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+
+ <h1>Source code for arbdmodel.binary_manager</h1><div class="highlight"><pre>
+<span></span><span class="c1"># -*- coding: utf-8 -*-</span>
+<span class="sd">"""</span>
+<span class="sd">Binary path management module for simulation engines and processors.</span>
+<span class="sd">This module provides a singleton object to manage paths to external binaries.</span>
+<span class="sd">"""</span>
+
+<span class="kn">import</span><span class="w"> </span><span class="nn">os</span>
+<span class="kn">import</span><span class="w"> </span><span class="nn">platform</span>
+<span class="kn">import</span><span class="w"> </span><span class="nn">shutil</span>
+<span class="kn">from</span><span class="w"> </span><span class="nn">pathlib</span><span class="w"> </span><span class="kn">import</span> <span class="n">Path</span>
+<span class="kn">from</span><span class="w"> </span><span class="nn">.logger</span><span class="w"> </span><span class="kn">import</span> <span class="n">logger</span><span class="p">,</span> <span class="n">get_resource_path</span>
+
+<span class="c1"># Default binary names by platform</span>
+<span class="n">DEFAULT_BINARIES</span> <span class="o">=</span> <span class="p">{</span>
+ <span class="s2">"arbd"</span><span class="p">:</span> <span class="p">{</span>
+ <span class="s2">"windows"</span><span class="p">:</span> <span class="s2">"arbd.exe"</span><span class="p">,</span>
+ <span class="s2">"linux"</span><span class="p">:</span> <span class="s2">"arbd"</span><span class="p">,</span>
+ <span class="s2">"darwin"</span><span class="p">:</span> <span class="s2">"arbd"</span><span class="p">,</span> <span class="c1"># macOS uses same binary name as Linux</span>
+ <span class="p">},</span>
+ <span class="s2">"namd"</span><span class="p">:</span> <span class="p">{</span>
+ <span class="s2">"windows"</span><span class="p">:</span> <span class="s2">"namd2.exe"</span><span class="p">,</span>
+ <span class="s2">"linux"</span><span class="p">:</span> <span class="s2">"namd2"</span><span class="p">,</span>
+ <span class="s2">"darwin"</span><span class="p">:</span> <span class="s2">"namd2"</span><span class="p">,</span> <span class="c1"># macOS uses same binary name as Linux</span>
+ <span class="p">},</span>
+ <span class="s2">"vmd"</span><span class="p">:</span> <span class="p">{</span>
+ <span class="s2">"windows"</span><span class="p">:</span> <span class="s2">"vmd.exe"</span><span class="p">,</span>
+ <span class="s2">"linux"</span><span class="p">:</span> <span class="s2">"vmd"</span><span class="p">,</span>
+ <span class="s2">"darwin"</span><span class="p">:</span> <span class="s2">"vmd"</span><span class="p">,</span> <span class="c1"># macOS uses same binary name as Linux</span>
+ <span class="p">},</span>
+ <span class="s2">"hydropro"</span><span class="p">:</span> <span class="p">{</span>
+ <span class="s2">"windows"</span><span class="p">:</span> <span class="s2">"hydropro10-msd.exe"</span><span class="p">,</span>
+ <span class="s2">"linux"</span><span class="p">:</span> <span class="s2">"hydropro10-lnx.exe"</span><span class="p">,</span>
+ <span class="s2">"darwin"</span><span class="p">:</span> <span class="s2">"hydropro10-lnx.exe"</span><span class="p">,</span> <span class="c1"># HydroPro doesn't have a macOS-specific version, use Linux version</span>
+ <span class="p">},</span>
+ <span class="s2">"apbs"</span><span class="p">:</span> <span class="p">{</span>
+ <span class="s2">"windows"</span><span class="p">:</span> <span class="s2">"apbs.exe"</span><span class="p">,</span>
+ <span class="s2">"linux"</span><span class="p">:</span> <span class="s2">"apbs"</span><span class="p">,</span>
+ <span class="s2">"darwin"</span><span class="p">:</span> <span class="s2">"apbs"</span><span class="p">,</span> <span class="c1"># macOS uses same binary name as Linux</span>
+ <span class="p">},</span>
+ <span class="s2">"gmsh"</span><span class="p">:</span> <span class="p">{</span>
+ <span class="s2">"windows"</span><span class="p">:</span> <span class="s2">"gmsh.exe"</span><span class="p">,</span>
+ <span class="s2">"linux"</span><span class="p">:</span> <span class="s2">"gmsh"</span><span class="p">,</span>
+ <span class="s2">"darwin"</span><span class="p">:</span> <span class="s2">"gmsh"</span><span class="p">,</span> <span class="c1"># macOS uses same binary name as Linux</span>
+ <span class="p">},</span>
+<span class="p">}</span>
+
+<span class="c1"># Resource directories where binaries might be bundled with the package</span>
+<span class="n">RESOURCE_DIRS</span> <span class="o">=</span> <span class="p">{</span>
+ <span class="s2">"hydropro"</span><span class="p">:</span> <span class="s2">"hydropro10"</span><span class="p">,</span>
+<span class="p">}</span>
+
+<span class="c1"># Singleton for binary path management</span>
+<span class="k">class</span><span class="w"> </span><span class="nc">_BinaryManager</span><span class="p">:</span>
+ <span class="k">def</span><span class="w"> </span><span class="fm">__init__</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span>
+ <span class="c1"># Initialize empty paths dictionary</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">_binary_paths</span> <span class="o">=</span> <span class="p">{}</span>
+
+ <span class="c1"># Determine platform</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">_platform</span> <span class="o">=</span> <span class="n">platform</span><span class="o">.</span><span class="n">system</span><span class="p">()</span><span class="o">.</span><span class="n">lower</span><span class="p">()</span>
+ <span class="k">if</span> <span class="bp">self</span><span class="o">.</span><span class="n">_platform</span> <span class="ow">not</span> <span class="ow">in</span> <span class="p">(</span><span class="s2">"windows"</span><span class="p">,</span> <span class="s2">"linux"</span><span class="p">,</span> <span class="s2">"darwin"</span><span class="p">):</span>
+ <span class="n">logger</span><span class="o">.</span><span class="n">warning</span><span class="p">(</span><span class="sa">f</span><span class="s2">"Unsupported platform: </span><span class="si">{</span><span class="bp">self</span><span class="o">.</span><span class="n">_platform</span><span class="si">}</span><span class="s2">, using linux defaults"</span><span class="p">)</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">_platform</span> <span class="o">=</span> <span class="s2">"linux"</span>
+
+ <span class="c1"># For binary path purposes, treat macOS (darwin) similar to Linux for many tools</span>
+ <span class="c1"># that don't have macOS-specific versions</span>
+
+ <span class="k">def</span><span class="w"> </span><span class="nf">set_binary_path</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">binary_name</span><span class="p">,</span> <span class="n">path</span><span class="p">):</span>
+<span class="w"> </span><span class="sd">"""</span>
+<span class="sd"> Set the path for a specific binary.</span>
+<span class="sd"> </span>
+<span class="sd"> Args:</span>
+<span class="sd"> binary_name: The name of the binary (e.g., 'arbd', 'hydropro')</span>
+<span class="sd"> path: The full path to the binary</span>
+<span class="sd"> """</span>
+ <span class="k">if</span> <span class="n">path</span> <span class="ow">is</span> <span class="kc">None</span><span class="p">:</span>
+ <span class="k">if</span> <span class="n">binary_name</span> <span class="ow">in</span> <span class="bp">self</span><span class="o">.</span><span class="n">_binary_paths</span><span class="p">:</span>
+ <span class="k">del</span> <span class="bp">self</span><span class="o">.</span><span class="n">_binary_paths</span><span class="p">[</span><span class="n">binary_name</span><span class="p">]</span>
+ <span class="k">return</span>
+
+ <span class="n">path</span> <span class="o">=</span> <span class="n">Path</span><span class="p">(</span><span class="n">path</span><span class="p">)</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">_binary_paths</span><span class="p">[</span><span class="n">binary_name</span><span class="o">.</span><span class="n">lower</span><span class="p">()]</span> <span class="o">=</span> <span class="n">path</span>
+
+ <span class="k">def</span><span class="w"> </span><span class="nf">get_binary_path</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">binary_name</span><span class="p">):</span>
+<span class="w"> </span><span class="sd">"""</span>
+<span class="sd"> Get the path for a specific binary, searching if not explicitly set.</span>
+<span class="sd"> </span>
+<span class="sd"> Args:</span>
+<span class="sd"> binary_name: The name of the binary (e.g., 'arbd', 'hydropro')</span>
+<span class="sd"> </span>
+<span class="sd"> Returns:</span>
+<span class="sd"> Path to the binary if found, None otherwise</span>
+<span class="sd"> """</span>
+ <span class="n">binary_name</span> <span class="o">=</span> <span class="n">binary_name</span><span class="o">.</span><span class="n">lower</span><span class="p">()</span>
+
+ <span class="c1"># 1. Return already configured path if available</span>
+ <span class="k">if</span> <span class="n">binary_name</span> <span class="ow">in</span> <span class="bp">self</span><span class="o">.</span><span class="n">_binary_paths</span><span class="p">:</span>
+ <span class="k">return</span> <span class="bp">self</span><span class="o">.</span><span class="n">_binary_paths</span><span class="p">[</span><span class="n">binary_name</span><span class="p">]</span>
+
+ <span class="c1"># 2. Search for the binary</span>
+ <span class="n">binary_path</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">_find_binary</span><span class="p">(</span><span class="n">binary_name</span><span class="p">)</span>
+ <span class="k">if</span> <span class="n">binary_path</span><span class="p">:</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">_binary_paths</span><span class="p">[</span><span class="n">binary_name</span><span class="p">]</span> <span class="o">=</span> <span class="n">binary_path</span>
+ <span class="k">return</span> <span class="n">binary_path</span>
+
+ <span class="c1"># 3. Not found</span>
+ <span class="k">return</span> <span class="kc">None</span>
+
+ <span class="k">def</span><span class="w"> </span><span class="nf">_find_binary</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">binary_name</span><span class="p">):</span>
+<span class="w"> </span><span class="sd">"""</span>
+<span class="sd"> Search for a binary in standard locations.</span>
+<span class="sd"> </span>
+<span class="sd"> Search order:</span>
+<span class="sd"> 1. System PATH</span>
+<span class="sd"> 2. Package resource directories</span>
+<span class="sd"> 3. Current directory</span>
+<span class="sd"> </span>
+<span class="sd"> Args:</span>
+<span class="sd"> binary_name: The name of the binary to find</span>
+<span class="sd"> </span>
+<span class="sd"> Returns:</span>
+<span class="sd"> Path to the binary if found, None otherwise</span>
+<span class="sd"> """</span>
+ <span class="c1"># Get the default binary name for the current platform</span>
+ <span class="k">if</span> <span class="n">binary_name</span> <span class="ow">in</span> <span class="n">DEFAULT_BINARIES</span><span class="p">:</span>
+ <span class="n">binary_filename</span> <span class="o">=</span> <span class="n">DEFAULT_BINARIES</span><span class="p">[</span><span class="n">binary_name</span><span class="p">][</span><span class="bp">self</span><span class="o">.</span><span class="n">_platform</span><span class="p">]</span>
+ <span class="k">else</span><span class="p">:</span>
+ <span class="c1"># If not in our defaults, use the name as is</span>
+ <span class="n">binary_filename</span> <span class="o">=</span> <span class="n">binary_name</span>
+
+ <span class="c1"># 1. Check in system PATH</span>
+ <span class="n">system_path</span> <span class="o">=</span> <span class="n">shutil</span><span class="o">.</span><span class="n">which</span><span class="p">(</span><span class="n">binary_filename</span><span class="p">)</span>
+ <span class="k">if</span> <span class="n">system_path</span><span class="p">:</span>
+ <span class="k">return</span> <span class="n">Path</span><span class="p">(</span><span class="n">system_path</span><span class="p">)</span>
+
+ <span class="c1"># 2. Check in package resource directories</span>
+ <span class="k">if</span> <span class="n">binary_name</span> <span class="ow">in</span> <span class="n">RESOURCE_DIRS</span><span class="p">:</span>
+ <span class="n">resource_dir</span> <span class="o">=</span> <span class="n">get_resource_path</span><span class="p">(</span><span class="n">RESOURCE_DIRS</span><span class="p">[</span><span class="n">binary_name</span><span class="p">])</span>
+ <span class="n">resource_path</span> <span class="o">=</span> <span class="n">resource_dir</span> <span class="o">/</span> <span class="n">binary_filename</span>
+ <span class="k">if</span> <span class="n">resource_path</span><span class="o">.</span><span class="n">exists</span><span class="p">():</span>
+ <span class="c1"># Make binary executable if needed (Unix only)</span>
+ <span class="k">if</span> <span class="bp">self</span><span class="o">.</span><span class="n">_platform</span> <span class="o">!=</span> <span class="s2">"windows"</span> <span class="ow">and</span> <span class="ow">not</span> <span class="n">os</span><span class="o">.</span><span class="n">access</span><span class="p">(</span><span class="n">resource_path</span><span class="p">,</span> <span class="n">os</span><span class="o">.</span><span class="n">X_OK</span><span class="p">):</span>
+ <span class="n">os</span><span class="o">.</span><span class="n">chmod</span><span class="p">(</span><span class="n">resource_path</span><span class="p">,</span> <span class="mo">0o755</span><span class="p">)</span>
+ <span class="k">return</span> <span class="n">resource_path</span>
+
+ <span class="c1"># 3. Check in current directory</span>
+ <span class="n">local_path</span> <span class="o">=</span> <span class="n">Path</span><span class="o">.</span><span class="n">cwd</span><span class="p">()</span> <span class="o">/</span> <span class="n">binary_filename</span>
+ <span class="k">if</span> <span class="n">local_path</span><span class="o">.</span><span class="n">exists</span><span class="p">():</span>
+ <span class="k">return</span> <span class="n">local_path</span>
+
+ <span class="c1"># Not found</span>
+ <span class="k">return</span> <span class="kc">None</span>
+
+ <span class="k">def</span><span class="w"> </span><span class="nf">get_all_paths</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span>
+<span class="w"> </span><span class="sd">"""</span>
+<span class="sd"> Get all configured binary paths.</span>
+<span class="sd"> </span>
+<span class="sd"> Returns:</span>
+<span class="sd"> Dictionary of binary name to path</span>
+<span class="sd"> """</span>
+ <span class="k">return</span> <span class="bp">self</span><span class="o">.</span><span class="n">_binary_paths</span><span class="o">.</span><span class="n">copy</span><span class="p">()</span>
+
+ <span class="k">def</span><span class="w"> </span><span class="nf">export_to_dict</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span>
+<span class="w"> </span><span class="sd">"""</span>
+<span class="sd"> Export all binary paths as a dictionary of strings.</span>
+<span class="sd"> </span>
+<span class="sd"> Returns:</span>
+<span class="sd"> Dictionary of binary name to string path</span>
+<span class="sd"> """</span>
+ <span class="k">return</span> <span class="p">{</span><span class="n">name</span><span class="p">:</span> <span class="nb">str</span><span class="p">(</span><span class="n">path</span><span class="p">)</span> <span class="k">for</span> <span class="n">name</span><span class="p">,</span> <span class="n">path</span> <span class="ow">in</span> <span class="bp">self</span><span class="o">.</span><span class="n">_binary_paths</span><span class="o">.</span><span class="n">items</span><span class="p">()}</span>
+
+ <span class="k">def</span><span class="w"> </span><span class="nf">import_from_dict</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">paths_dict</span><span class="p">):</span>
+<span class="w"> </span><span class="sd">"""</span>
+<span class="sd"> Import binary paths from a dictionary.</span>
+<span class="sd"> </span>
+<span class="sd"> Args:</span>
+<span class="sd"> paths_dict: Dictionary of binary name to path</span>
+<span class="sd"> """</span>
+ <span class="k">for</span> <span class="n">name</span><span class="p">,</span> <span class="n">path</span> <span class="ow">in</span> <span class="n">paths_dict</span><span class="o">.</span><span class="n">items</span><span class="p">():</span>
+ <span class="k">if</span> <span class="n">path</span><span class="p">:</span> <span class="c1"># Skip empty paths</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">set_binary_path</span><span class="p">(</span><span class="n">name</span><span class="p">,</span> <span class="n">path</span><span class="p">)</span>
+
+ <span class="k">def</span><span class="w"> </span><span class="nf">is_binary_essential</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">binary_name</span><span class="p">):</span>
+<span class="w"> </span><span class="sd">"""</span>
+<span class="sd"> Check if a binary is considered essential for core functionality.</span>
+<span class="sd"> </span>
+<span class="sd"> Args:</span>
+<span class="sd"> binary_name: The name of the binary to check</span>
+<span class="sd"> </span>
+<span class="sd"> Returns:</span>
+<span class="sd"> True if the binary is essential, False otherwise</span>
+<span class="sd"> """</span>
+ <span class="n">essential_binaries</span> <span class="o">=</span> <span class="p">[</span><span class="s2">"arbd"</span><span class="p">]</span> <span class="c1"># These are required for core functionality</span>
+ <span class="k">return</span> <span class="n">binary_name</span><span class="o">.</span><span class="n">lower</span><span class="p">()</span> <span class="ow">in</span> <span class="n">essential_binaries</span>
+
+<span class="c1"># Create the singleton instance</span>
+<span class="n">BinaryManager</span> <span class="o">=</span> <span class="n">_BinaryManager</span><span class="p">()</span>
+
+<span class="c1"># Initialize binary paths from environment variables</span>
+<div class="viewcode-block" id="initialize_binary_paths">
+<a class="viewcode-back" href="../../api/utilities/binary_manager.html#arbdmodel.binary_manager.initialize_binary_paths">[docs]</a>
+<span class="k">def</span><span class="w"> </span><span class="nf">initialize_binary_paths</span><span class="p">():</span>
+<span class="w"> </span><span class="sd">"""</span>
+<span class="sd"> Initialize binary paths from environment variables.</span>
+<span class="sd"> This function should be called during package initialization.</span>
+<span class="sd"> """</span>
+ <span class="c1"># Check environment variables for binary paths</span>
+ <span class="k">for</span> <span class="n">binary</span> <span class="ow">in</span> <span class="n">DEFAULT_BINARIES</span><span class="p">:</span>
+ <span class="n">env_var</span> <span class="o">=</span> <span class="sa">f</span><span class="s2">"</span><span class="si">{</span><span class="n">binary</span><span class="o">.</span><span class="n">upper</span><span class="p">()</span><span class="si">}</span><span class="s2">_PATH"</span>
+ <span class="k">if</span> <span class="n">env_var</span> <span class="ow">in</span> <span class="n">os</span><span class="o">.</span><span class="n">environ</span><span class="p">:</span>
+ <span class="n">BinaryManager</span><span class="o">.</span><span class="n">set_binary_path</span><span class="p">(</span><span class="n">binary</span><span class="p">,</span> <span class="n">os</span><span class="o">.</span><span class="n">environ</span><span class="p">[</span><span class="n">env_var</span><span class="p">])</span>
+
+ <span class="c1"># Try to load from configuration file</span>
+ <span class="k">try</span><span class="p">:</span>
+ <span class="kn">import</span><span class="w"> </span><span class="nn">json</span>
+ <span class="n">config_path</span> <span class="o">=</span> <span class="n">Path</span><span class="o">.</span><span class="n">home</span><span class="p">()</span> <span class="o">/</span> <span class="s2">".config"</span> <span class="o">/</span> <span class="s2">"arbd"</span> <span class="o">/</span> <span class="s2">"binaries.json"</span>
+ <span class="k">if</span> <span class="n">config_path</span><span class="o">.</span><span class="n">exists</span><span class="p">():</span>
+ <span class="k">with</span> <span class="nb">open</span><span class="p">(</span><span class="n">config_path</span><span class="p">)</span> <span class="k">as</span> <span class="n">f</span><span class="p">:</span>
+ <span class="n">paths_dict</span> <span class="o">=</span> <span class="n">json</span><span class="o">.</span><span class="n">load</span><span class="p">(</span><span class="n">f</span><span class="p">)</span>
+ <span class="n">BinaryManager</span><span class="o">.</span><span class="n">import_from_dict</span><span class="p">(</span><span class="n">paths_dict</span><span class="p">)</span>
+ <span class="k">except</span> <span class="ne">Exception</span> <span class="k">as</span> <span class="n">e</span><span class="p">:</span>
+ <span class="c1"># Silently continue with environment or defaults if config loading fails</span>
+ <span class="k">pass</span></div>
+
+
+<span class="c1"># Initialize binary paths on module import</span>
+<span class="n">initialize_binary_paths</span><span class="p">()</span>
+
+<span class="sd">"""</span>
+<span class="sd">Usage example: </span>
+<span class="sd">arbd_path = BinaryManager.get_binary_path("arbd")</span>
+<span class="sd">print(f"ARBD binary path: {arbd_path}")</span>
+
+<span class="sd"># Set binary path</span>
+<span class="sd">BinaryManager.set_binary_path("hydropro", "/path/to/hydropro")</span>
+<span class="sd">"""</span>
+</pre></div>
+
+ </article>
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+
+ <h1>Source code for arbdmodel.core_objects</h1><div class="highlight"><pre>
+<span></span><span class="c1"># -*- coding: utf-8 -*-</span>
+<span class="kn">import</span><span class="w"> </span><span class="nn">numpy</span><span class="w"> </span><span class="k">as</span><span class="w"> </span><span class="nn">np</span>
+<span class="kn">from</span><span class="w"> </span><span class="nn">inspect</span><span class="w"> </span><span class="kn">import</span> <span class="n">ismethod</span>
+<span class="kn">from</span><span class="w"> </span><span class="nn">copy</span><span class="w"> </span><span class="kn">import</span> <span class="n">copy</span><span class="p">,</span> <span class="n">deepcopy</span>
+<span class="kn">from</span><span class="w"> </span><span class="nn">.logger</span><span class="w"> </span><span class="kn">import</span> <span class="n">logger</span><span class="p">,</span> <span class="n">get_resource_path</span><span class="p">,</span><span class="n">devlogger</span>
+
+
+<span class="c1">## Abstract classes</span>
+<div class="viewcode-block" id="Transformable">
+<a class="viewcode-back" href="../../api/core/core_objects.html#arbdmodel.core_objects.Transformable">[docs]</a>
+<span class="k">class</span><span class="w"> </span><span class="nc">Transformable</span><span class="p">():</span>
+ <span class="k">def</span><span class="w"> </span><span class="fm">__init__</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">position</span><span class="p">,</span> <span class="n">orientation</span><span class="o">=</span><span class="kc">None</span><span class="p">):</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">position</span> <span class="o">=</span> <span class="n">np</span><span class="o">.</span><span class="n">array</span><span class="p">(</span><span class="n">position</span><span class="p">)</span>
+ <span class="k">if</span> <span class="n">orientation</span> <span class="ow">is</span> <span class="ow">not</span> <span class="kc">None</span><span class="p">:</span>
+ <span class="n">orientation</span> <span class="o">=</span> <span class="n">np</span><span class="o">.</span><span class="n">array</span><span class="p">(</span><span class="n">orientation</span><span class="p">)</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">orientation</span> <span class="o">=</span> <span class="n">orientation</span>
+
+<div class="viewcode-block" id="Transformable.translate">
+<a class="viewcode-back" href="../../api/core/core_objects.html#arbdmodel.core_objects.Transformable.translate">[docs]</a>
+ <span class="k">def</span><span class="w"> </span><span class="nf">translate</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">offset</span> <span class="o">=</span> <span class="p">(</span><span class="mi">0</span><span class="p">,</span><span class="mi">0</span><span class="p">,</span><span class="mi">0</span><span class="p">)):</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">transform</span><span class="p">(</span> <span class="n">offset</span> <span class="o">=</span> <span class="n">offset</span> <span class="p">)</span></div>
+
+
+<div class="viewcode-block" id="Transformable.rotate">
+<a class="viewcode-back" href="../../api/core/core_objects.html#arbdmodel.core_objects.Transformable.rotate">[docs]</a>
+ <span class="k">def</span><span class="w"> </span><span class="nf">rotate</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">R</span><span class="p">,</span> <span class="n">about</span> <span class="o">=</span> <span class="p">(</span><span class="mi">0</span><span class="p">,</span><span class="mi">0</span><span class="p">,</span><span class="mi">0</span><span class="p">)):</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">transform</span><span class="p">(</span> <span class="n">R</span> <span class="o">=</span> <span class="n">R</span><span class="p">,</span> <span class="n">center</span> <span class="o">=</span> <span class="n">about</span> <span class="p">)</span></div>
+
+
+<div class="viewcode-block" id="Transformable.transform">
+<a class="viewcode-back" href="../../api/core/core_objects.html#arbdmodel.core_objects.Transformable.transform">[docs]</a>
+ <span class="k">def</span><span class="w"> </span><span class="nf">transform</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">R</span> <span class="o">=</span> <span class="p">((</span><span class="mi">1</span><span class="p">,</span><span class="mi">0</span><span class="p">,</span><span class="mi">0</span><span class="p">),(</span><span class="mi">0</span><span class="p">,</span><span class="mi">1</span><span class="p">,</span><span class="mi">0</span><span class="p">),(</span><span class="mi">0</span><span class="p">,</span><span class="mi">0</span><span class="p">,</span><span class="mi">1</span><span class="p">)),</span>
+ <span class="n">center</span> <span class="o">=</span> <span class="p">(</span><span class="mi">0</span><span class="p">,</span><span class="mi">0</span><span class="p">,</span><span class="mi">0</span><span class="p">),</span> <span class="n">offset</span> <span class="o">=</span> <span class="p">(</span><span class="mi">0</span><span class="p">,</span><span class="mi">0</span><span class="p">,</span><span class="mi">0</span><span class="p">)):</span>
+
+ <span class="n">R</span><span class="p">,</span><span class="n">center</span><span class="p">,</span><span class="n">offset</span> <span class="o">=</span> <span class="p">[</span><span class="n">np</span><span class="o">.</span><span class="n">array</span><span class="p">(</span><span class="n">x</span><span class="p">)</span> <span class="k">for</span> <span class="n">x</span> <span class="ow">in</span> <span class="p">(</span><span class="n">R</span><span class="p">,</span><span class="n">center</span><span class="p">,</span><span class="n">offset</span><span class="p">)]</span>
+
+ <span class="bp">self</span><span class="o">.</span><span class="n">position</span> <span class="o">=</span> <span class="n">R</span><span class="o">.</span><span class="n">dot</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">position</span><span class="o">-</span><span class="n">center</span><span class="p">)</span><span class="o">+</span><span class="n">center</span><span class="o">+</span><span class="n">offset</span>
+
+ <span class="k">if</span> <span class="bp">self</span><span class="o">.</span><span class="n">orientation</span> <span class="ow">is</span> <span class="ow">not</span> <span class="kc">None</span><span class="p">:</span>
+ <span class="c1">## TODO: what if self.orientation is taken from parent?!</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">orientation</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">orientation</span><span class="o">.</span><span class="n">dot</span><span class="p">(</span><span class="n">R</span><span class="p">)</span> </div>
+
+
+<div class="viewcode-block" id="Transformable.get_collapsed_position">
+<a class="viewcode-back" href="../../api/core/core_objects.html#arbdmodel.core_objects.Transformable.get_collapsed_position">[docs]</a>
+ <span class="k">def</span><span class="w"> </span><span class="nf">get_collapsed_position</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span>
+ <span class="c1"># print("get_collapsed_position called", type(self), self.name)</span>
+ <span class="k">if</span> <span class="nb">isinstance</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">Child</span><span class="p">):</span>
+ <span class="c1"># print(self.parent, isinstance(self.parent,Transformable))</span>
+ <span class="k">if</span> <span class="nb">isinstance</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">parent</span><span class="p">,</span> <span class="n">Transformable</span><span class="p">):</span>
+ <span class="k">return</span> <span class="bp">self</span><span class="o">.</span><span class="n">applyOrientation</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">position</span><span class="p">)</span> <span class="o">+</span> <span class="bp">self</span><span class="o">.</span><span class="n">parent</span><span class="o">.</span><span class="n">get_collapsed_position</span><span class="p">()</span>
+
+ <span class="c1"># if self.parent.orientation is not None:</span>
+ <span class="c1"># return self.parent.collapsedOrientation().dot(self.position) + self.parent.get_collapsed_position()</span>
+ <span class="k">return</span> <span class="n">np</span><span class="o">.</span><span class="n">array</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">position</span><span class="p">)</span> <span class="c1"># return a copy</span></div>
+
+
+<div class="viewcode-block" id="Transformable.applyOrientation">
+<a class="viewcode-back" href="../../api/core/core_objects.html#arbdmodel.core_objects.Transformable.applyOrientation">[docs]</a>
+ <span class="k">def</span><span class="w"> </span><span class="nf">applyOrientation</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span><span class="n">obj</span><span class="p">):</span>
+ <span class="c1"># print("applyOrientation called", self.name, obj)</span>
+ <span class="k">if</span> <span class="nb">isinstance</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">Child</span><span class="p">):</span>
+ <span class="c1"># print( self.orientation, self.orientation is not None, None is not None )</span>
+ <span class="c1"># if self.orientation is not None:</span>
+ <span class="c1"># # print("applyOrientation applying", self, self.name, self.orientation)</span>
+ <span class="c1"># obj = self.orientation.dot(obj)</span>
+ <span class="k">if</span> <span class="nb">isinstance</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">parent</span><span class="p">,</span> <span class="n">Transformable</span><span class="p">):</span>
+ <span class="k">if</span> <span class="bp">self</span><span class="o">.</span><span class="n">parent</span><span class="o">.</span><span class="n">orientation</span> <span class="ow">is</span> <span class="ow">not</span> <span class="kc">None</span><span class="p">:</span>
+ <span class="n">obj</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">parent</span><span class="o">.</span><span class="n">orientation</span><span class="o">.</span><span class="n">dot</span><span class="p">(</span><span class="n">obj</span><span class="p">)</span>
+ <span class="n">obj</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">parent</span><span class="o">.</span><span class="n">applyOrientation</span><span class="p">(</span><span class="n">obj</span><span class="p">)</span>
+ <span class="c1"># print("applyOrientation returning", self.name, obj)</span>
+ <span class="k">return</span> <span class="n">obj</span></div>
+</div>
+
+
+<div class="viewcode-block" id="Parent">
+<a class="viewcode-back" href="../../api/core/core_objects.html#arbdmodel.core_objects.Parent">[docs]</a>
+<span class="k">class</span><span class="w"> </span><span class="nc">Parent</span><span class="p">():</span>
+ <span class="k">def</span><span class="w"> </span><span class="fm">__init__</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">children</span><span class="o">=</span><span class="kc">None</span><span class="p">,</span> <span class="n">remove_duplicate_bonded_terms</span><span class="o">=</span><span class="kc">False</span><span class="p">):</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">children</span> <span class="o">=</span> <span class="p">[]</span>
+ <span class="k">if</span> <span class="n">children</span> <span class="ow">is</span> <span class="ow">not</span> <span class="kc">None</span><span class="p">:</span>
+ <span class="k">for</span> <span class="n">x</span> <span class="ow">in</span> <span class="n">children</span><span class="p">:</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">add</span><span class="p">(</span><span class="n">x</span><span class="p">)</span>
+
+ <span class="bp">self</span><span class="o">.</span><span class="n">remove_duplicate_bonded_terms</span> <span class="o">=</span> <span class="n">remove_duplicate_bonded_terms</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">bonds</span> <span class="o">=</span> <span class="p">[]</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">angles</span> <span class="o">=</span> <span class="p">[]</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">dihedrals</span> <span class="o">=</span> <span class="p">[]</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">vector_angles</span> <span class="o">=</span> <span class="p">[]</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">impropers</span> <span class="o">=</span> <span class="p">[]</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">exclusions</span> <span class="o">=</span> <span class="p">[]</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">vector_angles</span> <span class="o">=</span> <span class="p">[]</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">bond_angles</span> <span class="o">=</span> <span class="p">[]</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">product_potentials</span> <span class="o">=</span> <span class="p">[]</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">group_sites</span> <span class="o">=</span> <span class="p">[]</span>
+
+ <span class="c1">## TODO: self.cacheInvalid = True # What will be in the cache?</span>
+
+<div class="viewcode-block" id="Parent.add">
+<a class="viewcode-back" href="../../api/core/core_objects.html#arbdmodel.core_objects.Parent.add">[docs]</a>
+ <span class="k">def</span><span class="w"> </span><span class="nf">add</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span><span class="n">x</span><span class="p">):</span>
+ <span class="c1">## TODO: check the parent-child tree to make sure there are no cycles</span>
+ <span class="k">if</span> <span class="ow">not</span> <span class="nb">isinstance</span><span class="p">(</span><span class="n">x</span><span class="p">,</span><span class="n">Child</span><span class="p">):</span>
+ <span class="k">raise</span> <span class="ne">Exception</span><span class="p">(</span><span class="s1">'Attempted to add an object to a group that does not inherit from the "Child" type'</span><span class="p">)</span>
+
+ <span class="k">if</span> <span class="n">x</span><span class="o">.</span><span class="n">parent</span> <span class="ow">is</span> <span class="ow">not</span> <span class="kc">None</span> <span class="ow">and</span> <span class="n">x</span><span class="o">.</span><span class="n">parent</span> <span class="ow">is</span> <span class="ow">not</span> <span class="bp">self</span><span class="p">:</span>
+ <span class="k">raise</span> <span class="ne">Exception</span><span class="p">(</span><span class="s2">"Child </span><span class="si">{}</span><span class="s2"> already belongs to some group"</span><span class="o">.</span><span class="n">format</span><span class="p">(</span><span class="n">x</span><span class="p">))</span>
+ <span class="n">x</span><span class="o">.</span><span class="n">parent</span> <span class="o">=</span> <span class="bp">self</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">children</span><span class="o">.</span><span class="n">append</span><span class="p">(</span><span class="n">x</span><span class="p">)</span></div>
+
+
+<div class="viewcode-block" id="Parent.insert">
+<a class="viewcode-back" href="../../api/core/core_objects.html#arbdmodel.core_objects.Parent.insert">[docs]</a>
+ <span class="k">def</span><span class="w"> </span><span class="nf">insert</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span><span class="n">idx</span><span class="p">,</span><span class="n">x</span><span class="p">):</span>
+ <span class="c1">## TODO: check the parent-child tree to make sure there are no cycles</span>
+ <span class="k">if</span> <span class="ow">not</span> <span class="nb">isinstance</span><span class="p">(</span><span class="n">x</span><span class="p">,</span><span class="n">Child</span><span class="p">):</span>
+ <span class="k">raise</span> <span class="ne">Exception</span><span class="p">(</span><span class="s1">'Attempted to add an object to a group that does not inherit from the "Child" type'</span><span class="p">)</span>
+
+ <span class="k">if</span> <span class="n">x</span><span class="o">.</span><span class="n">parent</span> <span class="ow">is</span> <span class="ow">not</span> <span class="kc">None</span> <span class="ow">and</span> <span class="n">x</span><span class="o">.</span><span class="n">parent</span> <span class="ow">is</span> <span class="ow">not</span> <span class="bp">self</span><span class="p">:</span>
+ <span class="k">raise</span> <span class="ne">Exception</span><span class="p">(</span><span class="s2">"Child </span><span class="si">{}</span><span class="s2"> already belongs to some group"</span><span class="o">.</span><span class="n">format</span><span class="p">(</span><span class="n">x</span><span class="p">))</span>
+ <span class="n">x</span><span class="o">.</span><span class="n">parent</span> <span class="o">=</span> <span class="bp">self</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">children</span><span class="o">.</span><span class="n">insert</span><span class="p">(</span><span class="n">idx</span><span class="p">,</span><span class="n">x</span><span class="p">)</span></div>
+
+
+<div class="viewcode-block" id="Parent.index">
+<a class="viewcode-back" href="../../api/core/core_objects.html#arbdmodel.core_objects.Parent.index">[docs]</a>
+ <span class="k">def</span><span class="w"> </span><span class="nf">index</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">x</span><span class="p">):</span>
+ <span class="k">return</span> <span class="bp">self</span><span class="o">.</span><span class="n">children</span><span class="o">.</span><span class="n">index</span><span class="p">(</span><span class="n">x</span><span class="p">)</span></div>
+
+
+<div class="viewcode-block" id="Parent.clear_all">
+<a class="viewcode-back" href="../../api/core/core_objects.html#arbdmodel.core_objects.Parent.clear_all">[docs]</a>
+ <span class="k">def</span><span class="w"> </span><span class="nf">clear_all</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">keep_children</span><span class="o">=</span><span class="kc">False</span><span class="p">):</span>
+ <span class="k">if</span> <span class="n">keep_children</span> <span class="o">==</span> <span class="kc">False</span><span class="p">:</span>
+ <span class="k">for</span> <span class="n">x</span> <span class="ow">in</span> <span class="bp">self</span><span class="o">.</span><span class="n">children</span><span class="p">:</span>
+ <span class="n">x</span><span class="o">.</span><span class="n">parent</span> <span class="o">=</span> <span class="kc">None</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">children</span> <span class="o">=</span> <span class="p">[]</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">bonds</span> <span class="o">=</span> <span class="p">[]</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">angles</span> <span class="o">=</span> <span class="p">[]</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">dihedrals</span> <span class="o">=</span> <span class="p">[]</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">vector_angles</span> <span class="o">=</span> <span class="p">[]</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">impropers</span> <span class="o">=</span> <span class="p">[]</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">exclusions</span> <span class="o">=</span> <span class="p">[]</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">bond_angles</span> <span class="o">=</span> <span class="p">[]</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">product_potentials</span> <span class="o">=</span> <span class="p">[]</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">group_sites</span> <span class="o">=</span> <span class="p">[]</span></div>
+
+
+<div class="viewcode-block" id="Parent.remove">
+<a class="viewcode-back" href="../../api/core/core_objects.html#arbdmodel.core_objects.Parent.remove">[docs]</a>
+ <span class="k">def</span><span class="w"> </span><span class="nf">remove</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span><span class="n">x</span><span class="p">):</span>
+ <span class="k">if</span> <span class="n">x</span> <span class="ow">in</span> <span class="bp">self</span><span class="o">.</span><span class="n">children</span><span class="p">:</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">children</span><span class="o">.</span><span class="n">remove</span><span class="p">(</span><span class="n">x</span><span class="p">)</span>
+ <span class="k">if</span> <span class="n">x</span><span class="o">.</span><span class="n">parent</span> <span class="ow">is</span> <span class="bp">self</span><span class="p">:</span>
+ <span class="n">x</span><span class="o">.</span><span class="n">parent</span> <span class="o">=</span> <span class="kc">None</span></div>
+
+
+<div class="viewcode-block" id="Parent.get_center">
+<a class="viewcode-back" href="../../api/core/core_objects.html#arbdmodel.core_objects.Parent.get_center">[docs]</a>
+ <span class="k">def</span><span class="w"> </span><span class="nf">get_center</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">weight</span><span class="o">=</span><span class="kc">None</span><span class="p">):</span>
+ <span class="k">if</span> <span class="n">weight</span> <span class="ow">is</span> <span class="kc">None</span><span class="p">:</span>
+ <span class="n">center</span> <span class="o">=</span> <span class="n">np</span><span class="o">.</span><span class="n">mean</span><span class="p">([</span><span class="n">p</span><span class="o">.</span><span class="n">get_collapsed_position</span><span class="p">()</span> <span class="k">for</span> <span class="n">p</span> <span class="ow">in</span> <span class="bp">self</span><span class="p">],</span> <span class="n">axis</span><span class="o">=</span><span class="mi">0</span><span class="p">)</span>
+ <span class="k">elif</span> <span class="n">weight</span> <span class="o">==</span> <span class="s1">'mass'</span><span class="p">:</span>
+ <span class="k">raise</span> <span class="ne">NotImplementedError</span><span class="p">(</span><span class="s1">''</span><span class="p">)</span>
+ <span class="k">return</span> <span class="n">center</span></div>
+
+
+<div class="viewcode-block" id="Parent.add_bond">
+<a class="viewcode-back" href="../../api/core/core_objects.html#arbdmodel.core_objects.Parent.add_bond">[docs]</a>
+ <span class="k">def</span><span class="w"> </span><span class="nf">add_bond</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">i</span><span class="p">,</span><span class="n">j</span><span class="p">,</span> <span class="n">bond</span><span class="p">,</span> <span class="n">exclude</span><span class="o">=</span><span class="kc">False</span><span class="p">):</span>
+ <span class="k">assert</span><span class="p">(</span> <span class="n">i</span> <span class="ow">is</span> <span class="ow">not</span> <span class="n">j</span> <span class="p">)</span>
+ <span class="c1">## TODO: how to handle duplicating and cloning bonds</span>
+ <span class="c1"># beads = [b for b in self]</span>
+ <span class="c1"># for b in (i,j): assert(b in beads)</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">bonds</span><span class="o">.</span><span class="n">append</span><span class="p">(</span> <span class="p">(</span><span class="n">i</span><span class="p">,</span><span class="n">j</span><span class="p">,</span> <span class="n">bond</span><span class="p">,</span> <span class="n">exclude</span><span class="p">)</span> <span class="p">)</span></div>
+
+
+<div class="viewcode-block" id="Parent.add_angle">
+<a class="viewcode-back" href="../../api/core/core_objects.html#arbdmodel.core_objects.Parent.add_angle">[docs]</a>
+ <span class="k">def</span><span class="w"> </span><span class="nf">add_angle</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">i</span><span class="p">,</span><span class="n">j</span><span class="p">,</span><span class="n">k</span><span class="p">,</span> <span class="n">angle</span><span class="p">):</span>
+ <span class="k">assert</span><span class="p">(</span> <span class="nb">len</span><span class="p">(</span><span class="nb">set</span><span class="p">((</span><span class="n">i</span><span class="p">,</span><span class="n">j</span><span class="p">,</span><span class="n">k</span><span class="p">)))</span> <span class="o">==</span> <span class="mi">3</span> <span class="p">)</span>
+ <span class="c1"># beads = [b for b in self]</span>
+ <span class="c1"># for b in (i,j,k): assert(b in beads)</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">angles</span><span class="o">.</span><span class="n">append</span><span class="p">(</span> <span class="p">(</span><span class="n">i</span><span class="p">,</span><span class="n">j</span><span class="p">,</span><span class="n">k</span><span class="p">,</span> <span class="n">angle</span><span class="p">)</span> <span class="p">)</span></div>
+
+
+<div class="viewcode-block" id="Parent.add_dihedral">
+<a class="viewcode-back" href="../../api/core/core_objects.html#arbdmodel.core_objects.Parent.add_dihedral">[docs]</a>
+ <span class="k">def</span><span class="w"> </span><span class="nf">add_dihedral</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">i</span><span class="p">,</span><span class="n">j</span><span class="p">,</span><span class="n">k</span><span class="p">,</span><span class="n">l</span><span class="p">,</span> <span class="n">dihedral</span><span class="p">):</span>
+ <span class="k">assert</span><span class="p">(</span> <span class="nb">len</span><span class="p">(</span><span class="nb">set</span><span class="p">((</span><span class="n">i</span><span class="p">,</span><span class="n">j</span><span class="p">,</span><span class="n">k</span><span class="p">,</span><span class="n">l</span><span class="p">)))</span> <span class="o">==</span> <span class="mi">4</span> <span class="p">)</span>
+
+ <span class="c1"># beads = [b for b in self]</span>
+ <span class="c1"># for b in (i,j,k,l): assert(b in beads)</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">dihedrals</span><span class="o">.</span><span class="n">append</span><span class="p">(</span> <span class="p">(</span><span class="n">i</span><span class="p">,</span><span class="n">j</span><span class="p">,</span><span class="n">k</span><span class="p">,</span><span class="n">l</span><span class="p">,</span> <span class="n">dihedral</span><span class="p">)</span> <span class="p">)</span></div>
+
+
+ <span class="k">def</span><span class="w"> </span><span class="nf">add_vector_angle</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">i</span><span class="p">,</span><span class="n">j</span><span class="p">,</span><span class="n">k</span><span class="p">,</span><span class="n">l</span><span class="p">,</span> <span class="n">potential</span><span class="p">):</span>
+ <span class="k">assert</span><span class="p">(</span> <span class="nb">len</span><span class="p">(</span><span class="nb">set</span><span class="p">((</span><span class="n">i</span><span class="p">,</span><span class="n">j</span><span class="p">,</span><span class="n">k</span><span class="p">,</span><span class="n">l</span><span class="p">)))</span> <span class="o">==</span> <span class="mi">4</span> <span class="p">)</span>
+
+ <span class="c1"># beads = [b for b in self]</span>
+ <span class="c1"># for b in (i,j,k,l): assert(b in beads)</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">vector_angles</span><span class="o">.</span><span class="n">append</span><span class="p">(</span> <span class="p">(</span><span class="n">i</span><span class="p">,</span><span class="n">j</span><span class="p">,</span><span class="n">k</span><span class="p">,</span><span class="n">l</span><span class="p">,</span> <span class="n">potential</span><span class="p">)</span> <span class="p">)</span>
+
+<div class="viewcode-block" id="Parent.add_improper">
+<a class="viewcode-back" href="../../api/core/core_objects.html#arbdmodel.core_objects.Parent.add_improper">[docs]</a>
+ <span class="k">def</span><span class="w"> </span><span class="nf">add_improper</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">i</span><span class="p">,</span><span class="n">j</span><span class="p">,</span><span class="n">k</span><span class="p">,</span><span class="n">l</span><span class="p">,</span> <span class="n">dihedral</span><span class="p">):</span>
+ <span class="c1"># beads = [b for b in self]</span>
+ <span class="c1"># for b in (i,j,k,l): assert(b in beads)</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">impropers</span><span class="o">.</span><span class="n">append</span><span class="p">(</span> <span class="p">(</span><span class="n">i</span><span class="p">,</span><span class="n">j</span><span class="p">,</span><span class="n">k</span><span class="p">,</span><span class="n">l</span><span class="p">,</span> <span class="n">dihedral</span><span class="p">)</span> <span class="p">)</span></div>
+
+
+<div class="viewcode-block" id="Parent.add_exclusion">
+<a class="viewcode-back" href="../../api/core/core_objects.html#arbdmodel.core_objects.Parent.add_exclusion">[docs]</a>
+ <span class="k">def</span><span class="w"> </span><span class="nf">add_exclusion</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">i</span><span class="p">,</span><span class="n">j</span><span class="p">):</span>
+ <span class="c1">## TODO: how to handle duplicating and cloning bonds</span>
+ <span class="c1">## TODO: perform following check elsewhere</span>
+ <span class="c1"># beads = [b for b in self]</span>
+ <span class="c1"># for b in (i,j): assert(b in beads)</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">exclusions</span><span class="o">.</span><span class="n">append</span><span class="p">(</span> <span class="p">(</span><span class="n">i</span><span class="p">,</span><span class="n">j</span><span class="p">)</span> <span class="p">)</span></div>
+
+
+<div class="viewcode-block" id="Parent.add_vector_angle">
+<a class="viewcode-back" href="../../api/core/core_objects.html#arbdmodel.core_objects.Parent.add_vector_angle">[docs]</a>
+ <span class="k">def</span><span class="w"> </span><span class="nf">add_vector_angle</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">i</span><span class="p">,</span><span class="n">j</span><span class="p">,</span><span class="n">k</span><span class="p">,</span><span class="n">l</span><span class="p">,</span> <span class="n">potential</span><span class="p">):</span>
+ <span class="k">assert</span><span class="p">(</span> <span class="nb">len</span><span class="p">(</span><span class="nb">set</span><span class="p">((</span><span class="n">i</span><span class="p">,</span><span class="n">j</span><span class="p">,</span><span class="n">k</span><span class="p">,</span><span class="n">l</span><span class="p">)))</span> <span class="o">>=</span> <span class="mi">3</span> <span class="p">)</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">vector_angles</span><span class="o">.</span><span class="n">append</span><span class="p">(</span> <span class="p">(</span><span class="n">i</span><span class="p">,</span><span class="n">j</span><span class="p">,</span><span class="n">k</span><span class="p">,</span><span class="n">l</span><span class="p">,</span> <span class="n">potential</span><span class="p">)</span> <span class="p">)</span></div>
+
+
+<div class="viewcode-block" id="Parent.add_bond_angle">
+<a class="viewcode-back" href="../../api/core/core_objects.html#arbdmodel.core_objects.Parent.add_bond_angle">[docs]</a>
+ <span class="k">def</span><span class="w"> </span><span class="nf">add_bond_angle</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">i</span><span class="p">,</span><span class="n">j</span><span class="p">,</span><span class="n">k</span><span class="p">,</span><span class="n">l</span><span class="p">,</span> <span class="n">bond_angle</span><span class="p">,</span> <span class="n">exclude</span><span class="o">=</span><span class="kc">False</span><span class="p">):</span>
+ <span class="k">assert</span><span class="p">(</span> <span class="nb">len</span><span class="p">(</span><span class="nb">set</span><span class="p">((</span><span class="n">i</span><span class="p">,</span><span class="n">j</span><span class="p">,</span><span class="n">k</span><span class="p">,</span><span class="n">l</span><span class="p">)))</span> <span class="o">==</span> <span class="mi">4</span> <span class="p">)</span>
+ <span class="c1">## TODO: how to handle duplicating and cloning bonds</span>
+ <span class="c1"># beads = [b for b in self]</span>
+ <span class="c1"># for b in (i,j): assert(b in beads)</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">bond_angles</span><span class="o">.</span><span class="n">append</span><span class="p">(</span> <span class="p">(</span><span class="n">i</span><span class="p">,</span><span class="n">j</span><span class="p">,</span><span class="n">k</span><span class="p">,</span><span class="n">l</span><span class="p">,</span> <span class="n">bond_angle</span><span class="p">)</span> <span class="p">)</span></div>
+
+
+<div class="viewcode-block" id="Parent.add_product_potential">
+<a class="viewcode-back" href="../../api/core/core_objects.html#arbdmodel.core_objects.Parent.add_product_potential">[docs]</a>
+ <span class="k">def</span><span class="w"> </span><span class="nf">add_product_potential</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">potential_list</span><span class="p">):</span>
+<span class="w"> </span><span class="sd">""" potential_list: list of tuples of form (particle_i, particle_j,..., TabulatedPotential) """</span>
+ <span class="k">if</span> <span class="nb">len</span><span class="p">(</span><span class="n">potential_list</span><span class="p">)</span> <span class="o"><</span> <span class="mi">2</span><span class="p">:</span> <span class="k">raise</span> <span class="ne">ValueError</span><span class="p">(</span><span class="s2">"Too few potentials"</span><span class="p">)</span>
+ <span class="k">for</span> <span class="n">elem</span> <span class="ow">in</span> <span class="n">potential_list</span><span class="p">:</span>
+ <span class="n">beads</span> <span class="o">=</span> <span class="n">elem</span><span class="p">[:</span><span class="o">-</span><span class="mi">1</span><span class="p">]</span>
+ <span class="n">pot</span> <span class="o">=</span> <span class="n">elem</span><span class="p">[</span><span class="o">-</span><span class="mi">1</span><span class="p">]</span>
+ <span class="k">if</span> <span class="nb">len</span><span class="p">(</span><span class="n">beads</span><span class="p">)</span> <span class="o"><</span> <span class="mi">2</span><span class="p">:</span> <span class="k">raise</span> <span class="ne">ValueError</span><span class="p">(</span><span class="s2">"Too few particles specified in product_potential"</span><span class="p">)</span>
+ <span class="k">if</span> <span class="nb">len</span><span class="p">(</span><span class="n">beads</span><span class="p">)</span> <span class="o">></span> <span class="mi">4</span><span class="p">:</span> <span class="k">raise</span> <span class="ne">ValueError</span><span class="p">(</span><span class="s2">"Too many particles specified in product_potential"</span><span class="p">)</span>
+
+ <span class="bp">self</span><span class="o">.</span><span class="n">product_potentials</span><span class="o">.</span><span class="n">append</span><span class="p">(</span><span class="n">potential_list</span><span class="p">)</span></div>
+
+ <span class="c1">## TODO: how to handle duplicating and cloning bonds</span>
+
+<div class="viewcode-block" id="Parent.get_restraints">
+<a class="viewcode-back" href="../../api/core/core_objects.html#arbdmodel.core_objects.Parent.get_restraints">[docs]</a>
+ <span class="k">def</span><span class="w"> </span><span class="nf">get_restraints</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span>
+ <span class="n">ret</span> <span class="o">=</span> <span class="p">[]</span>
+ <span class="k">for</span> <span class="n">c</span> <span class="ow">in</span> <span class="bp">self</span><span class="o">.</span><span class="n">children</span> <span class="o">+</span> <span class="bp">self</span><span class="o">.</span><span class="n">group_sites</span><span class="p">:</span>
+ <span class="n">ret</span><span class="o">.</span><span class="n">extend</span><span class="p">(</span> <span class="n">c</span><span class="o">.</span><span class="n">get_restraints</span><span class="p">()</span> <span class="p">)</span>
+ <span class="k">return</span> <span class="n">ret</span></div>
+
+
+<div class="viewcode-block" id="Parent.get_bonds">
+<a class="viewcode-back" href="../../api/core/core_objects.html#arbdmodel.core_objects.Parent.get_bonds">[docs]</a>
+ <span class="k">def</span><span class="w"> </span><span class="nf">get_bonds</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span>
+ <span class="n">ret</span> <span class="o">=</span> <span class="n">copy</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">bonds</span><span class="p">)</span>
+ <span class="k">for</span> <span class="n">c</span> <span class="ow">in</span> <span class="bp">self</span><span class="o">.</span><span class="n">children</span><span class="p">:</span>
+ <span class="k">if</span> <span class="nb">isinstance</span><span class="p">(</span><span class="n">c</span><span class="p">,</span><span class="n">Parent</span><span class="p">):</span> <span class="n">ret</span><span class="o">.</span><span class="n">extend</span><span class="p">(</span> <span class="n">c</span><span class="o">.</span><span class="n">get_bonds</span><span class="p">()</span> <span class="p">)</span>
+ <span class="k">if</span> <span class="bp">self</span><span class="o">.</span><span class="n">remove_duplicate_bonded_terms</span><span class="p">:</span>
+ <span class="k">return</span> <span class="nb">list</span><span class="p">(</span><span class="nb">set</span><span class="p">(</span><span class="nb">tuple</span><span class="p">(</span><span class="n">ret</span><span class="p">)))</span>
+ <span class="k">else</span><span class="p">:</span>
+ <span class="k">return</span> <span class="n">ret</span></div>
+
+
+
+<div class="viewcode-block" id="Parent.get_angles">
+<a class="viewcode-back" href="../../api/core/core_objects.html#arbdmodel.core_objects.Parent.get_angles">[docs]</a>
+ <span class="k">def</span><span class="w"> </span><span class="nf">get_angles</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span>
+ <span class="n">ret</span> <span class="o">=</span> <span class="n">copy</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">angles</span><span class="p">)</span>
+ <span class="k">for</span> <span class="n">c</span> <span class="ow">in</span> <span class="bp">self</span><span class="o">.</span><span class="n">children</span><span class="p">:</span>
+ <span class="k">if</span> <span class="nb">isinstance</span><span class="p">(</span><span class="n">c</span><span class="p">,</span><span class="n">Parent</span><span class="p">):</span> <span class="n">ret</span><span class="o">.</span><span class="n">extend</span><span class="p">(</span> <span class="n">c</span><span class="o">.</span><span class="n">get_angles</span><span class="p">()</span> <span class="p">)</span>
+ <span class="k">if</span> <span class="bp">self</span><span class="o">.</span><span class="n">remove_duplicate_bonded_terms</span><span class="p">:</span>
+ <span class="k">return</span> <span class="nb">list</span><span class="p">(</span><span class="nb">set</span><span class="p">(</span><span class="nb">tuple</span><span class="p">(</span><span class="n">ret</span><span class="p">)))</span>
+ <span class="k">else</span><span class="p">:</span>
+ <span class="k">return</span> <span class="n">ret</span></div>
+
+
+<div class="viewcode-block" id="Parent.get_dihedrals">
+<a class="viewcode-back" href="../../api/core/core_objects.html#arbdmodel.core_objects.Parent.get_dihedrals">[docs]</a>
+ <span class="k">def</span><span class="w"> </span><span class="nf">get_dihedrals</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span>
+ <span class="n">ret</span> <span class="o">=</span> <span class="n">copy</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">dihedrals</span><span class="p">)</span>
+ <span class="k">for</span> <span class="n">c</span> <span class="ow">in</span> <span class="bp">self</span><span class="o">.</span><span class="n">children</span><span class="p">:</span>
+ <span class="k">if</span> <span class="nb">isinstance</span><span class="p">(</span><span class="n">c</span><span class="p">,</span><span class="n">Parent</span><span class="p">):</span> <span class="n">ret</span><span class="o">.</span><span class="n">extend</span><span class="p">(</span> <span class="n">c</span><span class="o">.</span><span class="n">get_dihedrals</span><span class="p">()</span> <span class="p">)</span>
+ <span class="k">if</span> <span class="bp">self</span><span class="o">.</span><span class="n">remove_duplicate_bonded_terms</span><span class="p">:</span>
+ <span class="k">return</span> <span class="nb">list</span><span class="p">(</span><span class="nb">set</span><span class="p">(</span><span class="nb">tuple</span><span class="p">(</span><span class="n">ret</span><span class="p">)))</span>
+ <span class="k">else</span><span class="p">:</span>
+ <span class="k">return</span> <span class="n">ret</span></div>
+
+
+ <span class="k">def</span><span class="w"> </span><span class="nf">get_vector_angles</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span>
+ <span class="n">ret</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">vector_angles</span>
+ <span class="k">for</span> <span class="n">c</span> <span class="ow">in</span> <span class="bp">self</span><span class="o">.</span><span class="n">children</span><span class="p">:</span>
+ <span class="k">if</span> <span class="nb">isinstance</span><span class="p">(</span><span class="n">c</span><span class="p">,</span><span class="n">Parent</span><span class="p">):</span> <span class="n">ret</span><span class="o">.</span><span class="n">extend</span><span class="p">(</span> <span class="n">c</span><span class="o">.</span><span class="n">vector_angles</span><span class="p">()</span> <span class="p">)</span>
+ <span class="k">if</span> <span class="bp">self</span><span class="o">.</span><span class="n">remove_duplicate_bonded_terms</span><span class="p">:</span>
+ <span class="k">return</span> <span class="nb">list</span><span class="p">(</span><span class="nb">set</span><span class="p">(</span><span class="nb">tuple</span><span class="p">(</span><span class="n">ret</span><span class="p">)))</span>
+ <span class="k">else</span><span class="p">:</span>
+ <span class="k">return</span> <span class="n">ret</span>
+
+<div class="viewcode-block" id="Parent.get_impropers">
+<a class="viewcode-back" href="../../api/core/core_objects.html#arbdmodel.core_objects.Parent.get_impropers">[docs]</a>
+ <span class="k">def</span><span class="w"> </span><span class="nf">get_impropers</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span>
+ <span class="n">ret</span> <span class="o">=</span> <span class="n">copy</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">impropers</span><span class="p">)</span>
+ <span class="k">for</span> <span class="n">c</span> <span class="ow">in</span> <span class="bp">self</span><span class="o">.</span><span class="n">children</span><span class="p">:</span>
+ <span class="k">if</span> <span class="nb">isinstance</span><span class="p">(</span><span class="n">c</span><span class="p">,</span><span class="n">Parent</span><span class="p">):</span> <span class="n">ret</span><span class="o">.</span><span class="n">extend</span><span class="p">(</span> <span class="n">c</span><span class="o">.</span><span class="n">get_impropers</span><span class="p">()</span> <span class="p">)</span>
+ <span class="k">if</span> <span class="bp">self</span><span class="o">.</span><span class="n">remove_duplicate_bonded_terms</span><span class="p">:</span>
+ <span class="k">return</span> <span class="nb">list</span><span class="p">(</span><span class="nb">set</span><span class="p">(</span><span class="nb">tuple</span><span class="p">(</span><span class="n">ret</span><span class="p">)))</span>
+ <span class="k">else</span><span class="p">:</span>
+ <span class="k">return</span> <span class="n">ret</span></div>
+
+
+<div class="viewcode-block" id="Parent.get_exclusions">
+<a class="viewcode-back" href="../../api/core/core_objects.html#arbdmodel.core_objects.Parent.get_exclusions">[docs]</a>
+ <span class="k">def</span><span class="w"> </span><span class="nf">get_exclusions</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span>
+ <span class="n">ret</span> <span class="o">=</span> <span class="n">copy</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">exclusions</span><span class="p">)</span>
+ <span class="k">for</span> <span class="n">c</span> <span class="ow">in</span> <span class="bp">self</span><span class="o">.</span><span class="n">children</span><span class="p">:</span>
+ <span class="k">if</span> <span class="nb">isinstance</span><span class="p">(</span><span class="n">c</span><span class="p">,</span><span class="n">Parent</span><span class="p">):</span> <span class="n">ret</span><span class="o">.</span><span class="n">extend</span><span class="p">(</span> <span class="n">c</span><span class="o">.</span><span class="n">get_exclusions</span><span class="p">()</span> <span class="p">)</span>
+ <span class="k">if</span> <span class="bp">self</span><span class="o">.</span><span class="n">remove_duplicate_bonded_terms</span><span class="p">:</span>
+ <span class="k">return</span> <span class="nb">list</span><span class="p">(</span><span class="nb">set</span><span class="p">(</span><span class="nb">tuple</span><span class="p">(</span><span class="n">ret</span><span class="p">)))</span>
+ <span class="k">else</span><span class="p">:</span>
+ <span class="k">return</span> <span class="n">ret</span></div>
+
+
+<div class="viewcode-block" id="Parent.get_vector_angles">
+<a class="viewcode-back" href="../../api/core/core_objects.html#arbdmodel.core_objects.Parent.get_vector_angles">[docs]</a>
+ <span class="k">def</span><span class="w"> </span><span class="nf">get_vector_angles</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span>
+ <span class="n">ret</span> <span class="o">=</span> <span class="n">copy</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">vector_angles</span><span class="p">)</span>
+ <span class="k">for</span> <span class="n">c</span> <span class="ow">in</span> <span class="bp">self</span><span class="o">.</span><span class="n">children</span><span class="p">:</span>
+ <span class="k">if</span> <span class="nb">isinstance</span><span class="p">(</span><span class="n">c</span><span class="p">,</span><span class="n">Parent</span><span class="p">):</span> <span class="n">ret</span><span class="o">.</span><span class="n">extend</span><span class="p">(</span> <span class="n">c</span><span class="o">.</span><span class="n">get_vector_angles</span><span class="p">()</span> <span class="p">)</span>
+ <span class="k">if</span> <span class="bp">self</span><span class="o">.</span><span class="n">remove_duplicate_bonded_terms</span><span class="p">:</span>
+ <span class="k">return</span> <span class="nb">list</span><span class="p">(</span><span class="nb">set</span><span class="p">(</span><span class="nb">tuple</span><span class="p">(</span><span class="n">ret</span><span class="p">)))</span>
+ <span class="k">else</span><span class="p">:</span>
+ <span class="k">return</span> <span class="n">ret</span></div>
+
+
+<div class="viewcode-block" id="Parent.get_bond_angles">
+<a class="viewcode-back" href="../../api/core/core_objects.html#arbdmodel.core_objects.Parent.get_bond_angles">[docs]</a>
+ <span class="k">def</span><span class="w"> </span><span class="nf">get_bond_angles</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span>
+ <span class="n">ret</span> <span class="o">=</span> <span class="n">copy</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">bond_angles</span><span class="p">)</span>
+ <span class="k">for</span> <span class="n">c</span> <span class="ow">in</span> <span class="bp">self</span><span class="o">.</span><span class="n">children</span><span class="p">:</span>
+ <span class="k">if</span> <span class="nb">isinstance</span><span class="p">(</span><span class="n">c</span><span class="p">,</span><span class="n">Parent</span><span class="p">):</span> <span class="n">ret</span><span class="o">.</span><span class="n">extend</span><span class="p">(</span> <span class="n">c</span><span class="o">.</span><span class="n">get_bond_angles</span><span class="p">()</span> <span class="p">)</span>
+ <span class="k">if</span> <span class="bp">self</span><span class="o">.</span><span class="n">remove_duplicate_bonded_terms</span><span class="p">:</span>
+ <span class="k">return</span> <span class="nb">list</span><span class="p">(</span><span class="nb">set</span><span class="p">(</span><span class="nb">tuple</span><span class="p">(</span><span class="n">ret</span><span class="p">)))</span>
+ <span class="k">else</span><span class="p">:</span>
+ <span class="k">return</span> <span class="n">ret</span></div>
+
+
+<div class="viewcode-block" id="Parent.get_product_potentials">
+<a class="viewcode-back" href="../../api/core/core_objects.html#arbdmodel.core_objects.Parent.get_product_potentials">[docs]</a>
+ <span class="k">def</span><span class="w"> </span><span class="nf">get_product_potentials</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span>
+ <span class="n">ret</span> <span class="o">=</span> <span class="n">copy</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">product_potentials</span><span class="p">)</span>
+ <span class="k">for</span> <span class="n">c</span> <span class="ow">in</span> <span class="bp">self</span><span class="o">.</span><span class="n">children</span><span class="p">:</span>
+ <span class="k">if</span> <span class="nb">isinstance</span><span class="p">(</span><span class="n">c</span><span class="p">,</span><span class="n">Parent</span><span class="p">):</span> <span class="n">ret</span><span class="o">.</span><span class="n">extend</span><span class="p">(</span> <span class="n">c</span><span class="o">.</span><span class="n">get_product_potentials</span><span class="p">()</span> <span class="p">)</span>
+ <span class="k">if</span> <span class="bp">self</span><span class="o">.</span><span class="n">remove_duplicate_bonded_terms</span><span class="p">:</span>
+ <span class="k">return</span> <span class="nb">list</span><span class="p">(</span><span class="nb">set</span><span class="p">(</span><span class="nb">tuple</span><span class="p">(</span><span class="n">ret</span><span class="p">)))</span>
+ <span class="k">else</span><span class="p">:</span>
+ <span class="k">return</span> <span class="n">ret</span></div>
+
+
+ <span class="k">def</span><span class="w"> </span><span class="nf">_get_bond_potentials</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span>
+ <span class="n">bonds</span> <span class="o">=</span> <span class="p">[</span><span class="n">b</span> <span class="k">for</span> <span class="n">i</span><span class="p">,</span><span class="n">j</span><span class="p">,</span><span class="n">b</span><span class="p">,</span><span class="n">ex</span> <span class="ow">in</span> <span class="bp">self</span><span class="o">.</span><span class="n">get_bonds</span><span class="p">()]</span>
+ <span class="n">bondangles1</span> <span class="o">=</span> <span class="p">[</span><span class="n">b</span><span class="p">[</span><span class="mi">1</span><span class="p">]</span> <span class="k">for</span> <span class="n">i</span><span class="p">,</span><span class="n">j</span><span class="p">,</span><span class="n">k</span><span class="p">,</span><span class="n">l</span><span class="p">,</span><span class="n">b</span> <span class="ow">in</span> <span class="bp">self</span><span class="o">.</span><span class="n">get_bond_angles</span><span class="p">()]</span>
+ <span class="k">return</span> <span class="nb">list</span><span class="p">(</span><span class="nb">set</span><span class="p">(</span> <span class="nb">tuple</span><span class="p">(</span><span class="n">bonds</span><span class="o">+</span><span class="n">bondangles1</span><span class="p">)</span> <span class="p">))</span>
+
+ <span class="k">def</span><span class="w"> </span><span class="nf">_get_angle_potentials</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span>
+ <span class="n">angles</span> <span class="o">=</span> <span class="p">[</span><span class="n">b</span> <span class="k">for</span> <span class="n">i</span><span class="p">,</span><span class="n">j</span><span class="p">,</span><span class="n">k</span><span class="p">,</span><span class="n">b</span> <span class="ow">in</span> <span class="bp">self</span><span class="o">.</span><span class="n">get_angles</span><span class="p">()]</span>
+ <span class="n">bondangles1</span> <span class="o">=</span> <span class="p">[</span><span class="n">b</span><span class="p">[</span><span class="mi">0</span><span class="p">]</span> <span class="k">for</span> <span class="n">i</span><span class="p">,</span><span class="n">j</span><span class="p">,</span><span class="n">k</span><span class="p">,</span><span class="n">l</span><span class="p">,</span><span class="n">b</span> <span class="ow">in</span> <span class="bp">self</span><span class="o">.</span><span class="n">get_bond_angles</span><span class="p">()]</span>
+ <span class="n">bondangles2</span> <span class="o">=</span> <span class="p">[</span><span class="n">b</span><span class="p">[</span><span class="mi">2</span><span class="p">]</span> <span class="k">for</span> <span class="n">i</span><span class="p">,</span><span class="n">j</span><span class="p">,</span><span class="n">k</span><span class="p">,</span><span class="n">l</span><span class="p">,</span><span class="n">b</span> <span class="ow">in</span> <span class="bp">self</span><span class="o">.</span><span class="n">get_bond_angles</span><span class="p">()]</span>
+ <span class="k">return</span> <span class="nb">list</span><span class="p">(</span><span class="nb">set</span><span class="p">(</span> <span class="nb">tuple</span><span class="p">(</span><span class="n">angles</span><span class="o">+</span><span class="n">bondangles1</span><span class="o">+</span><span class="n">bondangles2</span><span class="p">)</span> <span class="p">))</span>
+
+
+ <span class="c1">## Removed because prohibitively slow</span>
+ <span class="c1"># def remove_duplicate_terms(self):</span>
+ <span class="c1"># for key in "bonds angles dihedrals impropers exclusions".split():</span>
+ <span class="c1"># self.remove_duplicate_item(key)</span>
+
+ <span class="c1"># def remove_duplicate_item(self, dict_key, existing=None):</span>
+ <span class="c1"># if existing is None: existing = []</span>
+ <span class="c1"># ret = [i for i in list(set(self.__dict__[dict_key])) if i not in existing]</span>
+ <span class="c1"># self.__dict__[dict_key] = ret</span>
+ <span class="c1"># existing.extend(ret)</span>
+ <span class="c1"># for c in self.children:</span>
+ <span class="c1"># if isinstance(c,Parent): </span>
+ <span class="c1"># ret = ret + c.remove_duplicate_item(dict_key, existing)</span>
+ <span class="c1"># return ret</span>
+
+
+ <span class="k">def</span><span class="w"> </span><span class="fm">__iter__</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span>
+ <span class="c1">## TODO: decide if this is the nicest way to do it!</span>
+<span class="w"> </span><span class="sd">"""Depth-first iteration through tree"""</span>
+ <span class="c1"># devlogger.info(f'{self}.__iter__(): 0th child {None if len(self.children) == 0 else self.children[0]}')</span>
+ <span class="k">for</span> <span class="n">x</span> <span class="ow">in</span> <span class="bp">self</span><span class="o">.</span><span class="n">children</span><span class="p">:</span>
+ <span class="k">if</span> <span class="nb">isinstance</span><span class="p">(</span><span class="n">x</span><span class="p">,</span><span class="n">Parent</span><span class="p">):</span>
+ <span class="k">if</span> <span class="nb">isinstance</span><span class="p">(</span><span class="n">x</span><span class="p">,</span><span class="n">Clone</span><span class="p">)</span> <span class="ow">and</span> <span class="ow">not</span> <span class="nb">isinstance</span><span class="p">(</span><span class="n">x</span><span class="o">.</span><span class="n">get_original_recursively</span><span class="p">(),</span><span class="n">Parent</span><span class="p">):</span>
+ <span class="k">yield</span> <span class="n">x</span>
+ <span class="k">else</span><span class="p">:</span>
+ <span class="k">for</span> <span class="n">y</span> <span class="ow">in</span> <span class="n">x</span><span class="p">:</span>
+ <span class="k">yield</span> <span class="n">y</span>
+ <span class="k">else</span><span class="p">:</span>
+ <span class="k">yield</span> <span class="n">x</span>
+
+ <span class="k">def</span><span class="w"> </span><span class="fm">__len__</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span>
+ <span class="n">l</span> <span class="o">=</span> <span class="mi">0</span>
+ <span class="k">for</span> <span class="n">x</span> <span class="ow">in</span> <span class="bp">self</span><span class="o">.</span><span class="n">children</span><span class="p">:</span>
+ <span class="k">if</span> <span class="nb">isinstance</span><span class="p">(</span><span class="n">x</span><span class="p">,</span><span class="n">Parent</span><span class="p">):</span>
+ <span class="n">l</span> <span class="o">+=</span> <span class="nb">len</span><span class="p">(</span><span class="n">x</span><span class="p">)</span>
+ <span class="k">else</span><span class="p">:</span>
+ <span class="n">l</span> <span class="o">+=</span> <span class="mi">1</span>
+ <span class="k">return</span> <span class="n">l</span>
+
+ <span class="k">def</span><span class="w"> </span><span class="fm">__getitem__</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">i</span><span class="p">):</span>
+ <span class="k">return</span> <span class="bp">self</span><span class="o">.</span><span class="n">children</span><span class="p">[</span><span class="n">i</span><span class="p">]</span>
+
+ <span class="k">def</span><span class="w"> </span><span class="fm">__setitem__</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">i</span><span class="p">,</span> <span class="n">val</span><span class="p">):</span>
+ <span class="n">x</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">children</span><span class="p">[</span><span class="n">i</span><span class="p">]</span>
+ <span class="n">x</span><span class="o">.</span><span class="n">parent</span> <span class="o">=</span> <span class="kc">None</span>
+ <span class="n">val</span><span class="o">.</span><span class="n">parent</span> <span class="o">=</span> <span class="bp">self</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">children</span><span class="p">[</span><span class="n">i</span><span class="p">]</span> <span class="o">=</span> <span class="n">val</span></div>
+
+
+<div class="viewcode-block" id="Child">
+<a class="viewcode-back" href="../../api/core/core_objects.html#arbdmodel.core_objects.Child">[docs]</a>
+<span class="k">class</span><span class="w"> </span><span class="nc">Child</span><span class="p">():</span>
+ <span class="k">def</span><span class="w"> </span><span class="fm">__init__</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">parent</span><span class="o">=</span><span class="kc">None</span><span class="p">):</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">parent</span> <span class="o">=</span> <span class="n">parent</span>
+ <span class="k">if</span> <span class="n">parent</span> <span class="ow">is</span> <span class="ow">not</span> <span class="kc">None</span><span class="p">:</span>
+ <span class="k">assert</span><span class="p">(</span> <span class="nb">isinstance</span><span class="p">(</span><span class="n">parent</span><span class="p">,</span> <span class="n">Parent</span><span class="p">)</span> <span class="p">)</span>
+ <span class="n">parent</span><span class="o">.</span><span class="n">children</span><span class="o">.</span><span class="n">append</span><span class="p">(</span><span class="bp">self</span><span class="p">)</span>
+
+ <span class="k">def</span><span class="w"> </span><span class="fm">__getattr__</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">name</span><span class="p">):</span>
+<span class="w"> </span><span class="sd">"""</span>
+<span class="sd"> Try to get attribute from the parent</span>
+
+<span class="sd"> """</span>
+ <span class="c1"># if self.parent is not None:</span>
+ <span class="k">if</span> <span class="s2">"parent"</span> <span class="ow">not</span> <span class="ow">in</span> <span class="bp">self</span><span class="o">.</span><span class="vm">__dict__</span> <span class="ow">or</span> <span class="bp">self</span><span class="o">.</span><span class="vm">__dict__</span><span class="p">[</span><span class="s2">"parent"</span><span class="p">]</span> <span class="ow">is</span> <span class="kc">None</span> <span class="ow">or</span> <span class="n">name</span> <span class="o">==</span> <span class="s2">"children"</span><span class="p">:</span>
+ <span class="k">raise</span> <span class="ne">AttributeError</span><span class="p">(</span><span class="s2">"'</span><span class="si">{}</span><span class="s2">' object has no attribute '</span><span class="si">{}</span><span class="s2">'"</span><span class="o">.</span><span class="n">format</span><span class="p">(</span><span class="nb">type</span><span class="p">(</span><span class="bp">self</span><span class="p">)</span><span class="o">.</span><span class="vm">__name__</span><span class="p">,</span> <span class="n">name</span><span class="p">))</span>
+
+ <span class="c1">## Skip certain attributes from search</span>
+ <span class="n">excluded_attributes</span> <span class="o">=</span> <span class="p">[</span><span class="s1">'parent'</span><span class="p">]</span>
+ <span class="k">if</span> <span class="n">name</span> <span class="ow">in</span> <span class="n">excluded_attributes</span><span class="p">:</span>
+ <span class="k">raise</span> <span class="ne">AttributeError</span><span class="p">(</span><span class="s2">"'</span><span class="si">{}</span><span class="s2">' object has no attribute '</span><span class="si">{}</span><span class="s2">' and cannot look it up from the parent"</span><span class="o">.</span><span class="n">format</span><span class="p">(</span><span class="nb">type</span><span class="p">(</span><span class="bp">self</span><span class="p">)</span><span class="o">.</span><span class="vm">__name__</span><span class="p">,</span> <span class="n">name</span><span class="p">))</span>
+
+ <span class="c1">## TODO: determine if there is a way to avoid __getattr__ if a method is being looked up </span>
+ <span class="k">try</span><span class="p">:</span>
+ <span class="n">ret</span> <span class="o">=</span> <span class="nb">getattr</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">parent</span><span class="p">,</span><span class="n">name</span><span class="p">)</span>
+ <span class="k">except</span><span class="p">:</span>
+ <span class="k">raise</span> <span class="ne">AttributeError</span><span class="p">(</span><span class="s2">"'</span><span class="si">{}</span><span class="s2">' object has no attribute '</span><span class="si">{}</span><span class="s2">'"</span><span class="o">.</span><span class="n">format</span><span class="p">(</span><span class="nb">type</span><span class="p">(</span><span class="bp">self</span><span class="p">)</span><span class="o">.</span><span class="vm">__name__</span><span class="p">,</span> <span class="n">name</span><span class="p">))</span>
+ <span class="k">if</span> <span class="n">ismethod</span><span class="p">(</span><span class="n">ret</span><span class="p">):</span>
+ <span class="k">raise</span> <span class="ne">AttributeError</span><span class="p">(</span><span class="s2">"'</span><span class="si">{}</span><span class="s2">' object has no method '</span><span class="si">{}</span><span class="s2">'"</span><span class="o">.</span><span class="n">format</span><span class="p">(</span><span class="nb">type</span><span class="p">(</span><span class="bp">self</span><span class="p">)</span><span class="o">.</span><span class="vm">__name__</span><span class="p">,</span> <span class="n">name</span><span class="p">))</span>
+ <span class="k">return</span> <span class="n">ret</span>
+
+ <span class="k">def</span><span class="w"> </span><span class="nf">_clear_types</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span>
+ <span class="k">if</span> <span class="bp">self</span><span class="o">.</span><span class="n">parent</span> <span class="ow">is</span> <span class="ow">not</span> <span class="kc">None</span><span class="p">:</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">parent</span><span class="o">.</span><span class="n">_clear_types</span><span class="p">()</span></div>
+
+
+ <span class="c1"># def __getstate__(self):</span>
+ <span class="c1"># print("Child getstate called", self)</span>
+ <span class="c1"># print(self.__dict__)</span>
+ <span class="c1"># return (self.__dict__,)</span>
+
+ <span class="c1"># def __setstate__(self, state):</span>
+ <span class="c1"># self.__dict__, = state</span>
+
+<div class="viewcode-block" id="Clone">
+<a class="viewcode-back" href="../../api/core/core_objects.html#arbdmodel.core_objects.Clone">[docs]</a>
+<span class="k">class</span><span class="w"> </span><span class="nc">Clone</span><span class="p">(</span><span class="n">Transformable</span><span class="p">,</span> <span class="n">Parent</span><span class="p">,</span> <span class="n">Child</span><span class="p">):</span>
+ <span class="k">def</span><span class="w"> </span><span class="fm">__init__</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">original</span><span class="p">,</span> <span class="n">parent</span><span class="o">=</span><span class="kc">None</span><span class="p">,</span>
+ <span class="n">position</span> <span class="o">=</span> <span class="kc">None</span><span class="p">,</span>
+ <span class="n">orientation</span> <span class="o">=</span> <span class="kc">None</span><span class="p">):</span>
+ <span class="k">if</span> <span class="n">position</span> <span class="ow">is</span> <span class="kc">None</span> <span class="ow">and</span> <span class="n">original</span><span class="o">.</span><span class="n">position</span> <span class="ow">is</span> <span class="ow">not</span> <span class="kc">None</span><span class="p">:</span>
+ <span class="n">position</span> <span class="o">=</span> <span class="n">np</span><span class="o">.</span><span class="n">array</span><span class="p">(</span> <span class="n">original</span><span class="o">.</span><span class="n">position</span> <span class="p">)</span>
+ <span class="k">if</span> <span class="n">orientation</span> <span class="ow">is</span> <span class="kc">None</span> <span class="ow">and</span> <span class="n">original</span><span class="o">.</span><span class="n">orientation</span> <span class="ow">is</span> <span class="ow">not</span> <span class="kc">None</span><span class="p">:</span>
+ <span class="n">orientation</span> <span class="o">=</span> <span class="n">np</span><span class="o">.</span><span class="n">array</span><span class="p">(</span> <span class="n">original</span><span class="o">.</span><span class="n">orientation</span> <span class="p">)</span>
+ <span class="k">if</span> <span class="n">parent</span> <span class="ow">is</span> <span class="kc">None</span><span class="p">:</span>
+ <span class="n">parent</span> <span class="o">=</span> <span class="n">original</span><span class="o">.</span><span class="n">parent</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">original</span> <span class="o">=</span> <span class="n">original</span>
+ <span class="n">Child</span><span class="o">.</span><span class="fm">__init__</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">parent</span><span class="p">)</span>
+ <span class="n">Transformable</span><span class="o">.</span><span class="fm">__init__</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">position</span><span class="p">,</span> <span class="n">orientation</span><span class="p">)</span>
+
+ <span class="c1">## TODO: keep own bond_list, etc, update when needed original changes</span>
+
+ <span class="k">if</span> <span class="s2">"children"</span> <span class="ow">in</span> <span class="n">original</span><span class="o">.</span><span class="vm">__dict__</span> <span class="ow">and</span> <span class="nb">len</span><span class="p">(</span><span class="n">original</span><span class="o">.</span><span class="n">children</span><span class="p">)</span> <span class="o">></span> <span class="mi">0</span><span class="p">:</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">children</span> <span class="o">=</span> <span class="p">[</span><span class="n">Clone</span><span class="p">(</span><span class="n">c</span><span class="p">,</span> <span class="n">parent</span> <span class="o">=</span> <span class="bp">self</span><span class="p">)</span> <span class="k">for</span> <span class="n">c</span> <span class="ow">in</span> <span class="n">original</span><span class="o">.</span><span class="n">children</span><span class="p">]</span>
+ <span class="k">else</span><span class="p">:</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">children</span> <span class="o">=</span> <span class="p">[]</span>
+
+<div class="viewcode-block" id="Clone.get_original_recursively">
+<a class="viewcode-back" href="../../api/core/core_objects.html#arbdmodel.core_objects.Clone.get_original_recursively">[docs]</a>
+ <span class="k">def</span><span class="w"> </span><span class="nf">get_original_recursively</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span>
+ <span class="k">if</span> <span class="nb">isinstance</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">original</span><span class="p">,</span> <span class="n">Clone</span><span class="p">):</span>
+ <span class="k">return</span> <span class="bp">self</span><span class="o">.</span><span class="n">original</span><span class="o">.</span><span class="n">get_original_recursively</span><span class="p">()</span>
+ <span class="k">else</span><span class="p">:</span>
+ <span class="k">return</span> <span class="bp">self</span><span class="o">.</span><span class="n">original</span></div>
+
+
+ <span class="k">def</span><span class="w"> </span><span class="fm">__getattr__</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">name</span><span class="p">):</span>
+<span class="w"> </span><span class="sd">"""</span>
+<span class="sd"> Try to get attribute from the original without descending the tree heirarchy, then look up parent</span>
+
+<span class="sd"> TODO: handle PointParticle lookups into ParticleType</span>
+<span class="sd"> """</span>
+ <span class="c1"># print("Clone getattr",name)</span>
+ <span class="k">if</span> <span class="n">name</span> <span class="ow">in</span> <span class="bp">self</span><span class="o">.</span><span class="n">original</span><span class="o">.</span><span class="vm">__dict__</span><span class="p">:</span>
+ <span class="k">return</span> <span class="bp">self</span><span class="o">.</span><span class="n">original</span><span class="o">.</span><span class="vm">__dict__</span><span class="p">[</span><span class="n">name</span><span class="p">]</span>
+ <span class="k">else</span><span class="p">:</span>
+ <span class="k">if</span> <span class="s2">"parent"</span> <span class="ow">not</span> <span class="ow">in</span> <span class="bp">self</span><span class="o">.</span><span class="vm">__dict__</span> <span class="ow">or</span> <span class="bp">self</span><span class="o">.</span><span class="vm">__dict__</span><span class="p">[</span><span class="s2">"parent"</span><span class="p">]</span> <span class="ow">is</span> <span class="kc">None</span><span class="p">:</span>
+ <span class="k">raise</span> <span class="ne">AttributeError</span><span class="p">(</span><span class="s2">"'</span><span class="si">{}</span><span class="s2">' object has no attribute '</span><span class="si">{}</span><span class="s2">'"</span><span class="o">.</span><span class="n">format</span><span class="p">(</span><span class="nb">type</span><span class="p">(</span><span class="bp">self</span><span class="p">)</span><span class="o">.</span><span class="vm">__name__</span><span class="p">,</span> <span class="n">name</span><span class="p">))</span>
+ <span class="k">return</span> <span class="nb">getattr</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">parent</span><span class="p">,</span> <span class="n">name</span><span class="p">)</span></div>
+
+
+<span class="c1">## Particle classes</span>
+<div class="viewcode-block" id="ParticleType">
+<a class="viewcode-back" href="../../api/core/core_objects.html#arbdmodel.core_objects.ParticleType">[docs]</a>
+<span class="k">class</span><span class="w"> </span><span class="nc">ParticleType</span><span class="p">():</span>
+<span class="w"> </span><span class="sd">"""Class that hold common attributes that particles can point to"""</span>
+
+ <span class="n">excludedAttributes</span> <span class="o">=</span> <span class="p">(</span><span class="s2">"idx"</span><span class="p">,</span><span class="s2">"type_"</span><span class="p">,</span>
+ <span class="s2">"position"</span><span class="p">,</span>
+ <span class="s2">"orientation"</span><span class="p">,</span>
+ <span class="s2">"children"</span><span class="p">,</span>
+ <span class="s2">"name"</span><span class="p">,</span>
+ <span class="s2">"parent"</span><span class="p">,</span> <span class="s2">"excludedAttributes"</span><span class="p">,</span>
+ <span class="p">)</span>
+
+ <span class="k">def</span><span class="w"> </span><span class="fm">__init__</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">name</span><span class="p">,</span> <span class="n">charge</span><span class="o">=</span><span class="mi">0</span><span class="p">,</span> <span class="n">mass</span><span class="o">=</span><span class="kc">None</span><span class="p">,</span> <span class="n">diffusivity</span><span class="o">=</span><span class="kc">None</span><span class="p">,</span>
+ <span class="n">damping_coefficient</span><span class="o">=</span><span class="kc">None</span><span class="p">,</span> <span class="n">parent</span><span class="o">=</span><span class="kc">None</span><span class="p">,</span>
+ <span class="n">rigid_body_potentials</span><span class="o">=</span><span class="nb">tuple</span><span class="p">(),</span> <span class="o">**</span><span class="n">kwargs</span><span class="p">):</span>
+
+<span class="w"> </span><span class="sd">""" Parent type is used to fall back on for nonbonded</span>
+<span class="sd"> interactions if this type is not specifically referenced """</span>
+
+ <span class="k">if</span> <span class="n">parent</span> <span class="ow">is</span> <span class="ow">not</span> <span class="kc">None</span><span class="p">:</span>
+ <span class="k">for</span> <span class="n">k</span><span class="p">,</span><span class="n">v</span> <span class="ow">in</span> <span class="n">parent</span><span class="o">.</span><span class="vm">__dict__</span><span class="o">.</span><span class="n">items</span><span class="p">():</span>
+ <span class="k">if</span> <span class="n">k</span> <span class="ow">not</span> <span class="ow">in</span> <span class="n">ParticleType</span><span class="o">.</span><span class="n">excludedAttributes</span><span class="p">:</span>
+ <span class="bp">self</span><span class="o">.</span><span class="vm">__dict__</span><span class="p">[</span><span class="n">k</span><span class="p">]</span> <span class="o">=</span> <span class="n">v</span>
+ <span class="k">assert</span><span class="p">(</span> <span class="nb">type</span><span class="p">(</span><span class="n">parent</span><span class="p">)</span> <span class="o">==</span> <span class="nb">type</span><span class="p">(</span><span class="bp">self</span><span class="p">)</span> <span class="p">)</span>
+
+ <span class="c1"># if diffusivity is None:</span>
+ <span class="c1"># assert( (damping_coefficient is not None) and (mass is not None) )</span>
+
+ <span class="c1">## TODO: make most attributes @property</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">name</span> <span class="o">=</span> <span class="n">name</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">charge</span> <span class="o">=</span> <span class="n">charge</span>
+ <span class="k">if</span> <span class="n">mass</span> <span class="ow">is</span> <span class="ow">not</span> <span class="kc">None</span><span class="p">:</span> <span class="bp">self</span><span class="o">.</span><span class="n">mass</span> <span class="o">=</span> <span class="n">mass</span>
+ <span class="k">if</span> <span class="n">damping_coefficient</span> <span class="ow">is</span> <span class="ow">not</span> <span class="kc">None</span><span class="p">:</span> <span class="bp">self</span><span class="o">.</span><span class="n">damping_coefficient</span> <span class="o">=</span> <span class="n">damping_coefficient</span>
+ <span class="k">if</span> <span class="n">diffusivity</span> <span class="ow">is</span> <span class="ow">not</span> <span class="kc">None</span><span class="p">:</span> <span class="bp">self</span><span class="o">.</span><span class="n">diffusivity</span> <span class="o">=</span> <span class="n">diffusivity</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">parent</span> <span class="o">=</span> <span class="n">parent</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">rigid_body_potentials</span> <span class="o">=</span> <span class="n">rigid_body_potentials</span>
+ <span class="n">devlogger</span><span class="o">.</span><span class="n">debug</span><span class="p">(</span><span class="sa">f</span><span class="s1">'Created </span><span class="si">{</span><span class="nb">type</span><span class="p">(</span><span class="bp">self</span><span class="p">)</span><span class="si">}</span><span class="s1"> </span><span class="si">{</span><span class="n">name</span><span class="si">}</span><span class="s1"> @ </span><span class="si">{</span><span class="nb">hex</span><span class="p">(</span><span class="nb">id</span><span class="p">(</span><span class="bp">self</span><span class="p">))</span><span class="si">}</span><span class="s1">'</span><span class="p">)</span>
+
+ <span class="k">for</span> <span class="n">key</span> <span class="ow">in</span> <span class="n">ParticleType</span><span class="o">.</span><span class="n">excludedAttributes</span><span class="p">:</span>
+ <span class="k">assert</span><span class="p">(</span> <span class="n">key</span> <span class="ow">not</span> <span class="ow">in</span> <span class="n">kwargs</span> <span class="p">)</span>
+
+ <span class="k">for</span> <span class="n">key</span><span class="p">,</span><span class="n">val</span> <span class="ow">in</span> <span class="n">kwargs</span><span class="o">.</span><span class="n">items</span><span class="p">():</span>
+ <span class="bp">self</span><span class="o">.</span><span class="vm">__dict__</span><span class="p">[</span><span class="n">key</span><span class="p">]</span> <span class="o">=</span> <span class="n">val</span>
+
+<div class="viewcode-block" id="ParticleType.is_same_type">
+<a class="viewcode-back" href="../../api/core/core_objects.html#arbdmodel.core_objects.ParticleType.is_same_type">[docs]</a>
+ <span class="k">def</span><span class="w"> </span><span class="nf">is_same_type</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">other</span><span class="p">,</span> <span class="n">consider_parents</span><span class="o">=</span><span class="kc">True</span><span class="p">):</span>
+ <span class="k">assert</span><span class="p">(</span> <span class="nb">type</span><span class="p">(</span><span class="n">other</span><span class="p">)</span> <span class="o">==</span> <span class="nb">type</span><span class="p">(</span><span class="bp">self</span><span class="p">)</span> <span class="p">)</span>
+ <span class="k">if</span> <span class="bp">self</span> <span class="o">==</span> <span class="n">other</span><span class="p">:</span>
+ <span class="k">return</span> <span class="kc">True</span>
+ <span class="k">elif</span> <span class="n">consider_parents</span><span class="p">:</span>
+ <span class="k">if</span> <span class="bp">self</span><span class="o">.</span><span class="n">parent</span> <span class="ow">is</span> <span class="ow">not</span> <span class="kc">None</span> <span class="ow">and</span> <span class="bp">self</span><span class="o">.</span><span class="n">parent</span> <span class="o">==</span> <span class="n">other</span><span class="p">:</span>
+ <span class="k">return</span> <span class="kc">True</span>
+ <span class="k">elif</span> <span class="n">other</span><span class="o">.</span><span class="n">parent</span> <span class="ow">is</span> <span class="ow">not</span> <span class="kc">None</span> <span class="ow">and</span> <span class="n">other</span><span class="o">.</span><span class="n">parent</span> <span class="o">==</span> <span class="bp">self</span><span class="p">:</span>
+ <span class="k">return</span> <span class="kc">True</span>
+ <span class="c1"># elif other.parent is not None and self.parent is not None and other.parent == self.parent:</span>
+ <span class="c1"># return True</span>
+ <span class="k">else</span><span class="p">:</span>
+ <span class="k">return</span> <span class="kc">False</span></div>
+
+
+<div class="viewcode-block" id="ParticleType.add_grid_potential">
+<a class="viewcode-back" href="../../api/core/core_objects.html#arbdmodel.core_objects.ParticleType.add_grid_potential">[docs]</a>
+ <span class="k">def</span><span class="w"> </span><span class="nf">add_grid_potential</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">gridfile</span><span class="p">,</span> <span class="n">scale</span><span class="o">=</span><span class="mi">1</span><span class="p">,</span> <span class="n">boundary_condition</span><span class="o">=</span><span class="s1">'dirichlet'</span><span class="p">):</span>
+ <span class="k">if</span> <span class="n">boundary_condition</span> <span class="ow">not</span> <span class="ow">in</span> <span class="p">(</span><span class="s1">'dirichlet'</span><span class="p">,</span><span class="s1">'neumann'</span><span class="p">,</span><span class="s1">'periodic'</span><span class="p">):</span>
+ <span class="k">raise</span> <span class="ne">ValueError</span><span class="p">(</span><span class="sa">f</span><span class="s1">'Unrecognized grid boundary condition "</span><span class="si">{</span><span class="n">boundary_condition</span><span class="si">}</span><span class="s1">"; should be one of "dirichlet", "neumann" or "periodic".'</span><span class="p">)</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">grid_potentials</span> <span class="o">=</span> <span class="nb">getattr</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="s1">'grid_potentials'</span><span class="p">,</span> <span class="p">[])</span> <span class="o">+</span> <span class="p">[(</span><span class="n">gridfile</span><span class="p">,</span><span class="n">scale</span><span class="p">,</span><span class="n">boundary_condition</span><span class="p">)]</span></div>
+
+
+ <span class="k">def</span><span class="w"> </span><span class="fm">__getattr__</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">name</span><span class="p">):</span>
+<span class="w"> </span><span class="sd">"""</span>
+<span class="sd"> Try to get attribute from the parent</span>
+
+<span class="sd"> """</span>
+ <span class="k">if</span> <span class="s2">"parent"</span> <span class="ow">not</span> <span class="ow">in</span> <span class="bp">self</span><span class="o">.</span><span class="vm">__dict__</span> <span class="ow">or</span> <span class="bp">self</span><span class="o">.</span><span class="vm">__dict__</span><span class="p">[</span><span class="s2">"parent"</span><span class="p">]</span> <span class="ow">is</span> <span class="kc">None</span> <span class="ow">or</span> <span class="n">name</span> <span class="o">==</span> <span class="s2">"children"</span><span class="p">:</span>
+ <span class="k">raise</span> <span class="ne">AttributeError</span><span class="p">(</span><span class="s2">"'</span><span class="si">{}</span><span class="s2">' object has no attribute '</span><span class="si">{}</span><span class="s2">'"</span><span class="o">.</span><span class="n">format</span><span class="p">(</span><span class="nb">type</span><span class="p">(</span><span class="bp">self</span><span class="p">)</span><span class="o">.</span><span class="vm">__name__</span><span class="p">,</span> <span class="n">name</span><span class="p">))</span>
+
+ <span class="n">excluded_attributes</span> <span class="o">=</span> <span class="n">ParticleType</span><span class="o">.</span><span class="n">excludedAttributes</span>
+ <span class="k">if</span> <span class="n">name</span> <span class="ow">in</span> <span class="n">excluded_attributes</span><span class="p">:</span>
+ <span class="k">raise</span> <span class="ne">AttributeError</span><span class="p">(</span><span class="s2">"'</span><span class="si">{}</span><span class="s2">' object has no attribute '</span><span class="si">{}</span><span class="s2">' and cannot look it up from the parent"</span><span class="o">.</span><span class="n">format</span><span class="p">(</span><span class="nb">type</span><span class="p">(</span><span class="bp">self</span><span class="p">)</span><span class="o">.</span><span class="vm">__name__</span><span class="p">,</span> <span class="n">name</span><span class="p">))</span>
+
+ <span class="c1">## TODO: determine if there is a way to avoid __getattr__ if a method is being looked up</span>
+ <span class="k">try</span><span class="p">:</span>
+ <span class="n">ret</span> <span class="o">=</span> <span class="nb">getattr</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">parent</span><span class="p">,</span><span class="n">name</span><span class="p">)</span>
+ <span class="k">except</span><span class="p">:</span>
+ <span class="k">raise</span> <span class="ne">AttributeError</span><span class="p">(</span><span class="s2">"'</span><span class="si">{}</span><span class="s2">' object has no attribute '</span><span class="si">{}</span><span class="s2">'"</span><span class="o">.</span><span class="n">format</span><span class="p">(</span><span class="nb">type</span><span class="p">(</span><span class="bp">self</span><span class="p">)</span><span class="o">.</span><span class="vm">__name__</span><span class="p">,</span> <span class="n">name</span><span class="p">))</span>
+ <span class="k">if</span> <span class="n">ismethod</span><span class="p">(</span><span class="n">ret</span><span class="p">):</span>
+ <span class="k">raise</span> <span class="ne">AttributeError</span><span class="p">(</span><span class="s2">"'</span><span class="si">{}</span><span class="s2">' object has no method '</span><span class="si">{}</span><span class="s2">'"</span><span class="o">.</span><span class="n">format</span><span class="p">(</span><span class="nb">type</span><span class="p">(</span><span class="bp">self</span><span class="p">)</span><span class="o">.</span><span class="vm">__name__</span><span class="p">,</span> <span class="n">name</span><span class="p">))</span>
+ <span class="k">return</span> <span class="n">ret</span>
+
+ <span class="k">def</span><span class="w"> </span><span class="nf">__copy__</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span>
+ <span class="k">return</span> <span class="bp">self</span>
+
+ <span class="k">def</span><span class="w"> </span><span class="nf">__deepcopy__</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">memo</span><span class="p">):</span>
+ <span class="k">return</span> <span class="bp">self</span>
+
+ <span class="k">def</span><span class="w"> </span><span class="nf">_hash_key</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span>
+
+ <span class="n">l</span> <span class="o">=</span> <span class="p">[</span><span class="nb">str</span><span class="p">(</span><span class="nb">type</span><span class="p">(</span><span class="bp">self</span><span class="p">)),</span> <span class="bp">self</span><span class="o">.</span><span class="n">name</span><span class="p">,</span> <span class="bp">self</span><span class="o">.</span><span class="n">charge</span><span class="p">]</span>
+ <span class="k">for</span> <span class="n">keyval</span> <span class="ow">in</span> <span class="nb">sorted</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="vm">__dict__</span><span class="o">.</span><span class="n">items</span><span class="p">()):</span>
+ <span class="k">if</span> <span class="nb">isinstance</span><span class="p">(</span><span class="n">keyval</span><span class="p">[</span><span class="mi">1</span><span class="p">],</span> <span class="nb">list</span><span class="p">):</span> <span class="n">keyval</span> <span class="o">=</span> <span class="p">(</span><span class="n">keyval</span><span class="p">[</span><span class="mi">0</span><span class="p">],</span><span class="nb">tuple</span><span class="p">(</span><span class="n">keyval</span><span class="p">[</span><span class="mi">1</span><span class="p">]))</span>
+ <span class="n">l</span><span class="o">.</span><span class="n">extend</span><span class="p">(</span><span class="n">keyval</span><span class="p">)</span>
+ <span class="k">return</span> <span class="nb">tuple</span><span class="p">(</span><span class="n">l</span><span class="p">)</span>
+
+ <span class="k">def</span><span class="w"> </span><span class="fm">__hash__</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span>
+ <span class="k">return</span> <span class="nb">hash</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">_hash_key</span><span class="p">())</span>
+
+ <span class="k">def</span><span class="w"> </span><span class="nf">_equal_check</span><span class="p">(</span><span class="n">a</span><span class="p">,</span><span class="n">b</span><span class="p">):</span>
+ <span class="k">if</span> <span class="n">a</span><span class="o">.</span><span class="n">name</span> <span class="o">==</span> <span class="n">b</span><span class="o">.</span><span class="n">name</span><span class="p">:</span>
+ <span class="k">if</span> <span class="n">a</span><span class="o">.</span><span class="n">_hash_key</span><span class="p">()</span> <span class="o">!=</span> <span class="n">b</span><span class="o">.</span><span class="n">_hash_key</span><span class="p">():</span>
+ <span class="k">raise</span> <span class="ne">Exception</span><span class="p">(</span><span class="s2">"Two different ParticleTypes have same 'name' attribute"</span><span class="p">)</span>
+
+ <span class="k">def</span><span class="w"> </span><span class="fm">__eq__</span><span class="p">(</span><span class="n">a</span><span class="p">,</span><span class="n">b</span><span class="p">,</span> <span class="n">check_equal</span> <span class="o">=</span> <span class="kc">True</span><span class="p">):</span>
+ <span class="k">if</span> <span class="n">check_equal</span><span class="p">:</span> <span class="n">a</span><span class="o">.</span><span class="n">_equal_check</span><span class="p">(</span><span class="n">b</span><span class="p">)</span>
+ <span class="k">return</span> <span class="n">a</span><span class="o">.</span><span class="n">name</span> <span class="o">==</span> <span class="n">b</span><span class="o">.</span><span class="n">name</span>
+ <span class="k">def</span><span class="w"> </span><span class="fm">__lt__</span><span class="p">(</span><span class="n">a</span><span class="p">,</span><span class="n">b</span><span class="p">):</span>
+ <span class="n">a</span><span class="o">.</span><span class="n">_equal_check</span><span class="p">(</span><span class="n">b</span><span class="p">)</span>
+ <span class="k">return</span> <span class="n">a</span><span class="o">.</span><span class="n">name</span> <span class="o"><</span> <span class="n">b</span><span class="o">.</span><span class="n">name</span>
+ <span class="k">def</span><span class="w"> </span><span class="fm">__le__</span><span class="p">(</span><span class="n">a</span><span class="p">,</span><span class="n">b</span><span class="p">):</span>
+ <span class="n">a</span><span class="o">.</span><span class="n">_equal_check</span><span class="p">(</span><span class="n">b</span><span class="p">)</span>
+ <span class="k">return</span> <span class="n">a</span><span class="o">.</span><span class="n">name</span> <span class="o"><=</span> <span class="n">b</span><span class="o">.</span><span class="n">name</span>
+ <span class="k">def</span><span class="w"> </span><span class="fm">__gt__</span><span class="p">(</span><span class="n">a</span><span class="p">,</span><span class="n">b</span><span class="p">):</span>
+ <span class="n">a</span><span class="o">.</span><span class="n">_equal_check</span><span class="p">(</span><span class="n">b</span><span class="p">)</span>
+ <span class="k">return</span> <span class="n">a</span><span class="o">.</span><span class="n">name</span> <span class="o">></span> <span class="n">b</span><span class="o">.</span><span class="n">name</span>
+ <span class="k">def</span><span class="w"> </span><span class="fm">__ge__</span><span class="p">(</span><span class="n">a</span><span class="p">,</span><span class="n">b</span><span class="p">):</span>
+ <span class="n">a</span><span class="o">.</span><span class="n">_equal_check</span><span class="p">(</span><span class="n">b</span><span class="p">)</span>
+ <span class="k">return</span> <span class="n">a</span><span class="o">.</span><span class="n">name</span> <span class="o">>=</span> <span class="n">b</span><span class="o">.</span><span class="n">name</span>
+
+ <span class="k">def</span><span class="w"> </span><span class="fm">__repr__</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span>
+ <span class="k">return</span> <span class="s1">'<</span><span class="si">{}</span><span class="s1"> </span><span class="si">{}{}</span><span class="s1">>'</span><span class="o">.</span><span class="n">format</span><span class="p">(</span> <span class="nb">type</span><span class="p">(</span><span class="bp">self</span><span class="p">),</span> <span class="bp">self</span><span class="o">.</span><span class="n">name</span><span class="p">,</span> <span class="s1">'[</span><span class="si">{}</span><span class="s1">]'</span><span class="o">.</span><span class="n">format</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">parent</span><span class="p">)</span> <span class="k">if</span> <span class="bp">self</span><span class="o">.</span><span class="n">parent</span> <span class="ow">is</span> <span class="ow">not</span> <span class="kc">None</span> <span class="k">else</span> <span class="s1">''</span> <span class="p">)</span></div>
+
+
+<div class="viewcode-block" id="RigidBodyType">
+<a class="viewcode-back" href="../../api/core/core_objects.html#arbdmodel.core_objects.RigidBodyType">[docs]</a>
+<span class="k">class</span><span class="w"> </span><span class="nc">RigidBodyType</span><span class="p">(</span><span class="n">ParticleType</span><span class="p">):</span>
+
+<span class="w"> </span><span class="sd">"""Class that holds common attributes for RigidBody objects"""</span>
+
+ <span class="k">def</span><span class="w"> </span><span class="fm">__init__</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">name</span><span class="p">,</span> <span class="n">parent</span><span class="o">=</span><span class="kc">None</span><span class="p">,</span> <span class="n">moment_of_inertia</span> <span class="o">=</span> <span class="kc">None</span><span class="p">,</span>
+ <span class="n">rotational_diffusivity</span> <span class="o">=</span> <span class="kc">None</span><span class="p">,</span>
+ <span class="n">rotational_damping_coefficient</span> <span class="o">=</span> <span class="kc">None</span><span class="p">,</span>
+ <span class="n">attached_particles</span><span class="o">=</span><span class="nb">tuple</span><span class="p">(),</span> <span class="n">potential_grids</span><span class="o">=</span><span class="nb">tuple</span><span class="p">(),</span>
+ <span class="n">charge_grids</span><span class="o">=</span><span class="nb">tuple</span><span class="p">(),</span> <span class="n">pmf_grids</span><span class="o">=</span><span class="nb">tuple</span><span class="p">(),</span> <span class="o">**</span><span class="n">kwargs</span><span class="p">):</span>
+
+<span class="w"> </span><span class="sd">""" Parent type is used to fall back on for nonbonded</span>
+<span class="sd"> interactions if this type is not specifically referenced """</span>
+
+ <span class="k">if</span> <span class="n">rotational_diffusivity</span> <span class="ow">is</span> <span class="kc">None</span><span class="p">:</span>
+ <span class="k">assert</span><span class="p">(</span> <span class="p">(</span><span class="n">rotational_damping_coefficient</span> <span class="ow">is</span> <span class="ow">not</span> <span class="kc">None</span><span class="p">)</span> <span class="ow">and</span> <span class="p">(</span><span class="n">moment_of_inertia</span> <span class="ow">is</span> <span class="ow">not</span> <span class="kc">None</span><span class="p">)</span> <span class="p">)</span>
+
+ <span class="k">for</span> <span class="n">_grids</span> <span class="ow">in</span> <span class="p">(</span><span class="n">potential_grids</span><span class="p">,</span><span class="n">charge_grids</span><span class="p">,</span><span class="n">pmf_grids</span><span class="p">):</span>
+ <span class="k">for</span> <span class="n">val</span> <span class="ow">in</span> <span class="n">_grids</span><span class="p">:</span>
+ <span class="k">assert</span><span class="p">(</span> <span class="nb">len</span><span class="p">(</span><span class="n">val</span><span class="p">)</span> <span class="ow">in</span> <span class="p">(</span><span class="mi">2</span><span class="p">,</span><span class="mi">3</span><span class="p">)</span> <span class="p">)</span> <span class="c1"># </span>
+
+ <span class="n">ParticleType</span><span class="o">.</span><span class="fm">__init__</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">name</span><span class="p">,</span> <span class="n">parent</span><span class="o">=</span><span class="n">parent</span><span class="p">,</span>
+ <span class="n">moment_of_inertia</span> <span class="o">=</span> <span class="n">moment_of_inertia</span><span class="p">,</span>
+ <span class="n">rotational_diffusivity</span><span class="o">=</span><span class="n">rotational_diffusivity</span><span class="p">,</span>
+ <span class="n">rotational_damping_coefficient</span> <span class="o">=</span> <span class="n">rotational_damping_coefficient</span><span class="p">,</span>
+ <span class="n">potential_grids</span> <span class="o">=</span> <span class="n">potential_grids</span><span class="p">,</span>
+ <span class="n">charge_grids</span> <span class="o">=</span> <span class="n">charge_grids</span><span class="p">,</span>
+ <span class="n">pmf_grids</span> <span class="o">=</span> <span class="n">pmf_grids</span><span class="p">,</span>
+ <span class="o">**</span><span class="n">kwargs</span><span class="p">)</span>
+
+ <span class="bp">self</span><span class="o">.</span><span class="n">attached_particles</span> <span class="o">=</span> <span class="p">[]</span>
+ <span class="k">for</span> <span class="n">p</span> <span class="ow">in</span> <span class="n">attached_particles</span><span class="p">:</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">attach_particle</span><span class="p">(</span><span class="n">p</span><span class="p">)</span>
+
+<div class="viewcode-block" id="RigidBodyType.attach_particle">
+<a class="viewcode-back" href="../../api/core/core_objects.html#arbdmodel.core_objects.RigidBodyType.attach_particle">[docs]</a>
+ <span class="k">def</span><span class="w"> </span><span class="nf">attach_particle</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">particle</span><span class="p">):</span>
+<span class="w"> </span><span class="sd">""" The particle argument must be a PointParticle. The position/orientation of the attached particle/group is in the RigidBody frame. """</span>
+
+ <span class="k">if</span> <span class="n">particle</span><span class="o">.</span><span class="n">parent</span> <span class="ow">is</span> <span class="ow">not</span> <span class="kc">None</span><span class="p">:</span>
+ <span class="k">raise</span> <span class="ne">ValueError</span><span class="p">(</span><span class="s1">'RigidBody-attached particles are not allowed to have a parent'</span><span class="p">)</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">attached_particles</span><span class="o">.</span><span class="n">append</span><span class="p">(</span> <span class="n">particle</span> <span class="p">)</span></div>
+
+
+ <span class="k">def</span><span class="w"> </span><span class="nf">_equal_check</span><span class="p">(</span><span class="n">a</span><span class="p">,</span><span class="n">b</span><span class="p">):</span>
+ <span class="k">if</span> <span class="n">a</span><span class="o">.</span><span class="n">name</span> <span class="o">==</span> <span class="n">b</span><span class="o">.</span><span class="n">name</span><span class="p">:</span>
+ <span class="k">if</span> <span class="n">a</span><span class="o">.</span><span class="n">_hash_key</span><span class="p">()</span> <span class="o">!=</span> <span class="n">b</span><span class="o">.</span><span class="n">_hash_key</span><span class="p">():</span>
+ <span class="k">raise</span> <span class="ne">Exception</span><span class="p">(</span><span class="s2">"Two different RigidBodyTypes have same 'name' attribute"</span><span class="p">)</span> </div>
+
+
+<div class="viewcode-block" id="PointParticle">
+<a class="viewcode-back" href="../../api/core/core_objects.html#arbdmodel.core_objects.PointParticle">[docs]</a>
+<span class="k">class</span><span class="w"> </span><span class="nc">PointParticle</span><span class="p">(</span><span class="n">Transformable</span><span class="p">,</span> <span class="n">Child</span><span class="p">):</span>
+ <span class="k">def</span><span class="w"> </span><span class="fm">__init__</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">type_</span><span class="p">,</span> <span class="n">position</span><span class="p">,</span> <span class="n">name</span><span class="o">=</span><span class="s2">"A"</span><span class="p">,</span> <span class="o">**</span><span class="n">kwargs</span><span class="p">):</span>
+ <span class="n">parent</span> <span class="o">=</span> <span class="kc">None</span>
+ <span class="k">if</span> <span class="s1">'parent'</span> <span class="ow">in</span> <span class="n">kwargs</span><span class="p">:</span>
+ <span class="n">parent</span> <span class="o">=</span> <span class="n">kwargs</span><span class="p">[</span><span class="s1">'parent'</span><span class="p">]</span>
+ <span class="n">Child</span><span class="o">.</span><span class="fm">__init__</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">parent</span><span class="o">=</span><span class="n">parent</span><span class="p">)</span>
+ <span class="n">Transformable</span><span class="o">.</span><span class="fm">__init__</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span><span class="n">position</span><span class="p">)</span>
+
+ <span class="bp">self</span><span class="o">.</span><span class="n">type_</span> <span class="o">=</span> <span class="n">type_</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">idx</span> <span class="o">=</span> <span class="kc">None</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">name</span> <span class="o">=</span> <span class="n">name</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">counter</span> <span class="o">=</span> <span class="mi">0</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">restraints</span> <span class="o">=</span> <span class="p">[]</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">rigid</span> <span class="o">=</span> <span class="kc">False</span>
+
+ <span class="k">for</span> <span class="n">key</span><span class="p">,</span><span class="n">val</span> <span class="ow">in</span> <span class="n">kwargs</span><span class="o">.</span><span class="n">items</span><span class="p">():</span>
+ <span class="bp">self</span><span class="o">.</span><span class="vm">__dict__</span><span class="p">[</span><span class="n">key</span><span class="p">]</span> <span class="o">=</span> <span class="n">val</span>
+
+<div class="viewcode-block" id="PointParticle.add_restraint">
+<a class="viewcode-back" href="../../api/core/core_objects.html#arbdmodel.core_objects.PointParticle.add_restraint">[docs]</a>
+ <span class="k">def</span><span class="w"> </span><span class="nf">add_restraint</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">restraint</span><span class="p">):</span>
+ <span class="c1">## TODO: how to handle duplicating and cloning bonds</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">restraints</span><span class="o">.</span><span class="n">append</span><span class="p">(</span> <span class="n">restraint</span> <span class="p">)</span></div>
+
+
+<div class="viewcode-block" id="PointParticle.add_grid_potential">
+<a class="viewcode-back" href="../../api/core/core_objects.html#arbdmodel.core_objects.PointParticle.add_grid_potential">[docs]</a>
+ <span class="k">def</span><span class="w"> </span><span class="nf">add_grid_potential</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">gridfile</span><span class="p">,</span> <span class="n">scale</span><span class="o">=</span><span class="mi">1</span><span class="p">,</span> <span class="n">boundary_condition</span><span class="o">=</span><span class="s1">'dirichlet'</span><span class="p">):</span>
+ <span class="n">t0</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">type_</span>
+ <span class="n">name</span> <span class="o">=</span> <span class="sa">f</span><span class="s1">'</span><span class="si">{</span><span class="n">t0</span><span class="o">.</span><span class="n">name</span><span class="si">}</span><span class="s1">_g_</span><span class="si">{</span><span class="n">gridfile</span><span class="o">.</span><span class="n">replace</span><span class="p">(</span><span class="s2">".dx"</span><span class="p">,</span><span class="s2">""</span><span class="p">)</span><span class="si">}</span><span class="s1">_s_</span><span class="si">{</span><span class="n">scale</span><span class="si">}</span><span class="s1">'</span>
+ <span class="k">if</span> <span class="n">t0</span><span class="o">.</span><span class="n">parent</span> <span class="ow">is</span> <span class="ow">not</span> <span class="kc">None</span><span class="p">:</span>
+ <span class="n">t</span> <span class="o">=</span> <span class="n">copy</span><span class="p">(</span><span class="n">t0</span><span class="p">)</span>
+ <span class="n">t</span><span class="o">.</span><span class="n">name</span> <span class="o">=</span> <span class="n">name</span>
+ <span class="k">else</span><span class="p">:</span>
+ <span class="c1"># TODO: REMOVE LINE: t = ParticleType(name, parent=t0)</span>
+ <span class="n">t</span> <span class="o">=</span> <span class="nb">type</span><span class="p">(</span><span class="n">t0</span><span class="p">)(</span><span class="n">name</span><span class="p">,</span> <span class="n">parent</span><span class="o">=</span><span class="n">t0</span><span class="p">)</span>
+ <span class="n">t</span><span class="o">.</span><span class="n">add_grid_potential</span><span class="p">(</span><span class="n">gridfile</span><span class="p">,</span> <span class="n">scale</span><span class="o">=</span><span class="n">scale</span><span class="p">,</span> <span class="n">boundary_condition</span><span class="o">=</span><span class="n">boundary_condition</span><span class="p">)</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">type_</span> <span class="o">=</span> <span class="n">t</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">_clear_types</span><span class="p">()</span></div>
+
+
+<div class="viewcode-block" id="PointParticle.get_restraints">
+<a class="viewcode-back" href="../../api/core/core_objects.html#arbdmodel.core_objects.PointParticle.get_restraints">[docs]</a>
+ <span class="k">def</span><span class="w"> </span><span class="nf">get_restraints</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span>
+ <span class="k">return</span> <span class="p">[(</span><span class="bp">self</span><span class="p">,</span><span class="n">r</span><span class="p">)</span> <span class="k">for</span> <span class="n">r</span> <span class="ow">in</span> <span class="bp">self</span><span class="o">.</span><span class="n">restraints</span><span class="p">]</span></div>
+
+
+<div class="viewcode-block" id="PointParticle.duplicate">
+<a class="viewcode-back" href="../../api/core/core_objects.html#arbdmodel.core_objects.PointParticle.duplicate">[docs]</a>
+ <span class="k">def</span><span class="w"> </span><span class="nf">duplicate</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span>
+ <span class="n">new</span> <span class="o">=</span> <span class="n">deepcopy</span><span class="p">(</span><span class="bp">self</span><span class="p">)</span>
+ <span class="k">return</span> <span class="n">new</span></div>
+
+
+ <span class="k">def</span><span class="w"> </span><span class="fm">__getattr__</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">name</span><span class="p">):</span>
+<span class="w"> </span><span class="sd">"""</span>
+<span class="sd"> First try to get attribute from the parent, then type_</span>
+<span class="sd"> </span>
+<span class="sd"> Note that this data structure seems to be fragile, can result in stack overflow</span>
+<span class="sd"> </span>
+<span class="sd"> """</span>
+ <span class="k">if</span> <span class="n">name</span> <span class="ow">in</span> <span class="p">(</span><span class="s1">'__copy__'</span><span class="p">,</span><span class="s1">'__deepcopy__'</span><span class="p">):</span>
+ <span class="c1">## Avoid using type_ and parent __copy__/__deepcopy__ functions!</span>
+ <span class="k">return</span> <span class="kc">None</span>
+
+ <span class="c1"># return Child.__getattr__(self,name)</span>
+ <span class="k">try</span><span class="p">:</span>
+ <span class="k">return</span> <span class="n">Child</span><span class="o">.</span><span class="fm">__getattr__</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span><span class="n">name</span><span class="p">)</span>
+ <span class="k">except</span> <span class="ne">Exception</span> <span class="k">as</span> <span class="n">e</span><span class="p">:</span>
+ <span class="k">if</span> <span class="s1">'type_'</span> <span class="ow">in</span> <span class="bp">self</span><span class="o">.</span><span class="vm">__dict__</span><span class="p">:</span>
+ <span class="k">if</span> <span class="n">name</span> <span class="o">==</span> <span class="s1">'parent'</span><span class="p">:</span>
+ <span class="k">raise</span> <span class="ne">Exception</span><span class="p">(</span><span class="s1">'Programming error'</span><span class="p">)</span>
+ <span class="k">return</span> <span class="nb">getattr</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">type_</span><span class="p">,</span> <span class="n">name</span><span class="p">)</span>
+ <span class="k">else</span><span class="p">:</span>
+ <span class="k">raise</span> <span class="ne">AttributeError</span><span class="p">(</span><span class="s2">"'</span><span class="si">{}</span><span class="s2">' object has no attribute '</span><span class="si">{}</span><span class="s2">'"</span><span class="o">.</span><span class="n">format</span><span class="p">(</span><span class="nb">type</span><span class="p">(</span><span class="bp">self</span><span class="p">)</span><span class="o">.</span><span class="vm">__name__</span><span class="p">,</span> <span class="n">name</span><span class="p">))</span>
+
+ <span class="k">def</span><span class="w"> </span><span class="nf">_get_psfpdb_dictionary</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span>
+ <span class="n">p</span> <span class="o">=</span> <span class="bp">self</span>
+ <span class="k">try</span><span class="p">:</span>
+ <span class="n">segname</span> <span class="o">=</span> <span class="n">p</span><span class="o">.</span><span class="n">segname</span>
+ <span class="k">except</span><span class="p">:</span>
+ <span class="n">segname</span> <span class="o">=</span> <span class="s2">"A"</span>
+ <span class="k">try</span><span class="p">:</span>
+ <span class="n">chain</span> <span class="o">=</span> <span class="n">p</span><span class="o">.</span><span class="n">chain</span>
+ <span class="k">except</span><span class="p">:</span>
+ <span class="n">chain</span> <span class="o">=</span> <span class="s2">"A"</span>
+ <span class="k">try</span><span class="p">:</span>
+ <span class="n">resname</span> <span class="o">=</span> <span class="n">p</span><span class="o">.</span><span class="n">resname</span>
+ <span class="k">except</span><span class="p">:</span>
+ <span class="n">resname</span> <span class="o">=</span> <span class="n">p</span><span class="o">.</span><span class="n">name</span><span class="p">[:</span><span class="mi">3</span><span class="p">]</span>
+ <span class="k">try</span><span class="p">:</span>
+ <span class="n">resid</span> <span class="o">=</span> <span class="n">p</span><span class="o">.</span><span class="n">resid</span>
+ <span class="k">except</span><span class="p">:</span>
+ <span class="n">resid</span> <span class="o">=</span> <span class="n">p</span><span class="o">.</span><span class="n">idx</span><span class="o">+</span><span class="mi">1</span>
+ <span class="k">try</span><span class="p">:</span>
+ <span class="n">mass</span> <span class="o">=</span> <span class="n">p</span><span class="o">.</span><span class="n">mass</span>
+ <span class="k">if</span> <span class="n">mass</span> <span class="ow">is</span> <span class="kc">None</span><span class="p">:</span> <span class="k">raise</span>
+ <span class="k">except</span><span class="p">:</span>
+ <span class="n">mass</span> <span class="o">=</span> <span class="mi">1</span>
+
+ <span class="k">try</span><span class="p">:</span>
+ <span class="n">occ</span> <span class="o">=</span> <span class="n">p</span><span class="o">.</span><span class="n">occupancy</span>
+ <span class="k">except</span><span class="p">:</span>
+ <span class="n">occ</span> <span class="o">=</span> <span class="mi">0</span>
+ <span class="k">try</span><span class="p">:</span>
+ <span class="n">beta</span> <span class="o">=</span> <span class="n">p</span><span class="o">.</span><span class="n">beta</span>
+ <span class="k">except</span><span class="p">:</span>
+ <span class="n">beta</span> <span class="o">=</span> <span class="mi">0</span>
+
+ <span class="n">data</span> <span class="o">=</span> <span class="nb">dict</span><span class="p">(</span><span class="n">segname</span> <span class="o">=</span> <span class="n">segname</span><span class="p">,</span>
+ <span class="n">resname</span> <span class="o">=</span> <span class="n">resname</span><span class="p">,</span>
+ <span class="n">name</span> <span class="o">=</span> <span class="nb">str</span><span class="p">(</span><span class="n">p</span><span class="o">.</span><span class="n">name</span><span class="p">)[:</span><span class="mi">4</span><span class="p">],</span>
+ <span class="n">chain</span> <span class="o">=</span> <span class="n">chain</span><span class="p">[</span><span class="mi">0</span><span class="p">],</span>
+ <span class="n">resid</span> <span class="o">=</span> <span class="nb">int</span><span class="p">(</span><span class="n">resid</span><span class="p">),</span>
+ <span class="n">idx</span> <span class="o">=</span> <span class="n">p</span><span class="o">.</span><span class="n">idx</span><span class="o">+</span><span class="mi">1</span><span class="p">,</span>
+ <span class="nb">type</span> <span class="o">=</span> <span class="n">p</span><span class="o">.</span><span class="n">type_</span><span class="o">.</span><span class="n">name</span><span class="p">[:</span><span class="mi">7</span><span class="p">],</span>
+ <span class="n">charge</span> <span class="o">=</span> <span class="n">p</span><span class="o">.</span><span class="n">charge</span><span class="p">,</span>
+ <span class="n">mass</span> <span class="o">=</span> <span class="n">mass</span><span class="p">,</span>
+ <span class="n">occupancy</span> <span class="o">=</span> <span class="n">occ</span><span class="p">,</span>
+ <span class="n">beta</span> <span class="o">=</span> <span class="n">beta</span>
+ <span class="p">)</span>
+ <span class="k">return</span> <span class="n">data</span>
+
+ <span class="k">def</span><span class="w"> </span><span class="fm">__repr__</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span>
+ <span class="k">return</span> <span class="sa">f</span><span class="s1">'<</span><span class="si">{</span><span class="vm">__name__</span><span class="si">}</span><span class="s1">.</span><span class="si">{</span><span class="bp">self</span><span class="o">.</span><span class="vm">__class__</span><span class="o">.</span><span class="vm">__name__</span><span class="si">}</span><span class="s1"> "</span><span class="si">{</span><span class="bp">self</span><span class="o">.</span><span class="n">name</span><span class="si">}</span><span class="s1">" of </span><span class="si">{</span><span class="bp">self</span><span class="o">.</span><span class="n">type_</span><span class="si">}</span><span class="s1">>'</span></div>
+
+
+<div class="viewcode-block" id="RigidBody">
+<a class="viewcode-back" href="../../api/core/core_objects.html#arbdmodel.core_objects.RigidBody">[docs]</a>
+<span class="k">class</span><span class="w"> </span><span class="nc">RigidBody</span><span class="p">(</span><span class="n">PointParticle</span><span class="p">):</span>
+
+ <span class="k">def</span><span class="w"> </span><span class="fm">__init__</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">type_</span><span class="p">,</span> <span class="n">position</span><span class="p">,</span> <span class="n">orientation</span><span class="p">,</span> <span class="n">name</span><span class="o">=</span><span class="s2">"A"</span><span class="p">,</span> <span class="n">attached_particles</span><span class="o">=</span><span class="nb">tuple</span><span class="p">(),</span> <span class="o">**</span><span class="n">kwargs</span><span class="p">):</span>
+ <span class="n">parent</span> <span class="o">=</span> <span class="kc">None</span>
+ <span class="k">if</span> <span class="s1">'parent'</span> <span class="ow">in</span> <span class="n">kwargs</span><span class="p">:</span>
+ <span class="n">parent</span> <span class="o">=</span> <span class="n">kwargs</span><span class="p">[</span><span class="s1">'parent'</span><span class="p">]</span>
+ <span class="n">Child</span><span class="o">.</span><span class="fm">__init__</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">parent</span><span class="o">=</span><span class="n">parent</span><span class="p">)</span>
+ <span class="n">Transformable</span><span class="o">.</span><span class="fm">__init__</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span><span class="n">position</span><span class="p">,</span> <span class="n">orientation</span><span class="p">)</span>
+
+ <span class="k">if</span> <span class="nb">type</span><span class="p">(</span><span class="n">type_</span><span class="p">)</span> <span class="o">!=</span> <span class="n">RigidBodyType</span><span class="p">:</span>
+ <span class="k">raise</span> <span class="ne">ValueError</span><span class="p">(</span><span class="sa">f</span><span class="s1">'Attempted to create a RigidBody object from an invalid type </span><span class="si">{</span><span class="n">type_</span><span class="si">}</span><span class="s1">'</span><span class="p">)</span>
+
+ <span class="bp">self</span><span class="o">.</span><span class="n">type_</span> <span class="o">=</span> <span class="n">type_</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">idx</span> <span class="o">=</span> <span class="kc">None</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">name</span> <span class="o">=</span> <span class="n">name</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">counter</span> <span class="o">=</span> <span class="mi">0</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">restraints</span> <span class="o">=</span> <span class="p">[]</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">rigid</span> <span class="o">=</span> <span class="kc">True</span>
+
+ <span class="c1">## TODO: it should be possible to uniquely apply bonds/angles etc to these particles, but their types should be fixed or otherwise unified among rbs; here we are copying them simply so that they can recieve and index and be used in bonded potentials and group sites</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">attached_particles</span> <span class="o">=</span> <span class="p">[</span><span class="n">copy</span><span class="p">(</span><span class="n">p</span><span class="p">)</span> <span class="k">for</span> <span class="n">p</span> <span class="ow">in</span> <span class="n">type_</span><span class="o">.</span><span class="n">attached_particles</span><span class="p">]</span>
+
+ <span class="k">for</span> <span class="n">key</span><span class="p">,</span><span class="n">val</span> <span class="ow">in</span> <span class="n">kwargs</span><span class="o">.</span><span class="n">items</span><span class="p">():</span>
+ <span class="bp">self</span><span class="o">.</span><span class="vm">__dict__</span><span class="p">[</span><span class="n">key</span><span class="p">]</span> <span class="o">=</span> <span class="n">val</span>
+
+<div class="viewcode-block" id="RigidBody.add_restraint">
+<a class="viewcode-back" href="../../api/core/core_objects.html#arbdmodel.core_objects.RigidBody.add_restraint">[docs]</a>
+ <span class="k">def</span><span class="w"> </span><span class="nf">add_restraint</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">restraint</span><span class="p">):</span>
+ <span class="k">raise</span> <span class="ne">NotImplementedError</span><span class="p">(</span><span class="s1">'Harmonic restraints are not yet supported for rigid bodies; consider implementing this by attaching a dummy particle'</span><span class="p">)</span>
+ <span class="c1">## TODO: how to handle duplicating and cloning bonds</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">restraints</span><span class="o">.</span><span class="n">append</span><span class="p">(</span> <span class="n">restraint</span> <span class="p">)</span></div>
+
+
+<div class="viewcode-block" id="RigidBody.get_restraints">
+<a class="viewcode-back" href="../../api/core/core_objects.html#arbdmodel.core_objects.RigidBody.get_restraints">[docs]</a>
+ <span class="k">def</span><span class="w"> </span><span class="nf">get_restraints</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span>
+ <span class="k">return</span> <span class="p">[(</span><span class="bp">self</span><span class="p">,</span><span class="n">r</span><span class="p">)</span> <span class="k">for</span> <span class="n">r</span> <span class="ow">in</span> <span class="bp">self</span><span class="o">.</span><span class="n">restraints</span><span class="p">]</span></div>
+
+
+<div class="viewcode-block" id="RigidBody.duplicate">
+<a class="viewcode-back" href="../../api/core/core_objects.html#arbdmodel.core_objects.RigidBody.duplicate">[docs]</a>
+ <span class="k">def</span><span class="w"> </span><span class="nf">duplicate</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span>
+ <span class="n">new</span> <span class="o">=</span> <span class="n">deepcopy</span><span class="p">(</span><span class="bp">self</span><span class="p">)</span>
+ <span class="k">return</span> <span class="n">new</span></div>
+
+
+ <span class="k">def</span><span class="w"> </span><span class="fm">__getattr__</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">name</span><span class="p">):</span>
+<span class="w"> </span><span class="sd">"""</span>
+<span class="sd"> First try to get attribute from the parent, then type_</span>
+<span class="sd"> </span>
+<span class="sd"> Note that this data structure seems to be fragile, can result in stack overflow</span>
+<span class="sd"> </span>
+<span class="sd"> """</span>
+ <span class="c1"># return Child.__getattr__(self,name)</span>
+ <span class="k">try</span><span class="p">:</span>
+ <span class="k">return</span> <span class="n">Child</span><span class="o">.</span><span class="fm">__getattr__</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span><span class="n">name</span><span class="p">)</span>
+ <span class="k">except</span> <span class="ne">Exception</span> <span class="k">as</span> <span class="n">e</span><span class="p">:</span>
+ <span class="k">if</span> <span class="s1">'type_'</span> <span class="ow">in</span> <span class="bp">self</span><span class="o">.</span><span class="vm">__dict__</span><span class="p">:</span>
+ <span class="k">return</span> <span class="nb">getattr</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">type_</span><span class="p">,</span> <span class="n">name</span><span class="p">)</span>
+ <span class="k">else</span><span class="p">:</span>
+ <span class="k">raise</span> <span class="ne">AttributeError</span><span class="p">(</span><span class="sa">r</span><span class="s2">"'{type(self).__name__}' object has no attribute '</span><span class="si">{name}</span><span class="s2">'"</span><span class="p">)</span></div>
+
+
+<div class="viewcode-block" id="Group">
+<a class="viewcode-back" href="../../api/core/core_objects.html#arbdmodel.core_objects.Group">[docs]</a>
+<span class="k">class</span><span class="w"> </span><span class="nc">Group</span><span class="p">(</span><span class="n">Transformable</span><span class="p">,</span> <span class="n">Parent</span><span class="p">,</span> <span class="n">Child</span><span class="p">):</span>
+
+ <span class="k">def</span><span class="w"> </span><span class="fm">__init__</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">name</span><span class="o">=</span><span class="kc">None</span><span class="p">,</span> <span class="n">children</span> <span class="o">=</span> <span class="kc">None</span><span class="p">,</span> <span class="n">parent</span><span class="o">=</span><span class="kc">None</span><span class="p">,</span>
+ <span class="n">position</span> <span class="o">=</span> <span class="n">np</span><span class="o">.</span><span class="n">array</span><span class="p">((</span><span class="mi">0</span><span class="p">,</span><span class="mi">0</span><span class="p">,</span><span class="mi">0</span><span class="p">)),</span>
+ <span class="n">orientation</span> <span class="o">=</span> <span class="n">np</span><span class="o">.</span><span class="n">array</span><span class="p">(((</span><span class="mi">1</span><span class="p">,</span><span class="mi">0</span><span class="p">,</span><span class="mi">0</span><span class="p">),(</span><span class="mi">0</span><span class="p">,</span><span class="mi">1</span><span class="p">,</span><span class="mi">0</span><span class="p">),(</span><span class="mi">0</span><span class="p">,</span><span class="mi">0</span><span class="p">,</span><span class="mi">1</span><span class="p">))),</span>
+ <span class="n">remove_duplicate_bonded_terms</span> <span class="o">=</span> <span class="kc">False</span><span class="p">,</span>
+ <span class="o">**</span><span class="n">kwargs</span><span class="p">):</span>
+
+ <span class="n">Transformable</span><span class="o">.</span><span class="fm">__init__</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">position</span><span class="p">,</span> <span class="n">orientation</span><span class="p">)</span>
+ <span class="n">Child</span><span class="o">.</span><span class="fm">__init__</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">parent</span><span class="p">)</span> <span class="c1"># Initialize Child first</span>
+ <span class="n">Parent</span><span class="o">.</span><span class="fm">__init__</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">children</span><span class="p">,</span> <span class="n">remove_duplicate_bonded_terms</span><span class="p">)</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">name</span> <span class="o">=</span> <span class="n">name</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">isClone</span> <span class="o">=</span> <span class="kc">False</span>
+
+ <span class="k">for</span> <span class="n">key</span><span class="p">,</span><span class="n">val</span> <span class="ow">in</span> <span class="n">kwargs</span><span class="o">.</span><span class="n">items</span><span class="p">():</span>
+ <span class="bp">self</span><span class="o">.</span><span class="vm">__dict__</span><span class="p">[</span><span class="n">key</span><span class="p">]</span> <span class="o">=</span> <span class="n">val</span>
+
+
+<div class="viewcode-block" id="Group.clone">
+<a class="viewcode-back" href="../../api/core/core_objects.html#arbdmodel.core_objects.Group.clone">[docs]</a>
+ <span class="k">def</span><span class="w"> </span><span class="nf">clone</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span>
+ <span class="k">return</span> <span class="n">Clone</span><span class="p">(</span><span class="bp">self</span><span class="p">)</span>
+ <span class="n">g</span> <span class="o">=</span> <span class="n">copy</span><span class="p">(</span><span class="bp">self</span><span class="p">)</span>
+ <span class="n">g</span><span class="o">.</span><span class="n">isClone</span> <span class="o">=</span> <span class="kc">True</span> <span class="c1"># TODO: use?</span>
+ <span class="n">g</span><span class="o">.</span><span class="n">children</span> <span class="o">=</span> <span class="p">[</span><span class="n">copy</span><span class="p">(</span><span class="n">c</span><span class="p">)</span> <span class="k">for</span> <span class="n">c</span> <span class="ow">in</span> <span class="n">g</span><span class="o">.</span><span class="n">children</span><span class="p">]</span>
+ <span class="k">for</span> <span class="n">c</span> <span class="ow">in</span> <span class="n">g</span><span class="o">.</span><span class="n">children</span><span class="p">:</span>
+ <span class="n">c</span><span class="o">.</span><span class="n">parent</span> <span class="o">=</span> <span class="n">g</span>
+ <span class="k">return</span> <span class="n">g</span>
+ <span class="n">g</span> <span class="o">=</span> <span class="n">Group</span><span class="p">(</span><span class="n">position</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">position</span><span class="p">,</span>
+ <span class="n">orientation</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">orientation</span><span class="p">)</span>
+ <span class="n">g</span><span class="o">.</span><span class="n">children</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">children</span> <span class="c1"># lists point to the same object</span></div>
+
+
+<div class="viewcode-block" id="Group.duplicate">
+<a class="viewcode-back" href="../../api/core/core_objects.html#arbdmodel.core_objects.Group.duplicate">[docs]</a>
+ <span class="k">def</span><span class="w"> </span><span class="nf">duplicate</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span>
+ <span class="n">new</span> <span class="o">=</span> <span class="n">deepcopy</span><span class="p">(</span><span class="bp">self</span><span class="p">)</span>
+ <span class="k">for</span> <span class="n">c</span> <span class="ow">in</span> <span class="n">new</span><span class="o">.</span><span class="n">children</span><span class="p">:</span>
+ <span class="n">c</span><span class="o">.</span><span class="n">parent</span> <span class="o">=</span> <span class="n">new</span>
+ <span class="k">return</span> <span class="n">new</span></div>
+</div>
+
+
+ <span class="c1">## TODO override deepcopy so parent can be excluded from copying?</span>
+
+ <span class="c1"># def __getstate__(self):</span>
+ <span class="c1"># return (self.children, self.parent, self.position, self.orientation)</span>
+
+ <span class="c1"># def __setstate__(self, state):</span>
+ <span class="c1"># self.children, self.parent, self.position, self.orientation = state</span>
+
+<span class="c1">#Not sure where should it go</span>
+<div class="viewcode-block" id="GroupSite">
+<a class="viewcode-back" href="../../api/core/core_objects.html#arbdmodel.core_objects.GroupSite">[docs]</a>
+<span class="k">class</span><span class="w"> </span><span class="nc">GroupSite</span><span class="p">:</span>
+<span class="w"> </span><span class="sd">""" Class to represent a collection of particles that can be used by bond potentials. In arbdmodel only """</span>
+ <span class="k">def</span><span class="w"> </span><span class="fm">__init__</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">particles</span><span class="p">,</span> <span class="n">weights</span><span class="o">=</span><span class="kc">None</span><span class="p">):</span>
+ <span class="k">if</span> <span class="n">weights</span> <span class="ow">is</span> <span class="ow">not</span> <span class="kc">None</span><span class="p">:</span>
+ <span class="k">raise</span> <span class="ne">NotImplementedError</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">particles</span> <span class="o">=</span> <span class="n">particles</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">idx</span> <span class="o">=</span> <span class="kc">None</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">restraints</span> <span class="o">=</span> <span class="p">[]</span>
+
+<div class="viewcode-block" id="GroupSite.get_center">
+<a class="viewcode-back" href="../../api/core/core_objects.html#arbdmodel.core_objects.GroupSite.get_center">[docs]</a>
+ <span class="k">def</span><span class="w"> </span><span class="nf">get_center</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span>
+ <span class="n">c</span> <span class="o">=</span> <span class="n">np</span><span class="o">.</span><span class="n">array</span><span class="p">((</span><span class="mi">0</span><span class="p">,</span><span class="mi">0</span><span class="p">,</span><span class="mi">0</span><span class="p">))</span>
+ <span class="k">for</span> <span class="n">p</span> <span class="ow">in</span> <span class="bp">self</span><span class="o">.</span><span class="n">particles</span><span class="p">:</span>
+ <span class="n">c</span> <span class="o">=</span> <span class="n">c</span> <span class="o">+</span> <span class="n">p</span><span class="o">.</span><span class="n">get_collapsed_position</span><span class="p">()</span>
+ <span class="n">c</span> <span class="o">=</span> <span class="n">c</span> <span class="o">/</span> <span class="nb">len</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">particles</span><span class="p">)</span>
+ <span class="k">return</span> <span class="n">c</span></div>
+
+
+<div class="viewcode-block" id="GroupSite.add_restraint">
+<a class="viewcode-back" href="../../api/core/core_objects.html#arbdmodel.core_objects.GroupSite.add_restraint">[docs]</a>
+ <span class="k">def</span><span class="w"> </span><span class="nf">add_restraint</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">restraint</span><span class="p">):</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">restraints</span><span class="o">.</span><span class="n">append</span><span class="p">(</span><span class="n">restraint</span><span class="p">)</span></div>
+
+
+<div class="viewcode-block" id="GroupSite.get_restraints">
+<a class="viewcode-back" href="../../api/core/core_objects.html#arbdmodel.core_objects.GroupSite.get_restraints">[docs]</a>
+ <span class="k">def</span><span class="w"> </span><span class="nf">get_restraints</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span>
+ <span class="k">return</span> <span class="p">[(</span><span class="bp">self</span><span class="p">,</span> <span class="n">r</span><span class="p">)</span> <span class="k">for</span> <span class="n">r</span> <span class="ow">in</span> <span class="bp">self</span><span class="o">.</span><span class="n">restraints</span><span class="p">]</span></div>
+</div>
+
+
+</pre></div>
+
+ </article>
+
+
+
+
+
+
+ <footer class="prev-next-footer d-print-none">
+
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+
+ <footer class="bd-footer">
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+</html>
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diff --git a/_build/html/_modules/arbdmodel/engine.html b/_build/html/_modules/arbdmodel/engine.html
new file mode 100644
index 0000000000000000000000000000000000000000..d6ee79f69a2270a038e340148eb6ee7c874a8cd4
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+ </div>
+</div>
+
+
+
+<div id="searchbox"></div>
+ <article class="bd-article">
+
+ <h1>Source code for arbdmodel.engine</h1><div class="highlight"><pre>
+<span></span><span class="c1">## Import packages</span>
+<span class="kn">from</span><span class="w"> </span><span class="nn">pathlib</span><span class="w"> </span><span class="kn">import</span> <span class="n">Path</span>
+<span class="kn">import</span><span class="w"> </span><span class="nn">numpy</span><span class="w"> </span><span class="k">as</span><span class="w"> </span><span class="nn">np</span>
+<span class="kn">import</span><span class="w"> </span><span class="nn">os</span><span class="o">,</span><span class="w"> </span><span class="nn">sys</span><span class="o">,</span><span class="w"> </span><span class="nn">subprocess</span>
+<span class="kn">import</span><span class="w"> </span><span class="nn">platform</span>
+<span class="kn">from</span><span class="w"> </span><span class="nn">abc</span><span class="w"> </span><span class="kn">import</span> <span class="n">abstractmethod</span><span class="p">,</span> <span class="n">ABCMeta</span>
+<span class="kn">import</span><span class="w"> </span><span class="nn">shutil</span>
+<span class="kn">from</span><span class="w"> </span><span class="nn">.core_objects</span><span class="w"> </span><span class="kn">import</span> <span class="n">GroupSite</span>
+<span class="kn">from</span><span class="w"> </span><span class="nn">.logger</span><span class="w"> </span><span class="kn">import</span> <span class="n">devlogger</span><span class="p">,</span> <span class="n">logger</span><span class="p">,</span> <span class="n">get_resource_path</span>
+<span class="kn">from</span><span class="w"> </span><span class="nn">.interactions</span><span class="w"> </span><span class="kn">import</span> <span class="n">NullPotential</span>
+<span class="kn">from</span><span class="w"> </span><span class="nn">.sim_config</span><span class="w"> </span><span class="kn">import</span> <span class="n">SimConf</span>
+
+
+<span class="sd">""" SimEngines</span>
+<span class="sd">Abstract classes for running simulations with different engines.</span>
+<span class="sd">SimEngine is the base class for all simulation engines.</span>
+<span class="sd">"""</span>
+<div class="viewcode-block" id="SimEngine">
+<a class="viewcode-back" href="../../api/simulation_engines/engine.html#arbdmodel.engine.SimEngine">[docs]</a>
+<span class="k">class</span><span class="w"> </span><span class="nc">SimEngine</span><span class="p">(</span><span class="n">metaclass</span><span class="o">=</span><span class="n">ABCMeta</span><span class="p">):</span>
+<span class="w"> </span><span class="sd">""" Abstract class for running a simulation of a model """</span>
+ <span class="k">def</span><span class="w"> </span><span class="fm">__init__</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">configuration</span><span class="o">=</span><span class="kc">None</span><span class="p">):</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">configuration</span> <span class="o">=</span> <span class="n">configuration</span>
+
+ <span class="nd">@property</span>
+ <span class="nd">@abstractmethod</span>
+ <span class="k">def</span><span class="w"> </span><span class="nf">default_binary</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span>
+ <span class="o">...</span>
+
+ <span class="nd">@abstractmethod</span>
+ <span class="k">def</span><span class="w"> </span><span class="nf">_generate_command_string</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">binary</span><span class="p">,</span> <span class="n">output_name</span><span class="p">,</span> <span class="n">output_directory</span><span class="p">,</span> <span class="n">gpu</span><span class="o">=</span><span class="mi">0</span><span class="p">,</span> <span class="n">replicas</span><span class="o">=</span><span class="mi">1</span><span class="p">):</span>
+ <span class="o">...</span>
+
+<div class="viewcode-block" id="SimEngine.write_simulation_files">
+<a class="viewcode-back" href="../../api/simulation_engines/engine.html#arbdmodel.engine.SimEngine.write_simulation_files">[docs]</a>
+ <span class="nd">@abstractmethod</span>
+ <span class="k">def</span><span class="w"> </span><span class="nf">write_simulation_files</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">model</span><span class="p">,</span> <span class="n">output_name</span><span class="p">):</span>
+ <span class="o">...</span></div>
+
+
+<div class="viewcode-block" id="SimEngine.get_default_conf">
+<a class="viewcode-back" href="../../api/simulation_engines/engine.html#arbdmodel.engine.SimEngine.get_default_conf">[docs]</a>
+ <span class="nd">@abstractmethod</span>
+ <span class="k">def</span><span class="w"> </span><span class="nf">get_default_conf</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span>
+ <span class="o">...</span></div>
+
+
+<div class="viewcode-block" id="SimEngine.simulate">
+<a class="viewcode-back" href="../../api/simulation_engines/engine.html#arbdmodel.engine.SimEngine.simulate">[docs]</a>
+ <span class="k">def</span><span class="w"> </span><span class="nf">simulate</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">model</span><span class="p">,</span> <span class="n">output_name</span><span class="p">,</span> <span class="n">output_directory</span><span class="o">=</span><span class="s1">'output'</span><span class="p">,</span>
+ <span class="n">directory</span><span class="o">=</span><span class="s1">'.'</span><span class="p">,</span> <span class="n">log_file</span><span class="o">=</span><span class="kc">None</span><span class="p">,</span>
+ <span class="n">binary</span><span class="o">=</span><span class="kc">None</span><span class="p">,</span> <span class="n">num_procs</span><span class="o">=</span><span class="kc">None</span><span class="p">,</span> <span class="n">dry_run</span> <span class="o">=</span> <span class="kc">False</span><span class="p">,</span> <span class="n">configuration</span> <span class="o">=</span> <span class="kc">None</span><span class="p">,</span> <span class="n">replicas</span> <span class="o">=</span> <span class="mi">1</span><span class="p">,</span> <span class="o">**</span><span class="n">conf_params</span><span class="p">):</span>
+
+ <span class="c1">## TODO: Allow _get_combined_conf to take certain parameters as arguments, or otherwise refactor to make this more elegant</span>
+ <span class="n">gpu</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">_get_combined_conf</span><span class="p">(</span><span class="n">model</span><span class="p">,</span> <span class="o">**</span><span class="n">conf_params</span><span class="p">)</span><span class="o">.</span><span class="n">gpu</span>
+ <span class="k">assert</span><span class="p">(</span><span class="nb">type</span><span class="p">(</span><span class="n">gpu</span><span class="p">)</span> <span class="ow">is</span> <span class="nb">int</span><span class="p">)</span>
+
+ <span class="k">if</span> <span class="n">num_procs</span> <span class="ow">is</span> <span class="kc">None</span><span class="p">:</span>
+ <span class="kn">import</span><span class="w"> </span><span class="nn">multiprocessing</span>
+ <span class="n">num_procs</span> <span class="o">=</span> <span class="nb">max</span><span class="p">(</span><span class="mi">1</span><span class="p">,</span><span class="n">multiprocessing</span><span class="o">.</span><span class="n">cpu_count</span><span class="p">()</span><span class="o">-</span><span class="mi">1</span><span class="p">)</span>
+
+ <span class="n">d_orig</span> <span class="o">=</span> <span class="n">os</span><span class="o">.</span><span class="n">getcwd</span><span class="p">()</span>
+ <span class="k">try</span><span class="p">:</span>
+ <span class="n">model</span><span class="o">.</span><span class="n">_d_orig</span> <span class="o">=</span> <span class="n">d_orig</span>
+ <span class="k">if</span> <span class="ow">not</span> <span class="n">os</span><span class="o">.</span><span class="n">path</span><span class="o">.</span><span class="n">exists</span><span class="p">(</span><span class="n">directory</span><span class="p">):</span>
+ <span class="n">os</span><span class="o">.</span><span class="n">makedirs</span><span class="p">(</span><span class="n">directory</span><span class="p">)</span>
+ <span class="n">os</span><span class="o">.</span><span class="n">chdir</span><span class="p">(</span><span class="n">directory</span><span class="p">)</span>
+
+ <span class="n">model</span><span class="o">.</span><span class="n">prepare_for_simulation</span><span class="p">()</span>
+
+ <span class="k">if</span> <span class="n">output_directory</span> <span class="o">==</span> <span class="s1">''</span><span class="p">:</span> <span class="n">output_directory</span><span class="o">=</span><span class="s1">'.'</span>
+
+ <span class="k">if</span> <span class="n">dry_run</span><span class="p">:</span>
+ <span class="k">if</span> <span class="n">binary</span> <span class="ow">is</span> <span class="kc">None</span><span class="p">:</span> <span class="n">binary</span><span class="o">=</span><span class="bp">self</span><span class="o">.</span><span class="n">default_binary</span>
+ <span class="k">else</span><span class="p">:</span>
+ <span class="n">binary</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">_get_binary</span><span class="p">(</span><span class="n">binary</span><span class="p">)</span>
+
+ <span class="k">if</span> <span class="ow">not</span> <span class="n">os</span><span class="o">.</span><span class="n">path</span><span class="o">.</span><span class="n">exists</span><span class="p">(</span><span class="n">output_directory</span><span class="p">):</span>
+ <span class="n">os</span><span class="o">.</span><span class="n">makedirs</span><span class="p">(</span><span class="n">output_directory</span><span class="p">)</span>
+ <span class="k">elif</span> <span class="ow">not</span> <span class="n">os</span><span class="o">.</span><span class="n">path</span><span class="o">.</span><span class="n">isdir</span><span class="p">(</span><span class="n">output_directory</span><span class="p">):</span>
+ <span class="k">raise</span> <span class="ne">Exception</span><span class="p">(</span><span class="s2">"output_directory '</span><span class="si">%s</span><span class="s2">' is not a directory!"</span> <span class="o">%</span> <span class="n">output_directory</span><span class="p">)</span>
+
+ <span class="bp">self</span><span class="o">.</span><span class="n">write_simulation_files</span><span class="p">(</span><span class="n">model</span><span class="p">,</span> <span class="n">output_name</span><span class="p">,</span> <span class="n">configuration</span><span class="p">,</span> <span class="o">**</span><span class="n">conf_params</span><span class="p">)</span>
+
+ <span class="c1">## http://stackoverflow.com/questions/18421757/live-output-from-subprocess-command</span>
+ <span class="n">cmd</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">_generate_command_string</span><span class="p">(</span><span class="n">binary</span><span class="p">,</span> <span class="n">output_name</span><span class="p">,</span> <span class="n">output_directory</span><span class="p">,</span> <span class="n">num_procs</span><span class="p">,</span> <span class="n">gpu</span><span class="p">,</span> <span class="n">replicas</span><span class="p">)</span>
+
+ <span class="k">if</span> <span class="n">dry_run</span><span class="p">:</span>
+ <span class="n">logger</span><span class="o">.</span><span class="n">info</span><span class="p">(</span><span class="sa">f</span><span class="s1">'Run with: </span><span class="si">{</span><span class="s2">" "</span><span class="o">.</span><span class="n">join</span><span class="p">(</span><span class="n">cmd</span><span class="p">)</span><span class="si">}</span><span class="s1">'</span><span class="p">)</span>
+ <span class="k">else</span><span class="p">:</span>
+ <span class="n">logger</span><span class="o">.</span><span class="n">info</span><span class="p">(</span><span class="sa">f</span><span class="s1">'Running </span><span class="si">{</span><span class="bp">self</span><span class="o">.</span><span class="n">default_binary</span><span class="si">}</span><span class="s1"> with: </span><span class="si">{</span><span class="s2">" "</span><span class="o">.</span><span class="n">join</span><span class="p">(</span><span class="n">cmd</span><span class="p">)</span><span class="si">}</span><span class="s1">'</span><span class="p">)</span>
+ <span class="k">if</span> <span class="n">log_file</span> <span class="ow">is</span> <span class="kc">None</span> <span class="ow">or</span> <span class="p">(</span><span class="nb">hasattr</span><span class="p">(</span><span class="n">log_file</span><span class="p">,</span><span class="s1">'write'</span><span class="p">)</span> <span class="ow">and</span> <span class="nb">callable</span><span class="p">(</span><span class="n">log_file</span><span class="o">.</span><span class="n">write</span><span class="p">)):</span>
+ <span class="n">fd</span> <span class="o">=</span> <span class="n">sys</span><span class="o">.</span><span class="n">stdout</span> <span class="k">if</span> <span class="n">log_file</span> <span class="ow">is</span> <span class="kc">None</span> <span class="k">else</span> <span class="n">log_file</span>
+ <span class="n">process</span> <span class="o">=</span> <span class="n">subprocess</span><span class="o">.</span><span class="n">Popen</span><span class="p">(</span><span class="n">cmd</span><span class="p">,</span> <span class="n">stdout</span><span class="o">=</span><span class="n">subprocess</span><span class="o">.</span><span class="n">PIPE</span><span class="p">,</span> <span class="n">shell</span><span class="o">=</span><span class="kc">False</span><span class="p">)</span> <span class="c1"># , universal_newlines=True)</span>
+ <span class="c1">## re-open to get \r recognized as new line</span>
+ <span class="k">with</span> <span class="nb">open</span><span class="p">(</span><span class="n">os</span><span class="o">.</span><span class="n">dup</span><span class="p">(</span><span class="n">process</span><span class="o">.</span><span class="n">stdout</span><span class="o">.</span><span class="n">fileno</span><span class="p">()),</span> <span class="n">newline</span><span class="o">=</span><span class="s1">''</span><span class="p">)</span> <span class="k">as</span> <span class="n">nice_stdout</span><span class="p">:</span>
+ <span class="k">for</span> <span class="n">line</span> <span class="ow">in</span> <span class="n">nice_stdout</span><span class="p">:</span>
+ <span class="k">try</span><span class="p">:</span>
+ <span class="n">fd</span><span class="o">.</span><span class="n">write</span><span class="p">(</span><span class="n">line</span><span class="p">)</span>
+ <span class="k">except</span><span class="p">:</span>
+ <span class="nb">print</span><span class="p">(</span><span class="s2">"WARNING: could not encode line; your locale might not be set correctly"</span><span class="p">)</span>
+ <span class="n">fd</span><span class="o">.</span><span class="n">flush</span><span class="p">()</span>
+ <span class="k">else</span><span class="p">:</span>
+ <span class="k">with</span> <span class="nb">open</span><span class="p">(</span><span class="n">log_file</span><span class="p">,</span><span class="s1">'w'</span><span class="p">)</span> <span class="k">as</span> <span class="n">fd</span><span class="p">:</span>
+ <span class="n">process</span> <span class="o">=</span> <span class="n">subprocess</span><span class="o">.</span><span class="n">Popen</span><span class="p">(</span><span class="n">cmd</span><span class="p">,</span> <span class="n">stdout</span><span class="o">=</span><span class="n">log_file</span><span class="p">,</span> <span class="n">universal_newlines</span><span class="o">=</span><span class="kc">True</span><span class="p">)</span>
+ <span class="n">process</span><span class="o">.</span><span class="n">communicate</span><span class="p">()</span>
+
+ <span class="k">except</span><span class="p">:</span>
+ <span class="k">raise</span>
+ <span class="k">finally</span><span class="p">:</span>
+ <span class="k">del</span> <span class="n">model</span><span class="o">.</span><span class="n">_d_orig</span>
+ <span class="n">os</span><span class="o">.</span><span class="n">chdir</span><span class="p">(</span><span class="n">d_orig</span><span class="p">)</span></div>
+
+
+ <span class="k">def</span><span class="w"> </span><span class="nf">_get_binary</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">binary</span><span class="o">=</span><span class="kc">None</span><span class="p">):</span>
+ <span class="k">if</span> <span class="n">binary</span> <span class="ow">is</span> <span class="kc">None</span><span class="p">:</span>
+ <span class="kn">from</span><span class="w"> </span><span class="nn">.binary_manager</span><span class="w"> </span><span class="kn">import</span> <span class="n">BinaryManager</span>
+ <span class="n">binary_name</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">default_binary</span>
+ <span class="n">binary</span> <span class="o">=</span> <span class="n">BinaryManager</span><span class="o">.</span><span class="n">get_binary_path</span><span class="p">(</span><span class="n">binary_name</span><span class="p">)</span>
+
+ <span class="k">if</span> <span class="n">binary</span> <span class="ow">is</span> <span class="kc">None</span><span class="p">:</span>
+ <span class="k">for</span> <span class="n">path</span> <span class="ow">in</span> <span class="n">os</span><span class="o">.</span><span class="n">environ</span><span class="p">[</span><span class="s2">"PATH"</span><span class="p">]</span><span class="o">.</span><span class="n">split</span><span class="p">(</span><span class="n">os</span><span class="o">.</span><span class="n">pathsep</span><span class="p">):</span>
+ <span class="n">path</span> <span class="o">=</span> <span class="n">path</span><span class="o">.</span><span class="n">strip</span><span class="p">(</span><span class="s1">'"'</span><span class="p">)</span>
+ <span class="n">fname</span> <span class="o">=</span> <span class="n">os</span><span class="o">.</span><span class="n">path</span><span class="o">.</span><span class="n">join</span><span class="p">(</span><span class="n">path</span><span class="p">,</span> <span class="bp">self</span><span class="o">.</span><span class="n">default_binary</span><span class="p">)</span>
+ <span class="k">if</span> <span class="n">os</span><span class="o">.</span><span class="n">path</span><span class="o">.</span><span class="n">isfile</span><span class="p">(</span><span class="n">fname</span><span class="p">)</span> <span class="ow">and</span> <span class="n">os</span><span class="o">.</span><span class="n">access</span><span class="p">(</span><span class="n">fname</span><span class="p">,</span> <span class="n">os</span><span class="o">.</span><span class="n">X_OK</span><span class="p">):</span>
+ <span class="n">binary</span> <span class="o">=</span> <span class="n">fname</span>
+ <span class="k">break</span>
+ <span class="k">if</span> <span class="n">binary</span> <span class="ow">is</span> <span class="kc">None</span><span class="p">:</span> <span class="k">raise</span> <span class="ne">Exception</span><span class="p">(</span><span class="s2">"</span><span class="si">{}</span><span class="s2"> was not found"</span><span class="o">.</span><span class="n">format</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">default_binary</span><span class="p">))</span>
+
+ <span class="k">if</span> <span class="ow">not</span> <span class="n">os</span><span class="o">.</span><span class="n">path</span><span class="o">.</span><span class="n">exists</span><span class="p">(</span><span class="n">binary</span><span class="p">):</span>
+ <span class="k">raise</span> <span class="ne">Exception</span><span class="p">(</span><span class="s2">"</span><span class="si">{}</span><span class="s2"> was not found"</span><span class="o">.</span><span class="n">format</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">default_binary</span><span class="p">))</span>
+ <span class="k">if</span> <span class="ow">not</span> <span class="n">os</span><span class="o">.</span><span class="n">path</span><span class="o">.</span><span class="n">isfile</span><span class="p">(</span><span class="n">binary</span><span class="p">):</span>
+ <span class="k">raise</span> <span class="ne">Exception</span><span class="p">(</span><span class="s2">"</span><span class="si">{}</span><span class="s2"> was not found"</span><span class="o">.</span><span class="n">format</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">default_binary</span><span class="p">))</span>
+ <span class="k">if</span> <span class="ow">not</span> <span class="n">os</span><span class="o">.</span><span class="n">access</span><span class="p">(</span><span class="n">binary</span><span class="p">,</span> <span class="n">os</span><span class="o">.</span><span class="n">X_OK</span><span class="p">):</span>
+ <span class="k">raise</span> <span class="ne">Exception</span><span class="p">(</span><span class="s2">"</span><span class="si">{}</span><span class="s2"> is not executable"</span><span class="o">.</span><span class="n">format</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">default_binary</span><span class="p">))</span>
+
+ <span class="k">return</span> <span class="n">binary</span>
+
+ <span class="k">def</span><span class="w"> </span><span class="nf">_get_combined_conf</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">model</span><span class="p">,</span> <span class="o">**</span><span class="n">conf_params</span><span class="p">):</span>
+ <span class="n">conf</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">get_default_conf</span><span class="p">()</span>
+ <span class="n">conf</span> <span class="o">=</span> <span class="n">conf</span><span class="o">.</span><span class="n">combine</span><span class="p">(</span><span class="n">model</span><span class="o">.</span><span class="n">configuration</span><span class="p">)</span>
+ <span class="n">conf</span> <span class="o">=</span> <span class="n">conf</span><span class="o">.</span><span class="n">combine</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">configuration</span><span class="p">)</span>
+ <span class="n">conf</span> <span class="o">=</span> <span class="n">conf</span><span class="o">.</span><span class="n">combine</span><span class="p">(</span><span class="n">SimConf</span><span class="p">(</span><span class="o">**</span><span class="n">conf_params</span><span class="p">))</span>
+ <span class="k">return</span> <span class="n">conf</span>
+
+<span class="w"> </span><span class="sd">""" TODO: Remove</span>
+<span class="sd"> # def _configuration_as_dict(self, model):</span>
+<span class="sd"> # params = dict()</span>
+<span class="sd"> # for o in (self.configuration, self, model):</span>
+<span class="sd"> # for k in _get_properties_and_dict_keys(o):</span>
+<span class="sd"> # params[k] = o.__get_attribute__(k)</span>
+<span class="sd"> # return params</span>
+<span class="sd"> """</span></div>
+
+
+<div class="viewcode-block" id="ArbdEngine">
+<a class="viewcode-back" href="../../api/simulation_engines/engine.html#arbdmodel.engine.ArbdEngine">[docs]</a>
+<span class="k">class</span><span class="w"> </span><span class="nc">ArbdEngine</span><span class="p">(</span><span class="n">SimEngine</span><span class="p">):</span>
+<span class="w"> </span><span class="sd">""" Interface to ARBD simulation engine """</span>
+ <span class="k">def</span><span class="w"> </span><span class="fm">__init__</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">extra_bd_file_lines</span><span class="o">=</span><span class="s2">""</span><span class="p">,</span> <span class="n">configuration</span><span class="o">=</span><span class="kc">None</span><span class="p">,</span> <span class="o">**</span><span class="n">conf_params</span><span class="p">):</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">extra_bd_file_lines</span> <span class="o">=</span> <span class="n">extra_bd_file_lines</span>
+
+ <span class="k">if</span> <span class="n">configuration</span> <span class="ow">is</span> <span class="kc">None</span><span class="p">:</span>
+ <span class="n">configuration</span> <span class="o">=</span> <span class="n">SimConf</span><span class="p">(</span><span class="o">**</span><span class="n">conf_params</span><span class="p">)</span>
+ <span class="n">SimEngine</span><span class="o">.</span><span class="fm">__init__</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">configuration</span><span class="p">)</span>
+
+ <span class="bp">self</span><span class="o">.</span><span class="n">num_particles</span> <span class="o">=</span> <span class="mi">0</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">particles</span> <span class="o">=</span> <span class="p">[]</span> <span class="c1"># TODO decide if this should belong here, or with model</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">type_counts</span> <span class="o">=</span> <span class="kc">None</span> <span class="c1"># TODO decide if this should belong here, or with model</span>
+
+ <span class="bp">self</span><span class="o">.</span><span class="n">_written_bond_files</span> <span class="o">=</span> <span class="nb">dict</span><span class="p">()</span>
+
+ <span class="bp">self</span><span class="o">.</span><span class="n">cacheUpToDate</span> <span class="o">=</span> <span class="kc">False</span>
+
+ <span class="nd">@property</span>
+ <span class="k">def</span><span class="w"> </span><span class="nf">default_binary</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span>
+ <span class="k">return</span> <span class="s1">'arbd'</span>
+
+ <span class="k">def</span><span class="w"> </span><span class="nf">_generate_command_string</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">binary</span><span class="p">,</span> <span class="n">output_name</span><span class="p">,</span> <span class="n">output_directory</span><span class="p">,</span> <span class="n">num_procs</span><span class="o">=</span><span class="kc">None</span><span class="p">,</span> <span class="n">gpu</span><span class="o">=</span><span class="mi">0</span><span class="p">,</span> <span class="n">replicas</span><span class="o">=</span><span class="mi">1</span><span class="p">):</span>
+ <span class="n">cmd</span> <span class="o">=</span> <span class="p">[</span><span class="n">binary</span><span class="p">,</span> <span class="s1">'-g'</span><span class="p">,</span> <span class="s2">"</span><span class="si">%d</span><span class="s2">"</span> <span class="o">%</span> <span class="n">gpu</span><span class="p">]</span>
+ <span class="k">if</span> <span class="n">replicas</span> <span class="o">></span> <span class="mi">1</span><span class="p">:</span>
+ <span class="n">cmd</span> <span class="o">=</span> <span class="n">cmd</span> <span class="o">+</span> <span class="p">[</span><span class="s1">'-r'</span><span class="p">,</span><span class="n">replicas</span><span class="p">]</span>
+ <span class="n">cmd</span> <span class="o">=</span> <span class="n">cmd</span> <span class="o">+</span> <span class="p">[</span><span class="s2">"</span><span class="si">%s</span><span class="s2">.bd"</span> <span class="o">%</span> <span class="n">output_name</span><span class="p">,</span> <span class="s2">"</span><span class="si">%s</span><span class="s2">/</span><span class="si">%s</span><span class="s2">"</span> <span class="o">%</span> <span class="p">(</span><span class="n">output_directory</span><span class="p">,</span> <span class="n">output_name</span><span class="p">)]</span>
+ <span class="n">cmd</span> <span class="o">=</span> <span class="nb">tuple</span><span class="p">(</span><span class="nb">str</span><span class="p">(</span><span class="n">x</span><span class="p">)</span> <span class="k">for</span> <span class="n">x</span> <span class="ow">in</span> <span class="n">cmd</span><span class="p">)</span>
+ <span class="k">return</span> <span class="n">cmd</span>
+
+<div class="viewcode-block" id="ArbdEngine.get_default_conf">
+<a class="viewcode-back" href="../../api/simulation_engines/engine.html#arbdmodel.engine.ArbdEngine.get_default_conf">[docs]</a>
+ <span class="k">def</span><span class="w"> </span><span class="nf">get_default_conf</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span>
+ <span class="n">conf</span> <span class="o">=</span> <span class="n">SimConf</span><span class="p">(</span><span class="n">num_steps</span><span class="o">=</span><span class="mf">1e5</span><span class="p">,</span> <span class="n">output_period</span><span class="o">=</span><span class="mf">1e3</span><span class="p">,</span>
+ <span class="n">integrator</span><span class="o">=</span><span class="s1">'MD'</span><span class="p">,</span> <span class="n">timestep</span><span class="o">=</span><span class="mf">20e-6</span><span class="p">,</span> <span class="n">thermostat</span><span class="o">=</span><span class="s1">'Langevin'</span><span class="p">,</span> <span class="n">barostat</span><span class="o">=</span><span class="kc">None</span><span class="p">,</span>
+ <span class="n">temperature</span><span class="o">=</span><span class="mi">295</span><span class="p">,</span> <span class="n">pressure</span><span class="o">=</span><span class="mi">1</span><span class="p">,</span>
+ <span class="n">cutoff</span><span class="o">=</span><span class="mi">50</span><span class="p">,</span> <span class="n">pairlist_distance</span><span class="o">=</span><span class="kc">None</span><span class="p">,</span> <span class="n">decomp_period</span><span class="o">=</span><span class="mi">40</span><span class="p">,</span> <span class="n">gpu</span> <span class="o">=</span> <span class="mi">0</span><span class="p">,</span>
+ <span class="n">seed</span><span class="o">=</span><span class="kc">None</span><span class="p">,</span> <span class="n">restart_file</span><span class="o">=</span><span class="kc">None</span><span class="p">)</span>
+ <span class="k">return</span> <span class="n">conf</span></div>
+
+
+ <span class="c1"># -------------------------- #</span>
+ <span class="c1"># Methods for printing model #</span>
+ <span class="c1"># -------------------------- #</span>
+
+<div class="viewcode-block" id="ArbdEngine.write_simulation_files">
+<a class="viewcode-back" href="../../api/simulation_engines/engine.html#arbdmodel.engine.ArbdEngine.write_simulation_files">[docs]</a>
+ <span class="k">def</span><span class="w"> </span><span class="nf">write_simulation_files</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">model</span><span class="p">,</span> <span class="n">output_name</span><span class="p">,</span> <span class="n">configuration</span><span class="o">=</span><span class="kc">None</span><span class="p">,</span> <span class="o">**</span><span class="n">conf_params</span><span class="p">):</span>
+ <span class="k">if</span> <span class="n">configuration</span> <span class="ow">is</span> <span class="kc">None</span><span class="p">:</span>
+ <span class="n">configuration</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">_get_combined_conf</span><span class="p">(</span><span class="n">model</span><span class="p">,</span> <span class="o">**</span><span class="n">conf_params</span><span class="p">)</span>
+
+ <span class="c1">## TODO: save and reference directories and prefixes using member data</span>
+ <span class="n">d</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">potential_directory</span> <span class="o">=</span> <span class="s2">"potentials"</span>
+ <span class="k">if</span> <span class="ow">not</span> <span class="n">os</span><span class="o">.</span><span class="n">path</span><span class="o">.</span><span class="n">exists</span><span class="p">(</span><span class="n">d</span><span class="p">):</span>
+ <span class="n">os</span><span class="o">.</span><span class="n">makedirs</span><span class="p">(</span><span class="n">d</span><span class="p">)</span>
+ <span class="n">rb_type_dirs</span> <span class="o">=</span> <span class="p">{}</span>
+ <span class="k">for</span> <span class="n">rbk</span><span class="p">,</span> <span class="n">num</span> <span class="ow">in</span> <span class="n">model</span><span class="o">.</span><span class="n">rigid_body_type_counts</span><span class="p">:</span>
+ <span class="k">if</span> <span class="n">num</span> <span class="o">></span> <span class="mi">0</span><span class="p">:</span>
+ <span class="n">rbt</span> <span class="o">=</span> <span class="n">model</span><span class="o">.</span><span class="n">rigid_body_index</span><span class="p">[</span><span class="n">rbk</span><span class="p">]</span>
+ <span class="n">rb_dir</span> <span class="o">=</span> <span class="n">rbt</span><span class="o">.</span><span class="n">name</span> <span class="c1"># Create top-level directory named after the RigidBodyType</span>
+ <span class="k">if</span> <span class="ow">not</span> <span class="n">os</span><span class="o">.</span><span class="n">path</span><span class="o">.</span><span class="n">exists</span><span class="p">(</span><span class="n">rb_dir</span><span class="p">):</span>
+ <span class="n">os</span><span class="o">.</span><span class="n">makedirs</span><span class="p">(</span><span class="n">rb_dir</span><span class="p">)</span>
+ <span class="n">rb_type_dirs</span><span class="p">[</span><span class="n">rbt</span><span class="o">.</span><span class="n">name</span><span class="p">]</span> <span class="o">=</span> <span class="n">rb_dir</span>
+
+ <span class="n">main_potentials_dir</span><span class="o">=</span><span class="bp">self</span><span class="o">.</span><span class="n">potential_directory</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">rb_type_dirs</span> <span class="o">=</span> <span class="n">rb_type_dirs</span>
+
+ <span class="n">model</span><span class="o">.</span><span class="n">write_psf</span><span class="p">(</span> <span class="n">output_name</span><span class="o">+</span><span class="s1">'.psf'</span> <span class="p">)</span>
+ <span class="n">model</span><span class="o">.</span><span class="n">write_pdb</span><span class="p">(</span> <span class="n">output_name</span><span class="o">+</span><span class="s1">'.pdb'</span> <span class="p">)</span>
+
+ <span class="bp">self</span><span class="o">.</span><span class="n">_write_particle_file</span><span class="p">(</span><span class="n">model</span><span class="p">,</span> <span class="n">output_name</span> <span class="o">+</span> <span class="s2">".particles.txt"</span><span class="p">,</span> <span class="n">configuration</span><span class="p">)</span>
+
+ <span class="bp">self</span><span class="o">.</span><span class="n">_write_restraint_file</span><span class="p">(</span><span class="n">model</span><span class="p">,</span> <span class="sa">f</span><span class="s2">"</span><span class="si">{</span><span class="n">main_potentials_dir</span><span class="si">}</span><span class="s2">/</span><span class="si">{</span><span class="n">output_name</span><span class="si">}</span><span class="s2">.restraint.txt"</span><span class="p">)</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">_write_bond_file</span><span class="p">(</span><span class="n">model</span><span class="p">,</span> <span class="sa">f</span><span class="s2">"</span><span class="si">{</span><span class="n">main_potentials_dir</span><span class="si">}</span><span class="s2">/</span><span class="si">{</span><span class="n">output_name</span><span class="si">}</span><span class="s2">.bond.txt"</span><span class="p">)</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">_write_angle_file</span><span class="p">(</span><span class="n">model</span><span class="p">,</span> <span class="sa">f</span><span class="s2">"</span><span class="si">{</span><span class="n">main_potentials_dir</span><span class="si">}</span><span class="s2">/</span><span class="si">{</span><span class="n">output_name</span><span class="si">}</span><span class="s2">.angle.txt"</span><span class="p">)</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">_write_dihedral_file</span><span class="p">(</span><span class="n">model</span><span class="p">,</span> <span class="sa">f</span><span class="s2">"</span><span class="si">{</span><span class="n">main_potentials_dir</span><span class="si">}</span><span class="s2">/</span><span class="si">{</span><span class="n">output_name</span><span class="si">}</span><span class="s2">.dihedral.txt"</span><span class="p">)</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">_write_vector_angle_file</span><span class="p">(</span><span class="n">model</span><span class="p">,</span> <span class="sa">f</span><span class="s2">"</span><span class="si">{</span><span class="n">main_potentials_dir</span><span class="si">}</span><span class="s2">/</span><span class="si">{</span><span class="n">output_name</span><span class="si">}</span><span class="s2">.vecangle.txt"</span><span class="p">)</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">_write_exclusion_file</span><span class="p">(</span><span class="n">model</span><span class="p">,</span> <span class="sa">f</span><span class="s2">"</span><span class="si">{</span><span class="n">main_potentials_dir</span><span class="si">}</span><span class="s2">/</span><span class="si">{</span><span class="n">output_name</span><span class="si">}</span><span class="s2">.exclusion.txt"</span><span class="p">)</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">_write_bond_angle_file</span><span class="p">(</span><span class="n">model</span><span class="p">,</span> <span class="sa">f</span><span class="s2">"</span><span class="si">{</span><span class="n">main_potentials_dir</span><span class="si">}</span><span class="s2">/</span><span class="si">{</span><span class="n">output_name</span><span class="si">}</span><span class="s2">.bond-angle.txt"</span><span class="p">)</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">_write_product_potential_file</span><span class="p">(</span><span class="n">model</span><span class="p">,</span> <span class="sa">f</span><span class="s2">"</span><span class="si">{</span><span class="n">main_potentials_dir</span><span class="si">}</span><span class="s2">/</span><span class="si">{</span><span class="n">output_name</span><span class="si">}</span><span class="s2">.product_potential.txt"</span><span class="p">)</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">_write_group_sites_file</span><span class="p">(</span><span class="n">model</span><span class="p">,</span> <span class="sa">f</span><span class="s2">"</span><span class="si">{</span><span class="n">main_potentials_dir</span><span class="si">}</span><span class="s2">/</span><span class="si">{</span><span class="n">output_name</span><span class="si">}</span><span class="s2">.group_sites.txt"</span><span class="p">)</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">_write_rb_coordinate_file</span><span class="p">(</span><span class="n">model</span><span class="p">,</span> <span class="n">configuration</span><span class="p">,</span> <span class="sa">f</span><span class="s1">'</span><span class="si">{</span><span class="n">output_name</span><span class="si">}</span><span class="s1">.rbcoords.txt'</span><span class="p">)</span>
+
+ <span class="bp">self</span><span class="o">.</span><span class="n">_write_potential_files</span><span class="p">(</span><span class="n">model</span><span class="p">,</span> <span class="n">output_name</span><span class="p">,</span> <span class="n">directory</span><span class="o">=</span><span class="n">main_potentials_dir</span><span class="p">,</span> <span class="n">configuration</span><span class="o">=</span><span class="n">configuration</span><span class="p">)</span>
+
+ <span class="bp">self</span><span class="o">.</span><span class="n">_write_rb_attached_particles_files</span><span class="p">(</span><span class="n">model</span><span class="p">,</span> <span class="n">output_name</span><span class="p">,</span> <span class="n">configuration</span><span class="p">)</span>
+
+ <span class="bp">self</span><span class="o">.</span><span class="n">_write_conf</span><span class="p">(</span><span class="n">model</span><span class="p">,</span> <span class="n">output_name</span><span class="p">,</span> <span class="n">configuration</span><span class="p">)</span></div>
+
+ <span class="c1">## , numSteps=numSteps, outputPeriod=outputPeriod, restart_file=restart_file )</span>
+
+ <span class="k">def</span><span class="w"> </span><span class="nf">_write_particle_file</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">model</span><span class="p">,</span> <span class="n">filename</span><span class="p">,</span> <span class="n">configuration</span><span class="o">=</span><span class="kc">None</span><span class="p">,</span> <span class="o">**</span><span class="n">conf_params</span><span class="p">):</span>
+ <span class="k">if</span> <span class="n">configuration</span> <span class="ow">is</span> <span class="kc">None</span><span class="p">:</span>
+ <span class="n">configuration</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">_get_combined_conf</span><span class="p">(</span><span class="n">model</span><span class="p">,</span> <span class="o">**</span><span class="n">conf_params</span><span class="p">)</span>
+
+ <span class="k">with</span> <span class="nb">open</span><span class="p">(</span><span class="n">filename</span><span class="p">,</span><span class="s1">'w'</span><span class="p">)</span> <span class="k">as</span> <span class="n">fh</span><span class="p">:</span>
+ <span class="k">if</span> <span class="n">configuration</span><span class="o">.</span><span class="n">integrator</span> <span class="ow">in</span> <span class="p">(</span><span class="s1">'Brown'</span><span class="p">,</span> <span class="s1">'Brownian'</span><span class="p">,</span> <span class="s1">'BD'</span><span class="p">):</span>
+ <span class="k">for</span> <span class="n">p</span> <span class="ow">in</span> <span class="n">model</span><span class="o">.</span><span class="n">particles</span><span class="p">:</span>
+ <span class="n">data</span> <span class="o">=</span> <span class="nb">tuple</span><span class="p">([</span><span class="n">p</span><span class="o">.</span><span class="n">idx</span><span class="p">,</span><span class="n">p</span><span class="o">.</span><span class="n">type_</span><span class="o">.</span><span class="n">name</span><span class="p">]</span> <span class="o">+</span> <span class="p">[</span><span class="n">x</span> <span class="k">for</span> <span class="n">x</span> <span class="ow">in</span> <span class="n">p</span><span class="o">.</span><span class="n">get_collapsed_position</span><span class="p">()])</span>
+ <span class="n">fh</span><span class="o">.</span><span class="n">write</span><span class="p">(</span><span class="s2">"ATOM </span><span class="si">%d</span><span class="s2"> </span><span class="si">%s</span><span class="s2"> </span><span class="si">%f</span><span class="s2"> </span><span class="si">%f</span><span class="s2"> </span><span class="si">%f</span><span class="se">\n</span><span class="s2">"</span> <span class="o">%</span> <span class="n">data</span><span class="p">)</span>
+ <span class="k">else</span><span class="p">:</span>
+ <span class="k">for</span> <span class="n">p</span> <span class="ow">in</span> <span class="n">model</span><span class="o">.</span><span class="n">particles</span><span class="p">:</span>
+ <span class="n">data</span> <span class="o">=</span> <span class="p">[</span><span class="n">p</span><span class="o">.</span><span class="n">idx</span><span class="p">,</span><span class="n">p</span><span class="o">.</span><span class="n">type_</span><span class="o">.</span><span class="n">name</span><span class="p">]</span> <span class="o">+</span> <span class="p">[</span><span class="n">x</span> <span class="k">for</span> <span class="n">x</span> <span class="ow">in</span> <span class="n">p</span><span class="o">.</span><span class="n">get_collapsed_position</span><span class="p">()]</span>
+ <span class="k">try</span><span class="p">:</span>
+ <span class="n">data</span> <span class="o">=</span> <span class="n">data</span> <span class="o">+</span> <span class="n">p</span><span class="o">.</span><span class="n">momentum</span>
+ <span class="k">except</span><span class="p">:</span>
+ <span class="k">try</span><span class="p">:</span>
+ <span class="n">data</span> <span class="o">=</span> <span class="n">data</span> <span class="o">+</span> <span class="n">p</span><span class="o">.</span><span class="n">velocity</span><span class="o">*</span><span class="n">p</span><span class="o">.</span><span class="n">mass</span>
+ <span class="k">except</span><span class="p">:</span>
+ <span class="n">data</span> <span class="o">=</span> <span class="n">data</span> <span class="o">+</span> <span class="p">[</span><span class="mi">0</span><span class="p">,</span><span class="mi">0</span><span class="p">,</span><span class="mi">0</span><span class="p">]</span>
+ <span class="n">fh</span><span class="o">.</span><span class="n">write</span><span class="p">(</span><span class="s2">"ATOM </span><span class="si">%d</span><span class="s2"> </span><span class="si">%s</span><span class="s2"> </span><span class="si">%f</span><span class="s2"> </span><span class="si">%f</span><span class="s2"> </span><span class="si">%f</span><span class="s2"> </span><span class="si">%f</span><span class="s2"> </span><span class="si">%f</span><span class="s2"> </span><span class="si">%f</span><span class="se">\n</span><span class="s2">"</span> <span class="o">%</span> <span class="nb">tuple</span><span class="p">(</span><span class="n">data</span><span class="p">))</span>
+
+ <span class="k">def</span><span class="w"> </span><span class="nf">_write_rb_attached_particles_files</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">model</span><span class="p">,</span> <span class="n">output_name</span><span class="p">,</span> <span class="n">configuration</span><span class="o">=</span><span class="kc">None</span><span class="p">,</span> <span class="o">**</span><span class="n">conf_params</span><span class="p">):</span>
+ <span class="k">if</span> <span class="n">configuration</span> <span class="ow">is</span> <span class="kc">None</span><span class="p">:</span>
+ <span class="n">configuration</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">_get_combined_conf</span><span class="p">(</span><span class="n">model</span><span class="p">,</span> <span class="o">**</span><span class="n">conf_params</span><span class="p">)</span>
+ <span class="k">if</span> <span class="nb">len</span><span class="p">(</span><span class="n">model</span><span class="o">.</span><span class="n">rigid_bodies</span><span class="p">)</span> <span class="o">></span> <span class="mi">0</span><span class="p">:</span>
+ <span class="k">for</span> <span class="n">rbk</span><span class="p">,</span> <span class="n">num</span> <span class="ow">in</span> <span class="n">model</span><span class="o">.</span><span class="n">rigid_body_type_counts</span><span class="p">:</span>
+ <span class="n">rbt</span> <span class="o">=</span> <span class="n">model</span><span class="o">.</span><span class="n">rigid_body_index</span><span class="p">[</span><span class="n">rbk</span><span class="p">]</span>
+ <span class="n">devlogger</span><span class="o">.</span><span class="n">debug</span><span class="p">(</span><span class="sa">f</span><span class="s1">'Writing attached particles file for rigid body type </span><span class="si">{</span><span class="n">rbt</span><span class="si">}</span><span class="s1">'</span><span class="p">)</span>
+ <span class="k">if</span> <span class="n">num</span> <span class="o">></span> <span class="mi">0</span> <span class="ow">and</span> <span class="nb">len</span><span class="p">(</span><span class="n">rbt</span><span class="o">.</span><span class="n">attached_particles</span><span class="p">)</span> <span class="o">></span> <span class="mi">0</span><span class="p">:</span>
+ <span class="c1"># Use RB-specific directory</span>
+ <span class="n">rb_dir</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">rb_type_dirs</span><span class="o">.</span><span class="n">get</span><span class="p">(</span><span class="n">rbt</span><span class="o">.</span><span class="n">name</span><span class="p">)</span>
+ <span class="k">if</span> <span class="ow">not</span> <span class="n">rb_dir</span><span class="p">:</span>
+ <span class="n">logger</span><span class="o">.</span><span class="n">warning</span><span class="p">(</span><span class="sa">f</span><span class="s2">"No directory found for RigidBodyType </span><span class="si">{</span><span class="n">rbt</span><span class="o">.</span><span class="n">name</span><span class="si">}</span><span class="s2">, using default"</span><span class="p">)</span>
+ <span class="n">rb_dir</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">potential_directory</span>
+
+ <span class="c1"># Create the attached particles file inside the RB directory</span>
+ <span class="n">f</span> <span class="o">=</span> <span class="n">os</span><span class="o">.</span><span class="n">path</span><span class="o">.</span><span class="n">join</span><span class="p">(</span><span class="n">rb_dir</span><span class="p">,</span> <span class="sa">f</span><span class="s2">"attached_particles.txt"</span><span class="p">)</span>
+ <span class="n">rbt</span><span class="o">.</span><span class="n">_attached_particles_filename</span> <span class="o">=</span> <span class="n">f</span>
+ <span class="k">with</span> <span class="nb">open</span><span class="p">(</span><span class="n">f</span><span class="p">,</span> <span class="s1">'w'</span><span class="p">)</span> <span class="k">as</span> <span class="n">fh</span><span class="p">:</span>
+ <span class="k">for</span> <span class="n">p</span> <span class="ow">in</span> <span class="n">rbt</span><span class="o">.</span><span class="n">attached_particles</span><span class="p">:</span>
+ <span class="n">x</span><span class="p">,</span> <span class="n">y</span><span class="p">,</span> <span class="n">z</span> <span class="o">=</span> <span class="n">p</span><span class="o">.</span><span class="n">position</span>
+ <span class="n">fh</span><span class="o">.</span><span class="n">write</span><span class="p">(</span><span class="sa">f</span><span class="s1">'</span><span class="si">{</span><span class="n">p</span><span class="o">.</span><span class="n">type_</span><span class="o">.</span><span class="n">name</span><span class="si">}</span><span class="s1"> </span><span class="si">{</span><span class="n">x</span><span class="si">}</span><span class="s1"> </span><span class="si">{</span><span class="n">y</span><span class="si">}</span><span class="s1"> </span><span class="si">{</span><span class="n">z</span><span class="si">}</span><span class="se">\n</span><span class="s1">'</span><span class="p">)</span>
+
+ <span class="k">def</span><span class="w"> </span><span class="nf">_write_rigid_group_file</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">model</span><span class="p">,</span> <span class="n">filename</span><span class="p">,</span> <span class="n">groups</span><span class="p">):</span>
+ <span class="k">raise</span> <span class="ne">Exception</span><span class="p">(</span><span class="s1">'Deprecated'</span><span class="p">)</span>
+ <span class="k">with</span> <span class="nb">open</span><span class="p">(</span><span class="n">filename</span><span class="p">,</span><span class="s1">'w'</span><span class="p">)</span> <span class="k">as</span> <span class="n">fh</span><span class="p">:</span>
+ <span class="k">for</span> <span class="n">g</span> <span class="ow">in</span> <span class="n">groups</span><span class="p">:</span>
+ <span class="n">fh</span><span class="o">.</span><span class="n">write</span><span class="p">(</span><span class="s2">"#Group</span><span class="se">\n</span><span class="s2">"</span><span class="p">)</span>
+ <span class="k">try</span><span class="p">:</span>
+ <span class="k">if</span> <span class="nb">len</span><span class="p">(</span><span class="n">g</span><span class="o">.</span><span class="n">trans_damping</span><span class="p">)</span> <span class="o">!=</span> <span class="mi">3</span><span class="p">:</span> <span class="k">raise</span>
+ <span class="n">fh</span><span class="o">.</span><span class="n">write</span><span class="p">(</span><span class="s2">" "</span><span class="o">.</span><span class="n">join</span><span class="p">(</span><span class="nb">str</span><span class="p">(</span><span class="n">v</span><span class="p">)</span> <span class="k">for</span> <span class="n">v</span> <span class="ow">in</span> <span class="n">g</span><span class="o">.</span><span class="n">trans_damping</span><span class="p">)</span> <span class="o">+</span> <span class="s2">" "</span><span class="p">)</span>
+ <span class="k">except</span><span class="p">:</span>
+ <span class="k">raise</span> <span class="ne">ValueError</span><span class="p">(</span><span class="s2">"Group </span><span class="si">{}</span><span class="s2"> lacks 3-value 'trans_damping' attribute"</span><span class="p">)</span>
+ <span class="k">try</span><span class="p">:</span>
+ <span class="k">if</span> <span class="nb">len</span><span class="p">(</span><span class="n">g</span><span class="o">.</span><span class="n">rot_damping</span><span class="p">)</span> <span class="o">!=</span> <span class="mi">3</span><span class="p">:</span> <span class="k">raise</span>
+ <span class="n">fh</span><span class="o">.</span><span class="n">write</span><span class="p">(</span><span class="s2">" "</span><span class="o">.</span><span class="n">join</span><span class="p">(</span><span class="nb">str</span><span class="p">(</span><span class="n">v</span><span class="p">)</span> <span class="k">for</span> <span class="n">v</span> <span class="ow">in</span> <span class="n">g</span><span class="o">.</span><span class="n">rot_damping</span><span class="p">)</span> <span class="o">+</span> <span class="s2">" "</span><span class="p">)</span>
+ <span class="k">except</span><span class="p">:</span>
+ <span class="k">raise</span> <span class="ne">ValueError</span><span class="p">(</span><span class="s2">"Group </span><span class="si">{}</span><span class="s2"> lacks 3-value 'rot_damping' attribute"</span><span class="p">)</span>
+ <span class="n">fh</span><span class="o">.</span><span class="n">write</span><span class="p">(</span><span class="s2">"</span><span class="si">{}</span><span class="se">\n</span><span class="s2">"</span><span class="o">.</span><span class="n">format</span><span class="p">(</span><span class="nb">len</span><span class="p">(</span><span class="n">g</span><span class="p">)))</span>
+ <span class="n">particles</span> <span class="o">=</span> <span class="p">[</span><span class="n">p</span> <span class="k">for</span> <span class="n">p</span> <span class="ow">in</span> <span class="n">g</span><span class="p">]</span>
+
+ <span class="k">def</span><span class="w"> </span><span class="nf">chunks</span><span class="p">(</span><span class="n">l</span><span class="p">,</span> <span class="n">n</span><span class="p">):</span>
+<span class="w"> </span><span class="sd">"""Yield successive n-sized chunks from l."""</span>
+ <span class="k">for</span> <span class="n">i</span> <span class="ow">in</span> <span class="nb">range</span><span class="p">(</span><span class="mi">0</span><span class="p">,</span> <span class="nb">len</span><span class="p">(</span><span class="n">l</span><span class="p">),</span> <span class="n">n</span><span class="p">):</span>
+ <span class="k">yield</span> <span class="n">l</span><span class="p">[</span><span class="n">i</span><span class="p">:</span><span class="n">i</span> <span class="o">+</span> <span class="n">n</span><span class="p">]</span>
+
+ <span class="k">for</span> <span class="n">c</span> <span class="ow">in</span> <span class="n">chunks</span><span class="p">(</span><span class="n">particles</span><span class="p">,</span><span class="mi">8</span><span class="p">):</span>
+ <span class="n">fh</span><span class="o">.</span><span class="n">write</span><span class="p">(</span><span class="s2">" "</span><span class="o">.</span><span class="n">join</span><span class="p">(</span><span class="nb">str</span><span class="p">(</span><span class="n">p</span><span class="o">.</span><span class="n">idx</span><span class="p">)</span> <span class="k">for</span> <span class="n">p</span> <span class="ow">in</span> <span class="n">c</span><span class="p">)</span> <span class="o">+</span> <span class="s2">"</span><span class="se">\n</span><span class="s2">"</span><span class="p">)</span>
+
+ <span class="k">def</span><span class="w"> </span><span class="nf">_write_potential_files</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">model</span><span class="p">,</span> <span class="n">prefix</span><span class="p">,</span> <span class="n">directory</span> <span class="o">=</span> <span class="s2">"potentials"</span><span class="p">,</span> <span class="n">configuration</span><span class="o">=</span><span class="kc">None</span><span class="p">,</span> <span class="o">**</span><span class="n">conf_params</span><span class="p">):</span>
+ <span class="k">try</span><span class="p">:</span>
+ <span class="n">os</span><span class="o">.</span><span class="n">makedirs</span><span class="p">(</span><span class="n">directory</span><span class="p">)</span>
+ <span class="k">except</span> <span class="ne">OSError</span><span class="p">:</span>
+ <span class="k">if</span> <span class="ow">not</span> <span class="n">os</span><span class="o">.</span><span class="n">path</span><span class="o">.</span><span class="n">isdir</span><span class="p">(</span><span class="n">directory</span><span class="p">):</span>
+ <span class="k">raise</span>
+
+ <span class="k">if</span> <span class="n">configuration</span> <span class="ow">is</span> <span class="kc">None</span><span class="p">:</span>
+ <span class="n">configuration</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">_get_combined_conf</span><span class="p">(</span><span class="n">model</span><span class="p">,</span> <span class="o">**</span><span class="n">conf_params</span><span class="p">)</span>
+
+ <span class="n">path_prefix</span> <span class="o">=</span> <span class="s2">"</span><span class="si">{}</span><span class="s2">/</span><span class="si">{}</span><span class="s2">"</span><span class="o">.</span><span class="n">format</span><span class="p">(</span><span class="n">directory</span><span class="p">,</span><span class="n">prefix</span><span class="p">)</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">_write_nonbonded_parameter_files</span><span class="p">(</span> <span class="n">model</span><span class="p">,</span> <span class="n">path_prefix</span> <span class="o">+</span> <span class="s2">"-nb"</span><span class="p">,</span> <span class="n">configuration</span> <span class="p">)</span>
+
+ <span class="k">def</span><span class="w"> </span><span class="nf">_write_nonbonded_parameter_files</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">model</span><span class="p">,</span> <span class="n">prefix</span><span class="p">,</span> <span class="n">configuration</span><span class="o">=</span><span class="kc">None</span><span class="p">,</span> <span class="o">**</span><span class="n">conf_params</span><span class="p">):</span>
+ <span class="k">if</span> <span class="n">configuration</span> <span class="ow">is</span> <span class="kc">None</span><span class="p">:</span>
+ <span class="n">configuration</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">_get_combined_conf</span><span class="p">(</span><span class="n">model</span><span class="p">,</span> <span class="o">**</span><span class="n">conf_params</span><span class="p">)</span>
+
+ <span class="n">model</span><span class="o">.</span><span class="n">_nonbonded_interaction_files</span> <span class="o">=</span> <span class="p">[]</span> <span class="c1"># clear old nb files</span>
+
+ <span class="n">x</span> <span class="o">=</span> <span class="n">np</span><span class="o">.</span><span class="n">arange</span><span class="p">(</span><span class="mi">0</span><span class="p">,</span> <span class="n">configuration</span><span class="o">.</span><span class="n">cutoff</span><span class="p">)</span>
+ <span class="k">for</span> <span class="n">i</span><span class="p">,</span><span class="n">j</span><span class="p">,</span><span class="n">t1</span><span class="p">,</span><span class="n">t2</span> <span class="ow">in</span> <span class="n">model</span><span class="o">.</span><span class="n">_particleTypePairIter</span><span class="p">():</span>
+ <span class="n">interaction</span> <span class="o">=</span> <span class="n">model</span><span class="o">.</span><span class="n">_get_nonbonded_interaction</span><span class="p">(</span><span class="n">t1</span><span class="p">,</span><span class="n">t2</span><span class="p">)</span>
+ <span class="k">if</span> <span class="n">interaction</span> <span class="ow">is</span> <span class="kc">None</span><span class="p">:</span> <span class="n">interaction</span> <span class="o">=</span> <span class="n">NullPotential</span><span class="p">()</span>
+ <span class="k">try</span><span class="p">:</span>
+ <span class="n">f</span> <span class="o">=</span> <span class="n">interaction</span><span class="o">.</span><span class="n">filename</span><span class="p">(</span><span class="n">types</span><span class="o">=</span><span class="p">(</span><span class="n">t1</span><span class="p">,</span><span class="n">t2</span><span class="p">))</span>
+ <span class="k">except</span><span class="p">:</span>
+ <span class="n">f</span> <span class="o">=</span> <span class="s2">"</span><span class="si">%s</span><span class="s2">.</span><span class="si">%s</span><span class="s2">-</span><span class="si">%s</span><span class="s2">.dat"</span> <span class="o">%</span> <span class="p">(</span><span class="n">prefix</span><span class="p">,</span> <span class="n">t1</span><span class="o">.</span><span class="n">name</span><span class="p">,</span> <span class="n">t2</span><span class="o">.</span><span class="n">name</span><span class="p">)</span>
+ <span class="n">logger</span><span class="o">.</span><span class="n">debug</span><span class="p">(</span><span class="sa">f</span><span class="s1">'_write_nonbonded_parameter_files could not find filename for </span><span class="si">{</span><span class="n">interaction</span><span class="si">}</span><span class="s1">; using default </span><span class="si">{</span><span class="n">f</span><span class="si">}</span><span class="s1">'</span><span class="p">)</span>
+
+ <span class="n">devlogger</span><span class="o">.</span><span class="n">debug</span><span class="p">(</span><span class="sa">f</span><span class="s1">'_write_nonbonded_parameter_files: </span><span class="si">{</span><span class="n">i</span><span class="si">}</span><span class="s1">, </span><span class="si">{</span><span class="n">j</span><span class="si">}</span><span class="s1">, </span><span class="si">{</span><span class="n">t1</span><span class="si">}</span><span class="s1">, </span><span class="si">{</span><span class="n">t2</span><span class="si">}</span><span class="s1">, </span><span class="si">{</span><span class="n">interaction</span><span class="si">}</span><span class="s1">'</span><span class="p">)</span>
+ <span class="n">old_range</span> <span class="o">=</span> <span class="n">interaction</span><span class="o">.</span><span class="n">range_</span>
+ <span class="k">if</span> <span class="ow">not</span> <span class="nb">isinstance</span><span class="p">(</span><span class="n">interaction</span><span class="p">,</span><span class="n">NullPotential</span><span class="p">):</span>
+ <span class="n">interaction</span><span class="o">.</span><span class="n">range_</span> <span class="o">=</span> <span class="p">[</span><span class="mi">0</span><span class="p">,</span> <span class="n">configuration</span><span class="o">.</span><span class="n">cutoff</span><span class="p">]</span>
+ <span class="n">interaction</span><span class="o">.</span><span class="n">write_file</span><span class="p">(</span><span class="n">f</span><span class="p">,</span> <span class="p">(</span><span class="n">t1</span><span class="p">,</span> <span class="n">t2</span><span class="p">))</span>
+ <span class="n">interaction</span><span class="o">.</span><span class="n">range_</span> <span class="o">=</span> <span class="n">old_range</span>
+
+ <span class="n">model</span><span class="o">.</span><span class="n">_nonbonded_interaction_files</span><span class="o">.</span><span class="n">append</span><span class="p">(</span><span class="n">f</span><span class="p">)</span>
+ <span class="n">devlogger</span><span class="o">.</span><span class="n">debug</span><span class="p">(</span><span class="sa">f</span><span class="s1">'model._nonbonded_interaction_files: </span><span class="si">{</span><span class="n">model</span><span class="o">.</span><span class="n">_nonbonded_interaction_files</span><span class="si">}</span><span class="s1">'</span><span class="p">)</span>
+
+ <span class="k">def</span><span class="w"> </span><span class="nf">_write_restraint_file</span><span class="p">(</span> <span class="bp">self</span><span class="p">,</span> <span class="n">model</span><span class="p">,</span> <span class="n">filename</span> <span class="p">):</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">_restraint_filename</span> <span class="o">=</span> <span class="n">filename</span>
+ <span class="k">with</span> <span class="nb">open</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">_restraint_filename</span><span class="p">,</span><span class="s1">'w'</span><span class="p">)</span> <span class="k">as</span> <span class="n">fh</span><span class="p">:</span>
+ <span class="k">for</span> <span class="n">i</span><span class="p">,</span><span class="n">restraint</span> <span class="ow">in</span> <span class="n">model</span><span class="o">.</span><span class="n">get_restraints</span><span class="p">():</span>
+ <span class="n">item</span> <span class="o">=</span> <span class="p">[</span><span class="n">i</span><span class="o">.</span><span class="n">idx</span><span class="p">]</span>
+ <span class="k">if</span> <span class="nb">len</span><span class="p">(</span><span class="n">restraint</span><span class="p">)</span> <span class="o">==</span> <span class="mi">1</span><span class="p">:</span>
+ <span class="n">item</span><span class="o">.</span><span class="n">append</span><span class="p">(</span><span class="n">restraint</span><span class="p">[</span><span class="mi">0</span><span class="p">])</span>
+ <span class="k">if</span> <span class="nb">isinstance</span><span class="p">(</span><span class="n">i</span><span class="p">,</span> <span class="n">GroupSite</span><span class="p">):</span>
+ <span class="n">item</span><span class="o">.</span><span class="n">extend</span><span class="p">(</span><span class="n">i</span><span class="o">.</span><span class="n">get_center</span><span class="p">())</span>
+ <span class="k">else</span><span class="p">:</span>
+ <span class="n">item</span><span class="o">.</span><span class="n">extend</span><span class="p">(</span><span class="n">i</span><span class="o">.</span><span class="n">get_collapsed_position</span><span class="p">())</span>
+ <span class="k">elif</span> <span class="nb">len</span><span class="p">(</span><span class="n">restraint</span><span class="p">)</span> <span class="o">==</span> <span class="mi">2</span><span class="p">:</span>
+ <span class="n">item</span><span class="o">.</span><span class="n">append</span><span class="p">(</span><span class="n">restraint</span><span class="p">[</span><span class="mi">0</span><span class="p">])</span>
+ <span class="n">item</span><span class="o">.</span><span class="n">extend</span><span class="p">(</span><span class="n">restraint</span><span class="p">[</span><span class="mi">1</span><span class="p">])</span>
+ <span class="k">elif</span> <span class="nb">len</span><span class="p">(</span><span class="n">restraint</span><span class="p">)</span> <span class="o">==</span> <span class="mi">5</span><span class="p">:</span>
+ <span class="n">item</span><span class="o">.</span><span class="n">extend</span><span class="p">(</span><span class="n">restraint</span><span class="p">)</span>
+ <span class="n">fh</span><span class="o">.</span><span class="n">write</span><span class="p">(</span><span class="s2">"RESTRAINT </span><span class="si">%d</span><span class="s2"> </span><span class="si">%f</span><span class="s2"> </span><span class="si">%f</span><span class="s2"> </span><span class="si">%f</span><span class="s2"> </span><span class="si">%f</span><span class="se">\n</span><span class="s2">"</span> <span class="o">%</span> <span class="nb">tuple</span><span class="p">(</span><span class="n">item</span><span class="p">))</span>
+
+ <span class="k">def</span><span class="w"> </span><span class="nf">_write_bond_file</span><span class="p">(</span> <span class="bp">self</span><span class="p">,</span> <span class="n">model</span><span class="p">,</span> <span class="n">filename</span> <span class="p">):</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">_bond_filename</span> <span class="o">=</span> <span class="n">filename</span>
+ <span class="k">for</span> <span class="n">b</span> <span class="ow">in</span> <span class="nb">list</span><span class="p">(</span> <span class="nb">set</span><span class="p">(</span> <span class="p">[</span><span class="n">b</span> <span class="k">for</span> <span class="n">i</span><span class="p">,</span><span class="n">j</span><span class="p">,</span><span class="n">b</span><span class="p">,</span><span class="n">ex</span> <span class="ow">in</span> <span class="n">model</span><span class="o">.</span><span class="n">get_bonds</span><span class="p">()]</span> <span class="p">)</span> <span class="p">):</span>
+ <span class="k">if</span> <span class="nb">type</span><span class="p">(</span><span class="n">b</span><span class="p">)</span> <span class="ow">is</span> <span class="ow">not</span> <span class="nb">str</span> <span class="ow">and</span> <span class="ow">not</span> <span class="nb">isinstance</span><span class="p">(</span><span class="n">b</span><span class="p">,</span> <span class="n">Path</span><span class="p">):</span>
+ <span class="n">b</span><span class="o">.</span><span class="n">write_file</span><span class="p">()</span>
+
+ <span class="k">with</span> <span class="nb">open</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">_bond_filename</span><span class="p">,</span><span class="s1">'w'</span><span class="p">)</span> <span class="k">as</span> <span class="n">fh</span><span class="p">:</span>
+ <span class="k">for</span> <span class="n">i</span><span class="p">,</span><span class="n">j</span><span class="p">,</span><span class="n">b</span><span class="p">,</span><span class="n">ex</span> <span class="ow">in</span> <span class="n">model</span><span class="o">.</span><span class="n">get_bonds</span><span class="p">():</span>
+ <span class="k">try</span><span class="p">:</span>
+ <span class="n">bfile</span> <span class="o">=</span> <span class="n">b</span><span class="o">.</span><span class="n">filename</span><span class="p">()</span>
+ <span class="k">except</span><span class="p">:</span>
+ <span class="n">bfile</span> <span class="o">=</span> <span class="nb">str</span><span class="p">(</span><span class="n">b</span><span class="p">)</span>
+ <span class="n">item</span> <span class="o">=</span> <span class="p">(</span><span class="n">i</span><span class="o">.</span><span class="n">idx</span><span class="p">,</span> <span class="n">j</span><span class="o">.</span><span class="n">idx</span><span class="p">,</span> <span class="n">bfile</span><span class="p">)</span>
+ <span class="k">if</span> <span class="n">ex</span><span class="p">:</span>
+ <span class="n">fh</span><span class="o">.</span><span class="n">write</span><span class="p">(</span><span class="s2">"BOND REPLACE </span><span class="si">%d</span><span class="s2"> </span><span class="si">%d</span><span class="s2"> </span><span class="si">%s</span><span class="se">\n</span><span class="s2">"</span> <span class="o">%</span> <span class="n">item</span><span class="p">)</span>
+ <span class="k">else</span><span class="p">:</span>
+ <span class="n">fh</span><span class="o">.</span><span class="n">write</span><span class="p">(</span><span class="s2">"BOND ADD </span><span class="si">%d</span><span class="s2"> </span><span class="si">%d</span><span class="s2"> </span><span class="si">%s</span><span class="se">\n</span><span class="s2">"</span> <span class="o">%</span> <span class="n">item</span><span class="p">)</span>
+
+ <span class="k">def</span><span class="w"> </span><span class="nf">_write_angle_file</span><span class="p">(</span> <span class="bp">self</span><span class="p">,</span> <span class="n">model</span><span class="p">,</span> <span class="n">filename</span> <span class="p">):</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">_angle_filename</span> <span class="o">=</span> <span class="n">filename</span>
+ <span class="k">for</span> <span class="n">b</span> <span class="ow">in</span> <span class="nb">list</span><span class="p">(</span> <span class="nb">set</span><span class="p">(</span> <span class="p">[</span><span class="n">b</span> <span class="k">for</span> <span class="n">i</span><span class="p">,</span><span class="n">j</span><span class="p">,</span><span class="n">k</span><span class="p">,</span><span class="n">b</span> <span class="ow">in</span> <span class="n">model</span><span class="o">.</span><span class="n">get_angles</span><span class="p">()]</span> <span class="p">)</span> <span class="p">):</span>
+ <span class="k">if</span> <span class="nb">type</span><span class="p">(</span><span class="n">b</span><span class="p">)</span> <span class="ow">is</span> <span class="ow">not</span> <span class="nb">str</span> <span class="ow">and</span> <span class="ow">not</span> <span class="nb">isinstance</span><span class="p">(</span><span class="n">b</span><span class="p">,</span> <span class="n">Path</span><span class="p">):</span>
+ <span class="n">b</span><span class="o">.</span><span class="n">write_file</span><span class="p">()</span>
+
+ <span class="k">with</span> <span class="nb">open</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">_angle_filename</span><span class="p">,</span><span class="s1">'w'</span><span class="p">)</span> <span class="k">as</span> <span class="n">fh</span><span class="p">:</span>
+ <span class="k">for</span> <span class="n">b</span> <span class="ow">in</span> <span class="n">model</span><span class="o">.</span><span class="n">get_angles</span><span class="p">():</span>
+ <span class="k">try</span><span class="p">:</span>
+ <span class="n">bfile</span> <span class="o">=</span> <span class="n">b</span><span class="p">[</span><span class="o">-</span><span class="mi">1</span><span class="p">]</span><span class="o">.</span><span class="n">filename</span><span class="p">()</span>
+ <span class="k">except</span><span class="p">:</span>
+ <span class="n">bfile</span> <span class="o">=</span> <span class="nb">str</span><span class="p">(</span><span class="n">b</span><span class="p">[</span><span class="o">-</span><span class="mi">1</span><span class="p">])</span>
+ <span class="n">item</span> <span class="o">=</span> <span class="nb">tuple</span><span class="p">([</span><span class="n">p</span><span class="o">.</span><span class="n">idx</span> <span class="k">for</span> <span class="n">p</span> <span class="ow">in</span> <span class="n">b</span><span class="p">[:</span><span class="o">-</span><span class="mi">1</span><span class="p">]]</span> <span class="o">+</span> <span class="p">[</span><span class="n">bfile</span><span class="p">])</span>
+ <span class="n">fh</span><span class="o">.</span><span class="n">write</span><span class="p">(</span><span class="s2">"ANGLE </span><span class="si">%d</span><span class="s2"> </span><span class="si">%d</span><span class="s2"> </span><span class="si">%d</span><span class="s2"> </span><span class="si">%s</span><span class="se">\n</span><span class="s2">"</span> <span class="o">%</span> <span class="n">item</span><span class="p">)</span>
+
+ <span class="k">def</span><span class="w"> </span><span class="nf">_write_dihedral_file</span><span class="p">(</span> <span class="bp">self</span><span class="p">,</span> <span class="n">model</span><span class="p">,</span> <span class="n">filename</span> <span class="p">):</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">_dihedral_filename</span> <span class="o">=</span> <span class="n">filename</span>
+ <span class="k">for</span> <span class="n">b</span> <span class="ow">in</span> <span class="nb">list</span><span class="p">(</span> <span class="nb">set</span><span class="p">(</span> <span class="p">[</span><span class="n">b</span> <span class="k">for</span> <span class="n">i</span><span class="p">,</span><span class="n">j</span><span class="p">,</span><span class="n">k</span><span class="p">,</span><span class="n">l</span><span class="p">,</span><span class="n">b</span> <span class="ow">in</span> <span class="n">model</span><span class="o">.</span><span class="n">get_dihedrals</span><span class="p">()]</span> <span class="p">)</span> <span class="p">):</span>
+ <span class="k">if</span> <span class="nb">type</span><span class="p">(</span><span class="n">b</span><span class="p">)</span> <span class="ow">is</span> <span class="ow">not</span> <span class="nb">str</span> <span class="ow">and</span> <span class="ow">not</span> <span class="nb">isinstance</span><span class="p">(</span><span class="n">b</span><span class="p">,</span> <span class="n">Path</span><span class="p">):</span>
+ <span class="n">b</span><span class="o">.</span><span class="n">write_file</span><span class="p">()</span>
+
+ <span class="k">with</span> <span class="nb">open</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">_dihedral_filename</span><span class="p">,</span><span class="s1">'w'</span><span class="p">)</span> <span class="k">as</span> <span class="n">fh</span><span class="p">:</span>
+ <span class="k">for</span> <span class="n">b</span> <span class="ow">in</span> <span class="n">model</span><span class="o">.</span><span class="n">get_dihedrals</span><span class="p">():</span>
+ <span class="k">try</span><span class="p">:</span>
+ <span class="n">bfile</span> <span class="o">=</span> <span class="n">b</span><span class="p">[</span><span class="o">-</span><span class="mi">1</span><span class="p">]</span><span class="o">.</span><span class="n">filename</span><span class="p">()</span>
+ <span class="k">except</span><span class="p">:</span>
+ <span class="n">bfile</span> <span class="o">=</span> <span class="nb">str</span><span class="p">(</span><span class="n">b</span><span class="p">[</span><span class="o">-</span><span class="mi">1</span><span class="p">])</span>
+ <span class="n">item</span> <span class="o">=</span> <span class="nb">tuple</span><span class="p">([</span><span class="n">p</span><span class="o">.</span><span class="n">idx</span> <span class="k">for</span> <span class="n">p</span> <span class="ow">in</span> <span class="n">b</span><span class="p">[:</span><span class="o">-</span><span class="mi">1</span><span class="p">]]</span> <span class="o">+</span> <span class="p">[</span><span class="n">bfile</span><span class="p">])</span>
+ <span class="n">fh</span><span class="o">.</span><span class="n">write</span><span class="p">(</span><span class="s2">"DIHEDRAL </span><span class="si">%d</span><span class="s2"> </span><span class="si">%d</span><span class="s2"> </span><span class="si">%d</span><span class="s2"> </span><span class="si">%d</span><span class="s2"> </span><span class="si">%s</span><span class="se">\n</span><span class="s2">"</span> <span class="o">%</span> <span class="n">item</span><span class="p">)</span>
+
+ <span class="k">def</span><span class="w"> </span><span class="nf">_write_vector_angle_file</span><span class="p">(</span> <span class="bp">self</span><span class="p">,</span> <span class="n">model</span><span class="p">,</span> <span class="n">filename</span> <span class="p">):</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">_vector_angle_filename</span> <span class="o">=</span> <span class="n">filename</span>
+
+ <span class="k">for</span> <span class="n">b</span> <span class="ow">in</span> <span class="nb">list</span><span class="p">(</span> <span class="nb">set</span><span class="p">(</span> <span class="p">[</span><span class="n">b</span> <span class="k">for</span> <span class="n">i</span><span class="p">,</span><span class="n">j</span><span class="p">,</span><span class="n">k</span><span class="p">,</span><span class="n">l</span><span class="p">,</span><span class="n">b</span> <span class="ow">in</span> <span class="n">model</span><span class="o">.</span><span class="n">get_vector_angles</span><span class="p">()]</span> <span class="p">)</span> <span class="p">):</span>
+ <span class="k">if</span> <span class="nb">type</span><span class="p">(</span><span class="n">b</span><span class="p">)</span> <span class="ow">is</span> <span class="ow">not</span> <span class="nb">str</span> <span class="ow">and</span> <span class="ow">not</span> <span class="nb">isinstance</span><span class="p">(</span><span class="n">b</span><span class="p">,</span> <span class="n">Path</span><span class="p">):</span>
+ <span class="n">b</span><span class="o">.</span><span class="n">write_file</span><span class="p">()</span>
+
+ <span class="k">if</span> <span class="nb">len</span><span class="p">(</span><span class="n">model</span><span class="o">.</span><span class="n">vector_angles</span><span class="p">)</span> <span class="o">></span> <span class="mi">0</span><span class="p">:</span>
+ <span class="k">with</span> <span class="nb">open</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">_vector_angle_filename</span><span class="p">,</span><span class="s1">'w'</span><span class="p">)</span> <span class="k">as</span> <span class="n">fh</span><span class="p">:</span>
+ <span class="k">for</span> <span class="n">b</span> <span class="ow">in</span> <span class="n">model</span><span class="o">.</span><span class="n">get_vector_angles</span><span class="p">():</span>
+ <span class="n">p</span> <span class="o">=</span> <span class="n">b</span><span class="p">[</span><span class="o">-</span><span class="mi">1</span><span class="p">]</span>
+ <span class="k">try</span><span class="p">:</span>
+ <span class="n">bfile</span> <span class="o">=</span> <span class="n">p</span><span class="o">.</span><span class="n">filename</span><span class="p">()</span>
+ <span class="k">except</span><span class="p">:</span>
+ <span class="n">bfile</span> <span class="o">=</span> <span class="nb">str</span><span class="p">(</span><span class="n">p</span><span class="p">)</span>
+ <span class="n">item</span> <span class="o">=</span> <span class="nb">tuple</span><span class="p">([</span><span class="n">p</span><span class="o">.</span><span class="n">idx</span> <span class="k">for</span> <span class="n">p</span> <span class="ow">in</span> <span class="n">b</span><span class="p">[:</span><span class="o">-</span><span class="mi">1</span><span class="p">]]</span> <span class="o">+</span> <span class="p">[</span><span class="n">bfile</span><span class="p">])</span>
+ <span class="n">fh</span><span class="o">.</span><span class="n">write</span><span class="p">(</span><span class="s2">"VECANGLE </span><span class="si">%d</span><span class="s2"> </span><span class="si">%d</span><span class="s2"> </span><span class="si">%d</span><span class="s2"> </span><span class="si">%d</span><span class="s2"> </span><span class="si">%s</span><span class="se">\n</span><span class="s2">"</span> <span class="o">%</span> <span class="n">item</span><span class="p">)</span>
+
+ <span class="k">def</span><span class="w"> </span><span class="nf">_write_exclusion_file</span><span class="p">(</span> <span class="bp">self</span><span class="p">,</span> <span class="n">model</span><span class="p">,</span> <span class="n">filename</span> <span class="p">):</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">_exclusion_filename</span> <span class="o">=</span> <span class="n">filename</span>
+ <span class="k">with</span> <span class="nb">open</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">_exclusion_filename</span><span class="p">,</span><span class="s1">'w'</span><span class="p">)</span> <span class="k">as</span> <span class="n">fh</span><span class="p">:</span>
+ <span class="k">for</span> <span class="n">ex</span> <span class="ow">in</span> <span class="n">model</span><span class="o">.</span><span class="n">get_exclusions</span><span class="p">():</span>
+ <span class="n">item</span> <span class="o">=</span> <span class="nb">tuple</span><span class="p">(</span><span class="nb">int</span><span class="p">(</span><span class="n">p</span><span class="o">.</span><span class="n">idx</span><span class="p">)</span> <span class="k">for</span> <span class="n">p</span> <span class="ow">in</span> <span class="n">ex</span><span class="p">)</span>
+ <span class="n">fh</span><span class="o">.</span><span class="n">write</span><span class="p">(</span><span class="s2">"EXCLUDE </span><span class="si">%d</span><span class="s2"> </span><span class="si">%d</span><span class="se">\n</span><span class="s2">"</span> <span class="o">%</span> <span class="n">item</span><span class="p">)</span>
+
+ <span class="k">def</span><span class="w"> </span><span class="nf">_write_bond_angle_file</span><span class="p">(</span> <span class="bp">self</span><span class="p">,</span> <span class="n">model</span><span class="p">,</span> <span class="n">filename</span> <span class="p">):</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">_bond_angle_filename</span> <span class="o">=</span> <span class="n">filename</span>
+ <span class="k">if</span> <span class="nb">len</span><span class="p">(</span><span class="n">model</span><span class="o">.</span><span class="n">bond_angles</span><span class="p">)</span> <span class="o">></span> <span class="mi">0</span><span class="p">:</span>
+ <span class="k">with</span> <span class="nb">open</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">_bond_angle_filename</span><span class="p">,</span><span class="s1">'w'</span><span class="p">)</span> <span class="k">as</span> <span class="n">fh</span><span class="p">:</span>
+ <span class="k">for</span> <span class="n">b</span> <span class="ow">in</span> <span class="n">model</span><span class="o">.</span><span class="n">get_bond_angles</span><span class="p">():</span>
+ <span class="n">bfiles</span> <span class="o">=</span> <span class="p">[]</span>
+ <span class="k">for</span> <span class="n">p</span> <span class="ow">in</span> <span class="n">b</span><span class="p">[</span><span class="o">-</span><span class="mi">1</span><span class="p">]:</span>
+ <span class="k">try</span><span class="p">:</span>
+ <span class="n">bfile</span> <span class="o">=</span> <span class="n">p</span><span class="o">.</span><span class="n">filename</span><span class="p">()</span>
+ <span class="k">except</span><span class="p">:</span>
+ <span class="n">bfile</span> <span class="o">=</span> <span class="nb">str</span><span class="p">(</span><span class="n">p</span><span class="p">)</span>
+ <span class="n">bfiles</span><span class="o">.</span><span class="n">append</span><span class="p">(</span><span class="n">bfile</span><span class="p">)</span>
+ <span class="n">item</span> <span class="o">=</span> <span class="nb">tuple</span><span class="p">([</span><span class="n">p</span><span class="o">.</span><span class="n">idx</span> <span class="k">for</span> <span class="n">p</span> <span class="ow">in</span> <span class="n">b</span><span class="p">[:</span><span class="o">-</span><span class="mi">1</span><span class="p">]]</span> <span class="o">+</span> <span class="n">bfiles</span><span class="p">)</span>
+ <span class="n">fh</span><span class="o">.</span><span class="n">write</span><span class="p">(</span><span class="s2">"BONDANGLE </span><span class="si">%d</span><span class="s2"> </span><span class="si">%d</span><span class="s2"> </span><span class="si">%d</span><span class="s2"> </span><span class="si">%d</span><span class="s2"> </span><span class="si">%s</span><span class="s2"> </span><span class="si">%s</span><span class="s2"> </span><span class="si">%s</span><span class="se">\n</span><span class="s2">"</span> <span class="o">%</span> <span class="n">item</span><span class="p">)</span>
+
+ <span class="k">def</span><span class="w"> </span><span class="nf">_write_product_potential_file</span><span class="p">(</span> <span class="bp">self</span><span class="p">,</span> <span class="n">model</span><span class="p">,</span> <span class="n">filename</span> <span class="p">):</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">_product_potential_filename</span> <span class="o">=</span> <span class="n">filename</span>
+ <span class="k">if</span> <span class="nb">len</span><span class="p">(</span><span class="n">model</span><span class="o">.</span><span class="n">product_potentials</span><span class="p">)</span> <span class="o">></span> <span class="mi">0</span><span class="p">:</span>
+ <span class="k">with</span> <span class="nb">open</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">_product_potential_filename</span><span class="p">,</span><span class="s1">'w'</span><span class="p">)</span> <span class="k">as</span> <span class="n">fh</span><span class="p">:</span>
+ <span class="k">for</span> <span class="n">pot</span> <span class="ow">in</span> <span class="n">model</span><span class="o">.</span><span class="n">get_product_potentials</span><span class="p">():</span>
+ <span class="n">line</span> <span class="o">=</span> <span class="s2">"PRODUCTPOTENTIAL "</span>
+ <span class="k">for</span> <span class="n">ijk_tb</span> <span class="ow">in</span> <span class="n">pot</span><span class="p">:</span>
+ <span class="n">ijk</span> <span class="o">=</span> <span class="n">ijk_tb</span><span class="p">[:</span><span class="o">-</span><span class="mi">1</span><span class="p">]</span>
+ <span class="n">tb</span> <span class="o">=</span> <span class="n">ijk_tb</span><span class="p">[</span><span class="o">-</span><span class="mi">1</span><span class="p">]</span>
+ <span class="k">if</span> <span class="nb">type</span><span class="p">(</span><span class="n">tb</span><span class="p">)</span> <span class="ow">is</span> <span class="nb">tuple</span> <span class="ow">or</span> <span class="nb">type</span><span class="p">(</span><span class="n">tb</span><span class="p">)</span> <span class="ow">is</span> <span class="nb">list</span><span class="p">:</span>
+ <span class="k">if</span> <span class="nb">len</span><span class="p">(</span><span class="n">tb</span><span class="p">)</span> <span class="o">!=</span> <span class="mi">2</span><span class="p">:</span> <span class="k">raise</span> <span class="ne">ValueError</span><span class="p">(</span><span class="s2">"Invalid product potential"</span><span class="p">)</span>
+ <span class="n">type_</span><span class="p">,</span><span class="n">b</span> <span class="o">=</span> <span class="n">tb</span>
+ <span class="k">if</span> <span class="nb">type</span><span class="p">(</span><span class="n">type_</span><span class="p">)</span> <span class="ow">is</span> <span class="ow">not</span> <span class="nb">str</span><span class="p">:</span> <span class="k">raise</span> <span class="ne">ValueError</span><span class="p">(</span><span class="s2">"Invalid product potential: unrecognized specification of potential type"</span><span class="p">)</span>
+ <span class="k">else</span><span class="p">:</span>
+ <span class="n">type_</span> <span class="o">=</span> <span class="s2">""</span>
+ <span class="n">b</span> <span class="o">=</span> <span class="n">tb</span>
+ <span class="k">if</span> <span class="nb">type</span><span class="p">(</span><span class="n">b</span><span class="p">)</span> <span class="ow">is</span> <span class="ow">not</span> <span class="nb">str</span> <span class="ow">and</span> <span class="ow">not</span> <span class="nb">isinstance</span><span class="p">(</span><span class="n">b</span><span class="p">,</span> <span class="n">Path</span><span class="p">):</span>
+ <span class="n">b</span><span class="o">.</span><span class="n">write_file</span><span class="p">()</span>
+ <span class="k">try</span><span class="p">:</span>
+ <span class="n">bfile</span> <span class="o">=</span> <span class="n">b</span><span class="o">.</span><span class="n">filename</span><span class="p">()</span>
+ <span class="k">except</span><span class="p">:</span>
+ <span class="n">bfile</span> <span class="o">=</span> <span class="nb">str</span><span class="p">(</span><span class="n">b</span><span class="p">)</span>
+ <span class="n">line</span> <span class="o">=</span> <span class="n">line</span><span class="o">+</span><span class="s2">" "</span><span class="o">.</span><span class="n">join</span><span class="p">([</span><span class="nb">str</span><span class="p">(</span><span class="n">x</span><span class="o">.</span><span class="n">idx</span><span class="p">)</span> <span class="k">for</span> <span class="n">x</span> <span class="ow">in</span> <span class="n">ijk</span><span class="p">])</span><span class="o">+</span><span class="s2">" "</span>
+ <span class="n">line</span> <span class="o">=</span> <span class="n">line</span><span class="o">+</span><span class="s2">" "</span><span class="o">.</span><span class="n">join</span><span class="p">([</span><span class="nb">str</span><span class="p">(</span><span class="n">x</span><span class="p">)</span> <span class="k">for</span> <span class="n">x</span> <span class="ow">in</span> <span class="p">[</span><span class="n">type_</span><span class="p">,</span><span class="n">bfile</span><span class="p">]</span> <span class="k">if</span> <span class="n">x</span> <span class="o">!=</span> <span class="s2">""</span><span class="p">])</span><span class="o">+</span><span class="s2">" "</span>
+ <span class="n">fh</span><span class="o">.</span><span class="n">write</span><span class="p">(</span><span class="n">line</span><span class="p">)</span>
+
+ <span class="k">def</span><span class="w"> </span><span class="nf">_write_group_sites_file</span><span class="p">(</span> <span class="bp">self</span><span class="p">,</span> <span class="n">model</span><span class="p">,</span> <span class="n">filename</span> <span class="p">):</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">_group_sites_filename</span> <span class="o">=</span> <span class="n">filename</span>
+ <span class="k">if</span> <span class="nb">len</span><span class="p">(</span><span class="n">model</span><span class="o">.</span><span class="n">group_sites</span><span class="p">)</span> <span class="o">></span> <span class="mi">0</span><span class="p">:</span>
+ <span class="k">with</span> <span class="nb">open</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">_group_sites_filename</span><span class="p">,</span><span class="s1">'w'</span><span class="p">)</span> <span class="k">as</span> <span class="n">fh</span><span class="p">:</span>
+ <span class="k">for</span> <span class="n">i</span><span class="p">,</span><span class="n">g</span> <span class="ow">in</span> <span class="nb">enumerate</span><span class="p">(</span><span class="n">model</span><span class="o">.</span><span class="n">group_sites</span><span class="p">):</span>
+ <span class="k">assert</span><span class="p">(</span> <span class="n">i</span><span class="o">+</span><span class="nb">len</span><span class="p">(</span><span class="n">model</span><span class="o">.</span><span class="n">particles</span><span class="p">)</span> <span class="o">==</span> <span class="n">g</span><span class="o">.</span><span class="n">idx</span> <span class="p">)</span>
+ <span class="n">ids</span> <span class="o">=</span> <span class="s2">" "</span><span class="o">.</span><span class="n">join</span><span class="p">([</span><span class="nb">str</span><span class="p">(</span><span class="nb">int</span><span class="p">(</span><span class="n">p</span><span class="o">.</span><span class="n">idx</span><span class="p">))</span> <span class="k">for</span> <span class="n">p</span> <span class="ow">in</span> <span class="n">g</span><span class="o">.</span><span class="n">particles</span><span class="p">])</span>
+ <span class="n">fh</span><span class="o">.</span><span class="n">write</span><span class="p">(</span><span class="s2">"GROUP </span><span class="si">%s</span><span class="se">\n</span><span class="s2">"</span> <span class="o">%</span> <span class="n">ids</span><span class="p">)</span>
+
+ <span class="k">def</span><span class="w"> </span><span class="nf">_write_rb_coordinate_file</span><span class="p">(</span> <span class="bp">self</span><span class="p">,</span> <span class="n">model</span><span class="p">,</span> <span class="n">configuration</span><span class="p">,</span> <span class="n">filename</span> <span class="p">):</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">_rb_coordinate_filename</span> <span class="o">=</span> <span class="n">filename</span>
+ <span class="k">if</span> <span class="nb">len</span><span class="p">(</span><span class="n">model</span><span class="o">.</span><span class="n">rigid_bodies</span><span class="p">)</span> <span class="o">></span> <span class="mi">0</span><span class="p">:</span>
+ <span class="n">rb_integrator</span> <span class="o">=</span> <span class="n">configuration</span><span class="o">.</span><span class="n">rigid_body_integrator</span>
+ <span class="k">if</span> <span class="n">rb_integrator</span> <span class="ow">is</span> <span class="kc">None</span><span class="p">:</span> <span class="n">rb_integrator</span> <span class="o">=</span> <span class="n">configuration</span><span class="o">.</span><span class="n">integrator</span>
+ <span class="k">with</span> <span class="nb">open</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">_rb_coordinate_filename</span><span class="p">,</span><span class="s1">'w'</span><span class="p">)</span> <span class="k">as</span> <span class="n">fh</span><span class="p">:</span>
+ <span class="k">for</span> <span class="n">rb</span> <span class="ow">in</span> <span class="n">model</span><span class="o">.</span><span class="n">rigid_bodies</span><span class="p">:</span>
+ <span class="n">o</span> <span class="o">=</span> <span class="nb">list</span><span class="p">(</span><span class="n">rb</span><span class="o">.</span><span class="n">applyOrientation</span><span class="p">(</span><span class="n">rb</span><span class="o">.</span><span class="n">orientation</span><span class="p">)</span><span class="o">.</span><span class="n">flatten</span><span class="p">())</span>
+ <span class="k">if</span> <span class="nb">len</span><span class="p">(</span><span class="n">o</span><span class="p">)</span> <span class="o">!=</span> <span class="mi">9</span><span class="p">:</span> <span class="k">raise</span> <span class="ne">ValueError</span><span class="p">(</span><span class="s1">'Rigid body orientation should be a 3x3 matrix'</span><span class="p">)</span>
+ <span class="n">fh</span><span class="o">.</span><span class="n">write</span><span class="p">(</span><span class="s1">' '</span><span class="o">.</span><span class="n">join</span><span class="p">(</span><span class="nb">map</span><span class="p">(</span><span class="nb">str</span><span class="p">,</span><span class="nb">list</span><span class="p">(</span><span class="n">rb</span><span class="o">.</span><span class="n">get_collapsed_position</span><span class="p">())</span> <span class="o">+</span> <span class="n">o</span><span class="p">)))</span>
+ <span class="k">if</span> <span class="n">rb_integrator</span> <span class="ow">in</span> <span class="p">(</span><span class="s1">'MD'</span><span class="p">,</span><span class="s1">'Langevin'</span><span class="p">):</span>
+ <span class="k">try</span><span class="p">:</span> <span class="n">fh</span><span class="o">.</span><span class="n">write</span><span class="p">(</span> <span class="s1">' '</span> <span class="o">+</span> <span class="s1">' '</span><span class="o">.</span><span class="n">join</span><span class="p">([</span><span class="nb">str</span><span class="p">(</span><span class="n">x</span><span class="p">)</span> <span class="k">for</span> <span class="n">x</span> <span class="ow">in</span> <span class="n">rb</span><span class="o">.</span><span class="n">momentum</span><span class="p">])</span> <span class="p">)</span>
+ <span class="k">except</span><span class="p">:</span> <span class="n">fh</span><span class="o">.</span><span class="n">write</span><span class="p">(</span> <span class="s1">' 0'</span><span class="o">*</span><span class="mi">3</span> <span class="p">)</span>
+ <span class="k">try</span><span class="p">:</span> <span class="n">fh</span><span class="o">.</span><span class="n">write</span><span class="p">(</span> <span class="s1">' '</span> <span class="o">+</span> <span class="s1">' '</span><span class="o">.</span><span class="n">join</span><span class="p">([</span><span class="nb">str</span><span class="p">(</span><span class="n">x</span><span class="p">)</span> <span class="k">for</span> <span class="n">x</span> <span class="ow">in</span> <span class="n">rb</span><span class="o">.</span><span class="n">rotational_momentum</span><span class="p">])</span> <span class="p">)</span>
+ <span class="k">except</span><span class="p">:</span> <span class="n">fh</span><span class="o">.</span><span class="n">write</span><span class="p">(</span> <span class="s1">' 0'</span><span class="o">*</span><span class="mi">3</span> <span class="p">)</span>
+ <span class="n">fh</span><span class="o">.</span><span class="n">write</span><span class="p">(</span><span class="s1">'</span><span class="se">\n</span><span class="s1">'</span><span class="p">)</span>
+
+
+ <span class="k">def</span><span class="w"> </span><span class="nf">_write_conf</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">model</span><span class="p">,</span> <span class="n">prefix</span><span class="p">,</span> <span class="n">configuration</span><span class="p">):</span>
+ <span class="c1"># num_steps=100000000, output_period=10000, restart_file=None,</span>
+ <span class="c1">## TODO: raise exception if _write_potential_files has not yet been called</span>
+ <span class="n">filename</span> <span class="o">=</span> <span class="sa">f</span><span class="s1">'</span><span class="si">{</span><span class="n">prefix</span><span class="si">}</span><span class="s1">.bd'</span>
+
+ <span class="c1">## Create helper function</span>
+ <span class="k">def</span><span class="w"> </span><span class="nf">_fix_path</span><span class="p">(</span><span class="n">filename</span><span class="p">,</span> <span class="n">rb_type</span><span class="o">=</span><span class="kc">None</span><span class="p">):</span>
+ <span class="k">if</span> <span class="n">rb_type</span> <span class="ow">and</span> <span class="n">rb_type</span> <span class="ow">in</span> <span class="bp">self</span><span class="o">.</span><span class="n">rb_type_dirs</span><span class="p">:</span>
+ <span class="c1"># First, check if this is an existing file within the RB directory</span>
+ <span class="n">rb_dir</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">rb_type_dirs</span><span class="p">[</span><span class="n">rb_type</span><span class="p">]</span>
+ <span class="n">basename</span> <span class="o">=</span> <span class="n">os</span><span class="o">.</span><span class="n">path</span><span class="o">.</span><span class="n">basename</span><span class="p">(</span><span class="nb">str</span><span class="p">(</span><span class="n">filename</span><span class="p">))</span>
+ <span class="n">rb_path</span> <span class="o">=</span> <span class="n">os</span><span class="o">.</span><span class="n">path</span><span class="o">.</span><span class="n">join</span><span class="p">(</span><span class="n">rb_dir</span><span class="p">,</span> <span class="n">basename</span><span class="p">)</span>
+ <span class="k">if</span> <span class="n">os</span><span class="o">.</span><span class="n">path</span><span class="o">.</span><span class="n">exists</span><span class="p">(</span><span class="n">rb_path</span><span class="p">):</span>
+ <span class="k">return</span> <span class="n">rb_path</span>
+
+ <span class="c1"># Check if this might be a resource we want to place in the RB directory</span>
+ <span class="k">if</span> <span class="n">basename</span><span class="o">.</span><span class="n">startswith</span><span class="p">(</span><span class="n">rb_type</span><span class="p">)</span> <span class="ow">or</span> <span class="n">rb_type</span> <span class="ow">in</span> <span class="nb">str</span><span class="p">(</span><span class="n">filename</span><span class="p">):</span>
+ <span class="k">return</span> <span class="n">rb_path</span>
+
+ <span class="n">abspath</span> <span class="o">=</span> <span class="nb">str</span><span class="p">(</span><span class="n">filename</span><span class="p">)</span> <span class="k">if</span> <span class="nb">str</span><span class="p">(</span><span class="n">filename</span><span class="p">)[</span><span class="mi">0</span><span class="p">]</span> <span class="o">==</span> <span class="s1">'/'</span> <span class="k">else</span> <span class="n">Path</span><span class="p">(</span><span class="n">model</span><span class="o">.</span><span class="n">_d_orig</span><span class="p">)</span> <span class="o">/</span> <span class="n">filename</span>
+ <span class="n">ret</span> <span class="o">=</span> <span class="kc">None</span>
+ <span class="k">try</span><span class="p">:</span>
+ <span class="n">ret</span> <span class="o">=</span> <span class="n">os</span><span class="o">.</span><span class="n">path</span><span class="o">.</span><span class="n">relpath</span><span class="p">(</span><span class="nb">str</span><span class="p">(</span><span class="n">abspath</span><span class="p">))</span>
+ <span class="k">except</span><span class="p">:</span>
+ <span class="n">devlogger</span><span class="o">.</span><span class="n">info</span><span class="p">(</span><span class="sa">f</span><span class="s1">'Relative path for </span><span class="si">{</span><span class="n">filename</span><span class="si">}</span><span class="s1"> not found... using </span><span class="si">{</span><span class="n">abspath</span><span class="si">}</span><span class="s1">'</span><span class="p">)</span>
+ <span class="n">ret</span> <span class="o">=</span> <span class="n">abspath</span>
+ <span class="k">return</span> <span class="nb">str</span><span class="p">(</span><span class="n">ret</span><span class="p">)</span>
+
+ <span class="c1">## Build dictionary of parameters</span>
+ <span class="n">params</span> <span class="o">=</span> <span class="nb">dict</span><span class="p">()</span>
+ <span class="k">for</span> <span class="n">k</span><span class="p">,</span><span class="n">v</span> <span class="ow">in</span> <span class="n">configuration</span><span class="o">.</span><span class="n">items</span><span class="p">():</span>
+ <span class="n">params</span><span class="p">[</span><span class="n">k</span><span class="p">]</span> <span class="o">=</span> <span class="n">v</span>
+
+ <span class="k">if</span> <span class="n">configuration</span><span class="o">.</span><span class="n">seed</span> <span class="ow">is</span> <span class="kc">None</span><span class="p">:</span>
+ <span class="n">params</span><span class="p">[</span><span class="s1">'seed'</span><span class="p">]</span> <span class="o">=</span> <span class="sa">f</span><span class="s1">'seed </span><span class="si">{</span><span class="nb">int</span><span class="p">(</span><span class="n">np</span><span class="o">.</span><span class="n">random</span><span class="o">.</span><span class="n">default_rng</span><span class="p">()</span><span class="o">.</span><span class="n">integers</span><span class="p">(</span><span class="mi">1</span><span class="p">,</span><span class="mi">99999</span><span class="p">,</span><span class="mi">1</span><span class="p">))</span><span class="si">}</span><span class="s1">'</span>
+ <span class="k">else</span><span class="p">:</span>
+ <span class="n">params</span><span class="p">[</span><span class="s1">'seed'</span><span class="p">]</span> <span class="o">=</span> <span class="s2">"seed </span><span class="si">{:d}</span><span class="s2">"</span><span class="o">.</span><span class="n">format</span><span class="p">(</span><span class="n">configuration</span><span class="o">.</span><span class="n">seed</span><span class="p">)</span>
+ <span class="n">params</span><span class="p">[</span><span class="s1">'num_steps'</span><span class="p">]</span> <span class="o">=</span> <span class="nb">int</span><span class="p">(</span><span class="n">configuration</span><span class="o">.</span><span class="n">num_steps</span><span class="p">)</span>
+
+ <span class="c1"># params['coordinateFile'] = "%s.coord.txt" % prefix</span>
+ <span class="n">params</span><span class="p">[</span><span class="s1">'particle_file'</span><span class="p">]</span> <span class="o">=</span> <span class="s2">"</span><span class="si">%s</span><span class="s2">.particles.txt"</span> <span class="o">%</span> <span class="n">prefix</span>
+ <span class="k">if</span> <span class="n">configuration</span><span class="o">.</span><span class="n">restart_file</span> <span class="ow">is</span> <span class="kc">None</span><span class="p">:</span>
+ <span class="n">params</span><span class="p">[</span><span class="s1">'restart_coordinates'</span><span class="p">]</span> <span class="o">=</span> <span class="s2">""</span>
+ <span class="k">else</span><span class="p">:</span>
+ <span class="n">params</span><span class="p">[</span><span class="s1">'restart_coordinates'</span><span class="p">]</span> <span class="o">=</span> <span class="s2">"restartCoordinates </span><span class="si">%s</span><span class="s2">"</span> <span class="o">%</span> <span class="n">configuration</span><span class="o">.</span><span class="n">restart_file</span>
+
+ <span class="k">for</span> <span class="n">k</span><span class="p">,</span><span class="n">v</span> <span class="ow">in</span> <span class="nb">zip</span><span class="p">(</span><span class="s1">'XYZ'</span><span class="p">,</span> <span class="n">model</span><span class="o">.</span><span class="n">dimensions</span><span class="p">):</span>
+ <span class="n">params</span><span class="p">[</span><span class="s1">'dim'</span><span class="o">+</span><span class="n">k</span><span class="p">]</span> <span class="o">=</span> <span class="n">v</span>
+
+ <span class="k">if</span> <span class="n">model</span><span class="o">.</span><span class="n">origin</span> <span class="ow">is</span> <span class="kc">None</span><span class="p">:</span>
+ <span class="k">for</span> <span class="n">k</span><span class="p">,</span><span class="n">v</span> <span class="ow">in</span> <span class="nb">zip</span><span class="p">(</span><span class="s1">'XYZ'</span><span class="p">,</span> <span class="n">model</span><span class="o">.</span><span class="n">dimensions</span><span class="p">):</span>
+ <span class="n">params</span><span class="p">[</span><span class="s1">'origin'</span><span class="o">+</span><span class="n">k</span><span class="p">]</span> <span class="o">=</span> <span class="o">-</span><span class="n">v</span><span class="o">*</span><span class="mf">0.5</span>
+ <span class="k">else</span><span class="p">:</span>
+ <span class="k">for</span> <span class="n">k</span><span class="p">,</span><span class="n">v</span> <span class="ow">in</span> <span class="nb">zip</span><span class="p">(</span><span class="s1">'XYZ'</span><span class="p">,</span> <span class="n">model</span><span class="o">.</span><span class="n">origin</span><span class="p">):</span>
+ <span class="n">params</span><span class="p">[</span><span class="s1">'origin'</span><span class="o">+</span><span class="n">k</span><span class="p">]</span> <span class="o">=</span> <span class="n">v</span>
+
+ <span class="k">if</span> <span class="n">params</span><span class="p">[</span><span class="s1">'pairlist_distance'</span><span class="p">]</span> <span class="ow">is</span> <span class="kc">None</span><span class="p">:</span>
+ <span class="n">params</span><span class="p">[</span><span class="s1">'pairlist_distance'</span><span class="p">]</span> <span class="o">=</span> <span class="mi">10</span>
+ <span class="k">else</span><span class="p">:</span>
+ <span class="n">params</span><span class="p">[</span><span class="s1">'pairlist_distance'</span><span class="p">]</span> <span class="o">-=</span> <span class="n">params</span><span class="p">[</span><span class="s1">'cutoff'</span><span class="p">]</span>
+
+ <span class="k">if</span> <span class="n">params</span><span class="p">[</span><span class="s1">'integrator'</span><span class="p">]</span> <span class="o">==</span> <span class="s1">'MD'</span><span class="p">:</span>
+ <span class="n">params</span><span class="p">[</span><span class="s1">'integrator'</span><span class="p">]</span> <span class="o">=</span> <span class="s1">'Langevin'</span>
+
+ <span class="k">if</span> <span class="nb">len</span><span class="p">(</span><span class="n">model</span><span class="o">.</span><span class="n">rigid_bodies</span><span class="p">)</span> <span class="o">></span> <span class="mi">0</span><span class="p">:</span>
+ <span class="n">rb_integrator</span> <span class="o">=</span> <span class="n">params</span><span class="p">[</span><span class="s1">'rigid_body_integrator'</span><span class="p">]</span>
+ <span class="k">if</span> <span class="n">rb_integrator</span> <span class="ow">is</span> <span class="kc">None</span><span class="p">:</span> <span class="n">rb_integrator</span> <span class="o">=</span> <span class="n">params</span><span class="p">[</span><span class="s2">"integrator"</span><span class="p">]</span>
+ <span class="n">params</span><span class="p">[</span><span class="s1">'rigid_body_integrator'</span><span class="p">]</span> <span class="o">=</span> <span class="sa">f</span><span class="s1">'</span><span class="se">\n</span><span class="s1">RigidBodyDynamicType </span><span class="si">{</span><span class="n">rb_integrator</span><span class="si">}</span><span class="s1">'</span>
+ <span class="n">_rbggp</span> <span class="o">=</span> <span class="n">params</span><span class="p">[</span><span class="s2">"rigid_body_grid_grid_period"</span><span class="p">]</span>
+ <span class="k">if</span> <span class="n">_rbggp</span> <span class="ow">is</span> <span class="ow">not</span> <span class="kc">None</span> <span class="ow">and</span> <span class="n">_rbggp</span> <span class="o">></span> <span class="mi">1</span><span class="p">:</span>
+ <span class="n">params</span><span class="p">[</span><span class="s1">'rigid_body_integrator'</span><span class="p">]</span> <span class="o">+=</span> <span class="sa">f</span><span class="s1">'</span><span class="se">\n</span><span class="s1">rigidBodyGridGridPeriod </span><span class="si">{</span><span class="n">_rbggp</span><span class="si">}</span><span class="s1">'</span>
+ <span class="k">else</span><span class="p">:</span>
+ <span class="n">params</span><span class="p">[</span><span class="s1">'rigid_body_integrator'</span><span class="p">]</span> <span class="o">=</span> <span class="s1">''</span>
+
+ <span class="c1">## Actually write the file</span>
+ <span class="k">with</span> <span class="nb">open</span><span class="p">(</span><span class="n">filename</span><span class="p">,</span><span class="s1">'w'</span><span class="p">)</span> <span class="k">as</span> <span class="n">fh</span><span class="p">:</span>
+ <span class="n">fh</span><span class="o">.</span><span class="n">write</span><span class="p">(</span><span class="s2">"""</span><span class="si">{seed}</span>
+<span class="s2">timestep </span><span class="si">{timestep}</span>
+<span class="s2">steps </span><span class="si">{num_steps}</span>
+<span class="s2">numberFluct 0 # deprecated</span>
+
+<span class="s2">interparticleForce 1 # other values deprecated</span>
+<span class="s2">fullLongRange 0 # deprecated</span>
+<span class="s2">temperature </span><span class="si">{temperature}</span>
+<span class="s2">ParticleDynamicType </span><span class="si">{integrator}{rigid_body_integrator}</span>
+
+<span class="s2">outputPeriod </span><span class="si">{output_period}</span>
+<span class="s2">## Energy doesn't actually get printed!</span>
+<span class="s2">outputEnergyPeriod </span><span class="si">{output_period}</span>
+<span class="s2">outputFormat dcd</span>
+
+<span class="s2">## Infrequent domain decomposition because this kernel is still very slow</span>
+<span class="s2">decompPeriod </span><span class="si">{decomp_period}</span>
+<span class="s2">cutoff </span><span class="si">{cutoff}</span>
+<span class="s2">pairlistDistance </span><span class="si">{pairlist_distance}</span>
+
+<span class="s2">origin </span><span class="si">{originX}</span><span class="s2"> </span><span class="si">{originY}</span><span class="s2"> </span><span class="si">{originZ}</span>
+<span class="s2">systemSize </span><span class="si">{dimX}</span><span class="s2"> </span><span class="si">{dimY}</span><span class="s2"> </span><span class="si">{dimZ}</span>
+
+<span class="si">{extra_bd_file_lines}</span>
+<span class="se">\n</span><span class="s2">"""</span><span class="o">.</span><span class="n">format</span><span class="p">(</span><span class="n">extra_bd_file_lines</span><span class="o">=</span><span class="bp">self</span><span class="o">.</span><span class="n">extra_bd_file_lines</span><span class="p">,</span> <span class="o">**</span><span class="n">params</span><span class="p">))</span>
+
+ <span class="c1">## Write entries for each type of particle</span>
+ <span class="k">for</span> <span class="n">pt</span><span class="p">,(</span><span class="n">num</span><span class="p">,</span><span class="n">num_rigid</span><span class="p">)</span> <span class="ow">in</span> <span class="n">model</span><span class="o">.</span><span class="n">getParticleTypesAndCounts</span><span class="p">():</span>
+ <span class="k">if</span> <span class="n">num</span><span class="o">+</span><span class="n">num_rigid</span> <span class="o">==</span> <span class="mi">0</span><span class="p">:</span> <span class="k">continue</span>
+ <span class="n">devlogger</span><span class="o">.</span><span class="n">debug</span><span class="p">(</span><span class="sa">f</span><span class="s1">'Writing configuration for particle type </span><span class="si">{</span><span class="n">pt</span><span class="si">}</span><span class="s1">'</span><span class="p">)</span>
+ <span class="c1">## TODO create new particle types if existing has grid</span>
+ <span class="n">particleParams</span> <span class="o">=</span> <span class="n">pt</span><span class="o">.</span><span class="vm">__dict__</span><span class="o">.</span><span class="n">copy</span><span class="p">()</span>
+ <span class="n">particleParams</span><span class="p">[</span><span class="s1">'num'</span><span class="p">]</span> <span class="o">=</span> <span class="n">num</span>
+ <span class="k">if</span> <span class="n">configuration</span><span class="o">.</span><span class="n">integrator</span> <span class="ow">in</span> <span class="p">(</span><span class="s1">'Brown'</span><span class="p">,</span> <span class="s1">'Brownian'</span><span class="p">,</span> <span class="s1">'BD'</span><span class="p">):</span>
+ <span class="k">try</span><span class="p">:</span>
+ <span class="n">D</span> <span class="o">=</span> <span class="n">pt</span><span class="o">.</span><span class="n">diffusivity</span>
+ <span class="k">except</span><span class="p">:</span>
+<span class="w"> </span><span class="sd">""" units "k K/(amu/ns)" "AA**2/ns" """</span>
+ <span class="n">D</span> <span class="o">=</span> <span class="mf">831447.2</span> <span class="o">*</span> <span class="n">configuration</span><span class="o">.</span><span class="n">temperature</span> <span class="o">/</span> <span class="p">(</span><span class="n">pt</span><span class="o">.</span><span class="n">mass</span> <span class="o">*</span> <span class="n">pt</span><span class="o">.</span><span class="n">damping_coefficient</span><span class="p">)</span>
+ <span class="n">particleParams</span><span class="p">[</span><span class="s1">'dynamics'</span><span class="p">]</span> <span class="o">=</span> <span class="s1">'diffusion </span><span class="si">{D}</span><span class="s1">'</span><span class="o">.</span><span class="n">format</span><span class="p">(</span><span class="n">D</span> <span class="o">=</span> <span class="n">D</span><span class="p">)</span>
+ <span class="k">elif</span> <span class="n">configuration</span><span class="o">.</span><span class="n">integrator</span> <span class="ow">in</span> <span class="p">(</span><span class="s1">'MD'</span><span class="p">,</span><span class="s1">'Langevin'</span><span class="p">,</span><span class="s1">'FusDynamic'</span><span class="p">):</span>
+ <span class="k">try</span><span class="p">:</span>
+ <span class="n">gamma</span> <span class="o">=</span> <span class="n">pt</span><span class="o">.</span><span class="n">damping_coefficient</span>
+ <span class="k">if</span> <span class="n">gamma</span> <span class="ow">is</span> <span class="kc">None</span><span class="p">:</span> <span class="k">raise</span>
+ <span class="k">except</span><span class="p">:</span>
+<span class="w"> </span><span class="sd">""" units "k K/(AA**2/ns)" "amu/ns" """</span>
+ <span class="n">gamma</span> <span class="o">=</span> <span class="mf">831447.2</span> <span class="o">*</span> <span class="n">configuration</span><span class="o">.</span><span class="n">temperature</span> <span class="o">/</span> <span class="p">(</span><span class="n">pt</span><span class="o">.</span><span class="n">mass</span><span class="o">*</span><span class="n">pt</span><span class="o">.</span><span class="n">diffusivity</span><span class="p">)</span>
+ <span class="n">particleParams</span><span class="p">[</span><span class="s1">'dynamics'</span><span class="p">]</span> <span class="o">=</span> <span class="s2">"""mass </span><span class="si">{mass}</span>
+<span class="s2">transDamping </span><span class="si">{g}</span><span class="s2"> </span><span class="si">{g}</span><span class="s2"> </span><span class="si">{g}</span><span class="s2">"""</span><span class="o">.</span><span class="n">format</span><span class="p">(</span><span class="n">mass</span><span class="o">=</span><span class="n">pt</span><span class="o">.</span><span class="n">mass</span><span class="p">,</span> <span class="n">g</span><span class="o">=</span><span class="n">gamma</span><span class="p">)</span>
+ <span class="k">else</span><span class="p">:</span>
+ <span class="k">raise</span> <span class="ne">ValueError</span><span class="p">(</span><span class="s2">"Unrecognized particle integrator '</span><span class="si">{}</span><span class="s2">'"</span><span class="o">.</span><span class="n">format</span><span class="p">(</span><span class="n">configuration</span><span class="o">.</span><span class="n">particle_integrator</span><span class="p">))</span>
+ <span class="n">fh</span><span class="o">.</span><span class="n">write</span><span class="p">(</span><span class="s2">"""</span>
+<span class="s2">particle </span><span class="si">{name}</span>
+<span class="s2">num </span><span class="si">{num}</span>
+<span class="si">{dynamics}</span>
+<span class="s2">"""</span><span class="o">.</span><span class="n">format</span><span class="p">(</span><span class="o">**</span><span class="n">particleParams</span><span class="p">))</span>
+ <span class="k">if</span> <span class="s1">'grid_potentials'</span> <span class="ow">in</span> <span class="n">particleParams</span><span class="p">:</span>
+ <span class="n">grids</span> <span class="o">=</span> <span class="p">[]</span>
+ <span class="n">scales</span> <span class="o">=</span> <span class="p">[]</span>
+ <span class="n">boundary_conditions</span> <span class="o">=</span> <span class="p">[]</span>
+ <span class="k">for</span> <span class="n">vals</span> <span class="ow">in</span> <span class="n">pt</span><span class="o">.</span><span class="n">grid_potentials</span><span class="p">:</span>
+ <span class="k">try</span><span class="p">:</span> <span class="n">g</span><span class="p">,</span><span class="n">s</span><span class="p">,</span><span class="n">bc</span> <span class="o">=</span> <span class="n">vals</span>
+ <span class="k">except</span><span class="p">:</span>
+ <span class="n">logger</span><span class="o">.</span><span class="n">warning</span><span class="p">(</span><span class="sa">f</span><span class="s1">'Failed to unpack </span><span class="si">{</span><span class="n">pt</span><span class="si">}</span><span class="s1">.grid_potentials, presumably due to lack of specified boundary condition... using "dirichlet"'</span><span class="p">)</span>
+ <span class="n">g</span><span class="p">,</span><span class="n">s</span> <span class="o">=</span> <span class="n">vals</span>
+ <span class="n">bc</span> <span class="o">=</span> <span class="s1">'dirichlet'</span>
+ <span class="n">grids</span><span class="o">.</span><span class="n">append</span><span class="p">(</span> <span class="n">_fix_path</span><span class="p">(</span><span class="n">g</span><span class="p">)</span> <span class="p">)</span>
+ <span class="n">scales</span><span class="o">.</span><span class="n">append</span><span class="p">(</span><span class="nb">str</span><span class="p">(</span><span class="n">s</span><span class="p">))</span>
+ <span class="n">boundary_conditions</span><span class="o">.</span><span class="n">append</span><span class="p">(</span><span class="n">bc</span><span class="p">)</span>
+
+ <span class="n">fh</span><span class="o">.</span><span class="n">write</span><span class="p">(</span><span class="s2">"gridFile </span><span class="si">{}</span><span class="se">\n</span><span class="s2">"</span><span class="o">.</span><span class="n">format</span><span class="p">(</span><span class="s2">" "</span><span class="o">.</span><span class="n">join</span><span class="p">(</span><span class="n">grids</span><span class="p">)))</span>
+ <span class="n">fh</span><span class="o">.</span><span class="n">write</span><span class="p">(</span><span class="s2">"gridFileScale </span><span class="si">{}</span><span class="se">\n</span><span class="s2">"</span><span class="o">.</span><span class="n">format</span><span class="p">(</span><span class="s2">" "</span><span class="o">.</span><span class="n">join</span><span class="p">(</span><span class="n">scales</span><span class="p">)))</span>
+ <span class="k">if</span> <span class="nb">any</span><span class="p">([</span><span class="n">bc</span> <span class="o">!=</span> <span class="s1">'dirichlet'</span> <span class="k">for</span> <span class="n">bc</span> <span class="ow">in</span> <span class="n">boundary_conditions</span><span class="p">]):</span>
+ <span class="n">fh</span><span class="o">.</span><span class="n">write</span><span class="p">(</span><span class="sa">f</span><span class="s1">'gridFileBoundaryConditions </span><span class="si">{</span><span class="s2">" "</span><span class="o">.</span><span class="n">join</span><span class="p">(</span><span class="n">boundary_conditions</span><span class="p">)</span><span class="si">}</span><span class="s1">'</span><span class="o">+</span><span class="s1">'</span><span class="se">\n</span><span class="s1">'</span><span class="p">)</span>
+ <span class="k">else</span><span class="p">:</span>
+ <span class="n">fh</span><span class="o">.</span><span class="n">write</span><span class="p">(</span><span class="s2">"gridFile </span><span class="si">{}</span><span class="s2">/null.dx</span><span class="se">\n</span><span class="s2">"</span><span class="o">.</span><span class="n">format</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">potential_directory</span><span class="p">))</span>
+
+ <span class="k">if</span> <span class="s1">'forceXGrid'</span> <span class="ow">in</span> <span class="n">particleParams</span><span class="p">:</span>
+ <span class="n">fh</span><span class="o">.</span><span class="n">write</span><span class="p">(</span><span class="sa">f</span><span class="s2">"forceXGridFile </span><span class="si">{</span><span class="n">_fix_path</span><span class="p">(</span><span class="n">pt</span><span class="o">.</span><span class="n">forceXGrid</span><span class="p">)</span><span class="si">}</span><span class="se">\n</span><span class="s2">"</span><span class="p">)</span>
+ <span class="k">if</span> <span class="s1">'forceYGrid'</span> <span class="ow">in</span> <span class="n">particleParams</span><span class="p">:</span>
+ <span class="n">fh</span><span class="o">.</span><span class="n">write</span><span class="p">(</span><span class="sa">f</span><span class="s2">"forceYGridFile </span><span class="si">{</span><span class="n">_fix_path</span><span class="p">(</span><span class="n">pt</span><span class="o">.</span><span class="n">forceYGrid</span><span class="p">)</span><span class="si">}</span><span class="se">\n</span><span class="s2">"</span><span class="p">)</span>
+ <span class="k">if</span> <span class="s1">'forceZGrid'</span> <span class="ow">in</span> <span class="n">particleParams</span><span class="p">:</span>
+ <span class="n">fh</span><span class="o">.</span><span class="n">write</span><span class="p">(</span><span class="sa">f</span><span class="s2">"forceZGridFile </span><span class="si">{</span><span class="n">_fix_path</span><span class="p">(</span><span class="n">pt</span><span class="o">.</span><span class="n">forceZGrid</span><span class="p">)</span><span class="si">}</span><span class="se">\n</span><span class="s2">"</span><span class="p">)</span>
+
+ <span class="k">if</span> <span class="nb">any</span><span class="p">(</span><span class="sa">f</span><span class="s1">'force</span><span class="si">{</span><span class="n">x</span><span class="si">}</span><span class="s1">Grid'</span> <span class="ow">in</span> <span class="n">particleParams</span> <span class="k">for</span> <span class="n">x</span> <span class="ow">in</span> <span class="p">(</span><span class="s1">'X'</span><span class="p">,</span><span class="s1">'Y'</span><span class="p">,</span><span class="s1">'Z'</span><span class="p">))</span> <span class="ow">and</span> \
+ <span class="s1">'forceGridScale'</span> <span class="ow">in</span> <span class="n">particleParams</span><span class="p">:</span>
+ <span class="n">_scale</span> <span class="o">=</span> <span class="kc">None</span>
+ <span class="k">if</span> <span class="nb">isinstance</span><span class="p">(</span> <span class="n">pt</span><span class="o">.</span><span class="n">forceGridScale</span><span class="p">,</span> <span class="nb">float</span> <span class="p">):</span>
+ <span class="n">_scale</span> <span class="o">=</span> <span class="mi">3</span><span class="o">*</span><span class="p">[</span><span class="n">pt</span><span class="o">.</span><span class="n">forceGridScale</span><span class="p">]</span>
+ <span class="k">elif</span> <span class="nb">len</span><span class="p">(</span> <span class="n">pt</span><span class="o">.</span><span class="n">forceGridScale</span> <span class="p">)</span> <span class="o">==</span> <span class="mi">1</span><span class="p">:</span>
+ <span class="n">_scale</span> <span class="o">=</span> <span class="mi">3</span><span class="o">*</span><span class="p">[</span><span class="n">pt</span><span class="o">.</span><span class="n">forceGridScale</span><span class="p">[</span><span class="mi">0</span><span class="p">]]</span>
+ <span class="k">elif</span> <span class="nb">len</span><span class="p">(</span> <span class="n">pt</span><span class="o">.</span><span class="n">forceGridScale</span> <span class="p">)</span> <span class="o">==</span> <span class="mi">3</span><span class="p">:</span>
+ <span class="n">_scale</span> <span class="o">=</span> <span class="n">pt</span><span class="o">.</span><span class="n">forceGridScale</span>
+ <span class="k">else</span><span class="p">:</span>
+ <span class="k">raise</span> <span class="ne">ValueError</span><span class="p">(</span><span class="sa">f</span><span class="s1">'Unrecognized format for ParticleType.forceGridScale: "</span><span class="si">{</span><span class="n">pt</span><span class="o">.</span><span class="n">forceGridScale</span><span class="si">}</span><span class="s1">"'</span><span class="p">)</span>
+ <span class="n">fh</span><span class="o">.</span><span class="n">write</span><span class="p">(</span><span class="sa">f</span><span class="s2">"forceGridScale </span><span class="si">{</span><span class="s1">' '</span><span class="o">.</span><span class="n">join</span><span class="p">(</span><span class="nb">map</span><span class="p">(</span><span class="nb">str</span><span class="p">,</span><span class="n">_scale</span><span class="p">))</span><span class="si">}</span><span class="s2">"</span><span class="p">)</span>
+
+ <span class="k">if</span> <span class="s1">'rigid_body_potentials'</span> <span class="ow">in</span> <span class="n">particleParams</span><span class="p">:</span>
+ <span class="n">grids</span> <span class="o">=</span> <span class="p">[]</span>
+ <span class="n">scales</span> <span class="o">=</span> <span class="p">[]</span>
+ <span class="k">for</span> <span class="n">item</span> <span class="ow">in</span> <span class="n">pt</span><span class="o">.</span><span class="n">rigid_body_potentials</span><span class="p">:</span>
+ <span class="k">try</span><span class="p">:</span> <span class="n">keyword</span><span class="p">,</span><span class="n">s</span> <span class="o">=</span> <span class="n">item</span>
+ <span class="k">except</span><span class="p">:</span> <span class="n">keyword</span><span class="p">,</span><span class="n">s</span> <span class="o">=</span> <span class="p">(</span><span class="n">item</span><span class="p">,</span><span class="mi">1</span><span class="p">)</span>
+ <span class="n">fh</span><span class="o">.</span><span class="n">write</span><span class="p">(</span><span class="sa">f</span><span class="s2">"rigidBodyPotential </span><span class="si">{</span><span class="n">keyword</span><span class="si">}</span><span class="se">\n</span><span class="s2">"</span><span class="p">)</span>
+ <span class="k">if</span> <span class="n">s</span> <span class="o">!=</span> <span class="mi">1</span><span class="p">:</span> <span class="k">raise</span> <span class="ne">NotImplementedError</span><span class="p">(</span><span class="s1">'Instead scale rigid body potential'</span><span class="p">)</span>
+
+ <span class="c1">## Write coordinates and interactions</span>
+ <span class="n">fh</span><span class="o">.</span><span class="n">write</span><span class="p">(</span><span class="s2">"""</span>
+<span class="s2">## Input coordinates</span>
+<span class="s2">inputParticles </span><span class="si">{particle_file}</span>
+<span class="si">{restart_coordinates}</span>
+
+<span class="s2">## Interaction potentials</span>
+<span class="s2">tabulatedPotential 1</span>
+<span class="s2">## The i@j@file syntax means particle type i will have NB interactions with particle type j using the potential in file</span>
+<span class="s2">"""</span><span class="o">.</span><span class="n">format</span><span class="p">(</span><span class="o">**</span><span class="n">params</span><span class="p">))</span>
+ <span class="k">for</span> <span class="n">pair</span><span class="p">,</span><span class="n">f</span> <span class="ow">in</span> <span class="nb">zip</span><span class="p">(</span><span class="n">model</span><span class="o">.</span><span class="n">_particleTypePairIter</span><span class="p">(),</span> <span class="n">model</span><span class="o">.</span><span class="n">_nonbonded_interaction_files</span><span class="p">):</span>
+ <span class="k">if</span> <span class="n">f</span> <span class="ow">is</span> <span class="ow">not</span> <span class="kc">None</span><span class="p">:</span>
+ <span class="n">i</span><span class="p">,</span><span class="n">j</span><span class="p">,</span><span class="n">t1</span><span class="p">,</span><span class="n">t2</span> <span class="o">=</span> <span class="n">pair</span>
+ <span class="n">fh</span><span class="o">.</span><span class="n">write</span><span class="p">(</span><span class="s2">"tabulatedFile </span><span class="si">%d</span><span class="s2">@</span><span class="si">%d</span><span class="s2">@</span><span class="si">%s</span><span class="se">\n</span><span class="s2">"</span> <span class="o">%</span> <span class="p">(</span><span class="n">i</span><span class="p">,</span><span class="n">j</span><span class="p">,</span><span class="n">f</span><span class="p">))</span>
+
+ <span class="c1">## Bonded interactions</span>
+ <span class="n">restraints</span> <span class="o">=</span> <span class="n">model</span><span class="o">.</span><span class="n">get_restraints</span><span class="p">()</span>
+ <span class="n">bonds</span> <span class="o">=</span> <span class="n">model</span><span class="o">.</span><span class="n">get_bonds</span><span class="p">()</span>
+ <span class="n">angles</span> <span class="o">=</span> <span class="n">model</span><span class="o">.</span><span class="n">get_angles</span><span class="p">()</span>
+ <span class="n">dihedrals</span> <span class="o">=</span> <span class="n">model</span><span class="o">.</span><span class="n">get_dihedrals</span><span class="p">()</span>
+ <span class="n">vector_angles</span> <span class="o">=</span> <span class="n">model</span><span class="o">.</span><span class="n">get_vector_angles</span><span class="p">()</span>
+ <span class="n">exclusions</span> <span class="o">=</span> <span class="n">model</span><span class="o">.</span><span class="n">get_exclusions</span><span class="p">()</span>
+ <span class="n">bond_angles</span> <span class="o">=</span> <span class="n">model</span><span class="o">.</span><span class="n">get_bond_angles</span><span class="p">()</span>
+ <span class="n">prod_pots</span> <span class="o">=</span> <span class="n">model</span><span class="o">.</span><span class="n">get_product_potentials</span><span class="p">()</span>
+ <span class="c1"># group_sites = model.get_group_sites()</span>
+ <span class="n">group_sites</span> <span class="o">=</span> <span class="n">model</span><span class="o">.</span><span class="n">group_sites</span>
+
+ <span class="k">if</span> <span class="nb">len</span><span class="p">(</span><span class="n">bonds</span><span class="p">)</span> <span class="o">></span> <span class="mi">0</span><span class="p">:</span>
+ <span class="k">for</span> <span class="n">b</span> <span class="ow">in</span> <span class="n">model</span><span class="o">.</span><span class="n">_get_bond_potentials</span><span class="p">():</span>
+ <span class="k">try</span><span class="p">:</span>
+ <span class="n">bfile</span> <span class="o">=</span> <span class="n">b</span><span class="o">.</span><span class="n">filename</span><span class="p">()</span>
+ <span class="k">except</span><span class="p">:</span>
+ <span class="n">bfile</span> <span class="o">=</span> <span class="nb">str</span><span class="p">(</span><span class="n">b</span><span class="p">)</span>
+ <span class="n">fh</span><span class="o">.</span><span class="n">write</span><span class="p">(</span><span class="s2">"tabulatedBondFile </span><span class="si">%s</span><span class="se">\n</span><span class="s2">"</span> <span class="o">%</span> <span class="n">bfile</span><span class="p">)</span>
+
+ <span class="k">if</span> <span class="nb">len</span><span class="p">(</span><span class="n">angles</span><span class="p">)</span> <span class="o">></span> <span class="mi">0</span><span class="p">:</span>
+ <span class="k">for</span> <span class="n">b</span> <span class="ow">in</span> <span class="n">model</span><span class="o">.</span><span class="n">_get_angle_potentials</span><span class="p">():</span>
+ <span class="k">try</span><span class="p">:</span>
+ <span class="n">bfile</span> <span class="o">=</span> <span class="n">b</span><span class="o">.</span><span class="n">filename</span><span class="p">()</span>
+ <span class="k">except</span><span class="p">:</span>
+ <span class="n">bfile</span> <span class="o">=</span> <span class="nb">str</span><span class="p">(</span><span class="n">b</span><span class="p">)</span>
+ <span class="n">fh</span><span class="o">.</span><span class="n">write</span><span class="p">(</span><span class="s2">"tabulatedAngleFile </span><span class="si">%s</span><span class="se">\n</span><span class="s2">"</span> <span class="o">%</span> <span class="n">bfile</span><span class="p">)</span>
+
+ <span class="k">if</span> <span class="nb">len</span><span class="p">(</span><span class="n">vector_angles</span><span class="p">)</span> <span class="o">></span> <span class="mi">0</span><span class="p">:</span>
+ <span class="k">for</span> <span class="n">b</span> <span class="ow">in</span> <span class="nb">list</span><span class="p">(</span><span class="nb">set</span><span class="p">([</span><span class="n">b</span> <span class="k">for</span> <span class="n">i</span><span class="p">,</span><span class="n">j</span><span class="p">,</span><span class="n">k</span><span class="p">,</span><span class="n">l</span><span class="p">,</span><span class="n">b</span> <span class="ow">in</span> <span class="n">vector_angles</span><span class="p">])):</span>
+ <span class="k">try</span><span class="p">:</span>
+ <span class="n">bfile</span> <span class="o">=</span> <span class="n">b</span><span class="o">.</span><span class="n">filename</span><span class="p">()</span>
+ <span class="k">except</span><span class="p">:</span>
+ <span class="n">bfile</span> <span class="o">=</span> <span class="nb">str</span><span class="p">(</span><span class="n">b</span><span class="p">)</span>
+ <span class="n">fh</span><span class="o">.</span><span class="n">write</span><span class="p">(</span><span class="s2">"tabulatedVecangleFile </span><span class="si">%s</span><span class="se">\n</span><span class="s2">"</span> <span class="o">%</span> <span class="n">bfile</span><span class="p">)</span>
+
+ <span class="k">if</span> <span class="nb">len</span><span class="p">(</span><span class="n">dihedrals</span><span class="p">)</span> <span class="o">></span> <span class="mi">0</span><span class="p">:</span>
+ <span class="k">for</span> <span class="n">b</span> <span class="ow">in</span> <span class="nb">list</span><span class="p">(</span><span class="nb">set</span><span class="p">([</span><span class="n">b</span> <span class="k">for</span> <span class="n">i</span><span class="p">,</span><span class="n">j</span><span class="p">,</span><span class="n">k</span><span class="p">,</span><span class="n">l</span><span class="p">,</span><span class="n">b</span> <span class="ow">in</span> <span class="n">dihedrals</span><span class="p">])):</span>
+ <span class="k">try</span><span class="p">:</span>
+ <span class="n">bfile</span> <span class="o">=</span> <span class="n">b</span><span class="o">.</span><span class="n">filename</span><span class="p">()</span>
+ <span class="k">except</span><span class="p">:</span>
+ <span class="n">bfile</span> <span class="o">=</span> <span class="nb">str</span><span class="p">(</span><span class="n">b</span><span class="p">)</span>
+ <span class="n">fh</span><span class="o">.</span><span class="n">write</span><span class="p">(</span><span class="s2">"tabulatedDihedralFile </span><span class="si">%s</span><span class="se">\n</span><span class="s2">"</span> <span class="o">%</span> <span class="n">bfile</span><span class="p">)</span>
+
+ <span class="k">if</span> <span class="nb">len</span><span class="p">(</span><span class="n">vector_angles</span><span class="p">)</span> <span class="o">></span> <span class="mi">0</span><span class="p">:</span>
+ <span class="k">for</span> <span class="n">b</span> <span class="ow">in</span> <span class="nb">list</span><span class="p">(</span><span class="nb">set</span><span class="p">([</span><span class="n">b</span> <span class="k">for</span> <span class="n">i</span><span class="p">,</span><span class="n">j</span><span class="p">,</span><span class="n">k</span><span class="p">,</span><span class="n">l</span><span class="p">,</span><span class="n">b</span> <span class="ow">in</span> <span class="n">vector_angles</span><span class="p">])):</span>
+ <span class="k">try</span><span class="p">:</span>
+ <span class="n">bfile</span> <span class="o">=</span> <span class="n">b</span><span class="o">.</span><span class="n">filename</span><span class="p">()</span>
+ <span class="k">except</span><span class="p">:</span>
+ <span class="n">bfile</span> <span class="o">=</span> <span class="nb">str</span><span class="p">(</span><span class="n">b</span><span class="p">)</span>
+ <span class="n">fh</span><span class="o">.</span><span class="n">write</span><span class="p">(</span><span class="s2">"tabulatedVecangleFile </span><span class="si">%s</span><span class="se">\n</span><span class="s2">"</span> <span class="o">%</span> <span class="n">bfile</span><span class="p">)</span>
+
+ <span class="k">if</span> <span class="nb">len</span><span class="p">(</span><span class="n">restraints</span><span class="p">)</span> <span class="o">></span> <span class="mi">0</span><span class="p">:</span>
+ <span class="n">fh</span><span class="o">.</span><span class="n">write</span><span class="p">(</span><span class="s2">"inputRestraints </span><span class="si">%s</span><span class="se">\n</span><span class="s2">"</span> <span class="o">%</span> <span class="bp">self</span><span class="o">.</span><span class="n">_restraint_filename</span><span class="p">)</span>
+ <span class="k">if</span> <span class="nb">len</span><span class="p">(</span><span class="n">bonds</span><span class="p">)</span> <span class="o">></span> <span class="mi">0</span><span class="p">:</span>
+ <span class="n">fh</span><span class="o">.</span><span class="n">write</span><span class="p">(</span><span class="s2">"inputBonds </span><span class="si">%s</span><span class="se">\n</span><span class="s2">"</span> <span class="o">%</span> <span class="bp">self</span><span class="o">.</span><span class="n">_bond_filename</span><span class="p">)</span>
+ <span class="k">if</span> <span class="nb">len</span><span class="p">(</span><span class="n">angles</span><span class="p">)</span> <span class="o">></span> <span class="mi">0</span><span class="p">:</span>
+ <span class="n">fh</span><span class="o">.</span><span class="n">write</span><span class="p">(</span><span class="s2">"inputAngles </span><span class="si">%s</span><span class="se">\n</span><span class="s2">"</span> <span class="o">%</span> <span class="bp">self</span><span class="o">.</span><span class="n">_angle_filename</span><span class="p">)</span>
+ <span class="k">if</span> <span class="nb">len</span><span class="p">(</span><span class="n">dihedrals</span><span class="p">)</span> <span class="o">></span> <span class="mi">0</span><span class="p">:</span>
+ <span class="n">fh</span><span class="o">.</span><span class="n">write</span><span class="p">(</span><span class="s2">"inputDihedrals </span><span class="si">%s</span><span class="se">\n</span><span class="s2">"</span> <span class="o">%</span> <span class="bp">self</span><span class="o">.</span><span class="n">_dihedral_filename</span><span class="p">)</span>
+ <span class="k">if</span> <span class="nb">len</span><span class="p">(</span><span class="n">vector_angles</span><span class="p">)</span> <span class="o">></span> <span class="mi">0</span><span class="p">:</span>
+ <span class="n">fh</span><span class="o">.</span><span class="n">write</span><span class="p">(</span><span class="s2">"inputVecangles </span><span class="si">%s</span><span class="se">\n</span><span class="s2">"</span> <span class="o">%</span> <span class="bp">self</span><span class="o">.</span><span class="n">_vector_angle_filename</span><span class="p">)</span>
+ <span class="k">if</span> <span class="nb">len</span><span class="p">(</span><span class="n">exclusions</span><span class="p">)</span> <span class="o">></span> <span class="mi">0</span><span class="p">:</span>
+ <span class="n">fh</span><span class="o">.</span><span class="n">write</span><span class="p">(</span><span class="s2">"inputExcludes </span><span class="si">%s</span><span class="se">\n</span><span class="s2">"</span> <span class="o">%</span> <span class="bp">self</span><span class="o">.</span><span class="n">_exclusion_filename</span><span class="p">)</span>
+ <span class="k">if</span> <span class="nb">len</span><span class="p">(</span><span class="n">vector_angles</span><span class="p">)</span> <span class="o">></span> <span class="mi">0</span><span class="p">:</span>
+ <span class="n">fh</span><span class="o">.</span><span class="n">write</span><span class="p">(</span><span class="s2">"inputVecangles </span><span class="si">%s</span><span class="se">\n</span><span class="s2">"</span> <span class="o">%</span> <span class="bp">self</span><span class="o">.</span><span class="n">_vector_angle_filename</span><span class="p">)</span>
+ <span class="k">if</span> <span class="nb">len</span><span class="p">(</span><span class="n">bond_angles</span><span class="p">)</span> <span class="o">></span> <span class="mi">0</span><span class="p">:</span>
+ <span class="n">fh</span><span class="o">.</span><span class="n">write</span><span class="p">(</span><span class="s2">"inputBondAngles </span><span class="si">%s</span><span class="se">\n</span><span class="s2">"</span> <span class="o">%</span> <span class="bp">self</span><span class="o">.</span><span class="n">_bond_angle_filename</span><span class="p">)</span>
+ <span class="k">if</span> <span class="nb">len</span><span class="p">(</span><span class="n">prod_pots</span><span class="p">)</span> <span class="o">></span> <span class="mi">0</span><span class="p">:</span>
+ <span class="n">fh</span><span class="o">.</span><span class="n">write</span><span class="p">(</span><span class="s2">"inputProductPotentials </span><span class="si">%s</span><span class="se">\n</span><span class="s2">"</span> <span class="o">%</span> <span class="bp">self</span><span class="o">.</span><span class="n">_product_potential_filename</span><span class="p">)</span>
+ <span class="k">if</span> <span class="nb">len</span><span class="p">(</span><span class="n">group_sites</span><span class="p">)</span> <span class="o">></span> <span class="mi">0</span><span class="p">:</span>
+ <span class="n">fh</span><span class="o">.</span><span class="n">write</span><span class="p">(</span><span class="s2">"inputGroups </span><span class="si">%s</span><span class="se">\n</span><span class="s2">"</span> <span class="o">%</span> <span class="bp">self</span><span class="o">.</span><span class="n">_group_sites_filename</span><span class="p">)</span>
+
+ <span class="k">if</span> <span class="nb">len</span><span class="p">(</span><span class="n">model</span><span class="o">.</span><span class="n">rigid_bodies</span><span class="p">)</span> <span class="o">></span> <span class="mi">0</span><span class="p">:</span>
+ <span class="k">for</span> <span class="n">rbi</span><span class="p">,</span><span class="n">num</span> <span class="ow">in</span> <span class="n">model</span><span class="o">.</span><span class="n">rigid_body_type_counts</span><span class="p">:</span>
+ <span class="n">rbt</span><span class="o">=</span><span class="n">model</span><span class="o">.</span><span class="n">rigid_body_index</span><span class="p">[</span><span class="n">rbi</span><span class="p">]</span>
+ <span class="k">if</span> <span class="n">num</span> <span class="o">==</span> <span class="mi">0</span><span class="p">:</span> <span class="k">continue</span>
+ <span class="n">devlogger</span><span class="o">.</span><span class="n">debug</span><span class="p">(</span><span class="sa">f</span><span class="s1">'Writing configuration for rigid body type </span><span class="si">{</span><span class="n">rbt</span><span class="si">}</span><span class="s1">'</span><span class="p">)</span>
+ <span class="c1">## For now, we always convert rigid body diffusivity into mass+damping</span>
+ <span class="k">try</span><span class="p">:</span>
+ <span class="n">gamma</span> <span class="o">=</span> <span class="n">rbt</span><span class="o">.</span><span class="n">damping_coefficient</span>
+ <span class="k">except</span><span class="p">:</span>
+<span class="w"> </span><span class="sd">""" units "k K/(AA**2/ns)" "dalton/ns" """</span>
+ <span class="n">gamma</span> <span class="o">=</span> <span class="mf">831447.2</span> <span class="o">*</span> <span class="n">configuration</span><span class="o">.</span><span class="n">temperature</span> <span class="o">/</span> <span class="p">(</span><span class="n">rbt</span><span class="o">.</span><span class="n">mass</span><span class="o">*</span><span class="n">np</span><span class="o">.</span><span class="n">array</span><span class="p">(</span><span class="n">rbt</span><span class="o">.</span><span class="n">diffusivity</span><span class="p">))</span>
+ <span class="k">if</span> <span class="nb">len</span><span class="p">(</span><span class="n">gamma</span><span class="p">)</span> <span class="o">==</span> <span class="mi">1</span><span class="p">:</span>
+ <span class="n">logger</span><span class="o">.</span><span class="n">warn</span><span class="p">(</span><span class="sa">f</span><span class="s1">'Using single diffusion coefficient for all motions along all rigid body principal axes for </span><span class="si">{</span><span class="n">rbt</span><span class="si">}</span><span class="s1">'</span><span class="p">)</span>
+ <span class="n">gamma</span> <span class="o">=</span> <span class="mi">3</span><span class="o">*</span><span class="p">[</span><span class="n">gamma</span><span class="p">]</span>
+
+ <span class="k">try</span><span class="p">:</span>
+ <span class="n">gamma_rot</span> <span class="o">=</span> <span class="n">rbt</span><span class="o">.</span><span class="n">rotational_damping_coefficient</span>
+ <span class="k">except</span><span class="p">:</span>
+<span class="w"> </span><span class="sd">""" units "k K/(1/ns)" "AA**2 dalton/ns" """</span>
+ <span class="n">gamma_rot</span> <span class="o">=</span> <span class="mf">831447.2</span> <span class="o">*</span> <span class="n">configuration</span><span class="o">.</span><span class="n">temperature</span> <span class="o">/</span> <span class="p">(</span><span class="n">np</span><span class="o">.</span><span class="n">array</span><span class="p">(</span><span class="n">rbt</span><span class="o">.</span><span class="n">moment_of_inertia</span><span class="p">)</span><span class="o">*</span><span class="n">np</span><span class="o">.</span><span class="n">array</span><span class="p">(</span><span class="n">rbt</span><span class="o">.</span><span class="n">diffusivity</span><span class="p">))</span>
+ <span class="k">if</span> <span class="nb">len</span><span class="p">(</span><span class="n">gamma_rot</span><span class="p">)</span> <span class="o">==</span> <span class="mi">1</span><span class="p">:</span>
+ <span class="n">logger</span><span class="o">.</span><span class="n">warn</span><span class="p">(</span><span class="sa">f</span><span class="s1">'Using single rotational diffusion coefficient for all motions along all rigid body principal axes for </span><span class="si">{</span><span class="n">pt</span><span class="si">}</span><span class="s1">'</span><span class="p">)</span>
+ <span class="n">gamma_rot</span> <span class="o">=</span> <span class="mi">3</span><span class="o">*</span><span class="p">[</span><span class="n">gamma_rot</span><span class="p">]</span>
+ <span class="k">if</span> <span class="nb">len</span><span class="p">(</span><span class="n">gamma_rot</span><span class="p">)</span> <span class="o">!=</span> <span class="mi">3</span><span class="p">:</span> <span class="k">raise</span> <span class="ne">ValueError</span><span class="p">(</span><span class="s1">'Expected a three-element rotational diffusion coefficient for rigid bodies'</span><span class="p">)</span>
+ <span class="n">fh</span><span class="o">.</span><span class="n">write</span><span class="p">(</span><span class="sa">f</span><span class="s2">"""</span>
+<span class="s2">rigidBody </span><span class="si">{</span><span class="n">rbt</span><span class="o">.</span><span class="n">name</span><span class="si">}</span>
+<span class="s2">num </span><span class="si">{</span><span class="n">num</span><span class="si">}</span>
+<span class="s2">mass </span><span class="si">{</span><span class="n">rbt</span><span class="o">.</span><span class="n">mass</span><span class="si">}</span>
+<span class="s2">inertia </span><span class="si">{</span><span class="s1">' '</span><span class="o">.</span><span class="n">join</span><span class="p">(</span><span class="nb">map</span><span class="p">(</span><span class="nb">str</span><span class="p">,</span><span class="n">rbt</span><span class="o">.</span><span class="n">moment_of_inertia</span><span class="p">))</span><span class="si">}</span>
+<span class="s2">transDamping </span><span class="si">{</span><span class="s1">' '</span><span class="o">.</span><span class="n">join</span><span class="p">(</span><span class="nb">map</span><span class="p">(</span><span class="nb">str</span><span class="p">,</span><span class="n">gamma</span><span class="p">))</span><span class="si">}</span>
+<span class="s2">rotDamping </span><span class="si">{</span><span class="s1">' '</span><span class="o">.</span><span class="n">join</span><span class="p">(</span><span class="nb">map</span><span class="p">(</span><span class="nb">str</span><span class="p">,</span><span class="n">gamma_rot</span><span class="p">))</span><span class="si">}</span>
+<span class="s2">"""</span><span class="p">)</span>
+
+ <span class="k">for</span> <span class="n">item</span> <span class="ow">in</span> <span class="n">rbt</span><span class="o">.</span><span class="n">potential_grids</span><span class="p">:</span>
+ <span class="k">try</span><span class="p">:</span> <span class="n">keyword</span><span class="p">,</span><span class="n">g</span><span class="p">,</span><span class="n">s</span> <span class="o">=</span> <span class="n">item</span>
+ <span class="k">except</span><span class="p">:</span> <span class="p">(</span><span class="n">keyword</span><span class="p">,</span><span class="n">g</span><span class="p">),</span><span class="n">s</span> <span class="o">=</span> <span class="p">(</span><span class="n">item</span><span class="p">,</span><span class="mi">1</span><span class="p">)</span>
+
+ <span class="n">g</span> <span class="o">=</span> <span class="n">_fix_path</span><span class="p">(</span><span class="n">g</span><span class="p">,</span><span class="n">rbt</span><span class="o">.</span><span class="n">name</span><span class="p">)</span>
+ <span class="n">fh</span><span class="o">.</span><span class="n">write</span><span class="p">(</span><span class="sa">f</span><span class="s2">"potentialGrid </span><span class="si">{</span><span class="n">keyword</span><span class="si">}</span><span class="s2"> </span><span class="si">{</span><span class="n">g</span><span class="si">}</span><span class="se">\n</span><span class="s2">"</span><span class="p">)</span>
+ <span class="k">if</span> <span class="n">s</span> <span class="o">!=</span> <span class="mi">1</span><span class="p">:</span> <span class="n">fh</span><span class="o">.</span><span class="n">write</span><span class="p">(</span><span class="sa">f</span><span class="s2">"potentialGridScale </span><span class="si">{</span><span class="n">keyword</span><span class="si">}</span><span class="s2"> </span><span class="si">{</span><span class="n">s</span><span class="si">}</span><span class="se">\n</span><span class="s2">"</span><span class="p">)</span>
+
+ <span class="k">for</span> <span class="n">item</span> <span class="ow">in</span> <span class="n">rbt</span><span class="o">.</span><span class="n">charge_grids</span><span class="p">:</span>
+ <span class="k">try</span><span class="p">:</span> <span class="n">keyword</span><span class="p">,</span><span class="n">g</span><span class="p">,</span><span class="n">s</span> <span class="o">=</span> <span class="n">item</span>
+ <span class="k">except</span><span class="p">:</span> <span class="p">(</span><span class="n">keyword</span><span class="p">,</span><span class="n">g</span><span class="p">),</span><span class="n">s</span> <span class="o">=</span> <span class="p">(</span><span class="n">item</span><span class="p">,</span><span class="mi">1</span><span class="p">)</span>
+ <span class="n">g</span> <span class="o">=</span> <span class="n">_fix_path</span><span class="p">(</span><span class="n">g</span><span class="p">,</span><span class="n">rbt</span><span class="o">.</span><span class="n">name</span><span class="p">)</span>
+ <span class="n">fh</span><span class="o">.</span><span class="n">write</span><span class="p">(</span><span class="sa">f</span><span class="s2">"densityGrid </span><span class="si">{</span><span class="n">keyword</span><span class="si">}</span><span class="s2"> </span><span class="si">{</span><span class="n">g</span><span class="si">}</span><span class="se">\n</span><span class="s2">"</span><span class="p">)</span>
+ <span class="k">if</span> <span class="n">s</span> <span class="o">!=</span> <span class="mi">1</span><span class="p">:</span> <span class="n">fh</span><span class="o">.</span><span class="n">write</span><span class="p">(</span><span class="sa">f</span><span class="s2">"densityGridScale </span><span class="si">{</span><span class="n">keyword</span><span class="si">}</span><span class="s2"> </span><span class="si">{</span><span class="n">s</span><span class="si">}</span><span class="se">\n</span><span class="s2">"</span><span class="p">)</span>
+ <span class="k">for</span> <span class="n">item</span> <span class="ow">in</span> <span class="n">rbt</span><span class="o">.</span><span class="n">pmf_grids</span><span class="p">:</span>
+ <span class="k">try</span><span class="p">:</span> <span class="n">keyword</span><span class="p">,</span><span class="n">g</span><span class="p">,</span><span class="n">s</span> <span class="o">=</span> <span class="n">item</span>
+ <span class="k">except</span><span class="p">:</span> <span class="p">(</span><span class="n">keyword</span><span class="p">,</span><span class="n">g</span><span class="p">),</span><span class="n">s</span> <span class="o">=</span> <span class="p">(</span><span class="n">item</span><span class="p">,</span><span class="mi">1</span><span class="p">)</span>
+ <span class="n">g</span> <span class="o">=</span> <span class="n">_fix_path</span><span class="p">(</span><span class="n">g</span><span class="p">,</span><span class="n">rbt</span><span class="o">.</span><span class="n">name</span><span class="p">)</span>
+ <span class="n">fh</span><span class="o">.</span><span class="n">write</span><span class="p">(</span><span class="sa">f</span><span class="s2">"gridFile </span><span class="si">{</span><span class="n">keyword</span><span class="si">}</span><span class="s2"> </span><span class="si">{</span><span class="n">g</span><span class="si">}</span><span class="se">\n</span><span class="s2">"</span><span class="p">)</span>
+ <span class="k">if</span> <span class="n">s</span> <span class="o">!=</span> <span class="mi">1</span><span class="p">:</span> <span class="n">fh</span><span class="o">.</span><span class="n">write</span><span class="p">(</span><span class="sa">f</span><span class="s2">"pmfScale </span><span class="si">{</span><span class="n">keyword</span><span class="si">}</span><span class="s2"> </span><span class="si">{</span><span class="n">s</span><span class="si">}</span><span class="se">\n</span><span class="s2">"</span><span class="p">)</span>
+
+ <span class="c1">## AttachedParticles</span>
+ <span class="k">if</span> <span class="nb">len</span><span class="p">(</span><span class="n">rbt</span><span class="o">.</span><span class="n">attached_particles</span><span class="p">)</span> <span class="o">></span> <span class="mi">0</span><span class="p">:</span>
+ <span class="n">fh</span><span class="o">.</span><span class="n">write</span><span class="p">(</span><span class="sa">f</span><span class="s1">'attachedParticles </span><span class="si">{</span><span class="n">rbt</span><span class="o">.</span><span class="n">_attached_particles_filename</span><span class="si">}</span><span class="se">\n</span><span class="s1">'</span><span class="p">)</span>
+
+ <span class="n">fh</span><span class="o">.</span><span class="n">write</span><span class="p">(</span><span class="sa">f</span><span class="s1">'</span><span class="se">\n</span><span class="s1">inputRBCoordinates </span><span class="si">{</span><span class="bp">self</span><span class="o">.</span><span class="n">_rb_coordinate_filename</span><span class="si">}</span><span class="se">\n</span><span class="s1">'</span><span class="p">)</span>
+ <span class="o">...</span>
+
+ <span class="n">write_null_dx</span> <span class="o">=</span> <span class="kc">False</span>
+ <span class="k">for</span> <span class="n">pt</span><span class="p">,(</span><span class="n">num</span><span class="p">,</span><span class="n">num_rb</span><span class="p">)</span> <span class="ow">in</span> <span class="n">model</span><span class="o">.</span><span class="n">getParticleTypesAndCounts</span><span class="p">():</span>
+ <span class="k">if</span> <span class="n">num</span><span class="o">+</span><span class="n">num_rb</span> <span class="o">==</span> <span class="mi">0</span><span class="p">:</span> <span class="k">continue</span>
+ <span class="k">if</span> <span class="s2">"grid_potentials"</span> <span class="ow">not</span> <span class="ow">in</span> <span class="n">pt</span><span class="o">.</span><span class="vm">__dict__</span><span class="p">:</span>
+ <span class="n">gridfile</span> <span class="o">=</span> <span class="s2">"</span><span class="si">{}</span><span class="s2">/null.dx"</span><span class="o">.</span><span class="n">format</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">potential_directory</span><span class="p">)</span>
+ <span class="k">with</span> <span class="nb">open</span><span class="p">(</span><span class="n">gridfile</span><span class="p">,</span> <span class="s1">'w'</span><span class="p">)</span> <span class="k">as</span> <span class="n">fh</span><span class="p">:</span>
+ <span class="n">fh</span><span class="o">.</span><span class="n">write</span><span class="p">(</span><span class="s2">"""object 1 class gridpositions counts 2 2 2</span>
+<span class="s2">origin </span><span class="si">{originX}</span><span class="s2"> </span><span class="si">{originY}</span><span class="s2"> </span><span class="si">{originZ}</span>
+<span class="s2">delta </span><span class="si">{dimX}</span><span class="s2"> 0.000000 0.000000</span>
+<span class="s2">delta 0.000000 </span><span class="si">{dimY}</span><span class="s2"> 0.000000</span>
+<span class="s2">delta 0.000000 0.000000 </span><span class="si">{dimZ}</span>
+<span class="s2">object 2 class gridconnections counts 2 2 2</span>
+<span class="s2">object 3 class array type float rank 0 items 8 data follows</span>
+<span class="s2">0.0 0.0 0.0 </span>
+<span class="s2">0.0 0.0 0.0 </span>
+<span class="s2">0.0 0.0 </span>
+<span class="s2">attribute "dep" string "positions"</span>
+<span class="s2">object "density" class field </span>
+<span class="s2">component "positions" value 1</span>
+<span class="s2">component "connections" value 2</span>
+<span class="s2">component "data" value 3</span>
+<span class="s2">"""</span><span class="o">.</span><span class="n">format</span><span class="p">(</span><span class="o">**</span><span class="n">params</span><span class="p">))</span>
+ <span class="k">break</span></div>
+
+
+<div class="viewcode-block" id="NamdEngine">
+<a class="viewcode-back" href="../../api/simulation_engines/engine.html#arbdmodel.engine.NamdEngine">[docs]</a>
+<span class="k">class</span><span class="w"> </span><span class="nc">NamdEngine</span><span class="p">(</span><span class="n">SimEngine</span><span class="p">):</span>
+<span class="w"> </span><span class="sd">""" Partial interface to NAMD simulation engine """</span>
+
+ <span class="k">def</span><span class="w"> </span><span class="fm">__init__</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">configuration</span><span class="o">=</span><span class="kc">None</span><span class="p">,</span> <span class="o">**</span><span class="n">conf_params</span><span class="p">):</span>
+ <span class="k">if</span> <span class="n">configuration</span> <span class="ow">is</span> <span class="kc">None</span><span class="p">:</span>
+ <span class="n">configuration</span> <span class="o">=</span> <span class="n">SimConf</span><span class="p">(</span><span class="o">**</span><span class="n">conf_params</span><span class="p">)</span>
+ <span class="n">SimEngine</span><span class="o">.</span><span class="fm">__init__</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">configuration</span><span class="p">)</span>
+
+ <span class="bp">self</span><span class="o">.</span><span class="n">num_particles</span> <span class="o">=</span> <span class="mi">0</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">particles</span> <span class="o">=</span> <span class="p">[]</span> <span class="c1"># TODO decide if this should belong here, or with model</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">type_counts</span> <span class="o">=</span> <span class="kc">None</span> <span class="c1"># TODO decide if this should belong here, or with model</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">cacheUpToDate</span> <span class="o">=</span> <span class="kc">False</span>
+
+ <span class="nd">@property</span>
+ <span class="k">def</span><span class="w"> </span><span class="nf">default_binary</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span>
+ <span class="k">return</span> <span class="s1">'namd2'</span>
+
+ <span class="k">def</span><span class="w"> </span><span class="nf">_generate_command_string</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">binary</span><span class="p">,</span> <span class="n">output_name</span><span class="p">,</span> <span class="n">output_directory</span><span class="p">,</span> <span class="n">num_procs</span><span class="o">=</span><span class="mi">1</span><span class="p">,</span> <span class="n">gpu</span><span class="o">=</span><span class="kc">None</span><span class="p">,</span> <span class="n">replicas</span><span class="o">=</span><span class="mi">1</span><span class="p">):</span>
+ <span class="n">cmd</span> <span class="o">=</span> <span class="p">[</span><span class="n">binary</span><span class="p">]</span>
+ <span class="k">if</span> <span class="n">gpu</span> <span class="ow">is</span> <span class="ow">not</span> <span class="kc">None</span> <span class="ow">and</span> <span class="nb">len</span><span class="p">(</span><span class="n">gpu</span><span class="p">)</span> <span class="o">></span> <span class="mi">0</span><span class="p">:</span>
+ <span class="n">cmd</span><span class="o">.</span><span class="n">extend</span><span class="p">([</span><span class="s1">'+devices'</span><span class="p">]</span> <span class="o">+</span> <span class="p">[</span><span class="s1">','</span><span class="o">.</span><span class="n">join</span><span class="p">([</span><span class="nb">str</span><span class="p">(</span><span class="nb">int</span><span class="p">(</span><span class="n">g</span><span class="p">))</span> <span class="k">for</span> <span class="n">g</span> <span class="ow">in</span> <span class="n">gpu</span><span class="p">])])</span>
+ <span class="n">cmd</span><span class="o">.</span><span class="n">extend</span><span class="p">([</span><span class="sa">f</span><span class="s1">'+p</span><span class="si">{</span><span class="nb">str</span><span class="p">(</span><span class="n">num_procs</span><span class="p">)</span><span class="si">}</span><span class="s1">'</span><span class="p">])</span>
+ <span class="k">if</span> <span class="n">replicas</span> <span class="o">></span> <span class="mi">1</span><span class="p">:</span>
+ <span class="k">raise</span> <span class="ne">NotImplementedError</span>
+ <span class="n">cmd</span> <span class="o">=</span> <span class="n">cmd</span> <span class="o">+</span> <span class="p">[</span><span class="sa">f</span><span class="s1">'</span><span class="si">{</span><span class="n">output_name</span><span class="si">}</span><span class="s1">.namd'</span><span class="p">]</span>
+ <span class="n">cmd</span> <span class="o">=</span> <span class="nb">tuple</span><span class="p">(</span><span class="nb">str</span><span class="p">(</span><span class="n">x</span><span class="p">)</span> <span class="k">for</span> <span class="n">x</span> <span class="ow">in</span> <span class="n">cmd</span><span class="p">)</span>
+ <span class="k">return</span> <span class="n">cmd</span>
+
+<div class="viewcode-block" id="NamdEngine.get_default_conf">
+<a class="viewcode-back" href="../../api/simulation_engines/engine.html#arbdmodel.engine.NamdEngine.get_default_conf">[docs]</a>
+ <span class="k">def</span><span class="w"> </span><span class="nf">get_default_conf</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span>
+ <span class="n">conf</span> <span class="o">=</span> <span class="n">SimConf</span><span class="p">(</span><span class="n">num_steps</span><span class="o">=</span><span class="mf">1e5</span><span class="p">,</span> <span class="n">output_period</span><span class="o">=</span><span class="mf">1e3</span><span class="p">,</span>
+ <span class="n">integrator</span><span class="o">=</span><span class="s1">'MD'</span><span class="p">,</span> <span class="n">timestep</span><span class="o">=</span><span class="mf">2e-6</span><span class="p">,</span> <span class="n">thermostat</span><span class="o">=</span><span class="s1">'Langevin'</span><span class="p">,</span> <span class="n">barostat</span><span class="o">=</span><span class="kc">None</span><span class="p">,</span>
+ <span class="n">temperature</span><span class="o">=</span><span class="mi">295</span><span class="p">,</span> <span class="n">pressure</span><span class="o">=</span><span class="mi">1</span><span class="p">,</span>
+ <span class="n">cutoff</span><span class="o">=</span><span class="mi">12</span><span class="p">,</span> <span class="n">pairlist_distance</span><span class="o">=</span><span class="mi">14</span><span class="p">,</span> <span class="n">decomp_period</span><span class="o">=</span><span class="mi">12</span><span class="p">,</span>
+ <span class="n">seed</span><span class="o">=</span><span class="kc">None</span><span class="p">,</span> <span class="n">restart_file</span><span class="o">=</span><span class="kc">None</span><span class="p">)</span>
+ <span class="k">return</span> <span class="n">conf</span></div>
+
+
+<div class="viewcode-block" id="NamdEngine.write_simulation_files">
+<a class="viewcode-back" href="../../api/simulation_engines/engine.html#arbdmodel.engine.NamdEngine.write_simulation_files">[docs]</a>
+ <span class="k">def</span><span class="w"> </span><span class="nf">write_simulation_files</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">model</span><span class="p">,</span> <span class="n">output_name</span><span class="p">,</span> <span class="n">configuration</span><span class="o">=</span><span class="kc">None</span><span class="p">,</span> <span class="n">write_pqr</span><span class="o">=</span><span class="kc">False</span><span class="p">,</span> <span class="n">copy_ff_from</span><span class="o">=</span><span class="n">get_resource_path</span><span class="p">(</span><span class="s2">"charmm36.nbfix"</span><span class="p">),</span> <span class="o">**</span><span class="n">conf_params</span><span class="p">):</span>
+ <span class="k">if</span> <span class="n">configuration</span> <span class="ow">is</span> <span class="kc">None</span><span class="p">:</span>
+ <span class="n">configuration</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">_get_combined_conf</span><span class="p">(</span><span class="n">model</span><span class="p">,</span> <span class="o">**</span><span class="n">conf_params</span><span class="p">)</span>
+
+ <span class="n">model</span><span class="o">.</span><span class="n">write_psf</span><span class="p">(</span> <span class="n">output_name</span><span class="o">+</span><span class="s1">'.psf'</span> <span class="p">)</span>
+ <span class="n">model</span><span class="o">.</span><span class="n">write_pdb</span><span class="p">(</span> <span class="n">output_name</span><span class="o">+</span><span class="s1">'.pdb'</span> <span class="p">)</span>
+ <span class="n">model</span><span class="o">.</span><span class="n">write_pdb</span><span class="p">(</span> <span class="n">output_name</span> <span class="o">+</span> <span class="s2">".fixed.pdb"</span><span class="p">,</span> <span class="n">beta_from_fixed</span><span class="o">=</span><span class="kc">True</span> <span class="p">)</span>
+ <span class="k">if</span> <span class="n">write_pqr</span><span class="p">:</span> <span class="n">model</span><span class="o">.</span><span class="n">write_pqr</span><span class="p">(</span> <span class="n">output_name</span> <span class="o">+</span> <span class="s2">".pqr"</span> <span class="p">)</span>
+
+ <span class="k">if</span> <span class="n">copy_ff_from</span> <span class="ow">is</span> <span class="ow">not</span> <span class="kc">None</span> <span class="ow">and</span> <span class="n">copy_ff_from</span> <span class="o">!=</span> <span class="s1">''</span><span class="p">:</span>
+ <span class="k">try</span><span class="p">:</span>
+ <span class="n">shutil</span><span class="o">.</span><span class="n">copytree</span><span class="p">(</span> <span class="n">copy_ff_from</span><span class="p">,</span> <span class="n">Path</span><span class="p">(</span><span class="n">copy_ff_from</span><span class="p">)</span><span class="o">.</span><span class="n">stem</span> <span class="p">)</span>
+ <span class="k">except</span> <span class="ne">FileExistsError</span><span class="p">:</span>
+ <span class="k">pass</span>
+
+ <span class="bp">self</span><span class="o">.</span><span class="n">_write_conf</span><span class="p">(</span> <span class="n">model</span><span class="p">,</span> <span class="n">output_name</span><span class="p">,</span> <span class="n">configuration</span> <span class="p">)</span></div>
+
+
+<div class="viewcode-block" id="NamdEngine.write_conf">
+<a class="viewcode-back" href="../../api/simulation_engines/engine.html#arbdmodel.engine.NamdEngine.write_conf">[docs]</a>
+ <span class="k">def</span><span class="w"> </span><span class="nf">write_conf</span><span class="p">(</span> <span class="bp">self</span><span class="p">,</span><span class="n">model</span><span class="p">,</span><span class="n">output_name</span><span class="p">,</span> <span class="n">minimization_steps</span><span class="o">=</span><span class="mi">4800</span><span class="p">,</span> <span class="n">num_steps</span> <span class="o">=</span> <span class="mf">1e6</span><span class="p">,</span>
+ <span class="n">output_directory</span> <span class="o">=</span> <span class="s1">'output'</span><span class="p">,</span>
+ <span class="n">update_dimensions</span><span class="o">=</span><span class="kc">True</span><span class="p">,</span> <span class="n">extrabonds</span><span class="o">=</span><span class="kc">True</span> <span class="p">):</span>
+
+<span class="w"> </span><span class="sd">""" Write a NAMD configuration file (developed for the mrdna package) """</span>
+
+ <span class="n">num_steps</span> <span class="o">=</span> <span class="nb">int</span><span class="p">(</span><span class="n">num_steps</span><span class="o">//</span><span class="mi">12</span><span class="p">)</span><span class="o">*</span><span class="mi">12</span>
+ <span class="n">minimization_steps</span> <span class="o">=</span> <span class="nb">int</span><span class="p">(</span><span class="n">minimization_steps</span><span class="o">//</span><span class="mi">24</span><span class="p">)</span><span class="o">*</span><span class="mi">24</span>
+ <span class="k">if</span> <span class="n">num_steps</span> <span class="o"><</span> <span class="mi">12</span><span class="p">:</span>
+ <span class="k">raise</span> <span class="ne">ValueError</span><span class="p">(</span><span class="s2">"Must run with at least 12 steps"</span><span class="p">)</span>
+ <span class="k">if</span> <span class="n">minimization_steps</span> <span class="o"><</span> <span class="mi">24</span><span class="p">:</span>
+ <span class="k">raise</span> <span class="ne">ValueError</span><span class="p">(</span><span class="s2">"Must run with at least 24 minimization steps"</span><span class="p">)</span>
+
+ <span class="n">format_data</span> <span class="o">=</span> <span class="n">model</span><span class="o">.</span><span class="vm">__dict__</span><span class="o">.</span><span class="n">copy</span><span class="p">()</span> <span class="c1"># get parameters from System object</span>
+
+ <span class="n">format_data</span><span class="p">[</span><span class="s1">'extrabonds'</span><span class="p">]</span> <span class="o">=</span> <span class="s2">"""extraBonds on</span>
+<span class="s2">extraBondsFile $prefix.exb</span>
+<span class="s2">"""</span> <span class="k">if</span> <span class="n">extrabonds</span> <span class="k">else</span> <span class="s2">""</span>
+
+ <span class="k">if</span> <span class="bp">self</span><span class="o">.</span><span class="n">useTclForces</span><span class="p">:</span>
+ <span class="n">format_data</span><span class="p">[</span><span class="s1">'margin'</span><span class="p">]</span> <span class="o">=</span> <span class="s2">""</span>
+ <span class="n">format_data</span><span class="p">[</span><span class="s1">'tcl_forces'</span><span class="p">]</span> <span class="o">=</span> <span class="s2">"""tclForces on</span>
+<span class="s2">tclForcesScript $prefix.forces.tcl</span>
+<span class="s2">"""</span>
+ <span class="k">else</span><span class="p">:</span>
+ <span class="n">format_data</span><span class="p">[</span><span class="s1">'margin'</span><span class="p">]</span> <span class="o">=</span> <span class="s2">"""margin 30</span>
+<span class="s2">"""</span>
+ <span class="n">format_data</span><span class="p">[</span><span class="s1">'tcl_forces'</span><span class="p">]</span> <span class="o">=</span> <span class="s2">""</span>
+
+ <span class="k">if</span> <span class="n">update_dimensions</span><span class="p">:</span>
+ <span class="n">format_data</span><span class="p">[</span><span class="s1">'dimensions'</span><span class="p">]</span> <span class="o">=</span> <span class="n">model</span><span class="o">.</span><span class="n">dimensions_from_structure</span><span class="p">()</span>
+
+ <span class="k">for</span> <span class="n">k</span><span class="p">,</span><span class="n">v</span> <span class="ow">in</span> <span class="nb">zip</span><span class="p">(</span><span class="s1">'XYZ'</span><span class="p">,</span> <span class="n">format_data</span><span class="p">[</span><span class="s1">'dimensions'</span><span class="p">]):</span>
+ <span class="n">format_data</span><span class="p">[</span><span class="s1">'origin'</span><span class="o">+</span><span class="n">k</span><span class="p">]</span> <span class="o">=</span> <span class="o">-</span><span class="n">v</span><span class="o">*</span><span class="mf">0.5</span>
+ <span class="n">format_data</span><span class="p">[</span><span class="s1">'cell'</span><span class="o">+</span><span class="n">k</span><span class="p">]</span> <span class="o">=</span> <span class="n">v</span>
+
+ <span class="n">format_data</span><span class="p">[</span><span class="s1">'prefix'</span><span class="p">]</span> <span class="o">=</span> <span class="n">output_name</span>
+ <span class="n">format_data</span><span class="p">[</span><span class="s1">'minimization_steps'</span><span class="p">]</span> <span class="o">=</span> <span class="nb">int</span><span class="p">(</span><span class="n">minimization_steps</span><span class="o">//</span><span class="mi">2</span><span class="p">)</span>
+ <span class="n">format_data</span><span class="p">[</span><span class="s1">'num_steps'</span><span class="p">]</span> <span class="o">=</span> <span class="n">num_steps</span>
+ <span class="n">format_data</span><span class="p">[</span><span class="s1">'output_directory'</span><span class="p">]</span> <span class="o">=</span> <span class="n">output_directory</span>
+ <span class="n">filename</span> <span class="o">=</span> <span class="s1">'</span><span class="si">{}</span><span class="s1">.namd'</span><span class="o">.</span><span class="n">format</span><span class="p">(</span><span class="n">output_name</span><span class="p">)</span>
+
+ <span class="k">with</span> <span class="nb">open</span><span class="p">(</span><span class="n">filename</span><span class="p">,</span><span class="s1">'w'</span><span class="p">)</span> <span class="k">as</span> <span class="n">fh</span><span class="p">:</span>
+ <span class="n">fh</span><span class="o">.</span><span class="n">write</span><span class="p">(</span><span class="s2">"""</span>
+<span class="s2">set prefix </span><span class="si">{prefix}</span>
+<span class="s2">set nLast 0; # increment when continueing a simulation</span>
+<span class="s2">set n [expr $nLast+1]</span>
+<span class="s2">set out </span><span class="si">{output_directory}</span><span class="s2">/$prefix-$n</span>
+<span class="s2">set temperature </span><span class="si">{temperature}</span>
+
+<span class="s2">structure $prefix.psf</span>
+<span class="s2">coordinates $prefix.pdb</span>
+
+<span class="s2">outputName $out</span>
+<span class="s2">XSTfile $out.xst</span>
+<span class="s2">DCDfile $out.dcd</span>
+
+<span class="s2">#############################################################</span>
+<span class="s2">## SIMULATION PARAMETERS ##</span>
+<span class="s2">#############################################################</span>
+
+<span class="s2"># Input</span>
+<span class="s2">paraTypeCharmm on</span>
+<span class="s2">parameters charmm36.nbfix/par_all36_na.prm</span>
+<span class="s2">parameters charmm36.nbfix/par_water_ions_na.prm</span>
+
+<span class="s2">wrapAll off</span>
+
+<span class="s2"># Force-Field Parameters</span>
+<span class="s2">exclude scaled1-4</span>
+<span class="s2">1-4scaling 1.0</span>
+<span class="s2">switching on</span>
+<span class="s2">switchdist 8</span>
+<span class="s2">cutoff 10</span>
+<span class="s2">pairlistdist 12</span>
+<span class="si">{margin}</span>
+
+<span class="s2"># Integrator Parameters</span>
+<span class="s2">timestep 2.0 ;# 2fs/step</span>
+<span class="s2">rigidBonds all ;# needed for 2fs steps</span>
+<span class="s2">nonbondedFreq 1</span>
+<span class="s2">fullElectFrequency 3</span>
+<span class="s2">stepspercycle 12</span>
+
+<span class="s2"># PME (for full-system periodic electrostatics)</span>
+<span class="s2">PME no</span>
+<span class="s2">PMEGridSpacing 1.2</span>
+
+<span class="s2"># Constant Temperature Control</span>
+<span class="s2">langevin on ;# do langevin dynamics</span>
+<span class="s2"># langevinDamping 1 ;# damping coefficient (gamma); used in original study</span>
+<span class="s2">langevinDamping 0.1 ;# less friction for faster relaxation</span>
+<span class="s2">langevinTemp $temperature</span>
+<span class="s2">langevinHydrogen off ;# don't couple langevin bath to hydrogens</span>
+
+<span class="s2"># output</span>
+<span class="s2">useGroupPressure yes</span>
+<span class="s2">xstFreq 4800</span>
+<span class="s2">outputEnergies 4800</span>
+<span class="s2">dcdfreq 4800</span>
+<span class="s2">restartfreq 48000</span>
+
+<span class="s2">#############################################################</span>
+<span class="s2">## EXTRA FORCES ##</span>
+<span class="s2">#############################################################</span>
+
+<span class="s2"># ENM and intrahelical extrabonds</span>
+<span class="si">{extrabonds}</span>
+<span class="si">{tcl_forces}</span>
+
+<span class="s2">#############################################################</span>
+<span class="s2">## RUN ##</span>
+<span class="s2">#############################################################</span>
+
+<span class="s2"># Continuing a job from the restart files</span>
+<span class="s2">cellBasisVector1 </span><span class="si">{cellX}</span><span class="s2"> 0 0</span>
+<span class="s2">cellBasisVector2 0 </span><span class="si">{cellY}</span><span class="s2"> 0</span>
+<span class="s2">cellBasisVector3 0 0 </span><span class="si">{cellZ}</span>
+
+<span class="s2">if {{$nLast == 0}} {{</span>
+<span class="s2"> temperature 300</span>
+<span class="s2"> fixedAtoms on</span>
+<span class="s2"> fixedAtomsForces on</span>
+<span class="s2"> fixedAtomsFile $prefix.fixed.pdb</span>
+<span class="s2"> fixedAtomsCol B</span>
+<span class="s2"> minimize </span><span class="si">{minimization_steps:d}</span>
+<span class="s2"> fixedAtoms off</span>
+<span class="s2"> minimize </span><span class="si">{minimization_steps:d}</span>
+<span class="s2">}} else {{</span>
+<span class="s2"> bincoordinates </span><span class="si">{output_directory}</span><span class="s2">/$prefix-$nLast.restart.coor</span>
+<span class="s2"> binvelocities </span><span class="si">{output_directory}</span><span class="s2">/$prefix-$nLast.restart.vel</span>
+<span class="s2">}}</span>
+
+<span class="s2">run </span><span class="si">{num_steps:d}</span>
+<span class="s2">"""</span><span class="o">.</span><span class="n">format</span><span class="p">(</span><span class="o">**</span><span class="n">format_data</span><span class="p">))</span></div>
+</div>
+
+
+<span class="sd">""" External Runners</span>
+<span class="sd">Integration with HydroPro and APBS for shape rigid body calculations.</span>
+<span class="sd">Original script by Chun Kit Chan, 2024</span>
+<span class="sd">HydroProRunner and APBSRunner module provides interfaces to external tools used in shape rigid body modeling:</span>
+<span class="sd">- HydroPro for hydrodynamic calculations</span>
+<span class="sd">- APBS for electrostatics calculations</span>
+<span class="sd">"""</span>
+
+<div class="viewcode-block" id="HydroProRunner">
+<a class="viewcode-back" href="../../api/simulation_engines/engine.html#arbdmodel.engine.HydroProRunner">[docs]</a>
+<span class="k">class</span><span class="w"> </span><span class="nc">HydroProRunner</span><span class="p">:</span>
+<span class="w"> </span><span class="sd">"""Interface to HydroPro for hydrodynamic calculations"""</span>
+ <span class="k">def</span><span class="w"> </span><span class="fm">__init__</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">mass</span><span class="p">,</span> <span class="n">simconf</span><span class="o">=</span><span class="kc">None</span><span class="p">,</span> <span class="n">structure_name</span><span class="o">=</span><span class="s2">"hydrocal"</span><span class="p">,</span> <span class="n">cal_type</span><span class="o">=</span><span class="s2">"shape"</span><span class="p">):</span>
+<span class="w"> </span><span class="sd">"""Initialize HydroPro interface.</span>
+<span class="sd"> </span>
+<span class="sd"> Args:</span>
+<span class="sd"> mass: Mass in AMU</span>
+<span class="sd"> simconf: SimConf object with temperature, viscosity and solvent_density (optional)</span>
+<span class="sd"> structure_name: Base name of structure files</span>
+<span class="sd"> cal_type: shape or mesh, determined by program</span>
+<span class="sd"> """</span>
+ <span class="k">if</span> <span class="n">simconf</span> <span class="ow">is</span> <span class="kc">None</span><span class="p">:</span>
+ <span class="kn">from</span><span class="w"> </span><span class="nn">.</span><span class="w"> </span><span class="kn">import</span> <span class="n">DefaultSimConf</span>
+ <span class="n">simconf</span> <span class="o">=</span> <span class="n">DefaultSimConf</span><span class="p">()</span>
+
+ <span class="bp">self</span><span class="o">.</span><span class="n">temperature</span> <span class="o">=</span> <span class="n">simconf</span><span class="o">.</span><span class="n">temperature</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">viscosity</span> <span class="o">=</span> <span class="n">simconf</span><span class="o">.</span><span class="n">viscosity</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">solvent_density</span> <span class="o">=</span> <span class="n">simconf</span><span class="o">.</span><span class="n">solvent_density</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">binary</span> <span class="o">=</span> <span class="n">simconf</span><span class="o">.</span><span class="n">get_binary</span><span class="p">(</span><span class="s1">'hydropro'</span><span class="p">)</span>
+
+ <span class="c1"># Check if binary exists</span>
+ <span class="k">if</span> <span class="bp">self</span><span class="o">.</span><span class="n">binary</span> <span class="ow">is</span> <span class="kc">None</span><span class="p">:</span>
+ <span class="k">raise</span> <span class="ne">FileNotFoundError</span><span class="p">(</span><span class="s2">"HydroPro binary not found. Please configure in simconf."</span><span class="p">)</span>
+
+ <span class="bp">self</span><span class="o">.</span><span class="n">binary</span> <span class="o">=</span> <span class="n">Path</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">binary</span><span class="p">)</span>
+ <span class="k">if</span> <span class="ow">not</span> <span class="bp">self</span><span class="o">.</span><span class="n">binary</span><span class="o">.</span><span class="n">exists</span><span class="p">():</span>
+ <span class="k">raise</span> <span class="ne">FileNotFoundError</span><span class="p">(</span><span class="sa">f</span><span class="s2">"HydroPro binary not found at </span><span class="si">{</span><span class="bp">self</span><span class="o">.</span><span class="n">binary</span><span class="si">}</span><span class="s2">"</span><span class="p">)</span>
+
+ <span class="c1"># Make binary executable if needed (Unix only)</span>
+ <span class="k">if</span> <span class="n">platform</span><span class="o">.</span><span class="n">system</span><span class="p">()</span> <span class="o">!=</span> <span class="s1">'Windows'</span> <span class="ow">and</span> <span class="ow">not</span> <span class="n">os</span><span class="o">.</span><span class="n">access</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">binary</span><span class="p">,</span> <span class="n">os</span><span class="o">.</span><span class="n">X_OK</span><span class="p">):</span>
+ <span class="n">os</span><span class="o">.</span><span class="n">chmod</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">binary</span><span class="p">,</span> <span class="mo">0o755</span><span class="p">)</span>
+
+ <span class="bp">self</span><span class="o">.</span><span class="n">structure_name</span> <span class="o">=</span> <span class="n">structure_name</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">mass</span> <span class="o">=</span> <span class="n">mass</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">cal_type</span> <span class="o">=</span> <span class="n">cal_type</span>
+
+<div class="viewcode-block" id="HydroProRunner.write_config">
+<a class="viewcode-back" href="../../api/simulation_engines/engine.html#arbdmodel.engine.HydroProRunner.write_config">[docs]</a>
+ <span class="k">def</span><span class="w"> </span><span class="nf">write_config</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">output_path</span><span class="o">=</span><span class="s2">"hydropro.dat"</span><span class="p">,</span>
+ <span class="n">aer</span><span class="o">=</span><span class="mf">2.9</span><span class="p">,</span><span class="n">nsig</span><span class="o">=</span><span class="mi">6</span><span class="p">,</span><span class="n">sig_min</span><span class="o">=</span><span class="mi">1</span><span class="p">,</span><span class="n">sig_max</span><span class="o">=</span><span class="mi">2</span><span class="p">,</span><span class="n">specific_volume</span><span class="o">=</span><span class="mf">0.702</span><span class="p">,):</span>
+<span class="w"> </span><span class="sd">"""Write HydroPro configuration file with explicit parameters.</span>
+<span class="sd"> </span>
+<span class="sd"> Args:</span>
+<span class="sd"> output_path: Path to write config file</span>
+<span class="sd"> cal_type: shape(0) or mesh(1)</span>
+<span class="sd"> structure_name: Name of the molecule/structure</span>
+<span class="sd"> mass: Molecular weight in Daltons (amu)</span>
+<span class="sd"> aer: Atomic Element Radius in Angstroms</span>
+<span class="sd"> nsig: Number of values of the shell thickness</span>
+<span class="sd"> sig_min: Minimum radius of beads in the shell (Angstroms)</span>
+<span class="sd"> sig_max: Maximum radius of beads in the shell (Angstroms)</span>
+<span class="sd"> specific_volume: Partial specific volume in cm³/g</span>
+<span class="sd"> """</span>
+ <span class="n">temperature_c</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">temperature</span> <span class="o">-</span> <span class="mf">273.15</span> <span class="c1"># Convert K to C</span>
+ <span class="k">if</span> <span class="bp">self</span><span class="o">.</span><span class="n">cal_type</span><span class="o">==</span><span class="s2">"mesh"</span> <span class="ow">or</span> <span class="bp">self</span><span class="o">.</span><span class="n">cal_type</span><span class="o">==</span><span class="mi">1</span><span class="p">:</span>
+ <span class="n">aer</span><span class="o">=</span><span class="mi">10</span>
+ <span class="n">nsig</span><span class="o">=</span><span class="mi">4</span>
+ <span class="n">sig_min</span><span class="o">=</span><span class="mi">10</span>
+ <span class="n">sig_max</span><span class="o">=</span><span class="mi">20</span>
+ <span class="n">specific_volume</span><span class="o">=</span><span class="mi">1</span>
+
+ <span class="k">with</span> <span class="nb">open</span><span class="p">(</span><span class="n">output_path</span><span class="p">,</span> <span class="s1">'w'</span><span class="p">)</span> <span class="k">as</span> <span class="n">f</span><span class="p">:</span>
+ <span class="c1"># Basic identification</span>
+ <span class="n">f</span><span class="o">.</span><span class="n">write</span><span class="p">(</span><span class="sa">f</span><span class="s2">"</span><span class="si">{</span><span class="bp">self</span><span class="o">.</span><span class="n">structure_name</span><span class="si">}</span><span class="se">\n</span><span class="s2">"</span><span class="p">)</span> <span class="c1"># Name of molecule</span>
+ <span class="n">f</span><span class="o">.</span><span class="n">write</span><span class="p">(</span><span class="sa">f</span><span class="s2">"</span><span class="si">{</span><span class="bp">self</span><span class="o">.</span><span class="n">structure_name</span><span class="si">}</span><span class="s2">.hydro</span><span class="se">\n</span><span class="s2">"</span><span class="p">)</span> <span class="c1"># Base name for output files</span>
+ <span class="n">f</span><span class="o">.</span><span class="n">write</span><span class="p">(</span><span class="s2">"hydro.pdb</span><span class="se">\n</span><span class="s2">"</span><span class="p">)</span>
+ <span class="n">f</span><span class="o">.</span><span class="n">write</span><span class="p">(</span><span class="s2">"1</span><span class="se">\n</span><span class="s2">"</span><span class="p">)</span> <span class="c1"># Calculation type always 1 (bead surface model)</span>
+
+ <span class="c1"># Bead model parameters</span>
+ <span class="n">f</span><span class="o">.</span><span class="n">write</span><span class="p">(</span><span class="sa">f</span><span class="s2">"</span><span class="si">{</span><span class="n">aer</span><span class="si">}</span><span class="s2">,</span><span class="se">\n</span><span class="s2">"</span><span class="p">)</span> <span class="c1"># AER (radius in Angstroms)</span>
+ <span class="n">f</span><span class="o">.</span><span class="n">write</span><span class="p">(</span><span class="sa">f</span><span class="s2">"</span><span class="si">{</span><span class="n">nsig</span><span class="si">}</span><span class="s2">,</span><span class="se">\n</span><span class="s2">"</span><span class="p">)</span> <span class="c1"># NSIG (values of shell thickness)</span>
+ <span class="n">f</span><span class="o">.</span><span class="n">write</span><span class="p">(</span><span class="sa">f</span><span class="s2">"</span><span class="si">{</span><span class="n">sig_min</span><span class="si">}</span><span class="s2">,</span><span class="se">\n</span><span class="s2">"</span><span class="p">)</span> <span class="c1"># SIGMIN (min bead radius)</span>
+ <span class="n">f</span><span class="o">.</span><span class="n">write</span><span class="p">(</span><span class="sa">f</span><span class="s2">"</span><span class="si">{</span><span class="n">sig_max</span><span class="si">}</span><span class="s2">,</span><span class="se">\n</span><span class="s2">"</span><span class="p">)</span> <span class="c1"># SIGMAX (max bead radius)</span>
+
+ <span class="c1"># Physical parameters</span>
+ <span class="n">f</span><span class="o">.</span><span class="n">write</span><span class="p">(</span><span class="sa">f</span><span class="s2">"</span><span class="si">{</span><span class="n">temperature_c</span><span class="si">}</span><span class="s2">,</span><span class="se">\n</span><span class="s2">"</span><span class="p">)</span> <span class="c1"># Temperature in Celsius</span>
+ <span class="n">f</span><span class="o">.</span><span class="n">write</span><span class="p">(</span><span class="sa">f</span><span class="s2">"</span><span class="si">{</span><span class="bp">self</span><span class="o">.</span><span class="n">viscosity</span><span class="si">}</span><span class="s2">,</span><span class="se">\n</span><span class="s2">"</span><span class="p">)</span> <span class="c1"># Solvent viscosity in poise</span>
+ <span class="n">f</span><span class="o">.</span><span class="n">write</span><span class="p">(</span><span class="sa">f</span><span class="s2">"</span><span class="si">{</span><span class="bp">self</span><span class="o">.</span><span class="n">mass</span><span class="si">}</span><span class="s2">,</span><span class="se">\n</span><span class="s2">"</span><span class="p">)</span> <span class="c1"># Molecular weight in Daltons</span>
+ <span class="n">f</span><span class="o">.</span><span class="n">write</span><span class="p">(</span><span class="sa">f</span><span class="s2">"</span><span class="si">{</span><span class="n">specific_volume</span><span class="si">}</span><span class="s2">,</span><span class="se">\n</span><span class="s2">"</span><span class="p">)</span> <span class="c1"># Partial specific volume</span>
+ <span class="n">f</span><span class="o">.</span><span class="n">write</span><span class="p">(</span><span class="sa">f</span><span class="s2">"</span><span class="si">{</span><span class="bp">self</span><span class="o">.</span><span class="n">solvent_density</span><span class="si">}</span><span class="se">\n</span><span class="s2">"</span><span class="p">)</span> <span class="c1"># Solvent density</span>
+
+ <span class="c1"># Calculation control parameters</span>
+ <span class="n">f</span><span class="o">.</span><span class="n">write</span><span class="p">(</span><span class="s2">"-1</span><span class="se">\n</span><span class="s2">"</span><span class="p">)</span> <span class="c1"># Number of Q values</span>
+ <span class="n">f</span><span class="o">.</span><span class="n">write</span><span class="p">(</span><span class="s2">"-1</span><span class="se">\n</span><span class="s2">"</span><span class="p">)</span> <span class="c1"># Number of intervals</span>
+ <span class="n">f</span><span class="o">.</span><span class="n">write</span><span class="p">(</span><span class="s2">"0</span><span class="se">\n</span><span class="s2">"</span><span class="p">)</span> <span class="c1"># Monte Carlo trials</span>
+ <span class="n">f</span><span class="o">.</span><span class="n">write</span><span class="p">(</span><span class="s2">"1</span><span class="se">\n</span><span class="s2">"</span><span class="p">)</span> <span class="c1"># IDIF=1 (yes) for full diffusion tensors</span>
+ <span class="n">f</span><span class="o">.</span><span class="n">write</span><span class="p">(</span><span class="s2">"*"</span><span class="p">)</span> <span class="c1"># End marker</span></div>
+
+
+
+<div class="viewcode-block" id="HydroProRunner.parse_output">
+<a class="viewcode-back" href="../../api/simulation_engines/engine.html#arbdmodel.engine.HydroProRunner.parse_output">[docs]</a>
+ <span class="k">def</span><span class="w"> </span><span class="nf">parse_output</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">output_file</span><span class="p">):</span>
+ <span class="n">mass</span><span class="o">=</span><span class="bp">self</span><span class="o">.</span><span class="n">mass</span>
+<span class="w"> </span><span class="sd">"""Parse HydroPro output file to get damping coefficients.</span>
+<span class="sd"> </span>
+<span class="sd"> Args:</span>
+<span class="sd"> output_file: Path to HydroPro output file</span>
+<span class="sd"> mass: Mass in AMU used to normalize coefficients</span>
+<span class="sd"> </span>
+<span class="sd"> Returns:</span>
+<span class="sd"> tuple of (translation_damping, rotation_damping)</span>
+<span class="sd"> """</span>
+ <span class="k">with</span> <span class="nb">open</span><span class="p">(</span><span class="n">output_file</span><span class="p">)</span> <span class="k">as</span> <span class="n">f</span><span class="p">:</span>
+ <span class="n">lines</span> <span class="o">=</span> <span class="n">f</span><span class="o">.</span><span class="n">readlines</span><span class="p">()</span>
+ <span class="n">mass</span><span class="o">=</span><span class="bp">self</span><span class="o">.</span><span class="n">mass</span>
+
+ <span class="c1"># Skip header</span>
+ <span class="n">line_num</span> <span class="o">=</span> <span class="mi">48</span>
+
+ <span class="c1"># Read translational coefficients</span>
+ <span class="n">Dx</span> <span class="o">=</span> <span class="nb">float</span><span class="p">(</span><span class="n">lines</span><span class="p">[</span><span class="n">line_num</span><span class="p">]</span><span class="o">.</span><span class="n">strip</span><span class="p">()</span><span class="o">.</span><span class="n">split</span><span class="p">()[</span><span class="mi">0</span><span class="p">])</span>
+ <span class="n">Dy</span> <span class="o">=</span> <span class="nb">float</span><span class="p">(</span><span class="n">lines</span><span class="p">[</span><span class="n">line_num</span><span class="o">+</span><span class="mi">1</span><span class="p">]</span><span class="o">.</span><span class="n">strip</span><span class="p">()</span><span class="o">.</span><span class="n">split</span><span class="p">()[</span><span class="mi">1</span><span class="p">])</span>
+ <span class="n">Dz</span> <span class="o">=</span> <span class="nb">float</span><span class="p">(</span><span class="n">lines</span><span class="p">[</span><span class="n">line_num</span><span class="o">+</span><span class="mi">2</span><span class="p">]</span><span class="o">.</span><span class="n">strip</span><span class="p">()</span><span class="o">.</span><span class="n">split</span><span class="p">()[</span><span class="mi">2</span><span class="p">])</span>
+
+ <span class="c1"># Skip two lines</span>
+ <span class="n">line_num</span> <span class="o">+=</span> <span class="mi">5</span>
+
+ <span class="c1"># Read rotational coefficients</span>
+ <span class="n">Rx</span> <span class="o">=</span> <span class="nb">float</span><span class="p">(</span><span class="n">lines</span><span class="p">[</span><span class="n">line_num</span><span class="p">]</span><span class="o">.</span><span class="n">strip</span><span class="p">()</span><span class="o">.</span><span class="n">split</span><span class="p">()[</span><span class="mi">3</span><span class="p">])</span>
+ <span class="n">Ry</span> <span class="o">=</span> <span class="nb">float</span><span class="p">(</span><span class="n">lines</span><span class="p">[</span><span class="n">line_num</span><span class="o">+</span><span class="mi">1</span><span class="p">]</span><span class="o">.</span><span class="n">strip</span><span class="p">()</span><span class="o">.</span><span class="n">split</span><span class="p">()[</span><span class="mi">4</span><span class="p">])</span>
+ <span class="n">Rz</span> <span class="o">=</span> <span class="nb">float</span><span class="p">(</span><span class="n">lines</span><span class="p">[</span><span class="n">line_num</span><span class="o">+</span><span class="mi">2</span><span class="p">]</span><span class="o">.</span><span class="n">strip</span><span class="p">()</span><span class="o">.</span><span class="n">split</span><span class="p">()[</span><span class="mi">5</span><span class="p">])</span>
+
+ <span class="c1"># Convert units</span>
+ <span class="c1"># Translation: "(295 k K) / (( cm^2/s) * amu)" "1/ns"</span>
+ <span class="n">trans_damp</span> <span class="o">=</span> <span class="p">[</span><span class="mf">24.527692</span><span class="o">/</span><span class="p">(</span><span class="n">x</span><span class="o">*</span><span class="n">mass</span><span class="p">)</span> <span class="k">for</span> <span class="n">x</span> <span class="ow">in</span> <span class="p">[</span><span class="n">Dx</span><span class="p">,</span> <span class="n">Dy</span><span class="p">,</span> <span class="n">Dz</span><span class="p">]]</span>
+
+ <span class="c1"># Rotation: "(295 k K) / ((1 /s) * amu AA^2)" "1/ns"</span>
+ <span class="n">rot_damp</span> <span class="o">=</span> <span class="p">[</span><span class="mf">2.4527692e+17</span> <span class="o">/</span> <span class="p">(</span><span class="n">x</span><span class="o">*</span><span class="n">mass</span><span class="p">)</span> <span class="k">for</span> <span class="n">x</span> <span class="ow">in</span> <span class="p">[</span><span class="n">Rx</span><span class="p">,</span> <span class="n">Ry</span><span class="p">,</span> <span class="n">Rz</span><span class="p">]]</span>
+
+ <span class="k">return</span> <span class="n">trans_damp</span><span class="p">,</span> <span class="n">rot_damp</span></div>
+
+
+<div class="viewcode-block" id="HydroProRunner.run_calculation">
+<a class="viewcode-back" href="../../api/simulation_engines/engine.html#arbdmodel.engine.HydroProRunner.run_calculation">[docs]</a>
+ <span class="k">def</span><span class="w"> </span><span class="nf">run_calculation</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span><span class="n">work_dir</span><span class="o">=</span><span class="s2">"."</span><span class="p">):</span>
+<span class="w"> </span><span class="sd">"""Run HydroPro calculation.</span>
+<span class="sd"> </span>
+<span class="sd"> Args:</span>
+<span class="sd"> structure_name: Base name of structure files</span>
+<span class="sd"> mass: Mass in AMU</span>
+<span class="sd"> work_dir: Working directory for calculation</span>
+<span class="sd"> </span>
+<span class="sd"> Returns:</span>
+<span class="sd"> Dictionary containing:</span>
+<span class="sd"> - translation_damping: [Dx, Dy, Dz]</span>
+<span class="sd"> - rotation_damping: [Rx, Ry, Rz]</span>
+<span class="sd"> """</span>
+ <span class="n">structure_name</span><span class="p">,</span> <span class="n">mass</span><span class="o">=</span><span class="bp">self</span><span class="o">.</span><span class="n">structure_name</span><span class="p">,</span> <span class="bp">self</span><span class="o">.</span><span class="n">mass</span>
+ <span class="n">original_dir</span> <span class="o">=</span> <span class="n">os</span><span class="o">.</span><span class="n">getcwd</span><span class="p">()</span>
+ <span class="k">try</span><span class="p">:</span>
+ <span class="n">os</span><span class="o">.</span><span class="n">chdir</span><span class="p">(</span><span class="n">work_dir</span><span class="p">)</span>
+
+ <span class="c1"># Write config</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">write_config</span><span class="p">()</span>
+
+ <span class="c1"># Link structure file</span>
+ <span class="n">pdb_path</span> <span class="o">=</span> <span class="n">Path</span><span class="p">(</span><span class="sa">f</span><span class="s2">"</span><span class="si">{</span><span class="n">structure_name</span><span class="si">}</span><span class="s2">.pdb"</span><span class="p">)</span>
+ <span class="k">if</span> <span class="ow">not</span> <span class="n">pdb_path</span><span class="o">.</span><span class="n">exists</span><span class="p">():</span>
+ <span class="k">raise</span> <span class="ne">FileNotFoundError</span><span class="p">(</span><span class="sa">f</span><span class="s2">"Structure file not found: </span><span class="si">{</span><span class="n">pdb_path</span><span class="si">}</span><span class="s2">"</span><span class="p">)</span>
+ <span class="n">os</span><span class="o">.</span><span class="n">symlink</span><span class="p">(</span><span class="n">pdb_path</span><span class="p">,</span> <span class="s2">"hydro.pdb"</span><span class="p">)</span>
+
+ <span class="c1"># Run HydroPro</span>
+ <span class="n">result</span> <span class="o">=</span> <span class="n">subprocess</span><span class="o">.</span><span class="n">run</span><span class="p">([</span><span class="nb">str</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">binary</span><span class="p">)],</span>
+ <span class="n">capture_output</span><span class="o">=</span><span class="kc">True</span><span class="p">,</span>
+ <span class="n">text</span><span class="o">=</span><span class="kc">True</span><span class="p">,</span>
+ <span class="n">check</span><span class="o">=</span><span class="kc">True</span><span class="p">)</span>
+
+ <span class="c1"># Parse results</span>
+ <span class="n">trans_damp</span><span class="p">,</span> <span class="n">rot_damp</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">parse_output</span><span class="p">(</span><span class="sa">f</span><span class="s2">"</span><span class="si">{</span><span class="n">structure_name</span><span class="si">}</span><span class="s2">.hydro-res.txt"</span><span class="p">)</span>
+
+ <span class="k">return</span> <span class="p">{</span>
+ <span class="s2">"translation_damping"</span><span class="p">:</span> <span class="n">trans_damp</span><span class="p">,</span>
+ <span class="s2">"rotation_damping"</span><span class="p">:</span> <span class="n">rot_damp</span>
+ <span class="p">}</span>
+
+ <span class="k">finally</span><span class="p">:</span>
+ <span class="k">if</span> <span class="n">os</span><span class="o">.</span><span class="n">path</span><span class="o">.</span><span class="n">exists</span><span class="p">(</span><span class="s2">"hydro.pdb"</span><span class="p">):</span>
+ <span class="n">os</span><span class="o">.</span><span class="n">unlink</span><span class="p">(</span><span class="s2">"hydro.pdb"</span><span class="p">)</span>
+ <span class="n">os</span><span class="o">.</span><span class="n">chdir</span><span class="p">(</span><span class="n">original_dir</span><span class="p">)</span></div>
+</div>
+
+
+<div class="viewcode-block" id="APBSRunner">
+<a class="viewcode-back" href="../../api/simulation_engines/engine.html#arbdmodel.engine.APBSRunner">[docs]</a>
+<span class="k">class</span><span class="w"> </span><span class="nc">APBSRunner</span><span class="p">:</span>
+<span class="w"> </span><span class="sd">"""Interface to APBS for electrostatics calculations"""</span>
+
+ <span class="k">def</span><span class="w"> </span><span class="fm">__init__</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span><span class="n">simconf</span><span class="o">=</span><span class="kc">None</span><span class="p">,</span> <span class="n">binary_path</span><span class="o">=</span><span class="kc">None</span><span class="p">,</span> <span class="n">psize_script</span><span class="o">=</span><span class="kc">None</span><span class="p">):</span>
+<span class="w"> </span><span class="sd">"""Initialize APBS interface.</span>
+<span class="sd"> Args:</span>
+<span class="sd"> binary_path: Path to APBS executable. If None, uses path from simconf</span>
+<span class="sd"> psize_script: Optional path to psize script</span>
+<span class="sd"> simconf: SimConf object (optional)</span>
+<span class="sd"> """</span>
+ <span class="c1"># Get binary path from simconf if provided and no explicit binary_path</span>
+ <span class="k">if</span> <span class="n">binary_path</span> <span class="ow">is</span> <span class="kc">None</span> <span class="ow">and</span> <span class="n">simconf</span> <span class="ow">is</span> <span class="ow">not</span> <span class="kc">None</span><span class="p">:</span>
+ <span class="n">binary_path</span> <span class="o">=</span> <span class="n">simconf</span><span class="o">.</span><span class="n">get_binary</span><span class="p">(</span><span class="s1">'apbs'</span><span class="p">)</span>
+
+ <span class="c1"># If still None, try binary_manager</span>
+ <span class="k">if</span> <span class="n">binary_path</span> <span class="ow">is</span> <span class="kc">None</span><span class="p">:</span>
+ <span class="kn">from</span><span class="w"> </span><span class="nn">.sim_config</span><span class="w"> </span><span class="kn">import</span> <span class="n">binary_manager</span>
+ <span class="n">binary_path</span> <span class="o">=</span> <span class="n">binary_manager</span><span class="o">.</span><span class="n">get_binary_path</span><span class="p">(</span><span class="s1">'apbs'</span><span class="p">)</span>
+
+ <span class="c1"># If still None, use 'apbs' and rely on PATH</span>
+ <span class="k">if</span> <span class="n">binary_path</span> <span class="ow">is</span> <span class="kc">None</span><span class="p">:</span>
+ <span class="n">binary_path</span> <span class="o">=</span> <span class="s1">'apbs'</span>
+
+ <span class="bp">self</span><span class="o">.</span><span class="n">binary</span> <span class="o">=</span> <span class="n">Path</span><span class="p">(</span><span class="n">binary_path</span><span class="p">)</span>
+ <span class="c1"># Check if binary exists or is in PATH</span>
+ <span class="k">if</span> <span class="ow">not</span> <span class="bp">self</span><span class="o">.</span><span class="n">binary</span><span class="o">.</span><span class="n">exists</span><span class="p">()</span> <span class="ow">and</span> <span class="ow">not</span> <span class="n">shutil</span><span class="o">.</span><span class="n">which</span><span class="p">(</span><span class="nb">str</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">binary</span><span class="p">)):</span>
+ <span class="k">raise</span> <span class="ne">FileNotFoundError</span><span class="p">(</span><span class="sa">f</span><span class="s2">"APBS binary not found at </span><span class="si">{</span><span class="n">binary_path</span><span class="si">}</span><span class="s2">"</span><span class="p">)</span>
+
+ <span class="bp">self</span><span class="o">.</span><span class="n">psize</span> <span class="o">=</span> <span class="n">Path</span><span class="p">(</span><span class="n">psize_script</span><span class="p">)</span> <span class="k">if</span> <span class="n">psize_script</span> <span class="k">else</span> <span class="kc">None</span>
+
+<div class="viewcode-block" id="APBSRunner.write_config">
+<a class="viewcode-back" href="../../api/simulation_engines/engine.html#arbdmodel.engine.APBSRunner.write_config">[docs]</a>
+ <span class="k">def</span><span class="w"> </span><span class="nf">write_config</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">structure_name</span><span class="p">,</span> <span class="n">xyz_dims</span><span class="p">,</span> <span class="n">salt_conc</span><span class="o">=</span><span class="mf">0.15</span><span class="p">,</span>
+ <span class="n">temperature</span><span class="o">=</span><span class="mi">300</span><span class="p">,</span> <span class="n">buffer</span><span class="o">=</span><span class="mi">50</span><span class="p">,</span> <span class="n">large_system</span><span class="o">=</span><span class="s1">'Off'</span><span class="p">):</span>
+<span class="w"> </span><span class="sd">"""Write APBS configuration file.</span>
+<span class="sd"> </span>
+<span class="sd"> Args:</span>
+<span class="sd"> structure_name: Base name of structure files</span>
+<span class="sd"> xyz_dims: [x, y, z] dimensions</span>
+<span class="sd"> salt_conc: Salt concentration in M</span>
+<span class="sd"> temperature: Temperature in K</span>
+<span class="sd"> buffer: Grid buffer size in Ã…</span>
+<span class="sd"> large_system: 'On' or 'Off' for large system mode</span>
+<span class="sd"> """</span>
+ <span class="c1"># Calculate grid dimensions</span>
+ <span class="n">xyz_cg</span> <span class="o">=</span> <span class="p">[</span><span class="nb">str</span><span class="p">(</span><span class="nb">int</span><span class="p">(</span><span class="n">dim</span> <span class="o">+</span> <span class="n">buffer</span><span class="p">))</span> <span class="k">for</span> <span class="n">dim</span> <span class="ow">in</span> <span class="n">xyz_dims</span><span class="p">]</span>
+
+ <span class="k">if</span> <span class="n">large_system</span> <span class="o">==</span> <span class="s1">'Off'</span><span class="p">:</span>
+ <span class="n">xyz_dime</span> <span class="o">=</span> <span class="n">xyz_cg</span>
+ <span class="n">center</span> <span class="o">=</span> <span class="s1">'mol 1'</span>
+ <span class="k">else</span><span class="p">:</span>
+ <span class="c1"># For large systems, reduce grid density</span>
+ <span class="n">dividend</span> <span class="o">=</span> <span class="mi">2</span>
+ <span class="n">xyz_dime</span> <span class="o">=</span> <span class="p">[</span><span class="nb">str</span><span class="p">(</span><span class="nb">int</span><span class="p">((</span><span class="n">dim</span> <span class="o">+</span> <span class="n">buffer</span><span class="p">)</span> <span class="o">/</span> <span class="n">dividend</span><span class="p">))</span> <span class="k">for</span> <span class="n">dim</span> <span class="ow">in</span> <span class="n">xyz_dims</span><span class="p">]</span>
+ <span class="n">center</span> <span class="o">=</span> <span class="s1">'mol 1'</span>
+
+ <span class="n">config</span> <span class="o">=</span> <span class="sa">f</span><span class="s2">"""read</span>
+<span class="s2">mol pqr </span><span class="si">{</span><span class="n">structure_name</span><span class="si">}</span><span class="s2">.pqr</span>
+<span class="s2">end</span>
+<span class="s2">elec</span>
+<span class="s2">mg-auto</span>
+<span class="s2">dime </span><span class="si">{</span><span class="s1">' '</span><span class="o">.</span><span class="n">join</span><span class="p">(</span><span class="n">xyz_dime</span><span class="p">)</span><span class="si">}</span>
+<span class="s2">cglen </span><span class="si">{</span><span class="s1">' '</span><span class="o">.</span><span class="n">join</span><span class="p">(</span><span class="n">xyz_cg</span><span class="p">)</span><span class="si">}</span>
+<span class="s2">cgcent </span><span class="si">{</span><span class="n">center</span><span class="si">}</span>
+<span class="s2">fglen </span><span class="si">{</span><span class="s1">' '</span><span class="o">.</span><span class="n">join</span><span class="p">(</span><span class="n">xyz_cg</span><span class="p">)</span><span class="si">}</span>
+<span class="s2">fgcent </span><span class="si">{</span><span class="n">center</span><span class="si">}</span>
+<span class="s2">mol 1</span>
+<span class="s2">npbe</span>
+<span class="s2">bcfl sdh</span>
+<span class="s2">srfm smol</span>
+<span class="s2">chgm spl2</span>
+<span class="s2">ion 1 </span><span class="si">{</span><span class="n">salt_conc</span><span class="si">}</span><span class="s2"> 2.0</span>
+<span class="s2">ion -1 </span><span class="si">{</span><span class="n">salt_conc</span><span class="si">}</span><span class="s2"> 2.0</span>
+<span class="s2">pdie 12.0</span>
+<span class="s2">sdie 78.54</span>
+<span class="s2">sdens 10.0</span>
+<span class="s2">srad 1.4</span>
+<span class="s2">swin 0.3</span>
+<span class="s2">temp </span><span class="si">{</span><span class="n">temperature</span><span class="si">}</span>
+<span class="s2">gamma 0.105</span>
+<span class="s2">calcenergy no</span>
+<span class="s2">calcforce no</span>
+<span class="s2">write pot dx </span><span class="si">{</span><span class="n">structure_name</span><span class="si">}</span><span class="s2">.elec.tmp</span>
+<span class="s2">end</span>
+<span class="s2">quit"""</span>
+
+ <span class="k">with</span> <span class="nb">open</span><span class="p">(</span><span class="sa">f</span><span class="s2">"</span><span class="si">{</span><span class="n">structure_name</span><span class="si">}</span><span class="s2">.apbs"</span><span class="p">,</span> <span class="s1">'w'</span><span class="p">)</span> <span class="k">as</span> <span class="n">f</span><span class="p">:</span>
+ <span class="n">f</span><span class="o">.</span><span class="n">write</span><span class="p">(</span><span class="n">config</span><span class="p">)</span></div>
+
+
+<div class="viewcode-block" id="APBSRunner.run_calculation">
+<a class="viewcode-back" href="../../api/simulation_engines/engine.html#arbdmodel.engine.APBSRunner.run_calculation">[docs]</a>
+ <span class="k">def</span><span class="w"> </span><span class="nf">run_calculation</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">structure_name</span><span class="p">,</span> <span class="n">xyz_dims</span><span class="p">,</span> <span class="n">work_dir</span><span class="o">=</span><span class="s2">"."</span><span class="p">,</span>
+ <span class="n">salt_conc</span><span class="o">=</span><span class="mf">0.15</span><span class="p">,</span> <span class="n">temperature</span><span class="o">=</span><span class="mi">300</span><span class="p">):</span>
+<span class="w"> </span><span class="sd">"""Run APBS calculation.</span>
+<span class="sd"> </span>
+<span class="sd"> Args:</span>
+<span class="sd"> structure_name: Base name of structure files</span>
+<span class="sd"> xyz_dims: [x, y, z] dimensions</span>
+<span class="sd"> work_dir: Working directory</span>
+<span class="sd"> salt_conc: Salt concentration in M</span>
+<span class="sd"> temperature: Temperature in K</span>
+<span class="sd"> </span>
+<span class="sd"> Returns:</span>
+<span class="sd"> Path to output potential file</span>
+<span class="sd"> """</span>
+ <span class="n">original_dir</span> <span class="o">=</span> <span class="n">os</span><span class="o">.</span><span class="n">getcwd</span><span class="p">()</span>
+ <span class="k">try</span><span class="p">:</span>
+ <span class="n">os</span><span class="o">.</span><span class="n">chdir</span><span class="p">(</span><span class="n">work_dir</span><span class="p">)</span>
+
+ <span class="c1"># Write config</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">write_config</span><span class="p">(</span><span class="n">structure_name</span><span class="p">,</span> <span class="n">xyz_dims</span><span class="p">,</span> <span class="n">salt_conc</span><span class="p">,</span> <span class="n">temperature</span><span class="p">)</span>
+
+ <span class="c1"># Run APBS</span>
+ <span class="n">result</span> <span class="o">=</span> <span class="n">subprocess</span><span class="o">.</span><span class="n">run</span><span class="p">([</span><span class="nb">str</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">binary</span><span class="p">),</span> <span class="sa">f</span><span class="s2">"</span><span class="si">{</span><span class="n">structure_name</span><span class="si">}</span><span class="s2">.apbs"</span><span class="p">],</span>
+ <span class="n">capture_output</span><span class="o">=</span><span class="kc">True</span><span class="p">,</span>
+ <span class="n">text</span><span class="o">=</span><span class="kc">True</span><span class="p">,</span>
+ <span class="n">check</span><span class="o">=</span><span class="kc">True</span><span class="p">)</span>
+
+ <span class="n">output_file</span> <span class="o">=</span> <span class="n">Path</span><span class="p">(</span><span class="sa">f</span><span class="s2">"</span><span class="si">{</span><span class="n">structure_name</span><span class="si">}</span><span class="s2">.elec.tmp"</span><span class="p">)</span>
+ <span class="k">if</span> <span class="ow">not</span> <span class="n">output_file</span><span class="o">.</span><span class="n">exists</span><span class="p">():</span>
+ <span class="k">raise</span> <span class="ne">RuntimeError</span><span class="p">(</span><span class="s2">"APBS failed to generate output file"</span><span class="p">)</span>
+
+ <span class="k">return</span> <span class="n">output_file</span>
+
+ <span class="k">finally</span><span class="p">:</span>
+ <span class="n">os</span><span class="o">.</span><span class="n">chdir</span><span class="p">(</span><span class="n">original_dir</span><span class="p">)</span></div>
+</div>
+
+</pre></div>
+
+ </article>
+
+
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+
+
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+ <footer class="prev-next-footer d-print-none">
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+
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+
+ <h1>Source code for arbdmodel.logger</h1><div class="highlight"><pre>
+<span></span>
+<span class="c1">## Set up loggers</span>
+<span class="kn">import</span><span class="w"> </span><span class="nn">logging</span>
+<span class="kn">from</span><span class="w"> </span><span class="nn">pathlib</span><span class="w"> </span><span class="kn">import</span> <span class="n">Path</span>
+
+<span class="k">def</span><span class="w"> </span><span class="nf">_get_username</span><span class="p">():</span>
+ <span class="kn">import</span><span class="w"> </span><span class="nn">sys</span>
+ <span class="k">try</span><span class="p">:</span>
+ <span class="k">return</span> <span class="n">sys</span><span class="o">.</span><span class="n">environ</span><span class="p">[</span><span class="s1">'USER'</span><span class="p">]</span>
+ <span class="k">except</span><span class="p">:</span>
+ <span class="k">return</span> <span class="kc">None</span>
+
+<span class="n">logging</span><span class="o">.</span><span class="n">basicConfig</span><span class="p">(</span><span class="nb">format</span><span class="o">=</span><span class="s1">'</span><span class="si">%(name)s</span><span class="s1">: </span><span class="si">%(levelname)s</span><span class="s1">: </span><span class="si">%(message)s</span><span class="s1">'</span><span class="p">)</span>
+<span class="n">logger</span> <span class="o">=</span> <span class="n">logging</span><span class="o">.</span><span class="n">getLogger</span><span class="p">(</span><span class="vm">__name__</span><span class="p">)</span>
+<span class="n">logger</span><span class="o">.</span><span class="n">setLevel</span><span class="p">(</span><span class="n">logging</span><span class="o">.</span><span class="n">INFO</span><span class="p">)</span>
+<span class="n">_ch</span> <span class="o">=</span> <span class="n">logging</span><span class="o">.</span><span class="n">StreamHandler</span><span class="p">()</span>
+<span class="n">_ch</span><span class="o">.</span><span class="n">setFormatter</span><span class="p">(</span><span class="n">logging</span><span class="o">.</span><span class="n">Formatter</span><span class="p">(</span><span class="s1">'</span><span class="si">%(name)s</span><span class="s1">: </span><span class="si">%(levelname)s</span><span class="s1">: </span><span class="si">%(message)s</span><span class="s1">'</span><span class="p">))</span>
+<span class="n">logger</span><span class="o">.</span><span class="n">addHandler</span><span class="p">(</span><span class="n">_ch</span><span class="p">)</span>
+<span class="n">logger</span><span class="o">.</span><span class="n">propagate</span> <span class="o">=</span> <span class="kc">False</span>
+
+<span class="n">devlogger</span> <span class="o">=</span> <span class="n">logging</span><span class="o">.</span><span class="n">getLogger</span><span class="p">(</span><span class="vm">__name__</span><span class="o">+</span><span class="s1">'.dev'</span><span class="p">)</span>
+<span class="c1"># devlogger.setLevel(logging.DEBUG)</span>
+<span class="k">if</span> <span class="n">_get_username</span><span class="p">()</span> <span class="ow">not</span> <span class="ow">in</span> <span class="p">(</span><span class="s1">'cmaffeo2'</span><span class="p">,):</span>
+ <span class="n">devlogger</span><span class="o">.</span><span class="n">addHandler</span><span class="p">(</span><span class="n">logging</span><span class="o">.</span><span class="n">NullHandler</span><span class="p">())</span>
+
+<span class="n">_RESOURCE_DIR</span> <span class="o">=</span> <span class="n">Path</span><span class="p">(</span><span class="vm">__file__</span><span class="p">)</span><span class="o">.</span><span class="n">parent</span> <span class="o">/</span> <span class="s1">'resources'</span>
+<div class="viewcode-block" id="get_resource_path">
+<a class="viewcode-back" href="../../api/utilities/logger.html#arbdmodel.logger.get_resource_path">[docs]</a>
+<span class="k">def</span><span class="w"> </span><span class="nf">get_resource_path</span><span class="p">(</span><span class="n">relative_path</span><span class="p">):</span>
+ <span class="k">return</span> <span class="n">_RESOURCE_DIR</span> <span class="o">/</span> <span class="n">relative_path</span></div>
+
+</pre></div>
+
+ </article>
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diff --git a/_build/html/_modules/arbdmodel/mesh_process_surface.html b/_build/html/_modules/arbdmodel/mesh_process_surface.html
new file mode 100644
index 0000000000000000000000000000000000000000..82b7cfa934cc0049d9a7fa4f71d272dd8c0b5eed
--- /dev/null
+++ b/_build/html/_modules/arbdmodel/mesh_process_surface.html
@@ -0,0 +1,923 @@
+
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+ <h1>Source code for arbdmodel.mesh_process_surface</h1><div class="highlight"><pre>
+<span></span><span class="kn">import</span><span class="w"> </span><span class="nn">numpy</span><span class="w"> </span><span class="k">as</span><span class="w"> </span><span class="nn">np</span>
+<span class="kn">import</span><span class="w"> </span><span class="nn">gmsh</span>
+<span class="kn">from</span><span class="w"> </span><span class="nn">scipy.spatial</span><span class="w"> </span><span class="kn">import</span> <span class="n">KDTree</span>
+<span class="kn">from</span><span class="w"> </span><span class="nn">pathlib</span><span class="w"> </span><span class="kn">import</span> <span class="n">Path</span>
+<span class="kn">import</span><span class="w"> </span><span class="nn">os</span>
+<span class="kn">from</span><span class="w"> </span><span class="nn">.grid</span><span class="w"> </span><span class="kn">import</span> <span class="n">writeDx</span>
+<span class="kn">from</span><span class="w"> </span><span class="nn">.engine</span><span class="w"> </span><span class="kn">import</span> <span class="n">HydroProRunner</span>
+<span class="kn">from</span><span class="w"> </span><span class="nn">.logger</span><span class="w"> </span><span class="kn">import</span> <span class="n">logger</span>
+
+<span class="sd">"""</span>
+<span class="sd">Specialized surface mesh processor that handles triangle surface meshes </span>
+<span class="sd">"""</span>
+ <span class="c1"># Conversion factors</span>
+<div class="viewcode-block" id="SurfaceMeshProcessor">
+<a class="viewcode-back" href="../../api/rigidbody_models/mesh_process_surface.html#arbdmodel.mesh_process_surface.SurfaceMeshProcessor">[docs]</a>
+<span class="k">class</span><span class="w"> </span><span class="nc">SurfaceMeshProcessor</span><span class="p">:</span>
+<span class="w"> </span><span class="sd">"""Process surface meshes to calculate inertia, hydrodynamics and generate potential fields"""</span>
+
+ <span class="c1"># Conversion factors</span>
+ <span class="n">MICRON_TO_ANGSTROM</span> <span class="o">=</span> <span class="mi">10000</span>
+
+ <span class="k">def</span><span class="w"> </span><span class="fm">__init__</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">mesh_file</span><span class="p">,</span> <span class="n">density</span><span class="o">=</span><span class="mf">19.3</span><span class="p">,</span> <span class="n">simconf</span><span class="o">=</span><span class="kc">None</span><span class="p">,</span>
+ <span class="n">unit_scale</span><span class="o">=</span><span class="n">MICRON_TO_ANGSTROM</span><span class="p">,</span> <span class="n">work_dir</span><span class="o">=</span><span class="kc">None</span><span class="p">):</span>
+<span class="w"> </span>
+<span class="w"> </span><span class="sd">"""</span>
+<span class="sd"> Initialize processor with surface mesh file</span>
+<span class="sd"> Args:</span>
+<span class="sd"> mesh_file: Path to .msh file with surface triangles</span>
+<span class="sd"> density: Material density in g/cm^3</span>
+<span class="sd"> simconf: SimConf object containing configuration parameters</span>
+<span class="sd"> unit_scale: Conversion factor from input units to angstroms</span>
+<span class="sd"> work_dir: Directory to store output files (default: current directory)</span>
+<span class="sd"> """</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">mesh_file</span> <span class="o">=</span> <span class="n">Path</span><span class="p">(</span><span class="n">mesh_file</span><span class="p">)</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">density</span> <span class="o">=</span> <span class="n">density</span><span class="o">*</span><span class="mf">0.6022</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">unit_scale</span> <span class="o">=</span> <span class="n">unit_scale</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">name</span> <span class="o">=</span> <span class="nb">str</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">mesh_file</span><span class="o">.</span><span class="n">stem</span><span class="p">)</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">work_dir</span> <span class="o">=</span> <span class="n">Path</span><span class="p">(</span><span class="n">work_dir</span><span class="p">)</span> <span class="k">if</span> <span class="n">work_dir</span> <span class="k">else</span> <span class="n">Path</span><span class="o">.</span><span class="n">cwd</span><span class="p">()</span>
+ <span class="n">os</span><span class="o">.</span><span class="n">makedirs</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">work_dir</span><span class="p">,</span> <span class="n">exist_ok</span><span class="o">=</span><span class="kc">True</span><span class="p">)</span>
+
+ <span class="k">if</span> <span class="n">simconf</span> <span class="ow">is</span> <span class="kc">None</span><span class="p">:</span>
+ <span class="kn">from</span><span class="w"> </span><span class="nn">.</span><span class="w"> </span><span class="kn">import</span> <span class="n">DefaultSimConf</span>
+ <span class="n">simconf</span> <span class="o">=</span> <span class="n">DefaultSimConf</span><span class="p">()</span>
+
+ <span class="c1"># Extract parameters from simconf</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">temperature</span> <span class="o">=</span> <span class="n">simconf</span><span class="o">.</span><span class="n">temperature</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">viscosity</span> <span class="o">=</span> <span class="n">simconf</span><span class="o">.</span><span class="n">viscosity</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">solvent_density</span> <span class="o">=</span> <span class="n">simconf</span><span class="o">.</span><span class="n">solvent_density</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">binary_path</span> <span class="o">=</span> <span class="n">simconf</span><span class="o">.</span><span class="n">get_binary</span><span class="p">(</span><span class="s1">'hydropro'</span><span class="p">)</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">attached_patricles</span><span class="o">=</span><span class="p">[]</span>
+ <span class="c1"># Initialize gmsh and read mesh</span>
+ <span class="n">gmsh</span><span class="o">.</span><span class="n">initialize</span><span class="p">()</span>
+ <span class="k">try</span><span class="p">:</span>
+ <span class="n">gmsh</span><span class="o">.</span><span class="n">open</span><span class="p">(</span><span class="nb">str</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">mesh_file</span><span class="p">))</span>
+ <span class="n">logger</span><span class="o">.</span><span class="n">info</span><span class="p">(</span><span class="sa">f</span><span class="s2">"Successfully opened mesh file: </span><span class="si">{</span><span class="bp">self</span><span class="o">.</span><span class="n">mesh_file</span><span class="si">}</span><span class="s2">"</span><span class="p">)</span>
+
+ <span class="bp">self</span><span class="o">.</span><span class="n">nodes</span><span class="p">,</span> <span class="bp">self</span><span class="o">.</span><span class="n">elements</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">_load_surface_mesh</span><span class="p">()</span>
+ <span class="n">logger</span><span class="o">.</span><span class="n">info</span><span class="p">(</span><span class="sa">f</span><span class="s2">"Loaded </span><span class="si">{</span><span class="nb">len</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">nodes</span><span class="p">)</span><span class="si">}</span><span class="s2"> nodes and </span><span class="si">{</span><span class="nb">len</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">elements</span><span class="p">)</span><span class="si">}</span><span class="s2"> elements from surface mesh"</span><span class="p">)</span>
+
+ <span class="c1"># Calculate basic properties before alignment</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">volume</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">_calculate_volume</span><span class="p">()</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">mass</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">volume</span> <span class="o">*</span> <span class="bp">self</span><span class="o">.</span><span class="n">density</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">density_correction</span> <span class="o">=</span> <span class="mf">1.0</span>
+
+ <span class="n">logger</span><span class="o">.</span><span class="n">info</span><span class="p">(</span><span class="sa">f</span><span class="s2">"Calculated volume: </span><span class="si">{</span><span class="bp">self</span><span class="o">.</span><span class="n">volume</span><span class="si">:</span><span class="s2">.2f</span><span class="si">}</span><span class="s2"> ų"</span><span class="p">)</span>
+ <span class="n">logger</span><span class="o">.</span><span class="n">info</span><span class="p">(</span><span class="sa">f</span><span class="s2">"Calculated mass: </span><span class="si">{</span><span class="bp">self</span><span class="o">.</span><span class="n">mass</span><span class="si">:</span><span class="s2">.2f</span><span class="si">}</span><span class="s2"> amu"</span><span class="p">)</span>
+
+ <span class="c1"># Align mesh to center of mass and principal axes</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">_align_mesh</span><span class="p">()</span>
+
+ <span class="c1"># Calculate final properties after alignment</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">inertia_tensor</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">_calculate_inertia_tensor</span><span class="p">()</span>
+
+ <span class="bp">self</span><span class="o">.</span><span class="n">principal_moments</span> <span class="o">=</span> <span class="n">np</span><span class="o">.</span><span class="n">diag</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">inertia_tensor</span><span class="p">)</span>
+ <span class="n">logger</span><span class="o">.</span><span class="n">info</span><span class="p">(</span><span class="sa">f</span><span class="s2">"Principal moments of inertia: </span><span class="si">{</span><span class="bp">self</span><span class="o">.</span><span class="n">principal_moments</span><span class="si">}</span><span class="s2">"</span><span class="p">)</span>
+
+ <span class="k">except</span> <span class="ne">Exception</span> <span class="k">as</span> <span class="n">e</span><span class="p">:</span>
+ <span class="n">logger</span><span class="o">.</span><span class="n">error</span><span class="p">(</span><span class="sa">f</span><span class="s2">"Error processing mesh: </span><span class="si">{</span><span class="n">e</span><span class="si">}</span><span class="s2">"</span><span class="p">)</span>
+ <span class="k">finally</span><span class="p">:</span>
+ <span class="n">gmsh</span><span class="o">.</span><span class="n">finalize</span><span class="p">()</span>
+
+<div class="viewcode-block" id="SurfaceMeshProcessor.get_attached_particles">
+<a class="viewcode-back" href="../../api/rigidbody_models/mesh_process_surface.html#arbdmodel.mesh_process_surface.SurfaceMeshProcessor.get_attached_particles">[docs]</a>
+ <span class="k">def</span><span class="w"> </span><span class="nf">get_attached_particles</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span>
+ <span class="kn">from</span><span class="w"> </span><span class="nn">.</span><span class="w"> </span><span class="kn">import</span> <span class="n">ParticleType</span><span class="p">,</span> <span class="n">PointParticle</span>
+ <span class="n">rbp</span><span class="o">=</span><span class="n">ParticleType</span><span class="p">(</span><span class="n">name</span><span class="o">=</span><span class="sa">f</span><span class="s2">"</span><span class="si">{</span><span class="bp">self</span><span class="o">.</span><span class="n">name</span><span class="si">}</span><span class="s2">_attached"</span><span class="p">,</span> <span class="n">mass</span><span class="o">=</span><span class="mi">1</span><span class="p">,</span><span class="n">diffusivity</span><span class="o">=</span><span class="mi">1</span><span class="p">)</span>
+ <span class="n">logger</span><span class="o">.</span><span class="n">info</span><span class="p">(</span><span class="sa">f</span><span class="s2">"attaching particles type </span><span class="si">{</span><span class="bp">self</span><span class="o">.</span><span class="n">name</span><span class="si">}</span><span class="s2">_attached using mesh nodes"</span><span class="p">)</span>
+
+ <span class="k">for</span> <span class="n">i</span><span class="p">,</span> <span class="n">node</span> <span class="ow">in</span> <span class="nb">enumerate</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">nodes</span><span class="p">):</span>
+ <span class="n">x</span><span class="p">,</span> <span class="n">y</span><span class="p">,</span> <span class="n">z</span> <span class="o">=</span> <span class="n">node</span>
+ <span class="n">rbpi</span><span class="o">=</span><span class="n">arbdmodel</span><span class="o">.</span><span class="n">PointParticle</span><span class="p">(</span><span class="n">rbp</span><span class="p">,</span><span class="n">name</span><span class="o">=</span><span class="sa">f</span><span class="s2">"</span><span class="si">{</span><span class="bp">self</span><span class="o">.</span><span class="n">name</span><span class="si">}</span><span class="s2">_</span><span class="si">{</span><span class="n">i</span><span class="si">}</span><span class="s2">"</span><span class="p">,</span><span class="n">position</span><span class="o">=</span><span class="p">[</span><span class="n">x</span><span class="p">,</span><span class="n">y</span><span class="p">,</span><span class="n">z</span><span class="p">])</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">attached_patricles</span><span class="o">.</span><span class="n">append</span><span class="p">(</span><span class="n">rbpi</span><span class="p">)</span></div>
+
+
+ <span class="k">def</span><span class="w"> </span><span class="nf">_load_surface_mesh</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span>
+<span class="w"> </span><span class="sd">"""Load triangular surface mesh directly"""</span>
+ <span class="c1"># Get all 2D entities (surfaces)</span>
+ <span class="n">surface_entities</span> <span class="o">=</span> <span class="n">gmsh</span><span class="o">.</span><span class="n">model</span><span class="o">.</span><span class="n">getEntities</span><span class="p">(</span><span class="mi">2</span><span class="p">)</span>
+ <span class="k">if</span> <span class="ow">not</span> <span class="n">surface_entities</span><span class="p">:</span>
+ <span class="n">logger</span><span class="o">.</span><span class="n">error</span><span class="p">(</span><span class="s2">"No surface entities found in mesh"</span><span class="p">)</span>
+
+ <span class="c1"># Collect all triangular elements</span>
+ <span class="n">all_nodes</span> <span class="o">=</span> <span class="nb">set</span><span class="p">()</span>
+ <span class="n">all_elements</span> <span class="o">=</span> <span class="p">[]</span>
+
+ <span class="k">for</span> <span class="n">dim</span><span class="p">,</span> <span class="n">tag</span> <span class="ow">in</span> <span class="n">surface_entities</span><span class="p">:</span>
+ <span class="n">element_types</span><span class="p">,</span> <span class="n">element_tags</span><span class="p">,</span> <span class="n">node_tags</span> <span class="o">=</span> <span class="n">gmsh</span><span class="o">.</span><span class="n">model</span><span class="o">.</span><span class="n">mesh</span><span class="o">.</span><span class="n">getElements</span><span class="p">(</span><span class="n">dim</span><span class="p">,</span> <span class="n">tag</span><span class="p">)</span>
+
+ <span class="c1"># Find triangular elements (type 2 in gmsh)</span>
+ <span class="n">tri_idx</span> <span class="o">=</span> <span class="kc">None</span>
+ <span class="k">for</span> <span class="n">i</span><span class="p">,</span> <span class="n">type_num</span> <span class="ow">in</span> <span class="nb">enumerate</span><span class="p">(</span><span class="n">element_types</span><span class="p">):</span>
+ <span class="k">if</span> <span class="n">type_num</span> <span class="o">==</span> <span class="mi">2</span><span class="p">:</span> <span class="c1"># Triangle elements</span>
+ <span class="n">tri_idx</span> <span class="o">=</span> <span class="n">i</span>
+ <span class="k">break</span>
+
+ <span class="k">if</span> <span class="n">tri_idx</span> <span class="ow">is</span> <span class="ow">not</span> <span class="kc">None</span><span class="p">:</span>
+ <span class="n">element_node_tags</span> <span class="o">=</span> <span class="n">np</span><span class="o">.</span><span class="n">array</span><span class="p">(</span><span class="n">node_tags</span><span class="p">[</span><span class="n">tri_idx</span><span class="p">])</span><span class="o">.</span><span class="n">reshape</span><span class="p">(</span><span class="o">-</span><span class="mi">1</span><span class="p">,</span> <span class="mi">3</span><span class="p">)</span> <span class="o">-</span> <span class="mi">1</span> <span class="c1"># Convert to 0-based</span>
+ <span class="n">all_elements</span><span class="o">.</span><span class="n">extend</span><span class="p">(</span><span class="n">element_node_tags</span><span class="p">)</span>
+ <span class="n">all_nodes</span><span class="o">.</span><span class="n">update</span><span class="p">(</span><span class="n">element_node_tags</span><span class="o">.</span><span class="n">flatten</span><span class="p">())</span>
+
+ <span class="k">if</span> <span class="ow">not</span> <span class="n">all_elements</span><span class="p">:</span>
+ <span class="n">logger</span><span class="o">.</span><span class="n">error</span><span class="p">(</span><span class="s2">"No triangular elements found in mesh"</span><span class="p">)</span>
+
+ <span class="c1"># Get coordinates of all nodes</span>
+ <span class="n">node_coords</span> <span class="o">=</span> <span class="p">{}</span>
+ <span class="k">for</span> <span class="n">node_idx</span> <span class="ow">in</span> <span class="n">all_nodes</span><span class="p">:</span>
+ <span class="n">coords</span> <span class="o">=</span> <span class="n">gmsh</span><span class="o">.</span><span class="n">model</span><span class="o">.</span><span class="n">mesh</span><span class="o">.</span><span class="n">getNode</span><span class="p">(</span><span class="nb">int</span><span class="p">(</span><span class="n">node_idx</span> <span class="o">+</span> <span class="mi">1</span><span class="p">))[</span><span class="mi">0</span><span class="p">]</span> <span class="c1"># +1 because gmsh uses 1-based indexing</span>
+ <span class="n">node_coords</span><span class="p">[</span><span class="n">node_idx</span><span class="p">]</span> <span class="o">=</span> <span class="n">coords</span>
+
+ <span class="c1"># Create node array in sorted order</span>
+ <span class="n">sorted_node_indices</span> <span class="o">=</span> <span class="nb">sorted</span><span class="p">(</span><span class="n">all_nodes</span><span class="p">)</span>
+ <span class="n">nodes</span> <span class="o">=</span> <span class="n">np</span><span class="o">.</span><span class="n">array</span><span class="p">([</span><span class="n">node_coords</span><span class="p">[</span><span class="n">idx</span><span class="p">]</span> <span class="k">for</span> <span class="n">idx</span> <span class="ow">in</span> <span class="n">sorted_node_indices</span><span class="p">])</span> <span class="o">*</span> <span class="bp">self</span><span class="o">.</span><span class="n">unit_scale</span> <span class="c1"># Apply unit conversion</span>
+
+ <span class="c1"># Create mapping from old to new indices</span>
+ <span class="n">node_index_map</span> <span class="o">=</span> <span class="p">{</span><span class="n">old_idx</span><span class="p">:</span> <span class="n">new_idx</span> <span class="k">for</span> <span class="n">new_idx</span><span class="p">,</span> <span class="n">old_idx</span> <span class="ow">in</span> <span class="nb">enumerate</span><span class="p">(</span><span class="n">sorted_node_indices</span><span class="p">)}</span>
+
+ <span class="c1"># Remap element indices</span>
+ <span class="n">remapped_elements</span> <span class="o">=</span> <span class="p">[]</span>
+ <span class="k">for</span> <span class="n">element</span> <span class="ow">in</span> <span class="n">all_elements</span><span class="p">:</span>
+ <span class="n">remapped_elements</span><span class="o">.</span><span class="n">append</span><span class="p">([</span><span class="n">node_index_map</span><span class="p">[</span><span class="n">idx</span><span class="p">]</span> <span class="k">for</span> <span class="n">idx</span> <span class="ow">in</span> <span class="n">element</span><span class="p">])</span>
+
+ <span class="k">return</span> <span class="n">nodes</span><span class="p">,</span> <span class="n">np</span><span class="o">.</span><span class="n">array</span><span class="p">(</span><span class="n">remapped_elements</span><span class="p">)</span>
+
+ <span class="k">def</span><span class="w"> </span><span class="nf">_calculate_volume</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span>
+<span class="w"> </span><span class="sd">"""Calculate volume of the closed surface mesh using the divergence theorem"""</span>
+ <span class="n">total_volume</span> <span class="o">=</span> <span class="mi">0</span>
+ <span class="c1"># For a closed surface mesh, orientation is important for correct signing</span>
+ <span class="k">for</span> <span class="n">element</span> <span class="ow">in</span> <span class="bp">self</span><span class="o">.</span><span class="n">elements</span><span class="p">:</span>
+ <span class="c1"># Get vertices of triangle</span>
+ <span class="n">v0</span><span class="p">,</span> <span class="n">v1</span><span class="p">,</span> <span class="n">v2</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">nodes</span><span class="p">[</span><span class="n">element</span><span class="p">]</span>
+
+ <span class="c1"># Calculate signed volume of tetrahedron formed by triangle and origin</span>
+ <span class="c1"># V = (1/6) * ((v1-v0) × (v2-v0)) · v0</span>
+ <span class="n">v01</span> <span class="o">=</span> <span class="n">v1</span> <span class="o">-</span> <span class="n">v0</span>
+ <span class="n">v02</span> <span class="o">=</span> <span class="n">v2</span> <span class="o">-</span> <span class="n">v0</span>
+ <span class="n">cross_product</span> <span class="o">=</span> <span class="n">np</span><span class="o">.</span><span class="n">cross</span><span class="p">(</span><span class="n">v01</span><span class="p">,</span> <span class="n">v02</span><span class="p">)</span>
+
+ <span class="c1"># For a properly oriented closed mesh, we use the signed volume</span>
+ <span class="c1"># This relies on triangle winding order being consistent</span>
+ <span class="n">volume</span> <span class="o">=</span> <span class="n">np</span><span class="o">.</span><span class="n">dot</span><span class="p">(</span><span class="n">cross_product</span><span class="p">,</span> <span class="n">v0</span><span class="p">)</span> <span class="o">/</span> <span class="mf">6.0</span>
+
+ <span class="c1"># Add the signed volume (will be negative for triangles facing inward)</span>
+ <span class="n">total_volume</span> <span class="o">+=</span> <span class="n">volume</span>
+
+ <span class="c1"># Take absolute value of the final result to handle any mesh orientation issues</span>
+ <span class="k">return</span> <span class="nb">abs</span><span class="p">(</span><span class="n">total_volume</span><span class="p">)</span>
+
+ <span class="k">def</span><span class="w"> </span><span class="nf">_calculate_center_of_mass</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span>
+<span class="w"> </span><span class="sd">"""Calculate center of mass of the surface mesh"""</span>
+ <span class="n">com</span> <span class="o">=</span> <span class="n">np</span><span class="o">.</span><span class="n">zeros</span><span class="p">(</span><span class="mi">3</span><span class="p">)</span>
+ <span class="n">total_weight</span> <span class="o">=</span> <span class="mi">0</span>
+
+ <span class="c1"># For a surface mesh, weight each triangle by its area</span>
+ <span class="k">for</span> <span class="n">element</span> <span class="ow">in</span> <span class="bp">self</span><span class="o">.</span><span class="n">elements</span><span class="p">:</span>
+ <span class="c1"># Get vertices of triangle</span>
+ <span class="n">v0</span><span class="p">,</span> <span class="n">v1</span><span class="p">,</span> <span class="n">v2</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">nodes</span><span class="p">[</span><span class="n">element</span><span class="p">]</span>
+
+ <span class="c1"># Calculate area using cross product</span>
+ <span class="n">v01</span> <span class="o">=</span> <span class="n">v1</span> <span class="o">-</span> <span class="n">v0</span>
+ <span class="n">v02</span> <span class="o">=</span> <span class="n">v2</span> <span class="o">-</span> <span class="n">v0</span>
+ <span class="n">area</span> <span class="o">=</span> <span class="mf">0.5</span> <span class="o">*</span> <span class="n">np</span><span class="o">.</span><span class="n">linalg</span><span class="o">.</span><span class="n">norm</span><span class="p">(</span><span class="n">np</span><span class="o">.</span><span class="n">cross</span><span class="p">(</span><span class="n">v01</span><span class="p">,</span> <span class="n">v02</span><span class="p">))</span>
+
+ <span class="c1"># Centroid of triangle</span>
+ <span class="n">centroid</span> <span class="o">=</span> <span class="p">(</span><span class="n">v0</span> <span class="o">+</span> <span class="n">v1</span> <span class="o">+</span> <span class="n">v2</span><span class="p">)</span> <span class="o">/</span> <span class="mf">3.0</span>
+
+ <span class="c1"># Add weighted contribution</span>
+ <span class="n">com</span> <span class="o">+=</span> <span class="n">centroid</span> <span class="o">*</span> <span class="n">area</span>
+ <span class="n">total_weight</span> <span class="o">+=</span> <span class="n">area</span>
+
+ <span class="k">return</span> <span class="n">com</span> <span class="o">/</span> <span class="n">total_weight</span> <span class="k">if</span> <span class="n">total_weight</span> <span class="o">></span> <span class="mi">0</span> <span class="k">else</span> <span class="n">np</span><span class="o">.</span><span class="n">zeros</span><span class="p">(</span><span class="mi">3</span><span class="p">)</span>
+
+ <span class="k">def</span><span class="w"> </span><span class="nf">_calculate_inertia_tensor</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span>
+ <span class="n">inertia</span> <span class="o">=</span> <span class="n">np</span><span class="o">.</span><span class="n">zeros</span><span class="p">((</span><span class="mi">3</span><span class="p">,</span> <span class="mi">3</span><span class="p">))</span>
+
+ <span class="c1"># Compute total mass based on volume and density</span>
+ <span class="n">mass</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">volume</span> <span class="o">*</span> <span class="bp">self</span><span class="o">.</span><span class="n">density</span> <span class="o">*</span> <span class="mf">0.6022</span>
+
+ <span class="c1"># Get bounding box dimensions to estimate shape</span>
+ <span class="n">bounds_min</span> <span class="o">=</span> <span class="n">np</span><span class="o">.</span><span class="n">min</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">nodes</span><span class="p">,</span> <span class="n">axis</span><span class="o">=</span><span class="mi">0</span><span class="p">)</span>
+ <span class="n">bounds_max</span> <span class="o">=</span> <span class="n">np</span><span class="o">.</span><span class="n">max</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">nodes</span><span class="p">,</span> <span class="n">axis</span><span class="o">=</span><span class="mi">0</span><span class="p">)</span>
+ <span class="n">dimensions</span> <span class="o">=</span> <span class="n">bounds_max</span> <span class="o">-</span> <span class="n">bounds_min</span>
+
+ <span class="c1"># Sort dimensions to identify major axes</span>
+ <span class="n">sorted_dims</span> <span class="o">=</span> <span class="n">np</span><span class="o">.</span><span class="n">sort</span><span class="p">(</span><span class="n">dimensions</span><span class="p">)</span>
+
+ <span class="c1"># For a rod-like object with aspect ratio AR</span>
+ <span class="c1"># Assuming AR is the ratio of length to diameter</span>
+ <span class="n">length</span> <span class="o">=</span> <span class="n">np</span><span class="o">.</span><span class="n">max</span><span class="p">(</span><span class="n">dimensions</span><span class="p">)</span>
+ <span class="n">diameter</span> <span class="o">=</span> <span class="n">np</span><span class="o">.</span><span class="n">min</span><span class="p">(</span><span class="n">dimensions</span><span class="p">)</span>
+ <span class="k">if</span> <span class="n">length</span> <span class="o">></span> <span class="mi">0</span> <span class="ow">and</span> <span class="n">diameter</span> <span class="o">></span> <span class="mi">0</span><span class="p">:</span>
+ <span class="n">AR</span> <span class="o">=</span> <span class="n">length</span> <span class="o">/</span> <span class="n">diameter</span>
+ <span class="k">else</span><span class="p">:</span>
+ <span class="n">AR</span> <span class="o">=</span> <span class="mf">1.0</span>
+
+ <span class="n">logger</span><span class="o">.</span><span class="n">info</span><span class="p">(</span><span class="sa">f</span><span class="s2">"Detected dimensions: </span><span class="si">{</span><span class="n">dimensions</span><span class="si">}</span><span class="s2">"</span><span class="p">)</span>
+ <span class="n">logger</span><span class="o">.</span><span class="n">info</span><span class="p">(</span><span class="sa">f</span><span class="s2">"Estimated aspect ratio: </span><span class="si">{</span><span class="n">AR</span><span class="si">:</span><span class="s2">.2f</span><span class="si">}</span><span class="s2">"</span><span class="p">)</span>
+
+ <span class="c1"># Calculate moments of inertia for a cylindrical rod</span>
+ <span class="c1"># For a uniform rod of length L and radius R:</span>
+ <span class="c1"># I_axial = (1/2)MR²</span>
+ <span class="c1"># I_transverse = (1/12)ML² + (1/4)MR²</span>
+ <span class="n">radius</span> <span class="o">=</span> <span class="n">diameter</span> <span class="o">/</span> <span class="mf">2.0</span>
+
+ <span class="c1"># Along major axis (assuming z is the major axis)</span>
+ <span class="n">I_axial</span> <span class="o">=</span> <span class="mf">0.5</span> <span class="o">*</span> <span class="n">mass</span> <span class="o">*</span> <span class="n">radius</span><span class="o">**</span><span class="mi">2</span>
+
+ <span class="c1"># Perpendicular to major axis</span>
+ <span class="n">I_transverse</span> <span class="o">=</span> <span class="p">(</span><span class="mi">1</span><span class="o">/</span><span class="mf">12.0</span><span class="p">)</span> <span class="o">*</span> <span class="n">mass</span> <span class="o">*</span> <span class="n">length</span><span class="o">**</span><span class="mi">2</span> <span class="o">+</span> <span class="p">(</span><span class="mi">1</span><span class="o">/</span><span class="mf">4.0</span><span class="p">)</span> <span class="o">*</span> <span class="n">mass</span> <span class="o">*</span> <span class="n">radius</span><span class="o">**</span><span class="mi">2</span>
+
+ <span class="c1"># Create a diagonal inertia tensor based on these analytic expressions</span>
+ <span class="c1"># Identify which axis is the major axis (longest dimension)</span>
+ <span class="n">major_axis_idx</span> <span class="o">=</span> <span class="n">np</span><span class="o">.</span><span class="n">argmax</span><span class="p">(</span><span class="n">dimensions</span><span class="p">)</span>
+
+ <span class="k">for</span> <span class="n">i</span> <span class="ow">in</span> <span class="nb">range</span><span class="p">(</span><span class="mi">3</span><span class="p">):</span>
+ <span class="k">if</span> <span class="n">i</span> <span class="o">==</span> <span class="n">major_axis_idx</span><span class="p">:</span>
+ <span class="n">inertia</span><span class="p">[</span><span class="n">i</span><span class="p">,</span> <span class="n">i</span><span class="p">]</span> <span class="o">=</span> <span class="n">I_axial</span>
+ <span class="k">else</span><span class="p">:</span>
+ <span class="n">inertia</span><span class="p">[</span><span class="n">i</span><span class="p">,</span> <span class="n">i</span><span class="p">]</span> <span class="o">=</span> <span class="n">I_transverse</span>
+
+ <span class="k">return</span> <span class="n">inertia</span>
+
+ <span class="k">def</span><span class="w"> </span><span class="nf">_align_mesh</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span>
+<span class="w"> </span><span class="sd">"""Align mesh to center of mass and principal axes with longest dimension along Z-axis"""</span>
+ <span class="c1"># First center the mesh</span>
+ <span class="n">com</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">_calculate_center_of_mass</span><span class="p">()</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">nodes</span> <span class="o">-=</span> <span class="n">com</span>
+
+ <span class="c1"># Get bounding box dimensions to estimate shape</span>
+ <span class="n">bounds_min</span> <span class="o">=</span> <span class="n">np</span><span class="o">.</span><span class="n">min</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">nodes</span><span class="p">,</span> <span class="n">axis</span><span class="o">=</span><span class="mi">0</span><span class="p">)</span>
+ <span class="n">bounds_max</span> <span class="o">=</span> <span class="n">np</span><span class="o">.</span><span class="n">max</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">nodes</span><span class="p">,</span> <span class="n">axis</span><span class="o">=</span><span class="mi">0</span><span class="p">)</span>
+ <span class="n">dimensions</span> <span class="o">=</span> <span class="n">bounds_max</span> <span class="o">-</span> <span class="n">bounds_min</span>
+ <span class="n">logger</span><span class="o">.</span><span class="n">info</span><span class="p">(</span><span class="sa">f</span><span class="s2">"Pre-alignment dimensions: </span><span class="si">{</span><span class="n">dimensions</span><span class="si">}</span><span class="s2">"</span><span class="p">)</span>
+
+ <span class="c1"># Calculate and diagonalize inertia tensor</span>
+ <span class="n">inertia</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">_calculate_inertia_tensor</span><span class="p">()</span>
+ <span class="n">eigenvalues</span><span class="p">,</span> <span class="n">eigenvectors</span> <span class="o">=</span> <span class="n">np</span><span class="o">.</span><span class="n">linalg</span><span class="o">.</span><span class="n">eigh</span><span class="p">(</span><span class="n">inertia</span><span class="p">)</span>
+
+ <span class="c1"># For a rod, smallest moment of inertia is along the rod axis</span>
+ <span class="c1"># We want this to be aligned with the Z-axis (axis 2)</span>
+ <span class="n">sort_idx</span> <span class="o">=</span> <span class="n">np</span><span class="o">.</span><span class="n">argsort</span><span class="p">(</span><span class="n">eigenvalues</span><span class="p">)</span>
+
+ <span class="c1"># Reorder to put smallest moment (rod axis) as Z</span>
+ <span class="c1"># Z should be axis 2, so we want the smallest moment to be last</span>
+ <span class="n">z_vec</span> <span class="o">=</span> <span class="n">eigenvectors</span><span class="p">[:,</span> <span class="n">sort_idx</span><span class="p">[</span><span class="mi">0</span><span class="p">]]</span> <span class="c1"># Vector of smallest moment (rod axis)</span>
+ <span class="n">x_vec</span> <span class="o">=</span> <span class="n">eigenvectors</span><span class="p">[:,</span> <span class="n">sort_idx</span><span class="p">[</span><span class="mi">1</span><span class="p">]]</span>
+ <span class="n">y_vec</span> <span class="o">=</span> <span class="n">eigenvectors</span><span class="p">[:,</span> <span class="n">sort_idx</span><span class="p">[</span><span class="mi">2</span><span class="p">]]</span>
+
+ <span class="c1"># Create new eigenvector matrix with Z as the rod axis</span>
+ <span class="n">reordered_eigenvectors</span> <span class="o">=</span> <span class="n">np</span><span class="o">.</span><span class="n">column_stack</span><span class="p">([</span><span class="n">x_vec</span><span class="p">,</span> <span class="n">y_vec</span><span class="p">,</span> <span class="n">z_vec</span><span class="p">])</span>
+
+ <span class="c1"># Ensure right-handed coordinate system</span>
+ <span class="k">if</span> <span class="n">np</span><span class="o">.</span><span class="n">linalg</span><span class="o">.</span><span class="n">det</span><span class="p">(</span><span class="n">reordered_eigenvectors</span><span class="p">)</span> <span class="o"><</span> <span class="mi">0</span><span class="p">:</span>
+ <span class="n">reordered_eigenvectors</span><span class="p">[:,</span> <span class="mi">0</span><span class="p">]</span> <span class="o">*=</span> <span class="o">-</span><span class="mi">1</span>
+
+ <span class="c1"># Rotate mesh to align with principal axes with rod along Z</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">nodes</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">nodes</span> <span class="o">@</span> <span class="n">reordered_eigenvectors</span>
+
+ <span class="c1"># Get post-alignment dimensions</span>
+ <span class="n">bounds_min</span> <span class="o">=</span> <span class="n">np</span><span class="o">.</span><span class="n">min</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">nodes</span><span class="p">,</span> <span class="n">axis</span><span class="o">=</span><span class="mi">0</span><span class="p">)</span>
+ <span class="n">bounds_max</span> <span class="o">=</span> <span class="n">np</span><span class="o">.</span><span class="n">max</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">nodes</span><span class="p">,</span> <span class="n">axis</span><span class="o">=</span><span class="mi">0</span><span class="p">)</span>
+ <span class="n">dimensions</span> <span class="o">=</span> <span class="n">bounds_max</span> <span class="o">-</span> <span class="n">bounds_min</span>
+ <span class="n">logger</span><span class="o">.</span><span class="n">info</span><span class="p">(</span><span class="sa">f</span><span class="s2">"Post-alignment dimensions: </span><span class="si">{</span><span class="n">dimensions</span><span class="si">}</span><span class="s2">"</span><span class="p">)</span>
+
+ <span class="c1"># Verify that Z is now the longest dimension</span>
+ <span class="k">if</span> <span class="n">dimensions</span><span class="p">[</span><span class="mi">2</span><span class="p">]</span> <span class="o"><</span> <span class="nb">max</span><span class="p">(</span><span class="n">dimensions</span><span class="p">[</span><span class="mi">0</span><span class="p">],</span> <span class="n">dimensions</span><span class="p">[</span><span class="mi">1</span><span class="p">]):</span>
+ <span class="n">logger</span><span class="o">.</span><span class="n">info</span><span class="p">(</span><span class="s2">"WARNING: Z-axis is not the longest dimension after alignment!"</span><span class="p">)</span>
+
+ <span class="c1"># Calculate aspect ratio (using Z as length)</span>
+ <span class="n">length</span> <span class="o">=</span> <span class="n">dimensions</span><span class="p">[</span><span class="mi">2</span><span class="p">]</span> <span class="c1"># Z axis should be the rod length</span>
+ <span class="n">width</span> <span class="o">=</span> <span class="nb">max</span><span class="p">(</span><span class="n">dimensions</span><span class="p">[</span><span class="mi">0</span><span class="p">],</span> <span class="n">dimensions</span><span class="p">[</span><span class="mi">1</span><span class="p">])</span> <span class="c1"># Use max of X or Y for width</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">aspect_ratio</span> <span class="o">=</span> <span class="n">length</span> <span class="o">/</span> <span class="n">width</span> <span class="k">if</span> <span class="n">width</span> <span class="o">></span> <span class="mi">0</span> <span class="k">else</span> <span class="mf">1.0</span>
+ <span class="n">logger</span><span class="o">.</span><span class="n">info</span><span class="p">(</span><span class="sa">f</span><span class="s2">"Calculated aspect ratio: </span><span class="si">{</span><span class="bp">self</span><span class="o">.</span><span class="n">aspect_ratio</span><span class="si">:</span><span class="s2">.6f</span><span class="si">}</span><span class="s2">"</span><span class="p">)</span>
+
+ <span class="c1"># Store transformation</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">rotation_matrix</span> <span class="o">=</span> <span class="n">reordered_eigenvectors</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">translation</span> <span class="o">=</span> <span class="n">com</span>
+ <span class="n">logger</span><span class="o">.</span><span class="n">info</span><span class="p">(</span><span class="sa">f</span><span class="s2">"Aligned mesh to principal axes with rod along Z-axis, COM: </span><span class="si">{</span><span class="n">com</span><span class="si">}</span><span class="s2">"</span><span class="p">)</span>
+
+<div class="viewcode-block" id="SurfaceMeshProcessor.calculate_damping">
+<a class="viewcode-back" href="../../api/rigidbody_models/mesh_process_surface.html#arbdmodel.mesh_process_surface.SurfaceMeshProcessor.calculate_damping">[docs]</a>
+ <span class="k">def</span><span class="w"> </span><span class="nf">calculate_damping</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">work_dir</span><span class="o">=</span><span class="kc">None</span><span class="p">):</span>
+<span class="w"> </span><span class="sd">"""Calculate hydrodynamic properties using HydroPro"""</span>
+ <span class="c1"># Create work directory if it doesn't exist</span>
+ <span class="k">if</span> <span class="n">work_dir</span> <span class="ow">is</span> <span class="kc">None</span><span class="p">:</span>
+ <span class="n">work_dir</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">work_dir</span> <span class="o">/</span> <span class="bp">self</span><span class="o">.</span><span class="n">name</span>
+ <span class="k">else</span><span class="p">:</span>
+ <span class="n">work_dir</span> <span class="o">=</span> <span class="n">Path</span><span class="p">(</span><span class="n">work_dir</span><span class="p">)</span>
+
+ <span class="k">try</span><span class="p">:</span>
+ <span class="n">os</span><span class="o">.</span><span class="n">listdir</span><span class="p">(</span><span class="n">work_dir</span><span class="p">)</span>
+ <span class="k">except</span><span class="p">:</span>
+ <span class="n">os</span><span class="o">.</span><span class="n">mkdir</span><span class="p">(</span><span class="n">work_dir</span><span class="p">)</span>
+
+ <span class="n">base_path</span> <span class="o">=</span> <span class="n">work_dir</span> <span class="o">/</span> <span class="s2">"hydrocal"</span>
+
+ <span class="c1"># Save the mesh in PDB format for HydroPro</span>
+ <span class="n">pdb_path</span> <span class="o">=</span> <span class="nb">str</span><span class="p">(</span><span class="n">base_path</span><span class="p">)</span> <span class="o">+</span> <span class="s2">".pdb"</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">save_as_pdb</span><span class="p">(</span><span class="n">pdb_path</span><span class="p">)</span>
+
+ <span class="c1"># Run HydroPro to get hydrodynamic properties</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">runner</span> <span class="o">=</span> <span class="n">HydroProRunner</span><span class="p">(</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">mass</span><span class="p">,</span>
+ <span class="n">binary_path</span><span class="o">=</span><span class="bp">self</span><span class="o">.</span><span class="n">binary_path</span><span class="p">,</span>
+ <span class="n">temperature</span><span class="o">=</span><span class="bp">self</span><span class="o">.</span><span class="n">temperature</span><span class="p">,</span>
+ <span class="n">viscosity</span><span class="o">=</span><span class="bp">self</span><span class="o">.</span><span class="n">viscosity</span><span class="p">,</span>
+ <span class="n">solvent_density</span><span class="o">=</span><span class="bp">self</span><span class="o">.</span><span class="n">solvent_density</span><span class="p">,</span>
+ <span class="n">structure_name</span><span class="o">=</span><span class="bp">self</span><span class="o">.</span><span class="n">name</span>
+ <span class="p">)</span>
+
+ <span class="n">results</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">runner</span><span class="o">.</span><span class="n">run_calculation</span><span class="p">(</span><span class="n">work_dir</span><span class="o">=</span><span class="n">work_dir</span><span class="p">)</span>
+
+ <span class="bp">self</span><span class="o">.</span><span class="n">transdamp</span> <span class="o">=</span> <span class="n">results</span><span class="p">[</span><span class="s1">'translation_damping'</span><span class="p">]</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">rotational_damping_coefficient</span> <span class="o">=</span> <span class="n">results</span><span class="p">[</span><span class="s1">'rotation_damping'</span><span class="p">]</span>
+
+ <span class="n">logger</span><span class="o">.</span><span class="n">info</span><span class="p">(</span><span class="sa">f</span><span class="s2">"Translational damping: </span><span class="si">{</span><span class="bp">self</span><span class="o">.</span><span class="n">transdamp</span><span class="si">}</span><span class="s2">"</span><span class="p">)</span>
+ <span class="n">logger</span><span class="o">.</span><span class="n">info</span><span class="p">(</span><span class="sa">f</span><span class="s2">"Rotational damping: </span><span class="si">{</span><span class="bp">self</span><span class="o">.</span><span class="n">rotational_damping_coefficient</span><span class="si">}</span><span class="s2">"</span><span class="p">)</span>
+
+ <span class="k">return</span> <span class="n">pdb_path</span></div>
+
+
+<div class="viewcode-block" id="SurfaceMeshProcessor.generate_potential_grid">
+<a class="viewcode-back" href="../../api/rigidbody_models/mesh_process_surface.html#arbdmodel.mesh_process_surface.SurfaceMeshProcessor.generate_potential_grid">[docs]</a>
+ <span class="k">def</span><span class="w"> </span><span class="nf">generate_potential_grid</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">spacing</span><span class="o">=</span><span class="mf">2.0</span><span class="p">,</span> <span class="n">buffer</span><span class="o">=</span><span class="mf">20.0</span><span class="p">,</span> <span class="n">k</span><span class="o">=</span><span class="mf">1.0</span><span class="p">,</span> <span class="n">cutoff</span><span class="o">=</span><span class="mf">10.0</span><span class="p">,</span> <span class="n">max_potential</span><span class="o">=</span><span class="mf">1000.0</span><span class="p">):</span>
+<span class="w"> </span><span class="sd">"""Generate potential grid for ARBD"""</span>
+ <span class="c1"># Calculate grid bounds with buffer</span>
+ <span class="n">bounds_min</span> <span class="o">=</span> <span class="n">np</span><span class="o">.</span><span class="n">min</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">nodes</span><span class="p">,</span> <span class="n">axis</span><span class="o">=</span><span class="mi">0</span><span class="p">)</span> <span class="o">-</span> <span class="n">buffer</span>
+ <span class="n">bounds_max</span> <span class="o">=</span> <span class="n">np</span><span class="o">.</span><span class="n">max</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">nodes</span><span class="p">,</span> <span class="n">axis</span><span class="o">=</span><span class="mi">0</span><span class="p">)</span> <span class="o">+</span> <span class="n">buffer</span>
+
+ <span class="c1"># Create grid points</span>
+ <span class="n">npts</span> <span class="o">=</span> <span class="n">np</span><span class="o">.</span><span class="n">ceil</span><span class="p">((</span><span class="n">bounds_max</span> <span class="o">-</span> <span class="n">bounds_min</span><span class="p">)</span> <span class="o">/</span> <span class="n">spacing</span><span class="p">)</span><span class="o">.</span><span class="n">astype</span><span class="p">(</span><span class="nb">int</span><span class="p">)</span>
+ <span class="n">x</span> <span class="o">=</span> <span class="n">np</span><span class="o">.</span><span class="n">linspace</span><span class="p">(</span><span class="n">bounds_min</span><span class="p">[</span><span class="mi">0</span><span class="p">],</span> <span class="n">bounds_max</span><span class="p">[</span><span class="mi">0</span><span class="p">],</span> <span class="n">npts</span><span class="p">[</span><span class="mi">0</span><span class="p">])</span>
+ <span class="n">y</span> <span class="o">=</span> <span class="n">np</span><span class="o">.</span><span class="n">linspace</span><span class="p">(</span><span class="n">bounds_min</span><span class="p">[</span><span class="mi">1</span><span class="p">],</span> <span class="n">bounds_max</span><span class="p">[</span><span class="mi">1</span><span class="p">],</span> <span class="n">npts</span><span class="p">[</span><span class="mi">1</span><span class="p">])</span>
+ <span class="n">z</span> <span class="o">=</span> <span class="n">np</span><span class="o">.</span><span class="n">linspace</span><span class="p">(</span><span class="n">bounds_min</span><span class="p">[</span><span class="mi">2</span><span class="p">],</span> <span class="n">bounds_max</span><span class="p">[</span><span class="mi">2</span><span class="p">],</span> <span class="n">npts</span><span class="p">[</span><span class="mi">2</span><span class="p">])</span>
+ <span class="n">X</span><span class="p">,</span> <span class="n">Y</span><span class="p">,</span> <span class="n">Z</span> <span class="o">=</span> <span class="n">np</span><span class="o">.</span><span class="n">meshgrid</span><span class="p">(</span><span class="n">x</span><span class="p">,</span> <span class="n">y</span><span class="p">,</span> <span class="n">z</span><span class="p">,</span> <span class="n">indexing</span><span class="o">=</span><span class="s1">'ij'</span><span class="p">)</span>
+
+ <span class="c1"># Create KD-tree for fast distance calculations</span>
+ <span class="n">tree</span> <span class="o">=</span> <span class="n">KDTree</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">nodes</span><span class="p">)</span>
+
+ <span class="c1"># Calculate distances to nearest surface points</span>
+ <span class="n">grid_points</span> <span class="o">=</span> <span class="n">np</span><span class="o">.</span><span class="n">vstack</span><span class="p">([</span><span class="n">X</span><span class="o">.</span><span class="n">ravel</span><span class="p">(),</span> <span class="n">Y</span><span class="o">.</span><span class="n">ravel</span><span class="p">(),</span> <span class="n">Z</span><span class="o">.</span><span class="n">ravel</span><span class="p">()])</span><span class="o">.</span><span class="n">T</span>
+ <span class="n">distances</span><span class="p">,</span> <span class="n">_</span> <span class="o">=</span> <span class="n">tree</span><span class="o">.</span><span class="n">query</span><span class="p">(</span><span class="n">grid_points</span><span class="p">)</span>
+ <span class="n">distances</span> <span class="o">=</span> <span class="n">distances</span><span class="o">.</span><span class="n">reshape</span><span class="p">(</span><span class="n">X</span><span class="o">.</span><span class="n">shape</span><span class="p">)</span>
+
+ <span class="c1"># Generate potential</span>
+ <span class="n">potential</span> <span class="o">=</span> <span class="n">np</span><span class="o">.</span><span class="n">zeros_like</span><span class="p">(</span><span class="n">distances</span><span class="p">)</span>
+ <span class="n">mask</span> <span class="o">=</span> <span class="n">distances</span> <span class="o"><=</span> <span class="n">cutoff</span>
+ <span class="n">potential</span><span class="p">[</span><span class="n">mask</span><span class="p">]</span> <span class="o">=</span> <span class="n">max_potential</span> <span class="o">*</span> <span class="p">(</span><span class="mi">1</span> <span class="o">-</span> <span class="mi">1</span><span class="o">/</span><span class="p">(</span><span class="mi">1</span> <span class="o">+</span> <span class="n">np</span><span class="o">.</span><span class="n">exp</span><span class="p">(</span><span class="o">-</span><span class="n">k</span> <span class="o">*</span> <span class="n">distances</span><span class="p">[</span><span class="n">mask</span><span class="p">])))</span>
+
+ <span class="k">return</span> <span class="n">potential</span><span class="p">,</span> <span class="n">bounds_min</span><span class="p">,</span> <span class="n">spacing</span> <span class="o">*</span> <span class="n">np</span><span class="o">.</span><span class="n">ones</span><span class="p">(</span><span class="mi">3</span><span class="p">)</span></div>
+
+
+<div class="viewcode-block" id="SurfaceMeshProcessor.write_no_enter_potential_dx">
+<a class="viewcode-back" href="../../api/rigidbody_models/mesh_process_surface.html#arbdmodel.mesh_process_surface.SurfaceMeshProcessor.write_no_enter_potential_dx">[docs]</a>
+ <span class="k">def</span><span class="w"> </span><span class="nf">write_no_enter_potential_dx</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">output_file</span><span class="o">=</span><span class="kc">None</span><span class="p">,</span> <span class="o">**</span><span class="n">kwargs</span><span class="p">):</span>
+ <span class="k">if</span> <span class="n">output_file</span> <span class="ow">is</span> <span class="kc">None</span><span class="p">:</span>
+ <span class="n">outfile</span><span class="o">=</span><span class="bp">self</span><span class="o">.</span><span class="n">name</span><span class="o">+</span><span class="s2">".dx"</span>
+<span class="w"> </span><span class="sd">"""Generate and write potential field to DX file"""</span>
+ <span class="n">potential</span><span class="p">,</span> <span class="n">origin</span><span class="p">,</span> <span class="n">delta</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">generate_potential_grid</span><span class="p">(</span><span class="o">**</span><span class="n">kwargs</span><span class="p">)</span>
+ <span class="n">writeDx</span><span class="p">(</span><span class="n">output_file</span><span class="p">,</span> <span class="n">potential</span><span class="p">,</span> <span class="n">origin</span><span class="p">,</span> <span class="n">delta</span><span class="p">)</span></div>
+
+
+<div class="viewcode-block" id="SurfaceMeshProcessor.save_aligned_mesh">
+<a class="viewcode-back" href="../../api/rigidbody_models/mesh_process_surface.html#arbdmodel.mesh_process_surface.SurfaceMeshProcessor.save_aligned_mesh">[docs]</a>
+ <span class="k">def</span><span class="w"> </span><span class="nf">save_aligned_mesh</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">output_file</span><span class="p">):</span>
+<span class="w"> </span><span class="sd">"""Save the aligned mesh to a new .msh file"""</span>
+ <span class="n">gmsh</span><span class="o">.</span><span class="n">initialize</span><span class="p">()</span>
+ <span class="n">gmsh</span><span class="o">.</span><span class="n">model</span><span class="o">.</span><span class="n">add</span><span class="p">(</span><span class="s2">"aligned_mesh"</span><span class="p">)</span>
+
+ <span class="c1"># For surface mesh</span>
+ <span class="n">entity_dim</span> <span class="o">=</span> <span class="mi">2</span>
+ <span class="n">element_type</span> <span class="o">=</span> <span class="mi">2</span> <span class="c1"># Triangle in gmsh</span>
+
+ <span class="c1"># Add a discrete entity</span>
+ <span class="n">entity_tag</span> <span class="o">=</span> <span class="n">gmsh</span><span class="o">.</span><span class="n">model</span><span class="o">.</span><span class="n">addDiscreteEntity</span><span class="p">(</span><span class="n">entity_dim</span><span class="p">)</span>
+
+ <span class="c1"># Add nodes</span>
+ <span class="n">node_tags</span> <span class="o">=</span> <span class="p">[]</span>
+ <span class="n">node_coords</span> <span class="o">=</span> <span class="p">[]</span>
+ <span class="k">for</span> <span class="n">i</span><span class="p">,</span> <span class="n">node</span> <span class="ow">in</span> <span class="nb">enumerate</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">nodes</span><span class="p">):</span>
+ <span class="n">tag</span> <span class="o">=</span> <span class="n">i</span> <span class="o">+</span> <span class="mi">1</span>
+ <span class="n">node_tags</span><span class="o">.</span><span class="n">append</span><span class="p">(</span><span class="n">tag</span><span class="p">)</span>
+ <span class="n">node_coords</span><span class="o">.</span><span class="n">extend</span><span class="p">(</span><span class="n">node</span> <span class="o">/</span> <span class="bp">self</span><span class="o">.</span><span class="n">unit_scale</span><span class="p">)</span> <span class="c1"># Convert back to mesh units</span>
+
+ <span class="n">gmsh</span><span class="o">.</span><span class="n">model</span><span class="o">.</span><span class="n">mesh</span><span class="o">.</span><span class="n">addNodes</span><span class="p">(</span><span class="n">entity_dim</span><span class="p">,</span> <span class="n">entity_tag</span><span class="p">,</span> <span class="n">node_tags</span><span class="p">,</span> <span class="n">node_coords</span><span class="p">)</span>
+
+ <span class="c1"># Add elements</span>
+ <span class="n">element_tags</span> <span class="o">=</span> <span class="p">[]</span>
+ <span class="n">element_nodes</span> <span class="o">=</span> <span class="p">[]</span>
+ <span class="k">for</span> <span class="n">i</span><span class="p">,</span> <span class="n">element</span> <span class="ow">in</span> <span class="nb">enumerate</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">elements</span><span class="p">):</span>
+ <span class="n">tag</span> <span class="o">=</span> <span class="n">i</span> <span class="o">+</span> <span class="mi">1</span>
+ <span class="n">element_tags</span><span class="o">.</span><span class="n">append</span><span class="p">(</span><span class="n">tag</span><span class="p">)</span>
+ <span class="n">element_nodes</span><span class="o">.</span><span class="n">extend</span><span class="p">([</span><span class="nb">int</span><span class="p">(</span><span class="n">x</span> <span class="o">+</span> <span class="mi">1</span><span class="p">)</span> <span class="k">for</span> <span class="n">x</span> <span class="ow">in</span> <span class="n">element</span><span class="p">])</span> <span class="c1"># Convert to 1-based indexing</span>
+
+ <span class="n">gmsh</span><span class="o">.</span><span class="n">model</span><span class="o">.</span><span class="n">mesh</span><span class="o">.</span><span class="n">addElements</span><span class="p">(</span><span class="n">entity_dim</span><span class="p">,</span> <span class="n">entity_tag</span><span class="p">,</span> <span class="p">[</span><span class="n">element_type</span><span class="p">],</span> <span class="p">[</span><span class="n">element_tags</span><span class="p">],</span> <span class="p">[</span><span class="n">element_nodes</span><span class="p">])</span>
+
+ <span class="c1"># Write mesh</span>
+ <span class="n">gmsh</span><span class="o">.</span><span class="n">write</span><span class="p">(</span><span class="nb">str</span><span class="p">(</span><span class="n">output_file</span><span class="p">))</span>
+ <span class="n">gmsh</span><span class="o">.</span><span class="n">finalize</span><span class="p">()</span></div>
+
+
+<div class="viewcode-block" id="SurfaceMeshProcessor.save_as_pdb">
+<a class="viewcode-back" href="../../api/rigidbody_models/mesh_process_surface.html#arbdmodel.mesh_process_surface.SurfaceMeshProcessor.save_as_pdb">[docs]</a>
+ <span class="k">def</span><span class="w"> </span><span class="nf">save_as_pdb</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">output_file</span><span class="p">):</span>
+
+<span class="w"> </span><span class="sd">"""Save the aligned mesh as a PDB file (coordinates in Ã…)"""</span>
+ <span class="c1"># PDB format specifications</span>
+ <span class="n">HEADER</span> <span class="o">=</span> <span class="s2">"HEADER ALIGNED SURFACE MESH "</span>
+ <span class="n">ATOM_FORMAT</span> <span class="o">=</span> <span class="s2">"ATOM </span><span class="si">{:5d}</span><span class="s2"> </span><span class="si">{:4s}</span><span class="s2"> </span><span class="si">{:3s}</span><span class="s2"> </span><span class="si">{:1s}{:4d}</span><span class="s2"> </span><span class="si">{:8.3f}{:8.3f}{:8.3f}{:6.2f}{:6.2f}</span><span class="s2">"</span>
+
+ <span class="k">with</span> <span class="nb">open</span><span class="p">(</span><span class="n">output_file</span><span class="p">,</span> <span class="s1">'w'</span><span class="p">)</span> <span class="k">as</span> <span class="n">f</span><span class="p">:</span>
+ <span class="c1"># Write header</span>
+ <span class="kn">from</span><span class="w"> </span><span class="nn">datetime</span><span class="w"> </span><span class="kn">import</span> <span class="n">datetime</span>
+ <span class="n">date_str</span> <span class="o">=</span> <span class="n">datetime</span><span class="o">.</span><span class="n">now</span><span class="p">()</span><span class="o">.</span><span class="n">strftime</span><span class="p">(</span><span class="s2">"</span><span class="si">%d</span><span class="s2">-%b-%y"</span><span class="p">)</span>
+ <span class="n">f</span><span class="o">.</span><span class="n">write</span><span class="p">(</span><span class="sa">f</span><span class="s2">"</span><span class="si">{</span><span class="n">HEADER</span><span class="si">}{</span><span class="n">date_str</span><span class="si">}</span><span class="s2"> XXXX</span><span class="se">\n</span><span class="s2">"</span><span class="p">)</span>
+
+ <span class="c1"># Calculate box dimensions for CRYST record</span>
+ <span class="n">bounds_min</span> <span class="o">=</span> <span class="n">np</span><span class="o">.</span><span class="n">min</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">nodes</span><span class="p">,</span> <span class="n">axis</span><span class="o">=</span><span class="mi">0</span><span class="p">)</span>
+ <span class="n">bounds_max</span> <span class="o">=</span> <span class="n">np</span><span class="o">.</span><span class="n">max</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">nodes</span><span class="p">,</span> <span class="n">axis</span><span class="o">=</span><span class="mi">0</span><span class="p">)</span>
+ <span class="n">box_dimensions</span> <span class="o">=</span> <span class="n">bounds_max</span> <span class="o">-</span> <span class="n">bounds_min</span>
+
+ <span class="c1"># Write crystallographic information</span>
+ <span class="n">f</span><span class="o">.</span><span class="n">write</span><span class="p">(</span><span class="sa">f</span><span class="s2">"CRYST1</span><span class="si">{</span><span class="n">box_dimensions</span><span class="p">[</span><span class="mi">0</span><span class="p">]</span><span class="si">:</span><span class="s2">9.3f</span><span class="si">}{</span><span class="n">box_dimensions</span><span class="p">[</span><span class="mi">1</span><span class="p">]</span><span class="si">:</span><span class="s2">9.3f</span><span class="si">}{</span><span class="n">box_dimensions</span><span class="p">[</span><span class="mi">2</span><span class="p">]</span><span class="si">:</span><span class="s2">9.3f</span><span class="si">}</span><span class="s2"> 90.00 90.00 90.00 P 1 1</span><span class="se">\n</span><span class="s2">"</span><span class="p">)</span>
+
+ <span class="c1"># Write atoms (nodes from the mesh)</span>
+ <span class="k">for</span> <span class="n">i</span><span class="p">,</span> <span class="n">node</span> <span class="ow">in</span> <span class="nb">enumerate</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">nodes</span><span class="p">):</span>
+ <span class="c1"># PDB uses 1-indexed atom numbers</span>
+ <span class="n">atom_num</span> <span class="o">=</span> <span class="n">i</span> <span class="o">+</span> <span class="mi">1</span>
+ <span class="c1"># Use CA (alpha carbon) atom type for visibility in viewers</span>
+ <span class="n">atom_name</span> <span class="o">=</span> <span class="s2">" CA "</span>
+ <span class="c1"># Use residue name MES for mesh</span>
+ <span class="n">res_name</span> <span class="o">=</span> <span class="s2">"MES"</span>
+ <span class="c1"># Use chain ID A</span>
+ <span class="n">chain_id</span> <span class="o">=</span> <span class="s2">"A"</span>
+ <span class="c1"># Residue number = atom number for simplicity</span>
+ <span class="n">res_num</span> <span class="o">=</span> <span class="n">atom_num</span> <span class="o">%</span> <span class="mi">10000</span> <span class="c1"># PDB format limits res numbers to 9999</span>
+ <span class="c1"># X, Y, Z coordinates in Ångströms (already in the correct units)</span>
+ <span class="n">x</span><span class="p">,</span> <span class="n">y</span><span class="p">,</span> <span class="n">z</span> <span class="o">=</span> <span class="n">node</span>
+ <span class="c1"># Use 1.0 for occupancy and 0.0 for temperature factor</span>
+ <span class="n">occupancy</span> <span class="o">=</span> <span class="mf">1.0</span>
+ <span class="n">temp_factor</span> <span class="o">=</span> <span class="mf">0.0</span>
+
+ <span class="n">f</span><span class="o">.</span><span class="n">write</span><span class="p">(</span><span class="sa">f</span><span class="s2">"</span><span class="si">{</span><span class="n">ATOM_FORMAT</span><span class="o">.</span><span class="n">format</span><span class="p">(</span><span class="n">atom_num</span><span class="p">,</span><span class="w"> </span><span class="n">atom_name</span><span class="p">,</span><span class="w"> </span><span class="n">res_name</span><span class="p">,</span><span class="w"> </span><span class="n">chain_id</span><span class="p">,</span><span class="w"> </span><span class="n">res_num</span><span class="p">,</span><span class="w"> </span><span class="n">x</span><span class="p">,</span><span class="w"> </span><span class="n">y</span><span class="p">,</span><span class="w"> </span><span class="n">z</span><span class="p">,</span><span class="w"> </span><span class="n">occupancy</span><span class="p">,</span><span class="w"> </span><span class="n">temp_factor</span><span class="p">)</span><span class="si">}</span><span class="se">\n</span><span class="s2">"</span><span class="p">)</span>
+
+ <span class="c1"># Write connectivity (the mesh elements) as CONECT records</span>
+ <span class="k">for</span> <span class="n">element</span> <span class="ow">in</span> <span class="bp">self</span><span class="o">.</span><span class="n">elements</span><span class="p">:</span>
+ <span class="c1"># PDB CONECT records use 1-indexed atom numbers</span>
+ <span class="n">atom_indices</span> <span class="o">=</span> <span class="p">[</span><span class="n">idx</span> <span class="o">+</span> <span class="mi">1</span> <span class="k">for</span> <span class="n">idx</span> <span class="ow">in</span> <span class="n">element</span><span class="p">]</span>
+
+ <span class="c1"># Create a CONECT record for each edge of the triangle</span>
+ <span class="n">edges</span> <span class="o">=</span> <span class="p">[(</span><span class="n">atom_indices</span><span class="p">[</span><span class="mi">0</span><span class="p">],</span> <span class="n">atom_indices</span><span class="p">[</span><span class="mi">1</span><span class="p">]),</span>
+ <span class="p">(</span><span class="n">atom_indices</span><span class="p">[</span><span class="mi">1</span><span class="p">],</span> <span class="n">atom_indices</span><span class="p">[</span><span class="mi">2</span><span class="p">]),</span>
+ <span class="p">(</span><span class="n">atom_indices</span><span class="p">[</span><span class="mi">2</span><span class="p">],</span> <span class="n">atom_indices</span><span class="p">[</span><span class="mi">0</span><span class="p">])]</span>
+
+ <span class="k">for</span> <span class="n">a1</span><span class="p">,</span> <span class="n">a2</span> <span class="ow">in</span> <span class="n">edges</span><span class="p">:</span>
+ <span class="n">f</span><span class="o">.</span><span class="n">write</span><span class="p">(</span><span class="sa">f</span><span class="s2">"CONECT</span><span class="si">{</span><span class="n">a1</span><span class="si">:</span><span class="s2">5d</span><span class="si">}{</span><span class="n">a2</span><span class="si">:</span><span class="s2">5d</span><span class="si">}</span><span class="se">\n</span><span class="s2">"</span><span class="p">)</span>
+
+ <span class="c1"># Write end of file</span>
+ <span class="n">f</span><span class="o">.</span><span class="n">write</span><span class="p">(</span><span class="s2">"END</span><span class="se">\n</span><span class="s2">"</span><span class="p">)</span>
+
+ <span class="n">logger</span><span class="o">.</span><span class="n">info</span><span class="p">(</span><span class="sa">f</span><span class="s2">"Saved aligned mesh as PDB: </span><span class="si">{</span><span class="n">output_file</span><span class="si">}</span><span class="s2">"</span><span class="p">)</span></div>
+
+
+<div class="viewcode-block" id="SurfaceMeshProcessor.save_aligned_mesh_both_formats">
+<a class="viewcode-back" href="../../api/rigidbody_models/mesh_process_surface.html#arbdmodel.mesh_process_surface.SurfaceMeshProcessor.save_aligned_mesh_both_formats">[docs]</a>
+ <span class="k">def</span><span class="w"> </span><span class="nf">save_aligned_mesh_both_formats</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">base_filename</span><span class="p">):</span>
+<span class="w"> </span><span class="sd">"""Save the aligned mesh in both MSH and PDB formats"""</span>
+ <span class="c1"># Save as MSH (in microns)</span>
+ <span class="n">msh_filename</span> <span class="o">=</span> <span class="sa">f</span><span class="s2">"</span><span class="si">{</span><span class="n">base_filename</span><span class="si">}</span><span class="s2">.msh"</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">save_aligned_mesh</span><span class="p">(</span><span class="n">msh_filename</span><span class="p">)</span>
+ <span class="n">logger</span><span class="o">.</span><span class="n">info</span><span class="p">(</span><span class="sa">f</span><span class="s2">"Saved aligned mesh as MSH: </span><span class="si">{</span><span class="n">msh_filename</span><span class="si">}</span><span class="s2">"</span><span class="p">)</span>
+
+ <span class="c1"># Save as PDB (in Ångströms)</span>
+ <span class="n">pdb_filename</span> <span class="o">=</span> <span class="sa">f</span><span class="s2">"</span><span class="si">{</span><span class="n">base_filename</span><span class="si">}</span><span class="s2">.pdb"</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">save_as_pdb</span><span class="p">(</span><span class="n">pdb_filename</span><span class="p">)</span>
+ <span class="n">logger</span><span class="o">.</span><span class="n">info</span><span class="p">(</span><span class="sa">f</span><span class="s2">"Saved aligned mesh as PDB: </span><span class="si">{</span><span class="n">pdb_filename</span><span class="si">}</span><span class="s2">"</span><span class="p">)</span></div>
+</div>
+
+
+
+<div class="viewcode-block" id="process_surface_mesh">
+<a class="viewcode-back" href="../../api/rigidbody_models/mesh_process_surface.html#arbdmodel.mesh_process_surface.process_surface_mesh">[docs]</a>
+<span class="k">def</span><span class="w"> </span><span class="nf">process_surface_mesh</span><span class="p">(</span><span class="n">mesh_file</span><span class="p">,</span> <span class="n">density</span><span class="o">=</span><span class="mf">19.3</span><span class="p">,</span> <span class="n">temperature</span><span class="o">=</span><span class="mi">303</span><span class="p">,</span> <span class="n">viscosity</span><span class="o">=</span><span class="mf">0.01</span><span class="p">,</span>
+ <span class="n">solvent_density</span><span class="o">=</span><span class="mf">1.0</span><span class="p">,</span> <span class="n">output_dx</span><span class="o">=</span><span class="s2">"surface_potential.dx"</span><span class="p">,</span>
+ <span class="n">output_mesh</span><span class="o">=</span><span class="s2">"aligned_surface.msh"</span><span class="p">,</span> <span class="n">binary_path</span><span class="o">=</span><span class="kc">None</span><span class="p">,</span> <span class="o">**</span><span class="n">kwargs</span><span class="p">):</span>
+<span class="w"> </span><span class="sd">"""</span>
+<span class="sd"> Process surface mesh file and calculate all properties</span>
+<span class="sd"> </span>
+<span class="sd"> Args:</span>
+<span class="sd"> mesh_file: Path to .msh file containing surface triangles</span>
+<span class="sd"> density: Material density in g/cm³</span>
+<span class="sd"> temperature: Temperature in Kelvin</span>
+<span class="sd"> viscosity: Solvent viscosity in poise</span>
+<span class="sd"> solvent_density: Solvent density in g/cm³</span>
+<span class="sd"> output_dx: Optional path to output potential DX file</span>
+<span class="sd"> output_mesh: Optional path to save aligned mesh</span>
+<span class="sd"> binary_path: Path to HydroPro executable</span>
+<span class="sd"> expected_mass: Optional expected mass in amu to calibrate calculations</span>
+<span class="sd"> expected_aspect_ratio: Optional expected aspect ratio to calibrate inertia</span>
+<span class="sd"> **kwargs: Additional arguments for potential generation</span>
+<span class="sd"> """</span>
+ <span class="n">processor</span> <span class="o">=</span> <span class="n">SurfaceMeshProcessor</span><span class="p">(</span>
+ <span class="n">mesh_file</span><span class="p">,</span>
+ <span class="n">density</span><span class="o">=</span><span class="n">density</span><span class="p">,</span>
+ <span class="n">temperature</span><span class="o">=</span><span class="n">temperature</span><span class="p">,</span>
+ <span class="n">viscosity</span><span class="o">=</span><span class="n">viscosity</span><span class="p">,</span>
+ <span class="n">solvent_density</span><span class="o">=</span><span class="n">solvent_density</span><span class="p">,</span>
+ <span class="n">binary_path</span><span class="o">=</span><span class="n">binary_path</span><span class="p">,</span>
+ <span class="p">)</span>
+
+ <span class="c1"># Calculate hydrodynamic properties</span>
+ <span class="n">processor</span><span class="o">.</span><span class="n">calculate_damping</span><span class="p">()</span>
+
+ <span class="n">logger</span><span class="o">.</span><span class="n">info</span><span class="p">(</span><span class="sa">f</span><span class="s2">"Mass: </span><span class="si">{</span><span class="n">processor</span><span class="o">.</span><span class="n">mass</span><span class="si">:</span><span class="s2">.3f</span><span class="si">}</span><span class="s2"> amu"</span><span class="p">)</span>
+ <span class="n">logger</span><span class="o">.</span><span class="n">info</span><span class="p">(</span><span class="sa">f</span><span class="s2">"Volume: </span><span class="si">{</span><span class="n">processor</span><span class="o">.</span><span class="n">volume</span><span class="si">:</span><span class="s2">.3f</span><span class="si">}</span><span class="s2"> ų"</span><span class="p">)</span>
+ <span class="n">logger</span><span class="o">.</span><span class="n">info</span><span class="p">(</span><span class="s2">"</span><span class="se">\n</span><span class="s2">Principal moments of inertia:"</span><span class="p">)</span>
+ <span class="n">logger</span><span class="o">.</span><span class="n">info</span><span class="p">(</span><span class="n">processor</span><span class="o">.</span><span class="n">principal_moments</span><span class="p">)</span>
+ <span class="n">logger</span><span class="o">.</span><span class="n">info</span><span class="p">(</span><span class="s2">"</span><span class="se">\n</span><span class="s2">Translational damping coefficients [1/ns]:"</span><span class="p">)</span>
+ <span class="n">logger</span><span class="o">.</span><span class="n">info</span><span class="p">(</span><span class="n">processor</span><span class="o">.</span><span class="n">transdamp</span><span class="p">)</span>
+ <span class="n">logger</span><span class="o">.</span><span class="n">info</span><span class="p">(</span><span class="s2">"</span><span class="se">\n</span><span class="s2">Rotational damping coefficients [1/ns]:"</span><span class="p">)</span>
+ <span class="n">logger</span><span class="o">.</span><span class="n">info</span><span class="p">(</span><span class="n">processor</span><span class="o">.</span><span class="n">rotational_damping_coefficient</span><span class="p">)</span>
+
+ <span class="k">if</span> <span class="n">output_dx</span><span class="p">:</span>
+ <span class="n">processor</span><span class="o">.</span><span class="n">write_no_enter_potential_dx</span><span class="p">()</span>
+
+ <span class="k">if</span> <span class="n">output_mesh</span><span class="p">:</span>
+ <span class="n">processor</span><span class="o">.</span><span class="n">save_aligned_mesh</span><span class="p">(</span><span class="n">output_mesh</span><span class="p">)</span>
+
+ <span class="k">return</span> <span class="n">processor</span></div>
+
+
+<span class="k">if</span> <span class="vm">__name__</span> <span class="o">==</span> <span class="s2">"__main__"</span><span class="p">:</span>
+ <span class="n">process_surface_mesh</span><span class="p">(</span><span class="s2">"surface_mesh.msh"</span><span class="p">)</span>
+</pre></div>
+
+ </article>
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+ <h1>Source code for arbdmodel.mesh_process_volume</h1><div class="highlight"><pre>
+<span></span><span class="kn">import</span><span class="w"> </span><span class="nn">numpy</span><span class="w"> </span><span class="k">as</span><span class="w"> </span><span class="nn">np</span>
+<span class="kn">import</span><span class="w"> </span><span class="nn">gmsh</span>
+<span class="kn">from</span><span class="w"> </span><span class="nn">scipy.spatial</span><span class="w"> </span><span class="kn">import</span> <span class="n">KDTree</span>
+<span class="kn">from</span><span class="w"> </span><span class="nn">pathlib</span><span class="w"> </span><span class="kn">import</span> <span class="n">Path</span>
+<span class="kn">import</span><span class="w"> </span><span class="nn">os</span>
+<span class="kn">from</span><span class="w"> </span><span class="nn">.grid</span><span class="w"> </span><span class="kn">import</span> <span class="n">writeDx</span>
+<span class="kn">from</span><span class="w"> </span><span class="nn">.engine</span><span class="w"> </span><span class="kn">import</span> <span class="n">HydroProRunner</span>
+<span class="kn">from</span><span class="w"> </span><span class="nn">.logger</span><span class="w"> </span><span class="kn">import</span> <span class="n">logger</span>
+
+<span class="sd">"""</span>
+<span class="sd">Improved mesh processor with corrected inertia calculations based purely on mesh geometry</span>
+<span class="sd">"""</span>
+
+<div class="viewcode-block" id="MeshProcessor">
+<a class="viewcode-back" href="../../api/rigidbody_models/mesh_process_volume.html#arbdmodel.mesh_process_volume.MeshProcessor">[docs]</a>
+<span class="k">class</span><span class="w"> </span><span class="nc">MeshProcessor</span><span class="p">:</span>
+<span class="w"> </span><span class="sd">"""Process gmsh files to calculate inertia, hydrodynamics and generate potential fields"""</span>
+ <span class="c1"># Conversion factors</span>
+ <span class="n">MICRON_TO_ANGSTROM</span> <span class="o">=</span> <span class="mi">10000</span>
+
+ <span class="k">def</span><span class="w"> </span><span class="fm">__init__</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">mesh_file</span><span class="p">,</span> <span class="n">density</span><span class="o">=</span><span class="mf">19.3</span><span class="p">,</span> <span class="n">simconf</span><span class="o">=</span><span class="kc">None</span><span class="p">,</span> <span class="n">unit_scale</span><span class="o">=</span><span class="n">MICRON_TO_ANGSTROM</span><span class="p">,</span>
+ <span class="n">work_dir</span><span class="o">=</span><span class="kc">None</span><span class="p">,</span> <span class="n">expected_mass</span><span class="o">=</span><span class="kc">None</span><span class="p">):</span>
+<span class="w"> </span><span class="sd">"""</span>
+<span class="sd"> Initialize processor with mesh file</span>
+<span class="sd"> </span>
+<span class="sd"> Args:</span>
+<span class="sd"> mesh_file: Path to .msh file</span>
+<span class="sd"> density: Material density in g/cm^3</span>
+<span class="sd"> simconf: SimConf object containing configuration parameters</span>
+<span class="sd"> unit_scale: Conversion factor from input units to angstroms</span>
+<span class="sd"> work_dir: Working directory</span>
+<span class="sd"> expected_mass: Optional expected mass in amu to calibrate calculations</span>
+<span class="sd"> """</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">mesh_file</span> <span class="o">=</span> <span class="n">Path</span><span class="p">(</span><span class="n">mesh_file</span><span class="p">)</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">density</span> <span class="o">=</span> <span class="n">density</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">unit_scale</span> <span class="o">=</span> <span class="n">unit_scale</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">expected_mass</span> <span class="o">=</span> <span class="n">expected_mass</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">work_dir</span> <span class="o">=</span> <span class="n">Path</span><span class="p">(</span><span class="n">work_dir</span><span class="p">)</span> <span class="k">if</span> <span class="n">work_dir</span> <span class="k">else</span> <span class="n">Path</span><span class="o">.</span><span class="n">cwd</span><span class="p">()</span>
+ <span class="n">os</span><span class="o">.</span><span class="n">makedirs</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">work_dir</span><span class="p">,</span> <span class="n">exist_ok</span><span class="o">=</span><span class="kc">True</span><span class="p">)</span>
+
+ <span class="k">if</span> <span class="n">simconf</span> <span class="ow">is</span> <span class="kc">None</span><span class="p">:</span>
+ <span class="kn">from</span><span class="w"> </span><span class="nn">.</span><span class="w"> </span><span class="kn">import</span> <span class="n">DefaultSimConf</span>
+ <span class="n">simconf</span><span class="o">=</span><span class="n">DefaultSimConf</span><span class="p">()</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">simconf</span><span class="o">=</span><span class="n">simconf</span>
+
+
+ <span class="c1"># Extract parameters from simconf</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">temperature</span> <span class="o">=</span> <span class="n">simconf</span><span class="o">.</span><span class="n">temperature</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">viscosity</span> <span class="o">=</span> <span class="n">simconf</span><span class="o">.</span><span class="n">viscosity</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">solvent_density</span> <span class="o">=</span> <span class="n">simconf</span><span class="o">.</span><span class="n">solvent_density</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">binary_path</span> <span class="o">=</span> <span class="n">simconf</span><span class="o">.</span><span class="n">get_binary</span><span class="p">(</span><span class="s1">'hydropro'</span><span class="p">)</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">name</span> <span class="o">=</span> <span class="nb">str</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">mesh_file</span><span class="o">.</span><span class="n">stem</span><span class="p">)</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">attached_patricles</span><span class="o">=</span><span class="p">[]</span>
+
+ <span class="c1"># Initialize gmsh and read mesh</span>
+ <span class="n">gmsh</span><span class="o">.</span><span class="n">initialize</span><span class="p">()</span>
+ <span class="k">try</span><span class="p">:</span>
+ <span class="n">gmsh</span><span class="o">.</span><span class="n">open</span><span class="p">(</span><span class="nb">str</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">mesh_file</span><span class="p">))</span>
+ <span class="n">logger</span><span class="o">.</span><span class="n">info</span><span class="p">(</span><span class="sa">f</span><span class="s2">"Successfully opened mesh file: </span><span class="si">{</span><span class="bp">self</span><span class="o">.</span><span class="n">mesh_file</span><span class="si">}</span><span class="s2">"</span><span class="p">)</span>
+
+ <span class="c1"># First, load the full volumetric mesh for physical calculations</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">volume_nodes</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">_get_nodes</span><span class="p">()</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">volume_elements</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">_get_elements</span><span class="p">()</span>
+ <span class="n">logger</span><span class="o">.</span><span class="n">info</span><span class="p">(</span><span class="sa">f</span><span class="s2">"Loaded </span><span class="si">{</span><span class="nb">len</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">volume_nodes</span><span class="p">)</span><span class="si">}</span><span class="s2"> nodes and </span><span class="si">{</span><span class="nb">len</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">volume_elements</span><span class="p">)</span><span class="si">}</span><span class="s2"> elements from volume mesh"</span><span class="p">)</span>
+
+ <span class="c1"># Then extract surface mesh for visualization and HydroPro</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">nodes</span><span class="p">,</span> <span class="bp">self</span><span class="o">.</span><span class="n">elements</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">_extract_surface_mesh</span><span class="p">()</span>
+ <span class="n">logger</span><span class="o">.</span><span class="n">info</span><span class="p">(</span><span class="sa">f</span><span class="s2">"Extracted </span><span class="si">{</span><span class="nb">len</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">nodes</span><span class="p">)</span><span class="si">}</span><span class="s2"> nodes and </span><span class="si">{</span><span class="nb">len</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">elements</span><span class="p">)</span><span class="si">}</span><span class="s2"> elements from surface mesh"</span><span class="p">)</span>
+
+ <span class="c1"># Calculate volume using volumetric mesh</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">volume</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">_calculate_volume</span><span class="p">()</span>
+
+ <span class="c1"># Calculate mass with density correction if needed</span>
+ <span class="k">if</span> <span class="bp">self</span><span class="o">.</span><span class="n">expected_mass</span><span class="p">:</span>
+ <span class="c1"># Use expected mass if provided</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">mass</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">expected_mass</span>
+ <span class="c1"># Update density to match expected mass</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">density_correction</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">expected_mass</span> <span class="o">/</span> <span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">volume</span> <span class="o">*</span> <span class="mf">0.6022</span><span class="p">)</span>
+ <span class="n">logger</span><span class="o">.</span><span class="n">info</span><span class="p">(</span><span class="sa">f</span><span class="s2">"Using expected mass: </span><span class="si">{</span><span class="bp">self</span><span class="o">.</span><span class="n">mass</span><span class="si">:</span><span class="s2">.2f</span><span class="si">}</span><span class="s2"> amu (density correction: </span><span class="si">{</span><span class="bp">self</span><span class="o">.</span><span class="n">density_correction</span><span class="si">:</span><span class="s2">.6f</span><span class="si">}</span><span class="s2">)"</span><span class="p">)</span>
+ <span class="k">else</span><span class="p">:</span>
+ <span class="c1"># Convert density from g/cm^3 to amu/Ã…^3</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">mass</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">volume</span> <span class="o">*</span> <span class="bp">self</span><span class="o">.</span><span class="n">density</span> <span class="o">*</span> <span class="mf">0.6022</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">density_correction</span> <span class="o">=</span> <span class="mf">1.0</span>
+
+ <span class="n">logger</span><span class="o">.</span><span class="n">info</span><span class="p">(</span><span class="sa">f</span><span class="s2">"Calculated volume: </span><span class="si">{</span><span class="bp">self</span><span class="o">.</span><span class="n">volume</span><span class="si">:</span><span class="s2">.2f</span><span class="si">}</span><span class="s2"> ų"</span><span class="p">)</span>
+ <span class="n">logger</span><span class="o">.</span><span class="n">info</span><span class="p">(</span><span class="sa">f</span><span class="s2">"Calculated mass: </span><span class="si">{</span><span class="bp">self</span><span class="o">.</span><span class="n">mass</span><span class="si">:</span><span class="s2">.2f</span><span class="si">}</span><span class="s2"> amu"</span><span class="p">)</span>
+
+ <span class="c1"># Align both meshes to center of mass and principal axes</span>
+ <span class="c1"># Important: Center of mass calculation needs to be fixed to use the volumetric mesh</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">_align_mesh</span><span class="p">()</span>
+
+ <span class="c1"># Calculate inertia tensor using volumetric mesh with corrected method</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">inertia_tensor</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">_calculate_correct_inertia_tensor</span><span class="p">()</span>
+
+ <span class="bp">self</span><span class="o">.</span><span class="n">principal_moments</span> <span class="o">=</span> <span class="n">np</span><span class="o">.</span><span class="n">diag</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">inertia_tensor</span><span class="p">)</span>
+ <span class="n">logger</span><span class="o">.</span><span class="n">info</span><span class="p">(</span><span class="sa">f</span><span class="s2">"Principal moments of inertia: </span><span class="si">{</span><span class="bp">self</span><span class="o">.</span><span class="n">principal_moments</span><span class="si">}</span><span class="s2">"</span><span class="p">)</span>
+
+ <span class="k">except</span> <span class="ne">Exception</span> <span class="k">as</span> <span class="n">e</span><span class="p">:</span>
+ <span class="n">logger</span><span class="o">.</span><span class="n">info</span><span class="p">(</span><span class="sa">f</span><span class="s2">"Error processing mesh: </span><span class="si">{</span><span class="n">e</span><span class="si">}</span><span class="s2">"</span><span class="p">)</span>
+ <span class="k">raise</span>
+ <span class="k">finally</span><span class="p">:</span>
+ <span class="n">gmsh</span><span class="o">.</span><span class="n">finalize</span><span class="p">()</span>
+
+<div class="viewcode-block" id="MeshProcessor.get_attached_particles">
+<a class="viewcode-back" href="../../api/rigidbody_models/mesh_process_volume.html#arbdmodel.mesh_process_volume.MeshProcessor.get_attached_particles">[docs]</a>
+ <span class="k">def</span><span class="w"> </span><span class="nf">get_attached_particles</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span>
+ <span class="kn">from</span><span class="w"> </span><span class="nn">.</span><span class="w"> </span><span class="kn">import</span> <span class="n">ParticleType</span><span class="p">,</span> <span class="n">PointParticle</span>
+ <span class="n">rbp</span><span class="o">=</span><span class="n">ParticleType</span><span class="p">(</span><span class="n">name</span><span class="o">=</span><span class="sa">f</span><span class="s2">"</span><span class="si">{</span><span class="bp">self</span><span class="o">.</span><span class="n">name</span><span class="si">}</span><span class="s2">_attached"</span><span class="p">,</span> <span class="n">mass</span><span class="o">=</span><span class="mi">1</span><span class="p">,</span><span class="n">diffusivity</span><span class="o">=</span><span class="mi">1</span><span class="p">)</span>
+ <span class="n">logger</span><span class="o">.</span><span class="n">info</span><span class="p">(</span><span class="sa">f</span><span class="s2">"attaching particles type </span><span class="si">{</span><span class="bp">self</span><span class="o">.</span><span class="n">name</span><span class="si">}</span><span class="s2">_attached using mesh nodes"</span><span class="p">)</span>
+
+ <span class="k">for</span> <span class="n">i</span><span class="p">,</span> <span class="n">node</span> <span class="ow">in</span> <span class="nb">enumerate</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">nodes</span><span class="p">):</span>
+ <span class="n">x</span><span class="p">,</span> <span class="n">y</span><span class="p">,</span> <span class="n">z</span> <span class="o">=</span> <span class="n">node</span>
+ <span class="n">rbpi</span><span class="o">=</span><span class="n">PointParticle</span><span class="p">(</span><span class="n">rbp</span><span class="p">,</span><span class="n">name</span><span class="o">=</span><span class="sa">f</span><span class="s2">"</span><span class="si">{</span><span class="bp">self</span><span class="o">.</span><span class="n">name</span><span class="si">}</span><span class="s2">_</span><span class="si">{</span><span class="n">i</span><span class="si">}</span><span class="s2">"</span><span class="p">,</span><span class="n">position</span><span class="o">=</span><span class="p">[</span><span class="n">x</span><span class="p">,</span><span class="n">y</span><span class="p">,</span><span class="n">z</span><span class="p">])</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">attached_patricles</span><span class="o">.</span><span class="n">append</span><span class="p">(</span><span class="n">rbpi</span><span class="p">)</span>
+
+ <span class="k">return</span> <span class="bp">self</span><span class="o">.</span><span class="n">attached_patricles</span></div>
+
+
+ <span class="k">def</span><span class="w"> </span><span class="nf">_get_nodes</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span>
+<span class="w"> </span><span class="sd">"""Get all mesh nodes with unit conversion"""</span>
+ <span class="n">node_tags</span><span class="p">,</span> <span class="n">node_coords</span><span class="p">,</span> <span class="n">_</span> <span class="o">=</span> <span class="n">gmsh</span><span class="o">.</span><span class="n">model</span><span class="o">.</span><span class="n">mesh</span><span class="o">.</span><span class="n">getNodes</span><span class="p">()</span>
+ <span class="n">coords</span> <span class="o">=</span> <span class="n">np</span><span class="o">.</span><span class="n">array</span><span class="p">(</span><span class="n">node_coords</span><span class="p">)</span><span class="o">.</span><span class="n">reshape</span><span class="p">(</span><span class="o">-</span><span class="mi">1</span><span class="p">,</span> <span class="mi">3</span><span class="p">)</span>
+ <span class="k">return</span> <span class="n">coords</span> <span class="o">*</span> <span class="bp">self</span><span class="o">.</span><span class="n">unit_scale</span> <span class="c1"># Convert to angstroms</span>
+
+ <span class="k">def</span><span class="w"> </span><span class="nf">_get_elements</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span>
+<span class="w"> </span><span class="sd">"""Get tetrahedral elements from the volume mesh"""</span>
+ <span class="n">element_types</span><span class="p">,</span> <span class="n">element_tags</span><span class="p">,</span> <span class="n">node_tags</span> <span class="o">=</span> <span class="n">gmsh</span><span class="o">.</span><span class="n">model</span><span class="o">.</span><span class="n">mesh</span><span class="o">.</span><span class="n">getElements</span><span class="p">(</span><span class="n">dim</span><span class="o">=</span><span class="mi">3</span><span class="p">)</span>
+ <span class="k">if</span> <span class="ow">not</span> <span class="n">element_types</span><span class="p">:</span> <span class="c1"># No volume elements found</span>
+ <span class="n">logger</span><span class="o">.</span><span class="n">error</span><span class="p">(</span><span class="s2">"No tetrahedral elements found in mesh"</span><span class="p">)</span>
+
+ <span class="c1"># Find tetrahedral elements (type 4 in gmsh)</span>
+ <span class="n">tet_idx</span> <span class="o">=</span> <span class="kc">None</span>
+ <span class="k">for</span> <span class="n">i</span><span class="p">,</span> <span class="n">type_num</span> <span class="ow">in</span> <span class="nb">enumerate</span><span class="p">(</span><span class="n">element_types</span><span class="p">):</span>
+ <span class="k">if</span> <span class="n">type_num</span> <span class="o">==</span> <span class="mi">4</span><span class="p">:</span> <span class="c1"># Tetrahedral elements</span>
+ <span class="n">tet_idx</span> <span class="o">=</span> <span class="n">i</span>
+ <span class="k">break</span>
+
+ <span class="k">if</span> <span class="n">tet_idx</span> <span class="ow">is</span> <span class="kc">None</span><span class="p">:</span>
+ <span class="n">logger</span><span class="o">.</span><span class="n">error</span><span class="p">(</span><span class="s2">"No tetrahedral elements found in mesh"</span><span class="p">)</span>
+ <span class="c1"># Convert to 0-based indexing and reshape to Nx4 array</span>
+ <span class="k">try</span><span class="p">:</span>
+ <span class="n">elements</span> <span class="o">=</span> <span class="n">np</span><span class="o">.</span><span class="n">array</span><span class="p">(</span><span class="n">node_tags</span><span class="p">[</span><span class="n">tet_idx</span><span class="p">])</span><span class="o">.</span><span class="n">reshape</span><span class="p">(</span><span class="o">-</span><span class="mi">1</span><span class="p">,</span> <span class="mi">4</span><span class="p">)</span> <span class="o">-</span> <span class="mi">1</span>
+ <span class="k">except</span><span class="p">:</span>
+ <span class="n">logger</span><span class="o">.</span><span class="n">error</span><span class="p">(</span><span class="s2">"You are not using a volume mesh"</span><span class="p">)</span>
+ <span class="k">return</span> <span class="n">elements</span>
+
+ <span class="k">def</span><span class="w"> </span><span class="nf">_extract_surface_mesh</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span>
+<span class="w"> </span><span class="sd">"""Extract surface mesh from a 3D volumetric mesh"""</span>
+ <span class="c1"># Get 3D elements</span>
+ <span class="n">dim3_entities</span> <span class="o">=</span> <span class="n">gmsh</span><span class="o">.</span><span class="n">model</span><span class="o">.</span><span class="n">getEntities</span><span class="p">(</span><span class="mi">3</span><span class="p">)</span>
+ <span class="k">if</span> <span class="ow">not</span> <span class="n">dim3_entities</span><span class="p">:</span>
+ <span class="n">logger</span><span class="o">.</span><span class="n">error</span><span class="p">(</span><span class="s2">"No 3D volume elements found in mesh"</span><span class="p">)</span>
+
+ <span class="n">logger</span><span class="o">.</span><span class="n">info</span><span class="p">(</span><span class="s2">"Found 3D volumetric mesh, extracting surface..."</span><span class="p">)</span>
+
+ <span class="c1"># Create topology for boundary extraction</span>
+ <span class="n">gmsh</span><span class="o">.</span><span class="n">model</span><span class="o">.</span><span class="n">mesh</span><span class="o">.</span><span class="n">createTopology</span><span class="p">()</span>
+
+ <span class="c1"># Get surface elements</span>
+ <span class="n">surface_dimtags</span> <span class="o">=</span> <span class="n">gmsh</span><span class="o">.</span><span class="n">model</span><span class="o">.</span><span class="n">getBoundary</span><span class="p">([(</span><span class="mi">3</span><span class="p">,</span> <span class="n">tag</span><span class="p">)</span> <span class="k">for</span> <span class="n">dim</span><span class="p">,</span> <span class="n">tag</span> <span class="ow">in</span> <span class="n">dim3_entities</span><span class="p">],</span>
+ <span class="n">combined</span><span class="o">=</span><span class="kc">False</span><span class="p">,</span> <span class="n">oriented</span><span class="o">=</span><span class="kc">False</span><span class="p">)</span>
+
+ <span class="c1"># Create a new physical group for the surface</span>
+ <span class="n">surface_tag</span> <span class="o">=</span> <span class="n">gmsh</span><span class="o">.</span><span class="n">model</span><span class="o">.</span><span class="n">addPhysicalGroup</span><span class="p">(</span><span class="mi">2</span><span class="p">,</span> <span class="p">[</span><span class="n">tag</span> <span class="k">for</span> <span class="n">dim</span><span class="p">,</span> <span class="n">tag</span> <span class="ow">in</span> <span class="n">surface_dimtags</span><span class="p">])</span>
+
+ <span class="c1"># Get nodes associated with surface elements</span>
+ <span class="n">all_surface_nodes</span> <span class="o">=</span> <span class="nb">set</span><span class="p">()</span>
+ <span class="n">surface_elements</span> <span class="o">=</span> <span class="p">[]</span>
+
+ <span class="k">for</span> <span class="n">dim</span><span class="p">,</span> <span class="n">tag</span> <span class="ow">in</span> <span class="n">surface_dimtags</span><span class="p">:</span>
+ <span class="n">element_types</span><span class="p">,</span> <span class="n">element_tags</span><span class="p">,</span> <span class="n">node_tags</span> <span class="o">=</span> <span class="n">gmsh</span><span class="o">.</span><span class="n">model</span><span class="o">.</span><span class="n">mesh</span><span class="o">.</span><span class="n">getElements</span><span class="p">(</span><span class="n">dim</span><span class="p">,</span> <span class="n">tag</span><span class="p">)</span>
+
+ <span class="c1"># We only want triangular elements (type 2)</span>
+ <span class="n">tri_idx</span> <span class="o">=</span> <span class="kc">None</span>
+ <span class="k">for</span> <span class="n">i</span><span class="p">,</span> <span class="n">type_num</span> <span class="ow">in</span> <span class="nb">enumerate</span><span class="p">(</span><span class="n">element_types</span><span class="p">):</span>
+ <span class="k">if</span> <span class="n">type_num</span> <span class="o">==</span> <span class="mi">2</span><span class="p">:</span> <span class="c1"># Triangle elements</span>
+ <span class="n">tri_idx</span> <span class="o">=</span> <span class="n">i</span>
+ <span class="k">break</span>
+
+ <span class="k">if</span> <span class="n">tri_idx</span> <span class="ow">is</span> <span class="ow">not</span> <span class="kc">None</span><span class="p">:</span>
+ <span class="n">node_tags_array</span> <span class="o">=</span> <span class="n">np</span><span class="o">.</span><span class="n">array</span><span class="p">(</span><span class="n">node_tags</span><span class="p">[</span><span class="n">tri_idx</span><span class="p">])</span><span class="o">.</span><span class="n">reshape</span><span class="p">(</span><span class="o">-</span><span class="mi">1</span><span class="p">,</span> <span class="mi">3</span><span class="p">)</span> <span class="o">-</span> <span class="mi">1</span> <span class="c1"># Convert to 0-based</span>
+ <span class="n">surface_elements</span><span class="o">.</span><span class="n">extend</span><span class="p">(</span><span class="n">node_tags_array</span><span class="p">)</span>
+ <span class="n">all_surface_nodes</span><span class="o">.</span><span class="n">update</span><span class="p">(</span><span class="n">node_tags_array</span><span class="o">.</span><span class="n">flatten</span><span class="p">())</span>
+
+ <span class="c1"># Get coordinates of surface nodes</span>
+ <span class="n">surface_nodes</span> <span class="o">=</span> <span class="p">[]</span>
+ <span class="n">node_index_map</span> <span class="o">=</span> <span class="p">{}</span> <span class="c1"># Map old indices to new ones</span>
+
+ <span class="k">for</span> <span class="n">i</span><span class="p">,</span> <span class="n">old_idx</span> <span class="ow">in</span> <span class="nb">enumerate</span><span class="p">(</span><span class="nb">sorted</span><span class="p">(</span><span class="n">all_surface_nodes</span><span class="p">)):</span>
+ <span class="n">coords</span> <span class="o">=</span> <span class="n">gmsh</span><span class="o">.</span><span class="n">model</span><span class="o">.</span><span class="n">mesh</span><span class="o">.</span><span class="n">getNode</span><span class="p">(</span><span class="nb">int</span><span class="p">(</span><span class="n">old_idx</span> <span class="o">+</span> <span class="mi">1</span><span class="p">))[</span><span class="mi">0</span><span class="p">]</span> <span class="c1"># +1 because gmsh uses 1-based indexing</span>
+ <span class="n">surface_nodes</span><span class="o">.</span><span class="n">append</span><span class="p">(</span><span class="n">coords</span><span class="p">)</span>
+ <span class="n">node_index_map</span><span class="p">[</span><span class="n">old_idx</span><span class="p">]</span> <span class="o">=</span> <span class="n">i</span>
+
+ <span class="c1"># Remap element indices</span>
+ <span class="n">remapped_elements</span> <span class="o">=</span> <span class="p">[]</span>
+ <span class="k">for</span> <span class="n">element</span> <span class="ow">in</span> <span class="n">surface_elements</span><span class="p">:</span>
+ <span class="n">remapped_elements</span><span class="o">.</span><span class="n">append</span><span class="p">([</span><span class="n">node_index_map</span><span class="p">[</span><span class="n">idx</span><span class="p">]</span> <span class="k">for</span> <span class="n">idx</span> <span class="ow">in</span> <span class="n">element</span><span class="p">])</span>
+
+ <span class="c1"># Convert to numpy arrays and apply unit conversion</span>
+ <span class="n">nodes</span> <span class="o">=</span> <span class="n">np</span><span class="o">.</span><span class="n">array</span><span class="p">(</span><span class="n">surface_nodes</span><span class="p">)</span> <span class="o">*</span> <span class="bp">self</span><span class="o">.</span><span class="n">unit_scale</span>
+ <span class="n">elements</span> <span class="o">=</span> <span class="n">np</span><span class="o">.</span><span class="n">array</span><span class="p">(</span><span class="n">remapped_elements</span><span class="p">)</span>
+
+ <span class="k">return</span> <span class="n">nodes</span><span class="p">,</span> <span class="n">elements</span>
+
+ <span class="k">def</span><span class="w"> </span><span class="nf">_calculate_correct_inertia_tensor</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span>
+<span class="w"> </span><span class="sd">"""Calculate inertia tensor correctly using tetrahedral elements from the volume mesh"""</span>
+ <span class="c1"># Initialize inertia tensor</span>
+ <span class="n">inertia</span> <span class="o">=</span> <span class="n">np</span><span class="o">.</span><span class="n">zeros</span><span class="p">((</span><span class="mi">3</span><span class="p">,</span> <span class="mi">3</span><span class="p">))</span>
+
+ <span class="c1"># Set density (including any correction factors)</span>
+ <span class="k">if</span> <span class="nb">hasattr</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="s1">'density_correction'</span><span class="p">):</span>
+ <span class="n">effective_density</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">density</span> <span class="o">*</span> <span class="bp">self</span><span class="o">.</span><span class="n">density_correction</span>
+ <span class="k">else</span><span class="p">:</span>
+ <span class="n">effective_density</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">density</span>
+
+ <span class="c1"># Conversion factor from g/cm^3 to amu/Ã…^3</span>
+ <span class="n">density_amu</span> <span class="o">=</span> <span class="n">effective_density</span> <span class="o">*</span> <span class="mf">0.6022</span>
+
+ <span class="c1"># For each tetrahedral element</span>
+ <span class="k">for</span> <span class="n">element</span> <span class="ow">in</span> <span class="bp">self</span><span class="o">.</span><span class="n">volume_elements</span><span class="p">:</span>
+ <span class="c1"># Get vertices of tetrahedron</span>
+ <span class="n">v0</span><span class="p">,</span> <span class="n">v1</span><span class="p">,</span> <span class="n">v2</span><span class="p">,</span> <span class="n">v3</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">volume_nodes</span><span class="p">[</span><span class="n">element</span><span class="p">]</span>
+
+ <span class="c1"># Calculate volume of tetrahedron</span>
+ <span class="c1"># V = (1/6) * |((v1-v0) × (v2-v0)) · (v3-v0)|</span>
+ <span class="n">v01</span> <span class="o">=</span> <span class="n">v1</span> <span class="o">-</span> <span class="n">v0</span>
+ <span class="n">v02</span> <span class="o">=</span> <span class="n">v2</span> <span class="o">-</span> <span class="n">v0</span>
+ <span class="n">v03</span> <span class="o">=</span> <span class="n">v3</span> <span class="o">-</span> <span class="n">v0</span>
+ <span class="n">volume</span> <span class="o">=</span> <span class="nb">abs</span><span class="p">(</span><span class="n">np</span><span class="o">.</span><span class="n">dot</span><span class="p">(</span><span class="n">np</span><span class="o">.</span><span class="n">cross</span><span class="p">(</span><span class="n">v01</span><span class="p">,</span> <span class="n">v02</span><span class="p">),</span> <span class="n">v03</span><span class="p">))</span> <span class="o">/</span> <span class="mf">6.0</span>
+
+ <span class="c1"># Mass of tetrahedron</span>
+ <span class="n">tetra_mass</span> <span class="o">=</span> <span class="n">volume</span> <span class="o">*</span> <span class="n">density_amu</span>
+
+ <span class="c1"># Centroid of tetrahedron</span>
+ <span class="n">centroid</span> <span class="o">=</span> <span class="p">(</span><span class="n">v0</span> <span class="o">+</span> <span class="n">v1</span> <span class="o">+</span> <span class="n">v2</span> <span class="o">+</span> <span class="n">v3</span><span class="p">)</span> <span class="o">/</span> <span class="mf">4.0</span>
+
+ <span class="c1"># Tetrahedron inertia tensor calculation</span>
+ <span class="c1"># For a tetrahedron, we need to integrate over the volume</span>
+ <span class="c1"># See: https://en.wikipedia.org/wiki/List_of_moments_of_inertia</span>
+
+ <span class="c1"># Set up vertices relative to centroid</span>
+ <span class="n">vertices_centered</span> <span class="o">=</span> <span class="n">np</span><span class="o">.</span><span class="n">vstack</span><span class="p">([</span>
+ <span class="n">v0</span> <span class="o">-</span> <span class="n">centroid</span><span class="p">,</span>
+ <span class="n">v1</span> <span class="o">-</span> <span class="n">centroid</span><span class="p">,</span>
+ <span class="n">v2</span> <span class="o">-</span> <span class="n">centroid</span><span class="p">,</span>
+ <span class="n">v3</span> <span class="o">-</span> <span class="n">centroid</span>
+ <span class="p">])</span>
+
+ <span class="c1"># Compute the inertia tensor for tetrahedron about its centroid</span>
+ <span class="c1"># We'll use the formula for a general tetrahedron</span>
+ <span class="n">local_inertia</span> <span class="o">=</span> <span class="n">np</span><span class="o">.</span><span class="n">zeros</span><span class="p">((</span><span class="mi">3</span><span class="p">,</span> <span class="mi">3</span><span class="p">))</span>
+
+ <span class="c1"># Set up a matrix with columns for each coordinate</span>
+ <span class="n">x</span> <span class="o">=</span> <span class="n">vertices_centered</span><span class="p">[:,</span> <span class="mi">0</span><span class="p">]</span>
+ <span class="n">y</span> <span class="o">=</span> <span class="n">vertices_centered</span><span class="p">[:,</span> <span class="mi">1</span><span class="p">]</span>
+ <span class="n">z</span> <span class="o">=</span> <span class="n">vertices_centered</span><span class="p">[:,</span> <span class="mi">2</span><span class="p">]</span>
+
+ <span class="c1"># Calculate second moments</span>
+ <span class="n">xx</span> <span class="o">=</span> <span class="n">np</span><span class="o">.</span><span class="n">sum</span><span class="p">(</span><span class="n">x</span> <span class="o">*</span> <span class="n">x</span><span class="p">)</span> <span class="o">/</span> <span class="mf">10.0</span>
+ <span class="n">yy</span> <span class="o">=</span> <span class="n">np</span><span class="o">.</span><span class="n">sum</span><span class="p">(</span><span class="n">y</span> <span class="o">*</span> <span class="n">y</span><span class="p">)</span> <span class="o">/</span> <span class="mf">10.0</span>
+ <span class="n">zz</span> <span class="o">=</span> <span class="n">np</span><span class="o">.</span><span class="n">sum</span><span class="p">(</span><span class="n">z</span> <span class="o">*</span> <span class="n">z</span><span class="p">)</span> <span class="o">/</span> <span class="mf">10.0</span>
+
+ <span class="n">xy</span> <span class="o">=</span> <span class="n">np</span><span class="o">.</span><span class="n">sum</span><span class="p">(</span><span class="n">x</span> <span class="o">*</span> <span class="n">y</span><span class="p">)</span> <span class="o">/</span> <span class="mf">10.0</span>
+ <span class="n">xz</span> <span class="o">=</span> <span class="n">np</span><span class="o">.</span><span class="n">sum</span><span class="p">(</span><span class="n">x</span> <span class="o">*</span> <span class="n">z</span><span class="p">)</span> <span class="o">/</span> <span class="mf">10.0</span>
+ <span class="n">yz</span> <span class="o">=</span> <span class="n">np</span><span class="o">.</span><span class="n">sum</span><span class="p">(</span><span class="n">y</span> <span class="o">*</span> <span class="n">z</span><span class="p">)</span> <span class="o">/</span> <span class="mf">10.0</span>
+
+ <span class="c1"># Fill in the local inertia tensor</span>
+ <span class="n">local_inertia</span><span class="p">[</span><span class="mi">0</span><span class="p">,</span> <span class="mi">0</span><span class="p">]</span> <span class="o">=</span> <span class="n">yy</span> <span class="o">+</span> <span class="n">zz</span>
+ <span class="n">local_inertia</span><span class="p">[</span><span class="mi">1</span><span class="p">,</span> <span class="mi">1</span><span class="p">]</span> <span class="o">=</span> <span class="n">xx</span> <span class="o">+</span> <span class="n">zz</span>
+ <span class="n">local_inertia</span><span class="p">[</span><span class="mi">2</span><span class="p">,</span> <span class="mi">2</span><span class="p">]</span> <span class="o">=</span> <span class="n">xx</span> <span class="o">+</span> <span class="n">yy</span>
+
+ <span class="n">local_inertia</span><span class="p">[</span><span class="mi">0</span><span class="p">,</span> <span class="mi">1</span><span class="p">]</span> <span class="o">=</span> <span class="n">local_inertia</span><span class="p">[</span><span class="mi">1</span><span class="p">,</span> <span class="mi">0</span><span class="p">]</span> <span class="o">=</span> <span class="o">-</span><span class="n">xy</span>
+ <span class="n">local_inertia</span><span class="p">[</span><span class="mi">0</span><span class="p">,</span> <span class="mi">2</span><span class="p">]</span> <span class="o">=</span> <span class="n">local_inertia</span><span class="p">[</span><span class="mi">2</span><span class="p">,</span> <span class="mi">0</span><span class="p">]</span> <span class="o">=</span> <span class="o">-</span><span class="n">xz</span>
+ <span class="n">local_inertia</span><span class="p">[</span><span class="mi">1</span><span class="p">,</span> <span class="mi">2</span><span class="p">]</span> <span class="o">=</span> <span class="n">local_inertia</span><span class="p">[</span><span class="mi">2</span><span class="p">,</span> <span class="mi">1</span><span class="p">]</span> <span class="o">=</span> <span class="o">-</span><span class="n">yz</span>
+
+ <span class="c1"># Scale by mass</span>
+ <span class="n">local_inertia</span> <span class="o">*=</span> <span class="n">tetra_mass</span>
+
+ <span class="c1"># Apply parallel axis theorem to get the inertia tensor about the origin</span>
+ <span class="c1"># I = I_cm + m * (d^2 * I_identity - d ⊗ d)</span>
+ <span class="c1"># where d is the distance vector from the origin to the centroid</span>
+
+ <span class="c1"># Distance squared from origin to centroid</span>
+ <span class="n">d_squared</span> <span class="o">=</span> <span class="n">np</span><span class="o">.</span><span class="n">sum</span><span class="p">(</span><span class="n">centroid</span> <span class="o">*</span> <span class="n">centroid</span><span class="p">)</span>
+
+ <span class="c1"># Dyadic product of centroid vector with itself</span>
+ <span class="n">d_dyadic</span> <span class="o">=</span> <span class="n">np</span><span class="o">.</span><span class="n">outer</span><span class="p">(</span><span class="n">centroid</span><span class="p">,</span> <span class="n">centroid</span><span class="p">)</span>
+
+ <span class="c1"># Parallel axis theorem</span>
+ <span class="n">parallel_axis_correction</span> <span class="o">=</span> <span class="n">tetra_mass</span> <span class="o">*</span> <span class="p">(</span><span class="n">d_squared</span> <span class="o">*</span> <span class="n">np</span><span class="o">.</span><span class="n">eye</span><span class="p">(</span><span class="mi">3</span><span class="p">)</span> <span class="o">-</span> <span class="n">d_dyadic</span><span class="p">)</span>
+
+ <span class="c1"># Add to total inertia</span>
+ <span class="n">inertia</span> <span class="o">+=</span> <span class="n">local_inertia</span> <span class="o">+</span> <span class="n">parallel_axis_correction</span>
+
+ <span class="c1"># Scale inertia tensor to match expected mass if provided</span>
+ <span class="k">if</span> <span class="bp">self</span><span class="o">.</span><span class="n">expected_mass</span><span class="p">:</span>
+ <span class="n">mass_scale</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">expected_mass</span> <span class="o">/</span> <span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">volume</span> <span class="o">*</span> <span class="n">density_amu</span><span class="p">)</span>
+ <span class="n">inertia</span> <span class="o">*=</span> <span class="n">mass_scale</span>
+
+ <span class="c1"># Verify that the inertia tensor is positive-definite</span>
+ <span class="n">eigenvalues</span> <span class="o">=</span> <span class="n">np</span><span class="o">.</span><span class="n">linalg</span><span class="o">.</span><span class="n">eigvalsh</span><span class="p">(</span><span class="n">inertia</span><span class="p">)</span>
+ <span class="k">if</span> <span class="n">np</span><span class="o">.</span><span class="n">any</span><span class="p">(</span><span class="n">eigenvalues</span> <span class="o"><=</span> <span class="mi">0</span><span class="p">):</span>
+ <span class="n">logger</span><span class="o">.</span><span class="n">info</span><span class="p">(</span><span class="s2">"WARNING: Inertia tensor is not positive-definite! Eigenvalues:"</span><span class="p">,</span> <span class="n">eigenvalues</span><span class="p">)</span>
+ <span class="c1"># Fix by making all eigenvalues positive</span>
+ <span class="n">inertia</span> <span class="o">+=</span> <span class="n">np</span><span class="o">.</span><span class="n">eye</span><span class="p">(</span><span class="mi">3</span><span class="p">)</span> <span class="o">*</span> <span class="nb">abs</span><span class="p">(</span><span class="nb">min</span><span class="p">(</span><span class="mi">0</span><span class="p">,</span> <span class="n">np</span><span class="o">.</span><span class="n">min</span><span class="p">(</span><span class="n">eigenvalues</span><span class="p">)))</span> <span class="o">*</span> <span class="mf">1.01</span>
+
+ <span class="k">return</span> <span class="n">inertia</span>
+
+ <span class="k">def</span><span class="w"> </span><span class="nf">_calculate_volume</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span>
+<span class="w"> </span><span class="sd">"""Calculate volume using the tetrahedral elements from volume mesh"""</span>
+ <span class="c1"># For tetrahedral mesh, calculate volume by summing volumes of all tetrahedra</span>
+ <span class="n">total_volume</span> <span class="o">=</span> <span class="mi">0</span>
+
+ <span class="k">for</span> <span class="n">element</span> <span class="ow">in</span> <span class="bp">self</span><span class="o">.</span><span class="n">volume_elements</span><span class="p">:</span>
+ <span class="c1"># Get vertices of tetrahedron</span>
+ <span class="n">v0</span><span class="p">,</span> <span class="n">v1</span><span class="p">,</span> <span class="n">v2</span><span class="p">,</span> <span class="n">v3</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">volume_nodes</span><span class="p">[</span><span class="n">element</span><span class="p">]</span>
+
+ <span class="c1"># Calculate volume of tetrahedron</span>
+ <span class="c1"># V = (1/6) * |((v1-v0) × (v2-v0)) · (v3-v0)|</span>
+ <span class="n">v01</span> <span class="o">=</span> <span class="n">v1</span> <span class="o">-</span> <span class="n">v0</span>
+ <span class="n">v02</span> <span class="o">=</span> <span class="n">v2</span> <span class="o">-</span> <span class="n">v0</span>
+ <span class="n">v03</span> <span class="o">=</span> <span class="n">v3</span> <span class="o">-</span> <span class="n">v0</span>
+ <span class="n">volume</span> <span class="o">=</span> <span class="nb">abs</span><span class="p">(</span><span class="n">np</span><span class="o">.</span><span class="n">dot</span><span class="p">(</span><span class="n">np</span><span class="o">.</span><span class="n">cross</span><span class="p">(</span><span class="n">v01</span><span class="p">,</span> <span class="n">v02</span><span class="p">),</span> <span class="n">v03</span><span class="p">))</span> <span class="o">/</span> <span class="mf">6.0</span>
+
+ <span class="n">total_volume</span> <span class="o">+=</span> <span class="n">volume</span>
+
+ <span class="k">return</span> <span class="n">total_volume</span>
+
+ <span class="k">def</span><span class="w"> </span><span class="nf">_calculate_center_of_mass_volume</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span>
+<span class="w"> </span><span class="sd">"""Calculate center of mass using tetrahedral elements from volume mesh"""</span>
+ <span class="n">com</span> <span class="o">=</span> <span class="n">np</span><span class="o">.</span><span class="n">zeros</span><span class="p">(</span><span class="mi">3</span><span class="p">)</span>
+ <span class="n">total_mass</span> <span class="o">=</span> <span class="mi">0</span>
+
+ <span class="k">for</span> <span class="n">element</span> <span class="ow">in</span> <span class="bp">self</span><span class="o">.</span><span class="n">volume_elements</span><span class="p">:</span>
+ <span class="c1"># Get vertices of tetrahedron</span>
+ <span class="n">v0</span><span class="p">,</span> <span class="n">v1</span><span class="p">,</span> <span class="n">v2</span><span class="p">,</span> <span class="n">v3</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">volume_nodes</span><span class="p">[</span><span class="n">element</span><span class="p">]</span>
+
+ <span class="c1"># Calculate volume</span>
+ <span class="n">v01</span> <span class="o">=</span> <span class="n">v1</span> <span class="o">-</span> <span class="n">v0</span>
+ <span class="n">v02</span> <span class="o">=</span> <span class="n">v2</span> <span class="o">-</span> <span class="n">v0</span>
+ <span class="n">v03</span> <span class="o">=</span> <span class="n">v3</span> <span class="o">-</span> <span class="n">v0</span>
+ <span class="n">volume</span> <span class="o">=</span> <span class="nb">abs</span><span class="p">(</span><span class="n">np</span><span class="o">.</span><span class="n">dot</span><span class="p">(</span><span class="n">np</span><span class="o">.</span><span class="n">cross</span><span class="p">(</span><span class="n">v01</span><span class="p">,</span> <span class="n">v02</span><span class="p">),</span> <span class="n">v03</span><span class="p">))</span> <span class="o">/</span> <span class="mf">6.0</span>
+
+ <span class="c1"># Mass of tetrahedron</span>
+ <span class="n">tetra_mass</span> <span class="o">=</span> <span class="n">volume</span> <span class="o">*</span> <span class="bp">self</span><span class="o">.</span><span class="n">density</span> <span class="o">*</span> <span class="mf">0.6022</span> <span class="c1"># Convert to amu</span>
+
+ <span class="c1"># Centroid of tetrahedron</span>
+ <span class="n">centroid</span> <span class="o">=</span> <span class="p">(</span><span class="n">v0</span> <span class="o">+</span> <span class="n">v1</span> <span class="o">+</span> <span class="n">v2</span> <span class="o">+</span> <span class="n">v3</span><span class="p">)</span> <span class="o">/</span> <span class="mf">4.0</span>
+
+ <span class="c1"># Add weighted contribution</span>
+ <span class="n">com</span> <span class="o">+=</span> <span class="n">centroid</span> <span class="o">*</span> <span class="n">tetra_mass</span>
+ <span class="n">total_mass</span> <span class="o">+=</span> <span class="n">tetra_mass</span>
+
+ <span class="k">return</span> <span class="n">com</span> <span class="o">/</span> <span class="n">total_mass</span> <span class="k">if</span> <span class="n">total_mass</span> <span class="o">></span> <span class="mi">0</span> <span class="k">else</span> <span class="n">np</span><span class="o">.</span><span class="n">zeros</span><span class="p">(</span><span class="mi">3</span><span class="p">)</span>
+
+ <span class="k">def</span><span class="w"> </span><span class="nf">_align_mesh</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span>
+<span class="w"> </span><span class="sd">"""Align mesh to center of mass and principal axes with rod along Z-axis"""</span>
+ <span class="c1"># First center the mesh using volume-based COM calculation</span>
+ <span class="n">com</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">_calculate_center_of_mass_volume</span><span class="p">()</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">volume_nodes</span> <span class="o">-=</span> <span class="n">com</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">nodes</span> <span class="o">-=</span> <span class="n">com</span>
+
+ <span class="c1"># Calculate inertia tensor for initial alignment</span>
+ <span class="n">inertia</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">_calculate_correct_inertia_tensor</span><span class="p">()</span>
+
+ <span class="c1"># Diagonalize to find principal axes</span>
+ <span class="n">eigenvalues</span><span class="p">,</span> <span class="n">eigenvectors</span> <span class="o">=</span> <span class="n">np</span><span class="o">.</span><span class="n">linalg</span><span class="o">.</span><span class="n">eigh</span><span class="p">(</span><span class="n">inertia</span><span class="p">)</span>
+
+ <span class="c1"># Sort by eigenvalues</span>
+ <span class="n">sort_idx</span> <span class="o">=</span> <span class="n">np</span><span class="o">.</span><span class="n">argsort</span><span class="p">(</span><span class="n">eigenvalues</span><span class="p">)</span>
+ <span class="n">eigenvalues</span> <span class="o">=</span> <span class="n">eigenvalues</span><span class="p">[</span><span class="n">sort_idx</span><span class="p">]</span>
+
+ <span class="c1"># For a rod-like object:</span>
+ <span class="c1"># The smallest moment of inertia is along the rod axis</span>
+ <span class="c1"># We want this to be aligned with the Z-axis (index 2)</span>
+
+ <span class="c1"># Reordering eigenvectors: </span>
+ <span class="c1"># - smallest moment (rod axis) should be last (Z-axis)</span>
+ <span class="n">z_vec</span> <span class="o">=</span> <span class="n">eigenvectors</span><span class="p">[:,</span> <span class="n">sort_idx</span><span class="p">[</span><span class="mi">0</span><span class="p">]]</span> <span class="c1"># Vector with smallest moment -> Z axis</span>
+ <span class="n">x_vec</span> <span class="o">=</span> <span class="n">eigenvectors</span><span class="p">[:,</span> <span class="n">sort_idx</span><span class="p">[</span><span class="mi">1</span><span class="p">]]</span>
+ <span class="n">y_vec</span> <span class="o">=</span> <span class="n">eigenvectors</span><span class="p">[:,</span> <span class="n">sort_idx</span><span class="p">[</span><span class="mi">2</span><span class="p">]]</span> <span class="c1"># Vector with largest moment -> Y axis</span>
+
+ <span class="c1"># Create new rotation matrix with correctly ordered eigenvectors</span>
+ <span class="n">rotation_matrix</span> <span class="o">=</span> <span class="n">np</span><span class="o">.</span><span class="n">column_stack</span><span class="p">([</span><span class="n">x_vec</span><span class="p">,</span> <span class="n">y_vec</span><span class="p">,</span> <span class="n">z_vec</span><span class="p">])</span>
+
+ <span class="c1"># Ensure right-handed coordinate system</span>
+ <span class="k">if</span> <span class="n">np</span><span class="o">.</span><span class="n">linalg</span><span class="o">.</span><span class="n">det</span><span class="p">(</span><span class="n">rotation_matrix</span><span class="p">)</span> <span class="o"><</span> <span class="mi">0</span><span class="p">:</span>
+ <span class="n">rotation_matrix</span><span class="p">[:,</span> <span class="mi">0</span><span class="p">]</span> <span class="o">*=</span> <span class="o">-</span><span class="mi">1</span> <span class="c1"># Flip X-axis</span>
+
+ <span class="c1"># Apply rotation to both meshes</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">volume_nodes</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">volume_nodes</span> <span class="o">@</span> <span class="n">rotation_matrix</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">nodes</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">nodes</span> <span class="o">@</span> <span class="n">rotation_matrix</span>
+
+ <span class="c1"># Store transformation</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">rotation_matrix</span> <span class="o">=</span> <span class="n">rotation_matrix</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">translation</span> <span class="o">=</span> <span class="n">com</span>
+
+ <span class="c1"># Verify dimensions after alignment</span>
+ <span class="n">bounds_min</span> <span class="o">=</span> <span class="n">np</span><span class="o">.</span><span class="n">min</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">volume_nodes</span><span class="p">,</span> <span class="n">axis</span><span class="o">=</span><span class="mi">0</span><span class="p">)</span>
+ <span class="n">bounds_max</span> <span class="o">=</span> <span class="n">np</span><span class="o">.</span><span class="n">max</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">volume_nodes</span><span class="p">,</span> <span class="n">axis</span><span class="o">=</span><span class="mi">0</span><span class="p">)</span>
+ <span class="n">dimensions</span> <span class="o">=</span> <span class="n">bounds_max</span> <span class="o">-</span> <span class="n">bounds_min</span>
+
+ <span class="n">logger</span><span class="o">.</span><span class="n">info</span><span class="p">(</span><span class="sa">f</span><span class="s2">"Aligned mesh to principal axes, COM: </span><span class="si">{</span><span class="n">com</span><span class="si">}</span><span class="s2">"</span><span class="p">)</span>
+ <span class="n">logger</span><span class="o">.</span><span class="n">info</span><span class="p">(</span><span class="sa">f</span><span class="s2">"Dimensions after alignment (X,Y,Z): </span><span class="si">{</span><span class="n">dimensions</span><span class="si">}</span><span class="s2">"</span><span class="p">)</span>
+
+ <span class="c1"># Calculate aspect ratio after alignment</span>
+ <span class="n">length</span> <span class="o">=</span> <span class="n">dimensions</span><span class="p">[</span><span class="mi">2</span><span class="p">]</span> <span class="c1"># Z dimension (rod axis)</span>
+ <span class="n">width</span> <span class="o">=</span> <span class="nb">max</span><span class="p">(</span><span class="n">dimensions</span><span class="p">[</span><span class="mi">0</span><span class="p">],</span> <span class="n">dimensions</span><span class="p">[</span><span class="mi">1</span><span class="p">])</span> <span class="c1"># Larger of X,Y (transverse)</span>
+ <span class="n">aspect_ratio</span> <span class="o">=</span> <span class="n">length</span> <span class="o">/</span> <span class="n">width</span> <span class="k">if</span> <span class="n">width</span> <span class="o">></span> <span class="mi">0</span> <span class="k">else</span> <span class="mf">1.0</span>
+ <span class="n">logger</span><span class="o">.</span><span class="n">info</span><span class="p">(</span><span class="sa">f</span><span class="s2">"Calculated aspect ratio after alignment: </span><span class="si">{</span><span class="n">aspect_ratio</span><span class="si">:</span><span class="s2">.2f</span><span class="si">}</span><span class="s2">"</span><span class="p">)</span>
+
+<div class="viewcode-block" id="MeshProcessor.calculate_damping">
+<a class="viewcode-back" href="../../api/rigidbody_models/mesh_process_volume.html#arbdmodel.mesh_process_volume.MeshProcessor.calculate_damping">[docs]</a>
+ <span class="k">def</span><span class="w"> </span><span class="nf">calculate_damping</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span>
+<span class="w"> </span><span class="sd">"""Calculate hydrodynamic properties using HydroPro"""</span>
+ <span class="c1"># Create work directory if it doesn't exist</span>
+ <span class="n">work_dir</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">work_dir</span>
+ <span class="k">try</span><span class="p">:</span>
+ <span class="n">os</span><span class="o">.</span><span class="n">listdir</span><span class="p">(</span><span class="n">work_dir</span><span class="p">)</span>
+ <span class="k">except</span><span class="p">:</span>
+ <span class="n">os</span><span class="o">.</span><span class="n">mkdir</span><span class="p">(</span><span class="n">work_dir</span><span class="p">)</span>
+
+ <span class="n">base_path</span> <span class="o">=</span> <span class="n">work_dir</span> <span class="o">/</span> <span class="s2">"hydrocal"</span>
+
+ <span class="c1"># Save the mesh in PDB format for HydroPro</span>
+ <span class="n">pdb_path</span> <span class="o">=</span> <span class="nb">str</span><span class="p">(</span><span class="n">base_path</span><span class="p">)</span> <span class="o">+</span> <span class="s2">".pdb"</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">save_as_pdb</span><span class="p">(</span><span class="n">pdb_path</span><span class="p">)</span>
+
+ <span class="c1"># Run HydroPro to get hydrodynamic properties</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">runner</span> <span class="o">=</span> <span class="n">HydroProRunner</span><span class="p">(</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">mass</span><span class="p">,</span><span class="bp">self</span><span class="o">.</span><span class="n">simconf</span><span class="p">,</span>
+ <span class="n">structure_name</span><span class="o">=</span><span class="s2">"hydrocal"</span><span class="p">,</span><span class="n">cal_type</span><span class="o">=</span><span class="s2">"mesh"</span>
+ <span class="p">)</span>
+
+ <span class="n">results</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">runner</span><span class="o">.</span><span class="n">run_calculation</span><span class="p">(</span><span class="n">work_dir</span><span class="o">=</span><span class="n">work_dir</span><span class="p">)</span>
+
+ <span class="bp">self</span><span class="o">.</span><span class="n">transdamp</span> <span class="o">=</span> <span class="n">results</span><span class="p">[</span><span class="s1">'translation_damping'</span><span class="p">]</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">rotdamp</span> <span class="o">=</span> <span class="n">results</span><span class="p">[</span><span class="s1">'rotation_damping'</span><span class="p">]</span>
+
+ <span class="n">logger</span><span class="o">.</span><span class="n">info</span><span class="p">(</span><span class="sa">f</span><span class="s2">"Translational damping: </span><span class="si">{</span><span class="bp">self</span><span class="o">.</span><span class="n">transdamp</span><span class="si">}</span><span class="s2">"</span><span class="p">)</span>
+ <span class="n">logger</span><span class="o">.</span><span class="n">info</span><span class="p">(</span><span class="sa">f</span><span class="s2">"Rotational damping: </span><span class="si">{</span><span class="bp">self</span><span class="o">.</span><span class="n">rotdamp</span><span class="si">}</span><span class="s2">"</span><span class="p">)</span>
+
+ <span class="k">return</span> <span class="n">pdb_path</span></div>
+
+
+<div class="viewcode-block" id="MeshProcessor.generate_potential_grid">
+<a class="viewcode-back" href="../../api/rigidbody_models/mesh_process_volume.html#arbdmodel.mesh_process_volume.MeshProcessor.generate_potential_grid">[docs]</a>
+ <span class="k">def</span><span class="w"> </span><span class="nf">generate_potential_grid</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">spacing</span><span class="o">=</span><span class="mf">2.0</span><span class="p">,</span> <span class="n">buffer</span><span class="o">=</span><span class="mf">20.0</span><span class="p">,</span> <span class="n">k</span><span class="o">=</span><span class="mf">1.0</span><span class="p">,</span> <span class="n">cutoff</span><span class="o">=</span><span class="mf">10.0</span><span class="p">,</span> <span class="n">max_potential</span><span class="o">=</span><span class="mf">1000.0</span><span class="p">):</span>
+<span class="w"> </span><span class="sd">"""Generate potential grid for ARBD"""</span>
+ <span class="c1"># Calculate grid bounds with buffer</span>
+ <span class="n">bounds_min</span> <span class="o">=</span> <span class="n">np</span><span class="o">.</span><span class="n">min</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">nodes</span><span class="p">,</span> <span class="n">axis</span><span class="o">=</span><span class="mi">0</span><span class="p">)</span> <span class="o">-</span> <span class="n">buffer</span>
+ <span class="n">bounds_max</span> <span class="o">=</span> <span class="n">np</span><span class="o">.</span><span class="n">max</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">nodes</span><span class="p">,</span> <span class="n">axis</span><span class="o">=</span><span class="mi">0</span><span class="p">)</span> <span class="o">+</span> <span class="n">buffer</span>
+
+ <span class="c1"># Create grid points</span>
+ <span class="n">npts</span> <span class="o">=</span> <span class="n">np</span><span class="o">.</span><span class="n">ceil</span><span class="p">((</span><span class="n">bounds_max</span> <span class="o">-</span> <span class="n">bounds_min</span><span class="p">)</span> <span class="o">/</span> <span class="n">spacing</span><span class="p">)</span><span class="o">.</span><span class="n">astype</span><span class="p">(</span><span class="nb">int</span><span class="p">)</span>
+ <span class="n">x</span> <span class="o">=</span> <span class="n">np</span><span class="o">.</span><span class="n">linspace</span><span class="p">(</span><span class="n">bounds_min</span><span class="p">[</span><span class="mi">0</span><span class="p">],</span> <span class="n">bounds_max</span><span class="p">[</span><span class="mi">0</span><span class="p">],</span> <span class="n">npts</span><span class="p">[</span><span class="mi">0</span><span class="p">])</span>
+ <span class="n">y</span> <span class="o">=</span> <span class="n">np</span><span class="o">.</span><span class="n">linspace</span><span class="p">(</span><span class="n">bounds_min</span><span class="p">[</span><span class="mi">1</span><span class="p">],</span> <span class="n">bounds_max</span><span class="p">[</span><span class="mi">1</span><span class="p">],</span> <span class="n">npts</span><span class="p">[</span><span class="mi">1</span><span class="p">])</span>
+ <span class="n">z</span> <span class="o">=</span> <span class="n">np</span><span class="o">.</span><span class="n">linspace</span><span class="p">(</span><span class="n">bounds_min</span><span class="p">[</span><span class="mi">2</span><span class="p">],</span> <span class="n">bounds_max</span><span class="p">[</span><span class="mi">2</span><span class="p">],</span> <span class="n">npts</span><span class="p">[</span><span class="mi">2</span><span class="p">])</span>
+ <span class="n">X</span><span class="p">,</span> <span class="n">Y</span><span class="p">,</span> <span class="n">Z</span> <span class="o">=</span> <span class="n">np</span><span class="o">.</span><span class="n">meshgrid</span><span class="p">(</span><span class="n">x</span><span class="p">,</span> <span class="n">y</span><span class="p">,</span> <span class="n">z</span><span class="p">,</span> <span class="n">indexing</span><span class="o">=</span><span class="s1">'ij'</span><span class="p">)</span>
+
+ <span class="c1"># Create KD-tree for fast distance calculations</span>
+ <span class="n">tree</span> <span class="o">=</span> <span class="n">KDTree</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">nodes</span><span class="p">)</span>
+
+ <span class="c1"># Calculate distances to nearest surface points</span>
+ <span class="n">grid_points</span> <span class="o">=</span> <span class="n">np</span><span class="o">.</span><span class="n">vstack</span><span class="p">([</span><span class="n">X</span><span class="o">.</span><span class="n">ravel</span><span class="p">(),</span> <span class="n">Y</span><span class="o">.</span><span class="n">ravel</span><span class="p">(),</span> <span class="n">Z</span><span class="o">.</span><span class="n">ravel</span><span class="p">()])</span><span class="o">.</span><span class="n">T</span>
+ <span class="n">distances</span><span class="p">,</span> <span class="n">_</span> <span class="o">=</span> <span class="n">tree</span><span class="o">.</span><span class="n">query</span><span class="p">(</span><span class="n">grid_points</span><span class="p">)</span>
+ <span class="n">distances</span> <span class="o">=</span> <span class="n">distances</span><span class="o">.</span><span class="n">reshape</span><span class="p">(</span><span class="n">X</span><span class="o">.</span><span class="n">shape</span><span class="p">)</span>
+
+ <span class="c1"># Generate potential</span>
+ <span class="n">potential</span> <span class="o">=</span> <span class="n">np</span><span class="o">.</span><span class="n">zeros_like</span><span class="p">(</span><span class="n">distances</span><span class="p">)</span>
+ <span class="n">mask</span> <span class="o">=</span> <span class="n">distances</span> <span class="o"><=</span> <span class="n">cutoff</span>
+ <span class="n">potential</span><span class="p">[</span><span class="n">mask</span><span class="p">]</span> <span class="o">=</span> <span class="n">max_potential</span> <span class="o">*</span> <span class="p">(</span><span class="mi">1</span> <span class="o">-</span> <span class="mi">1</span><span class="o">/</span><span class="p">(</span><span class="mi">1</span> <span class="o">+</span> <span class="n">np</span><span class="o">.</span><span class="n">exp</span><span class="p">(</span><span class="o">-</span><span class="n">k</span> <span class="o">*</span> <span class="n">distances</span><span class="p">[</span><span class="n">mask</span><span class="p">])))</span>
+
+ <span class="k">return</span> <span class="n">potential</span><span class="p">,</span> <span class="n">bounds_min</span><span class="p">,</span> <span class="n">spacing</span> <span class="o">*</span> <span class="n">np</span><span class="o">.</span><span class="n">ones</span><span class="p">(</span><span class="mi">3</span><span class="p">)</span></div>
+
+
+<div class="viewcode-block" id="MeshProcessor.write_no_enter_potential">
+<a class="viewcode-back" href="../../api/rigidbody_models/mesh_process_volume.html#arbdmodel.mesh_process_volume.MeshProcessor.write_no_enter_potential">[docs]</a>
+ <span class="k">def</span><span class="w"> </span><span class="nf">write_no_enter_potential</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">output_file</span><span class="o">=</span><span class="kc">None</span><span class="p">,</span> <span class="o">**</span><span class="n">kwargs</span><span class="p">):</span>
+<span class="w"> </span><span class="sd">"""Generate and write potential field to DX file so particles do not fall inside rigidbody."""</span>
+ <span class="k">if</span> <span class="n">output_file</span> <span class="ow">is</span> <span class="kc">None</span><span class="p">:</span>
+ <span class="n">output_file</span><span class="o">=</span><span class="bp">self</span><span class="o">.</span><span class="n">work_dir</span><span class="o">/</span><span class="sa">f</span><span class="s2">"</span><span class="si">{</span><span class="bp">self</span><span class="o">.</span><span class="n">name</span><span class="si">}</span><span class="s2">-no-enter.dx"</span>
+ <span class="k">else</span><span class="p">:</span>
+ <span class="k">if</span> <span class="ow">not</span> <span class="n">os</span><span class="o">.</span><span class="n">path</span><span class="o">.</span><span class="n">isabs</span><span class="p">(</span><span class="n">output_file</span><span class="p">):</span>
+ <span class="n">output_file</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">work_dir</span> <span class="o">/</span> <span class="n">output_file</span>
+
+ <span class="n">potential</span><span class="p">,</span> <span class="n">origin</span><span class="p">,</span> <span class="n">delta</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">generate_potential_grid</span><span class="p">(</span><span class="o">**</span><span class="n">kwargs</span><span class="p">)</span>
+ <span class="n">writeDx</span><span class="p">(</span><span class="n">output_file</span><span class="p">,</span> <span class="n">potential</span><span class="p">,</span> <span class="n">origin</span><span class="p">,</span> <span class="n">delta</span><span class="p">)</span>
+ <span class="k">return</span> <span class="n">output_file</span></div>
+
+
+<div class="viewcode-block" id="MeshProcessor.save_aligned_mesh">
+<a class="viewcode-back" href="../../api/rigidbody_models/mesh_process_volume.html#arbdmodel.mesh_process_volume.MeshProcessor.save_aligned_mesh">[docs]</a>
+ <span class="k">def</span><span class="w"> </span><span class="nf">save_aligned_mesh</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">output_file</span><span class="p">):</span>
+ <span class="k">if</span> <span class="ow">not</span> <span class="n">os</span><span class="o">.</span><span class="n">path</span><span class="o">.</span><span class="n">isabs</span><span class="p">(</span><span class="n">output_file</span><span class="p">):</span>
+ <span class="n">output_file</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">work_dir</span> <span class="o">/</span> <span class="n">output_file</span>
+
+<span class="w"> </span><span class="sd">"""Save the aligned mesh to a new .msh file"""</span>
+ <span class="n">gmsh</span><span class="o">.</span><span class="n">initialize</span><span class="p">()</span>
+ <span class="n">gmsh</span><span class="o">.</span><span class="n">model</span><span class="o">.</span><span class="n">add</span><span class="p">(</span><span class="s2">"aligned_mesh"</span><span class="p">)</span>
+
+ <span class="c1"># For surface mesh</span>
+ <span class="n">entity_dim</span> <span class="o">=</span> <span class="mi">2</span>
+ <span class="n">element_type</span> <span class="o">=</span> <span class="mi">2</span> <span class="c1"># Triangle in gmsh</span>
+
+ <span class="c1"># Add a discrete entity</span>
+ <span class="n">entity_tag</span> <span class="o">=</span> <span class="n">gmsh</span><span class="o">.</span><span class="n">model</span><span class="o">.</span><span class="n">addDiscreteEntity</span><span class="p">(</span><span class="n">entity_dim</span><span class="p">)</span>
+
+ <span class="c1"># Add nodes</span>
+ <span class="n">node_tags</span> <span class="o">=</span> <span class="p">[]</span>
+ <span class="n">node_coords</span> <span class="o">=</span> <span class="p">[]</span>
+ <span class="k">for</span> <span class="n">i</span><span class="p">,</span> <span class="n">node</span> <span class="ow">in</span> <span class="nb">enumerate</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">nodes</span><span class="p">):</span>
+ <span class="n">tag</span> <span class="o">=</span> <span class="n">i</span> <span class="o">+</span> <span class="mi">1</span>
+ <span class="n">node_tags</span><span class="o">.</span><span class="n">append</span><span class="p">(</span><span class="n">tag</span><span class="p">)</span>
+ <span class="n">node_coords</span><span class="o">.</span><span class="n">extend</span><span class="p">(</span><span class="n">node</span> <span class="o">/</span> <span class="bp">self</span><span class="o">.</span><span class="n">unit_scale</span><span class="p">)</span> <span class="c1"># Convert back to mesh units</span>
+
+ <span class="n">gmsh</span><span class="o">.</span><span class="n">model</span><span class="o">.</span><span class="n">mesh</span><span class="o">.</span><span class="n">addNodes</span><span class="p">(</span><span class="n">entity_dim</span><span class="p">,</span> <span class="n">entity_tag</span><span class="p">,</span> <span class="n">node_tags</span><span class="p">,</span> <span class="n">node_coords</span><span class="p">)</span>
+
+ <span class="c1"># Add elements</span>
+ <span class="n">element_tags</span> <span class="o">=</span> <span class="p">[]</span>
+ <span class="n">element_nodes</span> <span class="o">=</span> <span class="p">[]</span>
+ <span class="k">for</span> <span class="n">i</span><span class="p">,</span> <span class="n">element</span> <span class="ow">in</span> <span class="nb">enumerate</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">elements</span><span class="p">):</span>
+ <span class="n">tag</span> <span class="o">=</span> <span class="n">i</span> <span class="o">+</span> <span class="mi">1</span>
+ <span class="n">element_tags</span><span class="o">.</span><span class="n">append</span><span class="p">(</span><span class="n">tag</span><span class="p">)</span>
+ <span class="n">element_nodes</span><span class="o">.</span><span class="n">extend</span><span class="p">([</span><span class="nb">int</span><span class="p">(</span><span class="n">x</span> <span class="o">+</span> <span class="mi">1</span><span class="p">)</span> <span class="k">for</span> <span class="n">x</span> <span class="ow">in</span> <span class="n">element</span><span class="p">])</span> <span class="c1"># Convert to 1-based indexing</span>
+
+ <span class="n">gmsh</span><span class="o">.</span><span class="n">model</span><span class="o">.</span><span class="n">mesh</span><span class="o">.</span><span class="n">addElements</span><span class="p">(</span><span class="n">entity_dim</span><span class="p">,</span> <span class="n">entity_tag</span><span class="p">,</span> <span class="p">[</span><span class="n">element_type</span><span class="p">],</span> <span class="p">[</span><span class="n">element_tags</span><span class="p">],</span> <span class="p">[</span><span class="n">element_nodes</span><span class="p">])</span>
+
+ <span class="c1"># Write mesh</span>
+ <span class="n">gmsh</span><span class="o">.</span><span class="n">write</span><span class="p">(</span><span class="nb">str</span><span class="p">(</span><span class="n">output_file</span><span class="p">))</span>
+ <span class="n">gmsh</span><span class="o">.</span><span class="n">finalize</span><span class="p">()</span></div>
+
+
+<div class="viewcode-block" id="MeshProcessor.save_as_pdb">
+<a class="viewcode-back" href="../../api/rigidbody_models/mesh_process_volume.html#arbdmodel.mesh_process_volume.MeshProcessor.save_as_pdb">[docs]</a>
+ <span class="k">def</span><span class="w"> </span><span class="nf">save_as_pdb</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">output_file</span><span class="p">):</span>
+<span class="w"> </span><span class="sd">"""Save the aligned mesh as a PDB file (coordinates in Ã…)"""</span>
+ <span class="k">if</span> <span class="ow">not</span> <span class="n">os</span><span class="o">.</span><span class="n">path</span><span class="o">.</span><span class="n">isabs</span><span class="p">(</span><span class="n">output_file</span><span class="p">):</span>
+ <span class="n">output_file</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">work_dir</span> <span class="o">/</span> <span class="n">output_file</span>
+ <span class="c1"># PDB format specifications</span>
+ <span class="n">HEADER</span> <span class="o">=</span> <span class="s2">"HEADER ALIGNED MESH "</span>
+ <span class="n">ATOM_FORMAT</span> <span class="o">=</span> <span class="s2">"ATOM </span><span class="si">{:5d}</span><span class="s2"> </span><span class="si">{:4s}</span><span class="s2"> </span><span class="si">{:3s}</span><span class="s2"> </span><span class="si">{:1s}{:4d}</span><span class="s2"> </span><span class="si">{:8.3f}{:8.3f}{:8.3f}{:6.2f}{:6.2f}</span><span class="s2">"</span>
+
+ <span class="k">with</span> <span class="nb">open</span><span class="p">(</span><span class="n">output_file</span><span class="p">,</span> <span class="s1">'w'</span><span class="p">)</span> <span class="k">as</span> <span class="n">f</span><span class="p">:</span>
+ <span class="c1"># Write header</span>
+ <span class="kn">from</span><span class="w"> </span><span class="nn">datetime</span><span class="w"> </span><span class="kn">import</span> <span class="n">datetime</span>
+ <span class="n">date_str</span> <span class="o">=</span> <span class="n">datetime</span><span class="o">.</span><span class="n">now</span><span class="p">()</span><span class="o">.</span><span class="n">strftime</span><span class="p">(</span><span class="s2">"</span><span class="si">%d</span><span class="s2">-%b-%y"</span><span class="p">)</span>
+ <span class="n">f</span><span class="o">.</span><span class="n">write</span><span class="p">(</span><span class="sa">f</span><span class="s2">"</span><span class="si">{</span><span class="n">HEADER</span><span class="si">}{</span><span class="n">date_str</span><span class="si">}</span><span class="s2"> XXXX</span><span class="se">\n</span><span class="s2">"</span><span class="p">)</span>
+
+ <span class="c1"># Calculate box dimensions for CRYST record</span>
+ <span class="n">bounds_min</span> <span class="o">=</span> <span class="n">np</span><span class="o">.</span><span class="n">min</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">nodes</span><span class="p">,</span> <span class="n">axis</span><span class="o">=</span><span class="mi">0</span><span class="p">)</span>
+ <span class="n">bounds_max</span> <span class="o">=</span> <span class="n">np</span><span class="o">.</span><span class="n">max</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">nodes</span><span class="p">,</span> <span class="n">axis</span><span class="o">=</span><span class="mi">0</span><span class="p">)</span>
+ <span class="n">box_dimensions</span> <span class="o">=</span> <span class="n">bounds_max</span> <span class="o">-</span> <span class="n">bounds_min</span>
+
+ <span class="c1"># Write crystallographic information</span>
+ <span class="n">f</span><span class="o">.</span><span class="n">write</span><span class="p">(</span><span class="sa">f</span><span class="s2">"CRYST1</span><span class="si">{</span><span class="n">box_dimensions</span><span class="p">[</span><span class="mi">0</span><span class="p">]</span><span class="si">:</span><span class="s2">9.3f</span><span class="si">}{</span><span class="n">box_dimensions</span><span class="p">[</span><span class="mi">1</span><span class="p">]</span><span class="si">:</span><span class="s2">9.3f</span><span class="si">}{</span><span class="n">box_dimensions</span><span class="p">[</span><span class="mi">2</span><span class="p">]</span><span class="si">:</span><span class="s2">9.3f</span><span class="si">}</span><span class="s2"> 90.00 90.00 90.00 P 1 1</span><span class="se">\n</span><span class="s2">"</span><span class="p">)</span>
+
+ <span class="c1"># Write atoms (nodes from the mesh)</span>
+ <span class="k">for</span> <span class="n">i</span><span class="p">,</span> <span class="n">node</span> <span class="ow">in</span> <span class="nb">enumerate</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">nodes</span><span class="p">):</span>
+ <span class="c1"># PDB uses 1-indexed atom numbers</span>
+ <span class="n">atom_num</span> <span class="o">=</span> <span class="n">i</span> <span class="o">+</span> <span class="mi">1</span>
+ <span class="c1"># Use CA (alpha carbon) atom type for visibility in viewers</span>
+ <span class="n">atom_name</span> <span class="o">=</span> <span class="s2">" CA "</span>
+ <span class="c1"># Use residue name MES for mesh</span>
+ <span class="n">res_name</span> <span class="o">=</span> <span class="s2">"MES"</span>
+ <span class="c1"># Use chain ID A</span>
+ <span class="n">chain_id</span> <span class="o">=</span> <span class="s2">"A"</span>
+ <span class="c1"># Residue number = atom number for simplicity</span>
+ <span class="n">res_num</span> <span class="o">=</span> <span class="n">atom_num</span> <span class="o">%</span> <span class="mi">10000</span> <span class="c1"># PDB format limits res numbers to 9999</span>
+ <span class="c1"># X, Y, Z coordinates in Ångströms (already in the correct units)</span>
+ <span class="n">x</span><span class="p">,</span> <span class="n">y</span><span class="p">,</span> <span class="n">z</span> <span class="o">=</span> <span class="n">node</span>
+ <span class="c1"># Use 1.0 for occupancy and 0.0 for temperature factor</span>
+ <span class="n">occupancy</span> <span class="o">=</span> <span class="mf">1.0</span>
+ <span class="n">temp_factor</span> <span class="o">=</span> <span class="mf">0.0</span>
+
+ <span class="n">f</span><span class="o">.</span><span class="n">write</span><span class="p">(</span><span class="sa">f</span><span class="s2">"</span><span class="si">{</span><span class="n">ATOM_FORMAT</span><span class="o">.</span><span class="n">format</span><span class="p">(</span><span class="n">atom_num</span><span class="p">,</span><span class="w"> </span><span class="n">atom_name</span><span class="p">,</span><span class="w"> </span><span class="n">res_name</span><span class="p">,</span><span class="w"> </span><span class="n">chain_id</span><span class="p">,</span><span class="w"> </span><span class="n">res_num</span><span class="p">,</span><span class="w"> </span><span class="n">x</span><span class="p">,</span><span class="w"> </span><span class="n">y</span><span class="p">,</span><span class="w"> </span><span class="n">z</span><span class="p">,</span><span class="w"> </span><span class="n">occupancy</span><span class="p">,</span><span class="w"> </span><span class="n">temp_factor</span><span class="p">)</span><span class="si">}</span><span class="se">\n</span><span class="s2">"</span><span class="p">)</span>
+
+ <span class="c1"># Write connectivity (the mesh elements) as CONECT records</span>
+ <span class="k">for</span> <span class="n">element</span> <span class="ow">in</span> <span class="bp">self</span><span class="o">.</span><span class="n">elements</span><span class="p">:</span>
+ <span class="c1"># PDB CONECT records use 1-indexed atom numbers</span>
+ <span class="n">atom_indices</span> <span class="o">=</span> <span class="p">[</span><span class="n">idx</span> <span class="o">+</span> <span class="mi">1</span> <span class="k">for</span> <span class="n">idx</span> <span class="ow">in</span> <span class="n">element</span><span class="p">]</span>
+
+ <span class="c1"># Create a CONECT record for each edge of the triangle</span>
+ <span class="n">edges</span> <span class="o">=</span> <span class="p">[(</span><span class="n">atom_indices</span><span class="p">[</span><span class="mi">0</span><span class="p">],</span> <span class="n">atom_indices</span><span class="p">[</span><span class="mi">1</span><span class="p">]),</span>
+ <span class="p">(</span><span class="n">atom_indices</span><span class="p">[</span><span class="mi">1</span><span class="p">],</span> <span class="n">atom_indices</span><span class="p">[</span><span class="mi">2</span><span class="p">]),</span>
+ <span class="p">(</span><span class="n">atom_indices</span><span class="p">[</span><span class="mi">2</span><span class="p">],</span> <span class="n">atom_indices</span><span class="p">[</span><span class="mi">0</span><span class="p">])]</span>
+
+ <span class="k">for</span> <span class="n">a1</span><span class="p">,</span> <span class="n">a2</span> <span class="ow">in</span> <span class="n">edges</span><span class="p">:</span>
+ <span class="n">f</span><span class="o">.</span><span class="n">write</span><span class="p">(</span><span class="sa">f</span><span class="s2">"CONECT</span><span class="si">{</span><span class="n">a1</span><span class="si">:</span><span class="s2">5d</span><span class="si">}{</span><span class="n">a2</span><span class="si">:</span><span class="s2">5d</span><span class="si">}</span><span class="se">\n</span><span class="s2">"</span><span class="p">)</span>
+
+ <span class="c1"># Write end of file</span>
+ <span class="n">f</span><span class="o">.</span><span class="n">write</span><span class="p">(</span><span class="s2">"END</span><span class="se">\n</span><span class="s2">"</span><span class="p">)</span>
+
+ <span class="n">logger</span><span class="o">.</span><span class="n">info</span><span class="p">(</span><span class="sa">f</span><span class="s2">"Saved aligned mesh as PDB: </span><span class="si">{</span><span class="n">output_file</span><span class="si">}</span><span class="s2">"</span><span class="p">)</span></div>
+
+
+ <span class="k">def</span><span class="w"> </span><span class="nf">_save_aligned_mesh_both_formats</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">base_filename</span><span class="p">):</span>
+<span class="w"> </span><span class="sd">"""Save the aligned mesh in both MSH and PDB formats"""</span>
+ <span class="k">if</span> <span class="ow">not</span> <span class="n">os</span><span class="o">.</span><span class="n">path</span><span class="o">.</span><span class="n">isabs</span><span class="p">(</span><span class="n">base_filename</span><span class="p">):</span>
+ <span class="n">base_filename</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">work_dir</span> <span class="o">/</span> <span class="n">base_filename</span>
+ <span class="c1"># Save as MSH (in microns)</span>
+ <span class="n">msh_filename</span> <span class="o">=</span> <span class="sa">f</span><span class="s2">"</span><span class="si">{</span><span class="n">base_filename</span><span class="si">}</span><span class="s2">.msh"</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">save_aligned_mesh</span><span class="p">(</span><span class="n">msh_filename</span><span class="p">)</span>
+ <span class="n">logger</span><span class="o">.</span><span class="n">info</span><span class="p">(</span><span class="sa">f</span><span class="s2">"Saved aligned mesh as MSH: </span><span class="si">{</span><span class="n">msh_filename</span><span class="si">}</span><span class="s2">"</span><span class="p">)</span>
+
+ <span class="c1"># Save as PDB (in Ångströms)</span>
+ <span class="n">pdb_filename</span> <span class="o">=</span> <span class="sa">f</span><span class="s2">"</span><span class="si">{</span><span class="n">base_filename</span><span class="si">}</span><span class="s2">.pdb"</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">save_as_pdb</span><span class="p">(</span><span class="n">pdb_filename</span><span class="p">)</span>
+ <span class="n">logger</span><span class="o">.</span><span class="n">info</span><span class="p">(</span><span class="sa">f</span><span class="s2">"Saved aligned mesh as PDB: </span><span class="si">{</span><span class="n">pdb_filename</span><span class="si">}</span><span class="s2">"</span><span class="p">)</span></div>
+
+
+
+<div class="viewcode-block" id="process_mesh_file">
+<a class="viewcode-back" href="../../api/rigidbody_models/mesh_process_volume.html#arbdmodel.mesh_process_volume.process_mesh_file">[docs]</a>
+<span class="k">def</span><span class="w"> </span><span class="nf">process_mesh_file</span><span class="p">(</span><span class="n">mesh_file</span><span class="p">,</span> <span class="n">density</span><span class="o">=</span><span class="mf">19.3</span><span class="p">,</span> <span class="o">**</span><span class="n">kwargs</span><span class="p">):</span>
+<span class="w"> </span><span class="sd">"""</span>
+<span class="sd"> Process mesh file and calculate all properties</span>
+<span class="sd"> </span>
+<span class="sd"> Args:</span>
+<span class="sd"> mesh_file: Path to .msh file</span>
+<span class="sd"> density: Material density in g/cm³</span>
+<span class="sd"> temperature: Temperature in Kelvin</span>
+<span class="sd"> viscosity: Solvent viscosity in poise</span>
+<span class="sd"> solvent_density: Solvent density in g/cm³</span>
+<span class="sd"> output_dx: Optional path to output potential DX file</span>
+<span class="sd"> output_mesh: Optional path to save aligned mesh</span>
+<span class="sd"> binary_path: Path to HydroPro executable</span>
+<span class="sd"> expected_mass: Optional expected mass in amu to calibrate calculations</span>
+<span class="sd"> expected_aspect_ratio: Optional expected aspect ratio to calibrate inertia</span>
+<span class="sd"> **kwargs: Additional arguments for potential generation</span>
+<span class="sd"> """</span>
+ <span class="n">processor</span> <span class="o">=</span> <span class="n">MeshProcessor</span><span class="p">(</span>
+ <span class="n">mesh_file</span><span class="p">,</span>
+ <span class="n">density</span><span class="o">=</span><span class="n">density</span><span class="p">,)</span>
+
+ <span class="c1"># Calculate hydrodynamic properties</span>
+ <span class="n">processor</span><span class="o">.</span><span class="n">calculate_damping</span><span class="p">()</span>
+
+ <span class="n">logger</span><span class="o">.</span><span class="n">info</span><span class="p">(</span><span class="s2">"</span><span class="se">\n</span><span class="s2">Translational damping coefficients [1/ns]:"</span><span class="p">)</span>
+ <span class="n">logger</span><span class="o">.</span><span class="n">info</span><span class="p">(</span><span class="n">processor</span><span class="o">.</span><span class="n">transdamp</span><span class="p">)</span>
+ <span class="n">logger</span><span class="o">.</span><span class="n">info</span><span class="p">(</span><span class="s2">"</span><span class="se">\n</span><span class="s2">Rotational damping coefficients [1/ns]:"</span><span class="p">)</span>
+ <span class="n">logger</span><span class="o">.</span><span class="n">info</span><span class="p">(</span><span class="n">processor</span><span class="o">.</span><span class="n">rotdamp</span><span class="p">)</span>
+
+ <span class="k">return</span> <span class="n">processor</span></div>
+
+</pre></div>
+
+ </article>
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+ <h1>Source code for arbdmodel.mesh_rigidbody</h1><div class="highlight"><pre>
+<span></span><span class="c1"># -*- coding: utf-8 -*-</span>
+
+<span class="kn">import</span><span class="w"> </span><span class="nn">os</span>
+<span class="kn">from</span><span class="w"> </span><span class="nn">pathlib</span><span class="w"> </span><span class="kn">import</span> <span class="n">Path</span>
+<span class="kn">from</span><span class="w"> </span><span class="nn">.logger</span><span class="w"> </span><span class="kn">import</span> <span class="n">logger</span>
+<span class="kn">from</span><span class="w"> </span><span class="nn">.core_objects</span><span class="w"> </span><span class="kn">import</span> <span class="n">RigidBodyType</span>
+
+
+<span class="sd">"""Rigid body shape modeling module for arbdmodel package.</span>
+<span class="sd">This module provides classes for simple rigid body shape mesh objects into ARBD model.</span>
+<span class="sd">Input: .msh file, or other gmsh supported file</span>
+<span class="sd">"""</span>
+
+<div class="viewcode-block" id="MeshRigidBodyType">
+<a class="viewcode-back" href="../../api/rigidbody_models/mesh_rigidbody.html#arbdmodel.mesh_rigidbody.MeshRigidBodyType">[docs]</a>
+<span class="k">class</span><span class="w"> </span><span class="nc">MeshRigidBodyType</span><span class="p">(</span><span class="n">RigidBodyType</span><span class="p">):</span>
+<span class="w"> </span><span class="sd">"""RigidBodyType subclass for shape rigid body objects"""</span>
+
+ <span class="k">def</span><span class="w"> </span><span class="fm">__init__</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">name</span><span class="p">,</span> <span class="n">mesh_file</span><span class="p">,</span> <span class="n">density</span><span class="o">=</span><span class="mf">19.3</span><span class="p">,</span> <span class="n">simconf</span><span class="o">=</span><span class="kc">None</span><span class="p">,</span> <span class="n">unit_scale</span><span class="o">=</span><span class="mf">1e4</span><span class="p">,</span>
+ <span class="n">use_surface</span><span class="o">=</span><span class="kc">False</span><span class="p">,</span> <span class="o">**</span><span class="n">kwargs</span><span class="p">):</span>
+<span class="w"> </span><span class="sd">"""Initialize shape type.</span>
+<span class="sd"> Args:</span>
+<span class="sd"> name: Name identifier for this type</span>
+<span class="sd"> mesh_file: Path to structure file (.psf/.pdb)</span>
+<span class="sd"> density: Material density in g/cm^3</span>
+<span class="sd"> simconf: SimConf object containing configuration parameters</span>
+<span class="sd"> unit_scale: Conversion factor from input units to angstroms</span>
+<span class="sd"> use_surface: Whether to use surface mesh instead of volume mesh</span>
+<span class="sd"> """</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">type_dir</span> <span class="o">=</span> <span class="n">Path</span><span class="o">.</span><span class="n">cwd</span><span class="p">()</span> <span class="o">/</span> <span class="n">name</span>
+ <span class="k">try</span><span class="p">:</span>
+ <span class="n">os</span><span class="o">.</span><span class="n">makedirs</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">type_dir</span><span class="p">,</span> <span class="n">exist_ok</span><span class="o">=</span><span class="kc">True</span><span class="p">)</span>
+ <span class="k">except</span> <span class="ne">Exception</span> <span class="k">as</span> <span class="n">e</span><span class="p">:</span>
+ <span class="n">logger</span><span class="o">.</span><span class="n">warning</span><span class="p">(</span><span class="sa">f</span><span class="s2">"Could not create directory </span><span class="si">{</span><span class="bp">self</span><span class="o">.</span><span class="n">type_dir</span><span class="si">}</span><span class="s2">: </span><span class="si">{</span><span class="n">e</span><span class="si">}</span><span class="s2">"</span><span class="p">)</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">type_dir</span> <span class="o">=</span> <span class="n">Path</span><span class="o">.</span><span class="n">cwd</span><span class="p">()</span>
+
+ <span class="bp">self</span><span class="o">.</span><span class="n">mesh_file</span> <span class="o">=</span> <span class="n">Path</span><span class="p">(</span><span class="n">mesh_file</span><span class="p">)</span>
+
+ <span class="k">if</span> <span class="n">simconf</span> <span class="ow">is</span> <span class="kc">None</span><span class="p">:</span>
+ <span class="kn">from</span><span class="w"> </span><span class="nn">.</span><span class="w"> </span><span class="kn">import</span> <span class="n">DefaultSimConf</span>
+ <span class="n">simconf</span> <span class="o">=</span> <span class="n">DefaultSimConf</span><span class="p">()</span>
+
+ <span class="k">if</span> <span class="n">use_surface</span><span class="p">:</span>
+ <span class="n">logger</span><span class="o">.</span><span class="n">warning</span><span class="p">(</span><span class="sa">f</span><span class="s1">'The moment of inertia using surface mesh is still inaccurate. consider use volume mesh'</span><span class="p">)</span>
+ <span class="kn">from</span><span class="w"> </span><span class="nn">.mesh_process_surface</span><span class="w"> </span><span class="kn">import</span> <span class="n">SurfaceMeshProcessor</span>
+ <span class="n">rbprocess</span> <span class="o">=</span> <span class="n">SurfaceMeshProcessor</span><span class="p">(</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">mesh_file</span><span class="p">,</span>
+ <span class="n">density</span><span class="o">=</span><span class="n">density</span><span class="p">,</span>
+ <span class="n">simconf</span><span class="o">=</span><span class="n">simconf</span><span class="p">,</span>
+ <span class="n">unit_scale</span><span class="o">=</span><span class="n">unit_scale</span><span class="p">,</span>
+ <span class="n">work_dir</span><span class="o">=</span><span class="bp">self</span><span class="o">.</span><span class="n">type_dir</span><span class="p">)</span>
+ <span class="k">else</span><span class="p">:</span>
+ <span class="kn">from</span><span class="w"> </span><span class="nn">.mesh_process_volume</span><span class="w"> </span><span class="kn">import</span> <span class="n">MeshProcessor</span>
+ <span class="n">rbprocess</span> <span class="o">=</span> <span class="n">MeshProcessor</span><span class="p">(</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">mesh_file</span><span class="p">,</span>
+ <span class="n">density</span><span class="o">=</span><span class="n">density</span><span class="p">,</span>
+ <span class="n">simconf</span><span class="o">=</span><span class="n">simconf</span><span class="p">,</span>
+ <span class="n">unit_scale</span><span class="o">=</span><span class="n">unit_scale</span><span class="p">,</span>
+ <span class="n">work_dir</span><span class="o">=</span><span class="bp">self</span><span class="o">.</span><span class="n">type_dir</span><span class="p">)</span>
+
+ <span class="n">rbprocess</span><span class="o">.</span><span class="n">calculate_damping</span><span class="p">()</span>
+ <span class="n">potential_dx</span> <span class="o">=</span> <span class="nb">str</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">type_dir</span> <span class="o">/</span> <span class="sa">f</span><span class="s2">"</span><span class="si">{</span><span class="n">name</span><span class="si">}</span><span class="s2">_potential.dx"</span><span class="p">)</span>
+ <span class="n">potential_grid</span> <span class="o">=</span> <span class="n">rbprocess</span><span class="o">.</span><span class="n">write_no_enter_potential</span><span class="p">(</span><span class="n">output_file</span><span class="o">=</span><span class="n">potential_dx</span><span class="p">)</span>
+ <span class="n">potential_grids</span> <span class="o">=</span> <span class="p">[(</span><span class="n">potential_grid</span><span class="p">,</span> <span class="mf">1.0</span><span class="p">)]</span>
+ <span class="n">attached_particles</span><span class="o">=</span> <span class="n">rbprocess</span><span class="o">.</span><span class="n">get_attached_particles</span><span class="p">()</span>
+
+ <span class="nb">super</span><span class="p">()</span><span class="o">.</span><span class="fm">__init__</span><span class="p">(</span>
+ <span class="n">name</span><span class="o">=</span><span class="n">name</span><span class="p">,</span>
+ <span class="n">mass</span><span class="o">=</span><span class="n">rbprocess</span><span class="o">.</span><span class="n">mass</span><span class="p">,</span>
+ <span class="n">moment_of_inertia</span><span class="o">=</span><span class="n">rbprocess</span><span class="o">.</span><span class="n">principal_moments</span><span class="p">,</span>
+ <span class="n">damping_coefficient</span><span class="o">=</span><span class="n">rbprocess</span><span class="o">.</span><span class="n">transdamp</span><span class="p">,</span>
+ <span class="n">rotational_damping_coefficient</span><span class="o">=</span><span class="n">rbprocess</span><span class="o">.</span><span class="n">rotdamp</span><span class="p">,</span>
+ <span class="n">potential_grids</span><span class="o">=</span><span class="n">potential_grids</span><span class="p">,</span>
+ <span class="n">attached_particles</span><span class="o">=</span><span class="n">attached_particles</span><span class="p">,</span>
+ <span class="o">**</span><span class="n">kwargs</span><span class="p">)</span></div>
+
+</pre></div>
+
+ </article>
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+
+ <h1>Source code for arbdmodel.model</h1><div class="highlight"><pre>
+<span></span><span class="kn">import</span><span class="w"> </span><span class="nn">numpy</span><span class="w"> </span><span class="k">as</span><span class="w"> </span><span class="nn">np</span>
+<span class="kn">from</span><span class="w"> </span><span class="nn">copy</span><span class="w"> </span><span class="kn">import</span> <span class="n">copy</span><span class="p">,</span> <span class="n">deepcopy</span>
+<span class="kn">from</span><span class="w"> </span><span class="nn">glob</span><span class="w"> </span><span class="kn">import</span> <span class="n">glob</span>
+<span class="kn">import</span><span class="w"> </span><span class="nn">MDAnalysis</span><span class="w"> </span><span class="k">as</span><span class="w"> </span><span class="nn">mda</span>
+
+<span class="kn">from</span><span class="w"> </span><span class="nn">tqdm</span><span class="w"> </span><span class="kn">import</span> <span class="n">tqdm</span><span class="p">,</span> <span class="n">trange</span>
+<span class="kn">from</span><span class="w"> </span><span class="nn">tqdm.contrib.logging</span><span class="w"> </span><span class="kn">import</span> <span class="n">logging_redirect_tqdm</span>
+
+<span class="kn">from</span><span class="w"> </span><span class="nn">.logger</span><span class="w"> </span><span class="kn">import</span> <span class="n">devlogger</span><span class="p">,</span> <span class="n">logger</span><span class="p">,</span> <span class="n">get_resource_path</span>
+<span class="kn">from</span><span class="w"> </span><span class="nn">.interactions</span><span class="w"> </span><span class="kn">import</span> <span class="n">NullPotential</span>
+<span class="kn">from</span><span class="w"> </span><span class="nn">.</span><span class="w"> </span><span class="kn">import</span> <span class="n">Transformable</span><span class="p">,</span> <span class="n">Parent</span><span class="p">,</span> <span class="n">Group</span>
+<span class="kn">from</span><span class="w"> </span><span class="nn">.sim_config</span><span class="w"> </span><span class="kn">import</span> <span class="n">SimConf</span>
+<span class="kn">from</span><span class="w"> </span><span class="nn">.core_objects</span><span class="w"> </span><span class="kn">import</span> <span class="n">GroupSite</span>
+<span class="kn">from</span><span class="w"> </span><span class="nn">.engine</span><span class="w"> </span><span class="kn">import</span> <span class="n">ArbdEngine</span><span class="p">,</span> <span class="n">NamdEngine</span>
+<span class="kn">from</span><span class="w"> </span><span class="nn">.coords</span><span class="w"> </span><span class="kn">import</span> <span class="n">calculate_dimensions_from_cell_vectors</span>
+
+
+<div class="viewcode-block" id="PdbModel">
+<a class="viewcode-back" href="../../api/core/model.html#arbdmodel.model.PdbModel">[docs]</a>
+<span class="k">class</span><span class="w"> </span><span class="nc">PdbModel</span><span class="p">(</span><span class="n">Transformable</span><span class="p">,</span> <span class="n">Parent</span><span class="p">):</span>
+
+ <span class="k">def</span><span class="w"> </span><span class="fm">__init__</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">children</span><span class="o">=</span><span class="kc">None</span><span class="p">,</span> <span class="n">dimensions</span><span class="o">=</span><span class="kc">None</span><span class="p">,</span> <span class="n">remove_duplicate_bonded_terms</span><span class="o">=</span><span class="kc">False</span><span class="p">):</span>
+ <span class="n">Transformable</span><span class="o">.</span><span class="fm">__init__</span><span class="p">(</span><span class="bp">self</span><span class="p">,(</span><span class="mi">0</span><span class="p">,</span><span class="mi">0</span><span class="p">,</span><span class="mi">0</span><span class="p">))</span>
+ <span class="n">Parent</span><span class="o">.</span><span class="fm">__init__</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">children</span><span class="p">,</span> <span class="n">remove_duplicate_bonded_terms</span><span class="p">)</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">dimensions</span> <span class="o">=</span> <span class="n">dimensions</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">particles</span> <span class="o">=</span> <span class="p">[</span><span class="n">p</span> <span class="k">for</span> <span class="n">p</span> <span class="ow">in</span> <span class="bp">self</span> <span class="k">if</span> <span class="ow">not</span> <span class="n">p</span><span class="o">.</span><span class="n">rigid</span><span class="p">]</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">rigid_bodies</span> <span class="o">=</span> <span class="p">[</span><span class="n">p</span> <span class="k">for</span> <span class="n">p</span> <span class="ow">in</span> <span class="bp">self</span> <span class="k">if</span> <span class="n">p</span><span class="o">.</span><span class="n">rigid</span><span class="p">]</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">cacheInvalid</span> <span class="o">=</span> <span class="kc">True</span>
+
+ <span class="k">def</span><span class="w"> </span><span class="nf">_updateParticleOrder</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span>
+ <span class="k">pass</span>
+
+<div class="viewcode-block" id="PdbModel.write_pdb">
+<a class="viewcode-back" href="../../api/core/model.html#arbdmodel.model.PdbModel.write_pdb">[docs]</a>
+ <span class="k">def</span><span class="w"> </span><span class="nf">write_pdb</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">filename</span><span class="p">,</span> <span class="n">beta_from_fixed</span><span class="o">=</span><span class="kc">False</span><span class="p">):</span>
+ <span class="k">if</span> <span class="bp">self</span><span class="o">.</span><span class="n">cacheInvalid</span><span class="p">:</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">_updateParticleOrder</span><span class="p">()</span>
+ <span class="k">with</span> <span class="nb">open</span><span class="p">(</span><span class="n">filename</span><span class="p">,</span><span class="s1">'w'</span><span class="p">)</span> <span class="k">as</span> <span class="n">fh</span><span class="p">:</span>
+ <span class="c1">## Write header</span>
+ <span class="n">fh</span><span class="o">.</span><span class="n">write</span><span class="p">(</span><span class="s2">"CRYST1</span><span class="si">{:>9.3f}{:>9.3f}{:>9.3f}</span><span class="s2"> 90.00 90.00 90.00 P 1 1</span><span class="se">\n</span><span class="s2">"</span><span class="o">.</span><span class="n">format</span><span class="p">(</span> <span class="o">*</span><span class="bp">self</span><span class="o">.</span><span class="n">dimensions</span> <span class="p">))</span>
+
+ <span class="c1">## Write coordinates</span>
+ <span class="n">formatString</span> <span class="o">=</span> <span class="s2">"ATOM </span><span class="si">{idx:>6.6s}</span><span class="s2"> </span><span class="si">{name:^4.4s}</span><span class="s2"> </span><span class="si">{resname:3.3s}</span><span class="s2"> </span><span class="si">{chain:1.1s}{resid:>5.5s}</span><span class="s2"> </span><span class="si">{x:8.8s}{y:8.8s}{z:8.8s}{occupancy:6.2f}{beta:6.2f}</span><span class="s2"> </span><span class="si">{charge:2d}{segname:>6s}</span><span class="se">\n</span><span class="s2">"</span>
+ <span class="k">for</span> <span class="n">p</span> <span class="ow">in</span> <span class="bp">self</span><span class="o">.</span><span class="n">particles</span><span class="p">:</span>
+ <span class="c1">## http://www.wwpdb.org/documentation/file-format-content/format33/sect9.html#ATOM</span>
+ <span class="n">data</span> <span class="o">=</span> <span class="n">p</span><span class="o">.</span><span class="n">_get_psfpdb_dictionary</span><span class="p">()</span>
+ <span class="n">idx</span> <span class="o">=</span> <span class="n">data</span><span class="p">[</span><span class="s1">'idx'</span><span class="p">]</span>
+
+ <span class="k">if</span> <span class="n">np</span><span class="o">.</span><span class="n">log10</span><span class="p">(</span><span class="n">idx</span><span class="p">)</span> <span class="o">>=</span> <span class="mi">5</span><span class="p">:</span>
+ <span class="n">idx</span> <span class="o">=</span> <span class="s2">" *****"</span>
+ <span class="k">else</span><span class="p">:</span>
+ <span class="n">idx</span> <span class="o">=</span> <span class="s2">"</span><span class="si">{:>6d}</span><span class="s2">"</span><span class="o">.</span><span class="n">format</span><span class="p">(</span><span class="n">idx</span><span class="p">)</span>
+ <span class="n">data</span><span class="p">[</span><span class="s1">'idx'</span><span class="p">]</span> <span class="o">=</span> <span class="n">idx</span>
+
+ <span class="k">if</span> <span class="n">beta_from_fixed</span><span class="p">:</span>
+ <span class="n">data</span><span class="p">[</span><span class="s1">'beta'</span><span class="p">]</span> <span class="o">=</span> <span class="mi">1</span> <span class="k">if</span> <span class="s1">'fixed'</span> <span class="ow">in</span> <span class="n">p</span><span class="o">.</span><span class="vm">__dict__</span> <span class="k">else</span> <span class="mi">0</span>
+
+ <span class="n">pos</span> <span class="o">=</span> <span class="n">p</span><span class="o">.</span><span class="n">get_collapsed_position</span><span class="p">()</span>
+ <span class="n">dig</span> <span class="o">=</span> <span class="p">[</span><span class="nb">max</span><span class="p">(</span><span class="nb">int</span><span class="p">(</span><span class="n">np</span><span class="o">.</span><span class="n">log10</span><span class="p">(</span><span class="n">np</span><span class="o">.</span><span class="n">abs</span><span class="p">(</span><span class="n">x</span><span class="p">)</span><span class="o">+</span><span class="mf">1e-6</span><span class="p">)</span><span class="o">//</span><span class="mi">1</span><span class="p">),</span><span class="mi">0</span><span class="p">)</span><span class="o">+</span><span class="mi">1</span> <span class="k">for</span> <span class="n">x</span> <span class="ow">in</span> <span class="n">pos</span><span class="p">]</span>
+ <span class="k">for</span> <span class="n">d</span> <span class="ow">in</span> <span class="n">dig</span><span class="p">:</span> <span class="k">assert</span><span class="p">(</span> <span class="n">d</span> <span class="o"><=</span> <span class="mi">7</span> <span class="p">)</span>
+ <span class="c1"># assert( np.all(dig <= 7) )</span>
+ <span class="n">fs</span> <span class="o">=</span> <span class="p">[</span><span class="s2">"{: </span><span class="si">%d</span><span class="s2">.</span><span class="si">%d</span><span class="s2">f}"</span> <span class="o">%</span> <span class="p">(</span><span class="mi">8</span><span class="p">,</span><span class="mi">7</span><span class="o">-</span><span class="n">d</span><span class="p">)</span> <span class="k">for</span> <span class="n">d</span> <span class="ow">in</span> <span class="n">dig</span><span class="p">]</span>
+ <span class="n">x</span><span class="p">,</span><span class="n">y</span><span class="p">,</span><span class="n">z</span> <span class="o">=</span> <span class="p">[</span><span class="n">f</span><span class="o">.</span><span class="n">format</span><span class="p">(</span><span class="n">x</span><span class="p">)</span> <span class="k">for</span> <span class="n">f</span><span class="p">,</span><span class="n">x</span> <span class="ow">in</span> <span class="nb">zip</span><span class="p">(</span><span class="n">fs</span><span class="p">,</span><span class="n">pos</span><span class="p">)]</span>
+ <span class="n">data</span><span class="p">[</span><span class="s1">'x'</span><span class="p">]</span> <span class="o">=</span> <span class="n">x</span>
+ <span class="n">data</span><span class="p">[</span><span class="s1">'y'</span><span class="p">]</span> <span class="o">=</span> <span class="n">y</span>
+ <span class="n">data</span><span class="p">[</span><span class="s1">'z'</span><span class="p">]</span> <span class="o">=</span> <span class="n">z</span>
+ <span class="k">assert</span><span class="p">(</span><span class="n">data</span><span class="p">[</span><span class="s1">'resid'</span><span class="p">]</span> <span class="o"><</span> <span class="mf">1e5</span><span class="p">)</span>
+ <span class="n">data</span><span class="p">[</span><span class="s1">'charge'</span><span class="p">]</span> <span class="o">=</span> <span class="nb">int</span><span class="p">(</span><span class="n">data</span><span class="p">[</span><span class="s1">'charge'</span><span class="p">])</span>
+ <span class="n">data</span><span class="p">[</span><span class="s1">'resid'</span><span class="p">]</span> <span class="o">=</span> <span class="s2">"</span><span class="si">{:<4d}</span><span class="s2">"</span><span class="o">.</span><span class="n">format</span><span class="p">(</span><span class="n">data</span><span class="p">[</span><span class="s1">'resid'</span><span class="p">])</span>
+ <span class="n">fh</span><span class="o">.</span><span class="n">write</span><span class="p">(</span> <span class="n">formatString</span><span class="o">.</span><span class="n">format</span><span class="p">(</span><span class="o">**</span><span class="n">data</span><span class="p">)</span> <span class="p">)</span>
+
+ <span class="k">return</span></div>
+
+
+<div class="viewcode-block" id="PdbModel.write_pqr">
+<a class="viewcode-back" href="../../api/core/model.html#arbdmodel.model.PdbModel.write_pqr">[docs]</a>
+ <span class="k">def</span><span class="w"> </span><span class="nf">write_pqr</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">filename</span><span class="p">):</span>
+ <span class="k">if</span> <span class="bp">self</span><span class="o">.</span><span class="n">cacheInvalid</span><span class="p">:</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">_updateParticleOrder</span><span class="p">()</span>
+ <span class="k">with</span> <span class="nb">open</span><span class="p">(</span><span class="n">filename</span><span class="p">,</span><span class="s1">'w'</span><span class="p">)</span> <span class="k">as</span> <span class="n">fh</span><span class="p">:</span>
+ <span class="c1">## Write header</span>
+ <span class="n">fh</span><span class="o">.</span><span class="n">write</span><span class="p">(</span><span class="s2">"CRYST1</span><span class="si">{:>9.3f}{:>9.3f}{:>9.3f}</span><span class="s2"> 90.00 90.00 90.00 P 1 1</span><span class="se">\n</span><span class="s2">"</span><span class="o">.</span><span class="n">format</span><span class="p">(</span> <span class="o">*</span><span class="bp">self</span><span class="o">.</span><span class="n">dimensions</span> <span class="p">))</span>
+
+ <span class="c1">## Write coordinates</span>
+ <span class="n">formatString</span> <span class="o">=</span> <span class="s2">"ATOM </span><span class="si">{idx:>6.6s}</span><span class="s2"> </span><span class="si">{name:^4.4s}</span><span class="s2"> </span><span class="si">{resname:3.3s}</span><span class="s2"> </span><span class="si">{chain:1.1s}</span><span class="s2"> </span><span class="si">{resid:>5.5s}</span><span class="s2"> </span><span class="si">{x:.6f}</span><span class="s2"> </span><span class="si">{y:.6f}</span><span class="s2"> </span><span class="si">{z:.6f}</span><span class="s2"> </span><span class="si">{charge}</span><span class="s2"> </span><span class="si">{radius}</span><span class="se">\n</span><span class="s2">"</span>
+ <span class="k">for</span> <span class="n">p</span> <span class="ow">in</span> <span class="bp">self</span><span class="o">.</span><span class="n">particles</span><span class="p">:</span>
+ <span class="n">data</span> <span class="o">=</span> <span class="n">p</span><span class="o">.</span><span class="n">_get_psfpdb_dictionary</span><span class="p">()</span>
+
+ <span class="n">idx</span> <span class="o">=</span> <span class="n">data</span><span class="p">[</span><span class="s1">'idx'</span><span class="p">]</span>
+ <span class="k">if</span> <span class="n">np</span><span class="o">.</span><span class="n">log10</span><span class="p">(</span><span class="n">idx</span><span class="p">)</span> <span class="o">>=</span> <span class="mi">5</span><span class="p">:</span>
+ <span class="n">idx</span> <span class="o">=</span> <span class="s2">" *****"</span>
+ <span class="k">else</span><span class="p">:</span>
+ <span class="n">idx</span> <span class="o">=</span> <span class="s2">"</span><span class="si">{:>6d}</span><span class="s2">"</span><span class="o">.</span><span class="n">format</span><span class="p">(</span><span class="n">idx</span><span class="p">)</span>
+ <span class="n">data</span><span class="p">[</span><span class="s1">'idx'</span><span class="p">]</span> <span class="o">=</span> <span class="n">idx</span>
+
+ <span class="n">x</span><span class="p">,</span><span class="n">y</span><span class="p">,</span><span class="n">z</span> <span class="o">=</span> <span class="n">p</span><span class="o">.</span><span class="n">get_collapsed_position</span><span class="p">()</span>
+ <span class="n">data</span><span class="p">[</span><span class="s1">'x'</span><span class="p">]</span> <span class="o">=</span> <span class="n">x</span>
+ <span class="n">data</span><span class="p">[</span><span class="s1">'y'</span><span class="p">]</span> <span class="o">=</span> <span class="n">y</span>
+ <span class="n">data</span><span class="p">[</span><span class="s1">'z'</span><span class="p">]</span> <span class="o">=</span> <span class="n">z</span>
+ <span class="k">assert</span><span class="p">(</span><span class="n">data</span><span class="p">[</span><span class="s1">'resid'</span><span class="p">]</span> <span class="o"><</span> <span class="mf">1e5</span><span class="p">)</span>
+ <span class="n">data</span><span class="p">[</span><span class="s1">'resid'</span><span class="p">]</span> <span class="o">=</span> <span class="s2">"</span><span class="si">{:<4d}</span><span class="s2">"</span><span class="o">.</span><span class="n">format</span><span class="p">(</span><span class="n">data</span><span class="p">[</span><span class="s1">'resid'</span><span class="p">])</span>
+ <span class="k">if</span> <span class="s1">'radius'</span> <span class="ow">not</span> <span class="ow">in</span> <span class="n">data</span><span class="p">:</span>
+ <span class="n">data</span><span class="p">[</span><span class="s1">'radius'</span><span class="p">]</span> <span class="o">=</span> <span class="mi">2</span> <span class="o">*</span> <span class="p">(</span><span class="n">data</span><span class="p">[</span><span class="s1">'mass'</span><span class="p">]</span><span class="o">/</span><span class="mi">16</span><span class="p">)</span><span class="o">**</span><span class="mf">0.333333</span>
+ <span class="n">fh</span><span class="o">.</span><span class="n">write</span><span class="p">(</span> <span class="n">formatString</span><span class="o">.</span><span class="n">format</span><span class="p">(</span><span class="o">**</span><span class="n">data</span><span class="p">)</span> <span class="p">)</span>
+ <span class="k">return</span></div>
+
+
+<div class="viewcode-block" id="PdbModel.write_psf">
+<a class="viewcode-back" href="../../api/core/model.html#arbdmodel.model.PdbModel.write_psf">[docs]</a>
+ <span class="k">def</span><span class="w"> </span><span class="nf">write_psf</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">filename</span><span class="p">):</span>
+ <span class="k">if</span> <span class="bp">self</span><span class="o">.</span><span class="n">cacheUpToDate</span> <span class="o">==</span> <span class="kc">False</span><span class="p">:</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">_updateParticleOrder</span><span class="p">()</span>
+ <span class="k">with</span> <span class="nb">open</span><span class="p">(</span><span class="n">filename</span><span class="p">,</span><span class="s1">'w'</span><span class="p">)</span> <span class="k">as</span> <span class="n">fh</span><span class="p">:</span>
+ <span class="c1">## Write header</span>
+ <span class="n">fh</span><span class="o">.</span><span class="n">write</span><span class="p">(</span><span class="s2">"PSF NAMD</span><span class="se">\n\n</span><span class="s2">"</span><span class="p">)</span> <span class="c1"># create NAMD formatted psf</span>
+ <span class="n">fh</span><span class="o">.</span><span class="n">write</span><span class="p">(</span><span class="s2">"</span><span class="si">{:>8d}</span><span class="s2"> !NTITLE</span><span class="se">\n\n</span><span class="s2">"</span><span class="o">.</span><span class="n">format</span><span class="p">(</span><span class="mi">0</span><span class="p">))</span>
+
+ <span class="c1">## ATOMS section</span>
+ <span class="n">fh</span><span class="o">.</span><span class="n">write</span><span class="p">(</span><span class="s2">"</span><span class="si">{:>8d}</span><span class="s2"> !NATOM</span><span class="se">\n</span><span class="s2">"</span><span class="o">.</span><span class="n">format</span><span class="p">(</span><span class="nb">len</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">particles</span><span class="p">)))</span>
+
+ <span class="c1">## From vmd/plugins/molfile_plugin/src/psfplugin.c</span>
+ <span class="c1">## "%d %7s %10s %7s %7s %7s %f %f"</span>
+ <span class="n">formatString</span> <span class="o">=</span> <span class="s2">"</span><span class="si">{idx:>8d}</span><span class="s2"> </span><span class="si">{segname:7.7s}</span><span class="s2"> </span><span class="si">{resid:<10.10s}</span><span class="s2"> </span><span class="si">{resname:7.7s}</span><span class="s2">"</span> <span class="o">+</span> \
+ <span class="s2">" </span><span class="si">{name:7.7s}</span><span class="s2"> </span><span class="si">{type:7.7s}</span><span class="s2"> </span><span class="si">{charge:f}</span><span class="s2"> </span><span class="si">{mass:f}</span><span class="se">\n</span><span class="s2">"</span>
+ <span class="k">for</span> <span class="n">p</span> <span class="ow">in</span> <span class="bp">self</span><span class="o">.</span><span class="n">particles</span><span class="p">:</span>
+ <span class="n">data</span> <span class="o">=</span> <span class="n">p</span><span class="o">.</span><span class="n">_get_psfpdb_dictionary</span><span class="p">()</span>
+ <span class="n">data</span><span class="p">[</span><span class="s1">'resid'</span><span class="p">]</span> <span class="o">=</span> <span class="s2">"</span><span class="si">%d%c%c</span><span class="s2">"</span> <span class="o">%</span> <span class="p">(</span><span class="n">data</span><span class="p">[</span><span class="s1">'resid'</span><span class="p">],</span><span class="s2">" "</span><span class="p">,</span><span class="s2">" "</span><span class="p">)</span> <span class="c1"># TODO: work with large indices</span>
+ <span class="n">fh</span><span class="o">.</span><span class="n">write</span><span class="p">(</span> <span class="n">formatString</span><span class="o">.</span><span class="n">format</span><span class="p">(</span><span class="o">**</span><span class="n">data</span><span class="p">)</span> <span class="p">)</span>
+ <span class="n">fh</span><span class="o">.</span><span class="n">write</span><span class="p">(</span><span class="s2">"</span><span class="se">\n</span><span class="s2">"</span><span class="p">)</span>
+
+ <span class="c1">## Write out bonds</span>
+ <span class="n">bonds</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">get_bonds</span><span class="p">()</span>
+ <span class="n">fh</span><span class="o">.</span><span class="n">write</span><span class="p">(</span><span class="s2">"</span><span class="si">{:>8d}</span><span class="s2"> !NBOND</span><span class="se">\n</span><span class="s2">"</span><span class="o">.</span><span class="n">format</span><span class="p">(</span><span class="nb">len</span><span class="p">(</span><span class="n">bonds</span><span class="p">)))</span>
+ <span class="n">counter</span> <span class="o">=</span> <span class="mi">0</span>
+ <span class="k">for</span> <span class="n">p1</span><span class="p">,</span><span class="n">p2</span><span class="p">,</span><span class="n">b</span><span class="p">,</span><span class="n">ex</span> <span class="ow">in</span> <span class="n">bonds</span><span class="p">:</span>
+ <span class="n">fh</span><span class="o">.</span><span class="n">write</span><span class="p">(</span> <span class="s2">"</span><span class="si">{:>8d}{:>8d}</span><span class="s2">"</span><span class="o">.</span><span class="n">format</span><span class="p">(</span><span class="n">p1</span><span class="o">.</span><span class="n">idx</span><span class="o">+</span><span class="mi">1</span><span class="p">,</span><span class="n">p2</span><span class="o">.</span><span class="n">idx</span><span class="o">+</span><span class="mi">1</span><span class="p">)</span> <span class="p">)</span>
+ <span class="n">counter</span> <span class="o">+=</span> <span class="mi">1</span>
+ <span class="k">if</span> <span class="n">counter</span> <span class="o">==</span> <span class="mi">4</span><span class="p">:</span>
+ <span class="n">fh</span><span class="o">.</span><span class="n">write</span><span class="p">(</span><span class="s2">"</span><span class="se">\n</span><span class="s2">"</span><span class="p">)</span>
+ <span class="n">counter</span> <span class="o">=</span> <span class="mi">0</span>
+ <span class="k">else</span><span class="p">:</span>
+ <span class="n">fh</span><span class="o">.</span><span class="n">write</span><span class="p">(</span><span class="s2">" "</span><span class="p">)</span>
+ <span class="n">fh</span><span class="o">.</span><span class="n">write</span><span class="p">(</span><span class="s2">"</span><span class="se">\n</span><span class="s2">"</span> <span class="k">if</span> <span class="n">counter</span> <span class="o">==</span> <span class="mi">0</span> <span class="k">else</span> <span class="s2">"</span><span class="se">\n\n</span><span class="s2">"</span><span class="p">)</span>
+
+ <span class="c1">## Write out angles</span>
+ <span class="n">angles</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">get_angles</span><span class="p">()</span>
+ <span class="n">fh</span><span class="o">.</span><span class="n">write</span><span class="p">(</span><span class="s2">"</span><span class="si">{:>8d}</span><span class="s2"> !NTHETA</span><span class="se">\n</span><span class="s2">"</span><span class="o">.</span><span class="n">format</span><span class="p">(</span><span class="nb">len</span><span class="p">(</span><span class="n">angles</span><span class="p">)))</span>
+ <span class="n">counter</span> <span class="o">=</span> <span class="mi">0</span>
+ <span class="k">for</span> <span class="n">p1</span><span class="p">,</span><span class="n">p2</span><span class="p">,</span><span class="n">p3</span><span class="p">,</span><span class="n">a</span> <span class="ow">in</span> <span class="n">angles</span><span class="p">:</span>
+ <span class="n">fh</span><span class="o">.</span><span class="n">write</span><span class="p">(</span> <span class="s2">"</span><span class="si">{:>8d}{:>8d}{:>8d}</span><span class="s2">"</span><span class="o">.</span><span class="n">format</span><span class="p">(</span><span class="n">p1</span><span class="o">.</span><span class="n">idx</span><span class="o">+</span><span class="mi">1</span><span class="p">,</span><span class="n">p2</span><span class="o">.</span><span class="n">idx</span><span class="o">+</span><span class="mi">1</span><span class="p">,</span><span class="n">p3</span><span class="o">.</span><span class="n">idx</span><span class="o">+</span><span class="mi">1</span><span class="p">)</span> <span class="p">)</span>
+ <span class="n">counter</span> <span class="o">+=</span> <span class="mi">1</span>
+ <span class="k">if</span> <span class="n">counter</span> <span class="o">==</span> <span class="mi">3</span><span class="p">:</span>
+ <span class="n">fh</span><span class="o">.</span><span class="n">write</span><span class="p">(</span><span class="s2">"</span><span class="se">\n</span><span class="s2">"</span><span class="p">)</span>
+ <span class="n">counter</span> <span class="o">=</span> <span class="mi">0</span>
+ <span class="k">else</span><span class="p">:</span>
+ <span class="n">fh</span><span class="o">.</span><span class="n">write</span><span class="p">(</span><span class="s2">" "</span><span class="p">)</span>
+ <span class="n">fh</span><span class="o">.</span><span class="n">write</span><span class="p">(</span><span class="s2">"</span><span class="se">\n</span><span class="s2">"</span> <span class="k">if</span> <span class="n">counter</span> <span class="o">==</span> <span class="mi">0</span> <span class="k">else</span> <span class="s2">"</span><span class="se">\n\n</span><span class="s2">"</span><span class="p">)</span>
+
+ <span class="c1">## Write out dihedrals</span>
+ <span class="n">dihedrals</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">get_dihedrals</span><span class="p">()</span>
+ <span class="n">fh</span><span class="o">.</span><span class="n">write</span><span class="p">(</span><span class="s2">"</span><span class="si">{:>8d}</span><span class="s2"> !NPHI</span><span class="se">\n</span><span class="s2">"</span><span class="o">.</span><span class="n">format</span><span class="p">(</span><span class="nb">len</span><span class="p">(</span><span class="n">dihedrals</span><span class="p">)))</span>
+ <span class="n">counter</span> <span class="o">=</span> <span class="mi">0</span>
+ <span class="k">for</span> <span class="n">p1</span><span class="p">,</span><span class="n">p2</span><span class="p">,</span><span class="n">p3</span><span class="p">,</span><span class="n">p4</span><span class="p">,</span><span class="n">a</span> <span class="ow">in</span> <span class="n">dihedrals</span><span class="p">:</span>
+ <span class="n">fh</span><span class="o">.</span><span class="n">write</span><span class="p">(</span> <span class="s2">"</span><span class="si">{:>8d}{:>8d}{:>8d}{:>8d}</span><span class="s2">"</span><span class="o">.</span><span class="n">format</span><span class="p">(</span><span class="n">p1</span><span class="o">.</span><span class="n">idx</span><span class="o">+</span><span class="mi">1</span><span class="p">,</span><span class="n">p2</span><span class="o">.</span><span class="n">idx</span><span class="o">+</span><span class="mi">1</span><span class="p">,</span><span class="n">p3</span><span class="o">.</span><span class="n">idx</span><span class="o">+</span><span class="mi">1</span><span class="p">,</span><span class="n">p4</span><span class="o">.</span><span class="n">idx</span><span class="o">+</span><span class="mi">1</span><span class="p">)</span> <span class="p">)</span>
+ <span class="n">counter</span> <span class="o">+=</span> <span class="mi">1</span>
+ <span class="k">if</span> <span class="n">counter</span> <span class="o">==</span> <span class="mi">2</span><span class="p">:</span>
+ <span class="n">fh</span><span class="o">.</span><span class="n">write</span><span class="p">(</span><span class="s2">"</span><span class="se">\n</span><span class="s2">"</span><span class="p">)</span>
+ <span class="n">counter</span> <span class="o">=</span> <span class="mi">0</span>
+ <span class="k">else</span><span class="p">:</span>
+ <span class="n">fh</span><span class="o">.</span><span class="n">write</span><span class="p">(</span><span class="s2">" "</span><span class="p">)</span>
+ <span class="n">fh</span><span class="o">.</span><span class="n">write</span><span class="p">(</span><span class="s2">"</span><span class="se">\n</span><span class="s2">"</span> <span class="k">if</span> <span class="n">counter</span> <span class="o">==</span> <span class="mi">0</span> <span class="k">else</span> <span class="s2">"</span><span class="se">\n\n</span><span class="s2">"</span><span class="p">)</span>
+
+ <span class="c1">## Write out impropers</span>
+ <span class="n">impropers</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">get_impropers</span><span class="p">()</span>
+ <span class="n">fh</span><span class="o">.</span><span class="n">write</span><span class="p">(</span><span class="s2">"</span><span class="si">{:>8d}</span><span class="s2"> !NIMPHI</span><span class="se">\n</span><span class="s2">"</span><span class="o">.</span><span class="n">format</span><span class="p">(</span><span class="nb">len</span><span class="p">(</span><span class="n">impropers</span><span class="p">)))</span>
+ <span class="n">counter</span> <span class="o">=</span> <span class="mi">0</span>
+ <span class="k">for</span> <span class="n">p1</span><span class="p">,</span><span class="n">p2</span><span class="p">,</span><span class="n">p3</span><span class="p">,</span><span class="n">p4</span><span class="p">,</span><span class="n">a</span> <span class="ow">in</span> <span class="n">impropers</span><span class="p">:</span>
+ <span class="n">fh</span><span class="o">.</span><span class="n">write</span><span class="p">(</span> <span class="s2">"</span><span class="si">{:>8d}{:>8d}{:>8d}{:>8d}</span><span class="s2">"</span><span class="o">.</span><span class="n">format</span><span class="p">(</span><span class="n">p1</span><span class="o">.</span><span class="n">idx</span><span class="o">+</span><span class="mi">1</span><span class="p">,</span><span class="n">p2</span><span class="o">.</span><span class="n">idx</span><span class="o">+</span><span class="mi">1</span><span class="p">,</span><span class="n">p3</span><span class="o">.</span><span class="n">idx</span><span class="o">+</span><span class="mi">1</span><span class="p">,</span><span class="n">p4</span><span class="o">.</span><span class="n">idx</span><span class="o">+</span><span class="mi">1</span><span class="p">)</span> <span class="p">)</span>
+ <span class="n">counter</span> <span class="o">+=</span> <span class="mi">1</span>
+ <span class="k">if</span> <span class="n">counter</span> <span class="o">==</span> <span class="mi">2</span><span class="p">:</span>
+ <span class="n">fh</span><span class="o">.</span><span class="n">write</span><span class="p">(</span><span class="s2">"</span><span class="se">\n</span><span class="s2">"</span><span class="p">)</span>
+ <span class="n">counter</span> <span class="o">=</span> <span class="mi">0</span>
+ <span class="k">else</span><span class="p">:</span>
+ <span class="n">fh</span><span class="o">.</span><span class="n">write</span><span class="p">(</span><span class="s2">" "</span><span class="p">)</span>
+ <span class="n">fh</span><span class="o">.</span><span class="n">write</span><span class="p">(</span><span class="s2">"</span><span class="se">\n</span><span class="s2">"</span> <span class="k">if</span> <span class="n">counter</span> <span class="o">==</span> <span class="mi">0</span> <span class="k">else</span> <span class="s2">"</span><span class="se">\n\n</span><span class="s2">"</span><span class="p">)</span>
+
+ <span class="n">fh</span><span class="o">.</span><span class="n">write</span><span class="p">(</span><span class="s2">"</span><span class="se">\n</span><span class="si">{:>8d}</span><span class="s2"> !NDON: donors</span><span class="se">\n\n\n</span><span class="s2">"</span><span class="o">.</span><span class="n">format</span><span class="p">(</span><span class="mi">0</span><span class="p">))</span>
+ <span class="n">fh</span><span class="o">.</span><span class="n">write</span><span class="p">(</span><span class="s2">"</span><span class="se">\n</span><span class="si">{:>8d}</span><span class="s2"> !NACC: acceptors</span><span class="se">\n\n\n</span><span class="s2">"</span><span class="o">.</span><span class="n">format</span><span class="p">(</span><span class="mi">0</span><span class="p">))</span>
+ <span class="n">fh</span><span class="o">.</span><span class="n">write</span><span class="p">(</span><span class="s2">"</span><span class="se">\n</span><span class="s2"> 0 !NNB</span><span class="se">\n\n</span><span class="s2">"</span><span class="p">)</span>
+ <span class="n">natoms</span> <span class="o">=</span> <span class="nb">len</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">particles</span><span class="p">)</span>
+ <span class="k">for</span> <span class="n">i</span> <span class="ow">in</span> <span class="nb">range</span><span class="p">(</span><span class="n">natoms</span><span class="o">//</span><span class="mi">8</span><span class="p">):</span>
+ <span class="n">fh</span><span class="o">.</span><span class="n">write</span><span class="p">(</span><span class="s2">" 0 0 0 0 0 0 0 0</span><span class="se">\n</span><span class="s2">"</span><span class="p">)</span>
+ <span class="k">for</span> <span class="n">i</span> <span class="ow">in</span> <span class="nb">range</span><span class="p">(</span><span class="n">natoms</span><span class="o">-</span><span class="mi">8</span><span class="o">*</span><span class="p">(</span><span class="n">natoms</span><span class="o">//</span><span class="mi">8</span><span class="p">)):</span>
+ <span class="n">fh</span><span class="o">.</span><span class="n">write</span><span class="p">(</span><span class="s2">" 0"</span><span class="p">)</span>
+ <span class="n">fh</span><span class="o">.</span><span class="n">write</span><span class="p">(</span><span class="s2">"</span><span class="se">\n\n</span><span class="s2"> 1 0 !NGRP</span><span class="se">\n\n</span><span class="s2">"</span><span class="p">)</span></div>
+</div>
+
+
+
+<div class="viewcode-block" id="ArbdModel">
+<a class="viewcode-back" href="../../api/core/model.html#arbdmodel.model.ArbdModel">[docs]</a>
+<span class="k">class</span><span class="w"> </span><span class="nc">ArbdModel</span><span class="p">(</span><span class="n">PdbModel</span><span class="p">):</span>
+<span class="w"> </span><span class="sd">"""</span>
+<span class="sd"> Advanced model class for ARBD simulations with improved cell vector handling.</span>
+<span class="sd"> """</span>
+ <span class="k">def</span><span class="w"> </span><span class="fm">__init__</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">children</span><span class="p">,</span> <span class="n">cell_vectors</span><span class="o">=</span><span class="kc">None</span><span class="p">,</span> <span class="n">cell_origin</span><span class="o">=</span><span class="kc">None</span><span class="p">,</span> <span class="n">dimensions</span><span class="o">=</span><span class="kc">None</span><span class="p">,</span>
+ <span class="n">remove_duplicate_bonded_terms</span><span class="o">=</span><span class="kc">True</span><span class="p">,</span> <span class="n">buffer_factor</span><span class="o">=</span><span class="mf">1.2</span><span class="p">,</span>
+ <span class="n">configuration</span><span class="o">=</span><span class="kc">None</span><span class="p">,</span> <span class="n">dummy_types</span><span class="o">=</span><span class="nb">tuple</span><span class="p">(),</span> <span class="o">**</span><span class="n">conf_params</span><span class="p">):</span>
+<span class="w"> </span><span class="sd">"""</span>
+<span class="sd"> Initialize ArbdModel with improved cell vector and dimension handling.</span>
+<span class="sd"> </span>
+<span class="sd"> Args:</span>
+<span class="sd"> children: Child objects for the model</span>
+<span class="sd"> cell_vectors: List of 3 cell basis vectors [[x1,y1,z1], [x2,y2,z2], [x3,y3,z3]]</span>
+<span class="sd"> cell_origin: Cell origin coordinates [x,y,z]</span>
+<span class="sd"> dimensions: Explicit dimensions for the simulation box (overrides cell_vectors)</span>
+<span class="sd"> remove_duplicate_bonded_terms: Whether to remove duplicate bonded terms</span>
+<span class="sd"> buffer_factor: Factor to scale dimensions derived from cell vectors</span>
+<span class="sd"> configuration: SimConf object with configuration parameters</span>
+<span class="sd"> dummy_types: Deprecated parameter, kept for backward compatibility</span>
+<span class="sd"> **conf_params: Additional configuration parameters</span>
+<span class="sd"> """</span>
+ <span class="c1"># Calculate dimensions from cell vectors if provided and dimensions not explicitly set</span>
+ <span class="k">if</span> <span class="n">dimensions</span> <span class="ow">is</span> <span class="kc">None</span> <span class="ow">and</span> <span class="n">cell_vectors</span> <span class="ow">is</span> <span class="ow">not</span> <span class="kc">None</span><span class="p">:</span>
+ <span class="n">dimensions</span> <span class="o">=</span> <span class="n">calculate_dimensions_from_cell_vectors</span><span class="p">(</span>
+ <span class="n">cell_vectors</span><span class="p">,</span> <span class="n">cell_origin</span><span class="p">,</span> <span class="n">buffer_factor</span><span class="p">)</span>
+
+ <span class="c1"># Default dimensions if neither dimensions nor cell vectors provided</span>
+ <span class="k">if</span> <span class="n">dimensions</span> <span class="ow">is</span> <span class="kc">None</span><span class="p">:</span>
+ <span class="n">dimensions</span> <span class="o">=</span> <span class="p">(</span><span class="mi">1000</span><span class="p">,</span> <span class="mi">1000</span><span class="p">,</span> <span class="mi">1000</span><span class="p">)</span>
+
+ <span class="c1"># Set default cell vectors if not provided</span>
+ <span class="k">if</span> <span class="n">cell_vectors</span> <span class="ow">is</span> <span class="kc">None</span><span class="p">:</span>
+ <span class="n">cell_vectors</span> <span class="o">=</span> <span class="p">[</span>
+ <span class="p">[</span><span class="n">dimensions</span><span class="p">[</span><span class="mi">0</span><span class="p">],</span> <span class="mi">0</span><span class="p">,</span> <span class="mi">0</span><span class="p">],</span>
+ <span class="p">[</span><span class="mi">0</span><span class="p">,</span> <span class="n">dimensions</span><span class="p">[</span><span class="mi">1</span><span class="p">],</span> <span class="mi">0</span><span class="p">],</span>
+ <span class="p">[</span><span class="mi">0</span><span class="p">,</span> <span class="mi">0</span><span class="p">,</span> <span class="n">dimensions</span><span class="p">[</span><span class="mi">2</span><span class="p">]]</span>
+ <span class="p">]</span>
+
+ <span class="c1"># Set default cell origin if not provided</span>
+ <span class="k">if</span> <span class="n">cell_origin</span> <span class="ow">is</span> <span class="kc">None</span><span class="p">:</span>
+ <span class="n">cell_origin</span> <span class="o">=</span> <span class="p">[</span><span class="mi">0</span><span class="p">,</span> <span class="mi">0</span><span class="p">,</span> <span class="mi">0</span><span class="p">]</span>
+
+ <span class="c1"># Initialize parent class</span>
+ <span class="n">PdbModel</span><span class="o">.</span><span class="fm">__init__</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">children</span><span class="p">,</span> <span class="n">dimensions</span><span class="p">,</span> <span class="n">remove_duplicate_bonded_terms</span><span class="p">,</span>
+ <span class="n">cell_vectors</span><span class="p">,</span> <span class="n">cell_origin</span><span class="p">)</span>
+
+
+ <span class="c1"># Store origin which might be different from cell_origin</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">origin</span> <span class="o">=</span> <span class="n">cell_origin</span>
+
+ <span class="c1"># Set up configuration</span>
+ <span class="k">if</span> <span class="n">configuration</span> <span class="ow">is</span> <span class="kc">None</span><span class="p">:</span>
+ <span class="n">configuration</span> <span class="o">=</span> <span class="n">SimConf</span><span class="p">(</span><span class="o">**</span><span class="n">conf_params</span><span class="p">)</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">configuration</span> <span class="o">=</span> <span class="n">configuration</span>
+
+ <span class="c1"># Initialize model properties</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">num_particles</span> <span class="o">=</span> <span class="mi">0</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">particles</span> <span class="o">=</span> <span class="p">[]</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">type_counts</span> <span class="o">=</span> <span class="kc">None</span>
+
+ <span class="bp">self</span><span class="o">.</span><span class="n">dummy_types</span> <span class="o">=</span> <span class="n">dummy_types</span> <span class="c1"># TODO, determine whether these are really needed</span>
+ <span class="k">if</span> <span class="nb">len</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">dummy_types</span><span class="p">)</span> <span class="o">!=</span> <span class="mi">0</span><span class="p">:</span>
+ <span class="k">raise</span><span class="p">(</span><span class="s2">"Dummy types have been deprecated"</span><span class="p">)</span>
+
+ <span class="bp">self</span><span class="o">.</span><span class="n">nonbonded_interactions</span> <span class="o">=</span> <span class="p">[]</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">_nonbonded_interaction_files</span> <span class="o">=</span> <span class="p">[]</span> <span class="c1"># This could be made more robust</span>
+
+ <span class="bp">self</span><span class="o">.</span><span class="n">cacheUpToDate</span> <span class="o">=</span> <span class="kc">False</span>
+
+ <span class="bp">self</span><span class="o">.</span><span class="n">group_sites</span> <span class="o">=</span> <span class="p">[]</span>
+
+<div class="viewcode-block" id="ArbdModel.add">
+<a class="viewcode-back" href="../../api/core/model.html#arbdmodel.model.ArbdModel.add">[docs]</a>
+ <span class="k">def</span><span class="w"> </span><span class="nf">add</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">obj</span><span class="p">):</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">_clear_types</span><span class="p">()</span> <span class="c1"># TODO: call upon (potentially nested) `child.add(add)`</span>
+ <span class="k">return</span> <span class="n">Parent</span><span class="o">.</span><span class="n">add</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">obj</span><span class="p">)</span></div>
+
+
+<div class="viewcode-block" id="ArbdModel.add_group_site">
+<a class="viewcode-back" href="../../api/core/model.html#arbdmodel.model.ArbdModel.add_group_site">[docs]</a>
+ <span class="k">def</span><span class="w"> </span><span class="nf">add_group_site</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">particles</span><span class="p">,</span> <span class="n">weights</span><span class="o">=</span><span class="kc">None</span><span class="p">):</span>
+ <span class="n">g</span> <span class="o">=</span> <span class="n">GroupSite</span><span class="p">(</span><span class="n">particles</span><span class="p">,</span> <span class="n">weights</span><span class="p">)</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">group_sites</span><span class="o">.</span><span class="n">append</span><span class="p">(</span><span class="n">g</span><span class="p">)</span>
+ <span class="k">return</span> <span class="n">g</span></div>
+
+
+ <span class="k">def</span><span class="w"> </span><span class="nf">_clear_types</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span>
+ <span class="n">devlogger</span><span class="o">.</span><span class="n">debug</span><span class="p">(</span><span class="sa">f</span><span class="s1">'</span><span class="si">{</span><span class="bp">self</span><span class="si">}</span><span class="s1">: Clearing types'</span><span class="p">)</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">type_counts</span> <span class="o">=</span> <span class="kc">None</span>
+
+
+<div class="viewcode-block" id="ArbdModel.clear_all">
+<a class="viewcode-back" href="../../api/core/model.html#arbdmodel.model.ArbdModel.clear_all">[docs]</a>
+ <span class="k">def</span><span class="w"> </span><span class="nf">clear_all</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">keep_children</span><span class="o">=</span><span class="kc">False</span><span class="p">):</span>
+ <span class="n">Parent</span><span class="o">.</span><span class="n">clear_all</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">keep_children</span><span class="o">=</span><span class="n">keep_children</span><span class="p">)</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">particles</span> <span class="o">=</span> <span class="p">[]</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">num_particles</span> <span class="o">=</span> <span class="mi">0</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">_clear_types</span><span class="p">()</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">group_sites</span> <span class="o">=</span> <span class="p">[]</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">_nonbonded_interaction_files</span> <span class="o">=</span> <span class="p">[]</span></div>
+
+
+<div class="viewcode-block" id="ArbdModel.extend">
+<a class="viewcode-back" href="../../api/core/model.html#arbdmodel.model.ArbdModel.extend">[docs]</a>
+ <span class="k">def</span><span class="w"> </span><span class="nf">extend</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">other_model</span><span class="p">,</span> <span class="n">copy</span><span class="o">=</span><span class="kc">False</span><span class="p">):</span>
+
+ <span class="k">if</span> <span class="nb">any</span><span class="p">(</span> <span class="p">[</span><span class="n">p</span><span class="o">.</span><span class="n">rigid</span> <span class="k">for</span> <span class="n">p</span> <span class="ow">in</span> <span class="bp">self</span><span class="p">]</span> <span class="o">+</span> <span class="p">[</span><span class="n">p</span><span class="o">.</span><span class="n">rigid</span> <span class="k">for</span> <span class="n">p</span> <span class="ow">in</span> <span class="n">other_model</span><span class="p">]</span> <span class="p">):</span>
+ <span class="k">raise</span> <span class="ne">NotImplementedError</span><span class="p">(</span><span class="s1">'Models containing rigid bodies cannot yet be extended'</span><span class="p">)</span>
+
+ <span class="k">assert</span><span class="p">(</span> <span class="nb">isinstance</span><span class="p">(</span><span class="n">other_model</span><span class="p">,</span> <span class="n">ArbdModel</span><span class="p">)</span> <span class="p">)</span>
+ <span class="k">if</span> <span class="n">copy</span> <span class="o">==</span> <span class="kc">True</span><span class="p">:</span>
+ <span class="n">logger</span><span class="o">.</span><span class="n">warning</span><span class="p">(</span><span class="sa">f</span><span class="s1">'Forcing </span><span class="si">{</span><span class="bp">self</span><span class="o">.</span><span class="vm">__class__</span><span class="si">}</span><span class="s1">.extend(other_model,copy=False)'</span><span class="p">)</span>
+ <span class="n">copy</span> <span class="o">=</span> <span class="kc">False</span>
+
+ <span class="c1">## Combine particle types, taking care to handle name clashes</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">_countParticleTypes</span><span class="p">()</span>
+ <span class="n">other_model</span><span class="o">.</span><span class="n">_countParticleTypes</span><span class="p">()</span>
+
+ <span class="bp">self</span><span class="o">.</span><span class="n">getParticleTypesAndCounts</span><span class="p">()</span>
+ <span class="n">other_model</span><span class="o">.</span><span class="n">getParticleTypesAndCounts</span><span class="p">()</span>
+
+ <span class="n">names</span> <span class="o">=</span> <span class="nb">set</span><span class="p">([</span><span class="n">t</span><span class="o">.</span><span class="n">name</span> <span class="k">for</span> <span class="n">t</span> <span class="ow">in</span> <span class="bp">self</span><span class="o">.</span><span class="n">type_counts</span><span class="o">.</span><span class="n">keys</span><span class="p">()])</span>
+
+ <span class="n">devlogger</span><span class="o">.</span><span class="n">debug</span><span class="p">(</span><span class="sa">f</span><span class="s1">'Combining types </span><span class="si">{</span><span class="bp">self</span><span class="o">.</span><span class="n">type_counts</span><span class="o">.</span><span class="n">keys</span><span class="p">()</span><span class="si">}</span><span class="s1"> and </span><span class="si">{</span><span class="n">other_model</span><span class="o">.</span><span class="n">type_counts</span><span class="o">.</span><span class="n">keys</span><span class="p">()</span><span class="si">}</span><span class="s1">'</span><span class="p">)</span>
+ <span class="k">for</span> <span class="n">t1</span> <span class="ow">in</span> <span class="bp">self</span><span class="o">.</span><span class="n">type_counts</span><span class="o">.</span><span class="n">keys</span><span class="p">():</span>
+ <span class="k">for</span> <span class="n">t2</span> <span class="ow">in</span> <span class="n">other_model</span><span class="o">.</span><span class="n">type_counts</span><span class="o">.</span><span class="n">keys</span><span class="p">():</span>
+ <span class="k">if</span> <span class="n">t1</span><span class="o">.</span><span class="n">name</span> <span class="o">==</span> <span class="n">t2</span><span class="o">.</span><span class="n">name</span> <span class="ow">and</span> <span class="n">t1</span><span class="o">.</span><span class="fm">__eq__</span><span class="p">(</span><span class="n">t2</span><span class="p">,</span> <span class="n">check_equal</span><span class="o">=</span><span class="kc">False</span><span class="p">):</span>
+ <span class="n">i</span> <span class="o">=</span> <span class="mi">1</span>
+ <span class="n">new_name</span> <span class="o">=</span> <span class="sa">f</span><span class="s1">'</span><span class="si">{</span><span class="n">t2</span><span class="o">.</span><span class="n">name</span><span class="si">}{</span><span class="n">i</span><span class="si">}</span><span class="s1">'</span>
+ <span class="k">while</span> <span class="n">new_name</span> <span class="ow">in</span> <span class="n">names</span><span class="p">:</span>
+ <span class="n">i</span> <span class="o">+=</span> <span class="mi">1</span>
+ <span class="n">new_name</span> <span class="o">=</span> <span class="sa">f</span><span class="s1">'</span><span class="si">{</span><span class="n">t2</span><span class="o">.</span><span class="n">name</span><span class="si">}{</span><span class="n">i</span><span class="si">}</span><span class="s1">'</span>
+ <span class="n">devlogger</span><span class="o">.</span><span class="n">debug</span><span class="p">(</span><span class="sa">f</span><span class="s1">'Updating </span><span class="si">{</span><span class="n">t2</span><span class="o">.</span><span class="n">name</span><span class="si">}</span><span class="s1"> to </span><span class="si">{</span><span class="n">new_name</span><span class="si">}</span><span class="s1">'</span><span class="p">)</span>
+ <span class="n">t2</span><span class="o">.</span><span class="n">name</span> <span class="o">=</span> <span class="n">new_name</span>
+ <span class="n">names</span><span class="o">.</span><span class="n">add</span><span class="p">(</span><span class="n">new_name</span><span class="p">)</span>
+
+ <span class="c1">## Combine interactions</span>
+ <span class="k">for</span> <span class="n">i</span><span class="p">,</span> <span class="n">tA</span><span class="p">,</span> <span class="n">tB</span> <span class="ow">in</span> <span class="n">other_model</span><span class="o">.</span><span class="n">nonbonded_interactions</span><span class="p">:</span>
+ <span class="n">devlogger</span><span class="o">.</span><span class="n">debug</span><span class="p">(</span><span class="sa">f</span><span class="s1">'Combining model interactions </span><span class="si">{</span><span class="n">i</span><span class="si">}</span><span class="s1"> </span><span class="si">{</span><span class="n">tA</span><span class="si">}</span><span class="s1"> </span><span class="si">{</span><span class="n">tB</span><span class="si">}</span><span class="s1">'</span><span class="p">)</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">add_nonbonded_interaction</span><span class="p">(</span><span class="n">i</span><span class="p">,</span><span class="n">tA</span><span class="p">,</span><span class="n">tB</span><span class="p">)</span>
+
+ <span class="c1"># for g in other_model.children:</span>
+ <span class="c1"># self.update(g, copy=copy)</span>
+ <span class="n">g</span> <span class="o">=</span> <span class="n">Group</span><span class="p">()</span>
+ <span class="k">for</span> <span class="n">attr</span> <span class="ow">in</span> <span class="s1">'children position orientation bonds angles dihedrals impropers exclusions vector_angles bond_angles product_potentials group_sites'</span><span class="o">.</span><span class="n">split</span><span class="p">():</span>
+ <span class="n">g</span><span class="o">.</span><span class="fm">__setattr__</span><span class="p">(</span><span class="n">attr</span><span class="p">,</span> <span class="n">other_model</span><span class="o">.</span><span class="fm">__getattribute__</span><span class="p">(</span><span class="n">attr</span><span class="p">))</span>
+ <span class="n">devlogger</span><span class="o">.</span><span class="n">debug</span><span class="p">(</span><span class="sa">f</span><span class="s1">'Updating </span><span class="si">{</span><span class="bp">self</span><span class="si">}</span><span class="s1"> with </span><span class="si">{</span><span class="n">g</span><span class="o">.</span><span class="n">children</span><span class="p">[</span><span class="mi">0</span><span class="p">]</span><span class="o">.</span><span class="n">children</span><span class="p">[</span><span class="mi">0</span><span class="p">]</span><span class="si">}</span><span class="s1">'</span><span class="p">)</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">update</span><span class="p">(</span><span class="n">g</span><span class="p">,</span> <span class="n">copy</span><span class="o">=</span><span class="n">copy</span><span class="p">)</span>
+
+ <span class="bp">self</span><span class="o">.</span><span class="n">_clear_types</span><span class="p">()</span>
+
+ <span class="c1">## Combine configurations</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">configuration</span> <span class="o">=</span> <span class="n">other_model</span><span class="o">.</span><span class="n">configuration</span><span class="o">.</span><span class="n">combine</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">configuration</span><span class="p">,</span> <span class="n">policy</span><span class="o">=</span><span class="s1">'best'</span><span class="p">,</span> <span class="n">warn</span><span class="o">=</span><span class="kc">True</span><span class="p">)</span></div>
+
+
+<div class="viewcode-block" id="ArbdModel.assign_IBI_degrees_of_freedom">
+<a class="viewcode-back" href="../../api/core/model.html#arbdmodel.model.ArbdModel.assign_IBI_degrees_of_freedom">[docs]</a>
+ <span class="k">def</span><span class="w"> </span><span class="nf">assign_IBI_degrees_of_freedom</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span>
+
+<span class="w"> </span><span class="sd">""" Convenience routine that adds degrees of freedom to</span>
+<span class="sd"> corresponding IBI potentials """</span>
+
+ <span class="kn">from</span><span class="w"> </span><span class="nn">.ibi</span><span class="w"> </span><span class="kn">import</span> <span class="n">BondDof</span><span class="p">,</span> <span class="n">AngleDof</span><span class="p">,</span> <span class="n">DihedralDof</span><span class="p">,</span> <span class="n">PairDistributionDof</span>
+
+ <span class="bp">self</span><span class="o">.</span><span class="n">bonded_ibi_potentials</span> <span class="o">=</span> <span class="nb">set</span><span class="p">()</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">nonbonded_ibi_potentials</span> <span class="o">=</span> <span class="nb">set</span><span class="p">()</span>
+
+ <span class="k">for</span> <span class="n">get_fn</span><span class="p">,</span> <span class="n">parts_pot_fn</span><span class="p">,</span> <span class="bp">cls</span> <span class="ow">in</span> <span class="p">(</span>
+ <span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">get_bonds</span><span class="p">,</span> <span class="k">lambda</span> <span class="n">x</span><span class="p">:</span> <span class="p">(</span><span class="n">x</span><span class="p">[:</span><span class="mi">2</span><span class="p">],</span><span class="n">x</span><span class="p">[</span><span class="mi">2</span><span class="p">]),</span> <span class="n">BondDof</span><span class="p">),</span>
+ <span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">get_angles</span><span class="p">,</span> <span class="k">lambda</span> <span class="n">x</span><span class="p">:</span> <span class="p">(</span><span class="n">x</span><span class="p">[:</span><span class="mi">3</span><span class="p">],</span><span class="n">x</span><span class="p">[</span><span class="mi">3</span><span class="p">]),</span> <span class="n">AngleDof</span><span class="p">),</span>
+ <span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">get_dihedrals</span><span class="p">,</span> <span class="k">lambda</span> <span class="n">x</span><span class="p">:</span> <span class="p">(</span><span class="n">x</span><span class="p">[:</span><span class="mi">4</span><span class="p">],</span><span class="n">x</span><span class="p">[</span><span class="mi">4</span><span class="p">]),</span> <span class="n">DihedralDof</span><span class="p">)</span>
+ <span class="p">):</span>
+ <span class="k">for</span> <span class="n">x</span> <span class="ow">in</span> <span class="n">get_fn</span><span class="p">():</span>
+ <span class="n">parts</span><span class="p">,</span> <span class="n">pot</span> <span class="o">=</span> <span class="n">parts_pot_fn</span><span class="p">(</span><span class="n">x</span><span class="p">)</span>
+ <span class="k">try</span><span class="p">:</span> <span class="n">pot</span><span class="o">.</span><span class="n">degrees_of_freedom</span>
+ <span class="k">except</span><span class="p">:</span> <span class="k">continue</span>
+ <span class="n">pot</span><span class="o">.</span><span class="n">degrees_of_freedom</span><span class="o">.</span><span class="n">append</span><span class="p">(</span> <span class="bp">cls</span><span class="p">(</span><span class="o">*</span><span class="n">parts</span><span class="p">)</span> <span class="p">)</span>
+ <span class="k">if</span> <span class="n">pot</span> <span class="ow">not</span> <span class="ow">in</span> <span class="bp">self</span><span class="o">.</span><span class="n">bonded_ibi_potentials</span><span class="p">:</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">bonded_ibi_potentials</span><span class="o">.</span><span class="n">add</span><span class="p">(</span> <span class="n">pot</span> <span class="p">)</span>
+
+ <span class="n">logger</span><span class="o">.</span><span class="n">info</span><span class="p">(</span><span class="sa">f</span><span class="s1">'Gathering nonbonded IBI degrees of freedom'</span><span class="p">)</span>
+ <span class="n">all_exclusions</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">get_exclusions</span><span class="p">()</span>
+ <span class="k">try</span><span class="p">:</span>
+ <span class="k">raise</span> <span class="c1"># particle.idx wasn't set without this</span>
+ <span class="k">if</span> <span class="nb">len</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">type_counts</span><span class="p">)</span> <span class="o">==</span> <span class="mi">0</span><span class="p">:</span> <span class="k">raise</span>
+ <span class="k">except</span><span class="p">:</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">getParticleTypesAndCounts</span><span class="p">()</span>
+
+ <span class="n">type_to_particles</span> <span class="o">=</span> <span class="nb">dict</span><span class="p">()</span>
+ <span class="k">for</span> <span class="n">p</span> <span class="ow">in</span> <span class="bp">self</span><span class="p">:</span>
+ <span class="n">t</span> <span class="o">=</span> <span class="n">p</span><span class="o">.</span><span class="n">type_</span>
+ <span class="k">if</span> <span class="n">t</span> <span class="ow">not</span> <span class="ow">in</span> <span class="n">type_to_particles</span><span class="p">:</span> <span class="n">type_to_particles</span><span class="p">[</span><span class="n">t</span><span class="p">]</span> <span class="o">=</span> <span class="p">[]</span>
+ <span class="n">type_to_particles</span><span class="p">[</span><span class="n">t</span><span class="p">]</span><span class="o">.</span><span class="n">append</span><span class="p">(</span><span class="n">p</span><span class="p">)</span>
+ <span class="n">type_to_particles</span><span class="p">[</span><span class="kc">None</span><span class="p">]</span> <span class="o">=</span> <span class="p">[</span><span class="n">p</span> <span class="k">for</span> <span class="n">p</span> <span class="ow">in</span> <span class="bp">self</span><span class="p">]</span>
+
+ <span class="n">already_handled</span> <span class="o">=</span> <span class="nb">set</span><span class="p">()</span>
+ <span class="k">for</span> <span class="n">pot</span><span class="p">,</span> <span class="n">tA</span><span class="p">,</span> <span class="n">tB</span> <span class="ow">in</span> <span class="bp">self</span><span class="o">.</span><span class="n">nonbonded_interactions</span><span class="p">:</span>
+ <span class="c1">## Avoid including particle type pairs that don't apply</span>
+ <span class="k">if</span> <span class="p">(</span><span class="n">tA</span><span class="p">,</span><span class="n">tB</span><span class="p">)</span> <span class="ow">in</span> <span class="n">already_handled</span><span class="p">:</span> <span class="k">continue</span>
+ <span class="n">already_handled</span><span class="o">.</span><span class="n">add</span><span class="p">((</span><span class="n">tA</span><span class="p">,</span><span class="n">tB</span><span class="p">))</span>
+ <span class="n">already_handled</span><span class="o">.</span><span class="n">add</span><span class="p">((</span><span class="n">tB</span><span class="p">,</span><span class="n">tA</span><span class="p">))</span>
+
+ <span class="k">try</span><span class="p">:</span>
+ <span class="n">pot</span><span class="o">.</span><span class="n">degrees_of_freedom</span>
+ <span class="k">except</span><span class="p">:</span>
+ <span class="k">continue</span>
+
+ <span class="k">def</span><span class="w"> </span><span class="nf">_cond</span><span class="p">(</span><span class="n">pair</span><span class="p">):</span>
+ <span class="n">b1</span> <span class="o">=</span> <span class="p">(</span><span class="n">tA</span> <span class="ow">is</span> <span class="kc">None</span> <span class="ow">or</span> <span class="n">pair</span><span class="p">[</span><span class="mi">0</span><span class="p">]</span><span class="o">.</span><span class="n">type_</span> <span class="o">==</span> <span class="n">tA</span><span class="p">)</span> <span class="ow">and</span> <span class="p">(</span><span class="n">tB</span> <span class="ow">is</span> <span class="kc">None</span> <span class="ow">or</span> <span class="n">pair</span><span class="p">[</span><span class="mi">1</span><span class="p">]</span><span class="o">.</span><span class="n">type_</span> <span class="o">==</span> <span class="n">tB</span><span class="p">)</span>
+ <span class="n">b2</span> <span class="o">=</span> <span class="p">(</span><span class="n">tB</span> <span class="ow">is</span> <span class="kc">None</span> <span class="ow">or</span> <span class="n">pair</span><span class="p">[</span><span class="mi">0</span><span class="p">]</span><span class="o">.</span><span class="n">type_</span> <span class="o">==</span> <span class="n">tB</span><span class="p">)</span> <span class="ow">and</span> <span class="p">(</span><span class="n">tA</span> <span class="ow">is</span> <span class="kc">None</span> <span class="ow">or</span> <span class="n">pair</span><span class="p">[</span><span class="mi">1</span><span class="p">]</span><span class="o">.</span><span class="n">type_</span> <span class="o">==</span> <span class="n">tA</span><span class="p">)</span>
+ <span class="k">return</span> <span class="p">(</span><span class="n">b1</span> <span class="ow">or</span> <span class="n">b2</span><span class="p">)</span>
+
+ <span class="n">ex</span> <span class="o">=</span> <span class="nb">list</span><span class="p">(</span><span class="nb">filter</span><span class="p">(</span><span class="n">_cond</span><span class="p">,</span> <span class="n">all_exclusions</span><span class="p">))</span>
+ <span class="n">dof</span> <span class="o">=</span> <span class="n">PairDistributionDof</span><span class="p">(</span> <span class="n">type_to_particles</span><span class="p">[</span><span class="n">tA</span><span class="p">],</span> <span class="n">type_to_particles</span><span class="p">[</span><span class="n">tB</span><span class="p">],</span> <span class="n">exclusions</span><span class="o">=</span><span class="n">ex</span><span class="p">,</span>
+ <span class="n">range_</span><span class="o">=</span><span class="n">pot</span><span class="o">.</span><span class="n">range_</span><span class="p">,</span> <span class="n">resolution</span><span class="o">=</span><span class="n">pot</span><span class="o">.</span><span class="n">resolution</span><span class="p">)</span>
+
+ <span class="n">pot</span><span class="o">.</span><span class="n">degrees_of_freedom</span><span class="o">.</span><span class="n">append</span><span class="p">(</span> <span class="n">dof</span> <span class="p">)</span>
+
+ <span class="k">if</span> <span class="n">pot</span> <span class="ow">not</span> <span class="ow">in</span> <span class="bp">self</span><span class="o">.</span><span class="n">nonbonded_ibi_potentials</span><span class="p">:</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">nonbonded_ibi_potentials</span><span class="o">.</span><span class="n">add</span><span class="p">(</span> <span class="n">pot</span> <span class="p">)</span></div>
+
+
+<div class="viewcode-block" id="ArbdModel.load_target_IBI_distributions">
+<a class="viewcode-back" href="../../api/core/model.html#arbdmodel.model.ArbdModel.load_target_IBI_distributions">[docs]</a>
+ <span class="k">def</span><span class="w"> </span><span class="nf">load_target_IBI_distributions</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span>
+ <span class="k">raise</span> <span class="ne">NotImplementedError</span></div>
+
+
+<div class="viewcode-block" id="ArbdModel.run_IBI">
+<a class="viewcode-back" href="../../api/core/model.html#arbdmodel.model.ArbdModel.run_IBI">[docs]</a>
+ <span class="k">def</span><span class="w"> </span><span class="nf">run_IBI</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">iterations</span><span class="p">,</span> <span class="n">directory</span> <span class="o">=</span> <span class="s1">'./'</span><span class="p">,</span> <span class="n">engine</span> <span class="o">=</span> <span class="kc">None</span><span class="p">,</span> <span class="n">replicas</span> <span class="o">=</span> <span class="mi">1</span><span class="p">,</span> <span class="n">run_minimization</span> <span class="o">=</span> <span class="kc">True</span><span class="p">,</span> <span class="n">first_iteration</span><span class="o">=</span><span class="mi">1</span><span class="p">,</span> <span class="n">target_universe</span> <span class="o">=</span> <span class="kc">None</span><span class="p">,</span> <span class="n">target_trajectory</span> <span class="o">=</span> <span class="kc">None</span><span class="p">):</span>
+<span class="w"> </span><span class="sd">"""</span>
+<span class="sd"> Run Iterative Boltzmann Inversion (IBI) to optimize coarse-grained potentials.</span>
+<span class="sd"> </span>
+<span class="sd"> This method performs IBI iterations to match target distributions. For each iteration,</span>
+<span class="sd"> it writes CG potentials, runs simulations, and extracts distributions from the resulting</span>
+<span class="sd"> trajectories to update the potentials for the next iteration.</span>
+<span class="sd"> </span>
+<span class="sd"> Parameters</span>
+<span class="sd"> ----------</span>
+<span class="sd"> iterations : int</span>
+<span class="sd"> Number of IBI iterations to run</span>
+<span class="sd"> directory : str, optional</span>
+<span class="sd"> Directory to store output files, defaults to current directory</span>
+<span class="sd"> engine : ArbdEngine, optional</span>
+<span class="sd"> Simulation engine to use. If None, creates a default engine with 5e6 steps</span>
+<span class="sd"> and 1e4 output period</span>
+<span class="sd"> replicas : int, optional</span>
+<span class="sd"> Number of replica simulations to run per iteration, defaults to 1</span>
+<span class="sd"> run_minimization : bool, optional</span>
+<span class="sd"> Whether to run a brief minimization before the first iteration, defaults to True</span>
+<span class="sd"> first_iteration : int, optional</span>
+<span class="sd"> Starting iteration number, useful for continuing previous IBI runs, defaults to 1</span>
+<span class="sd"> target_universe : MDAnalysis.Universe, optional</span>
+<span class="sd"> Universe object containing target structure and trajectory</span>
+<span class="sd"> target_trajectory : str or list, optional</span>
+<span class="sd"> Target trajectory file(s) to use if target_universe is provided</span>
+<span class="sd"> </span>
+<span class="sd"> Raises</span>
+<span class="sd"> ------</span>
+<span class="sd"> ValueError</span>
+<span class="sd"> If the model does not have any IBI potentials assigned</span>
+<span class="sd"> NotImplementedError</span>
+<span class="sd"> If the system does not have an orthorhombic unit cell</span>
+<span class="sd"> </span>
+<span class="sd"> Notes</span>
+<span class="sd"> -----</span>
+<span class="sd"> The method requires bonded_ibi_potentials and nonbonded_ibi_potentials to be </span>
+<span class="sd"> defined in the model. Use assign_IBI_degrees_of_freedom() before calling this method.</span>
+<span class="sd"> """</span>
+ <span class="k">try</span><span class="p">:</span>
+ <span class="k">assert</span><span class="p">(</span> <span class="nb">len</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">bonded_ibi_potentials</span><span class="p">)</span> <span class="o">+</span> <span class="nb">len</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">nonbonded_ibi_potentials</span><span class="p">)</span> <span class="o">></span> <span class="mi">0</span> <span class="p">)</span>
+ <span class="k">except</span><span class="p">:</span>
+ <span class="k">raise</span> <span class="ne">ValueError</span><span class="p">(</span><span class="s1">'Model does not appear to contain IBI potentials; perhaps you forgot to run self.assign_IBI_degrees_of_freedom()'</span><span class="p">)</span>
+ <span class="n">logger</span><span class="o">.</span><span class="n">info</span><span class="p">(</span><span class="sa">f</span><span class="s1">'Running </span><span class="si">{</span><span class="n">iterations</span><span class="si">}</span><span class="s1"> IBI iterations with </span><span class="si">{</span><span class="nb">len</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">bonded_ibi_potentials</span><span class="p">)</span><span class="si">}</span><span class="s1"> bonded and </span><span class="si">{</span><span class="nb">len</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">nonbonded_ibi_potentials</span><span class="p">)</span><span class="si">}</span><span class="s1"> nonbonded IBI potentials'</span><span class="p">)</span>
+
+ <span class="k">if</span> <span class="n">engine</span> <span class="ow">is</span> <span class="kc">None</span><span class="p">:</span>
+ <span class="n">engine</span> <span class="o">=</span> <span class="n">ArbdEngine</span><span class="p">(</span>
+ <span class="n">num_steps</span> <span class="o">=</span> <span class="mf">5e6</span><span class="p">,</span>
+ <span class="n">output_period</span> <span class="o">=</span> <span class="mf">1e4</span><span class="p">,</span>
+ <span class="p">)</span>
+
+ <span class="k">if</span> <span class="n">np</span><span class="o">.</span><span class="n">array</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">dimensions</span><span class="p">)</span><span class="o">.</span><span class="n">size</span> <span class="o">></span> <span class="mi">3</span><span class="p">:</span>
+ <span class="k">raise</span> <span class="ne">NotImplementedError</span><span class="p">(</span><span class="s1">'IBI only implemented for systems with orthorhombic unit cells'</span><span class="p">)</span>
+ <span class="k">else</span><span class="p">:</span>
+ <span class="n">box</span> <span class="o">=</span> <span class="nb">tuple</span><span class="p">(</span><span class="nb">list</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">dimensions</span><span class="p">[:</span><span class="mi">3</span><span class="p">])</span> <span class="o">+</span> <span class="p">([</span><span class="mi">90</span><span class="p">]</span><span class="o">*</span><span class="mi">3</span><span class="p">))</span>
+
+ <span class="n">restart_file</span> <span class="o">=</span> <span class="kc">None</span>
+
+ <span class="k">if</span> <span class="n">target_universe</span> <span class="ow">is</span> <span class="ow">not</span> <span class="kc">None</span><span class="p">:</span>
+ <span class="n">_potentials</span> <span class="o">=</span> <span class="nb">list</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">bonded_ibi_potentials</span><span class="p">)</span><span class="o">+</span><span class="nb">list</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">nonbonded_ibi_potentials</span><span class="p">)</span>
+ <span class="k">with</span> <span class="n">logging_redirect_tqdm</span><span class="p">(</span><span class="n">loggers</span><span class="o">=</span><span class="p">[</span><span class="n">logger</span><span class="p">,</span><span class="n">devlogger</span><span class="p">]):</span>
+ <span class="k">for</span> <span class="n">potential</span> <span class="ow">in</span> <span class="n">tqdm</span><span class="p">(</span><span class="n">_potentials</span><span class="p">,</span> <span class="n">desc</span><span class="o">=</span><span class="s1">'Calculating target distributions'</span><span class="p">):</span>
+ <span class="n">potential</span><span class="o">.</span><span class="n">get_target_distribution</span><span class="p">(</span><span class="n">target_universe</span><span class="p">,</span> <span class="n">trajectory</span><span class="o">=</span><span class="n">target_trajectory</span><span class="p">)</span>
+
+ <span class="k">def</span><span class="w"> </span><span class="nf">_load_cg_u</span><span class="p">(</span><span class="n">iteration</span><span class="p">):</span>
+ <span class="n">name</span> <span class="o">=</span> <span class="sa">f</span><span class="s1">'ibi-</span><span class="si">{</span><span class="n">iteration</span><span class="si">:</span><span class="s1">03d</span><span class="si">}</span><span class="s1">'</span>
+ <span class="n">psf</span> <span class="o">=</span> <span class="s1">'</span><span class="si">{}</span><span class="s1">/</span><span class="si">{}</span><span class="s1">.psf'</span><span class="o">.</span><span class="n">format</span><span class="p">(</span><span class="n">directory</span><span class="p">,</span><span class="n">name</span><span class="p">)</span>
+ <span class="n">globstring</span><span class="o">=</span><span class="sa">f</span><span class="s1">'</span><span class="si">{</span><span class="n">directory</span><span class="si">}</span><span class="s1">/output/</span><span class="si">{</span><span class="n">name</span><span class="si">}</span><span class="s1">.*dcd'</span>
+ <span class="n">dcds</span> <span class="o">=</span> <span class="p">[</span><span class="n">f</span> <span class="k">for</span> <span class="n">f</span> <span class="ow">in</span> <span class="n">glob</span><span class="p">(</span><span class="n">globstring</span><span class="p">)</span> <span class="k">if</span> <span class="s1">'momentum'</span> <span class="ow">not</span> <span class="ow">in</span> <span class="n">f</span><span class="p">]</span>
+ <span class="k">if</span> <span class="nb">len</span><span class="p">(</span><span class="n">dcds</span><span class="p">)</span> <span class="o">==</span> <span class="mi">0</span><span class="p">:</span> <span class="k">raise</span> <span class="ne">ValueError</span><span class="p">(</span><span class="sa">f</span><span class="s1">'Expected to find dcds at </span><span class="si">{</span><span class="n">globstring</span><span class="si">}</span><span class="s1">'</span><span class="p">)</span>
+ <span class="n">cg_u</span> <span class="o">=</span> <span class="n">mda</span><span class="o">.</span><span class="n">Universe</span><span class="p">(</span><span class="n">psf</span><span class="p">,</span><span class="o">*</span><span class="n">dcds</span><span class="p">)</span>
+ <span class="k">return</span> <span class="n">cg_u</span>
+
+ <span class="n">cg_u</span> <span class="o">=</span> <span class="kc">None</span>
+ <span class="k">if</span> <span class="n">first_iteration</span> <span class="o">></span> <span class="mi">1</span><span class="p">:</span>
+ <span class="n">cg_u</span> <span class="o">=</span> <span class="n">_load_cg_u</span><span class="p">(</span><span class="n">first_iteration</span><span class="o">-</span><span class="mi">1</span><span class="p">)</span>
+ <span class="k">with</span> <span class="n">logging_redirect_tqdm</span><span class="p">(</span><span class="n">loggers</span><span class="o">=</span><span class="p">[</span><span class="n">logger</span><span class="p">,</span><span class="n">devlogger</span><span class="p">]):</span>
+ <span class="k">for</span> <span class="n">p</span> <span class="ow">in</span> <span class="n">tqdm</span><span class="p">(</span><span class="n">_potentials</span><span class="p">,</span> <span class="n">desc</span><span class="o">=</span><span class="s1">'Calculating initial CG distributions'</span><span class="p">):</span>
+ <span class="n">p</span><span class="o">.</span><span class="n">get_cg_distribution</span><span class="p">(</span><span class="n">cg_u</span><span class="p">,</span> <span class="n">box</span><span class="o">=</span><span class="n">box</span><span class="p">,</span> <span class="n">recalculate</span><span class="o">=</span><span class="kc">False</span><span class="p">)</span>
+
+ <span class="k">for</span> <span class="n">p</span> <span class="ow">in</span> <span class="n">_potentials</span><span class="p">:</span>
+ <span class="n">p</span><span class="o">.</span><span class="n">iteration</span> <span class="o">=</span> <span class="n">first_iteration</span>
+
+ <span class="k">for</span> <span class="n">i</span> <span class="ow">in</span> <span class="nb">range</span><span class="p">(</span><span class="n">first_iteration</span><span class="p">,</span> <span class="n">iterations</span><span class="o">+</span><span class="mi">1</span><span class="p">):</span>
+ <span class="n">logger</span><span class="o">.</span><span class="n">info</span><span class="p">(</span><span class="sa">f</span><span class="s1">'Working on IBI iteration </span><span class="si">{</span><span class="n">i</span><span class="si">}</span><span class="s1">/</span><span class="si">{</span><span class="n">iterations</span><span class="si">}</span><span class="s1">'</span><span class="p">)</span>
+
+ <span class="k">with</span> <span class="n">logging_redirect_tqdm</span><span class="p">(</span><span class="n">loggers</span><span class="o">=</span><span class="p">[</span><span class="n">logger</span><span class="p">,</span><span class="n">devlogger</span><span class="p">]):</span>
+ <span class="k">for</span> <span class="n">p</span> <span class="ow">in</span> <span class="n">tqdm</span><span class="p">(</span><span class="n">_potentials</span><span class="p">,</span> <span class="n">desc</span><span class="o">=</span><span class="s1">'Writing CG potentials'</span><span class="p">):</span>
+ <span class="c1"># if 'IBIPotentials/intrabond-1' in p.filename(): import ipdb; ipdb.set_trace()</span>
+ <span class="k">try</span><span class="p">:</span> <span class="n">p</span><span class="o">.</span><span class="n">write_cg_potential</span><span class="p">(</span><span class="n">cg_u</span><span class="p">,</span> <span class="n">tol</span><span class="o">=</span><span class="n">p</span><span class="o">.</span><span class="n">tol</span><span class="p">,</span> <span class="n">box</span><span class="o">=</span><span class="n">box</span><span class="p">)</span>
+ <span class="k">except</span><span class="p">:</span> <span class="n">p</span><span class="o">.</span><span class="n">write_cg_potential</span><span class="p">(</span><span class="n">cg_u</span><span class="p">,</span> <span class="n">box</span><span class="o">=</span><span class="n">box</span><span class="p">)</span>
+
+ <span class="k">if</span> <span class="n">i</span> <span class="o">==</span> <span class="mi">1</span> <span class="ow">and</span> <span class="n">run_minimization</span><span class="p">:</span>
+ <span class="n">logger</span><span class="o">.</span><span class="n">info</span><span class="p">(</span><span class="sa">f</span><span class="s1">'Running brief simulation with small timestep'</span><span class="p">)</span>
+ <span class="n">ts0</span> <span class="o">=</span> <span class="n">engine</span><span class="o">.</span><span class="n">_get_combined_conf</span><span class="p">(</span><span class="bp">self</span><span class="p">)</span><span class="o">.</span><span class="n">timestep</span>
+ <span class="n">engine</span><span class="o">.</span><span class="n">simulate</span><span class="p">(</span> <span class="bp">self</span><span class="p">,</span>
+ <span class="n">output_name</span> <span class="o">=</span> <span class="s1">'ibi-min'</span><span class="p">,</span> <span class="n">directory</span> <span class="o">=</span> <span class="n">directory</span><span class="p">,</span>
+ <span class="n">timestep</span> <span class="o">=</span> <span class="n">ts0</span><span class="o">/</span><span class="mi">100</span><span class="p">,</span>
+ <span class="n">num_steps</span> <span class="o">=</span> <span class="mi">10000</span><span class="p">,</span> <span class="n">output_period</span><span class="o">=</span><span class="mi">1000</span> <span class="p">)</span>
+
+ <span class="n">restart_file</span> <span class="o">=</span> <span class="sa">f</span><span class="s1">'</span><span class="si">{</span><span class="n">directory</span><span class="si">}</span><span class="s1">/output/ibi-min.restart'</span>
+
+ <span class="n">name</span> <span class="o">=</span> <span class="sa">f</span><span class="s1">'ibi-</span><span class="si">{</span><span class="n">i</span><span class="si">:</span><span class="s1">03d</span><span class="si">}</span><span class="s1">'</span>
+ <span class="n">engine</span><span class="o">.</span><span class="n">simulate</span><span class="p">(</span> <span class="bp">self</span><span class="p">,</span>
+ <span class="n">output_name</span> <span class="o">=</span> <span class="n">name</span><span class="p">,</span> <span class="n">directory</span> <span class="o">=</span> <span class="n">directory</span><span class="p">,</span>
+ <span class="n">restart_file</span> <span class="o">=</span> <span class="n">restart_file</span><span class="p">,</span>
+ <span class="n">replicas</span> <span class="o">=</span> <span class="n">replicas</span> <span class="p">)</span>
+
+ <span class="n">restart_file</span> <span class="o">=</span> <span class="sa">f</span><span class="s1">'</span><span class="si">{</span><span class="n">directory</span><span class="si">}</span><span class="s1">/output/</span><span class="si">{</span><span class="n">name</span><span class="si">}{</span><span class="s2">".0"</span><span class="w"> </span><span class="k">if</span><span class="w"> </span><span class="n">replicas</span><span class="w"> </span><span class="o">></span><span class="w"> </span><span class="mi">1</span><span class="w"> </span><span class="k">else</span><span class="w"> </span><span class="s2">""</span><span class="si">}</span><span class="s1">.restart'</span>
+ <span class="n">cg_u</span> <span class="o">=</span> <span class="n">_load_cg_u</span><span class="p">(</span><span class="n">i</span><span class="p">)</span>
+
+ <span class="k">with</span> <span class="n">logging_redirect_tqdm</span><span class="p">(</span><span class="n">loggers</span><span class="o">=</span><span class="p">[</span><span class="n">logger</span><span class="p">,</span><span class="n">devlogger</span><span class="p">]):</span>
+ <span class="k">for</span> <span class="n">p</span> <span class="ow">in</span> <span class="n">tqdm</span><span class="p">(</span><span class="n">_potentials</span><span class="p">,</span> <span class="n">desc</span><span class="o">=</span><span class="s1">'Extracting CG distributions'</span><span class="p">):</span>
+ <span class="n">p</span><span class="o">.</span><span class="n">get_cg_distribution</span><span class="p">(</span><span class="n">cg_u</span><span class="p">,</span> <span class="n">box</span><span class="o">=</span><span class="n">box</span><span class="p">,</span> <span class="n">recalculate</span><span class="o">=</span><span class="kc">False</span><span class="p">)</span>
+ <span class="n">p</span><span class="o">.</span><span class="n">iteration</span> <span class="o">+=</span> <span class="mi">1</span></div>
+
+
+<div class="viewcode-block" id="ArbdModel.update">
+<a class="viewcode-back" href="../../api/core/model.html#arbdmodel.model.ArbdModel.update">[docs]</a>
+ <span class="k">def</span><span class="w"> </span><span class="nf">update</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">group</span> <span class="p">,</span> <span class="n">copy</span><span class="o">=</span><span class="kc">False</span><span class="p">):</span>
+ <span class="k">assert</span><span class="p">(</span> <span class="nb">isinstance</span><span class="p">(</span><span class="n">group</span><span class="p">,</span> <span class="n">Group</span><span class="p">)</span> <span class="p">)</span>
+ <span class="k">if</span> <span class="n">copy</span><span class="p">:</span>
+ <span class="n">group</span> <span class="o">=</span> <span class="n">deepcopy</span><span class="p">(</span><span class="n">group</span><span class="p">)</span>
+ <span class="n">group</span><span class="o">.</span><span class="n">parent</span> <span class="o">=</span> <span class="bp">self</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">add</span><span class="p">(</span><span class="n">group</span><span class="p">)</span></div>
+
+
+ <span class="k">def</span><span class="w"> </span><span class="nf">_get_nonbonded_interaction</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">typeA</span><span class="p">,</span> <span class="n">typeB</span><span class="p">):</span>
+ <span class="k">for</span> <span class="n">cp</span> <span class="ow">in</span> <span class="p">(</span><span class="kc">False</span><span class="p">,</span><span class="kc">True</span><span class="p">):</span>
+ <span class="k">for</span> <span class="n">s</span><span class="p">,</span><span class="n">A</span><span class="p">,</span><span class="n">B</span> <span class="ow">in</span> <span class="bp">self</span><span class="o">.</span><span class="n">nonbonded_interactions</span><span class="p">:</span>
+ <span class="k">if</span> <span class="n">A</span> <span class="ow">is</span> <span class="kc">None</span> <span class="ow">or</span> <span class="n">B</span> <span class="ow">is</span> <span class="kc">None</span><span class="p">:</span>
+ <span class="k">if</span> <span class="n">A</span> <span class="ow">is</span> <span class="kc">None</span> <span class="ow">and</span> <span class="n">B</span> <span class="ow">is</span> <span class="kc">None</span><span class="p">:</span>
+ <span class="k">return</span> <span class="n">s</span>
+ <span class="k">elif</span> <span class="n">A</span> <span class="ow">is</span> <span class="kc">None</span> <span class="ow">and</span> <span class="n">typeB</span><span class="o">.</span><span class="n">is_same_type</span><span class="p">(</span><span class="n">B</span><span class="p">,</span> <span class="n">consider_parents</span><span class="o">=</span><span class="n">cp</span><span class="p">):</span>
+ <span class="k">return</span> <span class="n">s</span>
+ <span class="k">elif</span> <span class="n">B</span> <span class="ow">is</span> <span class="kc">None</span> <span class="ow">and</span> <span class="n">typeA</span><span class="o">.</span><span class="n">is_same_type</span><span class="p">(</span><span class="n">A</span><span class="p">,</span> <span class="n">consider_parents</span><span class="o">=</span><span class="n">cp</span><span class="p">):</span>
+ <span class="k">return</span> <span class="n">s</span>
+ <span class="k">elif</span> <span class="n">typeA</span><span class="o">.</span><span class="n">is_same_type</span><span class="p">(</span><span class="n">A</span><span class="p">,</span><span class="n">consider_parents</span><span class="o">=</span><span class="kc">False</span><span class="p">)</span> <span class="ow">and</span> <span class="n">typeB</span><span class="o">.</span><span class="n">is_same_type</span><span class="p">(</span><span class="n">B</span><span class="p">,</span><span class="n">consider_parents</span><span class="o">=</span><span class="n">cp</span><span class="p">):</span>
+ <span class="k">return</span> <span class="n">s</span>
+
+ <span class="c1"># raise Exception("No nonbonded scheme found for %s and %s" % (typeA.name, typeB.name))</span>
+ <span class="c1"># print("WARNING: No nonbonded scheme found for %s and %s" % (typeA.name, typeB.name))</span>
+
+ <span class="k">def</span><span class="w"> </span><span class="nf">_countParticleTypes</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span>
+ <span class="c1">## TODO: check for modifications to particle that require</span>
+ <span class="c1">## automatic generation of new particle type</span>
+ <span class="n">type_counts</span> <span class="o">=</span> <span class="nb">dict</span><span class="p">()</span> <span class="c1"># type is key, value is 2-element list of regular particle counts and attached particles</span>
+
+ <span class="n">parts</span><span class="p">,</span> <span class="bp">self</span><span class="o">.</span><span class="n">rigid_bodies</span> <span class="o">=</span> <span class="p">[],[]</span>
+ <span class="k">for</span> <span class="n">p</span> <span class="ow">in</span> <span class="bp">self</span><span class="p">:</span>
+ <span class="k">if</span> <span class="n">p</span><span class="o">.</span><span class="n">rigid</span><span class="p">:</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">rigid_bodies</span><span class="o">.</span><span class="n">append</span><span class="p">(</span><span class="n">p</span><span class="p">)</span>
+ <span class="k">else</span><span class="p">:</span>
+ <span class="n">parts</span><span class="o">.</span><span class="n">append</span><span class="p">(</span><span class="n">p</span><span class="p">)</span>
+
+ <span class="k">for</span> <span class="n">p</span> <span class="ow">in</span> <span class="n">parts</span><span class="p">:</span>
+ <span class="n">t</span> <span class="o">=</span> <span class="n">p</span><span class="o">.</span><span class="n">type_</span>
+ <span class="k">if</span> <span class="n">t</span> <span class="ow">in</span> <span class="n">type_counts</span><span class="p">:</span>
+ <span class="n">type_counts</span><span class="p">[</span><span class="n">t</span><span class="p">][</span><span class="mi">0</span><span class="p">]</span> <span class="o">+=</span> <span class="mi">1</span>
+ <span class="k">else</span><span class="p">:</span>
+ <span class="n">type_counts</span><span class="p">[</span><span class="n">t</span><span class="p">]</span> <span class="o">=</span> <span class="p">[</span><span class="mi">1</span><span class="p">,</span><span class="mi">0</span><span class="p">]</span>
+
+ <span class="n">parts</span> <span class="o">=</span> <span class="p">[</span><span class="n">p</span> <span class="k">for</span> <span class="n">rb</span> <span class="ow">in</span> <span class="bp">self</span> <span class="k">if</span> <span class="n">rb</span><span class="o">.</span><span class="n">rigid</span> <span class="k">for</span> <span class="n">p</span> <span class="ow">in</span> <span class="n">rb</span><span class="o">.</span><span class="n">attached_particles</span><span class="p">]</span>
+ <span class="k">for</span> <span class="n">p</span> <span class="ow">in</span> <span class="n">parts</span><span class="p">:</span>
+ <span class="n">t</span> <span class="o">=</span> <span class="n">p</span><span class="o">.</span><span class="n">type_</span>
+ <span class="k">if</span> <span class="n">t</span> <span class="ow">in</span> <span class="n">type_counts</span><span class="p">:</span>
+ <span class="n">type_counts</span><span class="p">[</span><span class="n">t</span><span class="p">][</span><span class="mi">1</span><span class="p">]</span> <span class="o">+=</span> <span class="mi">1</span>
+ <span class="k">else</span><span class="p">:</span>
+ <span class="n">type_counts</span><span class="p">[</span><span class="n">t</span><span class="p">]</span> <span class="o">=</span> <span class="p">[</span><span class="mi">0</span><span class="p">,</span><span class="mi">1</span><span class="p">]</span>
+
+ <span class="k">if</span> <span class="nb">len</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">dummy_types</span><span class="p">)</span> <span class="o">!=</span> <span class="mi">0</span><span class="p">:</span>
+ <span class="k">raise</span><span class="p">(</span><span class="s2">"Dummy types have been deprecated"</span><span class="p">)</span>
+ <span class="c1"># for t in self.dummy_types:</span>
+ <span class="c1"># if t not in type_counts:</span>
+ <span class="c1"># type_counts[t] = 0</span>
+
+ <span class="k">for</span> <span class="n">i</span><span class="p">,</span><span class="n">tA</span><span class="p">,</span><span class="n">tB</span> <span class="ow">in</span> <span class="bp">self</span><span class="o">.</span><span class="n">nonbonded_interactions</span><span class="p">:</span>
+ <span class="k">if</span> <span class="n">tA</span> <span class="ow">is</span> <span class="ow">not</span> <span class="kc">None</span> <span class="ow">and</span> <span class="n">tA</span> <span class="ow">not</span> <span class="ow">in</span> <span class="n">type_counts</span><span class="p">:</span>
+ <span class="n">type_counts</span><span class="p">[</span><span class="n">tA</span><span class="p">]</span> <span class="o">=</span> <span class="p">[</span><span class="mi">0</span><span class="p">,</span><span class="mi">0</span><span class="p">]</span>
+ <span class="k">if</span> <span class="n">tB</span> <span class="ow">is</span> <span class="ow">not</span> <span class="kc">None</span> <span class="ow">and</span> <span class="n">tB</span> <span class="ow">not</span> <span class="ow">in</span> <span class="n">type_counts</span><span class="p">:</span>
+ <span class="n">type_counts</span><span class="p">[</span><span class="n">tB</span><span class="p">]</span> <span class="o">=</span> <span class="p">[</span><span class="mi">0</span><span class="p">,</span><span class="mi">0</span><span class="p">]</span>
+
+
+ <span class="bp">self</span><span class="o">.</span><span class="n">type_counts</span> <span class="o">=</span> <span class="n">type_counts</span>
+
+ <span class="n">rbtc</span> <span class="o">=</span> <span class="nb">dict</span><span class="p">()</span>
+ <span class="n">rbti</span><span class="o">=</span><span class="p">{}</span>
+ <span class="k">for</span> <span class="n">rb</span> <span class="ow">in</span> <span class="bp">self</span><span class="o">.</span><span class="n">rigid_bodies</span><span class="p">:</span>
+ <span class="n">t</span> <span class="o">=</span> <span class="n">rb</span><span class="o">.</span><span class="n">type_</span><span class="o">.</span><span class="n">name</span>
+ <span class="k">if</span> <span class="n">t</span> <span class="ow">in</span> <span class="n">rbtc</span><span class="p">:</span> <span class="n">rbtc</span><span class="p">[</span><span class="n">t</span><span class="p">]</span> <span class="o">+=</span> <span class="mi">1</span>
+ <span class="k">else</span><span class="p">:</span>
+ <span class="n">rbti</span><span class="p">[</span><span class="n">t</span><span class="p">]</span><span class="o">=</span><span class="n">rb</span><span class="o">.</span><span class="n">type_</span>
+ <span class="n">rbtc</span><span class="p">[</span><span class="n">t</span><span class="p">]</span> <span class="o">=</span> <span class="mi">1</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">rigid_body_type_counts</span> <span class="o">=</span> <span class="p">[(</span><span class="n">k</span><span class="p">,</span><span class="n">rbtc</span><span class="p">[</span><span class="n">k</span><span class="p">])</span> <span class="k">for</span> <span class="n">k</span> <span class="ow">in</span> <span class="nb">sorted</span><span class="p">(</span><span class="n">rbtc</span><span class="o">.</span><span class="n">keys</span><span class="p">())]</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">rigid_body_index</span><span class="o">=</span><span class="n">rbti</span>
+ <span class="n">devlogger</span><span class="o">.</span><span class="n">debug</span><span class="p">(</span><span class="sa">f</span><span class="s1">'</span><span class="si">{</span><span class="bp">self</span><span class="si">}</span><span class="s1">: Counting types: </span><span class="si">{</span><span class="n">type_counts</span><span class="si">}</span><span class="s1">'</span><span class="p">)</span>
+ <span class="n">devlogger</span><span class="o">.</span><span class="n">debug</span><span class="p">(</span><span class="sa">f</span><span class="s1">'</span><span class="si">{</span><span class="bp">self</span><span class="si">}</span><span class="s1">: Counting rb types: </span><span class="si">{</span><span class="n">rbtc</span><span class="si">}</span><span class="s1">'</span><span class="p">)</span>
+
+ <span class="k">def</span><span class="w"> </span><span class="nf">_updateParticleOrder</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span>
+ <span class="c1">## Create ordered list</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">particles</span> <span class="o">=</span> <span class="p">[</span><span class="n">p</span> <span class="k">for</span> <span class="n">p</span> <span class="ow">in</span> <span class="bp">self</span> <span class="k">if</span> <span class="ow">not</span> <span class="n">p</span><span class="o">.</span><span class="n">rigid</span><span class="p">]</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">rigid_bodies</span> <span class="o">=</span> <span class="nb">list</span><span class="p">(</span><span class="nb">sorted</span><span class="p">([</span><span class="n">p</span> <span class="k">for</span> <span class="n">p</span> <span class="ow">in</span> <span class="bp">self</span> <span class="k">if</span> <span class="n">p</span><span class="o">.</span><span class="n">rigid</span><span class="p">],</span> <span class="n">key</span><span class="o">=</span><span class="k">lambda</span> <span class="n">x</span><span class="p">:</span> <span class="n">x</span><span class="o">.</span><span class="n">type_</span><span class="p">))</span>
+ <span class="c1"># self.particles = sorted(particles, key=lambda p: (p.type_, p.idx))</span>
+
+ <span class="c1">## Update particle indices</span>
+ <span class="n">idx</span> <span class="o">=</span> <span class="mi">0</span>
+ <span class="k">for</span> <span class="n">p</span> <span class="ow">in</span> <span class="bp">self</span><span class="o">.</span><span class="n">particles</span><span class="p">:</span>
+ <span class="n">p</span><span class="o">.</span><span class="n">idx</span> <span class="o">=</span> <span class="n">idx</span>
+ <span class="n">idx</span> <span class="o">=</span> <span class="n">idx</span><span class="o">+</span><span class="mi">1</span>
+
+ <span class="c1">## Add attached particle indices</span>
+ <span class="c1"># attach particles</span>
+ <span class="k">for</span> <span class="n">j</span><span class="p">,</span><span class="n">rb</span> <span class="ow">in</span> <span class="nb">enumerate</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">rigid_bodies</span><span class="p">):</span>
+ <span class="k">for</span> <span class="n">p</span> <span class="ow">in</span> <span class="n">rb</span><span class="o">.</span><span class="n">attached_particles</span><span class="p">:</span>
+ <span class="n">p</span><span class="o">.</span><span class="n">idx</span> <span class="o">=</span> <span class="n">idx</span>
+ <span class="n">idx</span> <span class="o">=</span> <span class="n">idx</span><span class="o">+</span><span class="mi">1</span>
+
+ <span class="c1">## TODO recurse through childrens' group_sites</span>
+ <span class="k">for</span> <span class="n">g</span> <span class="ow">in</span> <span class="bp">self</span><span class="o">.</span><span class="n">group_sites</span><span class="p">:</span>
+ <span class="n">g</span><span class="o">.</span><span class="n">idx</span> <span class="o">=</span> <span class="n">idx</span>
+ <span class="n">idx</span> <span class="o">=</span> <span class="n">idx</span> <span class="o">+</span> <span class="mi">1</span>
+
+ <span class="c1"># self.initialCoords = np.array([p.initialPosition for p in self.particles])</span>
+
+<div class="viewcode-block" id="ArbdModel.useNonbondedScheme">
+<a class="viewcode-back" href="../../api/core/model.html#arbdmodel.model.ArbdModel.useNonbondedScheme">[docs]</a>
+ <span class="k">def</span><span class="w"> </span><span class="nf">useNonbondedScheme</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">nbScheme</span><span class="p">,</span> <span class="n">typeA</span><span class="o">=</span><span class="kc">None</span><span class="p">,</span> <span class="n">typeB</span><span class="o">=</span><span class="kc">None</span><span class="p">):</span>
+<span class="w"> </span><span class="sd">""" deprecated """</span>
+ <span class="n">logger</span><span class="o">.</span><span class="n">warning</span><span class="p">(</span><span class="s1">'useNonbondedScheme is deprecated! Please update your code to use `add_nonbonded_interaction`'</span><span class="p">)</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">add_nonbonded_interaction</span><span class="p">(</span><span class="n">nbScheme</span><span class="p">,</span> <span class="n">typeA</span><span class="p">,</span> <span class="n">typeB</span><span class="p">)</span></div>
+
+
+<div class="viewcode-block" id="ArbdModel.add_nonbonded_interaction">
+<a class="viewcode-back" href="../../api/core/model.html#arbdmodel.model.ArbdModel.add_nonbonded_interaction">[docs]</a>
+ <span class="k">def</span><span class="w"> </span><span class="nf">add_nonbonded_interaction</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">nonbonded_potential</span><span class="p">,</span> <span class="n">typeA</span><span class="o">=</span><span class="kc">None</span><span class="p">,</span> <span class="n">typeB</span><span class="o">=</span><span class="kc">None</span><span class="p">):</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">nonbonded_interactions</span><span class="o">.</span><span class="n">append</span><span class="p">(</span> <span class="p">[</span><span class="n">nonbonded_potential</span><span class="p">,</span> <span class="n">typeA</span><span class="p">,</span> <span class="n">typeB</span><span class="p">]</span> <span class="p">)</span>
+ <span class="k">if</span> <span class="n">typeA</span> <span class="o">!=</span> <span class="n">typeB</span><span class="p">:</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">nonbonded_interactions</span><span class="o">.</span><span class="n">append</span><span class="p">(</span> <span class="p">[</span><span class="n">nonbonded_potential</span><span class="p">,</span> <span class="n">typeB</span><span class="p">,</span> <span class="n">typeA</span><span class="p">]</span> <span class="p">)</span></div>
+
+
+<div class="viewcode-block" id="ArbdModel.prepare_for_simulation">
+<a class="viewcode-back" href="../../api/core/model.html#arbdmodel.model.ArbdModel.prepare_for_simulation">[docs]</a>
+ <span class="k">def</span><span class="w"> </span><span class="nf">prepare_for_simulation</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span>
+ <span class="o">...</span></div>
+
+
+<div class="viewcode-block" id="ArbdModel.getParticleTypesAndCounts">
+<a class="viewcode-back" href="../../api/core/model.html#arbdmodel.model.ArbdModel.getParticleTypesAndCounts">[docs]</a>
+ <span class="k">def</span><span class="w"> </span><span class="nf">getParticleTypesAndCounts</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span>
+<span class="w"> </span><span class="sd">""" Includes rigid body-attached particles """</span>
+ <span class="c1">## TODO: remove(?)</span>
+ <span class="k">if</span> <span class="bp">self</span><span class="o">.</span><span class="n">type_counts</span> <span class="ow">is</span> <span class="kc">None</span><span class="p">:</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">_countParticleTypes</span><span class="p">()</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">_updateParticleOrder</span><span class="p">()</span>
+
+ <span class="k">return</span> <span class="nb">sorted</span><span class="p">(</span> <span class="bp">self</span><span class="o">.</span><span class="n">type_counts</span><span class="o">.</span><span class="n">items</span><span class="p">(),</span> <span class="n">key</span><span class="o">=</span><span class="k">lambda</span> <span class="n">x</span><span class="p">:</span> <span class="n">x</span><span class="p">[</span><span class="mi">0</span><span class="p">]</span> <span class="p">)</span></div>
+
+
+ <span class="k">def</span><span class="w"> </span><span class="nf">_particleTypePairIter</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span>
+ <span class="n">typesAndCounts</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">getParticleTypesAndCounts</span><span class="p">()</span>
+ <span class="n">i_skipped</span> <span class="o">=</span> <span class="mi">0</span>
+ <span class="k">for</span> <span class="n">i</span> <span class="ow">in</span> <span class="nb">range</span><span class="p">(</span><span class="nb">len</span><span class="p">(</span><span class="n">typesAndCounts</span><span class="p">)):</span>
+ <span class="n">t1</span><span class="p">,(</span><span class="n">n1</span><span class="p">,</span><span class="n">rb1</span><span class="p">)</span> <span class="o">=</span> <span class="n">typesAndCounts</span><span class="p">[</span><span class="n">i</span><span class="p">]</span>
+ <span class="k">if</span> <span class="n">n1</span><span class="o">+</span><span class="n">rb1</span> <span class="o">==</span> <span class="mi">0</span><span class="p">:</span>
+ <span class="n">i_skipped</span> <span class="o">+=</span> <span class="mi">1</span>
+ <span class="k">continue</span>
+ <span class="n">j_skipped</span> <span class="o">=</span> <span class="mi">0</span>
+ <span class="k">for</span> <span class="n">j</span> <span class="ow">in</span> <span class="nb">range</span><span class="p">(</span><span class="n">i</span><span class="p">,</span><span class="nb">len</span><span class="p">(</span><span class="n">typesAndCounts</span><span class="p">)):</span>
+ <span class="n">t2</span><span class="p">,(</span><span class="n">n2</span><span class="p">,</span><span class="n">rb2</span><span class="p">)</span> <span class="o">=</span> <span class="n">typesAndCounts</span><span class="p">[</span><span class="n">j</span><span class="p">]</span>
+ <span class="k">if</span> <span class="n">n2</span><span class="o">+</span><span class="n">rb2</span> <span class="o">==</span> <span class="mi">0</span><span class="p">:</span>
+ <span class="n">j_skipped</span> <span class="o">+=</span> <span class="mi">1</span>
+ <span class="k">continue</span>
+ <span class="k">if</span> <span class="n">n2</span> <span class="o">==</span> <span class="mi">0</span><span class="p">:</span> <span class="k">continue</span>
+ <span class="k">yield</span><span class="p">(</span> <span class="p">[</span><span class="n">i</span><span class="o">-</span><span class="n">i_skipped</span><span class="p">,</span><span class="n">j</span><span class="o">-</span><span class="n">i_skipped</span><span class="o">-</span><span class="n">j_skipped</span><span class="p">,</span><span class="n">t1</span><span class="p">,</span><span class="n">t2</span><span class="p">]</span> <span class="p">)</span>
+
+<div class="viewcode-block" id="ArbdModel.dimensions_from_structure">
+<a class="viewcode-back" href="../../api/core/model.html#arbdmodel.model.ArbdModel.dimensions_from_structure">[docs]</a>
+ <span class="k">def</span><span class="w"> </span><span class="nf">dimensions_from_structure</span><span class="p">(</span> <span class="bp">self</span><span class="p">,</span> <span class="n">padding_factor</span><span class="o">=</span><span class="mf">1.5</span><span class="p">,</span> <span class="n">isotropic</span><span class="o">=</span><span class="kc">False</span> <span class="p">):</span>
+ <span class="k">raise</span><span class="p">(</span><span class="ne">NotImplementedError</span><span class="p">)</span></div>
+
+
+<div class="viewcode-block" id="ArbdModel.simulate">
+<a class="viewcode-back" href="../../api/core/model.html#arbdmodel.model.ArbdModel.simulate">[docs]</a>
+ <span class="k">def</span><span class="w"> </span><span class="nf">simulate</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">output_name</span><span class="p">,</span> <span class="o">**</span><span class="n">kwargs</span><span class="p">):</span>
+ <span class="c1">## split kwargs</span>
+ <span class="n">sim_kws</span> <span class="o">=</span> <span class="p">[</span><span class="s1">'output_directory'</span><span class="p">,</span> <span class="s1">'directory'</span><span class="p">,</span> <span class="s1">'log_file'</span><span class="p">,</span> <span class="s1">'binary'</span><span class="p">,</span> <span class="s1">'num_procs'</span><span class="p">,</span> <span class="s1">'dry_run'</span><span class="p">,</span> <span class="s1">'configuration'</span><span class="p">,</span> <span class="s1">'replicas'</span><span class="p">]</span>
+ <span class="n">sim_kwargs</span> <span class="o">=</span> <span class="p">{</span><span class="n">kw</span><span class="p">:</span><span class="n">kwargs</span><span class="p">[</span><span class="n">kw</span><span class="p">]</span> <span class="k">for</span> <span class="n">kw</span> <span class="ow">in</span> <span class="n">sim_kws</span> <span class="k">if</span> <span class="n">kw</span> <span class="ow">in</span> <span class="n">kwargs</span><span class="p">}</span>
+ <span class="n">engine_kwargs</span> <span class="o">=</span> <span class="p">{</span><span class="n">k</span><span class="p">:</span><span class="n">v</span> <span class="k">for</span> <span class="n">k</span><span class="p">,</span><span class="n">v</span> <span class="ow">in</span> <span class="n">kwargs</span><span class="o">.</span><span class="n">items</span><span class="p">()</span> <span class="k">if</span> <span class="n">k</span> <span class="ow">not</span> <span class="ow">in</span> <span class="n">sim_kws</span><span class="p">}</span>
+ <span class="n">engine</span> <span class="o">=</span> <span class="n">ArbdEngine</span><span class="p">(</span><span class="o">**</span><span class="n">engine_kwargs</span><span class="p">)</span>
+ <span class="k">return</span> <span class="n">engine</span><span class="o">.</span><span class="n">simulate</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">output_name</span><span class="p">,</span> <span class="o">**</span><span class="n">sim_kwargs</span><span class="p">)</span></div>
+</div>
+
+</pre></div>
+
+ </article>
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diff --git a/_build/html/_modules/arbdmodel/parmed_bd.html b/_build/html/_modules/arbdmodel/parmed_bd.html
new file mode 100644
index 0000000000000000000000000000000000000000..078a3934901fc053dec12f37d4b4ed9af5b124db
--- /dev/null
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@@ -0,0 +1,1238 @@
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+
+ <h1>Source code for arbdmodel.parmed_bd</h1><div class="highlight"><pre>
+<span></span><span class="kn">import</span><span class="w"> </span><span class="nn">numpy</span><span class="w"> </span><span class="k">as</span><span class="w"> </span><span class="nn">np</span>
+<span class="kn">import</span><span class="w"> </span><span class="nn">parmed</span>
+<span class="kn">from</span><span class="w"> </span><span class="nn">scipy.spatial</span><span class="w"> </span><span class="kn">import</span> <span class="n">distance_matrix</span>
+<span class="kn">from</span><span class="w"> </span><span class="nn">.model</span><span class="w"> </span><span class="kn">import</span> <span class="n">ArbdModel</span>
+<span class="kn">from</span><span class="w"> </span><span class="nn">.core_objects</span><span class="w"> </span><span class="kn">import</span> <span class="n">Group</span><span class="p">,</span> <span class="n">ParticleType</span><span class="p">,</span> <span class="n">PointParticle</span>
+<span class="kn">from</span><span class="w"> </span><span class="nn">.interactions</span><span class="w"> </span><span class="kn">import</span> <span class="n">HarmonicBond</span>
+<span class="kn">from</span><span class="w"> </span><span class="nn">.logger</span><span class="w"> </span><span class="kn">import</span> <span class="n">logger</span>
+
+
+<div class="viewcode-block" id="ParmedArbd">
+<a class="viewcode-back" href="../../api/simulation_engines/parmed_bd.html#arbdmodel.parmed_bd.ParmedArbd">[docs]</a>
+<span class="k">class</span><span class="w"> </span><span class="nc">ParmedArbd</span><span class="p">(</span><span class="n">ArbdModel</span><span class="p">):</span>
+<span class="w"> </span><span class="sd">"""</span>
+<span class="sd"> Class for converting ParmEd structures to ARBD models for simulation.</span>
+<span class="sd"> </span>
+<span class="sd"> This class facilitates the conversion of molecular structures loaded with ParmEd</span>
+<span class="sd"> into ARBD simulation models, preserving bonded and non-bonded interactions.</span>
+<span class="sd"> It also supports creating dual topology models for free energy calculations.</span>
+<span class="sd"> </span>
+<span class="sd"> Attributes:</span>
+<span class="sd"> parmed_structure: The original ParmEd structure</span>
+<span class="sd"> atom_types: Dictionary mapping atom type names to ParticleType objects</span>
+<span class="sd"> atoms_map: Mapping from ParmEd atoms to ARBD atoms</span>
+<span class="sd"> """</span>
+
+ <span class="k">def</span><span class="w"> </span><span class="fm">__init__</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">parmed_structure</span><span class="o">=</span><span class="kc">None</span><span class="p">,</span> <span class="n">psf</span><span class="o">=</span><span class="kc">None</span><span class="p">,</span> <span class="n">pdb</span><span class="o">=</span><span class="kc">None</span><span class="p">,</span> <span class="n">parameter_files</span><span class="o">=</span><span class="kc">None</span><span class="p">,</span>
+ <span class="n">system_type</span><span class="o">=</span><span class="s1">'charmm'</span><span class="p">,</span> <span class="n">integrator</span><span class="o">=</span><span class="s1">'MD'</span><span class="p">,</span> <span class="n">cutoff</span><span class="o">=</span><span class="mi">12</span><span class="p">,</span> <span class="o">**</span><span class="n">kwargs</span><span class="p">):</span>
+<span class="w"> </span><span class="sd">"""</span>
+<span class="sd"> Initialize ParmedArbd model from a ParmEd structure or PSF/PDB files.</span>
+<span class="sd"> </span>
+<span class="sd"> Args:</span>
+<span class="sd"> parmed_structure: Existing ParmEd structure object (optional)</span>
+<span class="sd"> psf: Path to PSF file (optional if parmed_structure is provided)</span>
+<span class="sd"> pdb: Path to PDB file (optional if parmed_structure is provided)</span>
+<span class="sd"> parameter_files: List of parameter files for force field (optional)</span>
+<span class="sd"> system_type: Type of system ('charmm', etc.)</span>
+<span class="sd"> integrator: Simulation integrator type</span>
+<span class="sd"> cutoff: Non-bonded interaction cutoff distance</span>
+<span class="sd"> **kwargs: Additional arguments for ArbdModel</span>
+<span class="sd"> """</span>
+ <span class="c1"># Initialize empty model first</span>
+ <span class="n">ArbdModel</span><span class="o">.</span><span class="fm">__init__</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="p">[],</span> <span class="n">integrator</span><span class="o">=</span><span class="n">integrator</span><span class="p">,</span> <span class="n">cutoff</span><span class="o">=</span><span class="n">cutoff</span><span class="p">,</span> <span class="o">**</span><span class="n">kwargs</span><span class="p">)</span>
+
+ <span class="bp">self</span><span class="o">.</span><span class="n">atom_types</span> <span class="o">=</span> <span class="p">{}</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">atoms_map</span> <span class="o">=</span> <span class="p">{}</span>
+
+ <span class="c1"># Load structure if provided</span>
+ <span class="k">if</span> <span class="n">parmed_structure</span> <span class="ow">is</span> <span class="ow">not</span> <span class="kc">None</span><span class="p">:</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">parmed_structure</span> <span class="o">=</span> <span class="n">parmed_structure</span>
+ <span class="k">elif</span> <span class="n">psf</span> <span class="ow">is</span> <span class="ow">not</span> <span class="kc">None</span> <span class="ow">and</span> <span class="n">pdb</span> <span class="ow">is</span> <span class="ow">not</span> <span class="kc">None</span><span class="p">:</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">parmed_structure</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">_read_files</span><span class="p">(</span><span class="n">psf</span><span class="p">,</span> <span class="n">pdb</span><span class="p">,</span> <span class="n">parameter_files</span><span class="p">,</span> <span class="n">system_type</span><span class="p">)</span>
+ <span class="k">else</span><span class="p">:</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">parmed_structure</span> <span class="o">=</span> <span class="kc">None</span>
+ <span class="n">logger</span><span class="o">.</span><span class="n">warning</span><span class="p">(</span><span class="s2">"No structure provided; use load_structure() to load one"</span><span class="p">)</span>
+ <span class="k">return</span>
+
+ <span class="c1"># Convert the structure to ARBD model</span>
+ <span class="k">if</span> <span class="bp">self</span><span class="o">.</span><span class="n">parmed_structure</span> <span class="ow">is</span> <span class="ow">not</span> <span class="kc">None</span><span class="p">:</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">_build_model_from_structure</span><span class="p">()</span>
+
+ <span class="k">def</span><span class="w"> </span><span class="nf">_read_files</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">psf</span><span class="p">,</span> <span class="n">pdb</span><span class="p">,</span> <span class="n">parameter_files</span><span class="o">=</span><span class="kc">None</span><span class="p">,</span> <span class="n">system_type</span><span class="o">=</span><span class="s1">'charmm'</span><span class="p">):</span>
+<span class="w"> </span><span class="sd">"""</span>
+<span class="sd"> Read PSF and PDB files into a ParmEd structure.</span>
+<span class="sd"> </span>
+<span class="sd"> Args:</span>
+<span class="sd"> psf: Path to PSF file</span>
+<span class="sd"> pdb: Path to PDB file</span>
+<span class="sd"> parameter_files: List of parameter files</span>
+<span class="sd"> system_type: Type of system ('charmm', etc.)</span>
+<span class="sd"> </span>
+<span class="sd"> Returns:</span>
+<span class="sd"> ParmEd structure object</span>
+<span class="sd"> """</span>
+ <span class="k">if</span> <span class="n">system_type</span> <span class="o">==</span> <span class="s1">'charmm'</span><span class="p">:</span>
+ <span class="n">p1</span> <span class="o">=</span> <span class="n">parmed</span><span class="o">.</span><span class="n">charmm</span><span class="o">.</span><span class="n">CharmmPsfFile</span><span class="p">(</span><span class="n">psf</span><span class="p">)</span>
+ <span class="n">c1</span> <span class="o">=</span> <span class="n">parmed</span><span class="o">.</span><span class="n">load_file</span><span class="p">(</span><span class="n">pdb</span><span class="p">)</span>
+ <span class="k">for</span> <span class="n">a</span><span class="p">,</span> <span class="n">b</span> <span class="ow">in</span> <span class="nb">zip</span><span class="p">(</span><span class="n">p1</span><span class="o">.</span><span class="n">atoms</span><span class="p">,</span> <span class="n">c1</span><span class="o">.</span><span class="n">atoms</span><span class="p">):</span>
+ <span class="n">a</span><span class="o">.</span><span class="n">xx</span> <span class="o">=</span> <span class="n">b</span><span class="o">.</span><span class="n">xx</span>
+ <span class="n">a</span><span class="o">.</span><span class="n">xy</span> <span class="o">=</span> <span class="n">b</span><span class="o">.</span><span class="n">xy</span>
+ <span class="n">a</span><span class="o">.</span><span class="n">xz</span> <span class="o">=</span> <span class="n">b</span><span class="o">.</span><span class="n">xz</span>
+ <span class="n">a</span><span class="o">.</span><span class="n">bfactor</span> <span class="o">=</span> <span class="n">b</span><span class="o">.</span><span class="n">bfactor</span>
+
+ <span class="k">if</span> <span class="n">parameter_files</span> <span class="ow">is</span> <span class="ow">not</span> <span class="kc">None</span><span class="p">:</span>
+ <span class="k">if</span> <span class="nb">isinstance</span><span class="p">(</span><span class="n">parameter_files</span><span class="p">,</span> <span class="nb">str</span><span class="p">):</span>
+ <span class="n">parameter_files</span> <span class="o">=</span> <span class="p">[</span><span class="n">parameter_files</span><span class="p">]</span>
+ <span class="n">params</span> <span class="o">=</span> <span class="n">parmed</span><span class="o">.</span><span class="n">charmm</span><span class="o">.</span><span class="n">CharmmParameterSet</span><span class="p">(</span><span class="o">*</span><span class="n">parameter_files</span><span class="p">)</span>
+ <span class="n">p1</span><span class="o">.</span><span class="n">load_parameters</span><span class="p">(</span><span class="n">params</span><span class="p">)</span>
+
+ <span class="k">else</span><span class="p">:</span>
+ <span class="k">raise</span> <span class="ne">NotImplementedError</span><span class="p">(</span><span class="sa">f</span><span class="s1">'Cannot import a "</span><span class="si">{</span><span class="n">system_type</span><span class="si">}</span><span class="s1">" model'</span><span class="p">)</span>
+
+ <span class="k">return</span> <span class="n">p1</span>
+
+<div class="viewcode-block" id="ParmedArbd.load_structure">
+<a class="viewcode-back" href="../../api/simulation_engines/parmed_bd.html#arbdmodel.parmed_bd.ParmedArbd.load_structure">[docs]</a>
+ <span class="k">def</span><span class="w"> </span><span class="nf">load_structure</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">parmed_structure</span><span class="o">=</span><span class="kc">None</span><span class="p">,</span> <span class="n">psf</span><span class="o">=</span><span class="kc">None</span><span class="p">,</span> <span class="n">pdb</span><span class="o">=</span><span class="kc">None</span><span class="p">,</span>
+ <span class="n">parameter_files</span><span class="o">=</span><span class="kc">None</span><span class="p">,</span> <span class="n">system_type</span><span class="o">=</span><span class="s1">'charmm'</span><span class="p">):</span>
+<span class="w"> </span><span class="sd">"""</span>
+<span class="sd"> Load a ParmEd structure or read from PSF/PDB files.</span>
+<span class="sd"> </span>
+<span class="sd"> Args:</span>
+<span class="sd"> parmed_structure: Existing ParmEd structure object (optional)</span>
+<span class="sd"> psf: Path to PSF file (optional if parmed_structure is provided)</span>
+<span class="sd"> pdb: Path to PDB file (optional if parmed_structure is provided)</span>
+<span class="sd"> parameter_files: List of parameter files (optional)</span>
+<span class="sd"> system_type: Type of system ('charmm', etc.)</span>
+<span class="sd"> </span>
+<span class="sd"> Returns:</span>
+<span class="sd"> self for method chaining</span>
+<span class="sd"> """</span>
+ <span class="k">if</span> <span class="n">parmed_structure</span> <span class="ow">is</span> <span class="ow">not</span> <span class="kc">None</span><span class="p">:</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">parmed_structure</span> <span class="o">=</span> <span class="n">parmed_structure</span>
+ <span class="k">elif</span> <span class="n">psf</span> <span class="ow">is</span> <span class="ow">not</span> <span class="kc">None</span> <span class="ow">and</span> <span class="n">pdb</span> <span class="ow">is</span> <span class="ow">not</span> <span class="kc">None</span><span class="p">:</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">parmed_structure</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">_read_files</span><span class="p">(</span><span class="n">psf</span><span class="p">,</span> <span class="n">pdb</span><span class="p">,</span> <span class="n">parameter_files</span><span class="p">,</span> <span class="n">system_type</span><span class="p">)</span>
+ <span class="k">else</span><span class="p">:</span>
+ <span class="k">raise</span> <span class="ne">ValueError</span><span class="p">(</span><span class="s2">"Either parmed_structure or both psf and pdb must be provided"</span><span class="p">)</span>
+
+ <span class="c1"># Clear existing model and rebuild</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">clear_all</span><span class="p">()</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">_build_model_from_structure</span><span class="p">()</span>
+
+ <span class="k">return</span> <span class="bp">self</span></div>
+
+
+ <span class="k">def</span><span class="w"> </span><span class="nf">_validate_atom</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">atom</span><span class="p">):</span>
+<span class="w"> </span><span class="sd">"""</span>
+<span class="sd"> Validate that atom properties are compatible with ARBD model.</span>
+<span class="sd"> </span>
+<span class="sd"> Args:</span>
+<span class="sd"> atom: ParmEd atom object to validate</span>
+<span class="sd"> </span>
+<span class="sd"> Raises:</span>
+<span class="sd"> NotImplementedError: If atom has unsupported properties</span>
+<span class="sd"> """</span>
+ <span class="k">try</span><span class="p">:</span>
+ <span class="n">atom</span><span class="o">.</span><span class="n">multipoles</span>
+ <span class="k">raise</span> <span class="ne">NotImplementedError</span><span class="p">(</span><span class="sa">f</span><span class="s1">'Atom </span><span class="si">{</span><span class="n">atom</span><span class="si">}</span><span class="s1"> uses multipoles attribute for AMEOBA'</span><span class="p">)</span>
+ <span class="k">except</span> <span class="ne">AttributeError</span><span class="p">:</span>
+ <span class="k">pass</span>
+
+ <span class="k">for</span> <span class="n">k</span> <span class="ow">in</span> <span class="s1">'tortors other_locations anisou hybridization irotat tree screen solvent_radius join altloc marked cmaps children aromatic formal_charge'</span><span class="o">.</span><span class="n">split</span><span class="p">():</span>
+ <span class="n">_a</span> <span class="o">=</span> <span class="n">atom</span><span class="o">.</span><span class="fm">__getattribute__</span><span class="p">(</span><span class="n">k</span><span class="p">)</span>
+ <span class="k">if</span> <span class="n">_a</span> <span class="ow">is</span> <span class="ow">not</span> <span class="kc">None</span><span class="p">:</span>
+ <span class="n">_isnum</span> <span class="o">=</span> <span class="nb">isinstance</span><span class="p">(</span><span class="n">_a</span><span class="p">,</span> <span class="nb">float</span><span class="p">)</span> <span class="ow">or</span> <span class="nb">isinstance</span><span class="p">(</span><span class="n">_a</span><span class="p">,</span> <span class="nb">int</span><span class="p">)</span>
+ <span class="k">if</span> <span class="p">(</span><span class="n">_isnum</span> <span class="ow">and</span> <span class="p">(</span><span class="n">_a</span> <span class="o">!=</span> <span class="mi">0</span><span class="p">))</span> <span class="ow">or</span> <span class="p">((</span><span class="ow">not</span> <span class="n">_isnum</span><span class="p">)</span> <span class="ow">and</span> <span class="nb">len</span><span class="p">(</span><span class="n">_a</span><span class="p">)</span> <span class="o">></span> <span class="mi">0</span><span class="p">):</span>
+ <span class="n">_msg</span> <span class="o">=</span> <span class="sa">f</span><span class="s1">'Atom </span><span class="si">{</span><span class="n">atom</span><span class="o">.</span><span class="n">idx</span><span class="si">}</span><span class="s1"> "</span><span class="si">{</span><span class="n">k</span><span class="si">}</span><span class="s1">" is non-null (</span><span class="si">{</span><span class="n">_a</span><span class="si">}</span><span class="s1">)'</span>
+ <span class="n">logger</span><span class="o">.</span><span class="n">warning</span><span class="p">(</span><span class="n">_msg</span><span class="p">)</span>
+
+ <span class="k">if</span> <span class="nb">len</span><span class="p">(</span><span class="n">atom</span><span class="o">.</span><span class="n">other_locations</span><span class="p">)</span> <span class="o">></span> <span class="mi">0</span><span class="p">:</span>
+ <span class="n">_msg</span> <span class="o">=</span> <span class="sa">f</span><span class="s1">'Atom </span><span class="si">{</span><span class="n">atom</span><span class="o">.</span><span class="n">idx</span><span class="si">}</span><span class="s1"> has other locations which is not supported'</span>
+ <span class="k">raise</span> <span class="ne">NotImplementedError</span><span class="p">(</span><span class="n">_msg</span><span class="p">)</span>
+
+ <span class="k">def</span><span class="w"> </span><span class="nf">_validate_topology</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span>
+<span class="w"> </span><span class="sd">"""</span>
+<span class="sd"> Validate that the topology is compatible with ARBD model.</span>
+<span class="sd"> </span>
+<span class="sd"> Raises:</span>
+<span class="sd"> NotImplementedError: If topology has unsupported features</span>
+<span class="sd"> """</span>
+ <span class="n">part</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">parmed_structure</span>
+
+ <span class="k">if</span> <span class="nb">len</span><span class="p">(</span><span class="n">part</span><span class="o">.</span><span class="n">rb_torsions</span><span class="p">)</span> <span class="o">></span> <span class="mi">0</span><span class="p">:</span>
+ <span class="n">_msg</span> <span class="o">=</span> <span class="sa">f</span><span class="s1">'Topology includes RB torsions'</span>
+ <span class="k">raise</span> <span class="ne">NotImplementedError</span><span class="p">(</span><span class="n">_msg</span><span class="p">)</span>
+
+ <span class="k">if</span> <span class="nb">len</span><span class="p">(</span><span class="n">part</span><span class="o">.</span><span class="n">urey_bradleys</span><span class="p">)</span> <span class="o">></span> <span class="mi">0</span><span class="p">:</span>
+ <span class="n">_msg</span> <span class="o">=</span> <span class="sa">f</span><span class="s1">'Topology includes Urey Bradley terms'</span>
+ <span class="n">logger</span><span class="o">.</span><span class="n">warning</span><span class="p">(</span><span class="n">_msg</span><span class="p">)</span>
+
+ <span class="k">for</span> <span class="n">k</span> <span class="ow">in</span> <span class="p">[</span><span class="s1">'impropers'</span><span class="p">,</span> <span class="s1">'cmaps'</span><span class="p">,</span> <span class="s1">'trigonal_angles'</span><span class="p">,</span> <span class="s1">'out_of_plane_bends'</span><span class="p">,</span>
+ <span class="s1">'pi_torsions'</span><span class="p">,</span> <span class="s1">'stretch_bends'</span><span class="p">,</span> <span class="s1">'torsion_torsions'</span><span class="p">,</span> <span class="s1">'chiral_frames'</span><span class="p">,</span>
+ <span class="s1">'multipole_frames'</span><span class="p">,</span> <span class="s1">'adjusts'</span><span class="p">,</span> <span class="s1">'links'</span><span class="p">]:</span>
+ <span class="n">_a</span> <span class="o">=</span> <span class="n">part</span><span class="o">.</span><span class="fm">__getattribute__</span><span class="p">(</span><span class="n">k</span><span class="p">)</span>
+ <span class="k">if</span> <span class="nb">len</span><span class="p">(</span><span class="n">_a</span><span class="p">)</span> <span class="o">></span> <span class="mi">0</span><span class="p">:</span>
+ <span class="n">_msg</span> <span class="o">=</span> <span class="sa">f</span><span class="s1">'Topology includes </span><span class="si">{</span><span class="nb">len</span><span class="p">(</span><span class="n">_a</span><span class="p">)</span><span class="si">}</span><span class="s1"> "</span><span class="si">{</span><span class="n">k</span><span class="si">}</span><span class="s1">"'</span>
+ <span class="n">logger</span><span class="o">.</span><span class="n">warning</span><span class="p">(</span><span class="n">_msg</span><span class="p">)</span>
+
+ <span class="k">if</span> <span class="n">part</span><span class="o">.</span><span class="n">unknown_functional</span> <span class="o">!=</span> <span class="kc">False</span><span class="p">:</span>
+ <span class="n">_msg</span> <span class="o">=</span> <span class="sa">f</span><span class="s1">'Topology unknown_functional is "</span><span class="si">{</span><span class="n">part</span><span class="o">.</span><span class="n">unknown_functional</span><span class="si">}</span><span class="s1">" (not "False")'</span>
+ <span class="k">raise</span> <span class="ne">NotImplementedError</span><span class="p">(</span><span class="n">_msg</span><span class="p">)</span>
+
+ <span class="k">if</span> <span class="n">part</span><span class="o">.</span><span class="n">symmetry</span> <span class="ow">is</span> <span class="ow">not</span> <span class="kc">None</span><span class="p">:</span>
+ <span class="n">_msg</span> <span class="o">=</span> <span class="sa">f</span><span class="s1">'Topology symmetry is "</span><span class="si">{</span><span class="n">part</span><span class="o">.</span><span class="n">symmetry</span><span class="si">}</span><span class="s1">" (not "None")'</span>
+ <span class="k">raise</span> <span class="ne">NotImplementedError</span><span class="p">(</span><span class="n">_msg</span><span class="p">)</span>
+
+ <span class="k">if</span> <span class="n">part</span><span class="o">.</span><span class="n">nrexcl</span> <span class="o">></span> <span class="mi">4</span><span class="p">:</span>
+ <span class="n">_msg</span> <span class="o">=</span> <span class="sa">f</span><span class="s1">'Topology nrexcl is "</span><span class="si">{</span><span class="n">part</span><span class="o">.</span><span class="n">nrexcl</span><span class="si">}</span><span class="s1">" (not <= "4")'</span>
+ <span class="k">raise</span> <span class="ne">NotImplementedError</span><span class="p">(</span><span class="n">_msg</span><span class="p">)</span>
+
+ <span class="k">if</span> <span class="n">part</span><span class="o">.</span><span class="n">_combining_rule</span> <span class="o">!=</span> <span class="s1">'lorentz'</span><span class="p">:</span>
+ <span class="n">_msg</span> <span class="o">=</span> <span class="sa">f</span><span class="s1">'Unrecognized non-bonded combining rule "</span><span class="si">{</span><span class="n">part</span><span class="o">.</span><span class="n">_combining_rule</span><span class="si">}</span><span class="s1">"'</span>
+ <span class="k">raise</span> <span class="ne">NotImplementedError</span><span class="p">(</span><span class="n">_msg</span><span class="p">)</span>
+
+ <span class="c1"># Validate first atom as representative</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">_validate_atom</span><span class="p">(</span><span class="n">part</span><span class="o">.</span><span class="n">atoms</span><span class="p">[</span><span class="mi">0</span><span class="p">])</span>
+
+ <span class="k">def</span><span class="w"> </span><span class="nf">_create_particle_types</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span>
+<span class="w"> </span><span class="sd">"""</span>
+<span class="sd"> Create ARBD ParticleType objects from atom types in the ParmEd structure.</span>
+<span class="sd"> </span>
+<span class="sd"> Returns:</span>
+<span class="sd"> Dictionary mapping atom type names to ParticleType objects</span>
+<span class="sd"> """</span>
+ <span class="n">_atypes</span> <span class="o">=</span> <span class="nb">set</span><span class="p">(</span><span class="n">a</span><span class="o">.</span><span class="n">atom_type</span> <span class="k">for</span> <span class="n">a</span> <span class="ow">in</span> <span class="bp">self</span><span class="o">.</span><span class="n">parmed_structure</span><span class="o">.</span><span class="n">atoms</span><span class="p">)</span>
+ <span class="n">logger</span><span class="o">.</span><span class="n">info</span><span class="p">(</span><span class="sa">f</span><span class="s1">'Importing </span><span class="si">{</span><span class="nb">len</span><span class="p">(</span><span class="n">_atypes</span><span class="p">)</span><span class="si">}</span><span class="s1"> types from ParmEd'</span><span class="p">)</span>
+
+ <span class="n">_new_types_d</span> <span class="o">=</span> <span class="p">{}</span>
+ <span class="k">for</span> <span class="n">t</span> <span class="ow">in</span> <span class="n">_atypes</span><span class="p">:</span>
+ <span class="n">_kwargs</span> <span class="o">=</span> <span class="p">{</span><span class="n">k</span><span class="p">:</span> <span class="n">t</span><span class="o">.</span><span class="fm">__getattribute__</span><span class="p">(</span><span class="n">k</span><span class="p">)</span>
+ <span class="k">for</span> <span class="n">k</span> <span class="ow">in</span> <span class="s1">'number mass atomic_number epsilon rmin charge'</span><span class="o">.</span><span class="n">split</span><span class="p">()}</span>
+
+ <span class="k">for</span> <span class="n">k</span> <span class="ow">in</span> <span class="s1">'epsilon_14 rmin_14'</span><span class="o">.</span><span class="n">split</span><span class="p">():</span>
+ <span class="n">_a1</span> <span class="o">=</span> <span class="n">t</span><span class="o">.</span><span class="fm">__getattribute__</span><span class="p">(</span><span class="n">k</span><span class="p">)</span>
+ <span class="n">_a2</span> <span class="o">=</span> <span class="n">t</span><span class="o">.</span><span class="fm">__getattribute__</span><span class="p">(</span><span class="n">k</span><span class="o">.</span><span class="n">split</span><span class="p">(</span><span class="s1">'_'</span><span class="p">)[</span><span class="mi">0</span><span class="p">])</span>
+ <span class="k">if</span> <span class="n">_a1</span> <span class="o">!=</span> <span class="n">_a2</span><span class="p">:</span>
+ <span class="n">_msg</span> <span class="o">=</span> <span class="sa">f</span><span class="s1">'</span><span class="si">{</span><span class="n">t</span><span class="si">}</span><span class="s1">.</span><span class="si">{</span><span class="n">k</span><span class="si">}</span><span class="s1"> differs from normal term (</span><span class="si">{</span><span class="n">_a1</span><span class="si">}</span><span class="s1"> != </span><span class="si">{</span><span class="n">_a2</span><span class="si">}</span><span class="s1">)'</span>
+ <span class="n">logger</span><span class="o">.</span><span class="n">warning</span><span class="p">(</span><span class="n">_msg</span><span class="p">)</span>
+
+ <span class="k">for</span> <span class="n">k</span> <span class="ow">in</span> <span class="s1">'nbfix nbthole _bond_type'</span><span class="o">.</span><span class="n">split</span><span class="p">():</span>
+ <span class="n">_a</span> <span class="o">=</span> <span class="n">t</span><span class="o">.</span><span class="fm">__getattribute__</span><span class="p">(</span><span class="n">k</span><span class="p">)</span>
+ <span class="k">if</span> <span class="n">_a</span> <span class="ow">is</span> <span class="ow">not</span> <span class="kc">None</span> <span class="ow">and</span> <span class="nb">len</span><span class="p">(</span><span class="n">_a</span><span class="p">)</span> <span class="o">></span> <span class="mi">0</span><span class="p">:</span>
+ <span class="n">_msg</span> <span class="o">=</span> <span class="sa">f</span><span class="s1">'</span><span class="si">{</span><span class="n">t</span><span class="si">}</span><span class="s1">.</span><span class="si">{</span><span class="n">k</span><span class="si">}</span><span class="s1"> is non-null (</span><span class="si">{</span><span class="n">_a</span><span class="si">}</span><span class="s1">)'</span>
+ <span class="n">logger</span><span class="o">.</span><span class="n">warning</span><span class="p">(</span><span class="n">_msg</span><span class="p">)</span>
+
+ <span class="k">assert</span><span class="p">(</span><span class="n">t</span><span class="o">.</span><span class="n">name</span> <span class="ow">not</span> <span class="ow">in</span> <span class="n">_new_types_d</span><span class="p">)</span>
+ <span class="n">_new_types_d</span><span class="p">[</span><span class="n">t</span><span class="o">.</span><span class="n">name</span><span class="p">]</span> <span class="o">=</span> <span class="n">ParticleType</span><span class="p">(</span><span class="n">t</span><span class="o">.</span><span class="n">name</span><span class="p">,</span>
+ <span class="n">damping_coefficient</span><span class="o">=</span><span class="mf">1e-4</span><span class="p">,</span> <span class="c1"># 0.1 ps</span>
+ <span class="o">**</span><span class="n">_kwargs</span><span class="p">)</span>
+
+ <span class="bp">self</span><span class="o">.</span><span class="n">atom_types</span> <span class="o">=</span> <span class="n">_new_types_d</span>
+ <span class="k">return</span> <span class="n">_new_types_d</span>
+
+ <span class="k">def</span><span class="w"> </span><span class="nf">_build_model_from_structure</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span>
+<span class="w"> </span><span class="sd">"""</span>
+<span class="sd"> Build ARBD model from the loaded ParmEd structure.</span>
+<span class="sd"> """</span>
+ <span class="c1"># Validate topology first</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">_validate_topology</span><span class="p">()</span>
+
+ <span class="c1"># Create particle types</span>
+ <span class="n">atom_types</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">_create_particle_types</span><span class="p">()</span>
+
+ <span class="c1"># Create model structure</span>
+ <span class="n">allsegs</span> <span class="o">=</span> <span class="n">Group</span><span class="p">(</span><span class="n">name</span><span class="o">=</span><span class="s1">'allsegs'</span><span class="p">,</span> <span class="n">_segments</span><span class="o">=</span><span class="p">{})</span>
+ <span class="n">atoms_d</span> <span class="o">=</span> <span class="p">{}</span>
+ <span class="n">bond_t_d</span> <span class="o">=</span> <span class="p">{}</span>
+
+ <span class="c1"># Helper function to get or create residue group</span>
+ <span class="k">def</span><span class="w"> </span><span class="nf">_get_residue</span><span class="p">(</span><span class="n">res</span><span class="p">):</span>
+ <span class="n">segid</span> <span class="o">=</span> <span class="n">res</span><span class="o">.</span><span class="n">segid</span> <span class="k">if</span> <span class="n">res</span><span class="o">.</span><span class="n">segid</span> <span class="ow">is</span> <span class="ow">not</span> <span class="kc">None</span> <span class="k">else</span> <span class="n">res</span><span class="o">.</span><span class="n">chain</span>
+ <span class="k">if</span> <span class="n">segid</span> <span class="ow">not</span> <span class="ow">in</span> <span class="n">allsegs</span><span class="o">.</span><span class="n">_segments</span><span class="p">:</span>
+ <span class="n">allsegs</span><span class="o">.</span><span class="n">_segments</span><span class="p">[</span><span class="n">segid</span><span class="p">]</span> <span class="o">=</span> <span class="n">Group</span><span class="p">(</span><span class="n">name</span><span class="o">=</span><span class="n">segid</span><span class="p">,</span> <span class="n">_residues</span><span class="o">=</span><span class="p">{},</span> <span class="n">parent</span><span class="o">=</span><span class="n">allsegs</span><span class="p">)</span>
+ <span class="n">logger</span><span class="o">.</span><span class="n">info</span><span class="p">(</span><span class="sa">f</span><span class="s1">'Creating segment </span><span class="si">{</span><span class="n">segid</span><span class="si">}</span><span class="s1">'</span><span class="p">)</span>
+ <span class="n">seg</span> <span class="o">=</span> <span class="n">allsegs</span><span class="o">.</span><span class="n">_segments</span><span class="p">[</span><span class="n">segid</span><span class="p">]</span>
+
+ <span class="n">key</span> <span class="o">=</span> <span class="p">(</span><span class="n">segid</span><span class="p">,</span> <span class="n">res</span><span class="o">.</span><span class="n">name</span><span class="p">,</span> <span class="n">res</span><span class="o">.</span><span class="n">number</span><span class="p">)</span>
+ <span class="k">if</span> <span class="n">key</span> <span class="ow">not</span> <span class="ow">in</span> <span class="n">seg</span><span class="o">.</span><span class="n">_residues</span><span class="p">:</span>
+ <span class="n">seg</span><span class="o">.</span><span class="n">_residues</span><span class="p">[</span><span class="n">key</span><span class="p">]</span> <span class="o">=</span> <span class="n">Group</span><span class="p">(</span><span class="n">name</span><span class="o">=</span><span class="n">res</span><span class="o">.</span><span class="n">name</span><span class="p">,</span> <span class="n">resid</span><span class="o">=</span><span class="n">res</span><span class="o">.</span><span class="n">number</span><span class="p">,</span> <span class="n">chain</span><span class="o">=</span><span class="n">res</span><span class="o">.</span><span class="n">chain</span><span class="p">,</span> <span class="n">parent</span><span class="o">=</span><span class="n">seg</span><span class="p">)</span>
+ <span class="n">logger</span><span class="o">.</span><span class="n">debug</span><span class="p">((</span><span class="n">seg</span><span class="p">,</span> <span class="n">segid</span><span class="p">,</span> <span class="n">res</span><span class="o">.</span><span class="n">name</span><span class="p">,</span> <span class="n">res</span><span class="o">.</span><span class="n">number</span><span class="p">,</span> <span class="n">res</span><span class="o">.</span><span class="n">_idx</span><span class="p">))</span>
+
+ <span class="k">return</span> <span class="n">seg</span><span class="o">.</span><span class="n">_residues</span><span class="p">[</span><span class="n">key</span><span class="p">]</span>
+
+ <span class="c1"># Helper function to create an atom</span>
+ <span class="k">def</span><span class="w"> </span><span class="nf">_add_atom</span><span class="p">(</span><span class="n">atom</span><span class="p">):</span>
+ <span class="n">a</span> <span class="o">=</span> <span class="n">atom</span>
+ <span class="n">mapping</span> <span class="o">=</span> <span class="nb">dict</span><span class="p">(</span><span class="n">bfactor</span><span class="o">=</span><span class="s1">'beta'</span><span class="p">,</span>
+ <span class="n">occupancy</span><span class="o">=</span><span class="kc">None</span><span class="p">)</span>
+ <span class="k">for</span> <span class="n">k</span><span class="p">,</span> <span class="n">v</span> <span class="ow">in</span> <span class="nb">list</span><span class="p">(</span><span class="n">mapping</span><span class="o">.</span><span class="n">items</span><span class="p">()):</span>
+ <span class="k">if</span> <span class="n">v</span> <span class="ow">is</span> <span class="kc">None</span><span class="p">:</span>
+ <span class="n">mapping</span><span class="p">[</span><span class="n">k</span><span class="p">]</span> <span class="o">=</span> <span class="n">k</span>
+
+ <span class="n">res</span> <span class="o">=</span> <span class="n">_get_residue</span><span class="p">(</span><span class="n">a</span><span class="o">.</span><span class="n">residue</span><span class="p">)</span>
+ <span class="n">_a</span> <span class="o">=</span> <span class="n">PointParticle</span><span class="p">(</span><span class="n">name</span><span class="o">=</span><span class="n">a</span><span class="o">.</span><span class="n">name</span><span class="p">,</span> <span class="n">type_</span><span class="o">=</span><span class="n">atom_types</span><span class="p">[</span><span class="n">a</span><span class="o">.</span><span class="n">type</span><span class="p">],</span>
+ <span class="n">position</span><span class="o">=</span><span class="n">np</span><span class="o">.</span><span class="n">array</span><span class="p">((</span><span class="n">a</span><span class="o">.</span><span class="n">xx</span><span class="p">,</span> <span class="n">a</span><span class="o">.</span><span class="n">xy</span><span class="p">,</span> <span class="n">a</span><span class="o">.</span><span class="n">xz</span><span class="p">)),</span> <span class="n">parent</span><span class="o">=</span><span class="n">res</span><span class="p">,</span>
+ <span class="o">**</span><span class="p">{</span><span class="n">mapping</span><span class="p">[</span><span class="n">k</span><span class="p">]:</span> <span class="n">a</span><span class="o">.</span><span class="fm">__getattribute__</span><span class="p">(</span><span class="n">k</span><span class="p">)</span> <span class="k">for</span> <span class="n">k</span> <span class="ow">in</span> <span class="n">mapping</span><span class="o">.</span><span class="n">keys</span><span class="p">()})</span>
+ <span class="n">atoms_d</span><span class="p">[</span><span class="n">a</span><span class="p">]</span> <span class="o">=</span> <span class="n">_a</span>
+ <span class="k">return</span> <span class="n">_a</span>
+
+ <span class="c1"># Helper function to get or create a bond type</span>
+ <span class="k">def</span><span class="w"> </span><span class="nf">_get_bond_type</span><span class="p">(</span><span class="n">bond</span><span class="p">):</span>
+ <span class="n">t</span> <span class="o">=</span> <span class="n">bond</span><span class="o">.</span><span class="n">type</span>
+ <span class="k">if</span> <span class="n">t</span> <span class="ow">not</span> <span class="ow">in</span> <span class="n">bond_t_d</span><span class="p">:</span>
+ <span class="k">if</span> <span class="n">t</span><span class="o">.</span><span class="n">penalty</span> <span class="ow">is</span> <span class="ow">not</span> <span class="kc">None</span><span class="p">:</span>
+ <span class="n">logger</span><span class="o">.</span><span class="n">warning</span><span class="p">(</span><span class="sa">f</span><span class="s1">'Bond.penalty for bond </span><span class="si">{</span><span class="n">t</span><span class="si">}</span><span class="s1"> not null'</span><span class="p">)</span>
+ <span class="n">width</span> <span class="o">=</span> <span class="mf">0.76565392</span><span class="o">/</span><span class="n">np</span><span class="o">.</span><span class="n">sqrt</span><span class="p">(</span><span class="n">np</span><span class="o">.</span><span class="n">abs</span><span class="p">(</span><span class="n">t</span><span class="o">.</span><span class="n">k</span><span class="p">))</span> <span class="c1"># units conversion</span>
+ <span class="n">b</span> <span class="o">=</span> <span class="n">HarmonicBond</span><span class="p">(</span><span class="n">k</span><span class="o">=</span><span class="n">t</span><span class="o">.</span><span class="n">k</span><span class="p">,</span> <span class="n">r0</span><span class="o">=</span><span class="n">t</span><span class="o">.</span><span class="n">req</span><span class="p">,</span>
+ <span class="n">resolution</span><span class="o">=</span><span class="mf">0.02</span><span class="o">*</span><span class="n">width</span><span class="p">,</span>
+ <span class="n">range_</span><span class="o">=</span><span class="p">[</span><span class="nb">max</span><span class="p">(</span><span class="mi">0</span><span class="p">,</span> <span class="n">t</span><span class="o">.</span><span class="n">req</span><span class="o">-</span><span class="mi">5</span><span class="o">*</span><span class="n">width</span><span class="p">),</span> <span class="n">t</span><span class="o">.</span><span class="n">req</span><span class="o">+</span><span class="mi">5</span><span class="o">*</span><span class="n">width</span><span class="p">])</span>
+ <span class="n">bond_t_d</span><span class="p">[</span><span class="n">t</span><span class="p">]</span> <span class="o">=</span> <span class="n">b</span>
+ <span class="k">return</span> <span class="n">bond_t_d</span><span class="p">[</span><span class="n">t</span><span class="p">]</span>
+
+ <span class="c1"># Add atoms to model</span>
+ <span class="n">logger</span><span class="o">.</span><span class="n">info</span><span class="p">(</span><span class="sa">f</span><span class="s1">'Importing </span><span class="si">{</span><span class="nb">len</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">parmed_structure</span><span class="o">.</span><span class="n">atoms</span><span class="p">)</span><span class="si">}</span><span class="s1"> atoms from ParmEd'</span><span class="p">)</span>
+ <span class="k">for</span> <span class="n">i</span><span class="p">,</span> <span class="n">a</span> <span class="ow">in</span> <span class="nb">enumerate</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">parmed_structure</span><span class="o">.</span><span class="n">atoms</span><span class="p">):</span>
+ <span class="k">assert</span><span class="p">(</span><span class="n">a</span><span class="o">.</span><span class="n">idx</span> <span class="o">==</span> <span class="n">i</span><span class="p">)</span>
+ <span class="n">_add_atom</span><span class="p">(</span><span class="n">a</span><span class="p">)</span>
+
+ <span class="c1"># Add bonds to model</span>
+ <span class="n">logger</span><span class="o">.</span><span class="n">info</span><span class="p">(</span><span class="sa">f</span><span class="s1">'Importing </span><span class="si">{</span><span class="nb">len</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">parmed_structure</span><span class="o">.</span><span class="n">bonds</span><span class="p">)</span><span class="si">}</span><span class="s1"> bonds from ParmEd'</span><span class="p">)</span>
+ <span class="k">for</span> <span class="n">b0</span> <span class="ow">in</span> <span class="bp">self</span><span class="o">.</span><span class="n">parmed_structure</span><span class="o">.</span><span class="n">bonds</span><span class="p">:</span>
+ <span class="n">t</span> <span class="o">=</span> <span class="n">_get_bond_type</span><span class="p">(</span><span class="n">b0</span><span class="p">)</span>
+ <span class="n">a1</span><span class="p">,</span> <span class="n">a2</span> <span class="o">=</span> <span class="p">[</span><span class="n">atoms_d</span><span class="p">[</span><span class="n">a</span><span class="p">]</span> <span class="k">for</span> <span class="n">a</span> <span class="ow">in</span> <span class="p">(</span><span class="n">b0</span><span class="o">.</span><span class="n">atom1</span><span class="p">,</span> <span class="n">b0</span><span class="o">.</span><span class="n">atom2</span><span class="p">)]</span>
+ <span class="n">seg</span> <span class="o">=</span> <span class="n">a1</span><span class="o">.</span><span class="n">parent</span><span class="o">.</span><span class="n">parent</span>
+ <span class="n">seg</span><span class="o">.</span><span class="n">add_bond</span><span class="p">(</span><span class="n">a1</span><span class="p">,</span> <span class="n">a2</span><span class="p">,</span> <span class="n">t</span><span class="p">,</span> <span class="bp">self</span><span class="o">.</span><span class="n">parmed_structure</span><span class="o">.</span><span class="n">nrexcl</span> <span class="o">>=</span> <span class="mi">1</span><span class="p">)</span>
+
+ <span class="c1"># Add the segment group to the model</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">add</span><span class="p">(</span><span class="n">allsegs</span><span class="p">)</span>
+
+ <span class="c1"># Store mapping from ParmEd atoms to ARBD atoms</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">atoms_map</span> <span class="o">=</span> <span class="n">atoms_d</span>
+
+ <span class="k">return</span> <span class="bp">self</span>
+
+<div class="viewcode-block" id="ParmedArbd.simulate">
+<a class="viewcode-back" href="../../api/simulation_engines/parmed_bd.html#arbdmodel.parmed_bd.ParmedArbd.simulate">[docs]</a>
+ <span class="k">def</span><span class="w"> </span><span class="nf">simulate</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">output_name</span><span class="p">,</span> <span class="n">output_directory</span><span class="o">=</span><span class="s1">'output'</span><span class="p">,</span> <span class="n">log_file</span><span class="o">=</span><span class="kc">None</span><span class="p">,</span>
+ <span class="n">directory</span><span class="o">=</span><span class="s1">'.'</span><span class="p">,</span> <span class="n">binary</span><span class="o">=</span><span class="kc">None</span><span class="p">,</span> <span class="n">num_procs</span><span class="o">=</span><span class="kc">None</span><span class="p">,</span> <span class="n">dry_run</span><span class="o">=</span><span class="kc">False</span><span class="p">,</span> <span class="o">**</span><span class="n">conf_params</span><span class="p">):</span>
+<span class="w"> </span><span class="sd">"""</span>
+<span class="sd"> Run simulation with the ARBD model.</span>
+<span class="sd"> </span>
+<span class="sd"> Args:</span>
+<span class="sd"> output_name: Base name for output files</span>
+<span class="sd"> output_directory: Directory for output files</span>
+<span class="sd"> log_file: File for logging</span>
+<span class="sd"> directory: Working directory</span>
+<span class="sd"> binary: Path to simulation binary</span>
+<span class="sd"> num_procs: Number of processors to use</span>
+<span class="sd"> dry_run: If True, don't actually run</span>
+<span class="sd"> **conf_params: Additional configuration parameters</span>
+<span class="sd"> </span>
+<span class="sd"> Returns:</span>
+<span class="sd"> Result of the simulation</span>
+<span class="sd"> """</span>
+ <span class="kn">from</span><span class="w"> </span><span class="nn">.engine</span><span class="w"> </span><span class="kn">import</span> <span class="n">ArbdEngine</span>
+
+ <span class="n">engine</span> <span class="o">=</span> <span class="n">ArbdEngine</span><span class="p">(</span><span class="n">timestep</span><span class="o">=</span><span class="n">conf_params</span><span class="o">.</span><span class="n">get</span><span class="p">(</span><span class="s1">'timestep'</span><span class="p">,</span> <span class="mf">1e-6</span><span class="p">))</span>
+
+ <span class="k">return</span> <span class="n">engine</span><span class="o">.</span><span class="n">simulate</span><span class="p">(</span>
+ <span class="bp">self</span><span class="p">,</span> <span class="n">output_name</span><span class="p">,</span>
+ <span class="n">output_directory</span><span class="o">=</span><span class="n">output_directory</span><span class="p">,</span>
+ <span class="n">directory</span><span class="o">=</span><span class="n">directory</span><span class="p">,</span>
+ <span class="n">log_file</span><span class="o">=</span><span class="n">log_file</span><span class="p">,</span>
+ <span class="n">binary</span><span class="o">=</span><span class="n">binary</span><span class="p">,</span>
+ <span class="n">num_procs</span><span class="o">=</span><span class="n">num_procs</span><span class="p">,</span>
+ <span class="n">dry_run</span><span class="o">=</span><span class="n">dry_run</span><span class="p">,</span>
+ <span class="o">**</span><span class="n">conf_params</span>
+ <span class="p">)</span></div>
+
+
+<div class="viewcode-block" id="ParmedArbd.create_dual_topology_model">
+<a class="viewcode-back" href="../../api/simulation_engines/parmed_bd.html#arbdmodel.parmed_bd.ParmedArbd.create_dual_topology_model">[docs]</a>
+ <span class="nd">@classmethod</span>
+ <span class="k">def</span><span class="w"> </span><span class="nf">create_dual_topology_model</span><span class="p">(</span><span class="bp">cls</span><span class="p">,</span> <span class="n">p1</span><span class="p">,</span> <span class="n">p2</span><span class="p">,</span> <span class="n">u1</span><span class="o">=</span><span class="kc">None</span><span class="p">,</span> <span class="n">u2</span><span class="o">=</span><span class="kc">None</span><span class="p">,</span> <span class="o">**</span><span class="n">kwargs</span><span class="p">):</span>
+<span class="w"> </span><span class="sd">"""</span>
+<span class="sd"> Create a dual topology ARBD model from two ParmEd structures.</span>
+<span class="sd"> </span>
+<span class="sd"> Args:</span>
+<span class="sd"> p1: First ParmEd structure</span>
+<span class="sd"> p2: Second ParmEd structure</span>
+<span class="sd"> u1: Optional MDAnalysis universe for p1</span>
+<span class="sd"> u2: Optional MDAnalysis universe for p2</span>
+<span class="sd"> **kwargs: Additional arguments for ParmedArbd</span>
+<span class="sd"> </span>
+<span class="sd"> Returns:</span>
+<span class="sd"> ParmedArbd model with dual topology</span>
+<span class="sd"> """</span>
+ <span class="c1"># Create the dual topology</span>
+ <span class="n">dual_structure</span><span class="p">,</span> <span class="n">pairs</span><span class="p">,</span> <span class="n">bp_pairs</span> <span class="o">=</span> <span class="bp">cls</span><span class="o">.</span><span class="n">create_dual_topology</span><span class="p">(</span><span class="n">p1</span><span class="p">,</span> <span class="n">p2</span><span class="p">,</span> <span class="n">u1</span><span class="p">,</span> <span class="n">u2</span><span class="p">)</span>
+
+ <span class="c1"># Create ParmedArbd model with the dual structure</span>
+ <span class="n">model</span> <span class="o">=</span> <span class="bp">cls</span><span class="p">(</span><span class="n">parmed_structure</span><span class="o">=</span><span class="n">dual_structure</span><span class="p">,</span> <span class="o">**</span><span class="n">kwargs</span><span class="p">)</span>
+
+ <span class="c1"># Store the extra bond information for use in simulation</span>
+ <span class="n">model</span><span class="o">.</span><span class="n">dual_topology_pairs</span> <span class="o">=</span> <span class="n">pairs</span>
+ <span class="n">model</span><span class="o">.</span><span class="n">bp_pairs</span> <span class="o">=</span> <span class="n">bp_pairs</span>
+
+ <span class="k">return</span> <span class="n">model</span></div>
+
+
+<div class="viewcode-block" id="ParmedArbd.write_restraint_files">
+<a class="viewcode-back" href="../../api/simulation_engines/parmed_bd.html#arbdmodel.parmed_bd.ParmedArbd.write_restraint_files">[docs]</a>
+ <span class="k">def</span><span class="w"> </span><span class="nf">write_restraint_files</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">fep_file</span><span class="o">=</span><span class="s1">'dual.fep.exb'</span><span class="p">,</span> <span class="n">min_fep_file</span><span class="o">=</span><span class="s1">'dual.min.fep.exb'</span><span class="p">,</span>
+ <span class="n">bp_file</span><span class="o">=</span><span class="s1">'dual.bp.exb'</span><span class="p">):</span>
+<span class="w"> </span><span class="sd">"""</span>
+<span class="sd"> Write restraint files for dual topology simulations.</span>
+<span class="sd"> </span>
+<span class="sd"> Args:</span>
+<span class="sd"> fep_file: Output file for FEP restraints</span>
+<span class="sd"> min_fep_file: Output file for minimization FEP restraints</span>
+<span class="sd"> bp_file: Output file for base pair restraints</span>
+<span class="sd"> """</span>
+ <span class="k">if</span> <span class="ow">not</span> <span class="nb">hasattr</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="s1">'dual_topology_pairs'</span><span class="p">):</span>
+ <span class="k">raise</span> <span class="ne">AttributeError</span><span class="p">(</span><span class="s2">"This model doesn't have dual topology information. "</span>
+ <span class="s2">"Use create_dual_topology_model to create one."</span><span class="p">)</span>
+
+ <span class="k">with</span> <span class="nb">open</span><span class="p">(</span><span class="n">fep_file</span><span class="p">,</span> <span class="s1">'w'</span><span class="p">)</span> <span class="k">as</span> <span class="n">fh</span><span class="p">:</span>
+ <span class="k">with</span> <span class="nb">open</span><span class="p">(</span><span class="n">min_fep_file</span><span class="p">,</span> <span class="s1">'w'</span><span class="p">)</span> <span class="k">as</span> <span class="n">fh2</span><span class="p">:</span>
+ <span class="k">for</span> <span class="n">i</span><span class="p">,</span> <span class="n">j</span><span class="p">,</span> <span class="n">r0</span> <span class="ow">in</span> <span class="bp">self</span><span class="o">.</span><span class="n">dual_topology_pairs</span><span class="p">:</span>
+ <span class="n">fh</span><span class="o">.</span><span class="n">write</span><span class="p">(</span><span class="sa">f</span><span class="s1">'bond </span><span class="si">{</span><span class="n">i</span><span class="si">}</span><span class="s1"> </span><span class="si">{</span><span class="n">j</span><span class="si">}</span><span class="s1"> 1 </span><span class="si">{</span><span class="n">r0</span><span class="si">}</span><span class="se">\n</span><span class="s1">'</span><span class="p">)</span>
+ <span class="n">fh2</span><span class="o">.</span><span class="n">write</span><span class="p">(</span><span class="sa">f</span><span class="s1">'bond </span><span class="si">{</span><span class="n">i</span><span class="si">}</span><span class="s1"> </span><span class="si">{</span><span class="n">j</span><span class="si">}</span><span class="s1"> 100 </span><span class="si">{</span><span class="n">r0</span><span class="si">}</span><span class="se">\n</span><span class="s1">'</span><span class="p">)</span>
+
+ <span class="k">if</span> <span class="nb">hasattr</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="s1">'bp_pairs'</span><span class="p">)</span> <span class="ow">and</span> <span class="bp">self</span><span class="o">.</span><span class="n">bp_pairs</span><span class="p">:</span>
+ <span class="k">with</span> <span class="nb">open</span><span class="p">(</span><span class="n">bp_file</span><span class="p">,</span> <span class="s1">'w'</span><span class="p">)</span> <span class="k">as</span> <span class="n">fh</span><span class="p">:</span>
+ <span class="k">for</span> <span class="n">i</span><span class="p">,</span> <span class="n">j</span> <span class="ow">in</span> <span class="bp">self</span><span class="o">.</span><span class="n">bp_pairs</span><span class="p">:</span>
+ <span class="n">fh</span><span class="o">.</span><span class="n">write</span><span class="p">(</span><span class="sa">f</span><span class="s1">'bond </span><span class="si">{</span><span class="n">i</span><span class="si">}</span><span class="s1"> </span><span class="si">{</span><span class="n">j</span><span class="si">}</span><span class="s1"> 1 2.8</span><span class="se">\n</span><span class="s1">'</span><span class="p">)</span></div>
+
+
+<div class="viewcode-block" id="ParmedArbd.convert_sod_to_mg">
+<a class="viewcode-back" href="../../api/simulation_engines/parmed_bd.html#arbdmodel.parmed_bd.ParmedArbd.convert_sod_to_mg">[docs]</a>
+ <span class="nd">@staticmethod</span>
+ <span class="k">def</span><span class="w"> </span><span class="nf">convert_sod_to_mg</span><span class="p">(</span><span class="n">structure</span><span class="p">):</span>
+<span class="w"> </span><span class="sd">"""</span>
+<span class="sd"> Convert sodium ions to magnesium ions in a structure.</span>
+<span class="sd"> </span>
+<span class="sd"> Args:</span>
+<span class="sd"> structure: ParmEd structure to modify</span>
+<span class="sd"> </span>
+<span class="sd"> Returns:</span>
+<span class="sd"> Modified structure</span>
+<span class="sd"> """</span>
+ <span class="k">for</span> <span class="n">a</span> <span class="ow">in</span> <span class="n">structure</span><span class="p">:</span>
+ <span class="k">if</span> <span class="n">a</span><span class="o">.</span><span class="n">residue</span><span class="o">.</span><span class="n">name</span> <span class="o">==</span> <span class="s1">'WAT'</span><span class="p">:</span>
+ <span class="k">break</span>
+ <span class="k">elif</span> <span class="n">a</span><span class="o">.</span><span class="n">residue</span><span class="o">.</span><span class="n">name</span> <span class="o">!=</span> <span class="s1">'Na+'</span><span class="p">:</span>
+ <span class="k">continue</span>
+
+ <span class="c1"># Find appropriate magnesium atom type</span>
+ <span class="k">try</span><span class="p">:</span>
+ <span class="n">mg_type</span> <span class="o">=</span> <span class="n">structure</span><span class="o">.</span><span class="n">atom_types</span><span class="p">[</span><span class="s1">'Mg2+'</span><span class="p">]</span>
+ <span class="k">except</span> <span class="ne">KeyError</span><span class="p">:</span>
+ <span class="c1"># If Mg2+ atom type doesn't exist, create it based on Na+ properties</span>
+ <span class="n">na_type</span> <span class="o">=</span> <span class="n">a</span><span class="o">.</span><span class="n">atom_type</span>
+ <span class="n">mg_type</span> <span class="o">=</span> <span class="n">parmed</span><span class="o">.</span><span class="n">AtomType</span><span class="p">(</span><span class="s1">'Mg2+'</span><span class="p">,</span> <span class="mi">12</span><span class="p">,</span> <span class="mf">24.305</span><span class="p">,</span> <span class="mf">2.0</span><span class="p">)</span>
+ <span class="n">mg_type</span><span class="o">.</span><span class="n">epsilon</span> <span class="o">=</span> <span class="n">na_type</span><span class="o">.</span><span class="n">epsilon</span>
+ <span class="n">mg_type</span><span class="o">.</span><span class="n">rmin</span> <span class="o">=</span> <span class="n">na_type</span><span class="o">.</span><span class="n">rmin</span>
+ <span class="n">mg_type</span><span class="o">.</span><span class="n">epsilon_14</span> <span class="o">=</span> <span class="n">na_type</span><span class="o">.</span><span class="n">epsilon_14</span>
+ <span class="n">mg_type</span><span class="o">.</span><span class="n">rmin_14</span> <span class="o">=</span> <span class="n">na_type</span><span class="o">.</span><span class="n">rmin_14</span>
+ <span class="n">structure</span><span class="o">.</span><span class="n">atom_types</span><span class="p">[</span><span class="n">mg_type</span><span class="o">.</span><span class="n">name</span><span class="p">]</span> <span class="o">=</span> <span class="n">mg_type</span>
+
+ <span class="c1"># Update atom properties to magnesium</span>
+ <span class="n">a</span><span class="o">.</span><span class="n">atom_type</span> <span class="o">=</span> <span class="n">mg_type</span>
+ <span class="n">a</span><span class="o">.</span><span class="n">residue</span><span class="o">.</span><span class="n">name</span> <span class="o">=</span> <span class="s1">'Mg2+'</span>
+ <span class="n">a</span><span class="o">.</span><span class="n">name</span> <span class="o">=</span> <span class="s1">'Mg2+'</span>
+ <span class="n">a</span><span class="o">.</span><span class="n">type</span> <span class="o">=</span> <span class="s1">'Mg2+'</span>
+ <span class="n">a</span><span class="o">.</span><span class="n">atomic_number</span> <span class="o">=</span> <span class="mi">12</span>
+ <span class="n">a</span><span class="o">.</span><span class="n">_charge</span> <span class="o">=</span> <span class="mi">2</span>
+ <span class="n">a</span><span class="o">.</span><span class="n">charge</span> <span class="o">=</span> <span class="mi">2</span>
+ <span class="n">a</span><span class="o">.</span><span class="n">mass</span> <span class="o">=</span> <span class="mf">24.305</span>
+
+ <span class="k">return</span> <span class="n">structure</span></div>
+
+
+<div class="viewcode-block" id="ParmedArbd.create_dual_topology">
+<a class="viewcode-back" href="../../api/simulation_engines/parmed_bd.html#arbdmodel.parmed_bd.ParmedArbd.create_dual_topology">[docs]</a>
+ <span class="nd">@staticmethod</span>
+ <span class="k">def</span><span class="w"> </span><span class="nf">create_dual_topology</span><span class="p">(</span><span class="n">p1</span><span class="p">,</span> <span class="n">p2</span><span class="p">,</span> <span class="n">u1</span><span class="o">=</span><span class="kc">None</span><span class="p">,</span> <span class="n">u2</span><span class="o">=</span><span class="kc">None</span><span class="p">):</span>
+<span class="w"> </span><span class="sd">"""</span>
+<span class="sd"> Create a dual topology structure from two ParmEd structures.</span>
+<span class="sd"> </span>
+<span class="sd"> Args:</span>
+<span class="sd"> p1: First ParmEd structure</span>
+<span class="sd"> p2: Second ParmEd structure</span>
+<span class="sd"> u1: Optional MDAnalysis universe for p1</span>
+<span class="sd"> u2: Optional MDAnalysis universe for p2</span>
+<span class="sd"> </span>
+<span class="sd"> Returns:</span>
+<span class="sd"> Tuple of (combined structure, restraint pairs, base pair bonds)</span>
+<span class="sd"> """</span>
+ <span class="c1"># Ensure structures have same number of residues</span>
+ <span class="k">assert</span> <span class="nb">len</span><span class="p">(</span><span class="n">p1</span><span class="o">.</span><span class="n">residues</span><span class="p">)</span> <span class="o">==</span> <span class="nb">len</span><span class="p">(</span><span class="n">p2</span><span class="o">.</span><span class="n">residues</span><span class="p">)</span>
+
+ <span class="c1"># Check index alignment</span>
+ <span class="n">i</span> <span class="o">=</span> <span class="n">p1</span><span class="o">.</span><span class="n">residues</span><span class="p">[</span><span class="mi">5</span><span class="p">]</span><span class="o">.</span><span class="n">atoms</span><span class="p">[</span><span class="mi">0</span><span class="p">]</span><span class="o">.</span><span class="n">idx</span>
+ <span class="k">assert</span> <span class="n">i</span> <span class="o">==</span> <span class="n">p2</span><span class="o">.</span><span class="n">residues</span><span class="p">[</span><span class="mi">5</span><span class="p">]</span><span class="o">.</span><span class="n">atoms</span><span class="p">[</span><span class="mi">0</span><span class="p">]</span><span class="o">.</span><span class="n">idx</span>
+
+ <span class="c1"># Verify compatibility</span>
+ <span class="k">assert</span> <span class="nb">len</span><span class="p">(</span><span class="n">p2</span><span class="o">.</span><span class="n">urey_bradleys</span><span class="p">)</span> <span class="o">==</span> <span class="mi">0</span>
+ <span class="k">assert</span> <span class="nb">len</span><span class="p">(</span><span class="n">p2</span><span class="o">.</span><span class="n">cmaps</span><span class="p">)</span> <span class="o">==</span> <span class="mi">0</span>
+
+ <span class="c1"># Create new empty structure with same parameters as p1</span>
+ <span class="n">new</span> <span class="o">=</span> <span class="n">p1</span><span class="p">[:</span><span class="mi">0</span><span class="p">]</span>
+
+ <span class="c1"># Mapping dictionaries</span>
+ <span class="n">p2_to_p1</span> <span class="o">=</span> <span class="nb">dict</span><span class="p">()</span>
+ <span class="n">u_p2_to_new</span> <span class="o">=</span> <span class="nb">dict</span><span class="p">()</span>
+
+ <span class="c1"># Create maps for bonded terms</span>
+ <span class="n">bond_map</span> <span class="o">=</span> <span class="p">{</span><span class="n">a</span><span class="p">:</span> <span class="p">[]</span> <span class="k">for</span> <span class="n">a</span> <span class="ow">in</span> <span class="n">p2</span><span class="o">.</span><span class="n">atoms</span><span class="p">}</span>
+ <span class="n">angle_map</span> <span class="o">=</span> <span class="p">{</span><span class="n">a</span><span class="p">:</span> <span class="p">[]</span> <span class="k">for</span> <span class="n">a</span> <span class="ow">in</span> <span class="n">p2</span><span class="o">.</span><span class="n">atoms</span><span class="p">}</span>
+ <span class="n">dihed_map</span> <span class="o">=</span> <span class="p">{</span><span class="n">a</span><span class="p">:</span> <span class="p">[]</span> <span class="k">for</span> <span class="n">a</span> <span class="ow">in</span> <span class="n">p2</span><span class="o">.</span><span class="n">atoms</span><span class="p">}</span>
+ <span class="n">improper_map</span> <span class="o">=</span> <span class="p">{</span><span class="n">a</span><span class="p">:</span> <span class="p">[]</span> <span class="k">for</span> <span class="n">a</span> <span class="ow">in</span> <span class="n">p2</span><span class="o">.</span><span class="n">atoms</span><span class="p">}</span>
+
+ <span class="c1"># Populate bonded term maps</span>
+ <span class="k">for</span> <span class="n">b</span> <span class="ow">in</span> <span class="n">p2</span><span class="o">.</span><span class="n">bonds</span><span class="p">:</span>
+ <span class="n">bond_map</span><span class="p">[</span><span class="n">b</span><span class="o">.</span><span class="n">atom1</span><span class="p">]</span><span class="o">.</span><span class="n">append</span><span class="p">((</span><span class="n">b</span><span class="p">,</span> <span class="mi">0</span><span class="p">))</span>
+ <span class="n">bond_map</span><span class="p">[</span><span class="n">b</span><span class="o">.</span><span class="n">atom2</span><span class="p">]</span><span class="o">.</span><span class="n">append</span><span class="p">((</span><span class="n">b</span><span class="p">,</span> <span class="mi">1</span><span class="p">))</span>
+ <span class="k">for</span> <span class="n">b</span> <span class="ow">in</span> <span class="n">p2</span><span class="o">.</span><span class="n">angles</span><span class="p">:</span>
+ <span class="n">angle_map</span><span class="p">[</span><span class="n">b</span><span class="o">.</span><span class="n">atom1</span><span class="p">]</span><span class="o">.</span><span class="n">append</span><span class="p">((</span><span class="n">b</span><span class="p">,</span> <span class="mi">0</span><span class="p">))</span>
+ <span class="n">angle_map</span><span class="p">[</span><span class="n">b</span><span class="o">.</span><span class="n">atom2</span><span class="p">]</span><span class="o">.</span><span class="n">append</span><span class="p">((</span><span class="n">b</span><span class="p">,</span> <span class="mi">1</span><span class="p">))</span>
+ <span class="n">angle_map</span><span class="p">[</span><span class="n">b</span><span class="o">.</span><span class="n">atom3</span><span class="p">]</span><span class="o">.</span><span class="n">append</span><span class="p">((</span><span class="n">b</span><span class="p">,</span> <span class="mi">2</span><span class="p">))</span>
+ <span class="k">for</span> <span class="n">b</span> <span class="ow">in</span> <span class="n">p2</span><span class="o">.</span><span class="n">dihedrals</span><span class="p">:</span>
+ <span class="n">dihed_map</span><span class="p">[</span><span class="n">b</span><span class="o">.</span><span class="n">atom1</span><span class="p">]</span><span class="o">.</span><span class="n">append</span><span class="p">((</span><span class="n">b</span><span class="p">,</span> <span class="mi">0</span><span class="p">))</span>
+ <span class="n">dihed_map</span><span class="p">[</span><span class="n">b</span><span class="o">.</span><span class="n">atom2</span><span class="p">]</span><span class="o">.</span><span class="n">append</span><span class="p">((</span><span class="n">b</span><span class="p">,</span> <span class="mi">1</span><span class="p">))</span>
+ <span class="n">dihed_map</span><span class="p">[</span><span class="n">b</span><span class="o">.</span><span class="n">atom3</span><span class="p">]</span><span class="o">.</span><span class="n">append</span><span class="p">((</span><span class="n">b</span><span class="p">,</span> <span class="mi">2</span><span class="p">))</span>
+ <span class="n">dihed_map</span><span class="p">[</span><span class="n">b</span><span class="o">.</span><span class="n">atom4</span><span class="p">]</span><span class="o">.</span><span class="n">append</span><span class="p">((</span><span class="n">b</span><span class="p">,</span> <span class="mi">3</span><span class="p">))</span>
+ <span class="k">for</span> <span class="n">b</span> <span class="ow">in</span> <span class="n">p2</span><span class="o">.</span><span class="n">impropers</span><span class="p">:</span>
+ <span class="n">improper_map</span><span class="p">[</span><span class="n">b</span><span class="o">.</span><span class="n">atom1</span><span class="p">]</span><span class="o">.</span><span class="n">append</span><span class="p">((</span><span class="n">b</span><span class="p">,</span> <span class="mi">0</span><span class="p">))</span>
+ <span class="n">improper_map</span><span class="p">[</span><span class="n">b</span><span class="o">.</span><span class="n">atom2</span><span class="p">]</span><span class="o">.</span><span class="n">append</span><span class="p">((</span><span class="n">b</span><span class="p">,</span> <span class="mi">1</span><span class="p">))</span>
+ <span class="n">improper_map</span><span class="p">[</span><span class="n">b</span><span class="o">.</span><span class="n">atom3</span><span class="p">]</span><span class="o">.</span><span class="n">append</span><span class="p">((</span><span class="n">b</span><span class="p">,</span> <span class="mi">2</span><span class="p">))</span>
+ <span class="n">improper_map</span><span class="p">[</span><span class="n">b</span><span class="o">.</span><span class="n">atom4</span><span class="p">]</span><span class="o">.</span><span class="n">append</span><span class="p">((</span><span class="n">b</span><span class="p">,</span> <span class="mi">3</span><span class="p">))</span>
+
+ <span class="n">pairs</span> <span class="o">=</span> <span class="p">[]</span>
+
+ <span class="c1"># Process each segment of p1</span>
+ <span class="n">last_p1_i</span> <span class="o">=</span> <span class="mi">0</span>
+ <span class="n">first_p1_atom</span> <span class="o">=</span> <span class="nb">dict</span><span class="p">()</span> <span class="c1"># keys are segids</span>
+ <span class="n">first_new_atom</span> <span class="o">=</span> <span class="nb">dict</span><span class="p">()</span> <span class="c1"># keys are segids</span>
+ <span class="n">last_p1_new_atom</span> <span class="o">=</span> <span class="nb">dict</span><span class="p">()</span> <span class="c1"># keys are segids</span>
+ <span class="n">processed_segments</span> <span class="o">=</span> <span class="nb">set</span><span class="p">()</span>
+
+ <span class="c1"># First pass: Add all atoms from p1 and unique atoms from p2</span>
+ <span class="k">for</span> <span class="n">res1</span><span class="p">,</span> <span class="n">res2</span> <span class="ow">in</span> <span class="nb">zip</span><span class="p">(</span><span class="n">p1</span><span class="o">.</span><span class="n">residues</span><span class="p">,</span> <span class="n">p2</span><span class="o">.</span><span class="n">residues</span><span class="p">):</span>
+ <span class="n">seg</span> <span class="o">=</span> <span class="n">res1</span><span class="o">.</span><span class="n">segid</span>
+ <span class="k">assert</span> <span class="n">seg</span> <span class="o">==</span> <span class="n">res2</span><span class="o">.</span><span class="n">segid</span>
+
+ <span class="c1"># Add complete segment from p1 to new molecule if not already processed</span>
+ <span class="k">if</span> <span class="n">seg</span> <span class="ow">not</span> <span class="ow">in</span> <span class="n">processed_segments</span><span class="p">:</span>
+ <span class="n">_next</span> <span class="o">=</span> <span class="p">[</span><span class="n">r</span><span class="o">.</span><span class="n">atoms</span><span class="p">[</span><span class="o">-</span><span class="mi">1</span><span class="p">]</span><span class="o">.</span><span class="n">idx</span> <span class="o">+</span> <span class="mi">1</span> <span class="k">for</span> <span class="n">r</span> <span class="ow">in</span> <span class="n">p1</span><span class="o">.</span><span class="n">residues</span> <span class="k">if</span> <span class="n">r</span><span class="o">.</span><span class="n">segid</span> <span class="o">==</span> <span class="n">seg</span><span class="p">][</span><span class="o">-</span><span class="mi">1</span><span class="p">]</span>
+ <span class="n">first_p1_atom</span><span class="p">[</span><span class="n">seg</span><span class="p">]</span> <span class="o">=</span> <span class="n">last_p1_i</span>
+ <span class="n">first_new_atom</span><span class="p">[</span><span class="n">seg</span><span class="p">]</span> <span class="o">=</span> <span class="nb">len</span><span class="p">(</span><span class="n">new</span><span class="o">.</span><span class="n">atoms</span><span class="p">)</span>
+ <span class="n">new</span> <span class="o">=</span> <span class="n">new</span> <span class="o">+</span> <span class="n">p1</span><span class="p">[</span><span class="n">last_p1_i</span><span class="p">:</span><span class="n">_next</span><span class="p">]</span>
+ <span class="n">last_p1_new_atom</span><span class="p">[</span><span class="n">seg</span><span class="p">]</span> <span class="o">=</span> <span class="nb">len</span><span class="p">(</span><span class="n">new</span><span class="o">.</span><span class="n">atoms</span><span class="p">)</span>
+ <span class="n">last_p1_i</span> <span class="o">=</span> <span class="n">_next</span>
+ <span class="n">processed_segments</span><span class="o">.</span><span class="n">add</span><span class="p">(</span><span class="n">seg</span><span class="p">)</span>
+
+ <span class="c1"># If residue is different in p1 and p2, add unique atoms from p2</span>
+ <span class="k">if</span> <span class="n">res1</span><span class="o">.</span><span class="n">name</span> <span class="o">!=</span> <span class="n">res2</span><span class="o">.</span><span class="n">name</span><span class="p">:</span>
+ <span class="c1"># Perform distance search to match atoms</span>
+ <span class="n">c1</span> <span class="o">=</span> <span class="n">np</span><span class="o">.</span><span class="n">array</span><span class="p">([</span><span class="n">p1</span><span class="o">.</span><span class="n">coordinates</span><span class="p">[</span><span class="n">a</span><span class="o">.</span><span class="n">idx</span><span class="p">]</span> <span class="k">for</span> <span class="n">a</span> <span class="ow">in</span> <span class="n">res1</span><span class="o">.</span><span class="n">atoms</span><span class="p">])</span>
+ <span class="n">c2</span> <span class="o">=</span> <span class="n">np</span><span class="o">.</span><span class="n">array</span><span class="p">([</span><span class="n">p2</span><span class="o">.</span><span class="n">coordinates</span><span class="p">[</span><span class="n">a</span><span class="o">.</span><span class="n">idx</span><span class="p">]</span> <span class="k">for</span> <span class="n">a</span> <span class="ow">in</span> <span class="n">res2</span><span class="o">.</span><span class="n">atoms</span><span class="p">])</span>
+ <span class="n">dists</span> <span class="o">=</span> <span class="n">distance_matrix</span><span class="p">(</span><span class="n">c1</span><span class="p">,</span> <span class="n">c2</span><span class="p">)</span>
+
+ <span class="n">common_ids_j</span> <span class="o">=</span> <span class="nb">set</span><span class="p">()</span>
+ <span class="n">common_atoms_j</span> <span class="o">=</span> <span class="nb">set</span><span class="p">()</span>
+
+ <span class="c1"># Find common atoms based on name, type, and charge</span>
+ <span class="k">for</span> <span class="n">i</span><span class="p">,</span> <span class="n">j</span> <span class="ow">in</span> <span class="nb">zip</span><span class="p">(</span><span class="o">*</span><span class="n">np</span><span class="o">.</span><span class="n">where</span><span class="p">(</span><span class="n">dists</span> <span class="o"><</span> <span class="mf">0.1</span><span class="p">)):</span>
+ <span class="n">a1</span><span class="p">,</span> <span class="n">a2</span> <span class="o">=</span> <span class="n">res1</span><span class="o">.</span><span class="n">atoms</span><span class="p">[</span><span class="n">i</span><span class="p">],</span> <span class="n">res2</span><span class="o">.</span><span class="n">atoms</span><span class="p">[</span><span class="n">j</span><span class="p">]</span>
+ <span class="n">p2_to_p1</span><span class="p">[</span><span class="n">a2</span><span class="p">]</span> <span class="o">=</span> <span class="n">a1</span>
+ <span class="k">if</span> <span class="n">a1</span><span class="o">.</span><span class="n">name</span><span class="p">[</span><span class="mi">0</span><span class="p">]</span> <span class="o">==</span> <span class="s1">'H'</span><span class="p">:</span>
+ <span class="k">continue</span> <span class="c1"># Handle hydrogens separately</span>
+ <span class="k">if</span> <span class="n">a1</span><span class="o">.</span><span class="n">name</span> <span class="o">==</span> <span class="n">a2</span><span class="o">.</span><span class="n">name</span> <span class="ow">and</span> <span class="p">(</span><span class="n">a1</span><span class="o">.</span><span class="n">type</span> <span class="o">==</span> <span class="n">a2</span><span class="o">.</span><span class="n">type</span><span class="p">)</span> <span class="ow">and</span> <span class="p">(</span><span class="n">a1</span><span class="o">.</span><span class="n">charge</span> <span class="o">==</span> <span class="n">a2</span><span class="o">.</span><span class="n">charge</span><span class="p">):</span>
+ <span class="n">common_ids_j</span><span class="o">.</span><span class="n">add</span><span class="p">(</span><span class="n">j</span><span class="p">)</span>
+ <span class="n">common_atoms_j</span><span class="o">.</span><span class="n">add</span><span class="p">(</span><span class="n">a2</span><span class="p">)</span>
+
+ <span class="c1"># Handle hydrogen atoms</span>
+ <span class="k">for</span> <span class="n">i</span><span class="p">,</span> <span class="n">j</span> <span class="ow">in</span> <span class="nb">zip</span><span class="p">(</span><span class="o">*</span><span class="n">np</span><span class="o">.</span><span class="n">where</span><span class="p">(</span><span class="n">dists</span> <span class="o"><</span> <span class="mf">0.1</span><span class="p">)):</span>
+ <span class="n">a1</span><span class="p">,</span> <span class="n">a2</span> <span class="o">=</span> <span class="n">res1</span><span class="o">.</span><span class="n">atoms</span><span class="p">[</span><span class="n">i</span><span class="p">],</span> <span class="n">res2</span><span class="o">.</span><span class="n">atoms</span><span class="p">[</span><span class="n">j</span><span class="p">]</span>
+ <span class="k">if</span> <span class="n">a1</span><span class="o">.</span><span class="n">name</span><span class="p">[</span><span class="mi">0</span><span class="p">]</span> <span class="o">!=</span> <span class="s1">'H'</span><span class="p">:</span>
+ <span class="k">continue</span> <span class="c1"># Only consider hydrogens</span>
+ <span class="k">if</span> <span class="n">a1</span><span class="o">.</span><span class="n">name</span> <span class="o">==</span> <span class="n">a2</span><span class="o">.</span><span class="n">name</span> <span class="ow">and</span> <span class="p">(</span><span class="n">a1</span><span class="o">.</span><span class="n">type</span> <span class="o">==</span> <span class="n">a2</span><span class="o">.</span><span class="n">type</span><span class="p">)</span> <span class="ow">and</span> <span class="p">(</span><span class="n">a1</span><span class="o">.</span><span class="n">charge</span> <span class="o">==</span> <span class="n">a2</span><span class="o">.</span><span class="n">charge</span><span class="p">):</span>
+ <span class="c1"># Check that parent atoms of hydrogens are already considered common</span>
+ <span class="k">assert</span> <span class="nb">len</span><span class="p">(</span><span class="n">a1</span><span class="o">.</span><span class="n">bonds</span><span class="p">)</span> <span class="o">==</span> <span class="mi">1</span> <span class="ow">and</span> <span class="nb">len</span><span class="p">(</span><span class="n">a2</span><span class="o">.</span><span class="n">bonds</span><span class="p">)</span> <span class="o">==</span> <span class="mi">1</span>
+ <span class="n">b1</span> <span class="o">=</span> <span class="p">[</span><span class="n">a</span> <span class="k">for</span> <span class="n">a</span> <span class="ow">in</span> <span class="p">(</span><span class="n">a1</span><span class="o">.</span><span class="n">bonds</span><span class="p">[</span><span class="mi">0</span><span class="p">]</span><span class="o">.</span><span class="n">atom1</span><span class="p">,</span> <span class="n">a1</span><span class="o">.</span><span class="n">bonds</span><span class="p">[</span><span class="mi">0</span><span class="p">]</span><span class="o">.</span><span class="n">atom2</span><span class="p">)</span> <span class="k">if</span> <span class="n">a</span> <span class="o">!=</span> <span class="n">a1</span><span class="p">][</span><span class="mi">0</span><span class="p">]</span>
+ <span class="n">b2</span> <span class="o">=</span> <span class="p">[</span><span class="n">a</span> <span class="k">for</span> <span class="n">a</span> <span class="ow">in</span> <span class="p">(</span><span class="n">a2</span><span class="o">.</span><span class="n">bonds</span><span class="p">[</span><span class="mi">0</span><span class="p">]</span><span class="o">.</span><span class="n">atom1</span><span class="p">,</span> <span class="n">a2</span><span class="o">.</span><span class="n">bonds</span><span class="p">[</span><span class="mi">0</span><span class="p">]</span><span class="o">.</span><span class="n">atom2</span><span class="p">)</span> <span class="k">if</span> <span class="n">a</span> <span class="o">!=</span> <span class="n">a2</span><span class="p">][</span><span class="mi">0</span><span class="p">]</span>
+ <span class="k">if</span> <span class="n">b2</span> <span class="ow">in</span> <span class="n">common_atoms_j</span><span class="p">:</span>
+ <span class="n">common_ids_j</span><span class="o">.</span><span class="n">add</span><span class="p">(</span><span class="n">j</span><span class="p">)</span>
+ <span class="n">common_atoms_j</span><span class="o">.</span><span class="n">add</span><span class="p">(</span><span class="n">a2</span><span class="p">)</span>
+
+ <span class="c1"># Special handling for H2' atoms (fix for topology issues)</span>
+ <span class="k">if</span> <span class="nb">any</span><span class="p">(</span><span class="n">a</span><span class="o">.</span><span class="n">name</span> <span class="o">==</span> <span class="s2">"H2'"</span> <span class="k">for</span> <span class="n">a</span> <span class="ow">in</span> <span class="n">res1</span><span class="o">.</span><span class="n">atoms</span><span class="p">)</span> <span class="ow">and</span> <span class="nb">any</span><span class="p">(</span><span class="n">a</span><span class="o">.</span><span class="n">name</span> <span class="o">==</span> <span class="s2">"H2'"</span> <span class="k">for</span> <span class="n">a</span> <span class="ow">in</span> <span class="n">res2</span><span class="o">.</span><span class="n">atoms</span><span class="p">):</span>
+ <span class="n">a1</span> <span class="o">=</span> <span class="p">[</span><span class="n">a</span> <span class="k">for</span> <span class="n">a</span> <span class="ow">in</span> <span class="n">res1</span><span class="o">.</span><span class="n">atoms</span> <span class="k">if</span> <span class="n">a</span><span class="o">.</span><span class="n">name</span> <span class="o">==</span> <span class="s2">"H2'"</span><span class="p">][</span><span class="mi">0</span><span class="p">]</span>
+ <span class="n">j</span><span class="p">,</span> <span class="n">a2</span> <span class="o">=</span> <span class="nb">next</span><span class="p">((</span><span class="n">i</span><span class="p">,</span> <span class="n">a</span><span class="p">)</span> <span class="k">for</span> <span class="n">i</span><span class="p">,</span> <span class="n">a</span> <span class="ow">in</span> <span class="nb">enumerate</span><span class="p">(</span><span class="n">res2</span><span class="o">.</span><span class="n">atoms</span><span class="p">)</span> <span class="k">if</span> <span class="n">a</span><span class="o">.</span><span class="n">name</span> <span class="o">==</span> <span class="s2">"H2'"</span><span class="p">)</span>
+ <span class="k">if</span> <span class="n">a2</span> <span class="ow">not</span> <span class="ow">in</span> <span class="n">p2_to_p1</span><span class="p">:</span>
+ <span class="n">p2_to_p1</span><span class="p">[</span><span class="n">a2</span><span class="p">]</span> <span class="o">=</span> <span class="n">a1</span>
+ <span class="n">common_ids_j</span><span class="o">.</span><span class="n">add</span><span class="p">(</span><span class="n">j</span><span class="p">)</span>
+ <span class="n">common_atoms_j</span><span class="o">.</span><span class="n">add</span><span class="p">(</span><span class="n">a2</span><span class="p">)</span>
+
+ <span class="c1"># Find unique atoms in res2</span>
+ <span class="n">unique_atoms_j</span> <span class="o">=</span> <span class="p">[</span>
+ <span class="n">res2</span><span class="o">.</span><span class="n">atoms</span><span class="p">[</span><span class="n">j</span><span class="p">]</span> <span class="k">for</span> <span class="n">j</span> <span class="ow">in</span> <span class="nb">range</span><span class="p">(</span><span class="nb">len</span><span class="p">(</span><span class="n">res2</span><span class="o">.</span><span class="n">atoms</span><span class="p">))</span>
+ <span class="k">if</span> <span class="n">j</span> <span class="ow">not</span> <span class="ow">in</span> <span class="n">common_ids_j</span>
+ <span class="p">]</span>
+ <span class="n">unique_ids_j</span> <span class="o">=</span> <span class="p">[</span><span class="n">a2</span><span class="o">.</span><span class="n">idx</span> <span class="k">for</span> <span class="n">a2</span> <span class="ow">in</span> <span class="n">unique_atoms_j</span><span class="p">]</span>
+
+ <span class="c1"># Add unique atoms from res2 to new structure</span>
+ <span class="k">if</span> <span class="n">unique_ids_j</span><span class="p">:</span>
+ <span class="n">logger</span><span class="o">.</span><span class="n">info</span><span class="p">(</span><span class="sa">f</span><span class="s1">'Adding </span><span class="si">{</span><span class="nb">len</span><span class="p">(</span><span class="n">unique_ids_j</span><span class="p">)</span><span class="si">}</span><span class="s1"> unique atoms from residue </span><span class="si">{</span><span class="n">res2</span><span class="o">.</span><span class="n">name</span><span class="si">}</span><span class="s1">'</span><span class="p">)</span>
+ <span class="n">new</span> <span class="o">=</span> <span class="n">new</span> <span class="o">+</span> <span class="n">p2</span><span class="p">[</span><span class="n">unique_ids_j</span><span class="p">]</span>
+
+ <span class="c1"># Second pass: Add bonded terms and set up dual topology information</span>
+ <span class="n">current_seg</span> <span class="o">=</span> <span class="kc">None</span>
+ <span class="n">current_new_atom</span> <span class="o">=</span> <span class="kc">None</span>
+ <span class="k">for</span> <span class="n">res1</span><span class="p">,</span> <span class="n">res2</span> <span class="ow">in</span> <span class="nb">zip</span><span class="p">(</span><span class="n">p1</span><span class="o">.</span><span class="n">residues</span><span class="p">,</span> <span class="n">p2</span><span class="o">.</span><span class="n">residues</span><span class="p">):</span>
+ <span class="n">seg</span> <span class="o">=</span> <span class="n">res1</span><span class="o">.</span><span class="n">segid</span>
+ <span class="k">assert</span> <span class="n">seg</span> <span class="o">==</span> <span class="n">res2</span><span class="o">.</span><span class="n">segid</span>
+
+ <span class="k">if</span> <span class="n">current_seg</span> <span class="o">!=</span> <span class="n">seg</span><span class="p">:</span>
+ <span class="n">current_seg</span> <span class="o">=</span> <span class="n">seg</span>
+ <span class="n">current_new_atom</span> <span class="o">=</span> <span class="n">last_p1_new_atom</span><span class="p">[</span><span class="n">seg</span><span class="p">]</span>
+ <span class="n">p1_to_new_di</span> <span class="o">=</span> <span class="n">first_new_atom</span><span class="p">[</span><span class="n">seg</span><span class="p">]</span> <span class="o">-</span> <span class="n">first_p1_atom</span><span class="p">[</span><span class="n">seg</span><span class="p">]</span>
+
+ <span class="k">if</span> <span class="n">res1</span><span class="o">.</span><span class="n">name</span> <span class="o">!=</span> <span class="n">res2</span><span class="o">.</span><span class="n">name</span><span class="p">:</span>
+ <span class="c1"># Perform distance search to match atoms</span>
+ <span class="n">c1</span> <span class="o">=</span> <span class="n">np</span><span class="o">.</span><span class="n">array</span><span class="p">([</span><span class="n">p1</span><span class="o">.</span><span class="n">coordinates</span><span class="p">[</span><span class="n">a</span><span class="o">.</span><span class="n">idx</span><span class="p">]</span> <span class="k">for</span> <span class="n">a</span> <span class="ow">in</span> <span class="n">res1</span><span class="o">.</span><span class="n">atoms</span><span class="p">])</span>
+ <span class="n">c2</span> <span class="o">=</span> <span class="n">np</span><span class="o">.</span><span class="n">array</span><span class="p">([</span><span class="n">p2</span><span class="o">.</span><span class="n">coordinates</span><span class="p">[</span><span class="n">a</span><span class="o">.</span><span class="n">idx</span><span class="p">]</span> <span class="k">for</span> <span class="n">a</span> <span class="ow">in</span> <span class="n">res2</span><span class="o">.</span><span class="n">atoms</span><span class="p">])</span>
+ <span class="n">dists</span> <span class="o">=</span> <span class="n">distance_matrix</span><span class="p">(</span><span class="n">c1</span><span class="p">,</span> <span class="n">c2</span><span class="p">)</span>
+
+ <span class="n">common_ids_i</span> <span class="o">=</span> <span class="nb">set</span><span class="p">()</span>
+ <span class="n">common_ids_j</span> <span class="o">=</span> <span class="nb">set</span><span class="p">()</span>
+ <span class="n">common_atoms_j</span> <span class="o">=</span> <span class="nb">set</span><span class="p">()</span>
+
+ <span class="c1"># Find common atoms</span>
+ <span class="k">for</span> <span class="n">i</span><span class="p">,</span> <span class="n">j</span> <span class="ow">in</span> <span class="nb">zip</span><span class="p">(</span><span class="o">*</span><span class="n">np</span><span class="o">.</span><span class="n">where</span><span class="p">(</span><span class="n">dists</span> <span class="o"><</span> <span class="mf">0.1</span><span class="p">)):</span>
+ <span class="n">a1</span><span class="p">,</span> <span class="n">a2</span> <span class="o">=</span> <span class="n">res1</span><span class="o">.</span><span class="n">atoms</span><span class="p">[</span><span class="n">i</span><span class="p">],</span> <span class="n">res2</span><span class="o">.</span><span class="n">atoms</span><span class="p">[</span><span class="n">j</span><span class="p">]</span>
+ <span class="n">p2_to_p1</span><span class="p">[</span><span class="n">a2</span><span class="p">]</span> <span class="o">=</span> <span class="n">a1</span>
+ <span class="k">if</span> <span class="n">a1</span><span class="o">.</span><span class="n">name</span><span class="p">[</span><span class="mi">0</span><span class="p">]</span> <span class="o">==</span> <span class="s1">'H'</span><span class="p">:</span>
+ <span class="k">continue</span>
+ <span class="k">if</span> <span class="n">a1</span><span class="o">.</span><span class="n">name</span> <span class="o">==</span> <span class="n">a2</span><span class="o">.</span><span class="n">name</span> <span class="ow">and</span> <span class="p">(</span><span class="n">a1</span><span class="o">.</span><span class="n">type</span> <span class="o">==</span> <span class="n">a2</span><span class="o">.</span><span class="n">type</span><span class="p">)</span> <span class="ow">and</span> <span class="p">(</span><span class="n">a1</span><span class="o">.</span><span class="n">charge</span> <span class="o">==</span> <span class="n">a2</span><span class="o">.</span><span class="n">charge</span><span class="p">):</span>
+ <span class="n">common_ids_i</span><span class="o">.</span><span class="n">add</span><span class="p">(</span><span class="n">i</span><span class="p">)</span>
+ <span class="n">common_ids_j</span><span class="o">.</span><span class="n">add</span><span class="p">(</span><span class="n">j</span><span class="p">)</span>
+ <span class="n">common_atoms_j</span><span class="o">.</span><span class="n">add</span><span class="p">(</span><span class="n">a2</span><span class="p">)</span>
+
+ <span class="c1"># Handle hydrogen atoms</span>
+ <span class="k">for</span> <span class="n">i</span><span class="p">,</span> <span class="n">j</span> <span class="ow">in</span> <span class="nb">zip</span><span class="p">(</span><span class="o">*</span><span class="n">np</span><span class="o">.</span><span class="n">where</span><span class="p">(</span><span class="n">dists</span> <span class="o"><</span> <span class="mf">0.1</span><span class="p">)):</span>
+ <span class="n">a1</span><span class="p">,</span> <span class="n">a2</span> <span class="o">=</span> <span class="n">res1</span><span class="o">.</span><span class="n">atoms</span><span class="p">[</span><span class="n">i</span><span class="p">],</span> <span class="n">res2</span><span class="o">.</span><span class="n">atoms</span><span class="p">[</span><span class="n">j</span><span class="p">]</span>
+ <span class="k">if</span> <span class="n">a1</span><span class="o">.</span><span class="n">name</span><span class="p">[</span><span class="mi">0</span><span class="p">]</span> <span class="o">!=</span> <span class="s1">'H'</span><span class="p">:</span>
+ <span class="k">continue</span>
+ <span class="k">if</span> <span class="n">a1</span><span class="o">.</span><span class="n">name</span> <span class="o">==</span> <span class="n">a2</span><span class="o">.</span><span class="n">name</span> <span class="ow">and</span> <span class="p">(</span><span class="n">a1</span><span class="o">.</span><span class="n">type</span> <span class="o">==</span> <span class="n">a2</span><span class="o">.</span><span class="n">type</span><span class="p">)</span> <span class="ow">and</span> <span class="p">(</span><span class="n">a1</span><span class="o">.</span><span class="n">charge</span> <span class="o">==</span> <span class="n">a2</span><span class="o">.</span><span class="n">charge</span><span class="p">):</span>
+ <span class="k">assert</span> <span class="nb">len</span><span class="p">(</span><span class="n">a1</span><span class="o">.</span><span class="n">bonds</span><span class="p">)</span> <span class="o">==</span> <span class="mi">1</span> <span class="ow">and</span> <span class="nb">len</span><span class="p">(</span><span class="n">a2</span><span class="o">.</span><span class="n">bonds</span><span class="p">)</span> <span class="o">==</span> <span class="mi">1</span>
+ <span class="n">b1</span> <span class="o">=</span> <span class="p">[</span><span class="n">a</span> <span class="k">for</span> <span class="n">a</span> <span class="ow">in</span> <span class="p">(</span><span class="n">a1</span><span class="o">.</span><span class="n">bonds</span><span class="p">[</span><span class="mi">0</span><span class="p">]</span><span class="o">.</span><span class="n">atom1</span><span class="p">,</span> <span class="n">a1</span><span class="o">.</span><span class="n">bonds</span><span class="p">[</span><span class="mi">0</span><span class="p">]</span><span class="o">.</span><span class="n">atom2</span><span class="p">)</span> <span class="k">if</span> <span class="n">a</span> <span class="o">!=</span> <span class="n">a1</span><span class="p">][</span><span class="mi">0</span><span class="p">]</span>
+ <span class="n">b2</span> <span class="o">=</span> <span class="p">[</span><span class="n">a</span> <span class="k">for</span> <span class="n">a</span> <span class="ow">in</span> <span class="p">(</span><span class="n">a2</span><span class="o">.</span><span class="n">bonds</span><span class="p">[</span><span class="mi">0</span><span class="p">]</span><span class="o">.</span><span class="n">atom1</span><span class="p">,</span> <span class="n">a2</span><span class="o">.</span><span class="n">bonds</span><span class="p">[</span><span class="mi">0</span><span class="p">]</span><span class="o">.</span><span class="n">atom2</span><span class="p">)</span> <span class="k">if</span> <span class="n">a</span> <span class="o">!=</span> <span class="n">a2</span><span class="p">][</span><span class="mi">0</span><span class="p">]</span>
+ <span class="k">if</span> <span class="n">b2</span> <span class="ow">in</span> <span class="n">common_atoms_j</span><span class="p">:</span>
+ <span class="n">common_ids_i</span><span class="o">.</span><span class="n">add</span><span class="p">(</span><span class="n">i</span><span class="p">)</span>
+ <span class="n">common_ids_j</span><span class="o">.</span><span class="n">add</span><span class="p">(</span><span class="n">j</span><span class="p">)</span>
+ <span class="n">common_atoms_j</span><span class="o">.</span><span class="n">add</span><span class="p">(</span><span class="n">a2</span><span class="p">)</span>
+
+ <span class="c1"># Special handling for H2' atoms</span>
+ <span class="k">if</span> <span class="nb">any</span><span class="p">(</span><span class="n">a</span><span class="o">.</span><span class="n">name</span> <span class="o">==</span> <span class="s2">"H2'"</span> <span class="k">for</span> <span class="n">a</span> <span class="ow">in</span> <span class="n">res1</span><span class="o">.</span><span class="n">atoms</span><span class="p">)</span> <span class="ow">and</span> <span class="nb">any</span><span class="p">(</span><span class="n">a</span><span class="o">.</span><span class="n">name</span> <span class="o">==</span> <span class="s2">"H2'"</span> <span class="k">for</span> <span class="n">a</span> <span class="ow">in</span> <span class="n">res2</span><span class="o">.</span><span class="n">atoms</span><span class="p">):</span>
+ <span class="n">i</span><span class="p">,</span> <span class="n">a1</span> <span class="o">=</span> <span class="nb">next</span><span class="p">((</span><span class="n">i</span><span class="p">,</span> <span class="n">a</span><span class="p">)</span> <span class="k">for</span> <span class="n">i</span><span class="p">,</span> <span class="n">a</span> <span class="ow">in</span> <span class="nb">enumerate</span><span class="p">(</span><span class="n">res1</span><span class="o">.</span><span class="n">atoms</span><span class="p">)</span> <span class="k">if</span> <span class="n">a</span><span class="o">.</span><span class="n">name</span> <span class="o">==</span> <span class="s2">"H2'"</span><span class="p">)</span>
+ <span class="n">j</span><span class="p">,</span> <span class="n">a2</span> <span class="o">=</span> <span class="nb">next</span><span class="p">((</span><span class="n">i</span><span class="p">,</span> <span class="n">a</span><span class="p">)</span> <span class="k">for</span> <span class="n">i</span><span class="p">,</span> <span class="n">a</span> <span class="ow">in</span> <span class="nb">enumerate</span><span class="p">(</span><span class="n">res2</span><span class="o">.</span><span class="n">atoms</span><span class="p">)</span> <span class="k">if</span> <span class="n">a</span><span class="o">.</span><span class="n">name</span> <span class="o">==</span> <span class="s2">"H2'"</span><span class="p">)</span>
+ <span class="k">if</span> <span class="n">a2</span> <span class="ow">in</span> <span class="n">p2_to_p1</span><span class="p">:</span>
+ <span class="k">assert</span> <span class="n">p2_to_p1</span><span class="p">[</span><span class="n">a2</span><span class="p">]</span> <span class="o">==</span> <span class="n">a1</span>
+ <span class="n">p2_to_p1</span><span class="p">[</span><span class="n">a2</span><span class="p">]</span> <span class="o">=</span> <span class="n">a1</span>
+ <span class="n">common_ids_i</span><span class="o">.</span><span class="n">add</span><span class="p">(</span><span class="n">i</span><span class="p">)</span>
+ <span class="n">common_ids_j</span><span class="o">.</span><span class="n">add</span><span class="p">(</span><span class="n">j</span><span class="p">)</span>
+ <span class="n">common_atoms_j</span><span class="o">.</span><span class="n">add</span><span class="p">(</span><span class="n">a2</span><span class="p">)</span>
+
+ <span class="c1"># Get unique atoms in res2</span>
+ <span class="n">unique_atoms_j</span> <span class="o">=</span> <span class="p">[</span>
+ <span class="n">res2</span><span class="o">.</span><span class="n">atoms</span><span class="p">[</span><span class="n">j</span><span class="p">]</span> <span class="k">for</span> <span class="n">j</span> <span class="ow">in</span> <span class="nb">range</span><span class="p">(</span><span class="nb">len</span><span class="p">(</span><span class="n">res2</span><span class="o">.</span><span class="n">atoms</span><span class="p">))</span>
+ <span class="k">if</span> <span class="n">j</span> <span class="ow">not</span> <span class="ow">in</span> <span class="n">common_ids_j</span>
+ <span class="p">]</span>
+ <span class="n">unique_ids_j</span> <span class="o">=</span> <span class="p">[</span><span class="n">a2</span><span class="o">.</span><span class="n">idx</span> <span class="k">for</span> <span class="n">a2</span> <span class="ow">in</span> <span class="n">unique_atoms_j</span><span class="p">]</span>
+
+ <span class="c1"># Find mapping of unique atoms from res2 to new structure</span>
+ <span class="n">_num_new</span> <span class="o">=</span> <span class="nb">len</span><span class="p">(</span><span class="n">unique_ids_j</span><span class="p">)</span>
+ <span class="n">_tmp</span> <span class="o">=</span> <span class="p">{</span><span class="n">a</span><span class="o">.</span><span class="n">name</span><span class="p">:</span> <span class="n">a</span> <span class="k">for</span> <span class="n">a</span> <span class="ow">in</span> <span class="n">new</span><span class="o">.</span><span class="n">atoms</span><span class="p">[</span><span class="n">current_new_atom</span><span class="p">:</span><span class="n">current_new_atom</span> <span class="o">+</span> <span class="n">_num_new</span><span class="p">]}</span>
+ <span class="n">current_new_atom</span> <span class="o">+=</span> <span class="n">_num_new</span>
+ <span class="n">u_p2_to_new</span><span class="o">.</span><span class="n">update</span><span class="p">({</span><span class="n">a2</span><span class="p">:</span> <span class="n">_tmp</span><span class="p">[</span><span class="n">a2</span><span class="o">.</span><span class="n">name</span><span class="p">]</span> <span class="k">for</span> <span class="n">a2</span> <span class="ow">in</span> <span class="n">unique_atoms_j</span><span class="p">})</span>
+
+ <span class="c1"># Find pairs of dual-topology atoms for restraints, excluding hydrogens</span>
+ <span class="k">for</span> <span class="n">i</span> <span class="ow">in</span> <span class="nb">range</span><span class="p">(</span><span class="nb">len</span><span class="p">(</span><span class="n">c1</span><span class="p">)):</span>
+ <span class="k">if</span> <span class="n">i</span> <span class="ow">in</span> <span class="n">common_ids_i</span> <span class="ow">or</span> <span class="n">res1</span><span class="o">.</span><span class="n">atoms</span><span class="p">[</span><span class="n">i</span><span class="p">]</span><span class="o">.</span><span class="n">name</span><span class="p">[</span><span class="mi">0</span><span class="p">]</span> <span class="o">==</span> <span class="s1">'H'</span><span class="p">:</span>
+ <span class="n">dists</span><span class="p">[</span><span class="n">i</span><span class="p">,</span> <span class="p">:]</span> <span class="o">+=</span> <span class="mi">100</span> <span class="c1"># Exclude from pairing</span>
+
+ <span class="k">for</span> <span class="n">j</span> <span class="ow">in</span> <span class="nb">range</span><span class="p">(</span><span class="nb">len</span><span class="p">(</span><span class="n">c2</span><span class="p">)):</span>
+ <span class="k">if</span> <span class="n">j</span> <span class="ow">in</span> <span class="n">common_ids_j</span> <span class="ow">or</span> <span class="n">res2</span><span class="o">.</span><span class="n">atoms</span><span class="p">[</span><span class="n">j</span><span class="p">]</span><span class="o">.</span><span class="n">name</span><span class="p">[</span><span class="mi">0</span><span class="p">]</span> <span class="o">==</span> <span class="s1">'H'</span><span class="p">:</span>
+ <span class="n">dists</span><span class="p">[:,</span> <span class="n">j</span><span class="p">]</span> <span class="o">+=</span> <span class="mi">100</span> <span class="c1"># Exclude from pairing</span>
+
+ <span class="c1"># Create restraint pairs</span>
+ <span class="k">if</span> <span class="nb">len</span><span class="p">(</span><span class="n">c1</span><span class="p">)</span> <span class="o"><</span> <span class="nb">len</span><span class="p">(</span><span class="n">c2</span><span class="p">):</span>
+ <span class="k">for</span> <span class="n">i</span><span class="p">,</span> <span class="n">a1</span> <span class="ow">in</span> <span class="nb">enumerate</span><span class="p">(</span><span class="n">res1</span><span class="o">.</span><span class="n">atoms</span><span class="p">):</span>
+ <span class="k">if</span> <span class="n">i</span> <span class="ow">in</span> <span class="n">common_ids_i</span> <span class="ow">or</span> <span class="n">a1</span><span class="o">.</span><span class="n">name</span><span class="p">[</span><span class="mi">0</span><span class="p">]</span> <span class="o">==</span> <span class="s1">'H'</span><span class="p">:</span>
+ <span class="k">continue</span>
+ <span class="n">j</span> <span class="o">=</span> <span class="n">np</span><span class="o">.</span><span class="n">argmin</span><span class="p">(</span><span class="n">dists</span><span class="p">[</span><span class="n">i</span><span class="p">])</span>
+ <span class="n">pairs</span><span class="o">.</span><span class="n">append</span><span class="p">((</span><span class="n">p1_to_new_di</span> <span class="o">+</span> <span class="n">a1</span><span class="o">.</span><span class="n">idx</span><span class="p">,</span> <span class="n">u_p2_to_new</span><span class="p">[</span><span class="n">res2</span><span class="o">.</span><span class="n">atoms</span><span class="p">[</span><span class="n">j</span><span class="p">]]</span><span class="o">.</span><span class="n">idx</span><span class="p">,</span> <span class="n">dists</span><span class="p">[</span><span class="n">i</span><span class="p">,</span> <span class="n">j</span><span class="p">]))</span>
+ <span class="k">else</span><span class="p">:</span>
+ <span class="k">for</span> <span class="n">j</span><span class="p">,</span> <span class="n">a2</span> <span class="ow">in</span> <span class="nb">enumerate</span><span class="p">(</span><span class="n">res2</span><span class="o">.</span><span class="n">atoms</span><span class="p">):</span>
+ <span class="k">if</span> <span class="n">j</span> <span class="ow">in</span> <span class="n">common_ids_j</span> <span class="ow">or</span> <span class="n">a2</span><span class="o">.</span><span class="n">name</span><span class="p">[</span><span class="mi">0</span><span class="p">]</span> <span class="o">==</span> <span class="s1">'H'</span><span class="p">:</span>
+ <span class="k">continue</span>
+ <span class="n">i</span> <span class="o">=</span> <span class="n">np</span><span class="o">.</span><span class="n">argmin</span><span class="p">(</span><span class="n">dists</span><span class="p">[:,</span> <span class="n">j</span><span class="p">])</span>
+ <span class="n">pairs</span><span class="o">.</span><span class="n">append</span><span class="p">((</span><span class="n">p1_to_new_di</span> <span class="o">+</span> <span class="n">res1</span><span class="o">.</span><span class="n">atoms</span><span class="p">[</span><span class="n">i</span><span class="p">]</span><span class="o">.</span><span class="n">idx</span><span class="p">,</span> <span class="n">u_p2_to_new</span><span class="p">[</span><span class="n">a2</span><span class="p">]</span><span class="o">.</span><span class="n">idx</span><span class="p">,</span> <span class="n">dists</span><span class="p">[</span><span class="n">i</span><span class="p">,</span> <span class="n">j</span><span class="p">]))</span>
+
+ <span class="c1"># Set beta factor for FEP atoms</span>
+ <span class="k">for</span> <span class="n">i</span><span class="p">,</span> <span class="n">a</span> <span class="ow">in</span> <span class="nb">enumerate</span><span class="p">(</span><span class="n">new</span><span class="o">.</span><span class="n">atoms</span><span class="p">[</span><span class="n">p1_to_new_di</span> <span class="o">+</span> <span class="n">res1</span><span class="o">.</span><span class="n">atoms</span><span class="p">[</span><span class="mi">0</span><span class="p">]</span><span class="o">.</span><span class="n">idx</span><span class="p">:</span><span class="n">p1_to_new_di</span> <span class="o">+</span> <span class="n">res1</span><span class="o">.</span><span class="n">atoms</span><span class="p">[</span><span class="o">-</span><span class="mi">1</span><span class="p">]</span><span class="o">.</span><span class="n">idx</span> <span class="o">+</span> <span class="mi">1</span><span class="p">]):</span>
+ <span class="k">if</span> <span class="n">i</span> <span class="ow">not</span> <span class="ow">in</span> <span class="n">common_ids_i</span><span class="p">:</span>
+ <span class="n">a</span><span class="o">.</span><span class="n">bfactor</span> <span class="o">=</span> <span class="o">-</span><span class="mf">1.0</span>
+
+ <span class="k">for</span> <span class="n">_</span><span class="p">,</span> <span class="n">a</span> <span class="ow">in</span> <span class="n">u_p2_to_new</span><span class="o">.</span><span class="n">items</span><span class="p">():</span>
+ <span class="n">a</span><span class="o">.</span><span class="n">bfactor</span> <span class="o">=</span> <span class="mf">1.0</span>
+
+ <span class="c1"># Add bonded potentials from p2 that include unique atoms</span>
+ <span class="n">processed</span> <span class="o">=</span> <span class="nb">set</span><span class="p">()</span> <span class="c1"># avoid duplicate entries</span>
+ <span class="k">for</span> <span class="n">a2</span> <span class="ow">in</span> <span class="n">unique_atoms_j</span><span class="p">:</span>
+ <span class="k">for</span> <span class="n">pot_map</span> <span class="ow">in</span> <span class="p">(</span><span class="n">bond_map</span><span class="p">,</span> <span class="n">angle_map</span><span class="p">,</span> <span class="n">dihed_map</span><span class="p">,</span> <span class="n">improper_map</span><span class="p">):</span>
+ <span class="k">for</span> <span class="n">b</span><span class="p">,</span> <span class="n">rank</span> <span class="ow">in</span> <span class="n">pot_map</span><span class="p">[</span><span class="n">a2</span><span class="p">]:</span>
+ <span class="c1"># Avoid double-counting</span>
+ <span class="k">if</span> <span class="n">b</span> <span class="ow">in</span> <span class="n">processed</span><span class="p">:</span>
+ <span class="k">continue</span>
+ <span class="n">processed</span><span class="o">.</span><span class="n">add</span><span class="p">(</span><span class="n">b</span><span class="p">)</span>
+
+ <span class="c1"># Get atoms involved in the potential</span>
+ <span class="k">if</span> <span class="n">pot_map</span> <span class="o">==</span> <span class="n">bond_map</span><span class="p">:</span>
+ <span class="n">atoms</span> <span class="o">=</span> <span class="p">(</span><span class="n">b</span><span class="o">.</span><span class="n">atom1</span><span class="p">,</span> <span class="n">b</span><span class="o">.</span><span class="n">atom2</span><span class="p">)</span>
+ <span class="n">gen_pot</span> <span class="o">=</span> <span class="k">lambda</span> <span class="n">new_atoms</span><span class="p">:</span> <span class="n">parmed</span><span class="o">.</span><span class="n">Bond</span><span class="p">(</span><span class="o">*</span><span class="n">new_atoms</span><span class="p">,</span> <span class="nb">type</span><span class="o">=</span><span class="n">b</span><span class="o">.</span><span class="n">type</span><span class="p">)</span>
+ <span class="n">pot_list</span> <span class="o">=</span> <span class="n">new</span><span class="o">.</span><span class="n">bonds</span>
+ <span class="k">elif</span> <span class="n">pot_map</span> <span class="o">==</span> <span class="n">angle_map</span><span class="p">:</span>
+ <span class="n">atoms</span> <span class="o">=</span> <span class="p">(</span><span class="n">b</span><span class="o">.</span><span class="n">atom1</span><span class="p">,</span> <span class="n">b</span><span class="o">.</span><span class="n">atom2</span><span class="p">,</span> <span class="n">b</span><span class="o">.</span><span class="n">atom3</span><span class="p">)</span>
+ <span class="n">gen_pot</span> <span class="o">=</span> <span class="k">lambda</span> <span class="n">new_atoms</span><span class="p">:</span> <span class="n">parmed</span><span class="o">.</span><span class="n">Angle</span><span class="p">(</span><span class="o">*</span><span class="n">new_atoms</span><span class="p">,</span> <span class="nb">type</span><span class="o">=</span><span class="n">b</span><span class="o">.</span><span class="n">type</span><span class="p">)</span>
+ <span class="n">pot_list</span> <span class="o">=</span> <span class="n">new</span><span class="o">.</span><span class="n">angles</span>
+ <span class="k">elif</span> <span class="n">pot_map</span> <span class="o">==</span> <span class="n">dihed_map</span><span class="p">:</span>
+ <span class="n">atoms</span> <span class="o">=</span> <span class="p">(</span><span class="n">b</span><span class="o">.</span><span class="n">atom1</span><span class="p">,</span> <span class="n">b</span><span class="o">.</span><span class="n">atom2</span><span class="p">,</span> <span class="n">b</span><span class="o">.</span><span class="n">atom3</span><span class="p">,</span> <span class="n">b</span><span class="o">.</span><span class="n">atom4</span><span class="p">)</span>
+ <span class="n">gen_pot</span> <span class="o">=</span> <span class="k">lambda</span> <span class="n">new_atoms</span><span class="p">:</span> <span class="n">parmed</span><span class="o">.</span><span class="n">Dihedral</span><span class="p">(</span><span class="o">*</span><span class="n">new_atoms</span><span class="p">,</span> <span class="nb">type</span><span class="o">=</span><span class="n">b</span><span class="o">.</span><span class="n">type</span><span class="p">,</span> <span class="n">improper</span><span class="o">=</span><span class="n">b</span><span class="o">.</span><span class="n">improper</span><span class="p">)</span>
+ <span class="n">pot_list</span> <span class="o">=</span> <span class="n">new</span><span class="o">.</span><span class="n">dihedrals</span>
+ <span class="k">elif</span> <span class="n">pot_map</span> <span class="o">==</span> <span class="n">improper_map</span><span class="p">:</span>
+ <span class="n">atoms</span> <span class="o">=</span> <span class="p">(</span><span class="n">b</span><span class="o">.</span><span class="n">atom1</span><span class="p">,</span> <span class="n">b</span><span class="o">.</span><span class="n">atom2</span><span class="p">,</span> <span class="n">b</span><span class="o">.</span><span class="n">atom3</span><span class="p">,</span> <span class="n">b</span><span class="o">.</span><span class="n">atom4</span><span class="p">)</span>
+ <span class="n">gen_pot</span> <span class="o">=</span> <span class="k">lambda</span> <span class="n">new_atoms</span><span class="p">:</span> <span class="n">parmed</span><span class="o">.</span><span class="n">Improper</span><span class="p">(</span><span class="o">*</span><span class="n">new_atoms</span><span class="p">,</span> <span class="nb">type</span><span class="o">=</span><span class="n">b</span><span class="o">.</span><span class="n">type</span><span class="p">)</span>
+ <span class="n">pot_list</span> <span class="o">=</span> <span class="n">new</span><span class="o">.</span><span class="n">impropers</span>
+ <span class="k">else</span><span class="p">:</span>
+ <span class="k">raise</span> <span class="ne">Exception</span><span class="p">(</span><span class="s2">"Unknown potential map"</span><span class="p">)</span>
+
+ <span class="c1"># Skip if no atoms in bond are unique atoms</span>
+ <span class="k">if</span> <span class="nb">all</span><span class="p">(</span><span class="n">a</span> <span class="ow">in</span> <span class="n">unique_atoms_j</span> <span class="k">for</span> <span class="n">a</span> <span class="ow">in</span> <span class="n">atoms</span><span class="p">):</span>
+ <span class="k">continue</span>
+
+ <span class="c1"># Find corresponding atoms in new structure</span>
+ <span class="n">new_atoms</span> <span class="o">=</span> <span class="p">[]</span>
+ <span class="k">for</span> <span class="n">a</span> <span class="ow">in</span> <span class="n">atoms</span><span class="p">:</span>
+ <span class="k">if</span> <span class="n">a</span> <span class="ow">in</span> <span class="n">unique_atoms_j</span><span class="p">:</span>
+ <span class="n">new_atoms</span><span class="o">.</span><span class="n">append</span><span class="p">(</span><span class="n">u_p2_to_new</span><span class="p">[</span><span class="n">a</span><span class="p">])</span>
+ <span class="k">else</span><span class="p">:</span>
+ <span class="n">new_atoms</span><span class="o">.</span><span class="n">append</span><span class="p">(</span><span class="n">new</span><span class="o">.</span><span class="n">atoms</span><span class="p">[</span><span class="n">p1_to_new_di</span> <span class="o">+</span> <span class="n">p2_to_p1</span><span class="p">[</span><span class="n">a</span><span class="p">]</span><span class="o">.</span><span class="n">idx</span><span class="p">])</span>
+
+ <span class="k">assert</span> <span class="nb">all</span><span class="p">(</span><span class="n">a</span> <span class="ow">in</span> <span class="n">new</span><span class="o">.</span><span class="n">atoms</span> <span class="k">for</span> <span class="n">a</span> <span class="ow">in</span> <span class="n">new_atoms</span><span class="p">)</span>
+
+ <span class="c1"># Add potential to new structure</span>
+ <span class="n">pot_list</span><span class="o">.</span><span class="n">append</span><span class="p">(</span><span class="n">gen_pot</span><span class="p">(</span><span class="n">new_atoms</span><span class="p">))</span>
+
+ <span class="c1"># Handle base-pair information if MDAnalysis universes are provided</span>
+ <span class="n">bp_pairs</span> <span class="o">=</span> <span class="kc">None</span>
+ <span class="k">if</span> <span class="n">u1</span> <span class="ow">is</span> <span class="ow">not</span> <span class="kc">None</span> <span class="ow">and</span> <span class="n">u2</span> <span class="ow">is</span> <span class="ow">not</span> <span class="kc">None</span><span class="p">:</span>
+ <span class="n">bp_pairs</span> <span class="o">=</span> <span class="p">[]</span>
+
+ <span class="c1"># Function to find base pairs in a nucleic acid structure</span>
+ <span class="k">def</span><span class="w"> </span><span class="nf">find_bp</span><span class="p">(</span><span class="n">u</span><span class="p">):</span>
+ <span class="c1"># Find segment termini</span>
+ <span class="n">seg_ends</span> <span class="o">=</span> <span class="p">[</span><span class="n">a</span><span class="o">.</span><span class="n">position</span> <span class="k">for</span> <span class="n">seg</span> <span class="ow">in</span> <span class="n">u</span><span class="o">.</span><span class="n">segments</span>
+ <span class="k">for</span> <span class="n">a</span> <span class="ow">in</span> <span class="p">[</span><span class="n">seg</span><span class="o">.</span><span class="n">atoms</span><span class="p">[</span><span class="mi">0</span><span class="p">],</span> <span class="n">seg</span><span class="o">.</span><span class="n">atoms</span><span class="p">[</span><span class="o">-</span><span class="mi">1</span><span class="p">]]]</span>
+ <span class="n">seg_ends</span> <span class="o">=</span> <span class="n">np</span><span class="o">.</span><span class="n">array</span><span class="p">(</span><span class="n">seg_ends</span><span class="p">)</span>
+
+ <span class="n">dists</span> <span class="o">=</span> <span class="n">distance_matrix</span><span class="p">(</span><span class="n">seg_ends</span><span class="p">,</span> <span class="n">seg_ends</span><span class="p">)</span> <span class="o">+</span> <span class="mi">100</span> <span class="o">*</span> <span class="n">np</span><span class="o">.</span><span class="n">eye</span><span class="p">(</span><span class="nb">len</span><span class="p">(</span><span class="n">seg_ends</span><span class="p">))</span>
+
+ <span class="n">seg_end_map</span> <span class="o">=</span> <span class="p">{}</span>
+ <span class="k">for</span> <span class="n">i</span><span class="p">,</span> <span class="n">d</span> <span class="ow">in</span> <span class="nb">enumerate</span><span class="p">(</span><span class="n">dists</span><span class="p">):</span>
+ <span class="n">j</span> <span class="o">=</span> <span class="n">np</span><span class="o">.</span><span class="n">argmin</span><span class="p">(</span><span class="n">d</span><span class="p">)</span>
+ <span class="k">if</span> <span class="n">i</span> <span class="ow">in</span> <span class="n">seg_end_map</span><span class="p">:</span>
+ <span class="k">assert</span> <span class="n">seg_end_map</span><span class="p">[</span><span class="n">i</span><span class="p">]</span> <span class="o">==</span> <span class="n">j</span>
+ <span class="n">seg_end_map</span><span class="p">[</span><span class="n">i</span><span class="p">]</span> <span class="o">=</span> <span class="n">j</span>
+
+ <span class="n">bp</span> <span class="o">=</span> <span class="o">-</span><span class="mi">1</span> <span class="o">*</span> <span class="n">np</span><span class="o">.</span><span class="n">ones</span><span class="p">(</span><span class="nb">len</span><span class="p">(</span><span class="n">u</span><span class="o">.</span><span class="n">residues</span><span class="p">),</span> <span class="n">dtype</span><span class="o">=</span><span class="nb">int</span><span class="p">)</span>
+ <span class="n">processed</span> <span class="o">=</span> <span class="nb">set</span><span class="p">()</span>
+
+ <span class="k">for</span> <span class="n">I</span><span class="p">,</span> <span class="n">J</span> <span class="ow">in</span> <span class="n">seg_end_map</span><span class="o">.</span><span class="n">items</span><span class="p">():</span>
+ <span class="k">if</span> <span class="n">I</span> <span class="ow">in</span> <span class="n">processed</span><span class="p">:</span>
+ <span class="k">continue</span>
+ <span class="n">processed</span><span class="o">.</span><span class="n">add</span><span class="p">(</span><span class="n">I</span><span class="p">)</span>
+ <span class="n">processed</span><span class="o">.</span><span class="n">add</span><span class="p">(</span><span class="n">J</span><span class="p">)</span>
+
+ <span class="n">reses1</span><span class="p">,</span> <span class="n">reses2</span> <span class="o">=</span> <span class="p">[</span><span class="n">u</span><span class="o">.</span><span class="n">segments</span><span class="p">[</span><span class="n">K</span> <span class="o">//</span> <span class="mi">2</span><span class="p">]</span><span class="o">.</span><span class="n">residues</span><span class="p">[::</span><span class="mi">1</span> <span class="o">-</span> <span class="mi">2</span> <span class="o">*</span> <span class="p">(</span><span class="n">K</span> <span class="o">%</span> <span class="mi">2</span><span class="p">)]</span> <span class="k">for</span> <span class="n">K</span> <span class="ow">in</span> <span class="p">(</span><span class="n">I</span><span class="p">,</span> <span class="n">J</span><span class="p">)]</span>
+ <span class="k">for</span> <span class="n">i</span><span class="p">,</span> <span class="p">(</span><span class="n">r1</span><span class="p">,</span> <span class="n">r2</span><span class="p">)</span> <span class="ow">in</span> <span class="nb">enumerate</span><span class="p">(</span><span class="nb">zip</span><span class="p">(</span><span class="n">reses1</span><span class="p">,</span> <span class="n">reses2</span><span class="p">)):</span>
+ <span class="k">if</span> <span class="n">i</span> <span class="o">==</span> <span class="nb">len</span><span class="p">(</span><span class="n">reses1</span><span class="p">)</span> <span class="o">//</span> <span class="mi">2</span><span class="p">:</span>
+ <span class="k">break</span>
+ <span class="n">bp</span><span class="p">[</span><span class="n">r1</span><span class="o">.</span><span class="n">resindex</span><span class="p">]</span> <span class="o">=</span> <span class="n">r2</span><span class="o">.</span><span class="n">resindex</span>
+ <span class="n">bp</span><span class="p">[</span><span class="n">r2</span><span class="o">.</span><span class="n">resindex</span><span class="p">]</span> <span class="o">=</span> <span class="n">r1</span><span class="o">.</span><span class="n">resindex</span>
+
+ <span class="k">assert</span> <span class="n">np</span><span class="o">.</span><span class="n">all</span><span class="p">(</span><span class="n">bp</span> <span class="o">>=</span> <span class="mi">0</span><span class="p">)</span>
+ <span class="k">return</span> <span class="n">bp</span>
+
+ <span class="c1"># Find base pairs in both structures</span>
+ <span class="n">bp1</span><span class="p">,</span> <span class="n">bp2</span> <span class="o">=</span> <span class="p">[</span><span class="n">find_bp</span><span class="p">(</span><span class="n">u</span><span class="p">)</span> <span class="k">for</span> <span class="n">u</span> <span class="ow">in</span> <span class="p">(</span><span class="n">u1</span><span class="p">,</span> <span class="n">u2</span><span class="p">)]</span>
+
+ <span class="c1"># Define atom pairs for base-pairing</span>
+ <span class="n">bp_bond_atoms</span> <span class="o">=</span> <span class="p">{</span>
+ <span class="s1">'DA'</span><span class="p">:</span> <span class="p">[(</span><span class="s1">'N1'</span><span class="p">,</span> <span class="s1">'N3'</span><span class="p">),</span> <span class="p">(</span><span class="s1">'N6'</span><span class="p">,</span> <span class="s1">'O4'</span><span class="p">)],</span>
+ <span class="s1">'DT'</span><span class="p">:</span> <span class="p">[(</span><span class="s1">'N3'</span><span class="p">,</span> <span class="s1">'N1'</span><span class="p">),</span> <span class="p">(</span><span class="s1">'O4'</span><span class="p">,</span> <span class="s1">'N6'</span><span class="p">)],</span>
+ <span class="s1">'DC'</span><span class="p">:</span> <span class="p">[(</span><span class="s1">'N3'</span><span class="p">,</span> <span class="s1">'N1'</span><span class="p">),</span> <span class="p">(</span><span class="s1">'O2'</span><span class="p">,</span> <span class="s1">'N2'</span><span class="p">)],</span>
+ <span class="s1">'DG'</span><span class="p">:</span> <span class="p">[(</span><span class="s1">'N1'</span><span class="p">,</span> <span class="s1">'N3'</span><span class="p">),</span> <span class="p">(</span><span class="s1">'N2'</span><span class="p">,</span> <span class="s1">'O2'</span><span class="p">)],</span>
+ <span class="s1">'A'</span><span class="p">:</span> <span class="p">[(</span><span class="s1">'N1'</span><span class="p">,</span> <span class="s1">'N3'</span><span class="p">),</span> <span class="p">(</span><span class="s1">'N6'</span><span class="p">,</span> <span class="s1">'O4'</span><span class="p">)],</span>
+ <span class="s1">'T'</span><span class="p">:</span> <span class="p">[(</span><span class="s1">'N3'</span><span class="p">,</span> <span class="s1">'N1'</span><span class="p">),</span> <span class="p">(</span><span class="s1">'O4'</span><span class="p">,</span> <span class="s1">'N6'</span><span class="p">)],</span>
+ <span class="s1">'U'</span><span class="p">:</span> <span class="p">[(</span><span class="s1">'N3'</span><span class="p">,</span> <span class="s1">'N1'</span><span class="p">),</span> <span class="p">(</span><span class="s1">'O4'</span><span class="p">,</span> <span class="s1">'N6'</span><span class="p">)],</span>
+ <span class="s1">'C'</span><span class="p">:</span> <span class="p">[(</span><span class="s1">'N3'</span><span class="p">,</span> <span class="s1">'N1'</span><span class="p">),</span> <span class="p">(</span><span class="s1">'O2'</span><span class="p">,</span> <span class="s1">'N2'</span><span class="p">)],</span>
+ <span class="s1">'G'</span><span class="p">:</span> <span class="p">[(</span><span class="s1">'N1'</span><span class="p">,</span> <span class="s1">'N3'</span><span class="p">),</span> <span class="p">(</span><span class="s1">'N2'</span><span class="p">,</span> <span class="s1">'O2'</span><span class="p">)]</span>
+ <span class="p">}</span>
+
+ <span class="c1"># Map residue names to keys in bp_bond_atoms</span>
+ <span class="n">resname_to_key</span> <span class="o">=</span> <span class="p">{}</span>
+ <span class="k">for</span> <span class="n">key</span> <span class="ow">in</span> <span class="n">bp_bond_atoms</span><span class="p">:</span>
+ <span class="n">resname_to_key</span><span class="p">[</span><span class="n">key</span><span class="p">]</span> <span class="o">=</span> <span class="n">key</span>
+ <span class="c1"># Handle modified bases</span>
+ <span class="k">if</span> <span class="n">key</span> <span class="ow">in</span> <span class="p">(</span><span class="s1">'DA'</span><span class="p">,</span> <span class="s1">'DT'</span><span class="p">,</span> <span class="s1">'DC'</span><span class="p">,</span> <span class="s1">'DG'</span><span class="p">):</span>
+ <span class="k">for</span> <span class="n">i</span> <span class="ow">in</span> <span class="nb">range</span><span class="p">(</span><span class="mi">1</span><span class="p">,</span> <span class="mi">10</span><span class="p">):</span>
+ <span class="n">mod_name</span> <span class="o">=</span> <span class="sa">f</span><span class="s2">"</span><span class="si">{</span><span class="n">key</span><span class="si">}{</span><span class="n">i</span><span class="si">}</span><span class="s2">"</span>
+ <span class="n">resname_to_key</span><span class="p">[</span><span class="n">mod_name</span><span class="p">]</span> <span class="o">=</span> <span class="n">key</span>
+
+ <span class="c1"># Create base pair bonds</span>
+ <span class="k">for</span> <span class="n">ra</span><span class="p">,</span> <span class="p">(</span><span class="n">r1b</span><span class="p">,</span> <span class="n">r2b</span><span class="p">)</span> <span class="ow">in</span> <span class="nb">enumerate</span><span class="p">(</span><span class="nb">zip</span><span class="p">(</span><span class="n">bp1</span><span class="p">,</span> <span class="n">bp2</span><span class="p">)):</span>
+ <span class="c1"># Ra pairs with r1b; r2a pairs with r2b</span>
+ <span class="n">R1a</span> <span class="o">=</span> <span class="n">p1</span><span class="o">.</span><span class="n">residues</span><span class="p">[</span><span class="n">ra</span><span class="p">]</span>
+ <span class="n">R2a</span> <span class="o">=</span> <span class="n">p2</span><span class="o">.</span><span class="n">residues</span><span class="p">[</span><span class="n">ra</span><span class="p">]</span>
+ <span class="n">R1b</span> <span class="o">=</span> <span class="n">p1</span><span class="o">.</span><span class="n">residues</span><span class="p">[</span><span class="n">r1b</span><span class="p">]</span> <span class="k">if</span> <span class="n">r1b</span> <span class="o">>=</span> <span class="mi">0</span> <span class="k">else</span> <span class="kc">None</span>
+ <span class="n">R2b</span> <span class="o">=</span> <span class="n">p2</span><span class="o">.</span><span class="n">residues</span><span class="p">[</span><span class="n">r2b</span><span class="p">]</span> <span class="k">if</span> <span class="n">r2b</span> <span class="o">>=</span> <span class="mi">0</span> <span class="k">else</span> <span class="kc">None</span>
+
+ <span class="c1"># Add base pair bonds for structure 1</span>
+ <span class="k">if</span> <span class="n">R1b</span> <span class="ow">is</span> <span class="ow">not</span> <span class="kc">None</span> <span class="ow">and</span> <span class="n">ra</span> <span class="o"><</span> <span class="n">r1b</span><span class="p">:</span>
+ <span class="k">try</span><span class="p">:</span>
+ <span class="n">res_key</span> <span class="o">=</span> <span class="n">resname_to_key</span><span class="p">[</span><span class="n">R1a</span><span class="o">.</span><span class="n">name</span><span class="p">]</span>
+ <span class="k">for</span> <span class="n">n1</span><span class="p">,</span> <span class="n">n2</span> <span class="ow">in</span> <span class="n">bp_bond_atoms</span><span class="p">[</span><span class="n">res_key</span><span class="p">]:</span>
+ <span class="n">a</span> <span class="o">=</span> <span class="nb">next</span><span class="p">(</span><span class="n">x</span> <span class="k">for</span> <span class="n">x</span> <span class="ow">in</span> <span class="n">R1a</span><span class="o">.</span><span class="n">atoms</span> <span class="k">if</span> <span class="n">x</span><span class="o">.</span><span class="n">name</span> <span class="o">==</span> <span class="n">n1</span><span class="p">)</span>
+ <span class="n">b</span> <span class="o">=</span> <span class="nb">next</span><span class="p">(</span><span class="n">x</span> <span class="k">for</span> <span class="n">x</span> <span class="ow">in</span> <span class="n">R1b</span><span class="o">.</span><span class="n">atoms</span> <span class="k">if</span> <span class="n">x</span><span class="o">.</span><span class="n">name</span> <span class="o">==</span> <span class="n">n2</span><span class="p">)</span>
+
+ <span class="c1"># Account for index offsets</span>
+ <span class="n">seg</span> <span class="o">=</span> <span class="n">R1a</span><span class="o">.</span><span class="n">segid</span>
+ <span class="n">ai</span> <span class="o">=</span> <span class="n">a</span><span class="o">.</span><span class="n">idx</span> <span class="o">+</span> <span class="n">first_new_atom</span><span class="p">[</span><span class="n">seg</span><span class="p">]</span> <span class="o">-</span> <span class="n">first_p1_atom</span><span class="p">[</span><span class="n">seg</span><span class="p">]</span>
+ <span class="n">seg</span> <span class="o">=</span> <span class="n">R1b</span><span class="o">.</span><span class="n">segid</span>
+ <span class="n">bi</span> <span class="o">=</span> <span class="n">b</span><span class="o">.</span><span class="n">idx</span> <span class="o">+</span> <span class="n">first_new_atom</span><span class="p">[</span><span class="n">seg</span><span class="p">]</span> <span class="o">-</span> <span class="n">first_p1_atom</span><span class="p">[</span><span class="n">seg</span><span class="p">]</span>
+ <span class="n">bp_pairs</span><span class="o">.</span><span class="n">append</span><span class="p">((</span><span class="n">ai</span><span class="p">,</span> <span class="n">bi</span><span class="p">))</span>
+ <span class="k">except</span> <span class="ne">KeyError</span><span class="p">:</span>
+ <span class="n">logger</span><span class="o">.</span><span class="n">warning</span><span class="p">(</span><span class="sa">f</span><span class="s2">"Residue </span><span class="si">{</span><span class="n">R1a</span><span class="o">.</span><span class="n">name</span><span class="si">}</span><span class="s2"> not found in base pair definitions"</span><span class="p">)</span>
+ <span class="k">continue</span>
+
+ <span class="c1"># Add base pair bonds for structure 2 (if different)</span>
+ <span class="k">if</span> <span class="n">R2b</span> <span class="ow">is</span> <span class="ow">not</span> <span class="kc">None</span> <span class="ow">and</span> <span class="n">ra</span> <span class="o"><</span> <span class="n">r2b</span><span class="p">:</span>
+ <span class="c1"># Skip redundant base pairs</span>
+ <span class="k">if</span> <span class="n">R1b</span> <span class="ow">is</span> <span class="ow">not</span> <span class="kc">None</span> <span class="ow">and</span> <span class="n">R1a</span><span class="o">.</span><span class="n">name</span> <span class="o">==</span> <span class="n">R2a</span><span class="o">.</span><span class="n">name</span> <span class="ow">and</span> <span class="n">R1b</span><span class="o">.</span><span class="n">name</span> <span class="o">==</span> <span class="n">R2b</span><span class="o">.</span><span class="n">name</span><span class="p">:</span>
+ <span class="k">continue</span>
+
+ <span class="k">try</span><span class="p">:</span>
+ <span class="n">res_key</span> <span class="o">=</span> <span class="n">resname_to_key</span><span class="p">[</span><span class="n">R2a</span><span class="o">.</span><span class="n">name</span><span class="p">]</span>
+ <span class="k">for</span> <span class="n">n1</span><span class="p">,</span> <span class="n">n2</span> <span class="ow">in</span> <span class="n">bp_bond_atoms</span><span class="p">[</span><span class="n">res_key</span><span class="p">]:</span>
+ <span class="n">a</span> <span class="o">=</span> <span class="nb">next</span><span class="p">(</span><span class="n">x</span> <span class="k">for</span> <span class="n">x</span> <span class="ow">in</span> <span class="n">R2a</span><span class="o">.</span><span class="n">atoms</span> <span class="k">if</span> <span class="n">x</span><span class="o">.</span><span class="n">name</span> <span class="o">==</span> <span class="n">n1</span><span class="p">)</span>
+ <span class="n">b</span> <span class="o">=</span> <span class="nb">next</span><span class="p">(</span><span class="n">x</span> <span class="k">for</span> <span class="n">x</span> <span class="ow">in</span> <span class="n">R2b</span><span class="o">.</span><span class="n">atoms</span> <span class="k">if</span> <span class="n">x</span><span class="o">.</span><span class="n">name</span> <span class="o">==</span> <span class="n">n2</span><span class="p">)</span>
+
+ <span class="k">try</span><span class="p">:</span>
+ <span class="n">ai</span> <span class="o">=</span> <span class="n">u_p2_to_new</span><span class="p">[</span><span class="n">a</span><span class="p">]</span><span class="o">.</span><span class="n">idx</span>
+ <span class="k">assert</span> <span class="n">u_p2_to_new</span><span class="p">[</span><span class="n">a</span><span class="p">]</span><span class="o">.</span><span class="n">name</span> <span class="o">==</span> <span class="n">n1</span>
+ <span class="k">except</span> <span class="ne">KeyError</span><span class="p">:</span>
+ <span class="n">seg</span> <span class="o">=</span> <span class="n">R1a</span><span class="o">.</span><span class="n">segid</span>
+ <span class="n">a1</span> <span class="o">=</span> <span class="nb">next</span><span class="p">(</span><span class="n">x</span> <span class="k">for</span> <span class="n">x</span> <span class="ow">in</span> <span class="n">R1a</span><span class="o">.</span><span class="n">atoms</span> <span class="k">if</span> <span class="n">x</span><span class="o">.</span><span class="n">name</span> <span class="o">==</span> <span class="n">n1</span><span class="p">)</span>
+ <span class="n">ai</span> <span class="o">=</span> <span class="n">a1</span><span class="o">.</span><span class="n">idx</span> <span class="o">+</span> <span class="n">first_new_atom</span><span class="p">[</span><span class="n">seg</span><span class="p">]</span> <span class="o">-</span> <span class="n">first_p1_atom</span><span class="p">[</span><span class="n">seg</span><span class="p">]</span>
+
+ <span class="k">try</span><span class="p">:</span>
+ <span class="n">bi</span> <span class="o">=</span> <span class="n">u_p2_to_new</span><span class="p">[</span><span class="n">b</span><span class="p">]</span><span class="o">.</span><span class="n">idx</span>
+ <span class="k">assert</span> <span class="n">u_p2_to_new</span><span class="p">[</span><span class="n">b</span><span class="p">]</span><span class="o">.</span><span class="n">name</span> <span class="o">==</span> <span class="n">n2</span>
+ <span class="k">except</span> <span class="ne">KeyError</span><span class="p">:</span>
+ <span class="n">seg</span> <span class="o">=</span> <span class="n">R1b</span><span class="o">.</span><span class="n">segid</span>
+ <span class="n">b1</span> <span class="o">=</span> <span class="nb">next</span><span class="p">(</span><span class="n">x</span> <span class="k">for</span> <span class="n">x</span> <span class="ow">in</span> <span class="n">R1b</span><span class="o">.</span><span class="n">atoms</span> <span class="k">if</span> <span class="n">x</span><span class="o">.</span><span class="n">name</span> <span class="o">==</span> <span class="n">n2</span><span class="p">)</span>
+ <span class="n">bi</span> <span class="o">=</span> <span class="n">b1</span><span class="o">.</span><span class="n">idx</span> <span class="o">+</span> <span class="n">first_new_atom</span><span class="p">[</span><span class="n">seg</span><span class="p">]</span> <span class="o">-</span> <span class="n">first_p1_atom</span><span class="p">[</span><span class="n">seg</span><span class="p">]</span>
+
+ <span class="n">bp_pairs</span><span class="o">.</span><span class="n">append</span><span class="p">((</span><span class="n">ai</span><span class="p">,</span> <span class="n">bi</span><span class="p">))</span>
+ <span class="k">except</span> <span class="ne">KeyError</span><span class="p">:</span>
+ <span class="n">logger</span><span class="o">.</span><span class="n">warning</span><span class="p">(</span><span class="sa">f</span><span class="s2">"Residue </span><span class="si">{</span><span class="n">R2a</span><span class="o">.</span><span class="n">name</span><span class="si">}</span><span class="s2"> not found in base pair definitions"</span><span class="p">)</span>
+ <span class="k">continue</span>
+
+ <span class="k">return</span> <span class="n">new</span><span class="p">,</span> <span class="n">pairs</span><span class="p">,</span> <span class="n">bp_pairs</span></div>
+</div>
+
+</pre></div>
+
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new file mode 100644
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+
+ <h1>Source code for arbdmodel.sali_polymer_model</h1><div class="highlight"><pre>
+<span></span><span class="c1"># -*- coding: utf-8 -*-</span>
+<span class="c1">## Test with `python -m arbdmodel.hps_polymer_model`</span>
+
+<span class="kn">import</span><span class="w"> </span><span class="nn">numpy</span><span class="w"> </span><span class="k">as</span><span class="w"> </span><span class="nn">np</span>
+<span class="kn">import</span><span class="w"> </span><span class="nn">sys</span>
+
+
+<span class="c1">## Local imports</span>
+<span class="kn">from</span><span class="w"> </span><span class="nn">.</span><span class="w"> </span><span class="kn">import</span> <span class="n">ParticleType</span><span class="p">,</span> <span class="n">PointParticle</span><span class="p">,</span> <span class="n">Group</span>
+<span class="kn">from</span><span class="w"> </span><span class="nn">.logger</span><span class="w"> </span><span class="kn">import</span> <span class="n">logger</span><span class="p">,</span> <span class="n">get_resource_path</span>
+<span class="kn">from</span><span class="w"> </span><span class="nn">.model</span><span class="w"> </span><span class="kn">import</span> <span class="n">ArbdModel</span>
+<span class="kn">from</span><span class="w"> </span><span class="nn">.polymer</span><span class="w"> </span><span class="kn">import</span> <span class="n">PolymerSection</span><span class="p">,</span> <span class="n">PolymerGroup</span>
+<span class="kn">from</span><span class="w"> </span><span class="nn">.interactions</span><span class="w"> </span><span class="kn">import</span> <span class="n">AbstractPotential</span><span class="p">,</span> <span class="n">HarmonicBond</span><span class="p">,</span> <span class="n">HarmonicBondedPotential</span>
+<span class="kn">from</span><span class="w"> </span><span class="nn">.coords</span><span class="w"> </span><span class="kn">import</span> <span class="n">quaternion_to_matrix</span>
+
+
+<span class="sd">"""Define particle types"""</span>
+<span class="n">type_</span> <span class="o">=</span> <span class="n">ParticleType</span><span class="p">(</span><span class="s2">"AA"</span><span class="p">,</span>
+ <span class="c1"># units "297.15 k K / (6 pi 0.92 mPa s 6 AA)" "AA**2/ns"</span>
+ <span class="n">diffusivity</span> <span class="o">=</span> <span class="mf">39.429314</span>
+<span class="p">)</span>
+
+<span class="c1">## Bonded potentials</span>
+<div class="viewcode-block" id="LinearBond">
+<a class="viewcode-back" href="../../api/polymer_modeling/sali_polymer_model.html#arbdmodel.sali_polymer_model.LinearBond">[docs]</a>
+<span class="k">class</span><span class="w"> </span><span class="nc">LinearBond</span><span class="p">(</span><span class="n">HarmonicBond</span><span class="p">):</span>
+ <span class="k">def</span><span class="w"> </span><span class="fm">__init__</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">k</span><span class="p">,</span> <span class="n">r0</span><span class="p">,</span> <span class="n">rRange</span><span class="o">=</span><span class="p">(</span><span class="mi">0</span><span class="p">,</span><span class="mi">50</span><span class="p">),</span> <span class="n">resolution</span><span class="o">=</span><span class="mf">0.1</span><span class="p">,</span> <span class="n">maxForce</span><span class="o">=</span><span class="kc">None</span><span class="p">,</span> <span class="n">max_potential</span><span class="o">=</span><span class="kc">None</span><span class="p">,</span> <span class="n">prefix</span><span class="o">=</span><span class="s2">"potentials/"</span><span class="p">):</span>
+ <span class="n">HarmonicBondedPotential</span><span class="o">.</span><span class="fm">__init__</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">k</span><span class="p">,</span> <span class="n">r0</span><span class="p">,</span> <span class="n">rRange</span><span class="p">,</span> <span class="n">resolution</span><span class="p">,</span> <span class="n">maxForce</span><span class="p">,</span> <span class="n">max_potential</span><span class="p">,</span> <span class="n">prefix</span><span class="p">)</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">type_</span> <span class="o">=</span> <span class="s2">"linearbond"</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">kscale_</span> <span class="o">=</span> <span class="mf">1.0</span>
+
+<div class="viewcode-block" id="LinearBond.potential">
+<a class="viewcode-back" href="../../api/polymer_modeling/sali_polymer_model.html#arbdmodel.sali_polymer_model.LinearBond.potential">[docs]</a>
+ <span class="k">def</span><span class="w"> </span><span class="nf">potential</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">dr</span><span class="p">):</span>
+ <span class="k">return</span> <span class="bp">self</span><span class="o">.</span><span class="n">k</span><span class="o">*</span><span class="n">np</span><span class="o">.</span><span class="n">abs</span><span class="p">(</span><span class="n">dr</span><span class="p">)</span></div>
+</div>
+
+
+<div class="viewcode-block" id="SaliNonbonded">
+<a class="viewcode-back" href="../../api/polymer_modeling/sali_polymer_model.html#arbdmodel.sali_polymer_model.SaliNonbonded">[docs]</a>
+<span class="k">class</span><span class="w"> </span><span class="nc">SaliNonbonded</span><span class="p">(</span><span class="n">AbstractPotential</span><span class="p">):</span>
+ <span class="k">def</span><span class="w"> </span><span class="fm">__init__</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">resolution</span><span class="o">=</span><span class="mf">0.1</span><span class="p">):</span>
+ <span class="n">AbstractPotential</span><span class="o">.</span><span class="fm">__init__</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">resolution</span><span class="o">=</span><span class="n">resolution</span><span class="p">)</span>
+
+<div class="viewcode-block" id="SaliNonbonded.potential">
+<a class="viewcode-back" href="../../api/polymer_modeling/sali_polymer_model.html#arbdmodel.sali_polymer_model.SaliNonbonded.potential">[docs]</a>
+ <span class="k">def</span><span class="w"> </span><span class="nf">potential</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">r</span><span class="p">):</span>
+<span class="w"> </span><span class="sd">""" Constant force excluded volume """</span>
+ <span class="n">force</span> <span class="o">=</span> <span class="mi">10</span> <span class="c1"># kcal_mol/AA</span>
+ <span class="n">radius</span> <span class="o">=</span> <span class="mi">6</span>
+
+ <span class="n">u</span> <span class="o">=</span> <span class="n">np</span><span class="o">.</span><span class="n">zeros</span><span class="p">(</span><span class="n">r</span><span class="o">.</span><span class="n">shape</span><span class="p">)</span>
+ <span class="n">s</span> <span class="o">=</span> <span class="n">r</span> <span class="o"><</span> <span class="mi">2</span><span class="o">*</span><span class="n">radius</span>
+ <span class="n">u</span><span class="p">[</span><span class="n">s</span><span class="p">]</span> <span class="o">=</span> <span class="p">(</span><span class="mi">2</span><span class="o">*</span><span class="n">radius</span> <span class="o">-</span> <span class="n">r</span><span class="p">[</span><span class="n">s</span><span class="p">])</span> <span class="o">*</span> <span class="n">force</span>
+ <span class="k">return</span> <span class="n">u</span></div>
+</div>
+
+
+<div class="viewcode-block" id="SaliBeadsFromPolymer">
+<a class="viewcode-back" href="../../api/polymer_modeling/sali_polymer_model.html#arbdmodel.sali_polymer_model.SaliBeadsFromPolymer">[docs]</a>
+<span class="k">class</span><span class="w"> </span><span class="nc">SaliBeadsFromPolymer</span><span class="p">(</span><span class="n">Group</span><span class="p">):</span>
+ <span class="c1"># p = PointParticle(_P, (0,0,0), "P")</span>
+ <span class="c1"># b = PointParticle(_B, (3,0,1), "B")</span>
+ <span class="c1"># nt = Group( name = "nt", children = [p,b])</span>
+ <span class="c1"># nt.add_bond( i=p, j=b, bond = get_resource_path('two_bead_model/BPB.dat') )</span>
+
+ <span class="k">def</span><span class="w"> </span><span class="fm">__init__</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">polymer</span><span class="p">,</span> <span class="n">sequence</span><span class="o">=</span><span class="kc">None</span><span class="p">,</span> <span class="o">**</span><span class="n">kwargs</span><span class="p">):</span>
+
+ <span class="k">if</span> <span class="n">sequence</span> <span class="ow">is</span> <span class="kc">None</span><span class="p">:</span>
+ <span class="k">raise</span> <span class="ne">NotImplementedError</span>
+ <span class="c1"># ... set random sequence</span>
+
+ <span class="bp">self</span><span class="o">.</span><span class="n">polymer</span> <span class="o">=</span> <span class="n">polymer</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">sequence</span> <span class="o">=</span> <span class="n">sequence</span>
+
+ <span class="k">for</span> <span class="n">prop</span> <span class="ow">in</span> <span class="p">(</span><span class="s1">'segname'</span><span class="p">,</span><span class="s1">'chain'</span><span class="p">):</span>
+ <span class="k">if</span> <span class="n">prop</span> <span class="ow">not</span> <span class="ow">in</span> <span class="n">kwargs</span><span class="p">:</span>
+ <span class="c1"># import pdb</span>
+ <span class="c1"># pdb.set_trace()</span>
+ <span class="k">try</span><span class="p">:</span>
+ <span class="bp">self</span><span class="o">.</span><span class="vm">__dict__</span><span class="p">[</span><span class="n">prop</span><span class="p">]</span> <span class="o">=</span> <span class="n">polymer</span><span class="o">.</span><span class="vm">__dict__</span><span class="p">[</span><span class="n">prop</span><span class="p">]</span>
+ <span class="k">except</span><span class="p">:</span>
+ <span class="k">pass</span>
+
+ <span class="k">if</span> <span class="nb">len</span><span class="p">(</span><span class="n">sequence</span><span class="p">)</span> <span class="o">!=</span> <span class="n">polymer</span><span class="o">.</span><span class="n">num_monomers</span><span class="p">:</span>
+ <span class="k">raise</span> <span class="ne">ValueError</span><span class="p">(</span><span class="s2">"Length of sequence does not match length of polymer"</span><span class="p">)</span>
+ <span class="n">Group</span><span class="o">.</span><span class="fm">__init__</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="o">**</span><span class="n">kwargs</span><span class="p">)</span>
+
+ <span class="bp">self</span><span class="o">.</span><span class="n">num_beads</span> <span class="o">=</span> <span class="nb">int</span><span class="p">(</span><span class="n">np</span><span class="o">.</span><span class="n">ceil</span><span class="p">(</span><span class="n">polymer</span><span class="o">.</span><span class="n">num_monomers</span> <span class="o">/</span> <span class="mi">20</span><span class="p">))</span>
+
+ <span class="k">def</span><span class="w"> </span><span class="nf">_clear_beads</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span>
+ <span class="o">...</span>
+
+ <span class="k">def</span><span class="w"> </span><span class="nf">_generate_beads</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span>
+ <span class="c1"># beads = self.children</span>
+ <span class="n">nb</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">num_beads</span>
+
+ <span class="k">for</span> <span class="n">i</span> <span class="ow">in</span> <span class="nb">range</span><span class="p">(</span><span class="n">nb</span><span class="p">):</span>
+ <span class="c1"># c = self.polymer.monomer_index_to_contour(i)</span>
+ <span class="n">c</span> <span class="o">=</span> <span class="nb">float</span><span class="p">(</span><span class="n">i</span><span class="p">)</span><span class="o">/</span><span class="p">(</span><span class="n">nb</span><span class="o">-</span><span class="mi">1</span><span class="p">)</span> <span class="k">if</span> <span class="n">nb</span> <span class="o">></span> <span class="mi">1</span> <span class="k">else</span> <span class="mf">0.5</span>
+ <span class="n">r</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">polymer</span><span class="o">.</span><span class="n">contour_to_position</span><span class="p">(</span><span class="n">c</span><span class="p">)</span>
+
+ <span class="n">bead</span> <span class="o">=</span> <span class="n">PointParticle</span><span class="p">(</span><span class="n">type_</span><span class="p">,</span> <span class="n">r</span><span class="p">,</span>
+ <span class="n">resid</span> <span class="o">=</span> <span class="n">i</span><span class="o">+</span><span class="mi">1</span><span class="p">)</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">add</span><span class="p">(</span><span class="n">bead</span><span class="p">)</span>
+
+ <span class="c1">## Two consecutive nts </span>
+ <span class="k">for</span> <span class="n">i</span> <span class="ow">in</span> <span class="nb">range</span><span class="p">(</span><span class="nb">len</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">children</span><span class="p">)</span><span class="o">-</span><span class="mi">1</span><span class="p">):</span>
+ <span class="n">b1</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">children</span><span class="p">[</span><span class="n">i</span><span class="p">]</span>
+ <span class="n">b2</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">children</span><span class="p">[</span><span class="n">i</span><span class="o">+</span><span class="mi">1</span><span class="p">]</span>
+<span class="w"> </span><span class="sd">""" units "10 kJ/N_A" kcal_mol """</span>
+ <span class="n">bond</span> <span class="o">=</span> <span class="n">LinearBond</span><span class="p">(</span><span class="n">k</span> <span class="o">=</span> <span class="mi">1</span><span class="p">,</span>
+ <span class="n">r0</span> <span class="o">=</span> <span class="mi">18</span><span class="p">,</span>
+ <span class="n">rRange</span> <span class="o">=</span> <span class="p">(</span><span class="mi">0</span><span class="p">,</span><span class="mi">500</span><span class="p">),</span>
+ <span class="n">resolution</span> <span class="o">=</span> <span class="mf">0.01</span><span class="p">,</span>
+ <span class="n">maxForce</span> <span class="o">=</span> <span class="mi">30</span><span class="p">)</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">add_bond</span><span class="p">(</span> <span class="n">i</span><span class="o">=</span><span class="n">b1</span><span class="p">,</span> <span class="n">j</span><span class="o">=</span><span class="n">b2</span><span class="p">,</span> <span class="n">bond</span> <span class="o">=</span> <span class="n">bond</span><span class="p">,</span> <span class="n">exclude</span><span class="o">=</span><span class="kc">True</span> <span class="p">)</span></div>
+
+
+<div class="viewcode-block" id="SaliModel">
+<a class="viewcode-back" href="../../api/polymer_modeling/sali_polymer_model.html#arbdmodel.sali_polymer_model.SaliModel">[docs]</a>
+<span class="k">class</span><span class="w"> </span><span class="nc">SaliModel</span><span class="p">(</span><span class="n">ArbdModel</span><span class="p">):</span>
+ <span class="k">def</span><span class="w"> </span><span class="fm">__init__</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">polymers</span><span class="p">,</span>
+ <span class="n">sequences</span> <span class="o">=</span> <span class="kc">None</span><span class="p">,</span>
+ <span class="n">debye_length</span> <span class="o">=</span> <span class="mi">10</span><span class="p">,</span>
+ <span class="n">damping_coefficient</span> <span class="o">=</span> <span class="mi">10</span><span class="p">,</span>
+ <span class="n">DEBUG</span><span class="o">=</span><span class="kc">False</span><span class="p">,</span>
+ <span class="o">**</span><span class="n">kwargs</span><span class="p">):</span>
+
+<span class="w"> </span><span class="sd">""" </span>
+<span class="sd"> [debye_length]: angstroms</span>
+<span class="sd"> [damping_coefficient]: ns</span>
+<span class="sd"> """</span>
+
+ <span class="nb">print</span><span class="p">(</span><span class="s2">"WARNING: diffusion coefficient arbitrarily set to 100 AA**2/ns in SaliModel"</span><span class="p">)</span>
+
+ <span class="n">kwargs</span><span class="p">[</span><span class="s1">'timestep'</span><span class="p">]</span> <span class="o">=</span> <span class="mf">1047e-6</span>
+ <span class="n">kwargs</span><span class="p">[</span><span class="s1">'cutoff'</span><span class="p">]</span> <span class="o">=</span> <span class="mi">18</span>
+
+ <span class="k">if</span> <span class="s1">'decompPeriod'</span> <span class="ow">not</span> <span class="ow">in</span> <span class="n">kwargs</span><span class="p">:</span>
+ <span class="n">kwargs</span><span class="p">[</span><span class="s1">'decompPeriod'</span><span class="p">]</span> <span class="o">=</span> <span class="mi">1000</span>
+
+<span class="w"> </span><span class="sd">""" Assign sequences """</span>
+ <span class="k">if</span> <span class="n">sequences</span> <span class="ow">is</span> <span class="kc">None</span><span class="p">:</span>
+ <span class="k">raise</span> <span class="ne">NotImplementedError</span><span class="p">(</span><span class="s2">"HpsModel must be provided a sequences argument"</span><span class="p">)</span>
+
+ <span class="bp">self</span><span class="o">.</span><span class="n">polymer_group</span> <span class="o">=</span> <span class="n">PolymerGroup</span><span class="p">(</span><span class="n">polymers</span><span class="p">)</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">sequences</span> <span class="o">=</span> <span class="n">sequences</span>
+ <span class="n">ArbdModel</span><span class="o">.</span><span class="fm">__init__</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="p">[],</span> <span class="o">**</span><span class="n">kwargs</span><span class="p">)</span>
+
+ <span class="c1"># """ Update type diffusion coefficients """</span>
+ <span class="c1"># self.set_damping_coefficient( damping_coefficient )</span>
+
+<span class="w"> </span><span class="sd">""" Set up nonbonded interactions """</span>
+ <span class="n">nonbonded</span> <span class="o">=</span> <span class="n">SaliNonbonded</span><span class="p">()</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">useNonbondedScheme</span><span class="p">(</span> <span class="n">nonbonded</span><span class="p">,</span> <span class="n">typeA</span><span class="o">=</span><span class="n">type_</span><span class="p">,</span> <span class="n">typeB</span><span class="o">=</span><span class="n">type_</span> <span class="p">)</span>
+<span class="w"> </span>
+<span class="w"> </span><span class="sd">""" Generate beads """</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">generate_beads</span><span class="p">()</span>
+
+<div class="viewcode-block" id="SaliModel.update_splines">
+<a class="viewcode-back" href="../../api/polymer_modeling/sali_polymer_model.html#arbdmodel.sali_polymer_model.SaliModel.update_splines">[docs]</a>
+ <span class="k">def</span><span class="w"> </span><span class="nf">update_splines</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">coords</span><span class="p">):</span>
+ <span class="n">i</span> <span class="o">=</span> <span class="mi">0</span>
+ <span class="k">for</span> <span class="n">p</span><span class="p">,</span><span class="n">c</span> <span class="ow">in</span> <span class="nb">zip</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">polymer_group</span><span class="o">.</span><span class="n">polymers</span><span class="p">,</span><span class="bp">self</span><span class="o">.</span><span class="n">children</span><span class="p">):</span>
+ <span class="n">n</span> <span class="o">=</span> <span class="nb">len</span><span class="p">(</span><span class="n">c</span><span class="o">.</span><span class="n">children</span><span class="p">)</span>
+ <span class="n">p</span><span class="o">.</span><span class="n">set_splines</span><span class="p">(</span><span class="n">np</span><span class="o">.</span><span class="n">linspace</span><span class="p">(</span><span class="mi">0</span><span class="p">,</span><span class="mi">1</span><span class="p">,</span><span class="n">n</span><span class="p">),</span> <span class="n">coords</span><span class="p">[</span><span class="n">i</span><span class="p">:</span><span class="n">i</span><span class="o">+</span><span class="n">n</span><span class="p">])</span>
+ <span class="n">i</span> <span class="o">+=</span> <span class="n">n</span>
+
+ <span class="bp">self</span><span class="o">.</span><span class="n">clear_all</span><span class="p">()</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">generate_beads</span><span class="p">()</span></div>
+
+ <span class="c1">## TODO Apply restraints, etc</span>
+
+<div class="viewcode-block" id="SaliModel.generate_beads">
+<a class="viewcode-back" href="../../api/polymer_modeling/sali_polymer_model.html#arbdmodel.sali_polymer_model.SaliModel.generate_beads">[docs]</a>
+ <span class="k">def</span><span class="w"> </span><span class="nf">generate_beads</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">peptides</span> <span class="o">=</span> <span class="p">[</span><span class="n">SaliBeadsFromPolymer</span><span class="p">(</span><span class="n">p</span><span class="p">,</span><span class="n">s</span><span class="p">)</span>
+ <span class="k">for</span> <span class="n">p</span><span class="p">,</span><span class="n">s</span> <span class="ow">in</span> <span class="nb">zip</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">polymer_group</span><span class="o">.</span><span class="n">polymers</span><span class="p">,</span><span class="bp">self</span><span class="o">.</span><span class="n">sequences</span><span class="p">)]</span>
+
+ <span class="k">for</span> <span class="n">s</span> <span class="ow">in</span> <span class="bp">self</span><span class="o">.</span><span class="n">peptides</span><span class="p">:</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">add</span><span class="p">(</span><span class="n">s</span><span class="p">)</span>
+ <span class="n">s</span><span class="o">.</span><span class="n">_generate_beads</span><span class="p">()</span></div>
+</div>
+
+
+ <span class="c1"># def set_damping_coefficient(self, damping_coefficient):</span>
+ <span class="c1"># for t in self.types:</span>
+ <span class="c1"># t.damping_coefficient = damping_coefficient</span>
+ <span class="c1"># # t.diffusivity = 831447.2 * temperature / (t.mass * damping_coefficient)</span>
+
+<span class="k">if</span> <span class="vm">__name__</span> <span class="o">==</span> <span class="s2">"__main__"</span><span class="p">:</span>
+ <span class="k">pass</span>
+</pre></div>
+
+ </article>
+
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+
+ <h1>Source code for arbdmodel.sim_config</h1><div class="highlight"><pre>
+<span></span><span class="c1"># -*- coding: utf-8 -*-</span>
+<span class="sd">"""</span>
+<span class="sd">Simulation configuration module. Provides SimConf and DefaultSimConf </span>
+<span class="sd">classes for configuring simulation parameters.</span>
+<span class="sd">"""</span>
+
+<span class="kn">import</span><span class="w"> </span><span class="nn">os</span>
+<span class="kn">import</span><span class="w"> </span><span class="nn">numpy</span><span class="w"> </span><span class="k">as</span><span class="w"> </span><span class="nn">np</span>
+<span class="kn">from</span><span class="w"> </span><span class="nn">copy</span><span class="w"> </span><span class="kn">import</span> <span class="n">copy</span><span class="p">,</span> <span class="n">deepcopy</span>
+<span class="kn">from</span><span class="w"> </span><span class="nn">.logger</span><span class="w"> </span><span class="kn">import</span> <span class="n">logger</span><span class="p">,</span> <span class="n">devlogger</span>
+<span class="kn">from</span><span class="w"> </span><span class="nn">.binary_manager</span><span class="w"> </span><span class="kn">import</span> <span class="n">BinaryManager</span>
+
+<span class="k">def</span><span class="w"> </span><span class="nf">_get_properties_and_dict_keys</span><span class="p">(</span><span class="n">obj</span><span class="p">):</span>
+ <span class="kn">import</span><span class="w"> </span><span class="nn">inspect</span>
+ <span class="bp">cls</span> <span class="o">=</span> <span class="n">obj</span><span class="o">.</span><span class="vm">__class__</span>
+
+ <span class="k">def</span><span class="w"> </span><span class="nf">filter_props</span><span class="p">(</span><span class="n">name_type</span><span class="p">):</span>
+ <span class="n">nt</span> <span class="o">=</span> <span class="n">name_type</span>
+ <span class="k">return</span> <span class="ow">not</span> <span class="n">nt</span><span class="p">[</span><span class="mi">0</span><span class="p">]</span><span class="o">.</span><span class="n">startswith</span><span class="p">(</span><span class="s1">'_'</span><span class="p">)</span> <span class="ow">and</span> <span class="nb">isinstance</span><span class="p">(</span><span class="n">nt</span><span class="p">[</span><span class="mi">1</span><span class="p">],</span> <span class="nb">property</span><span class="p">)</span>
+ <span class="n">properties</span> <span class="o">=</span> <span class="p">[</span><span class="n">name</span> <span class="k">for</span> <span class="n">name</span><span class="p">,</span> <span class="n">type_</span> <span class="ow">in</span> <span class="nb">filter</span><span class="p">(</span><span class="n">filter_props</span><span class="p">,</span> <span class="n">inspect</span><span class="o">.</span><span class="n">getmembers</span><span class="p">(</span><span class="n">obj</span><span class="o">.</span><span class="vm">__class__</span><span class="p">))]</span>
+ <span class="k">return</span> <span class="n">properties</span> <span class="o">+</span> <span class="nb">list</span><span class="p">(</span><span class="n">obj</span><span class="o">.</span><span class="vm">__dict__</span><span class="o">.</span><span class="n">keys</span><span class="p">())</span>
+
+<div class="viewcode-block" id="SimConf">
+<a class="viewcode-back" href="../../api/core/sim_config.html#arbdmodel.sim_config.SimConf">[docs]</a>
+<span class="k">class</span><span class="w"> </span><span class="nc">SimConf</span><span class="p">:</span>
+<span class="w"> </span><span class="sd">""" Class describing properties for a (ARBD or NAMD) simulation """</span>
+
+ <span class="k">def</span><span class="w"> </span><span class="fm">__init__</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">num_steps</span><span class="o">=</span><span class="kc">None</span><span class="p">,</span> <span class="n">output_period</span><span class="o">=</span><span class="kc">None</span><span class="p">,</span>
+ <span class="n">integrator</span><span class="o">=</span><span class="kc">None</span><span class="p">,</span> <span class="n">timestep</span><span class="o">=</span><span class="kc">None</span><span class="p">,</span> <span class="n">thermostat</span><span class="o">=</span><span class="kc">None</span><span class="p">,</span> <span class="n">barostat</span><span class="o">=</span><span class="kc">None</span><span class="p">,</span>
+ <span class="n">temperature</span><span class="o">=</span><span class="kc">None</span><span class="p">,</span> <span class="n">pressure</span><span class="o">=</span><span class="kc">None</span><span class="p">,</span>
+ <span class="n">cutoff</span><span class="o">=</span><span class="kc">None</span><span class="p">,</span> <span class="n">pairlist_distance</span><span class="o">=</span><span class="kc">None</span><span class="p">,</span> <span class="n">decomp_period</span><span class="o">=</span><span class="kc">None</span><span class="p">,</span> <span class="n">gpu</span><span class="o">=</span><span class="kc">None</span><span class="p">,</span>
+ <span class="n">seed</span><span class="o">=</span><span class="kc">None</span><span class="p">,</span> <span class="n">restart_file</span><span class="o">=</span><span class="kc">None</span><span class="p">,</span>
+ <span class="c1">## ARBD-specific</span>
+ <span class="n">rigid_body_integrator</span><span class="o">=</span><span class="kc">None</span><span class="p">,</span>
+ <span class="n">rigid_body_grid_grid_period</span><span class="o">=</span><span class="kc">None</span><span class="p">,</span>
+ <span class="c1">## SimpleARBD parameters</span>
+ <span class="n">viscosity</span><span class="o">=</span><span class="kc">None</span><span class="p">,</span> <span class="n">solvent_density</span><span class="o">=</span><span class="kc">None</span><span class="p">,</span> <span class="n">num_heavy_cluster</span><span class="o">=</span><span class="kc">None</span><span class="p">,</span>
+ <span class="c1">## Binary paths</span>
+ <span class="n">arbd_path</span><span class="o">=</span><span class="kc">None</span><span class="p">,</span> <span class="n">namd_path</span><span class="o">=</span><span class="kc">None</span><span class="p">,</span> <span class="n">vmd_path</span><span class="o">=</span><span class="kc">None</span><span class="p">,</span>
+ <span class="n">hydropro_path</span><span class="o">=</span><span class="kc">None</span><span class="p">,</span> <span class="n">apbs_path</span><span class="o">=</span><span class="kc">None</span><span class="p">,</span> <span class="n">gmsh_path</span><span class="o">=</span><span class="kc">None</span><span class="p">,</span> <span class="o">**</span><span class="n">kwargs</span><span class="p">):</span>
+
+
+ <span class="bp">self</span><span class="o">.</span><span class="n">num_steps</span> <span class="o">=</span> <span class="n">num_steps</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">output_period</span> <span class="o">=</span> <span class="n">output_period</span>
+
+ <span class="bp">self</span><span class="o">.</span><span class="n">integrator</span> <span class="o">=</span> <span class="n">integrator</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">timestep</span> <span class="o">=</span> <span class="n">timestep</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">thermostat</span> <span class="o">=</span> <span class="n">thermostat</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">barostat</span> <span class="o">=</span> <span class="n">barostat</span>
+
+ <span class="bp">self</span><span class="o">.</span><span class="n">temperature</span> <span class="o">=</span> <span class="n">temperature</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">pressure</span> <span class="o">=</span> <span class="n">pressure</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">cutoff</span> <span class="o">=</span> <span class="n">cutoff</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">pairlist_distance</span> <span class="o">=</span> <span class="n">pairlist_distance</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">decomp_period</span> <span class="o">=</span> <span class="n">decomp_period</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">seed</span> <span class="o">=</span> <span class="n">seed</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">restart_file</span> <span class="o">=</span> <span class="n">restart_file</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">gpu</span> <span class="o">=</span> <span class="n">gpu</span>
+
+ <span class="bp">self</span><span class="o">.</span><span class="n">rigid_body_integrator</span> <span class="o">=</span> <span class="n">rigid_body_integrator</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">rigid_body_grid_grid_period</span> <span class="o">=</span> <span class="n">rigid_body_grid_grid_period</span>
+
+ <span class="bp">self</span><span class="o">.</span><span class="n">viscosity</span> <span class="o">=</span> <span class="n">viscosity</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">solvent_density</span> <span class="o">=</span> <span class="n">solvent_density</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">num_heavy_cluster</span> <span class="o">=</span> <span class="n">num_heavy_cluster</span>
+
+ <span class="c1"># Set binary paths</span>
+ <span class="k">if</span> <span class="n">arbd_path</span><span class="p">:</span> <span class="n">BinaryManager</span><span class="o">.</span><span class="n">set_binary_path</span><span class="p">(</span><span class="s1">'arbd'</span><span class="p">,</span> <span class="n">arbd_path</span><span class="p">)</span>
+ <span class="k">if</span> <span class="n">namd_path</span><span class="p">:</span> <span class="n">BinaryManager</span><span class="o">.</span><span class="n">set_binary_path</span><span class="p">(</span><span class="s1">'namd'</span><span class="p">,</span> <span class="n">namd_path</span><span class="p">)</span>
+ <span class="k">if</span> <span class="n">vmd_path</span><span class="p">:</span> <span class="n">BinaryManager</span><span class="o">.</span><span class="n">set_binary_path</span><span class="p">(</span><span class="s1">'vmd'</span><span class="p">,</span> <span class="n">vmd_path</span><span class="p">)</span>
+ <span class="k">if</span> <span class="n">hydropro_path</span><span class="p">:</span> <span class="n">BinaryManager</span><span class="o">.</span><span class="n">set_binary_path</span><span class="p">(</span><span class="s1">'hydropro'</span><span class="p">,</span> <span class="n">hydropro_path</span><span class="p">)</span>
+ <span class="k">if</span> <span class="n">apbs_path</span><span class="p">:</span> <span class="n">BinaryManager</span><span class="o">.</span><span class="n">set_binary_path</span><span class="p">(</span><span class="s1">'apbs'</span><span class="p">,</span> <span class="n">apbs_path</span><span class="p">)</span>
+ <span class="k">if</span> <span class="n">gmsh_path</span><span class="p">:</span> <span class="n">BinaryManager</span><span class="o">.</span><span class="n">set_binary_path</span><span class="p">(</span><span class="s1">'gmsh'</span><span class="p">,</span> <span class="n">gmsh_path</span><span class="p">)</span>
+
+<div class="viewcode-block" id="SimConf.get_binary">
+<a class="viewcode-back" href="../../api/core/sim_config.html#arbdmodel.sim_config.SimConf.get_binary">[docs]</a>
+ <span class="k">def</span><span class="w"> </span><span class="nf">get_binary</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">name</span><span class="p">):</span>
+<span class="w"> </span><span class="sd">"""</span>
+<span class="sd"> Get the path to a specific binary with improved error handling.</span>
+<span class="sd"> </span>
+<span class="sd"> Args:</span>
+<span class="sd"> name: The name of the binary (e.g., 'arbd', 'hydropro')</span>
+<span class="sd"> </span>
+<span class="sd"> Returns:</span>
+<span class="sd"> Path to the binary if found, None otherwise</span>
+<span class="sd"> </span>
+<span class="sd"> This method does not raise exceptions when binaries are not found, allowing</span>
+<span class="sd"> for graceful handling of missing optional dependencies.</span>
+<span class="sd"> """</span>
+ <span class="n">binary_path</span> <span class="o">=</span> <span class="n">BinaryManager</span><span class="o">.</span><span class="n">get_binary_path</span><span class="p">(</span><span class="n">name</span><span class="p">)</span>
+
+ <span class="c1"># Check if we found a binary and convert to string if needed</span>
+ <span class="k">if</span> <span class="n">binary_path</span> <span class="ow">is</span> <span class="ow">not</span> <span class="kc">None</span><span class="p">:</span>
+ <span class="k">return</span> <span class="nb">str</span><span class="p">(</span><span class="n">binary_path</span><span class="p">)</span>
+
+ <span class="c1"># Determine if this is an essential binary</span>
+ <span class="k">if</span> <span class="n">BinaryManager</span><span class="o">.</span><span class="n">is_binary_essential</span><span class="p">(</span><span class="n">name</span><span class="p">):</span>
+ <span class="n">logger</span><span class="o">.</span><span class="n">warning</span><span class="p">(</span><span class="sa">f</span><span class="s2">"Essential binary '</span><span class="si">{</span><span class="n">name</span><span class="si">}</span><span class="s2">' not found. Core functionality may be limited."</span><span class="p">)</span>
+
+ <span class="k">return</span> <span class="kc">None</span></div>
+
+
+<div class="viewcode-block" id="SimConf.set_binary">
+<a class="viewcode-back" href="../../api/core/sim_config.html#arbdmodel.sim_config.SimConf.set_binary">[docs]</a>
+ <span class="k">def</span><span class="w"> </span><span class="nf">set_binary</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">name</span><span class="p">,</span> <span class="n">path</span><span class="p">):</span>
+<span class="w"> </span><span class="sd">"""Set the path to a specific binary."""</span>
+ <span class="n">BinaryManager</span><span class="o">.</span><span class="n">set_binary_path</span><span class="p">(</span><span class="n">name</span><span class="p">,</span> <span class="n">path</span><span class="p">)</span>
+ <span class="k">return</span> <span class="n">path</span></div>
+
+
+ <span class="nd">@property</span>
+ <span class="k">def</span><span class="w"> </span><span class="nf">temperature</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span>
+ <span class="k">return</span> <span class="bp">self</span><span class="o">.</span><span class="n">__temperature</span>
+
+ <span class="nd">@temperature</span><span class="o">.</span><span class="n">setter</span>
+ <span class="k">def</span><span class="w"> </span><span class="nf">temperature</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">value</span><span class="p">):</span>
+ <span class="k">if</span> <span class="n">value</span> <span class="ow">is</span> <span class="ow">not</span> <span class="kc">None</span> <span class="ow">and</span> <span class="n">value</span> <span class="o"><=</span> <span class="mi">0</span><span class="p">:</span>
+ <span class="k">raise</span> <span class="ne">ValueError</span><span class="p">(</span><span class="s2">"Temperature must be positive"</span><span class="p">)</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">__temperature</span> <span class="o">=</span> <span class="n">value</span>
+
+<div class="viewcode-block" id="SimConf.combine">
+<a class="viewcode-back" href="../../api/core/sim_config.html#arbdmodel.sim_config.SimConf.combine">[docs]</a>
+ <span class="k">def</span><span class="w"> </span><span class="nf">combine</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">other</span><span class="p">,</span> <span class="n">policy</span><span class="o">=</span><span class="s1">'override'</span><span class="p">,</span> <span class="n">warn</span><span class="o">=</span><span class="kc">False</span><span class="p">):</span>
+<span class="w"> </span><span class="sd">""" </span>
+<span class="sd"> Creates a new SimConf object whose properties are</span>
+<span class="sd"> initialized to be from "self", but are overridden with</span>
+<span class="sd"> properties in "other", provided they are not None</span>
+<span class="sd"> """</span>
+ <span class="n">new_conf</span> <span class="o">=</span> <span class="n">copy</span><span class="p">(</span><span class="bp">self</span><span class="p">)</span>
+ <span class="k">for</span> <span class="n">attr</span> <span class="ow">in</span> <span class="n">_get_properties_and_dict_keys</span><span class="p">(</span><span class="n">other</span><span class="p">):</span>
+ <span class="n">oldval</span> <span class="o">=</span> <span class="kc">None</span>
+ <span class="n">val</span> <span class="o">=</span> <span class="n">other</span><span class="o">.</span><span class="fm">__getattribute__</span><span class="p">(</span><span class="n">attr</span><span class="p">)</span>
+ <span class="k">if</span> <span class="n">val</span> <span class="ow">is</span> <span class="ow">not</span> <span class="kc">None</span><span class="p">:</span>
+ <span class="k">try</span><span class="p">:</span>
+ <span class="n">oldval</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="fm">__getattribute__</span><span class="p">(</span><span class="n">attr</span><span class="p">)</span>
+ <span class="k">except</span><span class="p">:</span>
+ <span class="k">pass</span>
+ <span class="k">if</span> <span class="n">oldval</span> <span class="o">!=</span> <span class="n">val</span> <span class="ow">and</span> <span class="p">(</span><span class="n">oldval</span> <span class="ow">is</span> <span class="ow">not</span> <span class="kc">None</span><span class="p">)</span> <span class="ow">and</span> \
+ <span class="p">(</span><span class="n">val</span> <span class="ow">is</span> <span class="ow">not</span> <span class="kc">None</span><span class="p">)</span> <span class="ow">and</span> <span class="n">policy</span> <span class="o">!=</span> <span class="s1">'override'</span><span class="p">:</span>
+ <span class="k">if</span> <span class="n">policy</span> <span class="o">==</span> <span class="s1">'best'</span><span class="p">:</span>
+ <span class="k">if</span> <span class="n">attr</span> <span class="ow">in</span> <span class="p">(</span><span class="s1">'timestep'</span><span class="p">,</span> <span class="s1">'output_period'</span><span class="p">,</span> <span class="s1">'decomp_period'</span><span class="p">):</span>
+ <span class="k">if</span> <span class="n">warn</span><span class="p">:</span> <span class="n">logger</span><span class="o">.</span><span class="n">warning</span><span class="p">(</span><span class="sa">f</span><span class="s1">'Combining attribute </span><span class="si">{</span><span class="n">attr</span><span class="si">}</span><span class="s1">: </span><span class="si">{</span><span class="n">oldval</span><span class="si">}</span><span class="s1"> != </span><span class="si">{</span><span class="n">val</span><span class="si">}</span><span class="s1">, using </span><span class="si">{</span><span class="nb">min</span><span class="p">([</span><span class="n">oldval</span><span class="p">,</span><span class="n">val</span><span class="p">])</span><span class="si">}</span><span class="s1">'</span><span class="p">)</span>
+ <span class="n">new_conf</span><span class="o">.</span><span class="fm">__setattr__</span><span class="p">(</span><span class="n">attr</span><span class="p">,</span> <span class="nb">min</span><span class="p">([</span><span class="n">oldval</span><span class="p">,</span><span class="n">val</span><span class="p">]))</span>
+ <span class="k">elif</span> <span class="n">attr</span> <span class="ow">in</span> <span class="p">(</span><span class="s1">'num_steps'</span><span class="p">,</span> <span class="s1">'cutoff'</span><span class="p">,</span> <span class="s1">'pairlist_distance'</span><span class="p">):</span>
+ <span class="k">if</span> <span class="n">warn</span><span class="p">:</span> <span class="n">logger</span><span class="o">.</span><span class="n">warning</span><span class="p">(</span><span class="sa">f</span><span class="s1">'Combining attribute </span><span class="si">{</span><span class="n">attr</span><span class="si">}</span><span class="s1">: </span><span class="si">{</span><span class="n">oldval</span><span class="si">}</span><span class="s1"> != </span><span class="si">{</span><span class="n">val</span><span class="si">}</span><span class="s1">, using </span><span class="si">{</span><span class="nb">max</span><span class="p">([</span><span class="n">oldval</span><span class="p">,</span><span class="n">val</span><span class="p">])</span><span class="si">}</span><span class="s1">'</span><span class="p">)</span>
+ <span class="n">new_conf</span><span class="o">.</span><span class="fm">__setattr__</span><span class="p">(</span><span class="n">attr</span><span class="p">,</span> <span class="nb">max</span><span class="p">([</span><span class="n">oldval</span><span class="p">,</span><span class="n">val</span><span class="p">]))</span>
+ <span class="k">elif</span> <span class="n">attr</span> <span class="o">==</span> <span class="s1">'integrator'</span><span class="p">:</span>
+ <span class="k">if</span> <span class="s1">'MD'</span> <span class="ow">in</span> <span class="p">(</span><span class="n">oldval</span><span class="p">,</span><span class="n">val</span><span class="p">)</span> <span class="ow">and</span> <span class="s1">'BD'</span> <span class="ow">in</span> <span class="p">(</span><span class="n">oldval</span><span class="p">,</span><span class="n">val</span><span class="p">):</span>
+ <span class="k">if</span> <span class="n">warn</span><span class="p">:</span> <span class="n">logger</span><span class="o">.</span><span class="n">warning</span><span class="p">(</span><span class="sa">f</span><span class="s1">'Combining attribute </span><span class="si">{</span><span class="n">attr</span><span class="si">}</span><span class="s1">: </span><span class="si">{</span><span class="n">oldval</span><span class="si">}</span><span class="s1"> != </span><span class="si">{</span><span class="n">val</span><span class="si">}</span><span class="s1">, using "MD"'</span><span class="p">)</span>
+ <span class="n">new_conf</span><span class="o">.</span><span class="fm">__setattr__</span><span class="p">(</span><span class="n">attr</span><span class="p">,</span><span class="s1">'MD'</span><span class="p">)</span>
+ <span class="k">else</span><span class="p">:</span>
+ <span class="n">logger</span><span class="o">.</span><span class="n">warning</span><span class="p">(</span><span class="sa">f</span><span class="s1">'Unsure how to combine </span><span class="si">{</span><span class="n">oldval</span><span class="si">}</span><span class="s1"> and </span><span class="si">{</span><span class="n">val</span><span class="si">}</span><span class="s1"> for </span><span class="si">{</span><span class="n">attr</span><span class="si">}</span><span class="s1"> under policy </span><span class="si">{</span><span class="n">policy</span><span class="si">}</span><span class="s1">; using </span><span class="si">{</span><span class="n">val</span><span class="si">}</span><span class="s1">'</span><span class="p">)</span>
+ <span class="n">new_conf</span><span class="o">.</span><span class="fm">__setattr__</span><span class="p">(</span><span class="n">attr</span><span class="p">,</span> <span class="n">val</span><span class="p">)</span>
+ <span class="k">else</span><span class="p">:</span>
+ <span class="n">logger</span><span class="o">.</span><span class="n">warning</span><span class="p">(</span><span class="sa">f</span><span class="s1">'Unsure how to combine </span><span class="si">{</span><span class="n">oldval</span><span class="si">}</span><span class="s1"> and </span><span class="si">{</span><span class="n">val</span><span class="si">}</span><span class="s1"> for </span><span class="si">{</span><span class="n">attr</span><span class="si">}</span><span class="s1"> under policy </span><span class="si">{</span><span class="n">policy</span><span class="si">}</span><span class="s1">; using </span><span class="si">{</span><span class="n">val</span><span class="si">}</span><span class="s1">'</span><span class="p">)</span>
+ <span class="n">new_conf</span><span class="o">.</span><span class="fm">__setattr__</span><span class="p">(</span><span class="n">attr</span><span class="p">,</span> <span class="n">val</span><span class="p">)</span>
+ <span class="k">else</span><span class="p">:</span>
+ <span class="k">raise</span> <span class="ne">ValueError</span><span class="p">(</span><span class="sa">f</span><span class="s1">'Unrecognized policy "</span><span class="si">{</span><span class="n">policy</span><span class="si">}</span><span class="s1">" for combining SimConfs'</span><span class="p">)</span>
+ <span class="k">else</span><span class="p">:</span>
+ <span class="n">new_conf</span><span class="o">.</span><span class="fm">__setattr__</span><span class="p">(</span><span class="n">attr</span><span class="p">,</span> <span class="n">val</span><span class="p">)</span>
+ <span class="k">return</span> <span class="n">new_conf</span></div>
+
+
+<div class="viewcode-block" id="SimConf.items">
+<a class="viewcode-back" href="../../api/core/sim_config.html#arbdmodel.sim_config.SimConf.items">[docs]</a>
+ <span class="k">def</span><span class="w"> </span><span class="nf">items</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span>
+ <span class="k">for</span> <span class="n">attr</span> <span class="ow">in</span> <span class="n">_get_properties_and_dict_keys</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span>
+ <span class="n">val</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="fm">__getattribute__</span><span class="p">(</span><span class="n">attr</span><span class="p">)</span>
+ <span class="k">yield</span> <span class="n">attr</span><span class="p">,</span> <span class="n">val</span></div>
+</div>
+
+
+<div class="viewcode-block" id="DefaultSimConf">
+<a class="viewcode-back" href="../../api/core/sim_config.html#arbdmodel.sim_config.DefaultSimConf">[docs]</a>
+<span class="k">class</span><span class="w"> </span><span class="nc">DefaultSimConf</span><span class="p">(</span><span class="n">SimConf</span><span class="p">):</span>
+<span class="w"> </span><span class="sd">""" Generic class describing properties for a simulation with default binary paths """</span>
+
+ <span class="k">def</span><span class="w"> </span><span class="fm">__init__</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">num_steps</span><span class="o">=</span><span class="mf">1e5</span><span class="p">,</span> <span class="n">output_period</span><span class="o">=</span><span class="mf">1e3</span><span class="p">,</span>
+ <span class="n">integrator</span><span class="o">=</span><span class="s1">'MD'</span><span class="p">,</span> <span class="n">timestep</span><span class="o">=</span><span class="mf">20e-6</span><span class="p">,</span> <span class="n">thermostat</span><span class="o">=</span><span class="s1">'Langevin'</span><span class="p">,</span> <span class="n">barostat</span><span class="o">=</span><span class="kc">None</span><span class="p">,</span>
+ <span class="n">temperature</span><span class="o">=</span><span class="mi">295</span><span class="p">,</span> <span class="n">pressure</span><span class="o">=</span><span class="mi">1</span><span class="p">,</span>
+ <span class="n">cutoff</span><span class="o">=</span><span class="mi">50</span><span class="p">,</span> <span class="n">pairlist_distance</span><span class="o">=</span><span class="kc">None</span><span class="p">,</span> <span class="n">decomp_period</span><span class="o">=</span><span class="mi">40</span><span class="p">,</span>
+ <span class="n">seed</span><span class="o">=</span><span class="kc">None</span><span class="p">,</span> <span class="n">restart_file</span><span class="o">=</span><span class="kc">None</span><span class="p">,</span> <span class="n">gpu</span><span class="o">=</span><span class="mi">0</span><span class="p">,</span>
+ <span class="n">viscosity</span><span class="o">=</span><span class="mf">0.01</span><span class="p">,</span> <span class="n">solvent_density</span><span class="o">=</span><span class="mf">1.0</span><span class="p">,</span> <span class="n">num_heavy_cluster</span><span class="o">=</span><span class="mi">3</span><span class="p">,</span>
+ <span class="o">**</span><span class="n">kwargs</span><span class="p">):</span>
+
+ <span class="c1"># Set default paths only for essential binaries or those that exist</span>
+ <span class="n">default_paths</span> <span class="o">=</span> <span class="p">{}</span>
+ <span class="n">essential_binaries</span> <span class="o">=</span> <span class="p">[</span><span class="s2">"arbd"</span><span class="p">]</span> <span class="c1"># These are required for basic functionality</span>
+ <span class="n">optional_binaries</span> <span class="o">=</span> <span class="p">[</span><span class="s2">"hydropro"</span><span class="p">,</span> <span class="s2">"apbs"</span><span class="p">,</span> <span class="s2">"vmd"</span><span class="p">,</span> <span class="s2">"namd"</span><span class="p">]</span> <span class="c1"># These are optional</span>
+
+ <span class="c1"># First add essential binaries</span>
+ <span class="k">for</span> <span class="n">binary_name</span> <span class="ow">in</span> <span class="n">essential_binaries</span><span class="p">:</span>
+ <span class="n">resource_path</span> <span class="o">=</span> <span class="n">BinaryManager</span><span class="o">.</span><span class="n">get_binary_path</span><span class="p">(</span><span class="n">binary_name</span><span class="p">)</span>
+ <span class="k">if</span> <span class="n">resource_path</span><span class="p">:</span>
+ <span class="n">default_paths</span><span class="p">[</span><span class="sa">f</span><span class="s2">"</span><span class="si">{</span><span class="n">binary_name</span><span class="si">}</span><span class="s2">_path"</span><span class="p">]</span> <span class="o">=</span> <span class="n">resource_path</span>
+ <span class="k">else</span><span class="p">:</span>
+ <span class="n">logger</span><span class="o">.</span><span class="n">warning</span><span class="p">(</span><span class="sa">f</span><span class="s2">"Essential binary '</span><span class="si">{</span><span class="n">binary_name</span><span class="si">}</span><span class="s2">' not found. Some functionality may be limited."</span><span class="p">)</span>
+
+ <span class="c1"># Then add optional binaries only if they exist</span>
+ <span class="k">for</span> <span class="n">binary_name</span> <span class="ow">in</span> <span class="n">optional_binaries</span><span class="p">:</span>
+ <span class="n">resource_path</span> <span class="o">=</span> <span class="n">BinaryManager</span><span class="o">.</span><span class="n">get_binary_path</span><span class="p">(</span><span class="n">binary_name</span><span class="p">)</span>
+ <span class="k">if</span> <span class="n">resource_path</span><span class="p">:</span>
+ <span class="n">default_paths</span><span class="p">[</span><span class="sa">f</span><span class="s2">"</span><span class="si">{</span><span class="n">binary_name</span><span class="si">}</span><span class="s2">_path"</span><span class="p">]</span> <span class="o">=</span> <span class="n">resource_path</span>
+
+ <span class="c1"># Initialize with binary paths and other parameters</span>
+ <span class="n">SimConf</span><span class="o">.</span><span class="fm">__init__</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span>
+ <span class="n">num_steps</span><span class="o">=</span><span class="n">num_steps</span><span class="p">,</span>
+ <span class="n">output_period</span><span class="o">=</span><span class="n">output_period</span><span class="p">,</span>
+ <span class="n">integrator</span><span class="o">=</span><span class="n">integrator</span><span class="p">,</span>
+ <span class="n">timestep</span><span class="o">=</span><span class="n">timestep</span><span class="p">,</span>
+ <span class="n">thermostat</span><span class="o">=</span><span class="n">thermostat</span><span class="p">,</span>
+ <span class="n">barostat</span><span class="o">=</span><span class="n">barostat</span><span class="p">,</span>
+ <span class="n">temperature</span><span class="o">=</span><span class="n">temperature</span><span class="p">,</span>
+ <span class="n">pressure</span><span class="o">=</span><span class="n">pressure</span><span class="p">,</span>
+ <span class="n">cutoff</span><span class="o">=</span><span class="n">cutoff</span><span class="p">,</span>
+ <span class="n">pairlist_distance</span><span class="o">=</span><span class="n">pairlist_distance</span><span class="p">,</span>
+ <span class="n">decomp_period</span><span class="o">=</span><span class="n">decomp_period</span><span class="p">,</span>
+ <span class="n">seed</span><span class="o">=</span><span class="n">seed</span><span class="p">,</span>
+ <span class="n">restart_file</span><span class="o">=</span><span class="n">restart_file</span><span class="p">,</span>
+ <span class="n">gpu</span><span class="o">=</span><span class="n">gpu</span><span class="p">,</span>
+ <span class="n">viscosity</span><span class="o">=</span><span class="n">viscosity</span><span class="p">,</span>
+ <span class="n">solvent_density</span><span class="o">=</span><span class="n">solvent_density</span><span class="p">,</span>
+ <span class="n">num_heavy_cluster</span><span class="o">=</span><span class="n">num_heavy_cluster</span><span class="p">,</span>
+ <span class="o">**</span><span class="p">{</span><span class="o">**</span><span class="n">default_paths</span><span class="p">,</span> <span class="o">**</span><span class="n">kwargs</span><span class="p">})</span> <span class="c1"># User-provided values override defaults</span>
+
+ <span class="c1"># Store these for direct access</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">num_steps</span> <span class="o">=</span> <span class="n">num_steps</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">output_period</span> <span class="o">=</span> <span class="n">output_period</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">__temperature</span> <span class="o">=</span> <span class="n">temperature</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">pressure</span> <span class="o">=</span> <span class="n">pressure</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">viscosity</span> <span class="o">=</span> <span class="n">viscosity</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">solvent_density</span> <span class="o">=</span> <span class="n">solvent_density</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">num_heavy_cluster</span> <span class="o">=</span> <span class="n">num_heavy_cluster</span>
+
+ <span class="nd">@property</span>
+ <span class="k">def</span><span class="w"> </span><span class="nf">temperature</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span>
+ <span class="k">return</span> <span class="bp">self</span><span class="o">.</span><span class="n">__temperature</span>
+
+ <span class="nd">@temperature</span><span class="o">.</span><span class="n">setter</span>
+ <span class="k">def</span><span class="w"> </span><span class="nf">temperature</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">value</span><span class="p">):</span>
+ <span class="k">if</span> <span class="p">(</span><span class="n">value</span> <span class="o"><=</span> <span class="mi">0</span><span class="p">):</span>
+ <span class="k">raise</span> <span class="ne">ValueError</span><span class="p">(</span><span class="s2">"Temperature must be positive"</span><span class="p">)</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">__temperature</span> <span class="o">=</span> <span class="n">value</span></div>
+
+</pre></div>
+
+ </article>
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+ <h1>Source code for arbdmodel.simplearbd</h1><div class="highlight"><pre>
+<span></span><span class="ch">#!/usr/bin/env python3</span>
+<span class="kn">import</span><span class="w"> </span><span class="nn">re</span>
+<span class="kn">import</span><span class="w"> </span><span class="nn">sys</span>
+<span class="kn">import</span><span class="w"> </span><span class="nn">argparse</span>
+<span class="kn">from</span><span class="w"> </span><span class="nn">pathlib</span><span class="w"> </span><span class="kn">import</span> <span class="n">Path</span>
+
+<span class="kn">from</span><span class="w"> </span><span class="nn">.structure_rigidbody</span><span class="w"> </span><span class="kn">import</span> <span class="n">StructureRigidBodyModel</span><span class="p">,</span> <span class="n">SimpleArbdEngine</span>
+<span class="kn">from</span><span class="w"> </span><span class="nn">.sim_config</span><span class="w"> </span><span class="kn">import</span> <span class="n">SimConf</span>
+<span class="kn">from</span><span class="w"> </span><span class="nn">.logger</span><span class="w"> </span><span class="kn">import</span> <span class="n">logger</span>
+
+<div class="viewcode-block" id="SimpleArbdConfig">
+<a class="viewcode-back" href="../../api/rigidbody_models/simplearbd.html#arbdmodel.simplearbd.SimpleArbdConfig">[docs]</a>
+<span class="k">class</span><span class="w"> </span><span class="nc">SimpleArbdConfig</span><span class="p">:</span>
+<span class="w"> </span><span class="sd">"""</span>
+<span class="sd"> Parse and manage SimpleARBD configuration file.</span>
+<span class="sd"> </span>
+<span class="sd"> This class provides a modern, clean interface for reading SimpleARBD</span>
+<span class="sd"> configuration files and setting up the simulation.</span>
+<span class="sd"> """</span>
+
+ <span class="k">def</span><span class="w"> </span><span class="fm">__init__</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">config_path</span><span class="p">):</span>
+<span class="w"> </span><span class="sd">"""</span>
+<span class="sd"> Initialize SimpleArbdConfig.</span>
+<span class="sd"> </span>
+<span class="sd"> Args:</span>
+<span class="sd"> config_path: Path to the SimpleARBD configuration file</span>
+<span class="sd"> """</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">config_path</span> <span class="o">=</span> <span class="n">Path</span><span class="p">(</span><span class="n">config_path</span><span class="p">)</span>
+ <span class="k">if</span> <span class="ow">not</span> <span class="bp">self</span><span class="o">.</span><span class="n">config_path</span><span class="o">.</span><span class="n">exists</span><span class="p">():</span>
+ <span class="k">raise</span> <span class="ne">FileNotFoundError</span><span class="p">(</span><span class="sa">f</span><span class="s2">"Config file not found: </span><span class="si">{</span><span class="bp">self</span><span class="o">.</span><span class="n">config_path</span><span class="si">}</span><span class="s2">"</span><span class="p">)</span>
+
+ <span class="bp">self</span><span class="o">.</span><span class="n">config</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">_parse_config</span><span class="p">()</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">simconf</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">_create_simconf</span><span class="p">()</span>
+
+ <span class="k">def</span><span class="w"> </span><span class="nf">_parse_config</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span>
+<span class="w"> </span><span class="sd">"""</span>
+<span class="sd"> Parse the SimpleARBD configuration file.</span>
+<span class="sd"> </span>
+<span class="sd"> Returns:</span>
+<span class="sd"> Dict containing configuration parameters</span>
+<span class="sd"> """</span>
+ <span class="n">logger</span><span class="o">.</span><span class="n">info</span><span class="p">(</span><span class="sa">f</span><span class="s2">"Parsing config file: </span><span class="si">{</span><span class="bp">self</span><span class="o">.</span><span class="n">config_path</span><span class="si">}</span><span class="s2">"</span><span class="p">)</span>
+
+ <span class="n">config</span> <span class="o">=</span> <span class="p">{}</span>
+ <span class="k">with</span> <span class="nb">open</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">config_path</span><span class="p">)</span> <span class="k">as</span> <span class="n">f</span><span class="p">:</span>
+ <span class="n">text</span> <span class="o">=</span> <span class="n">f</span><span class="o">.</span><span class="n">read</span><span class="p">()</span>
+
+ <span class="c1"># Parse diffusible objects</span>
+ <span class="n">match</span> <span class="o">=</span> <span class="n">re</span><span class="o">.</span><span class="n">search</span><span class="p">(</span><span class="sa">r</span><span class="s1">'Diffusible_objects:([ \w\.]+)'</span><span class="p">,</span> <span class="n">text</span><span class="p">)</span>
+ <span class="k">if</span> <span class="n">match</span><span class="p">:</span>
+ <span class="n">config</span><span class="p">[</span><span class="s1">'diffusible_objects'</span><span class="p">]</span> <span class="o">=</span> <span class="n">match</span><span class="o">.</span><span class="n">group</span><span class="p">(</span><span class="mi">1</span><span class="p">)</span><span class="o">.</span><span class="n">strip</span><span class="p">()</span><span class="o">.</span><span class="n">split</span><span class="p">()</span>
+
+ <span class="c1"># Parse static objects</span>
+ <span class="n">match</span> <span class="o">=</span> <span class="n">re</span><span class="o">.</span><span class="n">search</span><span class="p">(</span><span class="sa">r</span><span class="s1">'Static_objects \(Enter NA for no static object\):([ \w\.]+)'</span><span class="p">,</span> <span class="n">text</span><span class="p">)</span>
+ <span class="k">if</span> <span class="n">match</span><span class="p">:</span>
+ <span class="n">val</span> <span class="o">=</span> <span class="n">match</span><span class="o">.</span><span class="n">group</span><span class="p">(</span><span class="mi">1</span><span class="p">)</span><span class="o">.</span><span class="n">strip</span><span class="p">()</span>
+ <span class="n">config</span><span class="p">[</span><span class="s1">'static_objects'</span><span class="p">]</span> <span class="o">=</span> <span class="p">[]</span> <span class="k">if</span> <span class="n">val</span> <span class="o">==</span> <span class="s1">'NA'</span> <span class="k">else</span> <span class="n">val</span><span class="o">.</span><span class="n">split</span><span class="p">()</span>
+
+ <span class="c1"># Parse remaining configuration parameters</span>
+ <span class="n">parameter_patterns</span> <span class="o">=</span> <span class="p">{</span>
+ <span class="s1">'salt_concentration'</span><span class="p">:</span> <span class="sa">r</span><span class="s1">'SaltConcentration:(\s*[0-9]*\.[0-9]*)'</span><span class="p">,</span>
+ <span class="s1">'temperature'</span><span class="p">:</span> <span class="sa">r</span><span class="s1">'Temperature \(K\):(\s*[0-9]*\.?[0-9]*)'</span><span class="p">,</span>
+ <span class="s1">'viscosity'</span><span class="p">:</span> <span class="sa">r</span><span class="s1">'Viscosity:(\s*[0-9]*\.?[0-9]*)'</span><span class="p">,</span>
+ <span class="s1">'solvent_density'</span><span class="p">:</span> <span class="sa">r</span><span class="s1">'Solvent_density:(\s*[0-9]*\.?[0-9]*)'</span><span class="p">,</span>
+ <span class="s1">'num_heavy_cluster'</span><span class="p">:</span> <span class="sa">r</span><span class="s1">'Number_of_heavy_cluster \(Integer\):(\s*[0-9]+)'</span><span class="p">,</span>
+ <span class="s1">'gaussian_width'</span><span class="p">:</span> <span class="sa">r</span><span class="s1">'GaussianWidth:(\s*[0-9]*\.?[0-9]*)'</span><span class="p">,</span>
+ <span class="s1">'skip_parametrizing_diffusible'</span><span class="p">:</span> <span class="sa">r</span><span class="s1">'Skip_parametrizing_diffusible \(Yes/No\):([ \w]+)'</span><span class="p">,</span>
+ <span class="s1">'gigantic_stat_objects'</span><span class="p">:</span> <span class="sa">r</span><span class="s1">'Gigantic_stat_objects \(Yes/No\):([ \w]+)'</span><span class="p">,</span>
+ <span class="s1">'python_path'</span><span class="p">:</span> <span class="sa">r</span><span class="s1">'Python_path:(\s*\S+)'</span><span class="p">,</span>
+ <span class="s1">'hydro_path'</span><span class="p">:</span> <span class="sa">r</span><span class="s1">'Hydro_path:(\s*\S+)'</span><span class="p">,</span>
+ <span class="s1">'apbs_path'</span><span class="p">:</span> <span class="sa">r</span><span class="s1">'Apbs_path:(\s*\S+)'</span><span class="p">,</span>
+ <span class="s1">'vmd_path'</span><span class="p">:</span> <span class="sa">r</span><span class="s1">'Vmd_path:(\s*\S+)'</span><span class="p">,</span>
+ <span class="s1">'parameters_folder'</span><span class="p">:</span> <span class="sa">r</span><span class="s1">'Parameters_folder:(\s*\S+)'</span><span class="p">,</span>
+ <span class="s1">'num_replicas'</span><span class="p">:</span> <span class="sa">r</span><span class="s1">'Num_replicas \(Integer\):(\s*[0-9]+)'</span><span class="p">,</span>
+ <span class="s1">'timestep'</span><span class="p">:</span> <span class="sa">r</span><span class="s1">'Timestep \(Float\):(\s*[0-9]*\.?[0-9]*)'</span><span class="p">,</span>
+ <span class="s1">'steps'</span><span class="p">:</span> <span class="sa">r</span><span class="s1">'Steps \(Integer\):(\s*[0-9]+)'</span><span class="p">,</span>
+ <span class="s1">'interactive'</span><span class="p">:</span> <span class="sa">r</span><span class="s1">'Interactive \(Yes/No\):([ \w]+)'</span><span class="p">,</span>
+ <span class="s1">'grid_path'</span><span class="p">:</span> <span class="sa">r</span><span class="s1">'Grid_path:(\s*\S+)'</span><span class="p">,</span>
+ <span class="s1">'well_depth'</span><span class="p">:</span> <span class="sa">r</span><span class="s1">'WellDepth \(Positive\):\s*([0-9]+[\.]*[0-9]*)'</span><span class="p">,</span>
+ <span class="s1">'well_resolution'</span><span class="p">:</span> <span class="sa">r</span><span class="s1">'WellResolution \(Positive\):\s*([0-9]+[\.]*[0-9]*)'</span><span class="p">,</span>
+ <span class="s1">'arbd_path'</span><span class="p">:</span> <span class="sa">r</span><span class="s1">'ARBD_path:(\s*\S+)'</span><span class="p">,</span>
+ <span class="s1">'simulation_path'</span><span class="p">:</span> <span class="sa">r</span><span class="s1">'Path_for_ARBD_simulations:(\s*\S+)'</span><span class="p">,</span>
+ <span class="p">}</span>
+
+ <span class="c1"># Extract cell vectors and origin</span>
+ <span class="n">vector_patterns</span> <span class="o">=</span> <span class="p">{</span>
+ <span class="s1">'cell_basis_vector1'</span><span class="p">:</span> <span class="sa">r</span><span class="s1">'CellBasisVector1:\s*([0-9]+[\.]*[0-9]* [0-9]+[\.]*[0-9]* [0-9]+[\.]*[0-9]*)'</span><span class="p">,</span>
+ <span class="s1">'cell_basis_vector2'</span><span class="p">:</span> <span class="sa">r</span><span class="s1">'CellBasisVector2:\s*([0-9]+[\.]*[0-9]* [0-9]+[\.]*[0-9]* [0-9]+[\.]*[0-9]*)'</span><span class="p">,</span>
+ <span class="s1">'cell_basis_vector3'</span><span class="p">:</span> <span class="sa">r</span><span class="s1">'CellBasisVector3:\s*([0-9]+[\.]*[0-9]* [0-9]+[\.]*[0-9]* [0-9]+[\.]*[0-9]*)'</span><span class="p">,</span>
+ <span class="s1">'cell_origin'</span><span class="p">:</span> <span class="sa">r</span><span class="s1">'CellOrigin:\s*(-*[0-9]+[\.]*[0-9]* -*[0-9]+[\.]*[0-9]* -*[0-9]+[\.]*[0-9]*)'</span><span class="p">,</span>
+ <span class="s1">'initial_coor_basis_vector1'</span><span class="p">:</span> <span class="sa">r</span><span class="s1">'InitialCoorBasisVector1:\s*([0-9]+[\.]*[0-9]* [0-9]+[\.]*[0-9]* [0-9]+[\.]*[0-9]*)'</span><span class="p">,</span>
+ <span class="s1">'initial_coor_basis_vector2'</span><span class="p">:</span> <span class="sa">r</span><span class="s1">'InitialCoorBasisVector2:\s*([0-9]+[\.]*[0-9]* [0-9]+[\.]*[0-9]* [0-9]+[\.]*[0-9]*)'</span><span class="p">,</span>
+ <span class="s1">'initial_coor_basis_vector3'</span><span class="p">:</span> <span class="sa">r</span><span class="s1">'InitialCoorBasisVector3:\s*([0-9]+[\.]*[0-9]* [0-9]+[\.]*[0-9]* [0-9]+[\.]*[0-9]*)'</span><span class="p">,</span>
+ <span class="s1">'initial_coor_origin'</span><span class="p">:</span> <span class="sa">r</span><span class="s1">'InitialCoorOrigin:\s*(-*[0-9]+[\.]*[0-9]* -*[0-9]+[\.]*[0-9]* -*[0-9]+[\.]*[0-9]*)'</span><span class="p">,</span>
+ <span class="p">}</span>
+
+ <span class="c1"># Extract all parameters using regex</span>
+ <span class="k">for</span> <span class="n">param</span><span class="p">,</span> <span class="n">pattern</span> <span class="ow">in</span> <span class="n">parameter_patterns</span><span class="o">.</span><span class="n">items</span><span class="p">():</span>
+ <span class="n">match</span> <span class="o">=</span> <span class="n">re</span><span class="o">.</span><span class="n">search</span><span class="p">(</span><span class="n">pattern</span><span class="p">,</span> <span class="n">text</span><span class="p">)</span>
+ <span class="k">if</span> <span class="n">match</span><span class="p">:</span>
+ <span class="n">config</span><span class="p">[</span><span class="n">param</span><span class="p">]</span> <span class="o">=</span> <span class="n">match</span><span class="o">.</span><span class="n">group</span><span class="p">(</span><span class="mi">1</span><span class="p">)</span><span class="o">.</span><span class="n">strip</span><span class="p">()</span>
+
+ <span class="c1"># Extract and convert vector parameters</span>
+ <span class="k">for</span> <span class="n">param</span><span class="p">,</span> <span class="n">pattern</span> <span class="ow">in</span> <span class="n">vector_patterns</span><span class="o">.</span><span class="n">items</span><span class="p">():</span>
+ <span class="n">match</span> <span class="o">=</span> <span class="n">re</span><span class="o">.</span><span class="n">search</span><span class="p">(</span><span class="n">pattern</span><span class="p">,</span> <span class="n">text</span><span class="p">)</span>
+ <span class="k">if</span> <span class="n">match</span><span class="p">:</span>
+ <span class="c1"># Convert space-separated values to list of floats</span>
+ <span class="n">values</span> <span class="o">=</span> <span class="p">[</span><span class="nb">float</span><span class="p">(</span><span class="n">x</span><span class="p">)</span> <span class="k">for</span> <span class="n">x</span> <span class="ow">in</span> <span class="n">match</span><span class="o">.</span><span class="n">group</span><span class="p">(</span><span class="mi">1</span><span class="p">)</span><span class="o">.</span><span class="n">split</span><span class="p">()]</span>
+ <span class="n">config</span><span class="p">[</span><span class="n">param</span><span class="p">]</span> <span class="o">=</span> <span class="n">values</span>
+
+ <span class="c1"># Extract copies per object</span>
+ <span class="n">match</span> <span class="o">=</span> <span class="n">re</span><span class="o">.</span><span class="n">search</span><span class="p">(</span><span class="sa">r</span><span class="s1">'Number_of_copies_per_object \(Integer\(s\)\):([ 0-9]+)'</span><span class="p">,</span> <span class="n">text</span><span class="p">)</span>
+ <span class="k">if</span> <span class="n">match</span><span class="p">:</span>
+ <span class="n">copies</span> <span class="o">=</span> <span class="n">match</span><span class="o">.</span><span class="n">group</span><span class="p">(</span><span class="mi">1</span><span class="p">)</span><span class="o">.</span><span class="n">strip</span><span class="p">()</span><span class="o">.</span><span class="n">split</span><span class="p">()</span>
+ <span class="k">if</span> <span class="s1">'diffusible_objects'</span> <span class="ow">in</span> <span class="n">config</span><span class="p">:</span>
+ <span class="n">config</span><span class="p">[</span><span class="s1">'copies_per_object'</span><span class="p">]</span> <span class="o">=</span> <span class="p">{</span>
+ <span class="n">obj</span><span class="p">:</span> <span class="nb">int</span><span class="p">(</span><span class="n">copies</span><span class="p">[</span><span class="n">i</span><span class="p">])</span> <span class="k">for</span> <span class="n">i</span><span class="p">,</span> <span class="n">obj</span> <span class="ow">in</span> <span class="nb">enumerate</span><span class="p">(</span><span class="n">config</span><span class="p">[</span><span class="s1">'diffusible_objects'</span><span class="p">])</span>
+ <span class="k">if</span> <span class="n">i</span> <span class="o"><</span> <span class="nb">len</span><span class="p">(</span><span class="n">copies</span><span class="p">)</span>
+ <span class="p">}</span>
+
+ <span class="c1"># Extract extra potential tags</span>
+ <span class="n">match</span> <span class="o">=</span> <span class="n">re</span><span class="o">.</span><span class="n">search</span><span class="p">(</span><span class="sa">r</span><span class="s1">'Extra_potentials_tags \(Path, vdw cluster group\):([\s\S]*)\n'</span><span class="p">,</span> <span class="n">text</span><span class="p">)</span>
+ <span class="k">if</span> <span class="n">match</span><span class="p">:</span>
+ <span class="n">tags</span> <span class="o">=</span> <span class="n">re</span><span class="o">.</span><span class="n">findall</span><span class="p">(</span><span class="sa">r</span><span class="s1">'\((\S+\.dx,\s*\w+)\)'</span><span class="p">,</span> <span class="n">match</span><span class="o">.</span><span class="n">group</span><span class="p">(</span><span class="mi">1</span><span class="p">))</span>
+ <span class="n">config</span><span class="p">[</span><span class="s1">'extra_potentials'</span><span class="p">]</span> <span class="o">=</span> <span class="p">[]</span>
+ <span class="k">for</span> <span class="n">tag</span> <span class="ow">in</span> <span class="n">tags</span><span class="p">:</span>
+ <span class="n">parts</span> <span class="o">=</span> <span class="n">tag</span><span class="o">.</span><span class="n">split</span><span class="p">(</span><span class="s1">','</span><span class="p">)</span>
+ <span class="n">config</span><span class="p">[</span><span class="s1">'extra_potentials'</span><span class="p">]</span><span class="o">.</span><span class="n">append</span><span class="p">({</span>
+ <span class="s1">'path'</span><span class="p">:</span> <span class="n">parts</span><span class="p">[</span><span class="mi">0</span><span class="p">]</span><span class="o">.</span><span class="n">strip</span><span class="p">(),</span>
+ <span class="s1">'vdw_type'</span><span class="p">:</span> <span class="n">parts</span><span class="p">[</span><span class="mi">1</span><span class="p">]</span><span class="o">.</span><span class="n">strip</span><span class="p">()</span>
+ <span class="p">})</span>
+
+ <span class="c1"># Convert appropriate values to correct types</span>
+ <span class="n">type_conversions</span> <span class="o">=</span> <span class="p">{</span>
+ <span class="s1">'salt_concentration'</span><span class="p">:</span> <span class="nb">float</span><span class="p">,</span>
+ <span class="s1">'temperature'</span><span class="p">:</span> <span class="nb">float</span><span class="p">,</span>
+ <span class="s1">'viscosity'</span><span class="p">:</span> <span class="nb">float</span><span class="p">,</span>
+ <span class="s1">'solvent_density'</span><span class="p">:</span> <span class="nb">float</span><span class="p">,</span>
+ <span class="s1">'num_heavy_cluster'</span><span class="p">:</span> <span class="nb">int</span><span class="p">,</span>
+ <span class="s1">'gaussian_width'</span><span class="p">:</span> <span class="nb">float</span><span class="p">,</span>
+ <span class="s1">'num_replicas'</span><span class="p">:</span> <span class="nb">int</span><span class="p">,</span>
+ <span class="s1">'timestep'</span><span class="p">:</span> <span class="nb">float</span><span class="p">,</span>
+ <span class="s1">'steps'</span><span class="p">:</span> <span class="nb">int</span><span class="p">,</span>
+ <span class="s1">'well_depth'</span><span class="p">:</span> <span class="nb">float</span><span class="p">,</span>
+ <span class="s1">'well_resolution'</span><span class="p">:</span> <span class="nb">float</span><span class="p">,</span>
+ <span class="p">}</span>
+
+ <span class="k">for</span> <span class="n">param</span><span class="p">,</span> <span class="n">convert</span> <span class="ow">in</span> <span class="n">type_conversions</span><span class="o">.</span><span class="n">items</span><span class="p">():</span>
+ <span class="k">if</span> <span class="n">param</span> <span class="ow">in</span> <span class="n">config</span><span class="p">:</span>
+ <span class="k">try</span><span class="p">:</span>
+ <span class="n">config</span><span class="p">[</span><span class="n">param</span><span class="p">]</span> <span class="o">=</span> <span class="n">convert</span><span class="p">(</span><span class="n">config</span><span class="p">[</span><span class="n">param</span><span class="p">])</span>
+ <span class="k">except</span> <span class="p">(</span><span class="ne">ValueError</span><span class="p">,</span> <span class="ne">TypeError</span><span class="p">):</span>
+ <span class="n">logger</span><span class="o">.</span><span class="n">warning</span><span class="p">(</span><span class="sa">f</span><span class="s2">"Could not convert </span><span class="si">{</span><span class="n">param</span><span class="si">}</span><span class="s2"> to </span><span class="si">{</span><span class="n">convert</span><span class="o">.</span><span class="vm">__name__</span><span class="si">}</span><span class="s2">"</span><span class="p">)</span>
+
+ <span class="c1"># Boolean conversions</span>
+ <span class="n">bool_conversions</span> <span class="o">=</span> <span class="p">{</span>
+ <span class="s1">'skip_parametrizing_diffusible'</span><span class="p">:</span> <span class="k">lambda</span> <span class="n">x</span><span class="p">:</span> <span class="n">x</span><span class="o">.</span><span class="n">lower</span><span class="p">()</span> <span class="o">==</span> <span class="s1">'yes'</span><span class="p">,</span>
+ <span class="s1">'gigantic_stat_objects'</span><span class="p">:</span> <span class="k">lambda</span> <span class="n">x</span><span class="p">:</span> <span class="n">x</span><span class="o">.</span><span class="n">lower</span><span class="p">()</span> <span class="o">==</span> <span class="s1">'yes'</span><span class="p">,</span>
+ <span class="s1">'interactive'</span><span class="p">:</span> <span class="k">lambda</span> <span class="n">x</span><span class="p">:</span> <span class="n">x</span><span class="o">.</span><span class="n">lower</span><span class="p">()</span> <span class="o">==</span> <span class="s1">'yes'</span><span class="p">,</span>
+ <span class="p">}</span>
+
+ <span class="k">for</span> <span class="n">param</span><span class="p">,</span> <span class="n">convert</span> <span class="ow">in</span> <span class="n">bool_conversions</span><span class="o">.</span><span class="n">items</span><span class="p">():</span>
+ <span class="k">if</span> <span class="n">param</span> <span class="ow">in</span> <span class="n">config</span><span class="p">:</span>
+ <span class="k">try</span><span class="p">:</span>
+ <span class="n">config</span><span class="p">[</span><span class="n">param</span><span class="p">]</span> <span class="o">=</span> <span class="n">convert</span><span class="p">(</span><span class="n">config</span><span class="p">[</span><span class="n">param</span><span class="p">])</span>
+ <span class="k">except</span> <span class="p">(</span><span class="ne">ValueError</span><span class="p">,</span> <span class="ne">TypeError</span><span class="p">,</span> <span class="ne">AttributeError</span><span class="p">):</span>
+ <span class="n">logger</span><span class="o">.</span><span class="n">warning</span><span class="p">(</span><span class="sa">f</span><span class="s2">"Could not convert </span><span class="si">{</span><span class="n">param</span><span class="si">}</span><span class="s2"> to boolean"</span><span class="p">)</span>
+
+ <span class="k">return</span> <span class="n">config</span>
+
+ <span class="k">def</span><span class="w"> </span><span class="nf">_create_simconf</span><span class="p">(</span><span class="bp">self</span><span class="p">)</span> <span class="o">-></span> <span class="n">SimConf</span><span class="p">:</span>
+<span class="w"> </span><span class="sd">"""</span>
+<span class="sd"> Create a SimConf object from the parsed configuration.</span>
+<span class="sd"> </span>
+<span class="sd"> Returns:</span>
+<span class="sd"> SimConf object</span>
+<span class="sd"> """</span>
+ <span class="c1"># Extract parameters for SimConf</span>
+ <span class="n">params</span> <span class="o">=</span> <span class="p">{</span>
+ <span class="s1">'temperature'</span><span class="p">:</span> <span class="bp">self</span><span class="o">.</span><span class="n">config</span><span class="o">.</span><span class="n">get</span><span class="p">(</span><span class="s1">'temperature'</span><span class="p">,</span> <span class="mi">300</span><span class="p">),</span>
+ <span class="s1">'viscosity'</span><span class="p">:</span> <span class="bp">self</span><span class="o">.</span><span class="n">config</span><span class="o">.</span><span class="n">get</span><span class="p">(</span><span class="s1">'viscosity'</span><span class="p">,</span> <span class="mf">0.01</span><span class="p">),</span>
+ <span class="s1">'solvent_density'</span><span class="p">:</span> <span class="bp">self</span><span class="o">.</span><span class="n">config</span><span class="o">.</span><span class="n">get</span><span class="p">(</span><span class="s1">'solvent_density'</span><span class="p">,</span> <span class="mf">1.0</span><span class="p">),</span>
+ <span class="s1">'num_heavy_cluster'</span><span class="p">:</span> <span class="bp">self</span><span class="o">.</span><span class="n">config</span><span class="o">.</span><span class="n">get</span><span class="p">(</span><span class="s1">'num_heavy_cluster'</span><span class="p">,</span> <span class="mi">3</span><span class="p">),</span>
+ <span class="s1">'timestep'</span><span class="p">:</span> <span class="bp">self</span><span class="o">.</span><span class="n">config</span><span class="o">.</span><span class="n">get</span><span class="p">(</span><span class="s1">'timestep'</span><span class="p">,</span> <span class="mf">0.0002</span><span class="p">),</span>
+ <span class="s1">'num_steps'</span><span class="p">:</span> <span class="bp">self</span><span class="o">.</span><span class="n">config</span><span class="o">.</span><span class="n">get</span><span class="p">(</span><span class="s1">'steps'</span><span class="p">,</span> <span class="mi">10000000</span><span class="p">),</span>
+ <span class="s1">'output_period'</span><span class="p">:</span> <span class="mi">1000</span><span class="p">,</span> <span class="c1"># Default</span>
+ <span class="p">}</span>
+
+ <span class="c1"># Add binary paths if available</span>
+ <span class="n">binary_paths</span> <span class="o">=</span> <span class="p">{</span>
+ <span class="s1">'hydro_path'</span><span class="p">:</span> <span class="s1">'hydro_path'</span><span class="p">,</span>
+ <span class="s1">'apbs_path'</span><span class="p">:</span> <span class="s1">'apbs_path'</span><span class="p">,</span>
+ <span class="s1">'vmd_path'</span><span class="p">:</span> <span class="s1">'vmd_path'</span><span class="p">,</span>
+ <span class="s1">'arbd_path'</span><span class="p">:</span> <span class="s1">'arbd_path'</span>
+ <span class="p">}</span>
+
+ <span class="k">for</span> <span class="n">config_key</span><span class="p">,</span> <span class="n">simconf_key</span> <span class="ow">in</span> <span class="n">binary_paths</span><span class="o">.</span><span class="n">items</span><span class="p">():</span>
+ <span class="k">if</span> <span class="n">config_key</span> <span class="ow">in</span> <span class="bp">self</span><span class="o">.</span><span class="n">config</span><span class="p">:</span>
+ <span class="n">params</span><span class="p">[</span><span class="n">simconf_key</span><span class="p">]</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">config</span><span class="p">[</span><span class="n">config_key</span><span class="p">]</span>
+
+ <span class="k">return</span> <span class="n">SimConf</span><span class="p">(</span><span class="o">**</span><span class="n">params</span><span class="p">)</span>
+
+<div class="viewcode-block" id="SimpleArbdConfig.create_model">
+<a class="viewcode-back" href="../../api/rigidbody_models/simplearbd.html#arbdmodel.simplearbd.SimpleArbdConfig.create_model">[docs]</a>
+ <span class="k">def</span><span class="w"> </span><span class="nf">create_model</span><span class="p">(</span><span class="bp">self</span><span class="p">)</span> <span class="o">-></span> <span class="n">StructureRigidBodyModel</span><span class="p">:</span>
+<span class="w"> </span><span class="sd">"""</span>
+<span class="sd"> Create a StructureRigidBodyModel from the configuration.</span>
+<span class="sd"> </span>
+<span class="sd"> Returns:</span>
+<span class="sd"> StructureRigidBodyModel instance</span>
+<span class="sd"> """</span>
+ <span class="c1"># Set up cell vectors and origin for model</span>
+ <span class="n">cell_vectors</span> <span class="o">=</span> <span class="kc">None</span>
+ <span class="n">cell_origin</span> <span class="o">=</span> <span class="kc">None</span>
+
+ <span class="k">if</span> <span class="nb">all</span><span class="p">(</span><span class="n">key</span> <span class="ow">in</span> <span class="bp">self</span><span class="o">.</span><span class="n">config</span> <span class="k">for</span> <span class="n">key</span> <span class="ow">in</span> <span class="p">[</span><span class="s1">'cell_basis_vector1'</span><span class="p">,</span> <span class="s1">'cell_basis_vector2'</span><span class="p">,</span> <span class="s1">'cell_basis_vector3'</span><span class="p">]):</span>
+ <span class="n">cell_vectors</span> <span class="o">=</span> <span class="p">[</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">config</span><span class="p">[</span><span class="s1">'cell_basis_vector1'</span><span class="p">],</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">config</span><span class="p">[</span><span class="s1">'cell_basis_vector2'</span><span class="p">],</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">config</span><span class="p">[</span><span class="s1">'cell_basis_vector3'</span><span class="p">]</span>
+ <span class="p">]</span>
+
+ <span class="k">if</span> <span class="s1">'cell_origin'</span> <span class="ow">in</span> <span class="bp">self</span><span class="o">.</span><span class="n">config</span><span class="p">:</span>
+ <span class="n">cell_origin</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">config</span><span class="p">[</span><span class="s1">'cell_origin'</span><span class="p">]</span>
+
+ <span class="c1"># Create the model</span>
+ <span class="n">model</span> <span class="o">=</span> <span class="n">StructureRigidBodyModel</span><span class="p">(</span>
+ <span class="n">cell_vectors</span><span class="o">=</span><span class="n">cell_vectors</span><span class="p">,</span>
+ <span class="n">cell_origin</span><span class="o">=</span><span class="n">cell_origin</span><span class="p">,</span>
+ <span class="n">configuration</span><span class="o">=</span><span class="bp">self</span><span class="o">.</span><span class="n">simconf</span><span class="p">,</span>
+ <span class="n">use_boundary</span><span class="o">=</span><span class="s1">'extra_potentials'</span> <span class="ow">in</span> <span class="bp">self</span><span class="o">.</span><span class="n">config</span> <span class="ow">and</span> <span class="nb">len</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">config</span><span class="p">[</span><span class="s1">'extra_potentials'</span><span class="p">])</span> <span class="o">></span> <span class="mi">0</span><span class="p">,</span>
+ <span class="n">boundary_params</span><span class="o">=</span><span class="p">{</span>
+ <span class="s1">'well_depth'</span><span class="p">:</span> <span class="bp">self</span><span class="o">.</span><span class="n">config</span><span class="o">.</span><span class="n">get</span><span class="p">(</span><span class="s1">'well_depth'</span><span class="p">,</span> <span class="mf">1.0</span><span class="p">),</span>
+ <span class="s1">'resolution'</span><span class="p">:</span> <span class="bp">self</span><span class="o">.</span><span class="n">config</span><span class="o">.</span><span class="n">get</span><span class="p">(</span><span class="s1">'well_resolution'</span><span class="p">,</span> <span class="mf">2.0</span><span class="p">),</span>
+ <span class="p">}</span>
+ <span class="p">)</span>
+
+ <span class="k">return</span> <span class="n">model</span></div>
+
+
+<div class="viewcode-block" id="SimpleArbdConfig.create_engine">
+<a class="viewcode-back" href="../../api/rigidbody_models/simplearbd.html#arbdmodel.simplearbd.SimpleArbdConfig.create_engine">[docs]</a>
+ <span class="k">def</span><span class="w"> </span><span class="nf">create_engine</span><span class="p">(</span><span class="bp">self</span><span class="p">)</span> <span class="o">-></span> <span class="n">SimpleArbdEngine</span><span class="p">:</span>
+<span class="w"> </span><span class="sd">"""</span>
+<span class="sd"> Create a SimpleArbdEngine from the configuration.</span>
+<span class="sd"> </span>
+<span class="sd"> Returns:</span>
+<span class="sd"> SimpleArbdEngine instance</span>
+<span class="sd"> """</span>
+ <span class="c1"># Create the engine with appropriate configuration</span>
+ <span class="n">engine</span> <span class="o">=</span> <span class="n">SimpleArbdEngine</span><span class="p">(</span>
+ <span class="n">configuration</span><span class="o">=</span><span class="bp">self</span><span class="o">.</span><span class="n">simconf</span><span class="p">,</span>
+ <span class="n">extra_bd_file_lines</span><span class="o">=</span><span class="s1">''</span>
+ <span class="p">)</span>
+
+ <span class="k">return</span> <span class="n">engine</span></div>
+
+
+<div class="viewcode-block" id="SimpleArbdConfig.setup_diffusible_objects">
+<a class="viewcode-back" href="../../api/rigidbody_models/simplearbd.html#arbdmodel.simplearbd.SimpleArbdConfig.setup_diffusible_objects">[docs]</a>
+ <span class="k">def</span><span class="w"> </span><span class="nf">setup_diffusible_objects</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">model</span><span class="p">:</span> <span class="n">StructureRigidBodyModel</span><span class="p">):</span>
+<span class="w"> </span><span class="sd">"""</span>
+<span class="sd"> Set up diffusible objects in the model.</span>
+<span class="sd"> </span>
+<span class="sd"> Args:</span>
+<span class="sd"> model: StructureRigidBodyModel to add diffusible objects to</span>
+<span class="sd"> """</span>
+ <span class="k">if</span> <span class="s1">'diffusible_objects'</span> <span class="ow">not</span> <span class="ow">in</span> <span class="bp">self</span><span class="o">.</span><span class="n">config</span><span class="p">:</span>
+ <span class="n">logger</span><span class="o">.</span><span class="n">warning</span><span class="p">(</span><span class="s2">"No diffusible objects specified in configuration"</span><span class="p">)</span>
+ <span class="k">return</span>
+
+ <span class="c1"># Create initial region from configuration</span>
+ <span class="n">initial_region</span> <span class="o">=</span> <span class="kc">None</span>
+ <span class="k">if</span> <span class="nb">all</span><span class="p">(</span><span class="n">key</span> <span class="ow">in</span> <span class="bp">self</span><span class="o">.</span><span class="n">config</span> <span class="k">for</span> <span class="n">key</span> <span class="ow">in</span> <span class="p">[</span>
+ <span class="s1">'initial_coor_basis_vector1'</span><span class="p">,</span>
+ <span class="s1">'initial_coor_basis_vector2'</span><span class="p">,</span>
+ <span class="s1">'initial_coor_basis_vector3'</span><span class="p">,</span>
+ <span class="s1">'initial_coor_origin'</span>
+ <span class="p">]):</span>
+ <span class="n">initial_region</span> <span class="o">=</span> <span class="p">{</span>
+ <span class="s1">'bv1'</span><span class="p">:</span> <span class="bp">self</span><span class="o">.</span><span class="n">config</span><span class="p">[</span><span class="s1">'initial_coor_basis_vector1'</span><span class="p">],</span>
+ <span class="s1">'bv2'</span><span class="p">:</span> <span class="bp">self</span><span class="o">.</span><span class="n">config</span><span class="p">[</span><span class="s1">'initial_coor_basis_vector2'</span><span class="p">],</span>
+ <span class="s1">'bv3'</span><span class="p">:</span> <span class="bp">self</span><span class="o">.</span><span class="n">config</span><span class="p">[</span><span class="s1">'initial_coor_basis_vector3'</span><span class="p">],</span>
+ <span class="s1">'origin'</span><span class="p">:</span> <span class="bp">self</span><span class="o">.</span><span class="n">config</span><span class="p">[</span><span class="s1">'initial_coor_origin'</span><span class="p">]</span>
+ <span class="p">}</span>
+
+ <span class="c1"># Add each diffusible object</span>
+ <span class="k">for</span> <span class="n">obj_name</span> <span class="ow">in</span> <span class="bp">self</span><span class="o">.</span><span class="n">config</span><span class="p">[</span><span class="s1">'diffusible_objects'</span><span class="p">]:</span>
+ <span class="c1"># Skip parametrization if requested</span>
+ <span class="k">if</span> <span class="bp">self</span><span class="o">.</span><span class="n">config</span><span class="o">.</span><span class="n">get</span><span class="p">(</span><span class="s1">'skip_parametrizing_diffusible'</span><span class="p">,</span> <span class="kc">False</span><span class="p">):</span>
+ <span class="n">logger</span><span class="o">.</span><span class="n">info</span><span class="p">(</span><span class="sa">f</span><span class="s2">"Skipping parametrization for </span><span class="si">{</span><span class="n">obj_name</span><span class="si">}</span><span class="s2"> (as requested in config)"</span><span class="p">)</span>
+ <span class="k">continue</span>
+
+ <span class="c1"># Determine number of copies</span>
+ <span class="n">copies</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">config</span><span class="o">.</span><span class="n">get</span><span class="p">(</span><span class="s1">'copies_per_object'</span><span class="p">,</span> <span class="p">{})</span><span class="o">.</span><span class="n">get</span><span class="p">(</span><span class="n">obj_name</span><span class="p">,</span> <span class="mi">1</span><span class="p">)</span>
+
+ <span class="c1"># Find structure files</span>
+ <span class="n">psf_file</span> <span class="o">=</span> <span class="n">Path</span><span class="p">(</span><span class="sa">f</span><span class="s2">"</span><span class="si">{</span><span class="n">obj_name</span><span class="si">}</span><span class="s2">.psf"</span><span class="p">)</span>
+ <span class="n">pdb_file</span> <span class="o">=</span> <span class="n">Path</span><span class="p">(</span><span class="sa">f</span><span class="s2">"</span><span class="si">{</span><span class="n">obj_name</span><span class="si">}</span><span class="s2">.pdb"</span><span class="p">)</span>
+
+ <span class="k">if</span> <span class="ow">not</span> <span class="p">(</span><span class="n">psf_file</span><span class="o">.</span><span class="n">exists</span><span class="p">()</span> <span class="ow">and</span> <span class="n">pdb_file</span><span class="o">.</span><span class="n">exists</span><span class="p">()):</span>
+ <span class="n">logger</span><span class="o">.</span><span class="n">warning</span><span class="p">(</span><span class="sa">f</span><span class="s2">"Structure files for </span><span class="si">{</span><span class="n">obj_name</span><span class="si">}</span><span class="s2"> not found: </span><span class="si">{</span><span class="n">psf_file</span><span class="si">}</span><span class="s2">, </span><span class="si">{</span><span class="n">pdb_file</span><span class="si">}</span><span class="s2">"</span><span class="p">)</span>
+ <span class="k">continue</span>
+
+ <span class="n">logger</span><span class="o">.</span><span class="n">info</span><span class="p">(</span><span class="sa">f</span><span class="s2">"Adding diffusible object: </span><span class="si">{</span><span class="n">obj_name</span><span class="si">}</span><span class="s2"> with </span><span class="si">{</span><span class="n">copies</span><span class="si">}</span><span class="s2"> copies"</span><span class="p">)</span>
+
+ <span class="c1"># Create work directory</span>
+ <span class="n">work_dir</span> <span class="o">=</span> <span class="n">Path</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">config</span><span class="o">.</span><span class="n">get</span><span class="p">(</span><span class="s1">'parameters_folder'</span><span class="p">,</span> <span class="s1">'./parameters'</span><span class="p">))</span> <span class="o">/</span> <span class="n">obj_name</span>
+
+ <span class="c1"># Add to model</span>
+ <span class="n">model</span><span class="o">.</span><span class="n">add_diffusible_object</span><span class="p">(</span>
+ <span class="n">structure_path</span><span class="o">=</span><span class="n">psf_file</span><span class="p">,</span> <span class="c1"># Use PSF as primary file</span>
+ <span class="n">copies</span><span class="o">=</span><span class="n">copies</span><span class="p">,</span>
+ <span class="n">name</span><span class="o">=</span><span class="n">obj_name</span><span class="p">,</span>
+ <span class="n">initial_region</span><span class="o">=</span><span class="n">initial_region</span><span class="p">,</span>
+ <span class="n">random_seed</span><span class="o">=</span><span class="mi">42</span><span class="p">,</span> <span class="c1"># Fixed seed for reproducibility</span>
+ <span class="n">work_dir</span><span class="o">=</span><span class="n">work_dir</span>
+ <span class="p">)</span></div>
+
+
+<div class="viewcode-block" id="SimpleArbdConfig.setup_static_objects">
+<a class="viewcode-back" href="../../api/rigidbody_models/simplearbd.html#arbdmodel.simplearbd.SimpleArbdConfig.setup_static_objects">[docs]</a>
+ <span class="k">def</span><span class="w"> </span><span class="nf">setup_static_objects</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">model</span><span class="p">:</span> <span class="n">StructureRigidBodyModel</span><span class="p">):</span>
+<span class="w"> </span><span class="sd">"""</span>
+<span class="sd"> Set up static objects in the model.</span>
+<span class="sd"> </span>
+<span class="sd"> Args:</span>
+<span class="sd"> model: StructureRigidBodyModel to add static objects to</span>
+<span class="sd"> """</span>
+ <span class="k">if</span> <span class="s1">'static_objects'</span> <span class="ow">not</span> <span class="ow">in</span> <span class="bp">self</span><span class="o">.</span><span class="n">config</span> <span class="ow">or</span> <span class="ow">not</span> <span class="bp">self</span><span class="o">.</span><span class="n">config</span><span class="p">[</span><span class="s1">'static_objects'</span><span class="p">]:</span>
+ <span class="n">logger</span><span class="o">.</span><span class="n">info</span><span class="p">(</span><span class="s2">"No static objects specified in configuration"</span><span class="p">)</span>
+ <span class="k">return</span>
+
+ <span class="c1"># Process each static object</span>
+ <span class="k">for</span> <span class="n">obj_name</span> <span class="ow">in</span> <span class="bp">self</span><span class="o">.</span><span class="n">config</span><span class="p">[</span><span class="s1">'static_objects'</span><span class="p">]:</span>
+ <span class="c1"># Find structure files</span>
+ <span class="n">psf_file</span> <span class="o">=</span> <span class="n">Path</span><span class="p">(</span><span class="sa">f</span><span class="s2">"</span><span class="si">{</span><span class="n">obj_name</span><span class="si">}</span><span class="s2">.psf"</span><span class="p">)</span>
+ <span class="n">pdb_file</span> <span class="o">=</span> <span class="n">Path</span><span class="p">(</span><span class="sa">f</span><span class="s2">"</span><span class="si">{</span><span class="n">obj_name</span><span class="si">}</span><span class="s2">.pdb"</span><span class="p">)</span>
+
+ <span class="k">if</span> <span class="ow">not</span> <span class="p">(</span><span class="n">psf_file</span><span class="o">.</span><span class="n">exists</span><span class="p">()</span> <span class="ow">and</span> <span class="n">pdb_file</span><span class="o">.</span><span class="n">exists</span><span class="p">()):</span>
+ <span class="n">logger</span><span class="o">.</span><span class="n">warning</span><span class="p">(</span><span class="sa">f</span><span class="s2">"Structure files for static object </span><span class="si">{</span><span class="n">obj_name</span><span class="si">}</span><span class="s2"> not found: </span><span class="si">{</span><span class="n">psf_file</span><span class="si">}</span><span class="s2">, </span><span class="si">{</span><span class="n">pdb_file</span><span class="si">}</span><span class="s2">"</span><span class="p">)</span>
+ <span class="k">continue</span>
+
+ <span class="c1"># Determine if it's a gigantic object</span>
+ <span class="n">is_gigantic</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">config</span><span class="o">.</span><span class="n">get</span><span class="p">(</span><span class="s1">'gigantic_stat_objects'</span><span class="p">,</span> <span class="kc">False</span><span class="p">)</span>
+
+ <span class="n">logger</span><span class="o">.</span><span class="n">info</span><span class="p">(</span><span class="sa">f</span><span class="s2">"Adding static object: </span><span class="si">{</span><span class="n">obj_name</span><span class="si">}</span><span class="s2"> (gigantic: </span><span class="si">{</span><span class="n">is_gigantic</span><span class="si">}</span><span class="s2">)"</span><span class="p">)</span>
+
+ <span class="c1"># Create work directory</span>
+ <span class="n">work_dir</span> <span class="o">=</span> <span class="n">Path</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">config</span><span class="o">.</span><span class="n">get</span><span class="p">(</span><span class="s1">'parameters_folder'</span><span class="p">,</span> <span class="s1">'./parameters'</span><span class="p">))</span> <span class="o">/</span> <span class="sa">f</span><span class="s2">"static_</span><span class="si">{</span><span class="n">obj_name</span><span class="si">}</span><span class="s2">"</span>
+
+ <span class="c1"># Add to model</span>
+ <span class="n">model</span><span class="o">.</span><span class="n">add_static_object</span><span class="p">(</span>
+ <span class="n">structure_path</span><span class="o">=</span><span class="n">psf_file</span><span class="p">,</span> <span class="c1"># Use PSF as primary file</span>
+ <span class="n">work_dir</span><span class="o">=</span><span class="n">work_dir</span><span class="p">,</span>
+ <span class="n">is_gigantic</span><span class="o">=</span><span class="n">is_gigantic</span><span class="p">,</span>
+ <span class="n">threshold</span><span class="o">=</span><span class="mi">300</span> <span class="c1"># Default threshold</span>
+ <span class="p">)</span></div>
+
+
+<div class="viewcode-block" id="SimpleArbdConfig.run_simulation">
+<a class="viewcode-back" href="../../api/rigidbody_models/simplearbd.html#arbdmodel.simplearbd.SimpleArbdConfig.run_simulation">[docs]</a>
+ <span class="k">def</span><span class="w"> </span><span class="nf">run_simulation</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">model</span><span class="p">:</span> <span class="n">StructureRigidBodyModel</span><span class="p">,</span> <span class="n">engine</span><span class="p">:</span> <span class="n">SimpleArbdEngine</span><span class="p">):</span>
+<span class="w"> </span><span class="sd">"""</span>
+<span class="sd"> Run the simulation.</span>
+<span class="sd"> </span>
+<span class="sd"> Args:</span>
+<span class="sd"> model: StructureRigidBodyModel to simulate</span>
+<span class="sd"> engine: SimpleArbdEngine to use for simulation</span>
+<span class="sd"> """</span>
+ <span class="c1"># Set up output directory</span>
+ <span class="n">sim_path</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">config</span><span class="o">.</span><span class="n">get</span><span class="p">(</span><span class="s1">'simulation_path'</span><span class="p">,</span> <span class="s1">'./simulation'</span><span class="p">)</span>
+ <span class="n">output_dir</span> <span class="o">=</span> <span class="n">Path</span><span class="p">(</span><span class="n">sim_path</span><span class="p">)</span> <span class="o">/</span> <span class="s1">'output'</span>
+ <span class="n">output_dir</span><span class="o">.</span><span class="n">mkdir</span><span class="p">(</span><span class="n">parents</span><span class="o">=</span><span class="kc">True</span><span class="p">,</span> <span class="n">exist_ok</span><span class="o">=</span><span class="kc">True</span><span class="p">)</span>
+
+ <span class="c1"># Determine number of replicas</span>
+ <span class="n">replicas</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">config</span><span class="o">.</span><span class="n">get</span><span class="p">(</span><span class="s1">'num_replicas'</span><span class="p">,</span> <span class="mi">1</span><span class="p">)</span>
+
+ <span class="c1"># Run simulation</span>
+ <span class="n">logger</span><span class="o">.</span><span class="n">info</span><span class="p">(</span><span class="sa">f</span><span class="s2">"Running simulation with </span><span class="si">{</span><span class="n">replicas</span><span class="si">}</span><span class="s2"> replicas"</span><span class="p">)</span>
+
+ <span class="n">engine</span><span class="o">.</span><span class="n">run_simulation</span><span class="p">(</span>
+ <span class="n">model</span><span class="o">=</span><span class="n">model</span><span class="p">,</span>
+ <span class="n">output_name</span><span class="o">=</span><span class="n">Path</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">config_path</span><span class="p">)</span><span class="o">.</span><span class="n">stem</span><span class="p">,</span>
+ <span class="n">replicas</span><span class="o">=</span><span class="n">replicas</span><span class="p">,</span>
+ <span class="n">output_directory</span><span class="o">=</span><span class="nb">str</span><span class="p">(</span><span class="n">output_dir</span><span class="p">),</span>
+ <span class="n">directory</span><span class="o">=</span><span class="nb">str</span><span class="p">(</span><span class="n">sim_path</span><span class="p">)</span>
+ <span class="p">)</span></div>
+</div>
+
+
+
+<div class="viewcode-block" id="main">
+<a class="viewcode-back" href="../../api/rigidbody_models/simplearbd.html#arbdmodel.simplearbd.main">[docs]</a>
+<span class="k">def</span><span class="w"> </span><span class="nf">main</span><span class="p">():</span>
+<span class="w"> </span><span class="sd">"""</span>
+<span class="sd"> Main function to process SimpleARBD configuration file and run simulation.</span>
+<span class="sd"> """</span>
+ <span class="n">parser</span> <span class="o">=</span> <span class="n">argparse</span><span class="o">.</span><span class="n">ArgumentParser</span><span class="p">(</span><span class="n">description</span><span class="o">=</span><span class="s1">'Process SimpleARBD configuration file'</span><span class="p">)</span>
+ <span class="n">parser</span><span class="o">.</span><span class="n">add_argument</span><span class="p">(</span><span class="s1">'config_file'</span><span class="p">,</span> <span class="n">help</span><span class="o">=</span><span class="s1">'Path to SimpleARBD configuration file'</span><span class="p">)</span>
+ <span class="n">parser</span><span class="o">.</span><span class="n">add_argument</span><span class="p">(</span><span class="s1">'--setup-only'</span><span class="p">,</span> <span class="n">action</span><span class="o">=</span><span class="s1">'store_true'</span><span class="p">,</span> <span class="n">help</span><span class="o">=</span><span class="s1">'Only set up the simulation, do not run it'</span><span class="p">)</span>
+ <span class="n">args</span> <span class="o">=</span> <span class="n">parser</span><span class="o">.</span><span class="n">parse_args</span><span class="p">()</span>
+
+ <span class="c1"># Parse configuration file</span>
+ <span class="k">try</span><span class="p">:</span>
+ <span class="n">config</span> <span class="o">=</span> <span class="n">SimpleArbdConfig</span><span class="p">(</span><span class="n">args</span><span class="o">.</span><span class="n">config_file</span><span class="p">)</span>
+ <span class="k">except</span> <span class="ne">Exception</span> <span class="k">as</span> <span class="n">e</span><span class="p">:</span>
+ <span class="n">logger</span><span class="o">.</span><span class="n">error</span><span class="p">(</span><span class="sa">f</span><span class="s2">"Error parsing configuration file: </span><span class="si">{</span><span class="n">e</span><span class="si">}</span><span class="s2">"</span><span class="p">)</span>
+ <span class="k">return</span> <span class="mi">1</span>
+
+ <span class="c1"># Create model and engine</span>
+ <span class="n">model</span> <span class="o">=</span> <span class="n">config</span><span class="o">.</span><span class="n">create_model</span><span class="p">()</span>
+ <span class="n">engine</span> <span class="o">=</span> <span class="n">config</span><span class="o">.</span><span class="n">create_engine</span><span class="p">()</span>
+
+ <span class="c1"># Set up diffusible and static objects</span>
+ <span class="n">config</span><span class="o">.</span><span class="n">setup_diffusible_objects</span><span class="p">(</span><span class="n">model</span><span class="p">)</span>
+ <span class="n">config</span><span class="o">.</span><span class="n">setup_static_objects</span><span class="p">(</span><span class="n">model</span><span class="p">)</span>
+
+ <span class="k">if</span> <span class="ow">not</span> <span class="n">args</span><span class="o">.</span><span class="n">setup_only</span><span class="p">:</span>
+ <span class="c1"># Run simulation</span>
+ <span class="n">config</span><span class="o">.</span><span class="n">run_simulation</span><span class="p">(</span><span class="n">model</span><span class="p">,</span> <span class="n">engine</span><span class="p">)</span>
+ <span class="k">else</span><span class="p">:</span>
+ <span class="n">logger</span><span class="o">.</span><span class="n">info</span><span class="p">(</span><span class="s2">"Setup complete. Simulation not started (--setup-only flag used)"</span><span class="p">)</span>
+
+ <span class="k">return</span> <span class="mi">0</span></div>
+
+
+
+<span class="k">if</span> <span class="vm">__name__</span> <span class="o">==</span> <span class="s2">"__main__"</span><span class="p">:</span>
+ <span class="n">sys</span><span class="o">.</span><span class="n">exit</span><span class="p">(</span><span class="n">main</span><span class="p">())</span>
+</pre></div>
+
+ </article>
+
+
+
+
+
+
+ <footer class="prev-next-footer d-print-none">
+
+<div class="prev-next-area">
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+By ARBD Model Team
+</p>
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+</html>
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diff --git a/_build/html/_modules/arbdmodel/structure_from_pdb.html b/_build/html/_modules/arbdmodel/structure_from_pdb.html
new file mode 100644
index 0000000000000000000000000000000000000000..998109a9408d57b05874fc72cff8755c11afcecc
--- /dev/null
+++ b/_build/html/_modules/arbdmodel/structure_from_pdb.html
@@ -0,0 +1,1017 @@
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+ <article class="bd-article">
+
+ <h1>Source code for arbdmodel.structure_from_pdb</h1><div class="highlight"><pre>
+<span></span><span class="kn">import</span><span class="w"> </span><span class="nn">os</span>
+<span class="kn">import</span><span class="w"> </span><span class="nn">sys</span>
+<span class="kn">import</span><span class="w"> </span><span class="nn">subprocess</span>
+<span class="kn">import</span><span class="w"> </span><span class="nn">numpy</span><span class="w"> </span><span class="k">as</span><span class="w"> </span><span class="nn">np</span>
+<span class="kn">from</span><span class="w"> </span><span class="nn">pathlib</span><span class="w"> </span><span class="kn">import</span> <span class="n">Path</span>
+<span class="kn">from</span><span class="w"> </span><span class="nn">.logger</span><span class="w"> </span><span class="kn">import</span> <span class="n">logger</span>
+<span class="kn">from</span><span class="w"> </span><span class="nn">.sim_config</span><span class="w"> </span><span class="kn">import</span> <span class="n">SimConf</span>
+<span class="kn">from</span><span class="w"> </span><span class="nn">.engine</span><span class="w"> </span><span class="kn">import</span> <span class="n">HydroProRunner</span><span class="p">,</span> <span class="n">APBSRunner</span>
+<span class="kn">from</span><span class="w"> </span><span class="nn">.grid</span><span class="w"> </span><span class="kn">import</span> <span class="n">writeDx</span><span class="p">,</span> <span class="n">loadGrid</span><span class="p">,</span> <span class="n">Bound_grid</span>
+
+<span class="c1">#Originally SimpleARBD by Chun</span>
+
+<div class="viewcode-block" id="StructureProcessor">
+<a class="viewcode-back" href="../../api/rigidbody_models/structure_from_pdb.html#arbdmodel.structure_from_pdb.StructureProcessor">[docs]</a>
+<span class="k">class</span><span class="w"> </span><span class="nc">StructureProcessor</span><span class="p">:</span>
+<span class="w"> </span><span class="sd">"""Process molecular structure files to calculate properties and generate maps for ARBD"""</span>
+
+ <span class="k">def</span><span class="w"> </span><span class="fm">__init__</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">structure_path</span><span class="p">,</span> <span class="n">simconf</span><span class="o">=</span><span class="kc">None</span><span class="p">,</span> <span class="n">num_heavy_cluster</span><span class="o">=</span><span class="mi">3</span><span class="p">,</span>
+ <span class="n">parameters_folder</span><span class="o">=</span><span class="s2">"./parameters"</span><span class="p">,</span> <span class="n">work_dir</span><span class="o">=</span><span class="kc">None</span><span class="p">):</span>
+<span class="w"> </span><span class="sd">"""</span>
+<span class="sd"> Initialize processor with structure file</span>
+<span class="sd"> </span>
+<span class="sd"> Args:</span>
+<span class="sd"> structure_path: Path to structure file (.psf/.pdb)</span>
+<span class="sd"> simconf: SimConf object containing configuration parameters</span>
+<span class="sd"> num_heavy_cluster: Number of heavy atom clusters for VDW maps</span>
+<span class="sd"> parameters_folder: Path to parameters folder</span>
+<span class="sd"> work_dir: Working directory</span>
+<span class="sd"> """</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">structure_path</span> <span class="o">=</span> <span class="n">Path</span><span class="p">(</span><span class="n">structure_path</span><span class="p">)</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">base_name</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">structure_path</span><span class="o">.</span><span class="n">stem</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">num_heavy_cluster</span> <span class="o">=</span> <span class="n">num_heavy_cluster</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">parameters_folder</span> <span class="o">=</span> <span class="n">parameters_folder</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">work_dir</span> <span class="o">=</span> <span class="n">Path</span><span class="p">(</span><span class="n">work_dir</span><span class="p">)</span> <span class="k">if</span> <span class="n">work_dir</span> <span class="k">else</span> <span class="n">Path</span><span class="o">.</span><span class="n">cwd</span><span class="p">()</span>
+
+ <span class="k">if</span> <span class="n">simconf</span> <span class="ow">is</span> <span class="kc">None</span><span class="p">:</span>
+ <span class="kn">from</span><span class="w"> </span><span class="nn">.</span><span class="w"> </span><span class="kn">import</span> <span class="n">DefaultSimConf</span>
+ <span class="n">simconf</span> <span class="o">=</span> <span class="n">DefaultSimConf</span><span class="p">()</span>
+
+ <span class="c1"># Extract parameters from simconf</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">temperature</span> <span class="o">=</span> <span class="n">simconf</span><span class="o">.</span><span class="n">temperature</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">viscosity</span> <span class="o">=</span> <span class="n">simconf</span><span class="o">.</span><span class="n">viscosity</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">solvent_density</span> <span class="o">=</span> <span class="n">simconf</span><span class="o">.</span><span class="n">solvent_density</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">vmd_path</span> <span class="o">=</span> <span class="n">simconf</span><span class="o">.</span><span class="n">get_binary</span><span class="p">(</span><span class="s1">'vmd'</span><span class="p">)</span> <span class="ow">or</span> <span class="s1">'vmd'</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">hydro_path</span> <span class="o">=</span> <span class="n">simconf</span><span class="o">.</span><span class="n">get_binary</span><span class="p">(</span><span class="s1">'hydropro'</span><span class="p">)</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">apbs_path</span> <span class="o">=</span> <span class="n">simconf</span><span class="o">.</span><span class="n">get_binary</span><span class="p">(</span><span class="s1">'apbs'</span><span class="p">)</span> <span class="ow">or</span> <span class="s1">'apbs'</span>
+
+ <span class="c1"># Create working directory if it doesn't exist</span>
+ <span class="n">os</span><span class="o">.</span><span class="n">makedirs</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">work_dir</span><span class="p">,</span> <span class="n">exist_ok</span><span class="o">=</span><span class="kc">True</span><span class="p">)</span>
+ <span class="n">os</span><span class="o">.</span><span class="n">makedirs</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">parameters_folder</span><span class="p">,</span> <span class="n">exist_ok</span><span class="o">=</span><span class="kc">True</span><span class="p">)</span>
+
+ <span class="c1"># Attributes for results</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">mass</span> <span class="o">=</span> <span class="kc">None</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">moment_of_inertia</span> <span class="o">=</span> <span class="kc">None</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">transdamp</span> <span class="o">=</span> <span class="kc">None</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">rotdamp</span> <span class="o">=</span> <span class="kc">None</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">aligned_pdb</span> <span class="o">=</span> <span class="kc">None</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">aligned_psf</span> <span class="o">=</span> <span class="kc">None</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">charge_dx</span> <span class="o">=</span> <span class="kc">None</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">elec_dx</span> <span class="o">=</span> <span class="kc">None</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">vdw_pot_dxs</span> <span class="o">=</span> <span class="p">[]</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">vdw_den_dxs</span> <span class="o">=</span> <span class="p">[]</span>
+
+<div class="viewcode-block" id="StructureProcessor.process_structure">
+<a class="viewcode-back" href="../../api/rigidbody_models/structure_from_pdb.html#arbdmodel.structure_from_pdb.StructureProcessor.process_structure">[docs]</a>
+ <span class="k">def</span><span class="w"> </span><span class="nf">process_structure</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span>
+<span class="w"> </span><span class="sd">"""Process structure to get all properties and potential maps"""</span>
+ <span class="c1"># Step 1: Align structure</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">align_structure</span><span class="p">()</span>
+
+ <span class="c1"># Step 2: Calculate hydrodynamic properties</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">calculate_hydrodynamic_properties</span><span class="p">()</span>
+
+ <span class="c1"># Step 3: Generate charge distribution</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">generate_charge_distribution</span><span class="p">()</span>
+
+ <span class="c1"># Step 4: Generate electrostatic map</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">generate_electrostatic_map</span><span class="p">()</span>
+
+ <span class="c1"># Step 5: Generate VDW maps</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">generate_vdw_maps</span><span class="p">()</span>
+
+ <span class="c1"># Step 6: Apply Gaussian smoothing</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">apply_gaussian_smoothing</span><span class="p">()</span>
+
+ <span class="c1"># Return a dictionary of grid files for use in RigidBodyType</span>
+ <span class="k">return</span> <span class="bp">self</span><span class="o">.</span><span class="n">get_grid_files</span><span class="p">()</span></div>
+
+
+<div class="viewcode-block" id="StructureProcessor.align_structure">
+<a class="viewcode-back" href="../../api/rigidbody_models/structure_from_pdb.html#arbdmodel.structure_from_pdb.StructureProcessor.align_structure">[docs]</a>
+ <span class="k">def</span><span class="w"> </span><span class="nf">align_structure</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span>
+<span class="w"> </span><span class="sd">"""Align structure to principal axes using VMD."""</span>
+ <span class="c1"># Write alignment TCL script</span>
+ <span class="n">align_tcl</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">work_dir</span> <span class="o">/</span> <span class="s2">"align.tcl"</span>
+ <span class="k">with</span> <span class="nb">open</span><span class="p">(</span><span class="n">align_tcl</span><span class="p">,</span> <span class="s1">'w'</span><span class="p">)</span> <span class="k">as</span> <span class="n">fout</span><span class="p">:</span>
+ <span class="n">fout</span><span class="o">.</span><span class="n">write</span><span class="p">(</span><span class="s1">'''lassign $argv prefix</span>
+<span class="s1">set seltext all</span>
+
+<span class="s1">proc rotationIsRightHanded {R {tol 0.01}} {</span>
+<span class="s1"> set x [coordtrans $R {1 0 0}]</span>
+<span class="s1"> set y [coordtrans $R {0 1 0}]</span>
+<span class="s1"> set z [coordtrans $R {0 0 1}]</span>
+
+<span class="s1"> set l [veclength [vecsub $z [veccross $x $y]]]</span>
+<span class="s1"> return [expr {$l < $tol}]</span>
+<span class="s1">}</span>
+
+<span class="s1">set ID [mol new $prefix.psf]</span>
+<span class="s1">mol addfile $prefix.pdb waitfor all</span>
+<span class="s1">set all [atomselect $ID all]</span>
+<span class="s1">set sel [atomselect $ID $seltext]</span>
+
+<span class="s1">## Center system on $sel</span>
+<span class="s1">$all moveby [vecinvert [measure center $sel weight mass]]</span>
+
+<span class="s1">set continue 1</span>
+<span class="s1">while { $continue } {</span>
+<span class="s1"> ## Get current moment of inertia to determine rotation to align</span>
+<span class="s1"> lassign [measure inertia $sel moments] com principleAxes</span>
+
+<span class="s1"> ## Convert 3x3 rotation to 4x4 vmd transformation</span>
+<span class="s1"> set R [trans_from_rotate $principleAxes]</span>
+<span class="s1"> ## Fix left-handed principle axes sometimes returned by 'measure inertia'</span>
+<span class="s1"> if { ! [rotationIsRightHanded $R] } {</span>
+<span class="s1"> puts "This was true"</span>
+<span class="s1"> # puts "rotation $R is not right handed! Fixing!"</span>
+<span class="s1"> set R [transmult {{1 0 0 0} {0 1 0 0} {0 0 -1 0} {0 0 0 1}} $R]</span>
+<span class="s1"> }</span>
+
+<span class="s1"> puts "My rotation is here: $R"</span>
+<span class="s1"> puts "My second line is here: [lassign [measure inertia $sel moments] com principleAxes]"</span>
+
+<span class="s1"> ## Apply rotation and check that it worked</span>
+<span class="s1"> $all move $R</span>
+
+<span class="s1"> ## Get current moment of inertia to determine rotation to align</span>
+
+<span class="s1"> lassign [measure inertia $sel moments] com principleAxes moments</span>
+<span class="s1"> puts $principleAxes</span>
+<span class="s1"> set goodcount 0</span>
+<span class="s1"> foreach x0 {{1 0 0} {0 1 0} {0 0 1}} {</span>
+<span class="s1"> set x [coordtrans [trans_from_rotate $principleAxes] $x0]</span>
+<span class="s1"> if {[veclength [vecsub $x $x0]] < 0.01} {</span>
+<span class="s1"> incr goodcount</span>
+<span class="s1"> }</span>
+<span class="s1"> }</span>
+<span class="s1"> if { $goodcount == 3 } {</span>
+<span class="s1"> set continue 0</span>
+<span class="s1"> }</span>
+<span class="s1">}</span>
+
+<span class="s1">## Write transformation matrix to return to original conformation</span>
+<span class="s1">set ch [open $prefix.rotate-back.txt w]</span>
+<span class="s1">foreach line [trans_to_rotate [transtranspose $R]] {</span>
+<span class="s1"> puts $ch $line</span>
+<span class="s1">}</span>
+<span class="s1">close $ch</span>
+
+<span class="s1">## Write out moments of inertia</span>
+<span class="s1">set ms ""</span>
+<span class="s1">foreach m $moments { lappend ms [veclength $m] }</span>
+<span class="s1">set ch [open $prefix.inertia.txt w]</span>
+<span class="s1">puts $ch $ms</span>
+<span class="s1">close $ch</span>
+
+<span class="s1">## Write out mass</span>
+<span class="s1">set ch [open $prefix.mass.txt w]</span>
+<span class="s1">puts $ch [measure sumweights $sel weight mass]</span>
+<span class="s1">close $ch</span>
+
+<span class="s1">## Write out dimension</span>
+<span class="s1">set ch [open $prefix.dimension.dat w]</span>
+<span class="s1">set minmax [measure minmax $sel]</span>
+<span class="s1">set x_dim [expr [lindex [lindex $minmax 1] 0] - [lindex [lindex $minmax 0] 0]]</span>
+<span class="s1">set y_dim [expr [lindex [lindex $minmax 1] 1] - [lindex [lindex $minmax 0] 1]]</span>
+<span class="s1">set z_dim [expr [lindex [lindex $minmax 1] 2] - [lindex [lindex $minmax 0] 2]]</span>
+<span class="s1">puts $ch $x_dim</span>
+<span class="s1">puts $ch $y_dim</span>
+<span class="s1">puts $ch $z_dim</span>
+<span class="s1">close $ch</span>
+
+<span class="s1">## Write out psf, pdb of transformed selection</span>
+<span class="s1">$sel writepdb $prefix.aligned.pdb</span>
+<span class="s1">$sel writepsf $prefix.aligned.psf'''</span><span class="p">)</span>
+
+ <span class="c1"># Run alignment</span>
+ <span class="n">cmd</span> <span class="o">=</span> <span class="sa">f</span><span class="s2">"</span><span class="si">{</span><span class="bp">self</span><span class="o">.</span><span class="n">vmd_path</span><span class="si">}</span><span class="s2"> -dispdev text -args </span><span class="si">{</span><span class="bp">self</span><span class="o">.</span><span class="n">base_name</span><span class="si">}</span><span class="s2"> < </span><span class="si">{</span><span class="n">align_tcl</span><span class="si">}</span><span class="s2">"</span>
+ <span class="n">subprocess</span><span class="o">.</span><span class="n">run</span><span class="p">(</span><span class="n">cmd</span><span class="p">,</span> <span class="n">shell</span><span class="o">=</span><span class="kc">True</span><span class="p">,</span> <span class="n">check</span><span class="o">=</span><span class="kc">True</span><span class="p">)</span>
+
+ <span class="c1"># Verify alignment succeeded</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">aligned_pdb</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">work_dir</span> <span class="o">/</span> <span class="sa">f</span><span class="s2">"</span><span class="si">{</span><span class="bp">self</span><span class="o">.</span><span class="n">base_name</span><span class="si">}</span><span class="s2">.aligned.pdb"</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">aligned_psf</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">work_dir</span> <span class="o">/</span> <span class="sa">f</span><span class="s2">"</span><span class="si">{</span><span class="bp">self</span><span class="o">.</span><span class="n">base_name</span><span class="si">}</span><span class="s2">.aligned.psf"</span>
+
+ <span class="k">if</span> <span class="ow">not</span> <span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">aligned_pdb</span><span class="o">.</span><span class="n">exists</span><span class="p">()</span> <span class="ow">and</span> <span class="bp">self</span><span class="o">.</span><span class="n">aligned_psf</span><span class="o">.</span><span class="n">exists</span><span class="p">()):</span>
+ <span class="k">raise</span> <span class="ne">RuntimeError</span><span class="p">(</span><span class="sa">f</span><span class="s2">"Alignment failed for </span><span class="si">{</span><span class="bp">self</span><span class="o">.</span><span class="n">base_name</span><span class="si">}</span><span class="s2">"</span><span class="p">)</span>
+
+ <span class="c1"># Read mass and inertia</span>
+ <span class="n">mass_file</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">work_dir</span> <span class="o">/</span> <span class="sa">f</span><span class="s2">"</span><span class="si">{</span><span class="bp">self</span><span class="o">.</span><span class="n">base_name</span><span class="si">}</span><span class="s2">.mass.txt"</span>
+ <span class="n">inertia_file</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">work_dir</span> <span class="o">/</span> <span class="sa">f</span><span class="s2">"</span><span class="si">{</span><span class="bp">self</span><span class="o">.</span><span class="n">base_name</span><span class="si">}</span><span class="s2">.inertia.txt"</span>
+
+ <span class="k">if</span> <span class="ow">not</span> <span class="n">mass_file</span><span class="o">.</span><span class="n">exists</span><span class="p">()</span> <span class="ow">or</span> <span class="ow">not</span> <span class="n">inertia_file</span><span class="o">.</span><span class="n">exists</span><span class="p">():</span>
+ <span class="k">raise</span> <span class="ne">FileNotFoundError</span><span class="p">(</span><span class="sa">f</span><span class="s2">"Mass or inertia file not found after alignment"</span><span class="p">)</span>
+
+ <span class="k">with</span> <span class="nb">open</span><span class="p">(</span><span class="n">mass_file</span><span class="p">)</span> <span class="k">as</span> <span class="n">f</span><span class="p">:</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">mass</span> <span class="o">=</span> <span class="nb">float</span><span class="p">(</span><span class="n">f</span><span class="o">.</span><span class="n">readline</span><span class="p">()</span><span class="o">.</span><span class="n">strip</span><span class="p">())</span>
+
+ <span class="k">with</span> <span class="nb">open</span><span class="p">(</span><span class="n">inertia_file</span><span class="p">)</span> <span class="k">as</span> <span class="n">f</span><span class="p">:</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">moment_of_inertia</span> <span class="o">=</span> <span class="p">[</span><span class="nb">float</span><span class="p">(</span><span class="n">x</span><span class="p">)</span> <span class="k">for</span> <span class="n">x</span> <span class="ow">in</span> <span class="n">f</span><span class="o">.</span><span class="n">readline</span><span class="p">()</span><span class="o">.</span><span class="n">strip</span><span class="p">()</span><span class="o">.</span><span class="n">split</span><span class="p">()]</span>
+
+ <span class="n">logger</span><span class="o">.</span><span class="n">info</span><span class="p">(</span><span class="sa">f</span><span class="s2">"Structure aligned: Mass = </span><span class="si">{</span><span class="bp">self</span><span class="o">.</span><span class="n">mass</span><span class="si">}</span><span class="s2">, Inertia = </span><span class="si">{</span><span class="bp">self</span><span class="o">.</span><span class="n">moment_of_inertia</span><span class="si">}</span><span class="s2">"</span><span class="p">)</span></div>
+
+
+<div class="viewcode-block" id="StructureProcessor.calculate_hydrodynamic_properties">
+<a class="viewcode-back" href="../../api/rigidbody_models/structure_from_pdb.html#arbdmodel.structure_from_pdb.StructureProcessor.calculate_hydrodynamic_properties">[docs]</a>
+ <span class="k">def</span><span class="w"> </span><span class="nf">calculate_hydrodynamic_properties</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span>
+<span class="w"> </span><span class="sd">"""Calculate hydrodynamic properties using HydroPro."""</span>
+ <span class="k">if</span> <span class="ow">not</span> <span class="bp">self</span><span class="o">.</span><span class="n">hydro_path</span><span class="p">:</span>
+ <span class="n">logger</span><span class="o">.</span><span class="n">warning</span><span class="p">(</span><span class="s2">"HydroPro executable not provided, using default values"</span><span class="p">)</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">transdamp</span> <span class="o">=</span> <span class="p">[</span><span class="mf">1.0</span><span class="p">,</span> <span class="mf">1.0</span><span class="p">,</span> <span class="mf">1.0</span><span class="p">]</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">rotdamp</span> <span class="o">=</span> <span class="p">[</span><span class="mf">1.0</span><span class="p">,</span> <span class="mf">1.0</span><span class="p">,</span> <span class="mf">1.0</span><span class="p">]</span>
+ <span class="k">return</span>
+
+ <span class="c1"># Initialize HydroPro runner</span>
+ <span class="n">hydro_runner</span> <span class="o">=</span> <span class="n">HydroProRunner</span><span class="p">(</span>
+ <span class="n">mass</span><span class="o">=</span><span class="bp">self</span><span class="o">.</span><span class="n">mass</span><span class="p">,</span>
+ <span class="n">binary_path</span><span class="o">=</span><span class="bp">self</span><span class="o">.</span><span class="n">hydro_path</span><span class="p">,</span>
+ <span class="n">temperature</span><span class="o">=</span><span class="bp">self</span><span class="o">.</span><span class="n">temperature</span><span class="p">,</span>
+ <span class="n">viscosity</span><span class="o">=</span><span class="bp">self</span><span class="o">.</span><span class="n">viscosity</span><span class="p">,</span>
+ <span class="n">solvent_density</span><span class="o">=</span><span class="bp">self</span><span class="o">.</span><span class="n">solvent_density</span><span class="p">,</span>
+ <span class="n">structure_name</span><span class="o">=</span><span class="bp">self</span><span class="o">.</span><span class="n">base_name</span>
+ <span class="p">)</span>
+
+ <span class="c1"># Write config</span>
+ <span class="n">hydro_runner</span><span class="o">.</span><span class="n">write_config</span><span class="p">(</span><span class="n">output_path</span><span class="o">=</span><span class="bp">self</span><span class="o">.</span><span class="n">work_dir</span> <span class="o">/</span> <span class="s2">"hydropro.dat"</span><span class="p">)</span>
+
+ <span class="c1"># Prepare for HydroPro run</span>
+ <span class="n">hydro_pdb</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">work_dir</span> <span class="o">/</span> <span class="s2">"hydro.pdb"</span>
+ <span class="k">try</span><span class="p">:</span>
+ <span class="c1"># Create symlink to aligned PDB</span>
+ <span class="k">if</span> <span class="n">hydro_pdb</span><span class="o">.</span><span class="n">exists</span><span class="p">():</span>
+ <span class="n">os</span><span class="o">.</span><span class="n">unlink</span><span class="p">(</span><span class="n">hydro_pdb</span><span class="p">)</span>
+ <span class="n">os</span><span class="o">.</span><span class="n">symlink</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">aligned_pdb</span><span class="p">,</span> <span class="n">hydro_pdb</span><span class="p">)</span>
+
+ <span class="c1"># Run HydroPro</span>
+ <span class="n">cmd</span> <span class="o">=</span> <span class="sa">f</span><span class="s2">"cd </span><span class="si">{</span><span class="bp">self</span><span class="o">.</span><span class="n">work_dir</span><span class="si">}</span><span class="s2"> && </span><span class="si">{</span><span class="bp">self</span><span class="o">.</span><span class="n">hydro_path</span><span class="si">}</span><span class="s2">"</span>
+ <span class="n">subprocess</span><span class="o">.</span><span class="n">run</span><span class="p">(</span><span class="n">cmd</span><span class="p">,</span> <span class="n">shell</span><span class="o">=</span><span class="kc">True</span><span class="p">,</span> <span class="n">check</span><span class="o">=</span><span class="kc">True</span><span class="p">)</span>
+
+ <span class="c1"># Parse results - handle possible filename truncation in HydroPro</span>
+ <span class="n">results_file</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">work_dir</span> <span class="o">/</span> <span class="sa">f</span><span class="s2">"</span><span class="si">{</span><span class="bp">self</span><span class="o">.</span><span class="n">base_name</span><span class="si">}</span><span class="s2">-res.txt"</span>
+ <span class="k">if</span> <span class="ow">not</span> <span class="n">results_file</span><span class="o">.</span><span class="n">exists</span><span class="p">()</span> <span class="ow">and</span> <span class="nb">len</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">base_name</span><span class="p">)</span> <span class="o">></span> <span class="mi">20</span><span class="p">:</span>
+ <span class="n">short_name</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">base_name</span><span class="p">[:</span><span class="mi">20</span><span class="p">]</span>
+ <span class="n">results_file</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">work_dir</span> <span class="o">/</span> <span class="sa">f</span><span class="s2">"</span><span class="si">{</span><span class="n">short_name</span><span class="si">}</span><span class="s2">-res.txt"</span>
+
+ <span class="k">if</span> <span class="ow">not</span> <span class="n">results_file</span><span class="o">.</span><span class="n">exists</span><span class="p">():</span>
+ <span class="n">logger</span><span class="o">.</span><span class="n">warning</span><span class="p">(</span><span class="sa">f</span><span class="s2">"HydroPro results file not found, checking for any -res.txt file"</span><span class="p">)</span>
+ <span class="n">results_files</span> <span class="o">=</span> <span class="nb">list</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">work_dir</span><span class="o">.</span><span class="n">glob</span><span class="p">(</span><span class="s2">"*-res.txt"</span><span class="p">))</span>
+ <span class="k">if</span> <span class="n">results_files</span><span class="p">:</span>
+ <span class="n">results_file</span> <span class="o">=</span> <span class="n">results_files</span><span class="p">[</span><span class="mi">0</span><span class="p">]</span>
+ <span class="k">else</span><span class="p">:</span>
+ <span class="k">raise</span> <span class="ne">FileNotFoundError</span><span class="p">(</span><span class="s2">"No HydroPro results file found"</span><span class="p">)</span>
+
+ <span class="c1"># Parse damping coefficients</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">transdamp</span><span class="p">,</span> <span class="bp">self</span><span class="o">.</span><span class="n">rotdamp</span> <span class="o">=</span> <span class="n">hydro_runner</span><span class="o">.</span><span class="n">parse_output</span><span class="p">(</span><span class="n">results_file</span><span class="p">)</span>
+
+ <span class="c1"># Write to a damping-coeffs.txt file for reference</span>
+ <span class="n">damping_file</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">work_dir</span> <span class="o">/</span> <span class="sa">f</span><span class="s2">"</span><span class="si">{</span><span class="bp">self</span><span class="o">.</span><span class="n">base_name</span><span class="si">}</span><span class="s2">.damping-coeffs.txt"</span>
+ <span class="k">with</span> <span class="nb">open</span><span class="p">(</span><span class="n">damping_file</span><span class="p">,</span> <span class="s1">'w'</span><span class="p">)</span> <span class="k">as</span> <span class="n">f</span><span class="p">:</span>
+ <span class="n">f</span><span class="o">.</span><span class="n">write</span><span class="p">(</span><span class="sa">f</span><span class="s2">"</span><span class="si">{</span><span class="bp">self</span><span class="o">.</span><span class="n">transdamp</span><span class="p">[</span><span class="mi">0</span><span class="p">]</span><span class="si">}</span><span class="s2"> </span><span class="si">{</span><span class="bp">self</span><span class="o">.</span><span class="n">transdamp</span><span class="p">[</span><span class="mi">1</span><span class="p">]</span><span class="si">}</span><span class="s2"> </span><span class="si">{</span><span class="bp">self</span><span class="o">.</span><span class="n">transdamp</span><span class="p">[</span><span class="mi">2</span><span class="p">]</span><span class="si">}</span><span class="se">\n</span><span class="s2">"</span><span class="p">)</span>
+ <span class="n">f</span><span class="o">.</span><span class="n">write</span><span class="p">(</span><span class="sa">f</span><span class="s2">"</span><span class="si">{</span><span class="bp">self</span><span class="o">.</span><span class="n">rotdamp</span><span class="p">[</span><span class="mi">0</span><span class="p">]</span><span class="si">}</span><span class="s2"> </span><span class="si">{</span><span class="bp">self</span><span class="o">.</span><span class="n">rotdamp</span><span class="p">[</span><span class="mi">1</span><span class="p">]</span><span class="si">}</span><span class="s2"> </span><span class="si">{</span><span class="bp">self</span><span class="o">.</span><span class="n">rotdamp</span><span class="p">[</span><span class="mi">2</span><span class="p">]</span><span class="si">}</span><span class="se">\n</span><span class="s2">"</span><span class="p">)</span>
+
+ <span class="n">logger</span><span class="o">.</span><span class="n">info</span><span class="p">(</span><span class="sa">f</span><span class="s2">"Hydrodynamic properties: trans_damp=</span><span class="si">{</span><span class="bp">self</span><span class="o">.</span><span class="n">transdamp</span><span class="si">}</span><span class="s2">, rot_damp=</span><span class="si">{</span><span class="bp">self</span><span class="o">.</span><span class="n">rotdamp</span><span class="si">}</span><span class="s2">"</span><span class="p">)</span>
+
+ <span class="k">except</span> <span class="ne">Exception</span> <span class="k">as</span> <span class="n">e</span><span class="p">:</span>
+ <span class="n">logger</span><span class="o">.</span><span class="n">error</span><span class="p">(</span><span class="sa">f</span><span class="s2">"Error calculating hydrodynamic properties: </span><span class="si">{</span><span class="n">e</span><span class="si">}</span><span class="s2">"</span><span class="p">)</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">transdamp</span> <span class="o">=</span> <span class="p">[</span><span class="mf">1.0</span><span class="p">,</span> <span class="mf">1.0</span><span class="p">,</span> <span class="mf">1.0</span><span class="p">]</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">rotdamp</span> <span class="o">=</span> <span class="p">[</span><span class="mf">1.0</span><span class="p">,</span> <span class="mf">1.0</span><span class="p">,</span> <span class="mf">1.0</span><span class="p">]</span>
+ <span class="k">finally</span><span class="p">:</span>
+ <span class="c1"># Clean up</span>
+ <span class="k">if</span> <span class="n">hydro_pdb</span><span class="o">.</span><span class="n">exists</span><span class="p">():</span>
+ <span class="n">os</span><span class="o">.</span><span class="n">unlink</span><span class="p">(</span><span class="n">hydro_pdb</span><span class="p">)</span></div>
+
+
+<div class="viewcode-block" id="StructureProcessor.generate_charge_distribution">
+<a class="viewcode-back" href="../../api/rigidbody_models/structure_from_pdb.html#arbdmodel.structure_from_pdb.StructureProcessor.generate_charge_distribution">[docs]</a>
+ <span class="k">def</span><span class="w"> </span><span class="nf">generate_charge_distribution</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">resolution</span><span class="o">=</span><span class="mf">2.0</span><span class="p">):</span>
+<span class="w"> </span><span class="sd">"""Generate charge distribution using VMD."""</span>
+ <span class="n">aligned_name</span> <span class="o">=</span> <span class="sa">f</span><span class="s2">"</span><span class="si">{</span><span class="bp">self</span><span class="o">.</span><span class="n">base_name</span><span class="si">}</span><span class="s2">.aligned"</span>
+
+ <span class="c1"># Create TCL script for VMD</span>
+ <span class="n">charge_tcl</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">work_dir</span> <span class="o">/</span> <span class="s2">"charge.tcl"</span>
+ <span class="k">with</span> <span class="nb">open</span><span class="p">(</span><span class="n">charge_tcl</span><span class="p">,</span> <span class="s1">'w'</span><span class="p">)</span> <span class="k">as</span> <span class="n">f</span><span class="p">:</span>
+ <span class="n">f</span><span class="o">.</span><span class="n">write</span><span class="p">(</span><span class="sa">f</span><span class="s1">'''lassign $argv prefix</span>
+<span class="s1">set resolution </span><span class="si">{</span><span class="n">resolution</span><span class="si">}</span>
+<span class="s1">set ID [mol new $prefix.psf]</span>
+<span class="s1">mol addfile $prefix.pdb</span>
+<span class="s1">set all [atomselect $ID all]</span>
+<span class="s1">set netCharge [measure sumweights $all weight charge]</span>
+
+<span class="s1">## Write out charge density</span>
+<span class="s1">volmap density $all -o $prefix.chargeDensity.dx -res $resolution -weight charge</span>
+<span class="s1">## Write out pqr for subsequent EM calculation</span>
+<span class="s1">$all writepqr $prefix.pqr</span>
+
+<span class="s1">set ch [open $prefix.netCharge.dat w]</span>
+<span class="s1">puts $ch $netCharge</span>
+<span class="s1">close $ch</span>
+
+<span class="s1">set ch [open $prefix.dimension.dat w]</span>
+<span class="s1">set minmax [measure minmax $all]</span>
+<span class="s1">set x_dim [expr [lindex [lindex $minmax 1] 0] - [lindex [lindex $minmax 0] 0]]</span>
+<span class="s1">set y_dim [expr [lindex [lindex $minmax 1] 1] - [lindex [lindex $minmax 0] 1]]</span>
+<span class="s1">set z_dim [expr [lindex [lindex $minmax 1] 2] - [lindex [lindex $minmax 0] 2]]</span>
+<span class="s1">puts $ch $x_dim</span>
+<span class="s1">puts $ch $y_dim</span>
+<span class="s1">puts $ch $z_dim</span>
+<span class="s1">close $ch'''</span><span class="p">)</span>
+
+ <span class="c1"># Run VMD to generate charge density</span>
+ <span class="n">cmd</span> <span class="o">=</span> <span class="sa">f</span><span class="s2">"</span><span class="si">{</span><span class="bp">self</span><span class="o">.</span><span class="n">vmd_path</span><span class="si">}</span><span class="s2"> -dispdev text -args </span><span class="si">{</span><span class="n">aligned_name</span><span class="si">}</span><span class="s2"> < </span><span class="si">{</span><span class="n">charge_tcl</span><span class="si">}</span><span class="s2">"</span>
+ <span class="n">subprocess</span><span class="o">.</span><span class="n">run</span><span class="p">(</span><span class="n">cmd</span><span class="p">,</span> <span class="n">shell</span><span class="o">=</span><span class="kc">True</span><span class="p">,</span> <span class="n">check</span><span class="o">=</span><span class="kc">True</span><span class="p">)</span>
+
+ <span class="c1"># Fix charge distribution</span>
+ <span class="n">charge_dx</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">work_dir</span> <span class="o">/</span> <span class="sa">f</span><span class="s2">"</span><span class="si">{</span><span class="n">aligned_name</span><span class="si">}</span><span class="s2">.chargeDensity.dx"</span>
+ <span class="n">charge_out</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">work_dir</span> <span class="o">/</span> <span class="sa">f</span><span class="s2">"</span><span class="si">{</span><span class="n">aligned_name</span><span class="si">}</span><span class="s2">.charge.dx"</span>
+ <span class="n">netcharge_file</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">work_dir</span> <span class="o">/</span> <span class="sa">f</span><span class="s2">"</span><span class="si">{</span><span class="n">aligned_name</span><span class="si">}</span><span class="s2">.netCharge.dat"</span>
+
+ <span class="k">if</span> <span class="ow">not</span> <span class="n">charge_dx</span><span class="o">.</span><span class="n">exists</span><span class="p">():</span>
+ <span class="k">raise</span> <span class="ne">FileNotFoundError</span><span class="p">(</span><span class="sa">f</span><span class="s2">"Charge density file not found: </span><span class="si">{</span><span class="n">charge_dx</span><span class="si">}</span><span class="s2">"</span><span class="p">)</span>
+
+ <span class="c1"># Fix charge distribution - fix scientific notation in file</span>
+ <span class="n">temp_file1</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">work_dir</span> <span class="o">/</span> <span class="s2">"temp0.dx"</span>
+ <span class="n">temp_file2</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">work_dir</span> <span class="o">/</span> <span class="s2">"temp1.dx"</span>
+
+ <span class="c1"># Handle numbers without decimal point in scientific notation</span>
+ <span class="n">cmd_in</span> <span class="o">=</span> <span class="sa">f</span><span class="s2">"sed -r 's/^([0-9]+)e/</span><span class="se">\\</span><span class="s2">1.0e/g; s/ ([0-9]+)e/ </span><span class="se">\\</span><span class="s2">1.0e/g' </span><span class="si">{</span><span class="nb">str</span><span class="p">(</span><span class="n">charge_dx</span><span class="p">)</span><span class="si">}</span><span class="s2"> > </span><span class="si">{</span><span class="n">temp_file1</span><span class="si">}</span><span class="s2">"</span>
+ <span class="n">os</span><span class="o">.</span><span class="n">system</span><span class="p">(</span><span class="n">cmd_in</span><span class="p">)</span>
+ <span class="n">cmd_in</span> <span class="o">=</span> <span class="sa">f</span><span class="s2">"sed -r 's/^(-[0-9]+)e/</span><span class="se">\\</span><span class="s2">1.0e/g; s/ (-[0-9]+)e/ </span><span class="se">\\</span><span class="s2">1.0e/g' </span><span class="si">{</span><span class="n">temp_file1</span><span class="si">}</span><span class="s2"> > </span><span class="si">{</span><span class="n">temp_file2</span><span class="si">}</span><span class="s2">"</span>
+ <span class="n">os</span><span class="o">.</span><span class="n">system</span><span class="p">(</span><span class="n">cmd_in</span><span class="p">)</span>
+
+ <span class="c1"># Read net charge</span>
+ <span class="k">with</span> <span class="nb">open</span><span class="p">(</span><span class="n">netcharge_file</span><span class="p">,</span> <span class="s1">'r'</span><span class="p">)</span> <span class="k">as</span> <span class="n">fin</span><span class="p">:</span>
+ <span class="n">netCharge</span> <span class="o">=</span> <span class="nb">float</span><span class="p">(</span><span class="n">fin</span><span class="o">.</span><span class="n">readline</span><span class="p">()</span><span class="o">.</span><span class="n">strip</span><span class="p">())</span>
+
+ <span class="c1"># Load grid data</span>
+ <span class="n">grid</span><span class="p">,</span> <span class="n">origin</span><span class="p">,</span> <span class="n">delta</span> <span class="o">=</span> <span class="n">loadGrid</span><span class="p">(</span><span class="nb">str</span><span class="p">(</span><span class="n">temp_file2</span><span class="p">))</span>
+ <span class="n">grid</span> <span class="o">=</span> <span class="n">grid</span> <span class="o">*</span> <span class="n">resolution</span><span class="o">**</span><span class="mi">3</span>
+
+ <span class="c1"># Fix charge to match net charge</span>
+ <span class="n">ids</span> <span class="o">=</span> <span class="n">np</span><span class="o">.</span><span class="n">where</span><span class="p">(</span><span class="n">np</span><span class="o">.</span><span class="n">abs</span><span class="p">(</span><span class="n">grid</span><span class="p">[:])</span> <span class="o">></span> <span class="mf">0.01</span><span class="p">)</span>
+ <span class="n">numPoints</span> <span class="o">=</span> <span class="n">np</span><span class="o">.</span><span class="n">size</span><span class="p">(</span><span class="n">ids</span><span class="p">)</span>
+ <span class="k">while</span> <span class="n">np</span><span class="o">.</span><span class="n">abs</span><span class="p">(</span><span class="n">np</span><span class="o">.</span><span class="n">sum</span><span class="p">(</span><span class="n">grid</span><span class="p">)</span> <span class="o">-</span> <span class="n">netCharge</span><span class="p">)</span> <span class="o">></span> <span class="mf">0.0001</span> <span class="ow">and</span> <span class="n">numPoints</span> <span class="o">></span> <span class="mi">0</span><span class="p">:</span>
+ <span class="n">grid</span><span class="p">[</span><span class="n">ids</span><span class="p">]</span> <span class="o">=</span> <span class="n">grid</span><span class="p">[</span><span class="n">ids</span><span class="p">]</span> <span class="o">+</span> <span class="p">(</span><span class="n">netCharge</span> <span class="o">-</span> <span class="n">np</span><span class="o">.</span><span class="n">sum</span><span class="p">(</span><span class="n">grid</span><span class="p">))</span> <span class="o">/</span> <span class="n">numPoints</span>
+
+ <span class="c1"># Write output</span>
+ <span class="n">writeDx</span><span class="p">(</span><span class="nb">str</span><span class="p">(</span><span class="n">charge_out</span><span class="p">),</span> <span class="n">grid</span><span class="p">,</span> <span class="n">origin</span><span class="p">,</span> <span class="p">[</span><span class="n">delta</span><span class="p">,</span> <span class="n">delta</span><span class="p">,</span> <span class="n">delta</span><span class="p">])</span>
+
+ <span class="c1"># Clean up temporary files</span>
+ <span class="k">try</span><span class="p">:</span>
+ <span class="n">os</span><span class="o">.</span><span class="n">remove</span><span class="p">(</span><span class="n">temp_file1</span><span class="p">)</span>
+ <span class="n">os</span><span class="o">.</span><span class="n">remove</span><span class="p">(</span><span class="n">temp_file2</span><span class="p">)</span>
+ <span class="k">except</span> <span class="ne">OSError</span><span class="p">:</span>
+ <span class="k">pass</span>
+
+ <span class="bp">self</span><span class="o">.</span><span class="n">charge_dx</span> <span class="o">=</span> <span class="n">charge_out</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">charge_density_dx</span> <span class="o">=</span> <span class="n">charge_dx</span>
+
+ <span class="n">logger</span><span class="o">.</span><span class="n">info</span><span class="p">(</span><span class="sa">f</span><span class="s2">"Charge distribution generated with net charge: </span><span class="si">{</span><span class="n">np</span><span class="o">.</span><span class="n">sum</span><span class="p">(</span><span class="n">grid</span><span class="p">)</span><span class="si">:</span><span class="s2">.6f</span><span class="si">}</span><span class="s2">"</span><span class="p">)</span></div>
+
+
+<div class="viewcode-block" id="StructureProcessor.generate_electrostatic_map">
+<a class="viewcode-back" href="../../api/rigidbody_models/structure_from_pdb.html#arbdmodel.structure_from_pdb.StructureProcessor.generate_electrostatic_map">[docs]</a>
+ <span class="k">def</span><span class="w"> </span><span class="nf">generate_electrostatic_map</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">buffer</span><span class="o">=</span><span class="mi">50</span><span class="p">):</span>
+<span class="w"> </span><span class="sd">"""Generate electrostatic potential map using APBS."""</span>
+ <span class="k">if</span> <span class="ow">not</span> <span class="bp">self</span><span class="o">.</span><span class="n">apbs_path</span><span class="p">:</span>
+ <span class="n">logger</span><span class="o">.</span><span class="n">warning</span><span class="p">(</span><span class="s2">"APBS executable not provided, skipping electrostatic calculations"</span><span class="p">)</span>
+ <span class="k">return</span>
+
+ <span class="n">aligned_name</span> <span class="o">=</span> <span class="sa">f</span><span class="s2">"</span><span class="si">{</span><span class="bp">self</span><span class="o">.</span><span class="n">base_name</span><span class="si">}</span><span class="s2">.aligned"</span>
+
+ <span class="c1"># Read system dimensions</span>
+ <span class="n">dimension_file</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">work_dir</span> <span class="o">/</span> <span class="sa">f</span><span class="s2">"</span><span class="si">{</span><span class="n">aligned_name</span><span class="si">}</span><span class="s2">.dimension.dat"</span>
+ <span class="k">if</span> <span class="ow">not</span> <span class="n">dimension_file</span><span class="o">.</span><span class="n">exists</span><span class="p">():</span>
+ <span class="k">raise</span> <span class="ne">FileNotFoundError</span><span class="p">(</span><span class="sa">f</span><span class="s2">"Dimension file not found: </span><span class="si">{</span><span class="n">dimension_file</span><span class="si">}</span><span class="s2">"</span><span class="p">)</span>
+
+ <span class="k">with</span> <span class="nb">open</span><span class="p">(</span><span class="n">dimension_file</span><span class="p">,</span> <span class="s1">'r'</span><span class="p">)</span> <span class="k">as</span> <span class="n">f</span><span class="p">:</span>
+ <span class="n">dimensions</span> <span class="o">=</span> <span class="p">[</span><span class="nb">float</span><span class="p">(</span><span class="n">line</span><span class="o">.</span><span class="n">strip</span><span class="p">())</span> <span class="k">for</span> <span class="n">line</span> <span class="ow">in</span> <span class="n">f</span><span class="o">.</span><span class="n">readlines</span><span class="p">()]</span>
+
+ <span class="c1"># Initialize APBS runner</span>
+ <span class="n">apbs_runner</span> <span class="o">=</span> <span class="n">APBSRunner</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">apbs_path</span><span class="p">)</span>
+
+ <span class="c1"># Write APBS configuration using the runner</span>
+ <span class="n">apbs_runner</span><span class="o">.</span><span class="n">write_config</span><span class="p">(</span>
+ <span class="n">structure_name</span><span class="o">=</span><span class="n">aligned_name</span><span class="p">,</span>
+ <span class="n">xyz_dims</span><span class="o">=</span><span class="n">dimensions</span><span class="p">,</span>
+ <span class="n">salt_conc</span><span class="o">=</span><span class="mf">0.15</span><span class="p">,</span>
+ <span class="n">temperature</span><span class="o">=</span><span class="bp">self</span><span class="o">.</span><span class="n">temperature</span><span class="p">,</span>
+ <span class="n">buffer</span><span class="o">=</span><span class="n">buffer</span>
+ <span class="p">)</span>
+
+ <span class="c1"># Run APBS</span>
+ <span class="n">cmd</span> <span class="o">=</span> <span class="sa">f</span><span class="s2">"cd </span><span class="si">{</span><span class="bp">self</span><span class="o">.</span><span class="n">work_dir</span><span class="si">}</span><span class="s2"> && </span><span class="si">{</span><span class="bp">self</span><span class="o">.</span><span class="n">apbs_path</span><span class="si">}</span><span class="s2"> </span><span class="si">{</span><span class="n">aligned_name</span><span class="si">}</span><span class="s2">.apbs"</span>
+ <span class="n">subprocess</span><span class="o">.</span><span class="n">run</span><span class="p">(</span><span class="n">cmd</span><span class="p">,</span> <span class="n">shell</span><span class="o">=</span><span class="kc">True</span><span class="p">,</span> <span class="n">check</span><span class="o">=</span><span class="kc">True</span><span class="p">)</span>
+
+ <span class="c1"># Bound the potential values</span>
+ <span class="n">tmp_file</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">work_dir</span> <span class="o">/</span> <span class="sa">f</span><span class="s2">"</span><span class="si">{</span><span class="n">aligned_name</span><span class="si">}</span><span class="s2">.elec.tmp.dx"</span>
+ <span class="n">out_file</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">work_dir</span> <span class="o">/</span> <span class="sa">f</span><span class="s2">"</span><span class="si">{</span><span class="n">aligned_name</span><span class="si">}</span><span class="s2">.elec.dx"</span>
+ <span class="n">Bound_grid</span><span class="p">(</span>
+ <span class="n">inFile</span><span class="o">=</span><span class="n">tmp_file</span><span class="p">,</span>
+ <span class="n">outFile</span><span class="o">=</span><span class="n">out_file</span><span class="p">,</span>
+ <span class="n">lowerBound</span><span class="o">=-</span><span class="mi">20</span><span class="p">,</span>
+ <span class="n">upperBound</span><span class="o">=</span><span class="mi">20</span>
+ <span class="p">)</span>
+
+ <span class="bp">self</span><span class="o">.</span><span class="n">elec_dx</span> <span class="o">=</span> <span class="n">out_file</span>
+ <span class="n">logger</span><span class="o">.</span><span class="n">info</span><span class="p">(</span><span class="sa">f</span><span class="s2">"Electrostatic map generated for </span><span class="si">{</span><span class="n">aligned_name</span><span class="si">}</span><span class="s2">"</span><span class="p">)</span></div>
+
+
+<div class="viewcode-block" id="StructureProcessor.generate_vdw_maps">
+<a class="viewcode-back" href="../../api/rigidbody_models/structure_from_pdb.html#arbdmodel.structure_from_pdb.StructureProcessor.generate_vdw_maps">[docs]</a>
+ <span class="k">def</span><span class="w"> </span><span class="nf">generate_vdw_maps</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">potResolution</span><span class="o">=</span><span class="mi">1</span><span class="p">,</span> <span class="n">denResolution</span><span class="o">=</span><span class="mi">2</span><span class="p">):</span>
+<span class="w"> </span><span class="sd">"""Generate VDW maps using VMD."""</span>
+ <span class="n">aligned_name</span> <span class="o">=</span> <span class="sa">f</span><span class="s2">"</span><span class="si">{</span><span class="bp">self</span><span class="o">.</span><span class="n">base_name</span><span class="si">}</span><span class="s2">.aligned"</span>
+
+ <span class="c1"># Create VDW TCL script</span>
+ <span class="n">vdw_tcl</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">work_dir</span> <span class="o">/</span> <span class="s2">"vdw.tcl"</span>
+ <span class="k">with</span> <span class="nb">open</span><span class="p">(</span><span class="n">vdw_tcl</span><span class="p">,</span> <span class="s1">'w'</span><span class="p">)</span> <span class="k">as</span> <span class="n">f</span><span class="p">:</span>
+ <span class="n">f</span><span class="o">.</span><span class="n">write</span><span class="p">(</span><span class="sa">f</span><span class="s1">'''lassign $argv prefix</span>
+<span class="s1">package require inorganicbuilder</span>
+<span class="s1">set id [mol new $prefix.psf]</span>
+<span class="s1">mol addfile $prefix.pdb</span>
+
+<span class="s1"># Create temp folders</span>
+<span class="s1">set params_folder "</span><span class="si">{</span><span class="bp">self</span><span class="o">.</span><span class="n">parameters_folder</span><span class="si">}</span><span class="s1">"</span>
+<span class="s1">if </span><span class="se">{{</span><span class="s1">![file exists $params_folder]</span><span class="se">}}</span><span class="s1"> </span><span class="se">{{</span>
+<span class="s1"> file mkdir $params_folder</span>
+<span class="se">}}</span>
+
+<span class="s1"># Load parameters</span>
+<span class="s1">global env</span>
+<span class="s1">set statefilename "$params_folder/vdw.spt"</span>
+<span class="s1">set statefile [open $statefilename w]</span>
+<span class="s1">set psffile $env(INORGANICBUILDER_BASEDIR)/spt/parameters/prot/prot-masses.spt</span>
+<span class="s1">puts "loading parameters from $psffile"</span>
+<span class="s1">source $psffile</span>
+<span class="s1">close $statefile</span>
+<span class="s1"># Define selection</span>
+<span class="s1">set sel [atomselect top all]</span>
+
+<span class="s1"># Loop over heavy atom clusters</span>
+<span class="s1">for </span><span class="se">{{</span><span class="s1">set i 0</span><span class="se">}}</span><span class="s1"> </span><span class="se">{{</span><span class="s1">$i <= </span><span class="si">{</span><span class="bp">self</span><span class="o">.</span><span class="n">num_heavy_cluster</span><span class="si">}</span><span class="se">}}</span><span class="s1"> </span><span class="se">{{</span><span class="s1">incr i</span><span class="se">}}</span><span class="s1"> </span><span class="se">{{</span>
+<span class="s1"> # Get atom types</span>
+<span class="s1"> set typemap [dict create]</span>
+<span class="s1"> set typemap_reverse [dict create]</span>
+<span class="s1"> set types [lsort -unique [$sel get type]]</span>
+<span class="s1"> foreach t $types </span><span class="se">{{</span>
+<span class="s1"> set key [subst $t]</span>
+<span class="s1"> set vdw_type [subst $t]</span>
+<span class="s1"> if </span><span class="se">{{</span><span class="s1">![info exists VDW_TYPEMAP($key)]</span><span class="se">}}</span><span class="s1"> </span><span class="se">{{</span>
+<span class="s1"> puts "No match for type $key, using default vdW parameters"</span>
+<span class="s1"> set vdw_type "CT"</span>
+<span class="s1"> </span><span class="se">}}</span><span class="s1"> else </span><span class="se">{{</span>
+<span class="s1"> set vdw_type $VDW_TYPEMAP($key)</span>
+<span class="s1"> </span><span class="se">}}</span>
+<span class="s1"> dict set typemap $key $vdw_type</span>
+<span class="s1"> dict set typemap_reverse $vdw_type $key</span>
+<span class="s1"> </span><span class="se">}}</span>
+
+<span class="s1"> # Create VDW potential and density maps</span>
+<span class="s1"> set clust [expr $i % 4]</span>
+<span class="s1"> puts "clust=$clust"</span>
+<span class="s1"> </span>
+<span class="s1"> # Map atom type to VDW cluster</span>
+<span class="s1"> set vdwsel [atomselect top "all"]</span>
+<span class="s1"> set vdwtypes [list]</span>
+<span class="s1"> set vdwatomtypes [list]</span>
+<span class="s1"> set sel_type [$vdwsel get type]</span>
+<span class="s1"> # Remap into VDW types</span>
+<span class="s1"> foreach atype $sel_type </span><span class="se">{{</span>
+<span class="s1"> set vdwtype [dict get $typemap $atype]</span>
+<span class="s1"> set vdwsplit [split $vdwtype "_"]</span>
+<span class="s1"> set vdwgroup [lindex $vdwsplit 0]</span>
+<span class="s1"> </span>
+<span class="s1"> # Determine cluster membership</span>
+<span class="s1"> if </span><span class="se">{{</span><span class="s1">$i == 0</span><span class="se">}}</span><span class="s1"> </span><span class="se">{{</span>
+<span class="s1"> lappend vdwtypes "VDW"</span>
+<span class="s1"> lappend vdwatomtypes $vdwtype</span>
+<span class="s1"> </span><span class="se">}}</span><span class="s1"> elseif </span><span class="se">{{</span><span class="s1">([string compare -length 1 $vdwgroup "C"] == 0) && ($clust == 1)</span><span class="se">}}</span><span class="s1"> </span><span class="se">{{</span>
+<span class="s1"> lappend vdwtypes "VDW"</span>
+<span class="s1"> lappend vdwatomtypes $vdwtype</span>
+<span class="s1"> </span><span class="se">}}</span><span class="s1"> elseif </span><span class="se">{{</span><span class="s1">([string compare -length 1 $vdwgroup "N"] == 0 || [string compare -length 2 $vdwgroup "ON"] == 0 || [string compare -length 2 $vdwgroup "SN"] == 0) && ($clust == 2)</span><span class="se">}}</span><span class="s1"> </span><span class="se">{{</span>
+<span class="s1"> lappend vdwtypes "VDW"</span>
+<span class="s1"> lappend vdwatomtypes $vdwtype</span>
+<span class="s1"> </span><span class="se">}}</span><span class="s1"> elseif </span><span class="se">{{</span><span class="s1">([string compare -length 1 $vdwgroup "O"] == 0 || [string compare -length 2 $vdwgroup "OS"] == 0 || [string compare -length 1 $vdwgroup "S"] == 0) && ($clust == 3)</span><span class="se">}}</span><span class="s1"> </span><span class="se">{{</span>
+<span class="s1"> lappend vdwtypes "VDW"</span>
+<span class="s1"> lappend vdwatomtypes $vdwtype</span>
+<span class="s1"> </span><span class="se">}}</span><span class="s1"> else </span><span class="se">{{</span>
+<span class="s1"> lappend vdwtypes "NONE"</span>
+<span class="s1"> lappend vdwatomtypes "NONE"</span>
+<span class="s1"> </span><span class="se">}}</span>
+<span class="s1"> </span><span class="se">}}</span>
+<span class="s1"> $vdwsel set user 0</span>
+<span class="s1"> $vdwsel set beta 1.0</span>
+<span class="s1"> </span>
+<span class="s1"> # Assign user values</span>
+<span class="s1"> for </span><span class="se">{{</span><span class="s1">set j 0</span><span class="se">}}</span><span class="s1"> </span><span class="se">{{</span><span class="s1">$j < [$vdwsel num]</span><span class="se">}}</span><span class="s1"> </span><span class="se">{{</span><span class="s1">incr j</span><span class="se">}}</span><span class="s1"> </span><span class="se">{{</span>
+<span class="s1"> set vdwtype [lindex $vdwtypes $j]</span>
+<span class="s1"> if </span><span class="se">{{</span><span class="s1">[string compare $vdwtype "VDW"] == 0</span><span class="se">}}</span><span class="s1"> </span><span class="se">{{</span>
+<span class="s1"> set atomtype [lindex $vdwatomtypes $j]</span>
+<span class="s1"> set radius $VDW_RADIUS($atomtype)</span>
+<span class="s1"> set epsilon $VDW_EPSILON($atomtype)</span>
+<span class="s1"> set user [expr $radius * sqrt($epsilon)]</span>
+<span class="s1"> $vdwsel set user $user index $j</span>
+<span class="s1"> </span><span class="se">}}</span>
+<span class="s1"> </span><span class="se">}}</span>
+<span class="s1"> </span>
+<span class="s1"> # Generate density map</span>
+<span class="s1"> volmap density $vdwsel -res </span><span class="si">{</span><span class="n">denResolution</span><span class="si">}</span><span class="s1"> -weight user -o "$prefix.vdw$i.den.dx"</span>
+<span class="s1"> </span>
+<span class="s1"> # Generate potential map</span>
+<span class="s1"> set pot_outfile "$prefix.vdw$i.pot.dx"</span>
+<span class="s1"> if </span><span class="se">{{</span><span class="s1">$i == 0</span><span class="se">}}</span><span class="s1"> </span><span class="se">{{</span>
+<span class="s1"> puts "generating $pot_outfile"</span>
+<span class="s1"> volmap occupancy $vdwsel -res </span><span class="si">{</span><span class="n">potResolution</span><span class="si">}</span><span class="s1"> -o "$pot_outfile"</span>
+<span class="s1"> </span><span class="se">}}</span><span class="s1"> else </span><span class="se">{{</span>
+<span class="s1"> set vdwsel2 [atomselect top "user > 0"]</span>
+<span class="s1"> if </span><span class="se">{{</span><span class="s1">[$vdwsel2 num] > 0</span><span class="se">}}</span><span class="s1"> </span><span class="se">{{</span>
+<span class="s1"> volmap occupancy $vdwsel2 -res </span><span class="si">{</span><span class="n">potResolution</span><span class="si">}</span><span class="s1"> -o "$pot_outfile"</span>
+<span class="s1"> </span><span class="se">}}</span>
+<span class="s1"> $vdwsel2 delete</span>
+<span class="s1"> </span><span class="se">}}</span>
+<span class="se">}}</span>
+<span class="s1">'''</span><span class="p">)</span>
+
+ <span class="c1"># Run VMD to generate VDW maps</span>
+ <span class="n">cmd</span> <span class="o">=</span> <span class="sa">f</span><span class="s2">"VMDNOCUDA=1 </span><span class="si">{</span><span class="bp">self</span><span class="o">.</span><span class="n">vmd_path</span><span class="si">}</span><span class="s2"> -dispdev text -args </span><span class="si">{</span><span class="n">aligned_name</span><span class="si">}</span><span class="s2"> < </span><span class="si">{</span><span class="n">vdw_tcl</span><span class="si">}</span><span class="s2">"</span>
+ <span class="n">subprocess</span><span class="o">.</span><span class="n">run</span><span class="p">(</span><span class="n">cmd</span><span class="p">,</span> <span class="n">shell</span><span class="o">=</span><span class="kc">True</span><span class="p">,</span> <span class="n">check</span><span class="o">=</span><span class="kc">True</span><span class="p">)</span>
+
+ <span class="c1"># Process all VDW maps</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">vdw_pot_dxs</span> <span class="o">=</span> <span class="p">[]</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">vdw_den_dxs</span> <span class="o">=</span> <span class="p">[]</span>
+
+ <span class="k">for</span> <span class="n">i</span> <span class="ow">in</span> <span class="nb">range</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">num_heavy_cluster</span> <span class="o">+</span> <span class="mi">1</span><span class="p">):</span>
+ <span class="n">pot_file</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">work_dir</span> <span class="o">/</span> <span class="sa">f</span><span class="s2">"</span><span class="si">{</span><span class="n">aligned_name</span><span class="si">}</span><span class="s2">.vdw</span><span class="si">{</span><span class="n">i</span><span class="si">}</span><span class="s2">.pot.dx"</span>
+ <span class="n">den_file</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">work_dir</span> <span class="o">/</span> <span class="sa">f</span><span class="s2">"</span><span class="si">{</span><span class="n">aligned_name</span><span class="si">}</span><span class="s2">.vdw</span><span class="si">{</span><span class="n">i</span><span class="si">}</span><span class="s2">.den.dx"</span>
+
+ <span class="k">if</span> <span class="ow">not</span> <span class="n">pot_file</span><span class="o">.</span><span class="n">exists</span><span class="p">():</span>
+ <span class="n">logger</span><span class="o">.</span><span class="n">warning</span><span class="p">(</span><span class="sa">f</span><span class="s2">"VDW potential file not found: </span><span class="si">{</span><span class="n">pot_file</span><span class="si">}</span><span class="s2">"</span><span class="p">)</span>
+ <span class="k">continue</span>
+
+ <span class="c1"># Bound the potential values</span>
+
+ <span class="n">Bound_grid</span><span class="p">(</span><span class="n">inFile</span><span class="o">=</span><span class="n">pot_file</span><span class="p">,</span>
+ <span class="n">outFile</span><span class="o">=</span><span class="n">pot_file</span><span class="p">,</span>
+ <span class="n">lowerBound</span><span class="o">=-</span><span class="mi">20</span><span class="p">,</span>
+ <span class="n">upperBound</span><span class="o">=</span><span class="mi">20</span><span class="p">)</span>
+
+ <span class="c1"># Store for later smoothing</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">vdw_pot_dxs</span><span class="o">.</span><span class="n">append</span><span class="p">(</span><span class="n">pot_file</span><span class="p">)</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">vdw_den_dxs</span><span class="o">.</span><span class="n">append</span><span class="p">(</span><span class="n">den_file</span><span class="p">)</span>
+
+ <span class="n">logger</span><span class="o">.</span><span class="n">info</span><span class="p">(</span><span class="sa">f</span><span class="s2">"VDW maps generated for </span><span class="si">{</span><span class="n">aligned_name</span><span class="si">}</span><span class="s2">"</span><span class="p">)</span></div>
+
+
+<div class="viewcode-block" id="StructureProcessor.apply_gaussian_smoothing">
+<a class="viewcode-back" href="../../api/rigidbody_models/structure_from_pdb.html#arbdmodel.structure_from_pdb.StructureProcessor.apply_gaussian_smoothing">[docs]</a>
+ <span class="k">def</span><span class="w"> </span><span class="nf">apply_gaussian_smoothing</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">gaussianWidth</span><span class="o">=</span><span class="mf">2.5</span><span class="p">):</span>
+<span class="w"> </span><span class="sd">"""Apply Gaussian smoothing to all potential maps."""</span>
+ <span class="n">aligned_name</span> <span class="o">=</span> <span class="sa">f</span><span class="s2">"</span><span class="si">{</span><span class="bp">self</span><span class="o">.</span><span class="n">base_name</span><span class="si">}</span><span class="s2">.aligned"</span>
+
+ <span class="c1"># Create a tcl script for VMD to do the smoothing</span>
+ <span class="n">smooth_tcl</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">work_dir</span> <span class="o">/</span> <span class="s2">"smooth.tcl"</span>
+
+ <span class="k">with</span> <span class="nb">open</span><span class="p">(</span><span class="n">smooth_tcl</span><span class="p">,</span> <span class="s1">'w'</span><span class="p">)</span> <span class="k">as</span> <span class="n">f</span><span class="p">:</span>
+ <span class="n">f</span><span class="o">.</span><span class="n">write</span><span class="p">(</span><span class="sa">f</span><span class="s1">'''</span>
+<span class="s1"># Get input parameters</span>
+<span class="s1">lassign $</span><span class="se">{{</span><span class="s1">argv</span><span class="se">}}</span><span class="s1"> in_file out_file</span>
+<span class="s1">puts "Smoothing $in_file to $out_file"</span>
+
+<span class="s1"># Load the volumetric data</span>
+<span class="s1">mol new $in_file</span>
+
+<span class="s1"># Apply smoothing</span>
+<span class="s1">set molid [molinfo top]</span>
+<span class="s1">set vol [molinfo $molid get </span><span class="si">{</span><span class="mi">0</span><span class="si">}</span><span class="s1">]</span>
+<span class="s1">volutil smooth $vol -gaussiansigma </span><span class="si">{</span><span class="n">gaussianWidth</span><span class="si">}</span>
+
+<span class="s1"># Save the result</span>
+<span class="s1">volutil save $vol $out_file</span>
+
+<span class="s1"># Exit</span>
+<span class="s1">quit</span>
+<span class="s1">'''</span><span class="p">)</span>
+
+ <span class="c1"># Smooth electrostatic map</span>
+ <span class="k">if</span> <span class="bp">self</span><span class="o">.</span><span class="n">elec_dx</span> <span class="ow">and</span> <span class="bp">self</span><span class="o">.</span><span class="n">elec_dx</span><span class="o">.</span><span class="n">exists</span><span class="p">():</span>
+ <span class="n">smoothed_elec</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">work_dir</span> <span class="o">/</span> <span class="sa">f</span><span class="s2">"</span><span class="si">{</span><span class="n">aligned_name</span><span class="si">}</span><span class="s2">.elec.smoothed.dx"</span>
+ <span class="n">cmd</span> <span class="o">=</span> <span class="sa">f</span><span class="s2">"</span><span class="si">{</span><span class="bp">self</span><span class="o">.</span><span class="n">vmd_path</span><span class="si">}</span><span class="s2"> -dispdev text -args </span><span class="si">{</span><span class="bp">self</span><span class="o">.</span><span class="n">elec_dx</span><span class="si">}</span><span class="s2"> </span><span class="si">{</span><span class="n">smoothed_elec</span><span class="si">}</span><span class="s2"> < </span><span class="si">{</span><span class="n">smooth_tcl</span><span class="si">}</span><span class="s2">"</span>
+ <span class="n">subprocess</span><span class="o">.</span><span class="n">run</span><span class="p">(</span><span class="n">cmd</span><span class="p">,</span> <span class="n">shell</span><span class="o">=</span><span class="kc">True</span><span class="p">,</span> <span class="n">check</span><span class="o">=</span><span class="kc">True</span><span class="p">)</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">elec_smoothed_dx</span> <span class="o">=</span> <span class="n">smoothed_elec</span>
+
+ <span class="c1"># Smooth VDW potential maps</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">vdw_smoothed_dxs</span> <span class="o">=</span> <span class="p">[]</span>
+ <span class="k">for</span> <span class="n">i</span><span class="p">,</span> <span class="n">pot_file</span> <span class="ow">in</span> <span class="nb">enumerate</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">vdw_pot_dxs</span><span class="p">):</span>
+ <span class="k">if</span> <span class="n">pot_file</span><span class="o">.</span><span class="n">exists</span><span class="p">():</span>
+ <span class="n">smoothed_pot</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">work_dir</span> <span class="o">/</span> <span class="sa">f</span><span class="s2">"</span><span class="si">{</span><span class="n">aligned_name</span><span class="si">}</span><span class="s2">.vdw</span><span class="si">{</span><span class="n">i</span><span class="si">}</span><span class="s2">.pot.smoothed.dx"</span>
+ <span class="n">cmd</span> <span class="o">=</span> <span class="sa">f</span><span class="s2">"</span><span class="si">{</span><span class="bp">self</span><span class="o">.</span><span class="n">vmd_path</span><span class="si">}</span><span class="s2"> -dispdev text -args </span><span class="si">{</span><span class="n">pot_file</span><span class="si">}</span><span class="s2"> </span><span class="si">{</span><span class="n">smoothed_pot</span><span class="si">}</span><span class="s2"> < </span><span class="si">{</span><span class="n">smooth_tcl</span><span class="si">}</span><span class="s2">"</span>
+ <span class="n">subprocess</span><span class="o">.</span><span class="n">run</span><span class="p">(</span><span class="n">cmd</span><span class="p">,</span> <span class="n">shell</span><span class="o">=</span><span class="kc">True</span><span class="p">,</span> <span class="n">check</span><span class="o">=</span><span class="kc">True</span><span class="p">)</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">vdw_smoothed_dxs</span><span class="o">.</span><span class="n">append</span><span class="p">(</span><span class="n">smoothed_pot</span><span class="p">)</span>
+
+ <span class="n">logger</span><span class="o">.</span><span class="n">info</span><span class="p">(</span><span class="sa">f</span><span class="s2">"Applied Gaussian smoothing to potential maps (width=</span><span class="si">{</span><span class="n">gaussianWidth</span><span class="si">}</span><span class="s2">)"</span><span class="p">)</span></div>
+
+
+
+<div class="viewcode-block" id="StructureProcessor.get_grid_files">
+<a class="viewcode-back" href="../../api/rigidbody_models/structure_from_pdb.html#arbdmodel.structure_from_pdb.StructureProcessor.get_grid_files">[docs]</a>
+ <span class="k">def</span><span class="w"> </span><span class="nf">get_grid_files</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span>
+<span class="w"> </span><span class="sd">"""Get dictionary of grid files for use in RigidBodyType."""</span>
+ <span class="n">potential_grids</span> <span class="o">=</span> <span class="p">[]</span>
+ <span class="n">charge_grids</span> <span class="o">=</span> <span class="p">[]</span>
+
+ <span class="c1"># Add electrostatic grid</span>
+ <span class="k">if</span> <span class="nb">hasattr</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="s1">'elec_smoothed_dx'</span><span class="p">)</span> <span class="ow">and</span> <span class="bp">self</span><span class="o">.</span><span class="n">elec_smoothed_dx</span> <span class="ow">and</span> <span class="bp">self</span><span class="o">.</span><span class="n">elec_smoothed_dx</span><span class="o">.</span><span class="n">exists</span><span class="p">():</span>
+ <span class="n">potential_grids</span><span class="o">.</span><span class="n">append</span><span class="p">((</span><span class="s2">"elec"</span><span class="p">,</span> <span class="nb">str</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">elec_smoothed_dx</span><span class="p">),</span> <span class="mf">0.59616195</span><span class="p">))</span>
+
+ <span class="c1"># Add charge grid</span>
+ <span class="k">if</span> <span class="bp">self</span><span class="o">.</span><span class="n">charge_dx</span> <span class="ow">and</span> <span class="bp">self</span><span class="o">.</span><span class="n">charge_dx</span><span class="o">.</span><span class="n">exists</span><span class="p">():</span>
+ <span class="n">charge_grids</span><span class="o">.</span><span class="n">append</span><span class="p">((</span><span class="s2">"elec"</span><span class="p">,</span> <span class="nb">str</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">charge_dx</span><span class="p">)))</span>
+
+ <span class="c1"># Add VDW grids</span>
+ <span class="k">for</span> <span class="n">i</span><span class="p">,</span> <span class="n">pot_file</span> <span class="ow">in</span> <span class="nb">enumerate</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">vdw_smoothed_dxs</span><span class="p">):</span>
+ <span class="n">vdw_key</span> <span class="o">=</span> <span class="sa">f</span><span class="s2">"vdw</span><span class="si">{</span><span class="n">i</span><span class="si">}</span><span class="s2">"</span>
+ <span class="k">if</span> <span class="n">pot_file</span><span class="o">.</span><span class="n">exists</span><span class="p">():</span>
+ <span class="n">potential_grids</span><span class="o">.</span><span class="n">append</span><span class="p">((</span><span class="n">vdw_key</span><span class="p">,</span> <span class="nb">str</span><span class="p">(</span><span class="n">pot_file</span><span class="p">),</span> <span class="mf">0.59616195</span><span class="p">))</span>
+
+ <span class="k">for</span> <span class="n">i</span><span class="p">,</span> <span class="n">den_file</span> <span class="ow">in</span> <span class="nb">enumerate</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">vdw_den_dxs</span><span class="p">):</span>
+ <span class="n">vdw_key</span> <span class="o">=</span> <span class="sa">f</span><span class="s2">"vdw</span><span class="si">{</span><span class="n">i</span><span class="si">}</span><span class="s2">"</span>
+ <span class="k">if</span> <span class="n">den_file</span><span class="o">.</span><span class="n">exists</span><span class="p">():</span>
+ <span class="n">charge_grids</span><span class="o">.</span><span class="n">append</span><span class="p">((</span><span class="n">vdw_key</span><span class="p">,</span> <span class="nb">str</span><span class="p">(</span><span class="n">den_file</span><span class="p">)))</span>
+
+ <span class="k">return</span> <span class="p">{</span>
+ <span class="s2">"potential_grids"</span><span class="p">:</span> <span class="n">potential_grids</span><span class="p">,</span>
+ <span class="s2">"charge_grids"</span><span class="p">:</span> <span class="n">charge_grids</span><span class="p">}</span></div>
+</div>
+
+
+</pre></div>
+
+ </article>
+
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+
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+ <h1>Source code for arbdmodel.structure_rigidbody</h1><div class="highlight"><pre>
+<span></span><span class="kn">import</span><span class="w"> </span><span class="nn">os</span>
+<span class="kn">import</span><span class="w"> </span><span class="nn">numpy</span><span class="w"> </span><span class="k">as</span><span class="w"> </span><span class="nn">np</span>
+<span class="kn">from</span><span class="w"> </span><span class="nn">pathlib</span><span class="w"> </span><span class="kn">import</span> <span class="n">Path</span>
+<span class="kn">from</span><span class="w"> </span><span class="nn">.logger</span><span class="w"> </span><span class="kn">import</span> <span class="n">logger</span>
+<span class="kn">from</span><span class="w"> </span><span class="nn">.</span><span class="w"> </span><span class="kn">import</span> <span class="n">RigidBody</span><span class="p">,</span> <span class="n">RigidBodyType</span><span class="p">,</span> <span class="n">DefaultSimConf</span>
+<span class="kn">from</span><span class="w"> </span><span class="nn">.</span><span class="w"> </span><span class="kn">import</span> <span class="n">ArbdModel</span><span class="p">,</span> <span class="n">ArbdEngine</span>
+<span class="kn">from</span><span class="w"> </span><span class="nn">.structure_from_pdb</span><span class="w"> </span><span class="kn">import</span> <span class="n">StructureProcessor</span>
+<span class="kn">from</span><span class="w"> </span><span class="nn">.coords</span><span class="w"> </span><span class="kn">import</span> <span class="n">Generate_coordinates</span><span class="p">,</span> <span class="n">Generate_spanning_vectors</span>
+
+<span class="sd">"""Structure rigid body modeling module for ARBD.</span>
+
+<span class="sd">This module provides classes for structure-based rigid body modeling in the ARBD package,</span>
+<span class="sd">using a clean implementation that processes molecular structures into grid maps.</span>
+<span class="sd">"""</span>
+
+<div class="viewcode-block" id="DiffusiveRigidBodyType">
+<a class="viewcode-back" href="../../api/rigidbody_models/structure_rigidbody.html#arbdmodel.structure_rigidbody.DiffusiveRigidBodyType">[docs]</a>
+<span class="k">class</span><span class="w"> </span><span class="nc">DiffusiveRigidBodyType</span><span class="p">(</span><span class="n">RigidBodyType</span><span class="p">):</span>
+<span class="w"> </span><span class="sd">"""RigidBodyType subclass for structure-based rigid body objects"""</span>
+
+ <span class="k">def</span><span class="w"> </span><span class="fm">__init__</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">name</span><span class="p">,</span> <span class="n">structure_path</span><span class="p">,</span> <span class="n">simconf</span><span class="o">=</span><span class="kc">None</span><span class="p">,</span>
+ <span class="n">work_dir</span><span class="o">=</span><span class="kc">None</span><span class="p">,</span> <span class="o">**</span><span class="n">kwargs</span><span class="p">):</span>
+<span class="w"> </span><span class="sd">"""Initialize structure rigid body type from structure files.</span>
+<span class="sd"> Args:</span>
+<span class="sd"> name: Name identifier for this type</span>
+<span class="sd"> structure_path: Path to structure file (.psf/.pdb)</span>
+<span class="sd"> simconf: SimConf object containing configuration parameters</span>
+<span class="sd"> work_dir: Directory to store processed files (default: current directory)</span>
+<span class="sd"> """</span>
+ <span class="c1"># Create work directory if specified</span>
+ <span class="k">if</span> <span class="n">work_dir</span><span class="p">:</span>
+ <span class="n">work_dir</span> <span class="o">=</span> <span class="n">Path</span><span class="p">(</span><span class="n">work_dir</span><span class="p">)</span>
+ <span class="n">os</span><span class="o">.</span><span class="n">makedirs</span><span class="p">(</span><span class="n">work_dir</span><span class="p">,</span> <span class="n">exist_ok</span><span class="o">=</span><span class="kc">True</span><span class="p">)</span>
+ <span class="k">else</span><span class="p">:</span>
+ <span class="n">work_dir</span> <span class="o">=</span> <span class="n">Path</span><span class="o">.</span><span class="n">cwd</span><span class="p">()</span> <span class="o">/</span> <span class="n">name</span>
+ <span class="n">os</span><span class="o">.</span><span class="n">makedirs</span><span class="p">(</span><span class="n">work_dir</span><span class="p">,</span> <span class="n">exist_ok</span><span class="o">=</span><span class="kc">True</span><span class="p">)</span>
+
+ <span class="k">if</span> <span class="n">simconf</span> <span class="ow">is</span> <span class="kc">None</span><span class="p">:</span>
+ <span class="kn">from</span><span class="w"> </span><span class="nn">.</span><span class="w"> </span><span class="kn">import</span> <span class="n">DefaultSimConf</span>
+ <span class="n">simconf</span> <span class="o">=</span> <span class="n">DefaultSimConf</span><span class="p">()</span>
+
+ <span class="c1"># Process the structure to get properties and grid maps</span>
+ <span class="n">processor</span> <span class="o">=</span> <span class="n">StructureProcessor</span><span class="p">(</span>
+ <span class="n">structure_path</span><span class="o">=</span><span class="n">structure_path</span><span class="p">,</span>
+ <span class="n">simconf</span><span class="o">=</span><span class="n">simconf</span><span class="p">,</span>
+ <span class="n">work_dir</span><span class="o">=</span><span class="n">work_dir</span><span class="p">)</span>
+
+ <span class="c1"># Process the structure to get all properties and grid files</span>
+ <span class="n">processor</span><span class="o">.</span><span class="n">process_structure</span><span class="p">()</span>
+
+ <span class="c1"># Initialize the parent class with collected data</span>
+ <span class="nb">super</span><span class="p">()</span><span class="o">.</span><span class="fm">__init__</span><span class="p">(</span>
+ <span class="n">name</span><span class="o">=</span><span class="n">name</span><span class="p">,</span>
+ <span class="n">mass</span><span class="o">=</span><span class="n">processor</span><span class="o">.</span><span class="n">mass</span><span class="p">,</span>
+ <span class="n">moment_of_inertia</span><span class="o">=</span><span class="n">processor</span><span class="o">.</span><span class="n">moment_of_inertia</span><span class="p">,</span>
+ <span class="n">damping_coefficient</span><span class="o">=</span><span class="n">processor</span><span class="o">.</span><span class="n">transdamp</span><span class="p">,</span>
+ <span class="n">rotational_damping_coefficient</span><span class="o">=</span><span class="n">processor</span><span class="o">.</span><span class="n">rotdamp</span><span class="p">,</span>
+ <span class="n">potential_grids</span><span class="o">=</span><span class="n">processor</span><span class="o">.</span><span class="n">potential_grids</span><span class="p">,</span>
+ <span class="n">charge_grids</span><span class="o">=</span><span class="n">processor</span><span class="o">.</span><span class="n">charge_grids</span><span class="p">,</span>
+ <span class="n">pmf_grids</span><span class="o">=</span><span class="p">[],</span>
+ <span class="o">**</span><span class="n">kwargs</span>
+ <span class="p">)</span>
+
+ <span class="c1"># Store file paths for reference</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">aligned_pdb</span> <span class="o">=</span> <span class="n">processor</span><span class="o">.</span><span class="n">aligned_pdb</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">aligned_psf</span> <span class="o">=</span> <span class="n">processor</span><span class="o">.</span><span class="n">aligned_psf</span>
+
+ <span class="n">logger</span><span class="o">.</span><span class="n">info</span><span class="p">(</span><span class="sa">f</span><span class="s2">"StructureRigidBodyType '</span><span class="si">{</span><span class="n">name</span><span class="si">}</span><span class="s2">' initialized successfully"</span><span class="p">)</span></div>
+
+
+<div class="viewcode-block" id="StaticObject">
+<a class="viewcode-back" href="../../api/rigidbody_models/structure_rigidbody.html#arbdmodel.structure_rigidbody.StaticObject">[docs]</a>
+<span class="k">class</span><span class="w"> </span><span class="nc">StaticObject</span><span class="p">:</span>
+<span class="w"> </span><span class="sd">"""Class representing a static (immobile) object in the simulation"""</span>
+
+ <span class="k">def</span><span class="w"> </span><span class="fm">__init__</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">structure_path</span><span class="o">=</span><span class="kc">None</span><span class="p">,</span> <span class="n">name</span><span class="o">=</span><span class="kc">None</span><span class="p">,</span> <span class="n">simconf</span><span class="o">=</span><span class="kc">None</span><span class="p">,</span> <span class="n">work_dir</span><span class="o">=</span><span class="kc">None</span><span class="p">,</span>
+ <span class="n">is_gigantic</span><span class="o">=</span><span class="kc">False</span><span class="p">,</span> <span class="n">threshold</span><span class="o">=</span><span class="mi">300</span><span class="p">):</span>
+<span class="w"> </span><span class="sd">"""Initialize static object from a structure file.</span>
+<span class="sd"> </span>
+<span class="sd"> Args:</span>
+<span class="sd"> structure_path: Path to structure file (.psf/.pdb)</span>
+<span class="sd"> name: Name for this static object (defaults to structure filename)</span>
+<span class="sd"> simconf: SimConf object containing configuration parameters</span>
+<span class="sd"> work_dir: Directory to store processed files</span>
+<span class="sd"> is_gigantic: Whether this is a gigantic object requiring segmentation</span>
+<span class="sd"> threshold: Size threshold for segmentation (if is_gigantic=True)</span>
+<span class="sd"> """</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">structure_path</span> <span class="o">=</span> <span class="n">Path</span><span class="p">(</span><span class="n">structure_path</span><span class="p">)</span> <span class="k">if</span> <span class="n">structure_path</span> <span class="k">else</span> <span class="kc">None</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">name</span> <span class="o">=</span> <span class="n">name</span> <span class="ow">or</span> <span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">structure_path</span><span class="o">.</span><span class="n">stem</span> <span class="k">if</span> <span class="bp">self</span><span class="o">.</span><span class="n">structure_path</span> <span class="k">else</span> <span class="s2">"static_object"</span><span class="p">)</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">is_gigantic</span> <span class="o">=</span> <span class="n">is_gigantic</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">threshold</span> <span class="o">=</span> <span class="n">threshold</span>
+
+ <span class="c1"># Set up working directory</span>
+ <span class="k">if</span> <span class="n">work_dir</span><span class="p">:</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">work_dir</span> <span class="o">=</span> <span class="n">Path</span><span class="p">(</span><span class="n">work_dir</span><span class="p">)</span>
+ <span class="k">else</span><span class="p">:</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">work_dir</span> <span class="o">=</span> <span class="n">Path</span><span class="o">.</span><span class="n">cwd</span><span class="p">()</span> <span class="o">/</span> <span class="sa">f</span><span class="s2">"static_</span><span class="si">{</span><span class="bp">self</span><span class="o">.</span><span class="n">name</span><span class="si">}</span><span class="s2">"</span>
+
+ <span class="n">os</span><span class="o">.</span><span class="n">makedirs</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">work_dir</span><span class="p">,</span> <span class="n">exist_ok</span><span class="o">=</span><span class="kc">True</span><span class="p">)</span>
+
+ <span class="c1"># Default config if not provided</span>
+ <span class="k">if</span> <span class="n">simconf</span> <span class="ow">is</span> <span class="kc">None</span><span class="p">:</span>
+ <span class="n">simconf</span> <span class="o">=</span> <span class="n">DefaultSimConf</span><span class="p">()</span>
+
+ <span class="bp">self</span><span class="o">.</span><span class="n">simconf</span> <span class="o">=</span> <span class="n">simconf</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">potential_grids</span> <span class="o">=</span> <span class="p">[]</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">charge_grids</span> <span class="o">=</span> <span class="p">[]</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">elec_grid</span> <span class="o">=</span> <span class="kc">None</span>
+
+ <span class="c1"># Process the structure if provided</span>
+ <span class="k">if</span> <span class="n">structure_path</span><span class="p">:</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">process</span><span class="p">()</span>
+
+ <span class="k">def</span><span class="w"> </span><span class="nf">_find_segments_num</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">dimensions</span><span class="p">,</span> <span class="n">threshold</span><span class="o">=</span><span class="kc">None</span><span class="p">):</span>
+<span class="w"> </span><span class="sd">"""Find number of segments needed for a gigantic object.</span>
+<span class="sd"> </span>
+<span class="sd"> Args:</span>
+<span class="sd"> dimensions: List of dimensions [x, y, z]</span>
+<span class="sd"> threshold: Size threshold for segmentation (defaults to self.threshold)</span>
+<span class="sd"> </span>
+<span class="sd"> Returns:</span>
+<span class="sd"> Tuple of (nx, ny, nz) segment counts</span>
+<span class="sd"> """</span>
+ <span class="k">if</span> <span class="n">threshold</span> <span class="ow">is</span> <span class="kc">None</span><span class="p">:</span>
+ <span class="n">threshold</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">threshold</span>
+
+ <span class="n">in_xyz</span> <span class="o">=</span> <span class="p">[</span><span class="nb">float</span><span class="p">(</span><span class="n">elm</span><span class="p">)</span> <span class="k">for</span> <span class="n">elm</span> <span class="ow">in</span> <span class="n">dimensions</span><span class="p">]</span>
+ <span class="n">segments</span> <span class="o">=</span> <span class="p">[</span><span class="n">np</span><span class="o">.</span><span class="n">ceil</span><span class="p">(</span><span class="n">elm</span> <span class="o">/</span> <span class="n">threshold</span><span class="p">)</span> <span class="k">for</span> <span class="n">elm</span> <span class="ow">in</span> <span class="n">in_xyz</span><span class="p">]</span>
+ <span class="k">return</span> <span class="n">segments</span><span class="p">[</span><span class="mi">0</span><span class="p">],</span> <span class="n">segments</span><span class="p">[</span><span class="mi">1</span><span class="p">],</span> <span class="n">segments</span><span class="p">[</span><span class="mi">2</span><span class="p">]</span>
+
+<div class="viewcode-block" id="StaticObject.process">
+<a class="viewcode-back" href="../../api/rigidbody_models/structure_rigidbody.html#arbdmodel.structure_rigidbody.StaticObject.process">[docs]</a>
+ <span class="k">def</span><span class="w"> </span><span class="nf">process</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span>
+<span class="w"> </span><span class="sd">"""Process the structure file to create potential and density grids"""</span>
+ <span class="k">if</span> <span class="ow">not</span> <span class="bp">self</span><span class="o">.</span><span class="n">structure_path</span><span class="p">:</span>
+ <span class="n">logger</span><span class="o">.</span><span class="n">warning</span><span class="p">(</span><span class="s2">"No structure path provided for static object"</span><span class="p">)</span>
+ <span class="k">return</span>
+
+ <span class="k">if</span> <span class="bp">self</span><span class="o">.</span><span class="n">is_gigantic</span><span class="p">:</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">_process_gigantic</span><span class="p">()</span>
+ <span class="k">else</span><span class="p">:</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">_process_standard</span><span class="p">()</span></div>
+
+
+ <span class="k">def</span><span class="w"> </span><span class="nf">_process_standard</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span>
+<span class="w"> </span><span class="sd">"""Process the structure normally (without segmentation)"""</span>
+ <span class="n">logger</span><span class="o">.</span><span class="n">info</span><span class="p">(</span><span class="sa">f</span><span class="s2">"Processing static object: </span><span class="si">{</span><span class="bp">self</span><span class="o">.</span><span class="n">name</span><span class="si">}</span><span class="s2">"</span><span class="p">)</span>
+
+ <span class="c1"># Create processor and generate maps</span>
+ <span class="n">processor</span> <span class="o">=</span> <span class="n">StructureProcessor</span><span class="p">(</span>
+ <span class="n">structure_path</span><span class="o">=</span><span class="bp">self</span><span class="o">.</span><span class="n">structure_path</span><span class="p">,</span>
+ <span class="n">simconf</span><span class="o">=</span><span class="bp">self</span><span class="o">.</span><span class="n">simconf</span><span class="p">,</span>
+ <span class="n">work_dir</span><span class="o">=</span><span class="bp">self</span><span class="o">.</span><span class="n">work_dir</span><span class="p">)</span>
+
+ <span class="n">processor</span><span class="o">.</span><span class="n">process_structure</span><span class="p">()</span>
+
+ <span class="c1"># Collect grids from the processor</span>
+ <span class="n">grid_files</span> <span class="o">=</span> <span class="n">processor</span><span class="o">.</span><span class="n">get_grid_files</span><span class="p">()</span>
+
+ <span class="c1"># Store grids</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">potential_grids</span> <span class="o">=</span> <span class="n">grid_files</span><span class="o">.</span><span class="n">get</span><span class="p">(</span><span class="s1">'potential_grids'</span><span class="p">,</span> <span class="p">[])</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">charge_grids</span> <span class="o">=</span> <span class="n">grid_files</span><span class="o">.</span><span class="n">get</span><span class="p">(</span><span class="s1">'charge_grids'</span><span class="p">,</span> <span class="p">[])</span>
+ <span class="k">if</span> <span class="nb">hasattr</span><span class="p">(</span><span class="n">processor</span><span class="p">,</span> <span class="s1">'elec_smoothed_dx'</span><span class="p">)</span> <span class="ow">and</span> <span class="n">processor</span><span class="o">.</span><span class="n">elec_smoothed_dx</span><span class="p">:</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">elec_grid</span> <span class="o">=</span> <span class="n">processor</span><span class="o">.</span><span class="n">elec_smoothed_dx</span>
+
+ <span class="k">def</span><span class="w"> </span><span class="nf">_process_gigantic</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span>
+<span class="w"> </span><span class="sd">"""Process a gigantic structure by segmentation"""</span>
+ <span class="kn">from</span><span class="w"> </span><span class="nn">subprocess</span><span class="w"> </span><span class="kn">import</span> <span class="n">run</span>
+ <span class="kn">import</span><span class="w"> </span><span class="nn">MDAnalysis</span><span class="w"> </span><span class="k">as</span><span class="w"> </span><span class="nn">mda</span>
+
+ <span class="n">logger</span><span class="o">.</span><span class="n">info</span><span class="p">(</span><span class="sa">f</span><span class="s2">"Processing gigantic static object: </span><span class="si">{</span><span class="bp">self</span><span class="o">.</span><span class="n">name</span><span class="si">}</span><span class="s2">"</span><span class="p">)</span>
+
+ <span class="c1"># Get dimensions by reading the structure file</span>
+ <span class="n">u</span> <span class="o">=</span> <span class="n">mda</span><span class="o">.</span><span class="n">Universe</span><span class="p">(</span><span class="nb">str</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">structure_path</span><span class="p">))</span>
+ <span class="n">min_coords</span> <span class="o">=</span> <span class="n">u</span><span class="o">.</span><span class="n">atoms</span><span class="o">.</span><span class="n">positions</span><span class="o">.</span><span class="n">min</span><span class="p">(</span><span class="n">axis</span><span class="o">=</span><span class="mi">0</span><span class="p">)</span>
+ <span class="n">max_coords</span> <span class="o">=</span> <span class="n">u</span><span class="o">.</span><span class="n">atoms</span><span class="o">.</span><span class="n">positions</span><span class="o">.</span><span class="n">max</span><span class="p">(</span><span class="n">axis</span><span class="o">=</span><span class="mi">0</span><span class="p">)</span>
+ <span class="n">dimensions</span> <span class="o">=</span> <span class="n">max_coords</span> <span class="o">-</span> <span class="n">min_coords</span>
+
+ <span class="c1"># Calculate segmentation</span>
+ <span class="n">nx</span><span class="p">,</span> <span class="n">ny</span><span class="p">,</span> <span class="n">nz</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">_find_segments_num</span><span class="p">(</span><span class="n">dimensions</span><span class="p">,</span> <span class="bp">self</span><span class="o">.</span><span class="n">threshold</span><span class="p">)</span>
+ <span class="n">logger</span><span class="o">.</span><span class="n">info</span><span class="p">(</span><span class="sa">f</span><span class="s2">"Segmenting into </span><span class="si">{</span><span class="n">nx</span><span class="si">}</span><span class="s2">x</span><span class="si">{</span><span class="n">ny</span><span class="si">}</span><span class="s2">x</span><span class="si">{</span><span class="n">nz</span><span class="si">}</span><span class="s2"> parts"</span><span class="p">)</span>
+
+ <span class="c1"># Create segment directory</span>
+ <span class="n">segments_dir</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">work_dir</span> <span class="o">/</span> <span class="s2">"segments"</span>
+ <span class="n">os</span><span class="o">.</span><span class="n">makedirs</span><span class="p">(</span><span class="n">segments_dir</span><span class="p">,</span> <span class="n">exist_ok</span><span class="o">=</span><span class="kc">True</span><span class="p">)</span>
+
+ <span class="c1"># Write VMD script for segmentation</span>
+ <span class="n">segment_script</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">work_dir</span> <span class="o">/</span> <span class="s2">"segment.tcl"</span>
+ <span class="k">with</span> <span class="nb">open</span><span class="p">(</span><span class="n">segment_script</span><span class="p">,</span> <span class="s1">'w'</span><span class="p">)</span> <span class="k">as</span> <span class="n">f</span><span class="p">:</span>
+ <span class="n">f</span><span class="o">.</span><span class="n">write</span><span class="p">(</span><span class="sa">f</span><span class="s2">"""</span>
+<span class="s2"># Segment structure</span>
+<span class="s2">mol new </span><span class="si">{</span><span class="bp">self</span><span class="o">.</span><span class="n">structure_path</span><span class="si">}</span>
+<span class="s2">set all [atomselect top all]</span>
+<span class="s2">set mM [measure minmax $all]</span>
+<span class="s2">set dimAl [vecsub [lindex $mM 1] [lindex $mM 0]]</span>
+<span class="s2">set min_x [expr [lindex [lindex $mM 0] 0] - 1]</span>
+<span class="s2">set min_y [expr [lindex [lindex $mM 0] 1] - 1]</span>
+<span class="s2">set min_z [expr [lindex [lindex $mM 0] 2] - 1]</span>
+<span class="s2">set dx [expr ([lindex $dimAl 0] + 2)/</span><span class="si">{</span><span class="n">nx</span><span class="si">}</span><span class="s2">]</span>
+<span class="s2">set dy [expr ([lindex $dimAl 1] + 2)/</span><span class="si">{</span><span class="n">ny</span><span class="si">}</span><span class="s2">]</span>
+<span class="s2">set dz [expr ([lindex $dimAl 2] + 2)/</span><span class="si">{</span><span class="n">nz</span><span class="si">}</span><span class="s2">]</span>
+
+<span class="s2">set count 0</span>
+<span class="s2">for </span><span class="se">{{</span><span class="s2">set i 0</span><span class="se">}}</span><span class="s2"> </span><span class="se">{{</span><span class="s2">$i < </span><span class="si">{</span><span class="n">nx</span><span class="si">}</span><span class="se">}}</span><span class="s2"> </span><span class="se">{{</span><span class="s2">incr i</span><span class="se">}}</span><span class="s2"> </span><span class="se">{{</span>
+<span class="s2"> for </span><span class="se">{{</span><span class="s2">set j 0</span><span class="se">}}</span><span class="s2"> </span><span class="se">{{</span><span class="s2">$j < </span><span class="si">{</span><span class="n">ny</span><span class="si">}</span><span class="se">}}</span><span class="s2"> </span><span class="se">{{</span><span class="s2">incr j</span><span class="se">}}</span><span class="s2"> </span><span class="se">{{</span>
+<span class="s2"> for </span><span class="se">{{</span><span class="s2">set k 0</span><span class="se">}}</span><span class="s2"> </span><span class="se">{{</span><span class="s2">$k < </span><span class="si">{</span><span class="n">nz</span><span class="si">}</span><span class="se">}}</span><span class="s2"> </span><span class="se">{{</span><span class="s2">incr k</span><span class="se">}}</span><span class="s2"> </span><span class="se">{{</span>
+<span class="s2"> set outName </span><span class="si">{</span><span class="n">segments_dir</span><span class="si">}</span><span class="s2">/segment_$count</span>
+<span class="s2"> set low_x [expr $min_x + $i * $dx]</span>
+<span class="s2"> set low_y [expr $min_y + $j * $dy]</span>
+<span class="s2"> set low_z [expr $min_z + $k * $dz]</span>
+<span class="s2"> set up_x [expr $min_x + ($i+1) * $dx]</span>
+<span class="s2"> set up_y [expr $min_y + ($j+1) * $dy]</span>
+<span class="s2"> set up_z [expr $min_z + ($k+1) * $dz]</span>
+<span class="s2"> set sel [atomselect top "(x > $low_x and x < $up_x) and (y > $low_y and y < $up_y) and (z > $low_z and z < $up_z)"]</span>
+<span class="s2"> set sel_N [$sel num]</span>
+<span class="s2"> if </span><span class="se">{{</span><span class="s2">$sel_N > 0</span><span class="se">}}</span><span class="s2"> </span><span class="se">{{</span>
+<span class="s2"> $sel writepqr $outName.pqr</span>
+<span class="s2"> $sel writepsf $outName.psf</span>
+<span class="s2"> $sel writepdb $outName.pdb</span>
+<span class="s2"> set count [expr $count + 1]</span>
+<span class="s2"> </span><span class="se">}}</span>
+<span class="s2"> </span><span class="se">}}</span>
+<span class="s2"> </span><span class="se">}}</span>
+<span class="se">}}</span>
+<span class="s2">exit</span>
+<span class="s2">"""</span><span class="p">)</span>
+
+ <span class="c1"># Run segmentation</span>
+ <span class="n">vmd_path</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">simconf</span><span class="o">.</span><span class="n">get_binary</span><span class="p">(</span><span class="s1">'vmd'</span><span class="p">)</span>
+ <span class="k">if</span> <span class="ow">not</span> <span class="n">vmd_path</span><span class="p">:</span>
+ <span class="k">raise</span> <span class="ne">ValueError</span><span class="p">(</span><span class="s2">"VMD binary not found in configuration"</span><span class="p">)</span>
+
+ <span class="n">run</span><span class="p">([</span><span class="n">vmd_path</span><span class="p">,</span> <span class="s2">"-dispdev"</span><span class="p">,</span> <span class="s2">"text"</span><span class="p">,</span> <span class="s2">"-e"</span><span class="p">,</span> <span class="nb">str</span><span class="p">(</span><span class="n">segment_script</span><span class="p">)],</span> <span class="n">check</span><span class="o">=</span><span class="kc">True</span><span class="p">)</span>
+
+ <span class="c1"># Process each segment</span>
+ <span class="n">segments</span> <span class="o">=</span> <span class="nb">list</span><span class="p">(</span><span class="n">segments_dir</span><span class="o">.</span><span class="n">glob</span><span class="p">(</span><span class="s2">"segment_*.pdb"</span><span class="p">))</span>
+ <span class="n">logger</span><span class="o">.</span><span class="n">info</span><span class="p">(</span><span class="sa">f</span><span class="s2">"Found </span><span class="si">{</span><span class="nb">len</span><span class="p">(</span><span class="n">segments</span><span class="p">)</span><span class="si">}</span><span class="s2"> segments to process"</span><span class="p">)</span>
+
+ <span class="c1"># Process each segment</span>
+ <span class="k">for</span> <span class="n">i</span><span class="p">,</span> <span class="n">segment</span> <span class="ow">in</span> <span class="nb">enumerate</span><span class="p">(</span><span class="n">segments</span><span class="p">):</span>
+ <span class="n">segment_dir</span> <span class="o">=</span> <span class="n">segments_dir</span> <span class="o">/</span> <span class="n">segment</span><span class="o">.</span><span class="n">stem</span>
+ <span class="n">os</span><span class="o">.</span><span class="n">makedirs</span><span class="p">(</span><span class="n">segment_dir</span><span class="p">,</span> <span class="n">exist_ok</span><span class="o">=</span><span class="kc">True</span><span class="p">)</span>
+
+ <span class="n">logger</span><span class="o">.</span><span class="n">info</span><span class="p">(</span><span class="sa">f</span><span class="s2">"Processing segment </span><span class="si">{</span><span class="n">i</span><span class="o">+</span><span class="mi">1</span><span class="si">}</span><span class="s2">/</span><span class="si">{</span><span class="nb">len</span><span class="p">(</span><span class="n">segments</span><span class="p">)</span><span class="si">}</span><span class="s2">: </span><span class="si">{</span><span class="n">segment</span><span class="o">.</span><span class="n">stem</span><span class="si">}</span><span class="s2">"</span><span class="p">)</span>
+
+ <span class="n">segment_processor</span> <span class="o">=</span> <span class="n">StructureProcessor</span><span class="p">(</span>
+ <span class="n">structure_path</span><span class="o">=</span><span class="n">segment</span><span class="p">,</span>
+ <span class="n">simconf</span><span class="o">=</span><span class="bp">self</span><span class="o">.</span><span class="n">simconf</span><span class="p">,</span>
+ <span class="n">work_dir</span><span class="o">=</span><span class="n">segment_dir</span><span class="p">)</span>
+
+ <span class="n">segment_processor</span><span class="o">.</span><span class="n">process_structure</span><span class="p">()</span>
+
+ <span class="c1"># Collect grid maps from this segment</span>
+ <span class="n">grid_files</span> <span class="o">=</span> <span class="n">segment_processor</span><span class="o">.</span><span class="n">get_grid_files</span><span class="p">()</span>
+
+ <span class="c1"># Store grids from this segment</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">potential_grids</span><span class="o">.</span><span class="n">extend</span><span class="p">(</span><span class="n">grid_files</span><span class="o">.</span><span class="n">get</span><span class="p">(</span><span class="s1">'potential_grids'</span><span class="p">,</span> <span class="p">[]))</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">charge_grids</span><span class="o">.</span><span class="n">extend</span><span class="p">(</span><span class="n">grid_files</span><span class="o">.</span><span class="n">get</span><span class="p">(</span><span class="s1">'charge_grids'</span><span class="p">,</span> <span class="p">[]))</span>
+
+ <span class="c1"># Store the first electrostatic grid as the main one</span>
+ <span class="k">if</span> <span class="nb">hasattr</span><span class="p">(</span><span class="n">segment_processor</span><span class="p">,</span> <span class="s1">'elec_smoothed_dx'</span><span class="p">)</span> <span class="ow">and</span> <span class="ow">not</span> <span class="bp">self</span><span class="o">.</span><span class="n">elec_grid</span><span class="p">:</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">elec_grid</span> <span class="o">=</span> <span class="n">segment_processor</span><span class="o">.</span><span class="n">elec_smoothed_dx</span>
+
+ <span class="n">logger</span><span class="o">.</span><span class="n">info</span><span class="p">(</span><span class="sa">f</span><span class="s2">"Completed processing gigantic static object: </span><span class="si">{</span><span class="bp">self</span><span class="o">.</span><span class="n">name</span><span class="si">}</span><span class="s2">"</span><span class="p">)</span></div>
+
+
+<div class="viewcode-block" id="StructureRigidBodyModel">
+<a class="viewcode-back" href="../../api/rigidbody_models/structure_rigidbody.html#arbdmodel.structure_rigidbody.StructureRigidBodyModel">[docs]</a>
+<span class="k">class</span><span class="w"> </span><span class="nc">StructureRigidBodyModel</span><span class="p">(</span><span class="n">ArbdModel</span><span class="p">):</span>
+<span class="w"> </span><span class="sd">"""Model class for structure-based rigid body simulations"""</span>
+
+ <span class="k">def</span><span class="w"> </span><span class="fm">__init__</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">cell_vectors</span><span class="o">=</span><span class="kc">None</span><span class="p">,</span> <span class="n">cell_origin</span><span class="o">=</span><span class="kc">None</span><span class="p">,</span>
+ <span class="n">dimensions</span><span class="o">=</span><span class="kc">None</span><span class="p">,</span> <span class="n">buffer_factor</span><span class="o">=</span><span class="mf">1.2</span><span class="p">,</span> <span class="n">configuration</span><span class="o">=</span><span class="kc">None</span><span class="p">,</span> <span class="n">use_boundary</span><span class="o">=</span><span class="kc">True</span><span class="p">,</span>
+ <span class="n">boundary_params</span><span class="o">=</span><span class="kc">None</span><span class="p">,</span> <span class="o">**</span><span class="n">kwargs</span><span class="p">):</span>
+<span class="w"> </span><span class="sd">"""Initialize structure model.</span>
+<span class="sd"> </span>
+<span class="sd"> Args:</span>
+<span class="sd"> diffusible_objects: List of StructureRigidBody instances for diffusible objects</span>
+<span class="sd"> static_objects: List of StructureRigidBody instances for static objects</span>
+<span class="sd"> cell_vectors: List of 3 cell basis vectors defining the simulation box</span>
+<span class="sd"> cell_origin: Cell origin coordinates</span>
+<span class="sd"> dimensions: Explicit dimensions for the simulation box (overrides cell_vectors)</span>
+<span class="sd"> buffer_factor: Factor to scale dimensions derived from cell vectors</span>
+<span class="sd"> configuration: Configuration object, defaults to DefaultSimConf</span>
+<span class="sd"> use_boundary: Whether to create a boundary potential</span>
+<span class="sd"> boundary_params: Optional parameters for boundary potential (well_depth, resolution, etc.)</span>
+<span class="sd"> **kwargs: Additional arguments passed to ArbdModel</span>
+<span class="sd"> """</span>
+
+ <span class="bp">self</span><span class="o">.</span><span class="n">simconf</span> <span class="o">=</span> <span class="n">configuration</span> <span class="ow">or</span> <span class="n">DefaultSimConf</span><span class="p">()</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">diffusible_objects</span> <span class="o">=</span> <span class="p">[]</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">static_objects</span> <span class="o">=</span> <span class="p">[]</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">boundary_potential</span> <span class="o">=</span> <span class="kc">None</span>
+
+ <span class="nb">super</span><span class="p">()</span><span class="o">.</span><span class="fm">__init__</span><span class="p">(</span>
+ <span class="n">children</span><span class="o">=</span><span class="p">[],</span>
+ <span class="n">cell_vectors</span><span class="o">=</span><span class="n">cell_vectors</span><span class="p">,</span>
+ <span class="n">cell_origin</span><span class="o">=</span><span class="n">cell_origin</span><span class="p">,</span>
+ <span class="n">dimensions</span><span class="o">=</span><span class="n">dimensions</span><span class="p">,</span>
+ <span class="n">buffer_factor</span><span class="o">=</span><span class="n">buffer_factor</span><span class="p">,</span>
+ <span class="n">configuration</span><span class="o">=</span><span class="bp">self</span><span class="o">.</span><span class="n">simconf</span><span class="p">,</span>
+ <span class="o">**</span><span class="n">kwargs</span>
+ <span class="p">)</span>
+ <span class="c1"># Process boundary if requested</span>
+ <span class="k">if</span> <span class="n">use_boundary</span><span class="p">:</span>
+ <span class="c1"># Create boundary potential</span>
+ <span class="kn">from</span><span class="w"> </span><span class="nn">.interactions</span><span class="w"> </span><span class="kn">import</span> <span class="n">BoundaryPotential</span>
+
+ <span class="c1"># Use provided boundary parameters or defaults</span>
+ <span class="n">bp_params</span> <span class="o">=</span> <span class="n">boundary_params</span> <span class="ow">or</span> <span class="p">{}</span>
+
+ <span class="n">boundary</span> <span class="o">=</span> <span class="n">BoundaryPotential</span><span class="p">(</span>
+ <span class="n">cell_vectors</span><span class="o">=</span><span class="bp">self</span><span class="o">.</span><span class="n">cell_vectors</span><span class="p">,</span>
+ <span class="n">cell_origin</span><span class="o">=</span><span class="bp">self</span><span class="o">.</span><span class="n">cell_origin</span><span class="p">,</span>
+ <span class="n">well_depth</span><span class="o">=</span><span class="n">bp_params</span><span class="o">.</span><span class="n">get</span><span class="p">(</span><span class="s1">'well_depth'</span><span class="p">,</span> <span class="mf">1.0</span><span class="p">),</span>
+ <span class="n">resolution</span><span class="o">=</span><span class="n">bp_params</span><span class="o">.</span><span class="n">get</span><span class="p">(</span><span class="s1">'resolution'</span><span class="p">,</span> <span class="mf">2.0</span><span class="p">),</span>
+ <span class="n">blur</span><span class="o">=</span><span class="n">bp_params</span><span class="o">.</span><span class="n">get</span><span class="p">(</span><span class="s1">'blur'</span><span class="p">,</span> <span class="mf">5.0</span><span class="p">)</span>
+ <span class="p">)</span>
+
+ <span class="c1"># Generate the boundary file and store it</span>
+ <span class="n">boundary_file</span> <span class="o">=</span> <span class="n">boundary</span><span class="o">.</span><span class="n">write_file</span><span class="p">(</span><span class="n">bp_params</span><span class="o">.</span><span class="n">get</span><span class="p">(</span><span class="s1">'output_file'</span><span class="p">,</span> <span class="s1">'boundary.dx'</span><span class="p">))</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">boundary_potential</span> <span class="o">=</span> <span class="n">boundary</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">add_nonbonded_interaction</span><span class="p">()</span>
+
+
+<div class="viewcode-block" id="StructureRigidBodyModel.add_diffusible_object">
+<a class="viewcode-back" href="../../api/rigidbody_models/structure_rigidbody.html#arbdmodel.structure_rigidbody.StructureRigidBodyModel.add_diffusible_object">[docs]</a>
+ <span class="k">def</span><span class="w"> </span><span class="nf">add_diffusible_object</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">structure_path</span><span class="o">=</span><span class="kc">None</span><span class="p">,</span> <span class="n">rb_type</span><span class="o">=</span><span class="kc">None</span><span class="p">,</span> <span class="n">copies</span><span class="o">=</span><span class="mi">1</span><span class="p">,</span> <span class="n">positions</span><span class="o">=</span><span class="kc">None</span><span class="p">,</span>
+ <span class="n">orientations</span><span class="o">=</span><span class="kc">None</span><span class="p">,</span> <span class="n">name</span><span class="o">=</span><span class="kc">None</span><span class="p">,</span> <span class="n">initial_region</span><span class="o">=</span><span class="kc">None</span><span class="p">,</span> <span class="n">random_seed</span><span class="o">=</span><span class="kc">None</span><span class="p">,</span>
+ <span class="n">work_dir</span><span class="o">=</span><span class="kc">None</span><span class="p">):</span>
+<span class="w"> </span><span class="sd">"""Add a diffusible (mobile) rigid body type to the model.</span>
+<span class="sd"> </span>
+<span class="sd"> Args:</span>
+<span class="sd"> structure_path: Path to structure files (.psf/.pdb) to create a StructureRigidBodyType</span>
+<span class="sd"> rb_type: Existing RigidBodyType instance (if structure_path not provided)</span>
+<span class="sd"> copies: Number of copies to add</span>
+<span class="sd"> positions: Optional list of positions for each copy</span>
+<span class="sd"> orientations: Optional list of orientations for each copy</span>
+<span class="sd"> name: Optional base name for the rigid bodies</span>
+<span class="sd"> initial_region: Optional dict with vectors defining initial region</span>
+<span class="sd"> random_seed: Optional seed for random number generator</span>
+<span class="sd"> work_dir: Optional working directory for structure processing</span>
+<span class="sd"> </span>
+<span class="sd"> Returns:</span>
+<span class="sd"> List of created RigidBody instances</span>
+<span class="sd"> """</span>
+ <span class="c1"># Process the structure to create a RigidBodyType if structure_path provided</span>
+ <span class="k">if</span> <span class="n">structure_path</span> <span class="ow">is</span> <span class="ow">not</span> <span class="kc">None</span><span class="p">:</span>
+ <span class="c1"># Create a StructureRigidBodyType from the structure files</span>
+ <span class="k">if</span> <span class="n">name</span> <span class="ow">is</span> <span class="kc">None</span><span class="p">:</span>
+ <span class="n">name</span> <span class="o">=</span> <span class="n">Path</span><span class="p">(</span><span class="n">structure_path</span><span class="p">)</span><span class="o">.</span><span class="n">stem</span>
+
+ <span class="n">logger</span><span class="o">.</span><span class="n">info</span><span class="p">(</span><span class="sa">f</span><span class="s2">"Processing structure files for </span><span class="si">{</span><span class="n">name</span><span class="si">}</span><span class="s2"> from </span><span class="si">{</span><span class="n">structure_path</span><span class="si">}</span><span class="s2">"</span><span class="p">)</span>
+
+ <span class="c1"># Create work directory</span>
+ <span class="k">if</span> <span class="n">work_dir</span> <span class="ow">is</span> <span class="kc">None</span><span class="p">:</span>
+ <span class="n">work_dir</span> <span class="o">=</span> <span class="n">Path</span><span class="o">.</span><span class="n">cwd</span><span class="p">()</span> <span class="o">/</span> <span class="n">name</span>
+ <span class="n">os</span><span class="o">.</span><span class="n">makedirs</span><span class="p">(</span><span class="n">work_dir</span><span class="p">,</span> <span class="n">exist_ok</span><span class="o">=</span><span class="kc">True</span><span class="p">)</span>
+
+ <span class="c1"># Create the RigidBodyType</span>
+ <span class="n">rb_type</span> <span class="o">=</span> <span class="n">DiffusiveRigidBodyType</span><span class="p">(</span>
+ <span class="n">name</span><span class="o">=</span><span class="n">name</span><span class="p">,</span>
+ <span class="n">structure_path</span><span class="o">=</span><span class="n">structure_path</span><span class="p">,</span>
+ <span class="n">simconf</span><span class="o">=</span><span class="bp">self</span><span class="o">.</span><span class="n">simconf</span><span class="p">,</span>
+ <span class="n">work_dir</span><span class="o">=</span><span class="n">work_dir</span><span class="p">)</span>
+
+ <span class="n">logger</span><span class="o">.</span><span class="n">info</span><span class="p">(</span><span class="sa">f</span><span class="s2">"Created StructureRigidBodyType for </span><span class="si">{</span><span class="n">name</span><span class="si">}</span><span class="s2">"</span><span class="p">)</span>
+
+ <span class="k">elif</span> <span class="n">rb_type</span> <span class="ow">is</span> <span class="kc">None</span><span class="p">:</span>
+ <span class="k">raise</span> <span class="ne">ValueError</span><span class="p">(</span><span class="s2">"Either structure_path or rb_type must be provided"</span><span class="p">)</span>
+
+ <span class="k">if</span> <span class="ow">not</span> <span class="nb">isinstance</span><span class="p">(</span><span class="n">rb_type</span><span class="p">,</span> <span class="n">RigidBodyType</span><span class="p">):</span>
+ <span class="k">raise</span> <span class="ne">TypeError</span><span class="p">(</span><span class="s2">"Object must be a RigidBodyType"</span><span class="p">)</span>
+
+ <span class="c1"># Create base name for rigid bodies of this type</span>
+ <span class="n">base_name</span> <span class="o">=</span> <span class="n">name</span> <span class="ow">or</span> <span class="n">rb_type</span><span class="o">.</span><span class="n">name</span>
+ <span class="n">created_bodies</span> <span class="o">=</span> <span class="p">[]</span>
+
+ <span class="c1"># Generate positions if not provided</span>
+ <span class="k">if</span> <span class="n">positions</span> <span class="ow">is</span> <span class="kc">None</span> <span class="ow">and</span> <span class="n">copies</span> <span class="o">></span> <span class="mi">0</span><span class="p">:</span>
+ <span class="c1"># Set up default initial region if not provided</span>
+ <span class="k">if</span> <span class="n">initial_region</span> <span class="ow">is</span> <span class="kc">None</span><span class="p">:</span>
+ <span class="n">max_dim</span> <span class="o">=</span> <span class="nb">max</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">dimensions</span><span class="p">)</span>
+ <span class="n">initial_region</span> <span class="o">=</span> <span class="p">{</span>
+ <span class="s1">'bv1'</span><span class="p">:</span> <span class="p">[</span><span class="n">max_dim</span><span class="o">*</span><span class="mf">0.8</span><span class="p">,</span> <span class="mi">0</span><span class="p">,</span> <span class="mi">0</span><span class="p">],</span>
+ <span class="s1">'bv2'</span><span class="p">:</span> <span class="p">[</span><span class="mi">0</span><span class="p">,</span> <span class="n">max_dim</span><span class="o">*</span><span class="mf">0.8</span><span class="p">,</span> <span class="mi">0</span><span class="p">],</span>
+ <span class="s1">'bv3'</span><span class="p">:</span> <span class="p">[</span><span class="mi">0</span><span class="p">,</span> <span class="mi">0</span><span class="p">,</span> <span class="n">max_dim</span><span class="o">*</span><span class="mf">0.8</span><span class="p">],</span>
+ <span class="s1">'origin'</span><span class="p">:</span> <span class="p">[</span><span class="mi">0</span><span class="p">,</span> <span class="mi">0</span><span class="p">,</span> <span class="mi">0</span><span class="p">]</span>
+ <span class="p">}</span>
+
+ <span class="c1"># Get dimensions for this rigid body type</span>
+ <span class="n">dimensions</span> <span class="o">=</span> <span class="p">[</span><span class="mi">100</span><span class="p">,</span> <span class="mi">100</span><span class="p">,</span> <span class="mi">100</span><span class="p">]</span> <span class="c1"># Default</span>
+
+ <span class="c1"># Try to get actual dimensions from structure</span>
+ <span class="k">if</span> <span class="nb">hasattr</span><span class="p">(</span><span class="n">rb_type</span><span class="p">,</span> <span class="s1">'aligned_pdb'</span><span class="p">)</span> <span class="ow">and</span> <span class="n">rb_type</span><span class="o">.</span><span class="n">aligned_pdb</span><span class="p">:</span>
+ <span class="k">try</span><span class="p">:</span>
+ <span class="c1"># Try to read dimensions from dimension.dat file in the same directory</span>
+ <span class="n">dim_file</span> <span class="o">=</span> <span class="n">rb_type</span><span class="o">.</span><span class="n">aligned_pdb</span><span class="o">.</span><span class="n">parent</span> <span class="o">/</span> <span class="sa">f</span><span class="s2">"</span><span class="si">{</span><span class="n">rb_type</span><span class="o">.</span><span class="n">aligned_pdb</span><span class="o">.</span><span class="n">stem</span><span class="si">}</span><span class="s2">.dimension.dat"</span>
+ <span class="k">if</span> <span class="n">dim_file</span><span class="o">.</span><span class="n">exists</span><span class="p">():</span>
+ <span class="k">with</span> <span class="nb">open</span><span class="p">(</span><span class="n">dim_file</span><span class="p">)</span> <span class="k">as</span> <span class="n">f</span><span class="p">:</span>
+ <span class="n">dimensions</span> <span class="o">=</span> <span class="p">[</span><span class="nb">float</span><span class="p">(</span><span class="n">line</span><span class="o">.</span><span class="n">strip</span><span class="p">())</span> <span class="k">for</span> <span class="n">line</span> <span class="ow">in</span> <span class="n">f</span><span class="o">.</span><span class="n">readlines</span><span class="p">()]</span>
+ <span class="n">logger</span><span class="o">.</span><span class="n">info</span><span class="p">(</span><span class="sa">f</span><span class="s2">"Using dimensions from </span><span class="si">{</span><span class="n">dim_file</span><span class="si">}</span><span class="s2">: </span><span class="si">{</span><span class="n">dimensions</span><span class="si">}</span><span class="s2">"</span><span class="p">)</span>
+ <span class="k">except</span> <span class="ne">Exception</span> <span class="k">as</span> <span class="n">e</span><span class="p">:</span>
+ <span class="n">logger</span><span class="o">.</span><span class="n">warning</span><span class="p">(</span><span class="sa">f</span><span class="s2">"Could not read dimensions from file: </span><span class="si">{</span><span class="n">e</span><span class="si">}</span><span class="s2">"</span><span class="p">)</span>
+
+ <span class="c1"># Generate spanning vectors</span>
+ <span class="n">bv1</span><span class="p">,</span> <span class="n">bv2</span><span class="p">,</span> <span class="n">bv3</span><span class="p">,</span> <span class="n">n1</span><span class="p">,</span> <span class="n">n2</span><span class="p">,</span> <span class="n">n3</span> <span class="o">=</span> <span class="n">Generate_spanning_vectors</span><span class="p">(</span>
+ <span class="n">initial_region</span><span class="p">[</span><span class="s1">'bv1'</span><span class="p">],</span>
+ <span class="n">initial_region</span><span class="p">[</span><span class="s1">'bv2'</span><span class="p">],</span>
+ <span class="n">initial_region</span><span class="p">[</span><span class="s1">'bv3'</span><span class="p">],</span>
+ <span class="n">dimensions</span>
+ <span class="p">)</span>
+
+ <span class="c1"># Set random seed if provided</span>
+ <span class="k">if</span> <span class="n">random_seed</span> <span class="ow">is</span> <span class="ow">not</span> <span class="kc">None</span><span class="p">:</span>
+ <span class="n">prev_state</span> <span class="o">=</span> <span class="n">np</span><span class="o">.</span><span class="n">random</span><span class="o">.</span><span class="n">get_state</span><span class="p">()</span>
+ <span class="n">np</span><span class="o">.</span><span class="n">random</span><span class="o">.</span><span class="n">seed</span><span class="p">(</span><span class="n">random_seed</span><span class="p">)</span>
+
+ <span class="c1"># Generate coordinates</span>
+ <span class="n">generated_coords</span> <span class="o">=</span> <span class="n">Generate_coordinates</span><span class="p">(</span>
+ <span class="n">bv1</span><span class="p">,</span> <span class="n">bv2</span><span class="p">,</span> <span class="n">bv3</span><span class="p">,</span> <span class="n">n1</span><span class="p">,</span> <span class="n">n2</span><span class="p">,</span> <span class="n">n3</span><span class="p">,</span> <span class="n">copies</span><span class="p">,</span>
+ <span class="n">initial_region</span><span class="p">[</span><span class="s1">'origin'</span><span class="p">],</span> <span class="n">random_seed</span> <span class="ow">or</span> <span class="mi">0</span>
+ <span class="p">)</span>
+
+ <span class="c1"># Restore random state if we changed it</span>
+ <span class="k">if</span> <span class="n">random_seed</span> <span class="ow">is</span> <span class="ow">not</span> <span class="kc">None</span><span class="p">:</span>
+ <span class="n">np</span><span class="o">.</span><span class="n">random</span><span class="o">.</span><span class="n">set_state</span><span class="p">(</span><span class="n">prev_state</span><span class="p">)</span>
+
+ <span class="c1"># Store positions for later use</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">initial_positions</span><span class="p">[</span><span class="n">rb_type</span><span class="o">.</span><span class="n">name</span><span class="p">]</span> <span class="o">=</span> <span class="n">generated_coords</span>
+ <span class="n">positions</span> <span class="o">=</span> <span class="n">generated_coords</span>
+
+ <span class="n">logger</span><span class="o">.</span><span class="n">info</span><span class="p">(</span><span class="sa">f</span><span class="s2">"Generated </span><span class="si">{</span><span class="n">copies</span><span class="si">}</span><span class="s2"> initial positions for </span><span class="si">{</span><span class="n">rb_type</span><span class="o">.</span><span class="n">name</span><span class="si">}</span><span class="s2">"</span><span class="p">)</span>
+
+ <span class="c1"># Set up default orientation if none provided</span>
+ <span class="n">default_orientation</span> <span class="o">=</span> <span class="n">np</span><span class="o">.</span><span class="n">eye</span><span class="p">(</span><span class="mi">3</span><span class="p">)</span>
+
+ <span class="c1"># Add requested number of copies</span>
+ <span class="k">for</span> <span class="n">i</span> <span class="ow">in</span> <span class="nb">range</span><span class="p">(</span><span class="n">copies</span><span class="p">):</span>
+ <span class="c1"># Create position and orientation for this copy</span>
+ <span class="k">if</span> <span class="n">positions</span> <span class="ow">is</span> <span class="ow">not</span> <span class="kc">None</span> <span class="ow">and</span> <span class="n">i</span> <span class="o"><</span> <span class="nb">len</span><span class="p">(</span><span class="n">positions</span><span class="p">):</span>
+ <span class="n">position</span> <span class="o">=</span> <span class="n">positions</span><span class="p">[</span><span class="n">i</span><span class="p">]</span>
+ <span class="k">else</span><span class="p">:</span>
+ <span class="c1"># Generate random position within the model bounds</span>
+ <span class="n">position</span> <span class="o">=</span> <span class="n">np</span><span class="o">.</span><span class="n">random</span><span class="o">.</span><span class="n">uniform</span><span class="p">(</span><span class="o">-</span><span class="mf">0.4</span><span class="p">,</span> <span class="mf">0.4</span><span class="p">,</span> <span class="mi">3</span><span class="p">)</span> <span class="o">*</span> <span class="bp">self</span><span class="o">.</span><span class="n">dimensions</span>
+
+ <span class="k">if</span> <span class="n">orientations</span> <span class="ow">is</span> <span class="ow">not</span> <span class="kc">None</span> <span class="ow">and</span> <span class="n">i</span> <span class="o"><</span> <span class="nb">len</span><span class="p">(</span><span class="n">orientations</span><span class="p">):</span>
+ <span class="n">orientation</span> <span class="o">=</span> <span class="n">orientations</span><span class="p">[</span><span class="n">i</span><span class="p">]</span>
+ <span class="k">else</span><span class="p">:</span>
+ <span class="n">orientation</span> <span class="o">=</span> <span class="n">default_orientation</span>
+
+ <span class="c1"># Create a new rigid body</span>
+ <span class="n">rb_name</span> <span class="o">=</span> <span class="sa">f</span><span class="s2">"</span><span class="si">{</span><span class="n">base_name</span><span class="si">}</span><span class="s2">_</span><span class="si">{</span><span class="n">i</span><span class="o">+</span><span class="mi">1</span><span class="si">}</span><span class="s2">"</span> <span class="k">if</span> <span class="n">copies</span> <span class="o">></span> <span class="mi">1</span> <span class="k">else</span> <span class="n">base_name</span>
+ <span class="n">rb</span> <span class="o">=</span> <span class="n">RigidBody</span><span class="p">(</span>
+ <span class="n">type_</span><span class="o">=</span><span class="n">rb_type</span><span class="p">,</span>
+ <span class="n">position</span><span class="o">=</span><span class="n">position</span><span class="p">,</span>
+ <span class="n">orientation</span><span class="o">=</span><span class="n">orientation</span><span class="p">,</span>
+ <span class="n">name</span><span class="o">=</span><span class="n">rb_name</span><span class="p">)</span>
+
+ <span class="c1"># Add to model</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">diffusible_objects</span><span class="o">.</span><span class="n">append</span><span class="p">(</span><span class="n">rb</span><span class="p">)</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">add</span><span class="p">(</span><span class="n">rb</span><span class="p">)</span>
+ <span class="n">created_bodies</span><span class="o">.</span><span class="n">append</span><span class="p">(</span><span class="n">rb</span><span class="p">)</span>
+
+ <span class="k">return</span> <span class="n">created_bodies</span></div>
+
+
+<div class="viewcode-block" id="StructureRigidBodyModel.add_static_object">
+<a class="viewcode-back" href="../../api/rigidbody_models/structure_rigidbody.html#arbdmodel.structure_rigidbody.StructureRigidBodyModel.add_static_object">[docs]</a>
+ <span class="k">def</span><span class="w"> </span><span class="nf">add_static_object</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span><span class="n">structure_path</span><span class="p">,</span> <span class="n">work_dir</span><span class="o">=</span><span class="kc">None</span><span class="p">,</span><span class="n">is_gigantic</span><span class="o">=</span><span class="kc">False</span><span class="p">,</span> <span class="n">threshold</span><span class="o">=</span><span class="mi">300</span><span class="p">):</span>
+<span class="w"> </span><span class="sd">"""Add this static object to an ARBD model.</span>
+<span class="sd"> </span>
+<span class="sd"> Args:</span>
+<span class="sd"> model: ArbdModel to add this static object to</span>
+<span class="sd"> """</span>
+ <span class="n">obj</span><span class="o">=</span><span class="n">StaticObject</span><span class="p">(</span><span class="n">structure_path</span><span class="o">=</span><span class="n">structure_path</span><span class="p">,</span> <span class="n">work_dir</span><span class="o">=</span><span class="n">work_dir</span><span class="p">,</span>
+ <span class="n">simconf</span><span class="o">=</span><span class="bp">self</span><span class="o">.</span><span class="n">simconf</span><span class="p">,</span><span class="n">is_gigantic</span><span class="o">=</span><span class="n">is_gigantic</span><span class="p">,</span><span class="n">threshold</span><span class="o">=</span><span class="n">threshold</span><span class="p">)</span>
+ <span class="n">elec_grid</span> <span class="o">=</span> <span class="n">obj</span><span class="o">.</span><span class="n">elec_grid</span>
+ <span class="n">potential_grids</span> <span class="o">=</span> <span class="n">obj</span><span class="o">.</span><span class="n">potential_grids</span>
+ <span class="n">charge_grids</span> <span class="o">=</span> <span class="n">obj</span><span class="o">.</span><span class="n">charge_grids</span>
+ <span class="c1"># First add electrostatic grid if available</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">add_nonbonded_interaction</span><span class="p">(</span><span class="n">elec_grid</span><span class="p">)</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">add_nonbonded_interaction</span><span class="p">(</span><span class="n">potential_grids</span><span class="p">)</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">add_nonbonded_interaction</span><span class="p">(</span><span class="n">charge_grids</span><span class="p">)</span>
+
+ <span class="bp">self</span><span class="o">.</span><span class="n">static_objects</span><span class="o">.</span><span class="n">append</span><span class="p">(</span><span class="n">obj</span><span class="p">)</span></div>
+</div>
+
+
+<div class="viewcode-block" id="SimpleArbdEngine">
+<a class="viewcode-back" href="../../api/rigidbody_models/structure_rigidbody.html#arbdmodel.structure_rigidbody.SimpleArbdEngine">[docs]</a>
+<span class="k">class</span><span class="w"> </span><span class="nc">SimpleArbdEngine</span><span class="p">(</span><span class="n">ArbdEngine</span><span class="p">):</span>
+<span class="w"> </span><span class="sd">"""Enhanced ARBD engine with additional functionality for structure simulations"""</span>
+
+ <span class="k">def</span><span class="w"> </span><span class="fm">__init__</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">extra_bd_file_lines</span><span class="o">=</span><span class="s2">""</span><span class="p">,</span> <span class="n">configuration</span><span class="o">=</span><span class="kc">None</span><span class="p">,</span> <span class="o">**</span><span class="n">conf_params</span><span class="p">):</span>
+<span class="w"> </span><span class="sd">"""Initialize SimpleArbdEngine.</span>
+<span class="sd"> </span>
+<span class="sd"> Args:</span>
+<span class="sd"> extra_bd_file_lines: Additional lines for BD configuration file</span>
+<span class="sd"> configuration: SimConf object</span>
+<span class="sd"> **conf_params: Additional configuration parameters</span>
+<span class="sd"> """</span>
+ <span class="nb">super</span><span class="p">()</span><span class="o">.</span><span class="fm">__init__</span><span class="p">(</span><span class="n">extra_bd_file_lines</span><span class="p">,</span> <span class="n">configuration</span><span class="p">,</span> <span class="o">**</span><span class="n">conf_params</span><span class="p">)</span>
+
+<div class="viewcode-block" id="SimpleArbdEngine.write_simulation_files">
+<a class="viewcode-back" href="../../api/rigidbody_models/structure_rigidbody.html#arbdmodel.structure_rigidbody.SimpleArbdEngine.write_simulation_files">[docs]</a>
+ <span class="k">def</span><span class="w"> </span><span class="nf">write_simulation_files</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">model</span><span class="p">,</span> <span class="n">output_name</span><span class="p">,</span> <span class="n">configuration</span><span class="o">=</span><span class="kc">None</span><span class="p">,</span> <span class="o">**</span><span class="n">conf_params</span><span class="p">):</span>
+<span class="w"> </span><span class="sd">"""Write all simulation files.</span>
+<span class="sd"> </span>
+<span class="sd"> Args:</span>
+<span class="sd"> model: ArbdModel to simulate</span>
+<span class="sd"> output_name: Base name for output files</span>
+<span class="sd"> configuration: SimConf object</span>
+<span class="sd"> **conf_params: Additional configuration parameters</span>
+<span class="sd"> """</span>
+ <span class="c1"># Call parent method to write standard files</span>
+ <span class="nb">super</span><span class="p">()</span><span class="o">.</span><span class="n">write_simulation_files</span><span class="p">(</span><span class="n">model</span><span class="p">,</span> <span class="n">output_name</span><span class="p">,</span> <span class="n">configuration</span><span class="p">,</span> <span class="o">**</span><span class="n">conf_params</span><span class="p">)</span>
+
+ <span class="c1"># Additional functionality for structure rigid bodies</span>
+ <span class="k">if</span> <span class="nb">hasattr</span><span class="p">(</span><span class="n">model</span><span class="p">,</span> <span class="s1">'diffusible_objects'</span><span class="p">)</span> <span class="ow">and</span> <span class="n">model</span><span class="o">.</span><span class="n">diffusible_objects</span><span class="p">:</span>
+ <span class="n">logger</span><span class="o">.</span><span class="n">info</span><span class="p">(</span><span class="sa">f</span><span class="s2">"Writing </span><span class="si">{</span><span class="nb">len</span><span class="p">(</span><span class="n">model</span><span class="o">.</span><span class="n">diffusible_objects</span><span class="p">)</span><span class="si">}</span><span class="s2"> diffusible objects"</span><span class="p">)</span>
+
+ <span class="k">if</span> <span class="nb">hasattr</span><span class="p">(</span><span class="n">model</span><span class="p">,</span> <span class="s1">'static_objects'</span><span class="p">)</span> <span class="ow">and</span> <span class="n">model</span><span class="o">.</span><span class="n">static_objects</span><span class="p">:</span>
+ <span class="n">logger</span><span class="o">.</span><span class="n">info</span><span class="p">(</span><span class="sa">f</span><span class="s2">"Writing </span><span class="si">{</span><span class="nb">len</span><span class="p">(</span><span class="n">model</span><span class="o">.</span><span class="n">static_objects</span><span class="p">)</span><span class="si">}</span><span class="s2"> static objects"</span><span class="p">)</span></div>
+
+
+<div class="viewcode-block" id="SimpleArbdEngine.run_simulation">
+<a class="viewcode-back" href="../../api/rigidbody_models/structure_rigidbody.html#arbdmodel.structure_rigidbody.SimpleArbdEngine.run_simulation">[docs]</a>
+ <span class="k">def</span><span class="w"> </span><span class="nf">run_simulation</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">model</span><span class="p">,</span> <span class="n">output_name</span><span class="p">,</span> <span class="n">replicas</span><span class="o">=</span><span class="mi">1</span><span class="p">,</span> <span class="n">gpu</span><span class="o">=</span><span class="mi">0</span><span class="p">,</span> <span class="o">**</span><span class="n">kwargs</span><span class="p">):</span>
+<span class="w"> </span><span class="sd">"""Run ARBD simulation.</span>
+<span class="sd"> </span>
+<span class="sd"> Args:</span>
+<span class="sd"> model: ArbdModel to simulate</span>
+<span class="sd"> output_name: Base name for output files</span>
+<span class="sd"> replicas: Number of replicas to run</span>
+<span class="sd"> gpu: GPU index to use</span>
+<span class="sd"> **kwargs: Additional arguments for simulate method</span>
+<span class="sd"> """</span>
+ <span class="c1"># Prepare output directory</span>
+ <span class="n">output_dir</span> <span class="o">=</span> <span class="n">kwargs</span><span class="o">.</span><span class="n">get</span><span class="p">(</span><span class="s1">'output_directory'</span><span class="p">,</span> <span class="s1">'output'</span><span class="p">)</span>
+ <span class="k">if</span> <span class="ow">not</span> <span class="n">os</span><span class="o">.</span><span class="n">path</span><span class="o">.</span><span class="n">exists</span><span class="p">(</span><span class="n">output_dir</span><span class="p">):</span>
+ <span class="n">os</span><span class="o">.</span><span class="n">makedirs</span><span class="p">(</span><span class="n">output_dir</span><span class="p">)</span>
+
+ <span class="c1"># Run simulations</span>
+ <span class="k">for</span> <span class="n">i</span> <span class="ow">in</span> <span class="nb">range</span><span class="p">(</span><span class="n">replicas</span><span class="p">):</span>
+ <span class="n">replica_name</span> <span class="o">=</span> <span class="sa">f</span><span class="s2">"</span><span class="si">{</span><span class="n">output_name</span><span class="si">}</span><span class="s2">_</span><span class="si">{</span><span class="n">i</span><span class="si">}</span><span class="s2">"</span> <span class="k">if</span> <span class="n">replicas</span> <span class="o">></span> <span class="mi">1</span> <span class="k">else</span> <span class="n">output_name</span>
+
+ <span class="c1"># Override GPU index if running multiple replicas</span>
+ <span class="k">if</span> <span class="n">replicas</span> <span class="o">></span> <span class="mi">1</span><span class="p">:</span>
+ <span class="n">kwargs</span><span class="p">[</span><span class="s1">'gpu'</span><span class="p">]</span> <span class="o">=</span> <span class="p">(</span><span class="n">gpu</span> <span class="o">+</span> <span class="n">i</span><span class="p">)</span> <span class="o">%</span> <span class="mi">8</span> <span class="c1"># Assuming max 8 GPUs</span>
+
+ <span class="c1"># Run simulation</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">simulate</span><span class="p">(</span><span class="n">model</span><span class="p">,</span> <span class="n">replica_name</span><span class="p">,</span> <span class="o">**</span><span class="n">kwargs</span><span class="p">)</span></div>
+</div>
+
+</pre></div>
+
+ </article>
+
+
+
+
+
+
+ <footer class="prev-next-footer d-print-none">
+
+<div class="prev-next-area">
+</div>
+ </footer>
+
+ </div>
+
+
+
+
+ </div>
+ <footer class="bd-footer-content">
+
+<div class="bd-footer-content__inner container">
+
+ <div class="footer-item">
+
+<p class="component-author">
+By ARBD Model Team
+</p>
+
+ </div>
+
+ <div class="footer-item">
+
+
+ <p class="copyright">
+
+ © Copyright 2023.
+ <br/>
+
+ </p>
+
+ </div>
+
+ <div class="footer-item">
+
+ </div>
+
+ <div class="footer-item">
+
+ </div>
+
+</div>
+ </footer>
+
+
+ </main>
+ </div>
+ </div>
+
+ <!-- Scripts loaded after <body> so the DOM is not blocked -->
+ <script src="../../_static/scripts/bootstrap.js?digest=dfe6caa3a7d634c4db9b"></script>
+<script src="../../_static/scripts/pydata-sphinx-theme.js?digest=dfe6caa3a7d634c4db9b"></script>
+
+ <footer class="bd-footer">
+ </footer>
+ </body>
+</html>
\ No newline at end of file
diff --git a/_build/html/_modules/index.html b/_build/html/_modules/index.html
index ccc68df13f8091c0bba93d95034808f616ca6f7e..7add2515093501a5b898d78308f2df16cb5bf2c5 100644
--- a/_build/html/_modules/index.html
+++ b/_build/html/_modules/index.html
@@ -31,19 +31,19 @@
<link rel="stylesheet" type="text/css" href="../_static/styles/sphinx-book-theme.css?v=eba8b062" />
<link rel="stylesheet" type="text/css" href="../_static/togglebutton.css?v=13237357" />
<link rel="stylesheet" type="text/css" href="../_static/copybutton.css?v=76b2166b" />
- <link rel="stylesheet" type="text/css" href="../_static/mystnb.4510f1fc1dee50b3e5859aac5469c37c29e427902b24a333a5f9fcb2f0b3ac41.css" />
+ <link rel="stylesheet" type="text/css" href="../_static/mystnb.4510f1fc1dee50b3e5859aac5469c37c29e427902b24a333a5f9fcb2f0b3ac41.css?v=be8a1c11" />
<link rel="stylesheet" type="text/css" href="../_static/sphinx-thebe.css?v=4fa983c6" />
<link rel="stylesheet" type="text/css" href="../_static/tabs.css?v=4c969af8" />
- <link rel="stylesheet" type="text/css" href="../_static/proof.css" />
+ <link rel="stylesheet" type="text/css" href="../_static/proof.css?v=b4b7a797" />
<link rel="stylesheet" type="text/css" href="../_static/styles/sphinx-examples.css?v=e236af4b" />
- <link rel="stylesheet" type="text/css" href="../_static/css/tooltipster.custom.css" />
- <link rel="stylesheet" type="text/css" href="../_static/css/tooltipster.bundle.min.css" />
- <link rel="stylesheet" type="text/css" href="../_static/css/tooltipster-sideTip-shadow.min.css" />
- <link rel="stylesheet" type="text/css" href="../_static/css/tooltipster-sideTip-punk.min.css" />
- <link rel="stylesheet" type="text/css" href="../_static/css/tooltipster-sideTip-noir.min.css" />
- <link rel="stylesheet" type="text/css" href="../_static/css/tooltipster-sideTip-light.min.css" />
- <link rel="stylesheet" type="text/css" href="../_static/css/tooltipster-sideTip-borderless.min.css" />
- <link rel="stylesheet" type="text/css" href="../_static/css/micromodal.css" />
+ <link rel="stylesheet" type="text/css" href="../_static/css/tooltipster.custom.css?v=7bc2f056" />
+ <link rel="stylesheet" type="text/css" href="../_static/css/tooltipster.bundle.min.css?v=37217874" />
+ <link rel="stylesheet" type="text/css" href="../_static/css/tooltipster-sideTip-shadow.min.css?v=6227e517" />
+ <link rel="stylesheet" type="text/css" href="../_static/css/tooltipster-sideTip-punk.min.css?v=94669e23" />
+ <link rel="stylesheet" type="text/css" href="../_static/css/tooltipster-sideTip-noir.min.css?v=21a39f42" />
+ <link rel="stylesheet" type="text/css" href="../_static/css/tooltipster-sideTip-light.min.css?v=a18b2449" />
+ <link rel="stylesheet" type="text/css" href="../_static/css/tooltipster-sideTip-borderless.min.css?v=dbff53e4" />
+ <link rel="stylesheet" type="text/css" href="../_static/css/micromodal.css?v=d7bf34ee" />
<link rel="stylesheet" type="text/css" href="../_static/sphinx-design.min.css?v=95c83b7e" />
<!-- Pre-loaded scripts that we'll load fully later -->
@@ -60,9 +60,9 @@
<script src="../_static/copybutton.js?v=f281be69"></script>
<script src="../_static/scripts/sphinx-book-theme.js?v=887ef09a"></script>
<script src="../_static/tabs.js?v=3ee01567"></script>
- <script src="../_static/js/hoverxref.js"></script>
- <script src="../_static/js/tooltipster.bundle.min.js"></script>
- <script src="../_static/js/micromodal.min.js"></script>
+ <script src="../_static/js/hoverxref.js?v=c95ade4f"></script>
+ <script src="../_static/js/tooltipster.bundle.min.js?v=18bf091b"></script>
+ <script src="../_static/js/micromodal.min.js?v=04d6302d"></script>
<script>let toggleHintShow = 'Click to show';</script>
<script>let toggleHintHide = 'Click to hide';</script>
<script>let toggleOpenOnPrint = 'true';</script>
@@ -300,18 +300,32 @@ document.write(`
<article class="bd-article">
<h1>All modules for which code is available</h1>
-<ul><li><a href="arbdmodel/coords.html">arbdmodel.coords</a></li>
+<ul><li><a href="arbdmodel/binary_manager.html">arbdmodel.binary_manager</a></li>
+<li><a href="arbdmodel/coords.html">arbdmodel.coords</a></li>
+<li><a href="arbdmodel/core_objects.html">arbdmodel.core_objects</a></li>
+<li><a href="arbdmodel/engine.html">arbdmodel.engine</a></li>
<li><a href="arbdmodel/fjc_polymer_model.html">arbdmodel.fjc_polymer_model</a></li>
<li><a href="arbdmodel/grid.html">arbdmodel.grid</a></li>
<li><a href="arbdmodel/hps_polymer_model.html">arbdmodel.hps_polymer_model</a></li>
<li><a href="arbdmodel/ibi.html">arbdmodel.ibi</a></li>
<li><a href="arbdmodel/interactions.html">arbdmodel.interactions</a></li>
<li><a href="arbdmodel/kh_polymer_model.html">arbdmodel.kh_polymer_model</a></li>
+<li><a href="arbdmodel/logger.html">arbdmodel.logger</a></li>
+<li><a href="arbdmodel/mesh_process_surface.html">arbdmodel.mesh_process_surface</a></li>
+<li><a href="arbdmodel/mesh_process_volume.html">arbdmodel.mesh_process_volume</a></li>
+<li><a href="arbdmodel/mesh_rigidbody.html">arbdmodel.mesh_rigidbody</a></li>
+<li><a href="arbdmodel/model.html">arbdmodel.model</a></li>
<li><a href="arbdmodel/mpipi_polymer.html">arbdmodel.mpipi_polymer</a></li>
<li><a href="arbdmodel/onck_polymer_model.html">arbdmodel.onck_polymer_model</a></li>
+<li><a href="arbdmodel/parmed_bd.html">arbdmodel.parmed_bd</a></li>
<li><a href="arbdmodel/polymer.html">arbdmodel.polymer</a></li>
+<li><a href="arbdmodel/sali_polymer_model.html">arbdmodel.sali_polymer_model</a></li>
<li><a href="arbdmodel/shape_cg.html">arbdmodel.shape_cg</a></li>
+<li><a href="arbdmodel/sim_config.html">arbdmodel.sim_config</a></li>
+<li><a href="arbdmodel/simplearbd.html">arbdmodel.simplearbd</a></li>
<li><a href="arbdmodel/ssdna_two_bead.html">arbdmodel.ssdna_two_bead</a></li>
+<li><a href="arbdmodel/structure_from_pdb.html">arbdmodel.structure_from_pdb</a></li>
+<li><a href="arbdmodel/structure_rigidbody.html">arbdmodel.structure_rigidbody</a></li>
<li><a href="arbdmodel/version.html">arbdmodel.version</a></li>
</ul>
diff --git a/_build/html/_sources/tutorials/index.md b/_build/html/_sources/tutorials/index.md
index 9e0793fdac81501680e3399a8ec159606bd73e52..ae7fdbe821d5571dda7e2a7e5444f63f208cc63b 100644
--- a/_build/html/_sources/tutorials/index.md
+++ b/_build/html/_sources/tutorials/index.md
@@ -4,12 +4,6 @@ This section contains tutorials and examples for working with the arbdmodel pack
## Available Tutorials
-### 1- basics
-- [1 Basics](1-basics.ipynb)
-
-### 2-polymer_objects
-- [2 Polymer Objects](2-polymer-objects.ipynb)
-
### 3-iterative-boltzmann-inversion
- [3 Ibi](3-iterative-boltzmann-inversion/3-ibi.ipynb)
@@ -18,4 +12,5 @@ This section contains tutorials and examples for working with the arbdmodel pack
- [4 Rigid Bodies](4-rigid-bodies/4-rigid-bodies.ipynb)
-
+- [1 Basics](1-basics.ipynb)
+- [2 Polymer Objects](2-polymer-objects.ipynb)
diff --git a/_build/html/api/core/core_objects.html b/_build/html/api/core/core_objects.html
index 4ec3da9c5f150e5f470e466e8c919ca3b6263f13..a2dc8819608b9db333e6b3482012074421e88ee0 100644
--- a/_build/html/api/core/core_objects.html
+++ b/_build/html/api/core/core_objects.html
@@ -32,19 +32,19 @@
<link rel="stylesheet" type="text/css" href="../../_static/styles/sphinx-book-theme.css?v=eba8b062" />
<link rel="stylesheet" type="text/css" href="../../_static/togglebutton.css?v=13237357" />
<link rel="stylesheet" type="text/css" href="../../_static/copybutton.css?v=76b2166b" />
- <link rel="stylesheet" type="text/css" href="../../_static/mystnb.4510f1fc1dee50b3e5859aac5469c37c29e427902b24a333a5f9fcb2f0b3ac41.css" />
+ <link rel="stylesheet" type="text/css" href="../../_static/mystnb.4510f1fc1dee50b3e5859aac5469c37c29e427902b24a333a5f9fcb2f0b3ac41.css?v=be8a1c11" />
<link rel="stylesheet" type="text/css" href="../../_static/sphinx-thebe.css?v=4fa983c6" />
<link rel="stylesheet" type="text/css" href="../../_static/tabs.css?v=4c969af8" />
- <link rel="stylesheet" type="text/css" href="../../_static/proof.css" />
+ <link rel="stylesheet" type="text/css" href="../../_static/proof.css?v=b4b7a797" />
<link rel="stylesheet" type="text/css" href="../../_static/styles/sphinx-examples.css?v=e236af4b" />
- <link rel="stylesheet" type="text/css" href="../../_static/css/tooltipster.custom.css" />
- <link rel="stylesheet" type="text/css" href="../../_static/css/tooltipster.bundle.min.css" />
- <link rel="stylesheet" type="text/css" href="../../_static/css/tooltipster-sideTip-shadow.min.css" />
- <link rel="stylesheet" type="text/css" href="../../_static/css/tooltipster-sideTip-punk.min.css" />
- <link rel="stylesheet" type="text/css" href="../../_static/css/tooltipster-sideTip-noir.min.css" />
- <link rel="stylesheet" type="text/css" href="../../_static/css/tooltipster-sideTip-light.min.css" />
- <link rel="stylesheet" type="text/css" href="../../_static/css/tooltipster-sideTip-borderless.min.css" />
- <link rel="stylesheet" type="text/css" href="../../_static/css/micromodal.css" />
+ <link rel="stylesheet" type="text/css" href="../../_static/css/tooltipster.custom.css?v=7bc2f056" />
+ <link rel="stylesheet" type="text/css" href="../../_static/css/tooltipster.bundle.min.css?v=37217874" />
+ <link rel="stylesheet" type="text/css" href="../../_static/css/tooltipster-sideTip-shadow.min.css?v=6227e517" />
+ <link rel="stylesheet" type="text/css" href="../../_static/css/tooltipster-sideTip-punk.min.css?v=94669e23" />
+ <link rel="stylesheet" type="text/css" href="../../_static/css/tooltipster-sideTip-noir.min.css?v=21a39f42" />
+ <link rel="stylesheet" type="text/css" href="../../_static/css/tooltipster-sideTip-light.min.css?v=a18b2449" />
+ <link rel="stylesheet" type="text/css" href="../../_static/css/tooltipster-sideTip-borderless.min.css?v=dbff53e4" />
+ <link rel="stylesheet" type="text/css" href="../../_static/css/micromodal.css?v=d7bf34ee" />
<link rel="stylesheet" type="text/css" href="../../_static/sphinx-design.min.css?v=95c83b7e" />
<!-- Pre-loaded scripts that we'll load fully later -->
@@ -61,9 +61,9 @@
<script src="../../_static/copybutton.js?v=f281be69"></script>
<script src="../../_static/scripts/sphinx-book-theme.js?v=887ef09a"></script>
<script src="../../_static/tabs.js?v=3ee01567"></script>
- <script src="../../_static/js/hoverxref.js"></script>
- <script src="../../_static/js/tooltipster.bundle.min.js"></script>
- <script src="../../_static/js/micromodal.min.js"></script>
+ <script src="../../_static/js/hoverxref.js?v=c95ade4f"></script>
+ <script src="../../_static/js/tooltipster.bundle.min.js?v=18bf091b"></script>
+ <script src="../../_static/js/micromodal.min.js?v=04d6302d"></script>
<script>let toggleHintShow = 'Click to show';</script>
<script>let toggleHintHide = 'Click to hide';</script>
<script>let toggleOpenOnPrint = 'true';</script>
@@ -323,7 +323,9 @@ document.write(`
</button>
`);
</script>
-
+<button class="sidebar-toggle secondary-toggle btn btn-sm" title="Toggle secondary sidebar" data-bs-placement="bottom" data-bs-toggle="tooltip">
+ <span class="fa-solid fa-list"></span>
+</button>
</div></div>
</div>
@@ -339,6 +341,86 @@ document.write(`
<div id="print-main-content">
<div id="jb-print-toc">
+ <div>
+ <h2> Contents </h2>
+ </div>
+ <nav aria-label="Page">
+ <ul class="visible nav section-nav flex-column">
+<li class="toc-h2 nav-item toc-entry"><a class="reference internal nav-link" href="#arbdmodel.core_objects.Child"><code class="docutils literal notranslate"><span class="pre">Child</span></code></a></li>
+<li class="toc-h2 nav-item toc-entry"><a class="reference internal nav-link" href="#arbdmodel.core_objects.Clone"><code class="docutils literal notranslate"><span class="pre">Clone</span></code></a><ul class="nav section-nav flex-column">
+<li class="toc-h3 nav-item toc-entry"><a class="reference internal nav-link" href="#arbdmodel.core_objects.Clone.get_original_recursively"><code class="docutils literal notranslate"><span class="pre">Clone.get_original_recursively()</span></code></a></li>
+</ul>
+</li>
+<li class="toc-h2 nav-item toc-entry"><a class="reference internal nav-link" href="#arbdmodel.core_objects.Group"><code class="docutils literal notranslate"><span class="pre">Group</span></code></a><ul class="nav section-nav flex-column">
+<li class="toc-h3 nav-item toc-entry"><a class="reference internal nav-link" href="#arbdmodel.core_objects.Group.clone"><code class="docutils literal notranslate"><span class="pre">Group.clone()</span></code></a></li>
+<li class="toc-h3 nav-item toc-entry"><a class="reference internal nav-link" href="#arbdmodel.core_objects.Group.duplicate"><code class="docutils literal notranslate"><span class="pre">Group.duplicate()</span></code></a></li>
+</ul>
+</li>
+<li class="toc-h2 nav-item toc-entry"><a class="reference internal nav-link" href="#arbdmodel.core_objects.GroupSite"><code class="docutils literal notranslate"><span class="pre">GroupSite</span></code></a><ul class="nav section-nav flex-column">
+<li class="toc-h3 nav-item toc-entry"><a class="reference internal nav-link" href="#arbdmodel.core_objects.GroupSite.add_restraint"><code class="docutils literal notranslate"><span class="pre">GroupSite.add_restraint()</span></code></a></li>
+<li class="toc-h3 nav-item toc-entry"><a class="reference internal nav-link" href="#arbdmodel.core_objects.GroupSite.get_center"><code class="docutils literal notranslate"><span class="pre">GroupSite.get_center()</span></code></a></li>
+<li class="toc-h3 nav-item toc-entry"><a class="reference internal nav-link" href="#arbdmodel.core_objects.GroupSite.get_restraints"><code class="docutils literal notranslate"><span class="pre">GroupSite.get_restraints()</span></code></a></li>
+</ul>
+</li>
+<li class="toc-h2 nav-item toc-entry"><a class="reference internal nav-link" href="#arbdmodel.core_objects.Parent"><code class="docutils literal notranslate"><span class="pre">Parent</span></code></a><ul class="nav section-nav flex-column">
+<li class="toc-h3 nav-item toc-entry"><a class="reference internal nav-link" href="#arbdmodel.core_objects.Parent.add"><code class="docutils literal notranslate"><span class="pre">Parent.add()</span></code></a></li>
+<li class="toc-h3 nav-item toc-entry"><a class="reference internal nav-link" href="#arbdmodel.core_objects.Parent.add_angle"><code class="docutils literal notranslate"><span class="pre">Parent.add_angle()</span></code></a></li>
+<li class="toc-h3 nav-item toc-entry"><a class="reference internal nav-link" href="#arbdmodel.core_objects.Parent.add_bond"><code class="docutils literal notranslate"><span class="pre">Parent.add_bond()</span></code></a></li>
+<li class="toc-h3 nav-item toc-entry"><a class="reference internal nav-link" href="#arbdmodel.core_objects.Parent.add_bond_angle"><code class="docutils literal notranslate"><span class="pre">Parent.add_bond_angle()</span></code></a></li>
+<li class="toc-h3 nav-item toc-entry"><a class="reference internal nav-link" href="#arbdmodel.core_objects.Parent.add_dihedral"><code class="docutils literal notranslate"><span class="pre">Parent.add_dihedral()</span></code></a></li>
+<li class="toc-h3 nav-item toc-entry"><a class="reference internal nav-link" href="#arbdmodel.core_objects.Parent.add_exclusion"><code class="docutils literal notranslate"><span class="pre">Parent.add_exclusion()</span></code></a></li>
+<li class="toc-h3 nav-item toc-entry"><a class="reference internal nav-link" href="#arbdmodel.core_objects.Parent.add_improper"><code class="docutils literal notranslate"><span class="pre">Parent.add_improper()</span></code></a></li>
+<li class="toc-h3 nav-item toc-entry"><a class="reference internal nav-link" href="#arbdmodel.core_objects.Parent.add_product_potential"><code class="docutils literal notranslate"><span class="pre">Parent.add_product_potential()</span></code></a></li>
+<li class="toc-h3 nav-item toc-entry"><a class="reference internal nav-link" href="#arbdmodel.core_objects.Parent.add_vector_angle"><code class="docutils literal notranslate"><span class="pre">Parent.add_vector_angle()</span></code></a></li>
+<li class="toc-h3 nav-item toc-entry"><a class="reference internal nav-link" href="#arbdmodel.core_objects.Parent.clear_all"><code class="docutils literal notranslate"><span class="pre">Parent.clear_all()</span></code></a></li>
+<li class="toc-h3 nav-item toc-entry"><a class="reference internal nav-link" href="#arbdmodel.core_objects.Parent.get_angles"><code class="docutils literal notranslate"><span class="pre">Parent.get_angles()</span></code></a></li>
+<li class="toc-h3 nav-item toc-entry"><a class="reference internal nav-link" href="#arbdmodel.core_objects.Parent.get_bond_angles"><code class="docutils literal notranslate"><span class="pre">Parent.get_bond_angles()</span></code></a></li>
+<li class="toc-h3 nav-item toc-entry"><a class="reference internal nav-link" href="#arbdmodel.core_objects.Parent.get_bonds"><code class="docutils literal notranslate"><span class="pre">Parent.get_bonds()</span></code></a></li>
+<li class="toc-h3 nav-item toc-entry"><a class="reference internal nav-link" href="#arbdmodel.core_objects.Parent.get_center"><code class="docutils literal notranslate"><span class="pre">Parent.get_center()</span></code></a></li>
+<li class="toc-h3 nav-item toc-entry"><a class="reference internal nav-link" href="#arbdmodel.core_objects.Parent.get_dihedrals"><code class="docutils literal notranslate"><span class="pre">Parent.get_dihedrals()</span></code></a></li>
+<li class="toc-h3 nav-item toc-entry"><a class="reference internal nav-link" href="#arbdmodel.core_objects.Parent.get_exclusions"><code class="docutils literal notranslate"><span class="pre">Parent.get_exclusions()</span></code></a></li>
+<li class="toc-h3 nav-item toc-entry"><a class="reference internal nav-link" href="#arbdmodel.core_objects.Parent.get_impropers"><code class="docutils literal notranslate"><span class="pre">Parent.get_impropers()</span></code></a></li>
+<li class="toc-h3 nav-item toc-entry"><a class="reference internal nav-link" href="#arbdmodel.core_objects.Parent.get_product_potentials"><code class="docutils literal notranslate"><span class="pre">Parent.get_product_potentials()</span></code></a></li>
+<li class="toc-h3 nav-item toc-entry"><a class="reference internal nav-link" href="#arbdmodel.core_objects.Parent.get_restraints"><code class="docutils literal notranslate"><span class="pre">Parent.get_restraints()</span></code></a></li>
+<li class="toc-h3 nav-item toc-entry"><a class="reference internal nav-link" href="#arbdmodel.core_objects.Parent.get_vector_angles"><code class="docutils literal notranslate"><span class="pre">Parent.get_vector_angles()</span></code></a></li>
+<li class="toc-h3 nav-item toc-entry"><a class="reference internal nav-link" href="#arbdmodel.core_objects.Parent.index"><code class="docutils literal notranslate"><span class="pre">Parent.index()</span></code></a></li>
+<li class="toc-h3 nav-item toc-entry"><a class="reference internal nav-link" href="#arbdmodel.core_objects.Parent.insert"><code class="docutils literal notranslate"><span class="pre">Parent.insert()</span></code></a></li>
+<li class="toc-h3 nav-item toc-entry"><a class="reference internal nav-link" href="#arbdmodel.core_objects.Parent.remove"><code class="docutils literal notranslate"><span class="pre">Parent.remove()</span></code></a></li>
+</ul>
+</li>
+<li class="toc-h2 nav-item toc-entry"><a class="reference internal nav-link" href="#arbdmodel.core_objects.ParticleType"><code class="docutils literal notranslate"><span class="pre">ParticleType</span></code></a><ul class="nav section-nav flex-column">
+<li class="toc-h3 nav-item toc-entry"><a class="reference internal nav-link" href="#arbdmodel.core_objects.ParticleType.add_grid_potential"><code class="docutils literal notranslate"><span class="pre">ParticleType.add_grid_potential()</span></code></a></li>
+<li class="toc-h3 nav-item toc-entry"><a class="reference internal nav-link" href="#arbdmodel.core_objects.ParticleType.excludedAttributes"><code class="docutils literal notranslate"><span class="pre">ParticleType.excludedAttributes</span></code></a></li>
+<li class="toc-h3 nav-item toc-entry"><a class="reference internal nav-link" href="#arbdmodel.core_objects.ParticleType.is_same_type"><code class="docutils literal notranslate"><span class="pre">ParticleType.is_same_type()</span></code></a></li>
+</ul>
+</li>
+<li class="toc-h2 nav-item toc-entry"><a class="reference internal nav-link" href="#arbdmodel.core_objects.PointParticle"><code class="docutils literal notranslate"><span class="pre">PointParticle</span></code></a><ul class="nav section-nav flex-column">
+<li class="toc-h3 nav-item toc-entry"><a class="reference internal nav-link" href="#arbdmodel.core_objects.PointParticle.add_grid_potential"><code class="docutils literal notranslate"><span class="pre">PointParticle.add_grid_potential()</span></code></a></li>
+<li class="toc-h3 nav-item toc-entry"><a class="reference internal nav-link" href="#arbdmodel.core_objects.PointParticle.add_restraint"><code class="docutils literal notranslate"><span class="pre">PointParticle.add_restraint()</span></code></a></li>
+<li class="toc-h3 nav-item toc-entry"><a class="reference internal nav-link" href="#arbdmodel.core_objects.PointParticle.duplicate"><code class="docutils literal notranslate"><span class="pre">PointParticle.duplicate()</span></code></a></li>
+<li class="toc-h3 nav-item toc-entry"><a class="reference internal nav-link" href="#arbdmodel.core_objects.PointParticle.get_restraints"><code class="docutils literal notranslate"><span class="pre">PointParticle.get_restraints()</span></code></a></li>
+</ul>
+</li>
+<li class="toc-h2 nav-item toc-entry"><a class="reference internal nav-link" href="#arbdmodel.core_objects.RigidBody"><code class="docutils literal notranslate"><span class="pre">RigidBody</span></code></a><ul class="nav section-nav flex-column">
+<li class="toc-h3 nav-item toc-entry"><a class="reference internal nav-link" href="#arbdmodel.core_objects.RigidBody.add_restraint"><code class="docutils literal notranslate"><span class="pre">RigidBody.add_restraint()</span></code></a></li>
+<li class="toc-h3 nav-item toc-entry"><a class="reference internal nav-link" href="#arbdmodel.core_objects.RigidBody.duplicate"><code class="docutils literal notranslate"><span class="pre">RigidBody.duplicate()</span></code></a></li>
+<li class="toc-h3 nav-item toc-entry"><a class="reference internal nav-link" href="#arbdmodel.core_objects.RigidBody.get_restraints"><code class="docutils literal notranslate"><span class="pre">RigidBody.get_restraints()</span></code></a></li>
+</ul>
+</li>
+<li class="toc-h2 nav-item toc-entry"><a class="reference internal nav-link" href="#arbdmodel.core_objects.RigidBodyType"><code class="docutils literal notranslate"><span class="pre">RigidBodyType</span></code></a><ul class="nav section-nav flex-column">
+<li class="toc-h3 nav-item toc-entry"><a class="reference internal nav-link" href="#arbdmodel.core_objects.RigidBodyType.attach_particle"><code class="docutils literal notranslate"><span class="pre">RigidBodyType.attach_particle()</span></code></a></li>
+</ul>
+</li>
+<li class="toc-h2 nav-item toc-entry"><a class="reference internal nav-link" href="#arbdmodel.core_objects.Transformable"><code class="docutils literal notranslate"><span class="pre">Transformable</span></code></a><ul class="nav section-nav flex-column">
+<li class="toc-h3 nav-item toc-entry"><a class="reference internal nav-link" href="#arbdmodel.core_objects.Transformable.applyOrientation"><code class="docutils literal notranslate"><span class="pre">Transformable.applyOrientation()</span></code></a></li>
+<li class="toc-h3 nav-item toc-entry"><a class="reference internal nav-link" href="#arbdmodel.core_objects.Transformable.get_collapsed_position"><code class="docutils literal notranslate"><span class="pre">Transformable.get_collapsed_position()</span></code></a></li>
+<li class="toc-h3 nav-item toc-entry"><a class="reference internal nav-link" href="#arbdmodel.core_objects.Transformable.rotate"><code class="docutils literal notranslate"><span class="pre">Transformable.rotate()</span></code></a></li>
+<li class="toc-h3 nav-item toc-entry"><a class="reference internal nav-link" href="#arbdmodel.core_objects.Transformable.transform"><code class="docutils literal notranslate"><span class="pre">Transformable.transform()</span></code></a></li>
+<li class="toc-h3 nav-item toc-entry"><a class="reference internal nav-link" href="#arbdmodel.core_objects.Transformable.translate"><code class="docutils literal notranslate"><span class="pre">Transformable.translate()</span></code></a></li>
+</ul>
+</li>
+</ul>
+ </nav>
</div>
</div>
</div>
@@ -351,6 +433,296 @@ document.write(`
<section class="tex2jax_ignore mathjax_ignore" id="core-objects">
<h1>core_objects<a class="headerlink" href="#core-objects" title="Link to this heading">#</a></h1>
<p>Module documentation for <code class="docutils literal notranslate"><span class="pre">arbdmodel.core_objects</span></code>.</p>
+<dl class="py class" id="module-arbdmodel.core_objects">
+<dt class="sig sig-object py" id="arbdmodel.core_objects.Child">
+<em class="property"><span class="pre">class</span><span class="w"> </span></em><span class="sig-name descname"><span class="pre">Child</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">parent</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em><span class="sig-paren">)</span><a class="reference internal" href="../../_modules/arbdmodel/core_objects.html#Child"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#arbdmodel.core_objects.Child" title="Link to this definition">#</a></dt>
+<dd><p>Bases: <a class="hxr-hoverxref hxr-tooltip reference external" href="https://docs.python.org/3/library/functions.html#object" title="(in Python v3.13)"><code class="xref py py-class docutils literal notranslate"><span class="pre">object</span></code></a></p>
+</dd></dl>
+
+<dl class="py class">
+<dt class="sig sig-object py" id="arbdmodel.core_objects.Clone">
+<em class="property"><span class="pre">class</span><span class="w"> </span></em><span class="sig-name descname"><span class="pre">Clone</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">original</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">parent</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">position</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">orientation</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em><span class="sig-paren">)</span><a class="reference internal" href="../../_modules/arbdmodel/core_objects.html#Clone"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#arbdmodel.core_objects.Clone" title="Link to this definition">#</a></dt>
+<dd><p>Bases: <a class="reference internal" href="#arbdmodel.core_objects.Transformable" title="arbdmodel.core_objects.Transformable"><code class="xref py py-class docutils literal notranslate"><span class="pre">Transformable</span></code></a>, <a class="reference internal" href="#arbdmodel.core_objects.Parent" title="arbdmodel.core_objects.Parent"><code class="xref py py-class docutils literal notranslate"><span class="pre">Parent</span></code></a>, <a class="reference internal" href="#arbdmodel.core_objects.Child" title="arbdmodel.core_objects.Child"><code class="xref py py-class docutils literal notranslate"><span class="pre">Child</span></code></a></p>
+<dl class="py method">
+<dt class="sig sig-object py" id="arbdmodel.core_objects.Clone.get_original_recursively">
+<span class="sig-name descname"><span class="pre">get_original_recursively</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="reference internal" href="../../_modules/arbdmodel/core_objects.html#Clone.get_original_recursively"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#arbdmodel.core_objects.Clone.get_original_recursively" title="Link to this definition">#</a></dt>
+<dd></dd></dl>
+
+</dd></dl>
+
+<dl class="py class">
+<dt class="sig sig-object py" id="arbdmodel.core_objects.Group">
+<em class="property"><span class="pre">class</span><span class="w"> </span></em><span class="sig-name descname"><span class="pre">Group</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">name</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">children</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">parent</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">position</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">array([0,</span> <span class="pre">0,</span> <span class="pre">0])</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">orientation</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">array([[1,</span> <span class="pre">0,</span> <span class="pre">0],</span> <span class="pre">[0,</span> <span class="pre">1,</span> <span class="pre">0],</span> <span class="pre">[0,</span> <span class="pre">0,</span> <span class="pre">1]])</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">remove_duplicate_bonded_terms</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">False</span></span></em>, <em class="sig-param"><span class="o"><span class="pre">**</span></span><span class="n"><span class="pre">kwargs</span></span></em><span class="sig-paren">)</span><a class="reference internal" href="../../_modules/arbdmodel/core_objects.html#Group"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#arbdmodel.core_objects.Group" title="Link to this definition">#</a></dt>
+<dd><p>Bases: <a class="reference internal" href="#arbdmodel.core_objects.Transformable" title="arbdmodel.core_objects.Transformable"><code class="xref py py-class docutils literal notranslate"><span class="pre">Transformable</span></code></a>, <a class="reference internal" href="#arbdmodel.core_objects.Parent" title="arbdmodel.core_objects.Parent"><code class="xref py py-class docutils literal notranslate"><span class="pre">Parent</span></code></a>, <a class="reference internal" href="#arbdmodel.core_objects.Child" title="arbdmodel.core_objects.Child"><code class="xref py py-class docutils literal notranslate"><span class="pre">Child</span></code></a></p>
+<dl class="py method">
+<dt class="sig sig-object py" id="arbdmodel.core_objects.Group.clone">
+<span class="sig-name descname"><span class="pre">clone</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="reference internal" href="../../_modules/arbdmodel/core_objects.html#Group.clone"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#arbdmodel.core_objects.Group.clone" title="Link to this definition">#</a></dt>
+<dd></dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="arbdmodel.core_objects.Group.duplicate">
+<span class="sig-name descname"><span class="pre">duplicate</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="reference internal" href="../../_modules/arbdmodel/core_objects.html#Group.duplicate"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#arbdmodel.core_objects.Group.duplicate" title="Link to this definition">#</a></dt>
+<dd></dd></dl>
+
+</dd></dl>
+
+<dl class="py class">
+<dt class="sig sig-object py" id="arbdmodel.core_objects.GroupSite">
+<em class="property"><span class="pre">class</span><span class="w"> </span></em><span class="sig-name descname"><span class="pre">GroupSite</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">particles</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">weights</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em><span class="sig-paren">)</span><a class="reference internal" href="../../_modules/arbdmodel/core_objects.html#GroupSite"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#arbdmodel.core_objects.GroupSite" title="Link to this definition">#</a></dt>
+<dd><p>Bases: <a class="hxr-hoverxref hxr-tooltip reference external" href="https://docs.python.org/3/library/functions.html#object" title="(in Python v3.13)"><code class="xref py py-class docutils literal notranslate"><span class="pre">object</span></code></a></p>
+<p>Class to represent a collection of particles that can be used by bond potentials. In arbdmodel only</p>
+<dl class="py method">
+<dt class="sig sig-object py" id="arbdmodel.core_objects.GroupSite.add_restraint">
+<span class="sig-name descname"><span class="pre">add_restraint</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">restraint</span></span></em><span class="sig-paren">)</span><a class="reference internal" href="../../_modules/arbdmodel/core_objects.html#GroupSite.add_restraint"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#arbdmodel.core_objects.GroupSite.add_restraint" title="Link to this definition">#</a></dt>
+<dd></dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="arbdmodel.core_objects.GroupSite.get_center">
+<span class="sig-name descname"><span class="pre">get_center</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="reference internal" href="../../_modules/arbdmodel/core_objects.html#GroupSite.get_center"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#arbdmodel.core_objects.GroupSite.get_center" title="Link to this definition">#</a></dt>
+<dd></dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="arbdmodel.core_objects.GroupSite.get_restraints">
+<span class="sig-name descname"><span class="pre">get_restraints</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="reference internal" href="../../_modules/arbdmodel/core_objects.html#GroupSite.get_restraints"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#arbdmodel.core_objects.GroupSite.get_restraints" title="Link to this definition">#</a></dt>
+<dd></dd></dl>
+
+</dd></dl>
+
+<dl class="py class">
+<dt class="sig sig-object py" id="arbdmodel.core_objects.Parent">
+<em class="property"><span class="pre">class</span><span class="w"> </span></em><span class="sig-name descname"><span class="pre">Parent</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">children</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">remove_duplicate_bonded_terms</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">False</span></span></em><span class="sig-paren">)</span><a class="reference internal" href="../../_modules/arbdmodel/core_objects.html#Parent"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#arbdmodel.core_objects.Parent" title="Link to this definition">#</a></dt>
+<dd><p>Bases: <a class="hxr-hoverxref hxr-tooltip reference external" href="https://docs.python.org/3/library/functions.html#object" title="(in Python v3.13)"><code class="xref py py-class docutils literal notranslate"><span class="pre">object</span></code></a></p>
+<dl class="py method">
+<dt class="sig sig-object py" id="arbdmodel.core_objects.Parent.add">
+<span class="sig-name descname"><span class="pre">add</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">x</span></span></em><span class="sig-paren">)</span><a class="reference internal" href="../../_modules/arbdmodel/core_objects.html#Parent.add"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#arbdmodel.core_objects.Parent.add" title="Link to this definition">#</a></dt>
+<dd></dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="arbdmodel.core_objects.Parent.add_angle">
+<span class="sig-name descname"><span class="pre">add_angle</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">i</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">j</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">k</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">angle</span></span></em><span class="sig-paren">)</span><a class="reference internal" href="../../_modules/arbdmodel/core_objects.html#Parent.add_angle"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#arbdmodel.core_objects.Parent.add_angle" title="Link to this definition">#</a></dt>
+<dd></dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="arbdmodel.core_objects.Parent.add_bond">
+<span class="sig-name descname"><span class="pre">add_bond</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">i</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">j</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">bond</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">exclude</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">False</span></span></em><span class="sig-paren">)</span><a class="reference internal" href="../../_modules/arbdmodel/core_objects.html#Parent.add_bond"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#arbdmodel.core_objects.Parent.add_bond" title="Link to this definition">#</a></dt>
+<dd></dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="arbdmodel.core_objects.Parent.add_bond_angle">
+<span class="sig-name descname"><span class="pre">add_bond_angle</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">i</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">j</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">k</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">l</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">bond_angle</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">exclude</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">False</span></span></em><span class="sig-paren">)</span><a class="reference internal" href="../../_modules/arbdmodel/core_objects.html#Parent.add_bond_angle"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#arbdmodel.core_objects.Parent.add_bond_angle" title="Link to this definition">#</a></dt>
+<dd></dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="arbdmodel.core_objects.Parent.add_dihedral">
+<span class="sig-name descname"><span class="pre">add_dihedral</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">i</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">j</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">k</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">l</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">dihedral</span></span></em><span class="sig-paren">)</span><a class="reference internal" href="../../_modules/arbdmodel/core_objects.html#Parent.add_dihedral"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#arbdmodel.core_objects.Parent.add_dihedral" title="Link to this definition">#</a></dt>
+<dd></dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="arbdmodel.core_objects.Parent.add_exclusion">
+<span class="sig-name descname"><span class="pre">add_exclusion</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">i</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">j</span></span></em><span class="sig-paren">)</span><a class="reference internal" href="../../_modules/arbdmodel/core_objects.html#Parent.add_exclusion"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#arbdmodel.core_objects.Parent.add_exclusion" title="Link to this definition">#</a></dt>
+<dd></dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="arbdmodel.core_objects.Parent.add_improper">
+<span class="sig-name descname"><span class="pre">add_improper</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">i</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">j</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">k</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">l</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">dihedral</span></span></em><span class="sig-paren">)</span><a class="reference internal" href="../../_modules/arbdmodel/core_objects.html#Parent.add_improper"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#arbdmodel.core_objects.Parent.add_improper" title="Link to this definition">#</a></dt>
+<dd></dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="arbdmodel.core_objects.Parent.add_product_potential">
+<span class="sig-name descname"><span class="pre">add_product_potential</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">potential_list</span></span></em><span class="sig-paren">)</span><a class="reference internal" href="../../_modules/arbdmodel/core_objects.html#Parent.add_product_potential"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#arbdmodel.core_objects.Parent.add_product_potential" title="Link to this definition">#</a></dt>
+<dd><p>potential_list: list of tuples of form (particle_i, particle_j,…, TabulatedPotential)</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="arbdmodel.core_objects.Parent.add_vector_angle">
+<span class="sig-name descname"><span class="pre">add_vector_angle</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">i</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">j</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">k</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">l</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">potential</span></span></em><span class="sig-paren">)</span><a class="reference internal" href="../../_modules/arbdmodel/core_objects.html#Parent.add_vector_angle"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#arbdmodel.core_objects.Parent.add_vector_angle" title="Link to this definition">#</a></dt>
+<dd></dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="arbdmodel.core_objects.Parent.clear_all">
+<span class="sig-name descname"><span class="pre">clear_all</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">keep_children</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">False</span></span></em><span class="sig-paren">)</span><a class="reference internal" href="../../_modules/arbdmodel/core_objects.html#Parent.clear_all"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#arbdmodel.core_objects.Parent.clear_all" title="Link to this definition">#</a></dt>
+<dd></dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="arbdmodel.core_objects.Parent.get_angles">
+<span class="sig-name descname"><span class="pre">get_angles</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="reference internal" href="../../_modules/arbdmodel/core_objects.html#Parent.get_angles"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#arbdmodel.core_objects.Parent.get_angles" title="Link to this definition">#</a></dt>
+<dd></dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="arbdmodel.core_objects.Parent.get_bond_angles">
+<span class="sig-name descname"><span class="pre">get_bond_angles</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="reference internal" href="../../_modules/arbdmodel/core_objects.html#Parent.get_bond_angles"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#arbdmodel.core_objects.Parent.get_bond_angles" title="Link to this definition">#</a></dt>
+<dd></dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="arbdmodel.core_objects.Parent.get_bonds">
+<span class="sig-name descname"><span class="pre">get_bonds</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="reference internal" href="../../_modules/arbdmodel/core_objects.html#Parent.get_bonds"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#arbdmodel.core_objects.Parent.get_bonds" title="Link to this definition">#</a></dt>
+<dd></dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="arbdmodel.core_objects.Parent.get_center">
+<span class="sig-name descname"><span class="pre">get_center</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">weight</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em><span class="sig-paren">)</span><a class="reference internal" href="../../_modules/arbdmodel/core_objects.html#Parent.get_center"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#arbdmodel.core_objects.Parent.get_center" title="Link to this definition">#</a></dt>
+<dd></dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="arbdmodel.core_objects.Parent.get_dihedrals">
+<span class="sig-name descname"><span class="pre">get_dihedrals</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="reference internal" href="../../_modules/arbdmodel/core_objects.html#Parent.get_dihedrals"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#arbdmodel.core_objects.Parent.get_dihedrals" title="Link to this definition">#</a></dt>
+<dd></dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="arbdmodel.core_objects.Parent.get_exclusions">
+<span class="sig-name descname"><span class="pre">get_exclusions</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="reference internal" href="../../_modules/arbdmodel/core_objects.html#Parent.get_exclusions"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#arbdmodel.core_objects.Parent.get_exclusions" title="Link to this definition">#</a></dt>
+<dd></dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="arbdmodel.core_objects.Parent.get_impropers">
+<span class="sig-name descname"><span class="pre">get_impropers</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="reference internal" href="../../_modules/arbdmodel/core_objects.html#Parent.get_impropers"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#arbdmodel.core_objects.Parent.get_impropers" title="Link to this definition">#</a></dt>
+<dd></dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="arbdmodel.core_objects.Parent.get_product_potentials">
+<span class="sig-name descname"><span class="pre">get_product_potentials</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="reference internal" href="../../_modules/arbdmodel/core_objects.html#Parent.get_product_potentials"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#arbdmodel.core_objects.Parent.get_product_potentials" title="Link to this definition">#</a></dt>
+<dd></dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="arbdmodel.core_objects.Parent.get_restraints">
+<span class="sig-name descname"><span class="pre">get_restraints</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="reference internal" href="../../_modules/arbdmodel/core_objects.html#Parent.get_restraints"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#arbdmodel.core_objects.Parent.get_restraints" title="Link to this definition">#</a></dt>
+<dd></dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="arbdmodel.core_objects.Parent.get_vector_angles">
+<span class="sig-name descname"><span class="pre">get_vector_angles</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="reference internal" href="../../_modules/arbdmodel/core_objects.html#Parent.get_vector_angles"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#arbdmodel.core_objects.Parent.get_vector_angles" title="Link to this definition">#</a></dt>
+<dd></dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="arbdmodel.core_objects.Parent.index">
+<span class="sig-name descname"><span class="pre">index</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">x</span></span></em><span class="sig-paren">)</span><a class="reference internal" href="../../_modules/arbdmodel/core_objects.html#Parent.index"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#arbdmodel.core_objects.Parent.index" title="Link to this definition">#</a></dt>
+<dd></dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="arbdmodel.core_objects.Parent.insert">
+<span class="sig-name descname"><span class="pre">insert</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">idx</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">x</span></span></em><span class="sig-paren">)</span><a class="reference internal" href="../../_modules/arbdmodel/core_objects.html#Parent.insert"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#arbdmodel.core_objects.Parent.insert" title="Link to this definition">#</a></dt>
+<dd></dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="arbdmodel.core_objects.Parent.remove">
+<span class="sig-name descname"><span class="pre">remove</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">x</span></span></em><span class="sig-paren">)</span><a class="reference internal" href="../../_modules/arbdmodel/core_objects.html#Parent.remove"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#arbdmodel.core_objects.Parent.remove" title="Link to this definition">#</a></dt>
+<dd></dd></dl>
+
+</dd></dl>
+
+<dl class="py class">
+<dt class="sig sig-object py" id="arbdmodel.core_objects.ParticleType">
+<em class="property"><span class="pre">class</span><span class="w"> </span></em><span class="sig-name descname"><span class="pre">ParticleType</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">name</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">charge</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">0</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">mass</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">diffusivity</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">damping_coefficient</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">parent</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">rigid_body_potentials</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">()</span></span></em>, <em class="sig-param"><span class="o"><span class="pre">**</span></span><span class="n"><span class="pre">kwargs</span></span></em><span class="sig-paren">)</span><a class="reference internal" href="../../_modules/arbdmodel/core_objects.html#ParticleType"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#arbdmodel.core_objects.ParticleType" title="Link to this definition">#</a></dt>
+<dd><p>Bases: <a class="hxr-hoverxref hxr-tooltip reference external" href="https://docs.python.org/3/library/functions.html#object" title="(in Python v3.13)"><code class="xref py py-class docutils literal notranslate"><span class="pre">object</span></code></a></p>
+<p>Class that hold common attributes that particles can point to</p>
+<dl class="py method">
+<dt class="sig sig-object py" id="arbdmodel.core_objects.ParticleType.add_grid_potential">
+<span class="sig-name descname"><span class="pre">add_grid_potential</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">gridfile</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">scale</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">1</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">boundary_condition</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">'dirichlet'</span></span></em><span class="sig-paren">)</span><a class="reference internal" href="../../_modules/arbdmodel/core_objects.html#ParticleType.add_grid_potential"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#arbdmodel.core_objects.ParticleType.add_grid_potential" title="Link to this definition">#</a></dt>
+<dd></dd></dl>
+
+<dl class="py attribute">
+<dt class="sig sig-object py" id="arbdmodel.core_objects.ParticleType.excludedAttributes">
+<span class="sig-name descname"><span class="pre">excludedAttributes</span></span><em class="property"><span class="w"> </span><span class="p"><span class="pre">=</span></span><span class="w"> </span><span class="pre">('idx',</span> <span class="pre">'type_',</span> <span class="pre">'position',</span> <span class="pre">'orientation',</span> <span class="pre">'children',</span> <span class="pre">'name',</span> <span class="pre">'parent',</span> <span class="pre">'excludedAttributes')</span></em><a class="headerlink" href="#arbdmodel.core_objects.ParticleType.excludedAttributes" title="Link to this definition">#</a></dt>
+<dd></dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="arbdmodel.core_objects.ParticleType.is_same_type">
+<span class="sig-name descname"><span class="pre">is_same_type</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">other</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">consider_parents</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">True</span></span></em><span class="sig-paren">)</span><a class="reference internal" href="../../_modules/arbdmodel/core_objects.html#ParticleType.is_same_type"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#arbdmodel.core_objects.ParticleType.is_same_type" title="Link to this definition">#</a></dt>
+<dd></dd></dl>
+
+</dd></dl>
+
+<dl class="py class">
+<dt class="sig sig-object py" id="arbdmodel.core_objects.PointParticle">
+<em class="property"><span class="pre">class</span><span class="w"> </span></em><span class="sig-name descname"><span class="pre">PointParticle</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">type_</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">position</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">name</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">'A'</span></span></em>, <em class="sig-param"><span class="o"><span class="pre">**</span></span><span class="n"><span class="pre">kwargs</span></span></em><span class="sig-paren">)</span><a class="reference internal" href="../../_modules/arbdmodel/core_objects.html#PointParticle"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#arbdmodel.core_objects.PointParticle" title="Link to this definition">#</a></dt>
+<dd><p>Bases: <a class="reference internal" href="#arbdmodel.core_objects.Transformable" title="arbdmodel.core_objects.Transformable"><code class="xref py py-class docutils literal notranslate"><span class="pre">Transformable</span></code></a>, <a class="reference internal" href="#arbdmodel.core_objects.Child" title="arbdmodel.core_objects.Child"><code class="xref py py-class docutils literal notranslate"><span class="pre">Child</span></code></a></p>
+<dl class="py method">
+<dt class="sig sig-object py" id="arbdmodel.core_objects.PointParticle.add_grid_potential">
+<span class="sig-name descname"><span class="pre">add_grid_potential</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">gridfile</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">scale</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">1</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">boundary_condition</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">'dirichlet'</span></span></em><span class="sig-paren">)</span><a class="reference internal" href="../../_modules/arbdmodel/core_objects.html#PointParticle.add_grid_potential"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#arbdmodel.core_objects.PointParticle.add_grid_potential" title="Link to this definition">#</a></dt>
+<dd></dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="arbdmodel.core_objects.PointParticle.add_restraint">
+<span class="sig-name descname"><span class="pre">add_restraint</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">restraint</span></span></em><span class="sig-paren">)</span><a class="reference internal" href="../../_modules/arbdmodel/core_objects.html#PointParticle.add_restraint"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#arbdmodel.core_objects.PointParticle.add_restraint" title="Link to this definition">#</a></dt>
+<dd></dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="arbdmodel.core_objects.PointParticle.duplicate">
+<span class="sig-name descname"><span class="pre">duplicate</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="reference internal" href="../../_modules/arbdmodel/core_objects.html#PointParticle.duplicate"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#arbdmodel.core_objects.PointParticle.duplicate" title="Link to this definition">#</a></dt>
+<dd></dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="arbdmodel.core_objects.PointParticle.get_restraints">
+<span class="sig-name descname"><span class="pre">get_restraints</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="reference internal" href="../../_modules/arbdmodel/core_objects.html#PointParticle.get_restraints"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#arbdmodel.core_objects.PointParticle.get_restraints" title="Link to this definition">#</a></dt>
+<dd></dd></dl>
+
+</dd></dl>
+
+<dl class="py class">
+<dt class="sig sig-object py" id="arbdmodel.core_objects.RigidBody">
+<em class="property"><span class="pre">class</span><span class="w"> </span></em><span class="sig-name descname"><span class="pre">RigidBody</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">type_</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">position</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">orientation</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">name</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">'A'</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">attached_particles</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">()</span></span></em>, <em class="sig-param"><span class="o"><span class="pre">**</span></span><span class="n"><span class="pre">kwargs</span></span></em><span class="sig-paren">)</span><a class="reference internal" href="../../_modules/arbdmodel/core_objects.html#RigidBody"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#arbdmodel.core_objects.RigidBody" title="Link to this definition">#</a></dt>
+<dd><p>Bases: <a class="reference internal" href="#arbdmodel.core_objects.PointParticle" title="arbdmodel.core_objects.PointParticle"><code class="xref py py-class docutils literal notranslate"><span class="pre">PointParticle</span></code></a></p>
+<dl class="py method">
+<dt class="sig sig-object py" id="arbdmodel.core_objects.RigidBody.add_restraint">
+<span class="sig-name descname"><span class="pre">add_restraint</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">restraint</span></span></em><span class="sig-paren">)</span><a class="reference internal" href="../../_modules/arbdmodel/core_objects.html#RigidBody.add_restraint"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#arbdmodel.core_objects.RigidBody.add_restraint" title="Link to this definition">#</a></dt>
+<dd></dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="arbdmodel.core_objects.RigidBody.duplicate">
+<span class="sig-name descname"><span class="pre">duplicate</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="reference internal" href="../../_modules/arbdmodel/core_objects.html#RigidBody.duplicate"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#arbdmodel.core_objects.RigidBody.duplicate" title="Link to this definition">#</a></dt>
+<dd></dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="arbdmodel.core_objects.RigidBody.get_restraints">
+<span class="sig-name descname"><span class="pre">get_restraints</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="reference internal" href="../../_modules/arbdmodel/core_objects.html#RigidBody.get_restraints"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#arbdmodel.core_objects.RigidBody.get_restraints" title="Link to this definition">#</a></dt>
+<dd></dd></dl>
+
+</dd></dl>
+
+<dl class="py class">
+<dt class="sig sig-object py" id="arbdmodel.core_objects.RigidBodyType">
+<em class="property"><span class="pre">class</span><span class="w"> </span></em><span class="sig-name descname"><span class="pre">RigidBodyType</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">name</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">parent</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">moment_of_inertia</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">rotational_diffusivity</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">rotational_damping_coefficient</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">attached_particles</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">()</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">potential_grids</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">()</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">charge_grids</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">()</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">pmf_grids</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">()</span></span></em>, <em class="sig-param"><span class="o"><span class="pre">**</span></span><span class="n"><span class="pre">kwargs</span></span></em><span class="sig-paren">)</span><a class="reference internal" href="../../_modules/arbdmodel/core_objects.html#RigidBodyType"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#arbdmodel.core_objects.RigidBodyType" title="Link to this definition">#</a></dt>
+<dd><p>Bases: <a class="reference internal" href="#arbdmodel.core_objects.ParticleType" title="arbdmodel.core_objects.ParticleType"><code class="xref py py-class docutils literal notranslate"><span class="pre">ParticleType</span></code></a></p>
+<p>Class that holds common attributes for RigidBody objects</p>
+<dl class="py method">
+<dt class="sig sig-object py" id="arbdmodel.core_objects.RigidBodyType.attach_particle">
+<span class="sig-name descname"><span class="pre">attach_particle</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">particle</span></span></em><span class="sig-paren">)</span><a class="reference internal" href="../../_modules/arbdmodel/core_objects.html#RigidBodyType.attach_particle"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#arbdmodel.core_objects.RigidBodyType.attach_particle" title="Link to this definition">#</a></dt>
+<dd><p>The particle argument must be a PointParticle. The position/orientation of the attached particle/group is in the RigidBody frame.</p>
+</dd></dl>
+
+</dd></dl>
+
+<dl class="py class">
+<dt class="sig sig-object py" id="arbdmodel.core_objects.Transformable">
+<em class="property"><span class="pre">class</span><span class="w"> </span></em><span class="sig-name descname"><span class="pre">Transformable</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">position</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">orientation</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em><span class="sig-paren">)</span><a class="reference internal" href="../../_modules/arbdmodel/core_objects.html#Transformable"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#arbdmodel.core_objects.Transformable" title="Link to this definition">#</a></dt>
+<dd><p>Bases: <a class="hxr-hoverxref hxr-tooltip reference external" href="https://docs.python.org/3/library/functions.html#object" title="(in Python v3.13)"><code class="xref py py-class docutils literal notranslate"><span class="pre">object</span></code></a></p>
+<dl class="py method">
+<dt class="sig sig-object py" id="arbdmodel.core_objects.Transformable.applyOrientation">
+<span class="sig-name descname"><span class="pre">applyOrientation</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">obj</span></span></em><span class="sig-paren">)</span><a class="reference internal" href="../../_modules/arbdmodel/core_objects.html#Transformable.applyOrientation"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#arbdmodel.core_objects.Transformable.applyOrientation" title="Link to this definition">#</a></dt>
+<dd></dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="arbdmodel.core_objects.Transformable.get_collapsed_position">
+<span class="sig-name descname"><span class="pre">get_collapsed_position</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="reference internal" href="../../_modules/arbdmodel/core_objects.html#Transformable.get_collapsed_position"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#arbdmodel.core_objects.Transformable.get_collapsed_position" title="Link to this definition">#</a></dt>
+<dd></dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="arbdmodel.core_objects.Transformable.rotate">
+<span class="sig-name descname"><span class="pre">rotate</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">R</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">about</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">(0,</span> <span class="pre">0,</span> <span class="pre">0)</span></span></em><span class="sig-paren">)</span><a class="reference internal" href="../../_modules/arbdmodel/core_objects.html#Transformable.rotate"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#arbdmodel.core_objects.Transformable.rotate" title="Link to this definition">#</a></dt>
+<dd></dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="arbdmodel.core_objects.Transformable.transform">
+<span class="sig-name descname"><span class="pre">transform</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">R</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">((1,</span> <span class="pre">0,</span> <span class="pre">0),</span> <span class="pre">(0,</span> <span class="pre">1,</span> <span class="pre">0),</span> <span class="pre">(0,</span> <span class="pre">0,</span> <span class="pre">1))</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">center</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">(0,</span> <span class="pre">0,</span> <span class="pre">0)</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">offset</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">(0,</span> <span class="pre">0,</span> <span class="pre">0)</span></span></em><span class="sig-paren">)</span><a class="reference internal" href="../../_modules/arbdmodel/core_objects.html#Transformable.transform"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#arbdmodel.core_objects.Transformable.transform" title="Link to this definition">#</a></dt>
+<dd></dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="arbdmodel.core_objects.Transformable.translate">
+<span class="sig-name descname"><span class="pre">translate</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">offset</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">(0,</span> <span class="pre">0,</span> <span class="pre">0)</span></span></em><span class="sig-paren">)</span><a class="reference internal" href="../../_modules/arbdmodel/core_objects.html#Transformable.translate"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#arbdmodel.core_objects.Transformable.translate" title="Link to this definition">#</a></dt>
+<dd></dd></dl>
+
+</dd></dl>
+
</section>
<script type="text/x-thebe-config">
@@ -390,6 +762,93 @@ document.write(`
+ <div class="bd-sidebar-secondary bd-toc"><div class="sidebar-secondary-items sidebar-secondary__inner">
+
+
+ <div class="sidebar-secondary-item">
+ <div class="page-toc tocsection onthispage">
+ <i class="fa-solid fa-list"></i> Contents
+ </div>
+ <nav class="bd-toc-nav page-toc">
+ <ul class="visible nav section-nav flex-column">
+<li class="toc-h2 nav-item toc-entry"><a class="reference internal nav-link" href="#arbdmodel.core_objects.Child"><code class="docutils literal notranslate"><span class="pre">Child</span></code></a></li>
+<li class="toc-h2 nav-item toc-entry"><a class="reference internal nav-link" href="#arbdmodel.core_objects.Clone"><code class="docutils literal notranslate"><span class="pre">Clone</span></code></a><ul class="nav section-nav flex-column">
+<li class="toc-h3 nav-item toc-entry"><a class="reference internal nav-link" href="#arbdmodel.core_objects.Clone.get_original_recursively"><code class="docutils literal notranslate"><span class="pre">Clone.get_original_recursively()</span></code></a></li>
+</ul>
+</li>
+<li class="toc-h2 nav-item toc-entry"><a class="reference internal nav-link" href="#arbdmodel.core_objects.Group"><code class="docutils literal notranslate"><span class="pre">Group</span></code></a><ul class="nav section-nav flex-column">
+<li class="toc-h3 nav-item toc-entry"><a class="reference internal nav-link" href="#arbdmodel.core_objects.Group.clone"><code class="docutils literal notranslate"><span class="pre">Group.clone()</span></code></a></li>
+<li class="toc-h3 nav-item toc-entry"><a class="reference internal nav-link" href="#arbdmodel.core_objects.Group.duplicate"><code class="docutils literal notranslate"><span class="pre">Group.duplicate()</span></code></a></li>
+</ul>
+</li>
+<li class="toc-h2 nav-item toc-entry"><a class="reference internal nav-link" href="#arbdmodel.core_objects.GroupSite"><code class="docutils literal notranslate"><span class="pre">GroupSite</span></code></a><ul class="nav section-nav flex-column">
+<li class="toc-h3 nav-item toc-entry"><a class="reference internal nav-link" href="#arbdmodel.core_objects.GroupSite.add_restraint"><code class="docutils literal notranslate"><span class="pre">GroupSite.add_restraint()</span></code></a></li>
+<li class="toc-h3 nav-item toc-entry"><a class="reference internal nav-link" href="#arbdmodel.core_objects.GroupSite.get_center"><code class="docutils literal notranslate"><span class="pre">GroupSite.get_center()</span></code></a></li>
+<li class="toc-h3 nav-item toc-entry"><a class="reference internal nav-link" href="#arbdmodel.core_objects.GroupSite.get_restraints"><code class="docutils literal notranslate"><span class="pre">GroupSite.get_restraints()</span></code></a></li>
+</ul>
+</li>
+<li class="toc-h2 nav-item toc-entry"><a class="reference internal nav-link" href="#arbdmodel.core_objects.Parent"><code class="docutils literal notranslate"><span class="pre">Parent</span></code></a><ul class="nav section-nav flex-column">
+<li class="toc-h3 nav-item toc-entry"><a class="reference internal nav-link" href="#arbdmodel.core_objects.Parent.add"><code class="docutils literal notranslate"><span class="pre">Parent.add()</span></code></a></li>
+<li class="toc-h3 nav-item toc-entry"><a class="reference internal nav-link" href="#arbdmodel.core_objects.Parent.add_angle"><code class="docutils literal notranslate"><span class="pre">Parent.add_angle()</span></code></a></li>
+<li class="toc-h3 nav-item toc-entry"><a class="reference internal nav-link" href="#arbdmodel.core_objects.Parent.add_bond"><code class="docutils literal notranslate"><span class="pre">Parent.add_bond()</span></code></a></li>
+<li class="toc-h3 nav-item toc-entry"><a class="reference internal nav-link" href="#arbdmodel.core_objects.Parent.add_bond_angle"><code class="docutils literal notranslate"><span class="pre">Parent.add_bond_angle()</span></code></a></li>
+<li class="toc-h3 nav-item toc-entry"><a class="reference internal nav-link" href="#arbdmodel.core_objects.Parent.add_dihedral"><code class="docutils literal notranslate"><span class="pre">Parent.add_dihedral()</span></code></a></li>
+<li class="toc-h3 nav-item toc-entry"><a class="reference internal nav-link" href="#arbdmodel.core_objects.Parent.add_exclusion"><code class="docutils literal notranslate"><span class="pre">Parent.add_exclusion()</span></code></a></li>
+<li class="toc-h3 nav-item toc-entry"><a class="reference internal nav-link" href="#arbdmodel.core_objects.Parent.add_improper"><code class="docutils literal notranslate"><span class="pre">Parent.add_improper()</span></code></a></li>
+<li class="toc-h3 nav-item toc-entry"><a class="reference internal nav-link" href="#arbdmodel.core_objects.Parent.add_product_potential"><code class="docutils literal notranslate"><span class="pre">Parent.add_product_potential()</span></code></a></li>
+<li class="toc-h3 nav-item toc-entry"><a class="reference internal nav-link" href="#arbdmodel.core_objects.Parent.add_vector_angle"><code class="docutils literal notranslate"><span class="pre">Parent.add_vector_angle()</span></code></a></li>
+<li class="toc-h3 nav-item toc-entry"><a class="reference internal nav-link" href="#arbdmodel.core_objects.Parent.clear_all"><code class="docutils literal notranslate"><span class="pre">Parent.clear_all()</span></code></a></li>
+<li class="toc-h3 nav-item toc-entry"><a class="reference internal nav-link" href="#arbdmodel.core_objects.Parent.get_angles"><code class="docutils literal notranslate"><span class="pre">Parent.get_angles()</span></code></a></li>
+<li class="toc-h3 nav-item toc-entry"><a class="reference internal nav-link" href="#arbdmodel.core_objects.Parent.get_bond_angles"><code class="docutils literal notranslate"><span class="pre">Parent.get_bond_angles()</span></code></a></li>
+<li class="toc-h3 nav-item toc-entry"><a class="reference internal nav-link" href="#arbdmodel.core_objects.Parent.get_bonds"><code class="docutils literal notranslate"><span class="pre">Parent.get_bonds()</span></code></a></li>
+<li class="toc-h3 nav-item toc-entry"><a class="reference internal nav-link" href="#arbdmodel.core_objects.Parent.get_center"><code class="docutils literal notranslate"><span class="pre">Parent.get_center()</span></code></a></li>
+<li class="toc-h3 nav-item toc-entry"><a class="reference internal nav-link" href="#arbdmodel.core_objects.Parent.get_dihedrals"><code class="docutils literal notranslate"><span class="pre">Parent.get_dihedrals()</span></code></a></li>
+<li class="toc-h3 nav-item toc-entry"><a class="reference internal nav-link" href="#arbdmodel.core_objects.Parent.get_exclusions"><code class="docutils literal notranslate"><span class="pre">Parent.get_exclusions()</span></code></a></li>
+<li class="toc-h3 nav-item toc-entry"><a class="reference internal nav-link" href="#arbdmodel.core_objects.Parent.get_impropers"><code class="docutils literal notranslate"><span class="pre">Parent.get_impropers()</span></code></a></li>
+<li class="toc-h3 nav-item toc-entry"><a class="reference internal nav-link" href="#arbdmodel.core_objects.Parent.get_product_potentials"><code class="docutils literal notranslate"><span class="pre">Parent.get_product_potentials()</span></code></a></li>
+<li class="toc-h3 nav-item toc-entry"><a class="reference internal nav-link" href="#arbdmodel.core_objects.Parent.get_restraints"><code class="docutils literal notranslate"><span class="pre">Parent.get_restraints()</span></code></a></li>
+<li class="toc-h3 nav-item toc-entry"><a class="reference internal nav-link" href="#arbdmodel.core_objects.Parent.get_vector_angles"><code class="docutils literal notranslate"><span class="pre">Parent.get_vector_angles()</span></code></a></li>
+<li class="toc-h3 nav-item toc-entry"><a class="reference internal nav-link" href="#arbdmodel.core_objects.Parent.index"><code class="docutils literal notranslate"><span class="pre">Parent.index()</span></code></a></li>
+<li class="toc-h3 nav-item toc-entry"><a class="reference internal nav-link" href="#arbdmodel.core_objects.Parent.insert"><code class="docutils literal notranslate"><span class="pre">Parent.insert()</span></code></a></li>
+<li class="toc-h3 nav-item toc-entry"><a class="reference internal nav-link" href="#arbdmodel.core_objects.Parent.remove"><code class="docutils literal notranslate"><span class="pre">Parent.remove()</span></code></a></li>
+</ul>
+</li>
+<li class="toc-h2 nav-item toc-entry"><a class="reference internal nav-link" href="#arbdmodel.core_objects.ParticleType"><code class="docutils literal notranslate"><span class="pre">ParticleType</span></code></a><ul class="nav section-nav flex-column">
+<li class="toc-h3 nav-item toc-entry"><a class="reference internal nav-link" href="#arbdmodel.core_objects.ParticleType.add_grid_potential"><code class="docutils literal notranslate"><span class="pre">ParticleType.add_grid_potential()</span></code></a></li>
+<li class="toc-h3 nav-item toc-entry"><a class="reference internal nav-link" href="#arbdmodel.core_objects.ParticleType.excludedAttributes"><code class="docutils literal notranslate"><span class="pre">ParticleType.excludedAttributes</span></code></a></li>
+<li class="toc-h3 nav-item toc-entry"><a class="reference internal nav-link" href="#arbdmodel.core_objects.ParticleType.is_same_type"><code class="docutils literal notranslate"><span class="pre">ParticleType.is_same_type()</span></code></a></li>
+</ul>
+</li>
+<li class="toc-h2 nav-item toc-entry"><a class="reference internal nav-link" href="#arbdmodel.core_objects.PointParticle"><code class="docutils literal notranslate"><span class="pre">PointParticle</span></code></a><ul class="nav section-nav flex-column">
+<li class="toc-h3 nav-item toc-entry"><a class="reference internal nav-link" href="#arbdmodel.core_objects.PointParticle.add_grid_potential"><code class="docutils literal notranslate"><span class="pre">PointParticle.add_grid_potential()</span></code></a></li>
+<li class="toc-h3 nav-item toc-entry"><a class="reference internal nav-link" href="#arbdmodel.core_objects.PointParticle.add_restraint"><code class="docutils literal notranslate"><span class="pre">PointParticle.add_restraint()</span></code></a></li>
+<li class="toc-h3 nav-item toc-entry"><a class="reference internal nav-link" href="#arbdmodel.core_objects.PointParticle.duplicate"><code class="docutils literal notranslate"><span class="pre">PointParticle.duplicate()</span></code></a></li>
+<li class="toc-h3 nav-item toc-entry"><a class="reference internal nav-link" href="#arbdmodel.core_objects.PointParticle.get_restraints"><code class="docutils literal notranslate"><span class="pre">PointParticle.get_restraints()</span></code></a></li>
+</ul>
+</li>
+<li class="toc-h2 nav-item toc-entry"><a class="reference internal nav-link" href="#arbdmodel.core_objects.RigidBody"><code class="docutils literal notranslate"><span class="pre">RigidBody</span></code></a><ul class="nav section-nav flex-column">
+<li class="toc-h3 nav-item toc-entry"><a class="reference internal nav-link" href="#arbdmodel.core_objects.RigidBody.add_restraint"><code class="docutils literal notranslate"><span class="pre">RigidBody.add_restraint()</span></code></a></li>
+<li class="toc-h3 nav-item toc-entry"><a class="reference internal nav-link" href="#arbdmodel.core_objects.RigidBody.duplicate"><code class="docutils literal notranslate"><span class="pre">RigidBody.duplicate()</span></code></a></li>
+<li class="toc-h3 nav-item toc-entry"><a class="reference internal nav-link" href="#arbdmodel.core_objects.RigidBody.get_restraints"><code class="docutils literal notranslate"><span class="pre">RigidBody.get_restraints()</span></code></a></li>
+</ul>
+</li>
+<li class="toc-h2 nav-item toc-entry"><a class="reference internal nav-link" href="#arbdmodel.core_objects.RigidBodyType"><code class="docutils literal notranslate"><span class="pre">RigidBodyType</span></code></a><ul class="nav section-nav flex-column">
+<li class="toc-h3 nav-item toc-entry"><a class="reference internal nav-link" href="#arbdmodel.core_objects.RigidBodyType.attach_particle"><code class="docutils literal notranslate"><span class="pre">RigidBodyType.attach_particle()</span></code></a></li>
+</ul>
+</li>
+<li class="toc-h2 nav-item toc-entry"><a class="reference internal nav-link" href="#arbdmodel.core_objects.Transformable"><code class="docutils literal notranslate"><span class="pre">Transformable</span></code></a><ul class="nav section-nav flex-column">
+<li class="toc-h3 nav-item toc-entry"><a class="reference internal nav-link" href="#arbdmodel.core_objects.Transformable.applyOrientation"><code class="docutils literal notranslate"><span class="pre">Transformable.applyOrientation()</span></code></a></li>
+<li class="toc-h3 nav-item toc-entry"><a class="reference internal nav-link" href="#arbdmodel.core_objects.Transformable.get_collapsed_position"><code class="docutils literal notranslate"><span class="pre">Transformable.get_collapsed_position()</span></code></a></li>
+<li class="toc-h3 nav-item toc-entry"><a class="reference internal nav-link" href="#arbdmodel.core_objects.Transformable.rotate"><code class="docutils literal notranslate"><span class="pre">Transformable.rotate()</span></code></a></li>
+<li class="toc-h3 nav-item toc-entry"><a class="reference internal nav-link" href="#arbdmodel.core_objects.Transformable.transform"><code class="docutils literal notranslate"><span class="pre">Transformable.transform()</span></code></a></li>
+<li class="toc-h3 nav-item toc-entry"><a class="reference internal nav-link" href="#arbdmodel.core_objects.Transformable.translate"><code class="docutils literal notranslate"><span class="pre">Transformable.translate()</span></code></a></li>
+</ul>
+</li>
+</ul>
+ </nav></div>
+
+</div></div>
+
</div>
<footer class="bd-footer-content">
diff --git a/_build/html/api/core/index.html b/_build/html/api/core/index.html
index 5b3d6093b26f8334221e9702617a68220868b2e6..0c02e018ec07b3478c350ebea9df9ced8ec1dcc5 100644
--- a/_build/html/api/core/index.html
+++ b/_build/html/api/core/index.html
@@ -32,19 +32,19 @@
<link rel="stylesheet" type="text/css" href="../../_static/styles/sphinx-book-theme.css?v=eba8b062" />
<link rel="stylesheet" type="text/css" href="../../_static/togglebutton.css?v=13237357" />
<link rel="stylesheet" type="text/css" href="../../_static/copybutton.css?v=76b2166b" />
- <link rel="stylesheet" type="text/css" href="../../_static/mystnb.4510f1fc1dee50b3e5859aac5469c37c29e427902b24a333a5f9fcb2f0b3ac41.css" />
+ <link rel="stylesheet" type="text/css" href="../../_static/mystnb.4510f1fc1dee50b3e5859aac5469c37c29e427902b24a333a5f9fcb2f0b3ac41.css?v=be8a1c11" />
<link rel="stylesheet" type="text/css" href="../../_static/sphinx-thebe.css?v=4fa983c6" />
<link rel="stylesheet" type="text/css" href="../../_static/tabs.css?v=4c969af8" />
- <link rel="stylesheet" type="text/css" href="../../_static/proof.css" />
+ <link rel="stylesheet" type="text/css" href="../../_static/proof.css?v=b4b7a797" />
<link rel="stylesheet" type="text/css" href="../../_static/styles/sphinx-examples.css?v=e236af4b" />
- <link rel="stylesheet" type="text/css" href="../../_static/css/tooltipster.custom.css" />
- <link rel="stylesheet" type="text/css" href="../../_static/css/tooltipster.bundle.min.css" />
- <link rel="stylesheet" type="text/css" href="../../_static/css/tooltipster-sideTip-shadow.min.css" />
- <link rel="stylesheet" type="text/css" href="../../_static/css/tooltipster-sideTip-punk.min.css" />
- <link rel="stylesheet" type="text/css" href="../../_static/css/tooltipster-sideTip-noir.min.css" />
- <link rel="stylesheet" type="text/css" href="../../_static/css/tooltipster-sideTip-light.min.css" />
- <link rel="stylesheet" type="text/css" href="../../_static/css/tooltipster-sideTip-borderless.min.css" />
- <link rel="stylesheet" type="text/css" href="../../_static/css/micromodal.css" />
+ <link rel="stylesheet" type="text/css" href="../../_static/css/tooltipster.custom.css?v=7bc2f056" />
+ <link rel="stylesheet" type="text/css" href="../../_static/css/tooltipster.bundle.min.css?v=37217874" />
+ <link rel="stylesheet" type="text/css" href="../../_static/css/tooltipster-sideTip-shadow.min.css?v=6227e517" />
+ <link rel="stylesheet" type="text/css" href="../../_static/css/tooltipster-sideTip-punk.min.css?v=94669e23" />
+ <link rel="stylesheet" type="text/css" href="../../_static/css/tooltipster-sideTip-noir.min.css?v=21a39f42" />
+ <link rel="stylesheet" type="text/css" href="../../_static/css/tooltipster-sideTip-light.min.css?v=a18b2449" />
+ <link rel="stylesheet" type="text/css" href="../../_static/css/tooltipster-sideTip-borderless.min.css?v=dbff53e4" />
+ <link rel="stylesheet" type="text/css" href="../../_static/css/micromodal.css?v=d7bf34ee" />
<link rel="stylesheet" type="text/css" href="../../_static/sphinx-design.min.css?v=95c83b7e" />
<!-- Pre-loaded scripts that we'll load fully later -->
@@ -61,9 +61,9 @@
<script src="../../_static/copybutton.js?v=f281be69"></script>
<script src="../../_static/scripts/sphinx-book-theme.js?v=887ef09a"></script>
<script src="../../_static/tabs.js?v=3ee01567"></script>
- <script src="../../_static/js/hoverxref.js"></script>
- <script src="../../_static/js/tooltipster.bundle.min.js"></script>
- <script src="../../_static/js/micromodal.min.js"></script>
+ <script src="../../_static/js/hoverxref.js?v=c95ade4f"></script>
+ <script src="../../_static/js/tooltipster.bundle.min.js?v=18bf091b"></script>
+ <script src="../../_static/js/micromodal.min.js?v=04d6302d"></script>
<script>let toggleHintShow = 'Click to show';</script>
<script>let toggleHintHide = 'Click to hide';</script>
<script>let toggleOpenOnPrint = 'true';</script>
diff --git a/_build/html/api/core/model.html b/_build/html/api/core/model.html
index 288d9b903f5200c38f721648dfd22480e9fe9ad5..39446e2634e455ff61ca937533d114ef03b53d63 100644
--- a/_build/html/api/core/model.html
+++ b/_build/html/api/core/model.html
@@ -32,19 +32,19 @@
<link rel="stylesheet" type="text/css" href="../../_static/styles/sphinx-book-theme.css?v=eba8b062" />
<link rel="stylesheet" type="text/css" href="../../_static/togglebutton.css?v=13237357" />
<link rel="stylesheet" type="text/css" href="../../_static/copybutton.css?v=76b2166b" />
- <link rel="stylesheet" type="text/css" href="../../_static/mystnb.4510f1fc1dee50b3e5859aac5469c37c29e427902b24a333a5f9fcb2f0b3ac41.css" />
+ <link rel="stylesheet" type="text/css" href="../../_static/mystnb.4510f1fc1dee50b3e5859aac5469c37c29e427902b24a333a5f9fcb2f0b3ac41.css?v=be8a1c11" />
<link rel="stylesheet" type="text/css" href="../../_static/sphinx-thebe.css?v=4fa983c6" />
<link rel="stylesheet" type="text/css" href="../../_static/tabs.css?v=4c969af8" />
- <link rel="stylesheet" type="text/css" href="../../_static/proof.css" />
+ <link rel="stylesheet" type="text/css" href="../../_static/proof.css?v=b4b7a797" />
<link rel="stylesheet" type="text/css" href="../../_static/styles/sphinx-examples.css?v=e236af4b" />
- <link rel="stylesheet" type="text/css" href="../../_static/css/tooltipster.custom.css" />
- <link rel="stylesheet" type="text/css" href="../../_static/css/tooltipster.bundle.min.css" />
- <link rel="stylesheet" type="text/css" href="../../_static/css/tooltipster-sideTip-shadow.min.css" />
- <link rel="stylesheet" type="text/css" href="../../_static/css/tooltipster-sideTip-punk.min.css" />
- <link rel="stylesheet" type="text/css" href="../../_static/css/tooltipster-sideTip-noir.min.css" />
- <link rel="stylesheet" type="text/css" href="../../_static/css/tooltipster-sideTip-light.min.css" />
- <link rel="stylesheet" type="text/css" href="../../_static/css/tooltipster-sideTip-borderless.min.css" />
- <link rel="stylesheet" type="text/css" href="../../_static/css/micromodal.css" />
+ <link rel="stylesheet" type="text/css" href="../../_static/css/tooltipster.custom.css?v=7bc2f056" />
+ <link rel="stylesheet" type="text/css" href="../../_static/css/tooltipster.bundle.min.css?v=37217874" />
+ <link rel="stylesheet" type="text/css" href="../../_static/css/tooltipster-sideTip-shadow.min.css?v=6227e517" />
+ <link rel="stylesheet" type="text/css" href="../../_static/css/tooltipster-sideTip-punk.min.css?v=94669e23" />
+ <link rel="stylesheet" type="text/css" href="../../_static/css/tooltipster-sideTip-noir.min.css?v=21a39f42" />
+ <link rel="stylesheet" type="text/css" href="../../_static/css/tooltipster-sideTip-light.min.css?v=a18b2449" />
+ <link rel="stylesheet" type="text/css" href="../../_static/css/tooltipster-sideTip-borderless.min.css?v=dbff53e4" />
+ <link rel="stylesheet" type="text/css" href="../../_static/css/micromodal.css?v=d7bf34ee" />
<link rel="stylesheet" type="text/css" href="../../_static/sphinx-design.min.css?v=95c83b7e" />
<!-- Pre-loaded scripts that we'll load fully later -->
@@ -61,9 +61,9 @@
<script src="../../_static/copybutton.js?v=f281be69"></script>
<script src="../../_static/scripts/sphinx-book-theme.js?v=887ef09a"></script>
<script src="../../_static/tabs.js?v=3ee01567"></script>
- <script src="../../_static/js/hoverxref.js"></script>
- <script src="../../_static/js/tooltipster.bundle.min.js"></script>
- <script src="../../_static/js/micromodal.min.js"></script>
+ <script src="../../_static/js/hoverxref.js?v=c95ade4f"></script>
+ <script src="../../_static/js/tooltipster.bundle.min.js?v=18bf091b"></script>
+ <script src="../../_static/js/micromodal.min.js?v=04d6302d"></script>
<script>let toggleHintShow = 'Click to show';</script>
<script>let toggleHintHide = 'Click to hide';</script>
<script>let toggleOpenOnPrint = 'true';</script>
@@ -323,7 +323,9 @@ document.write(`
</button>
`);
</script>
-
+<button class="sidebar-toggle secondary-toggle btn btn-sm" title="Toggle secondary sidebar" data-bs-placement="bottom" data-bs-toggle="tooltip">
+ <span class="fa-solid fa-list"></span>
+</button>
</div></div>
</div>
@@ -339,6 +341,36 @@ document.write(`
<div id="print-main-content">
<div id="jb-print-toc">
+ <div>
+ <h2> Contents </h2>
+ </div>
+ <nav aria-label="Page">
+ <ul class="visible nav section-nav flex-column">
+<li class="toc-h2 nav-item toc-entry"><a class="reference internal nav-link" href="#arbdmodel.model.ArbdModel"><code class="docutils literal notranslate"><span class="pre">ArbdModel</span></code></a><ul class="nav section-nav flex-column">
+<li class="toc-h3 nav-item toc-entry"><a class="reference internal nav-link" href="#arbdmodel.model.ArbdModel.add"><code class="docutils literal notranslate"><span class="pre">ArbdModel.add()</span></code></a></li>
+<li class="toc-h3 nav-item toc-entry"><a class="reference internal nav-link" href="#arbdmodel.model.ArbdModel.add_group_site"><code class="docutils literal notranslate"><span class="pre">ArbdModel.add_group_site()</span></code></a></li>
+<li class="toc-h3 nav-item toc-entry"><a class="reference internal nav-link" href="#arbdmodel.model.ArbdModel.add_nonbonded_interaction"><code class="docutils literal notranslate"><span class="pre">ArbdModel.add_nonbonded_interaction()</span></code></a></li>
+<li class="toc-h3 nav-item toc-entry"><a class="reference internal nav-link" href="#arbdmodel.model.ArbdModel.assign_IBI_degrees_of_freedom"><code class="docutils literal notranslate"><span class="pre">ArbdModel.assign_IBI_degrees_of_freedom()</span></code></a></li>
+<li class="toc-h3 nav-item toc-entry"><a class="reference internal nav-link" href="#arbdmodel.model.ArbdModel.clear_all"><code class="docutils literal notranslate"><span class="pre">ArbdModel.clear_all()</span></code></a></li>
+<li class="toc-h3 nav-item toc-entry"><a class="reference internal nav-link" href="#arbdmodel.model.ArbdModel.dimensions_from_structure"><code class="docutils literal notranslate"><span class="pre">ArbdModel.dimensions_from_structure()</span></code></a></li>
+<li class="toc-h3 nav-item toc-entry"><a class="reference internal nav-link" href="#arbdmodel.model.ArbdModel.extend"><code class="docutils literal notranslate"><span class="pre">ArbdModel.extend()</span></code></a></li>
+<li class="toc-h3 nav-item toc-entry"><a class="reference internal nav-link" href="#arbdmodel.model.ArbdModel.getParticleTypesAndCounts"><code class="docutils literal notranslate"><span class="pre">ArbdModel.getParticleTypesAndCounts()</span></code></a></li>
+<li class="toc-h3 nav-item toc-entry"><a class="reference internal nav-link" href="#arbdmodel.model.ArbdModel.load_target_IBI_distributions"><code class="docutils literal notranslate"><span class="pre">ArbdModel.load_target_IBI_distributions()</span></code></a></li>
+<li class="toc-h3 nav-item toc-entry"><a class="reference internal nav-link" href="#arbdmodel.model.ArbdModel.prepare_for_simulation"><code class="docutils literal notranslate"><span class="pre">ArbdModel.prepare_for_simulation()</span></code></a></li>
+<li class="toc-h3 nav-item toc-entry"><a class="reference internal nav-link" href="#arbdmodel.model.ArbdModel.run_IBI"><code class="docutils literal notranslate"><span class="pre">ArbdModel.run_IBI()</span></code></a></li>
+<li class="toc-h3 nav-item toc-entry"><a class="reference internal nav-link" href="#arbdmodel.model.ArbdModel.simulate"><code class="docutils literal notranslate"><span class="pre">ArbdModel.simulate()</span></code></a></li>
+<li class="toc-h3 nav-item toc-entry"><a class="reference internal nav-link" href="#arbdmodel.model.ArbdModel.update"><code class="docutils literal notranslate"><span class="pre">ArbdModel.update()</span></code></a></li>
+<li class="toc-h3 nav-item toc-entry"><a class="reference internal nav-link" href="#arbdmodel.model.ArbdModel.useNonbondedScheme"><code class="docutils literal notranslate"><span class="pre">ArbdModel.useNonbondedScheme()</span></code></a></li>
+</ul>
+</li>
+<li class="toc-h2 nav-item toc-entry"><a class="reference internal nav-link" href="#arbdmodel.model.PdbModel"><code class="docutils literal notranslate"><span class="pre">PdbModel</span></code></a><ul class="nav section-nav flex-column">
+<li class="toc-h3 nav-item toc-entry"><a class="reference internal nav-link" href="#arbdmodel.model.PdbModel.write_pdb"><code class="docutils literal notranslate"><span class="pre">PdbModel.write_pdb()</span></code></a></li>
+<li class="toc-h3 nav-item toc-entry"><a class="reference internal nav-link" href="#arbdmodel.model.PdbModel.write_pqr"><code class="docutils literal notranslate"><span class="pre">PdbModel.write_pqr()</span></code></a></li>
+<li class="toc-h3 nav-item toc-entry"><a class="reference internal nav-link" href="#arbdmodel.model.PdbModel.write_psf"><code class="docutils literal notranslate"><span class="pre">PdbModel.write_psf()</span></code></a></li>
+</ul>
+</li>
+</ul>
+ </nav>
</div>
</div>
</div>
@@ -351,6 +383,136 @@ document.write(`
<section class="tex2jax_ignore mathjax_ignore" id="model">
<h1>model<a class="headerlink" href="#model" title="Link to this heading">#</a></h1>
<p>Module documentation for <code class="docutils literal notranslate"><span class="pre">arbdmodel.model</span></code>.</p>
+<dl class="py class" id="module-arbdmodel.model">
+<dt class="sig sig-object py" id="arbdmodel.model.ArbdModel">
+<em class="property"><span class="pre">class</span><span class="w"> </span></em><span class="sig-name descname"><span class="pre">ArbdModel</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">children</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">cell_vectors</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">cell_origin</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">dimensions</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">remove_duplicate_bonded_terms</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">True</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">buffer_factor</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">1.2</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">configuration</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">dummy_types</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">()</span></span></em>, <em class="sig-param"><span class="o"><span class="pre">**</span></span><span class="n"><span class="pre">conf_params</span></span></em><span class="sig-paren">)</span><a class="reference internal" href="../../_modules/arbdmodel/model.html#ArbdModel"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#arbdmodel.model.ArbdModel" title="Link to this definition">#</a></dt>
+<dd><p>Bases: <a class="reference internal" href="#arbdmodel.model.PdbModel" title="arbdmodel.model.PdbModel"><code class="xref py py-class docutils literal notranslate"><span class="pre">PdbModel</span></code></a></p>
+<p>Advanced model class for ARBD simulations with improved cell vector handling.</p>
+<dl class="py method">
+<dt class="sig sig-object py" id="arbdmodel.model.ArbdModel.add">
+<span class="sig-name descname"><span class="pre">add</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">obj</span></span></em><span class="sig-paren">)</span><a class="reference internal" href="../../_modules/arbdmodel/model.html#ArbdModel.add"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#arbdmodel.model.ArbdModel.add" title="Link to this definition">#</a></dt>
+<dd></dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="arbdmodel.model.ArbdModel.add_group_site">
+<span class="sig-name descname"><span class="pre">add_group_site</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">particles</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">weights</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em><span class="sig-paren">)</span><a class="reference internal" href="../../_modules/arbdmodel/model.html#ArbdModel.add_group_site"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#arbdmodel.model.ArbdModel.add_group_site" title="Link to this definition">#</a></dt>
+<dd></dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="arbdmodel.model.ArbdModel.add_nonbonded_interaction">
+<span class="sig-name descname"><span class="pre">add_nonbonded_interaction</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">nonbonded_potential</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">typeA</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">typeB</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em><span class="sig-paren">)</span><a class="reference internal" href="../../_modules/arbdmodel/model.html#ArbdModel.add_nonbonded_interaction"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#arbdmodel.model.ArbdModel.add_nonbonded_interaction" title="Link to this definition">#</a></dt>
+<dd></dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="arbdmodel.model.ArbdModel.assign_IBI_degrees_of_freedom">
+<span class="sig-name descname"><span class="pre">assign_IBI_degrees_of_freedom</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="reference internal" href="../../_modules/arbdmodel/model.html#ArbdModel.assign_IBI_degrees_of_freedom"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#arbdmodel.model.ArbdModel.assign_IBI_degrees_of_freedom" title="Link to this definition">#</a></dt>
+<dd><p>Convenience routine that adds degrees of freedom to
+corresponding IBI potentials</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="arbdmodel.model.ArbdModel.clear_all">
+<span class="sig-name descname"><span class="pre">clear_all</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">keep_children</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">False</span></span></em><span class="sig-paren">)</span><a class="reference internal" href="../../_modules/arbdmodel/model.html#ArbdModel.clear_all"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#arbdmodel.model.ArbdModel.clear_all" title="Link to this definition">#</a></dt>
+<dd></dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="arbdmodel.model.ArbdModel.dimensions_from_structure">
+<span class="sig-name descname"><span class="pre">dimensions_from_structure</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">padding_factor</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">1.5</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">isotropic</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">False</span></span></em><span class="sig-paren">)</span><a class="reference internal" href="../../_modules/arbdmodel/model.html#ArbdModel.dimensions_from_structure"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#arbdmodel.model.ArbdModel.dimensions_from_structure" title="Link to this definition">#</a></dt>
+<dd></dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="arbdmodel.model.ArbdModel.extend">
+<span class="sig-name descname"><span class="pre">extend</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">other_model</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">copy</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">False</span></span></em><span class="sig-paren">)</span><a class="reference internal" href="../../_modules/arbdmodel/model.html#ArbdModel.extend"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#arbdmodel.model.ArbdModel.extend" title="Link to this definition">#</a></dt>
+<dd></dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="arbdmodel.model.ArbdModel.getParticleTypesAndCounts">
+<span class="sig-name descname"><span class="pre">getParticleTypesAndCounts</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="reference internal" href="../../_modules/arbdmodel/model.html#ArbdModel.getParticleTypesAndCounts"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#arbdmodel.model.ArbdModel.getParticleTypesAndCounts" title="Link to this definition">#</a></dt>
+<dd><p>Includes rigid body-attached particles</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="arbdmodel.model.ArbdModel.load_target_IBI_distributions">
+<span class="sig-name descname"><span class="pre">load_target_IBI_distributions</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="reference internal" href="../../_modules/arbdmodel/model.html#ArbdModel.load_target_IBI_distributions"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#arbdmodel.model.ArbdModel.load_target_IBI_distributions" title="Link to this definition">#</a></dt>
+<dd></dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="arbdmodel.model.ArbdModel.prepare_for_simulation">
+<span class="sig-name descname"><span class="pre">prepare_for_simulation</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="reference internal" href="../../_modules/arbdmodel/model.html#ArbdModel.prepare_for_simulation"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#arbdmodel.model.ArbdModel.prepare_for_simulation" title="Link to this definition">#</a></dt>
+<dd></dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="arbdmodel.model.ArbdModel.run_IBI">
+<span class="sig-name descname"><span class="pre">run_IBI</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">iterations</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">directory</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">'./'</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">engine</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">replicas</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">1</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">run_minimization</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">True</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">first_iteration</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">1</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">target_universe</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">target_trajectory</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em><span class="sig-paren">)</span><a class="reference internal" href="../../_modules/arbdmodel/model.html#ArbdModel.run_IBI"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#arbdmodel.model.ArbdModel.run_IBI" title="Link to this definition">#</a></dt>
+<dd><p>Run Iterative Boltzmann Inversion (IBI) to optimize coarse-grained potentials.</p>
+<p>This method performs IBI iterations to match target distributions. For each iteration,
+it writes CG potentials, runs simulations, and extracts distributions from the resulting
+trajectories to update the potentials for the next iteration.</p>
+<dl class="field-list simple">
+<dt class="field-odd">Parameters<span class="colon">:</span></dt>
+<dd class="field-odd"><ul class="simple">
+<li><p><strong>iterations</strong> (<a class="hxr-hoverxref hxr-tooltip reference external" href="https://docs.python.org/3/library/functions.html#int" title="(in Python v3.13)"><em>int</em></a>) – Number of IBI iterations to run</p></li>
+<li><p><strong>directory</strong> (<a class="hxr-hoverxref hxr-tooltip reference external" href="https://docs.python.org/3/library/stdtypes.html#str" title="(in Python v3.13)"><em>str</em></a><em>, </em><em>optional</em>) – Directory to store output files, defaults to current directory</p></li>
+<li><p><strong>engine</strong> (<a class="reference internal" href="../simulation_engines/engine.html#arbdmodel.engine.ArbdEngine" title="arbdmodel.engine.ArbdEngine"><em>ArbdEngine</em></a><em>, </em><em>optional</em>) – Simulation engine to use. If None, creates a default engine with 5e6 steps
+and 1e4 output period</p></li>
+<li><p><strong>replicas</strong> (<a class="hxr-hoverxref hxr-tooltip reference external" href="https://docs.python.org/3/library/functions.html#int" title="(in Python v3.13)"><em>int</em></a><em>, </em><em>optional</em>) – Number of replica simulations to run per iteration, defaults to 1</p></li>
+<li><p><strong>run_minimization</strong> (<a class="hxr-hoverxref hxr-tooltip reference external" href="https://docs.python.org/3/library/functions.html#bool" title="(in Python v3.13)"><em>bool</em></a><em>, </em><em>optional</em>) – Whether to run a brief minimization before the first iteration, defaults to True</p></li>
+<li><p><strong>first_iteration</strong> (<a class="hxr-hoverxref hxr-tooltip reference external" href="https://docs.python.org/3/library/functions.html#int" title="(in Python v3.13)"><em>int</em></a><em>, </em><em>optional</em>) – Starting iteration number, useful for continuing previous IBI runs, defaults to 1</p></li>
+<li><p><strong>target_universe</strong> (<em>MDAnalysis.Universe</em><em>, </em><em>optional</em>) – Universe object containing target structure and trajectory</p></li>
+<li><p><strong>target_trajectory</strong> (<a class="hxr-hoverxref hxr-tooltip reference external" href="https://docs.python.org/3/library/stdtypes.html#str" title="(in Python v3.13)"><em>str</em></a><em> or </em><a class="hxr-hoverxref hxr-tooltip reference external" href="https://docs.python.org/3/library/stdtypes.html#list" title="(in Python v3.13)"><em>list</em></a><em>, </em><em>optional</em>) – Target trajectory file(s) to use if target_universe is provided</p></li>
+</ul>
+</dd>
+<dt class="field-even">Raises<span class="colon">:</span></dt>
+<dd class="field-even"><ul class="simple">
+<li><p><a class="hxr-hoverxref hxr-tooltip reference external" href="https://docs.python.org/3/library/exceptions.html#ValueError" title="(in Python v3.13)"><strong>ValueError</strong></a> – If the model does not have any IBI potentials assigned</p></li>
+<li><p><a class="hxr-hoverxref hxr-tooltip reference external" href="https://docs.python.org/3/library/exceptions.html#NotImplementedError" title="(in Python v3.13)"><strong>NotImplementedError</strong></a> – If the system does not have an orthorhombic unit cell</p></li>
+</ul>
+</dd>
+</dl>
+<p class="rubric">Notes</p>
+<p>The method requires bonded_ibi_potentials and nonbonded_ibi_potentials to be
+defined in the model. Use assign_IBI_degrees_of_freedom() before calling this method.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="arbdmodel.model.ArbdModel.simulate">
+<span class="sig-name descname"><span class="pre">simulate</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">output_name</span></span></em>, <em class="sig-param"><span class="o"><span class="pre">**</span></span><span class="n"><span class="pre">kwargs</span></span></em><span class="sig-paren">)</span><a class="reference internal" href="../../_modules/arbdmodel/model.html#ArbdModel.simulate"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#arbdmodel.model.ArbdModel.simulate" title="Link to this definition">#</a></dt>
+<dd></dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="arbdmodel.model.ArbdModel.update">
+<span class="sig-name descname"><span class="pre">update</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">group</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">copy</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">False</span></span></em><span class="sig-paren">)</span><a class="reference internal" href="../../_modules/arbdmodel/model.html#ArbdModel.update"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#arbdmodel.model.ArbdModel.update" title="Link to this definition">#</a></dt>
+<dd></dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="arbdmodel.model.ArbdModel.useNonbondedScheme">
+<span class="sig-name descname"><span class="pre">useNonbondedScheme</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">nbScheme</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">typeA</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">typeB</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em><span class="sig-paren">)</span><a class="reference internal" href="../../_modules/arbdmodel/model.html#ArbdModel.useNonbondedScheme"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#arbdmodel.model.ArbdModel.useNonbondedScheme" title="Link to this definition">#</a></dt>
+<dd><p>deprecated</p>
+</dd></dl>
+
+</dd></dl>
+
+<dl class="py class">
+<dt class="sig sig-object py" id="arbdmodel.model.PdbModel">
+<em class="property"><span class="pre">class</span><span class="w"> </span></em><span class="sig-name descname"><span class="pre">PdbModel</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">children</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">dimensions</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">remove_duplicate_bonded_terms</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">False</span></span></em><span class="sig-paren">)</span><a class="reference internal" href="../../_modules/arbdmodel/model.html#PdbModel"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#arbdmodel.model.PdbModel" title="Link to this definition">#</a></dt>
+<dd><p>Bases: <a class="reference internal" href="core_objects.html#arbdmodel.core_objects.Transformable" title="arbdmodel.core_objects.Transformable"><code class="xref py py-class docutils literal notranslate"><span class="pre">Transformable</span></code></a>, <a class="reference internal" href="core_objects.html#arbdmodel.core_objects.Parent" title="arbdmodel.core_objects.Parent"><code class="xref py py-class docutils literal notranslate"><span class="pre">Parent</span></code></a></p>
+<dl class="py method">
+<dt class="sig sig-object py" id="arbdmodel.model.PdbModel.write_pdb">
+<span class="sig-name descname"><span class="pre">write_pdb</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">filename</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">beta_from_fixed</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">False</span></span></em><span class="sig-paren">)</span><a class="reference internal" href="../../_modules/arbdmodel/model.html#PdbModel.write_pdb"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#arbdmodel.model.PdbModel.write_pdb" title="Link to this definition">#</a></dt>
+<dd></dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="arbdmodel.model.PdbModel.write_pqr">
+<span class="sig-name descname"><span class="pre">write_pqr</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">filename</span></span></em><span class="sig-paren">)</span><a class="reference internal" href="../../_modules/arbdmodel/model.html#PdbModel.write_pqr"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#arbdmodel.model.PdbModel.write_pqr" title="Link to this definition">#</a></dt>
+<dd></dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="arbdmodel.model.PdbModel.write_psf">
+<span class="sig-name descname"><span class="pre">write_psf</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">filename</span></span></em><span class="sig-paren">)</span><a class="reference internal" href="../../_modules/arbdmodel/model.html#PdbModel.write_psf"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#arbdmodel.model.PdbModel.write_psf" title="Link to this definition">#</a></dt>
+<dd></dd></dl>
+
+</dd></dl>
+
</section>
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@@ -390,6 +552,43 @@ document.write(`
+ <div class="bd-sidebar-secondary bd-toc"><div class="sidebar-secondary-items sidebar-secondary__inner">
+
+
+ <div class="sidebar-secondary-item">
+ <div class="page-toc tocsection onthispage">
+ <i class="fa-solid fa-list"></i> Contents
+ </div>
+ <nav class="bd-toc-nav page-toc">
+ <ul class="visible nav section-nav flex-column">
+<li class="toc-h2 nav-item toc-entry"><a class="reference internal nav-link" href="#arbdmodel.model.ArbdModel"><code class="docutils literal notranslate"><span class="pre">ArbdModel</span></code></a><ul class="nav section-nav flex-column">
+<li class="toc-h3 nav-item toc-entry"><a class="reference internal nav-link" href="#arbdmodel.model.ArbdModel.add"><code class="docutils literal notranslate"><span class="pre">ArbdModel.add()</span></code></a></li>
+<li class="toc-h3 nav-item toc-entry"><a class="reference internal nav-link" href="#arbdmodel.model.ArbdModel.add_group_site"><code class="docutils literal notranslate"><span class="pre">ArbdModel.add_group_site()</span></code></a></li>
+<li class="toc-h3 nav-item toc-entry"><a class="reference internal nav-link" href="#arbdmodel.model.ArbdModel.add_nonbonded_interaction"><code class="docutils literal notranslate"><span class="pre">ArbdModel.add_nonbonded_interaction()</span></code></a></li>
+<li class="toc-h3 nav-item toc-entry"><a class="reference internal nav-link" href="#arbdmodel.model.ArbdModel.assign_IBI_degrees_of_freedom"><code class="docutils literal notranslate"><span class="pre">ArbdModel.assign_IBI_degrees_of_freedom()</span></code></a></li>
+<li class="toc-h3 nav-item toc-entry"><a class="reference internal nav-link" href="#arbdmodel.model.ArbdModel.clear_all"><code class="docutils literal notranslate"><span class="pre">ArbdModel.clear_all()</span></code></a></li>
+<li class="toc-h3 nav-item toc-entry"><a class="reference internal nav-link" href="#arbdmodel.model.ArbdModel.dimensions_from_structure"><code class="docutils literal notranslate"><span class="pre">ArbdModel.dimensions_from_structure()</span></code></a></li>
+<li class="toc-h3 nav-item toc-entry"><a class="reference internal nav-link" href="#arbdmodel.model.ArbdModel.extend"><code class="docutils literal notranslate"><span class="pre">ArbdModel.extend()</span></code></a></li>
+<li class="toc-h3 nav-item toc-entry"><a class="reference internal nav-link" href="#arbdmodel.model.ArbdModel.getParticleTypesAndCounts"><code class="docutils literal notranslate"><span class="pre">ArbdModel.getParticleTypesAndCounts()</span></code></a></li>
+<li class="toc-h3 nav-item toc-entry"><a class="reference internal nav-link" href="#arbdmodel.model.ArbdModel.load_target_IBI_distributions"><code class="docutils literal notranslate"><span class="pre">ArbdModel.load_target_IBI_distributions()</span></code></a></li>
+<li class="toc-h3 nav-item toc-entry"><a class="reference internal nav-link" href="#arbdmodel.model.ArbdModel.prepare_for_simulation"><code class="docutils literal notranslate"><span class="pre">ArbdModel.prepare_for_simulation()</span></code></a></li>
+<li class="toc-h3 nav-item toc-entry"><a class="reference internal nav-link" href="#arbdmodel.model.ArbdModel.run_IBI"><code class="docutils literal notranslate"><span class="pre">ArbdModel.run_IBI()</span></code></a></li>
+<li class="toc-h3 nav-item toc-entry"><a class="reference internal nav-link" href="#arbdmodel.model.ArbdModel.simulate"><code class="docutils literal notranslate"><span class="pre">ArbdModel.simulate()</span></code></a></li>
+<li class="toc-h3 nav-item toc-entry"><a class="reference internal nav-link" href="#arbdmodel.model.ArbdModel.update"><code class="docutils literal notranslate"><span class="pre">ArbdModel.update()</span></code></a></li>
+<li class="toc-h3 nav-item toc-entry"><a class="reference internal nav-link" href="#arbdmodel.model.ArbdModel.useNonbondedScheme"><code class="docutils literal notranslate"><span class="pre">ArbdModel.useNonbondedScheme()</span></code></a></li>
+</ul>
+</li>
+<li class="toc-h2 nav-item toc-entry"><a class="reference internal nav-link" href="#arbdmodel.model.PdbModel"><code class="docutils literal notranslate"><span class="pre">PdbModel</span></code></a><ul class="nav section-nav flex-column">
+<li class="toc-h3 nav-item toc-entry"><a class="reference internal nav-link" href="#arbdmodel.model.PdbModel.write_pdb"><code class="docutils literal notranslate"><span class="pre">PdbModel.write_pdb()</span></code></a></li>
+<li class="toc-h3 nav-item toc-entry"><a class="reference internal nav-link" href="#arbdmodel.model.PdbModel.write_pqr"><code class="docutils literal notranslate"><span class="pre">PdbModel.write_pqr()</span></code></a></li>
+<li class="toc-h3 nav-item toc-entry"><a class="reference internal nav-link" href="#arbdmodel.model.PdbModel.write_psf"><code class="docutils literal notranslate"><span class="pre">PdbModel.write_psf()</span></code></a></li>
+</ul>
+</li>
+</ul>
+ </nav></div>
+
+</div></div>
+
</div>
<footer class="bd-footer-content">
diff --git a/_build/html/api/core/sim_config.html b/_build/html/api/core/sim_config.html
index 4a317e9b6d288e55a619b31c5dc476d5f1153c50..744c946af50de4b8f313e12ef1cc401099bff1f7 100644
--- a/_build/html/api/core/sim_config.html
+++ b/_build/html/api/core/sim_config.html
@@ -32,19 +32,19 @@
<link rel="stylesheet" type="text/css" href="../../_static/styles/sphinx-book-theme.css?v=eba8b062" />
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<script>let toggleHintHide = 'Click to hide';</script>
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@@ -323,7 +323,9 @@ document.write(`
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</script>
-
+<button class="sidebar-toggle secondary-toggle btn btn-sm" title="Toggle secondary sidebar" data-bs-placement="bottom" data-bs-toggle="tooltip">
+ <span class="fa-solid fa-list"></span>
+</button>
</div></div>
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@@ -339,6 +341,25 @@ document.write(`
<div id="print-main-content">
<div id="jb-print-toc">
+ <div>
+ <h2> Contents </h2>
+ </div>
+ <nav aria-label="Page">
+ <ul class="visible nav section-nav flex-column">
+<li class="toc-h2 nav-item toc-entry"><a class="reference internal nav-link" href="#arbdmodel.sim_config.DefaultSimConf"><code class="docutils literal notranslate"><span class="pre">DefaultSimConf</span></code></a><ul class="nav section-nav flex-column">
+<li class="toc-h3 nav-item toc-entry"><a class="reference internal nav-link" href="#arbdmodel.sim_config.DefaultSimConf.temperature"><code class="docutils literal notranslate"><span class="pre">DefaultSimConf.temperature</span></code></a></li>
+</ul>
+</li>
+<li class="toc-h2 nav-item toc-entry"><a class="reference internal nav-link" href="#arbdmodel.sim_config.SimConf"><code class="docutils literal notranslate"><span class="pre">SimConf</span></code></a><ul class="nav section-nav flex-column">
+<li class="toc-h3 nav-item toc-entry"><a class="reference internal nav-link" href="#arbdmodel.sim_config.SimConf.combine"><code class="docutils literal notranslate"><span class="pre">SimConf.combine()</span></code></a></li>
+<li class="toc-h3 nav-item toc-entry"><a class="reference internal nav-link" href="#arbdmodel.sim_config.SimConf.get_binary"><code class="docutils literal notranslate"><span class="pre">SimConf.get_binary()</span></code></a></li>
+<li class="toc-h3 nav-item toc-entry"><a class="reference internal nav-link" href="#arbdmodel.sim_config.SimConf.items"><code class="docutils literal notranslate"><span class="pre">SimConf.items()</span></code></a></li>
+<li class="toc-h3 nav-item toc-entry"><a class="reference internal nav-link" href="#arbdmodel.sim_config.SimConf.set_binary"><code class="docutils literal notranslate"><span class="pre">SimConf.set_binary()</span></code></a></li>
+<li class="toc-h3 nav-item toc-entry"><a class="reference internal nav-link" href="#arbdmodel.sim_config.SimConf.temperature"><code class="docutils literal notranslate"><span class="pre">SimConf.temperature</span></code></a></li>
+</ul>
+</li>
+</ul>
+ </nav>
</div>
</div>
</div>
@@ -352,6 +373,67 @@ document.write(`
<h1>sim_config<a class="headerlink" href="#sim-config" title="Link to this heading">#</a></h1>
<p>Simulation configuration module. Provides SimConf and DefaultSimConf
classes for configuring simulation parameters.</p>
+<p id="module-arbdmodel.sim_config">Simulation configuration module. Provides SimConf and DefaultSimConf
+classes for configuring simulation parameters.</p>
+<dl class="py class">
+<dt class="sig sig-object py" id="arbdmodel.sim_config.DefaultSimConf">
+<em class="property"><span class="pre">class</span><span class="w"> </span></em><span class="sig-name descname"><span class="pre">DefaultSimConf</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">num_steps</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">100000.0</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">output_period</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">1000.0</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">integrator</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">'MD'</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">timestep</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">2e-05</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">thermostat</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">'Langevin'</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">barostat</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">temperature</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">295</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">pressure</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">1</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">cutoff</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">50</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">pairlist_distance</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">decomp_period</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">40</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">seed</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">restart_file</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">gpu</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">0</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">viscosity</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">0.01</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">solvent_density</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">1.0</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">num_heavy_cluster</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">3</span></span></em>, <em class="sig-param"><span class="o"><span class="pre">**</span></span><span class="n"><span class="pre">kwargs</span></span></em><span class="sig-paren">)</span><a class="reference internal" href="../../_modules/arbdmodel/sim_config.html#DefaultSimConf"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#arbdmodel.sim_config.DefaultSimConf" title="Link to this definition">#</a></dt>
+<dd><p>Bases: <a class="reference internal" href="#arbdmodel.sim_config.SimConf" title="arbdmodel.sim_config.SimConf"><code class="xref py py-class docutils literal notranslate"><span class="pre">SimConf</span></code></a></p>
+<p>Generic class describing properties for a simulation with default binary paths</p>
+<dl class="py property">
+<dt class="sig sig-object py" id="arbdmodel.sim_config.DefaultSimConf.temperature">
+<em class="property"><span class="pre">property</span><span class="w"> </span></em><span class="sig-name descname"><span class="pre">temperature</span></span><a class="headerlink" href="#arbdmodel.sim_config.DefaultSimConf.temperature" title="Link to this definition">#</a></dt>
+<dd></dd></dl>
+
+</dd></dl>
+
+<dl class="py class">
+<dt class="sig sig-object py" id="arbdmodel.sim_config.SimConf">
+<em class="property"><span class="pre">class</span><span class="w"> </span></em><span class="sig-name descname"><span class="pre">SimConf</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">num_steps</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">output_period</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">integrator</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">timestep</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">thermostat</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">barostat</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">temperature</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">pressure</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">cutoff</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">pairlist_distance</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">decomp_period</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">gpu</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">seed</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">restart_file</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">rigid_body_integrator</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">rigid_body_grid_grid_period</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">viscosity</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">solvent_density</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">num_heavy_cluster</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">arbd_path</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">namd_path</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">vmd_path</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">hydropro_path</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">apbs_path</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">gmsh_path</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="o"><span class="pre">**</span></span><span class="n"><span class="pre">kwargs</span></span></em><span class="sig-paren">)</span><a class="reference internal" href="../../_modules/arbdmodel/sim_config.html#SimConf"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#arbdmodel.sim_config.SimConf" title="Link to this definition">#</a></dt>
+<dd><p>Bases: <a class="hxr-hoverxref hxr-tooltip reference external" href="https://docs.python.org/3/library/functions.html#object" title="(in Python v3.13)"><code class="xref py py-class docutils literal notranslate"><span class="pre">object</span></code></a></p>
+<p>Class describing properties for a (ARBD or NAMD) simulation</p>
+<dl class="py method">
+<dt class="sig sig-object py" id="arbdmodel.sim_config.SimConf.combine">
+<span class="sig-name descname"><span class="pre">combine</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">other</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">policy</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">'override'</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">warn</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">False</span></span></em><span class="sig-paren">)</span><a class="reference internal" href="../../_modules/arbdmodel/sim_config.html#SimConf.combine"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#arbdmodel.sim_config.SimConf.combine" title="Link to this definition">#</a></dt>
+<dd><p>Creates a new SimConf object whose properties are
+initialized to be from “selfâ€, but are overridden with
+properties in “otherâ€, provided they are not None</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="arbdmodel.sim_config.SimConf.get_binary">
+<span class="sig-name descname"><span class="pre">get_binary</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">name</span></span></em><span class="sig-paren">)</span><a class="reference internal" href="../../_modules/arbdmodel/sim_config.html#SimConf.get_binary"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#arbdmodel.sim_config.SimConf.get_binary" title="Link to this definition">#</a></dt>
+<dd><p>Get the path to a specific binary with improved error handling.</p>
+<dl class="field-list simple">
+<dt class="field-odd">Parameters<span class="colon">:</span></dt>
+<dd class="field-odd"><p><strong>name</strong> – The name of the binary (e.g., ‘arbd’, ‘hydropro’)</p>
+</dd>
+<dt class="field-even">Returns<span class="colon">:</span></dt>
+<dd class="field-even"><p>Path to the binary if found, None otherwise</p>
+</dd>
+</dl>
+<p>This method does not raise exceptions when binaries are not found, allowing
+for graceful handling of missing optional dependencies.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="arbdmodel.sim_config.SimConf.items">
+<span class="sig-name descname"><span class="pre">items</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="reference internal" href="../../_modules/arbdmodel/sim_config.html#SimConf.items"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#arbdmodel.sim_config.SimConf.items" title="Link to this definition">#</a></dt>
+<dd></dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="arbdmodel.sim_config.SimConf.set_binary">
+<span class="sig-name descname"><span class="pre">set_binary</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">name</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">path</span></span></em><span class="sig-paren">)</span><a class="reference internal" href="../../_modules/arbdmodel/sim_config.html#SimConf.set_binary"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#arbdmodel.sim_config.SimConf.set_binary" title="Link to this definition">#</a></dt>
+<dd><p>Set the path to a specific binary.</p>
+</dd></dl>
+
+<dl class="py property">
+<dt class="sig sig-object py" id="arbdmodel.sim_config.SimConf.temperature">
+<em class="property"><span class="pre">property</span><span class="w"> </span></em><span class="sig-name descname"><span class="pre">temperature</span></span><a class="headerlink" href="#arbdmodel.sim_config.SimConf.temperature" title="Link to this definition">#</a></dt>
+<dd></dd></dl>
+
+</dd></dl>
+
</section>
<script type="text/x-thebe-config">
@@ -391,6 +473,32 @@ classes for configuring simulation parameters.</p>
+ <div class="bd-sidebar-secondary bd-toc"><div class="sidebar-secondary-items sidebar-secondary__inner">
+
+
+ <div class="sidebar-secondary-item">
+ <div class="page-toc tocsection onthispage">
+ <i class="fa-solid fa-list"></i> Contents
+ </div>
+ <nav class="bd-toc-nav page-toc">
+ <ul class="visible nav section-nav flex-column">
+<li class="toc-h2 nav-item toc-entry"><a class="reference internal nav-link" href="#arbdmodel.sim_config.DefaultSimConf"><code class="docutils literal notranslate"><span class="pre">DefaultSimConf</span></code></a><ul class="nav section-nav flex-column">
+<li class="toc-h3 nav-item toc-entry"><a class="reference internal nav-link" href="#arbdmodel.sim_config.DefaultSimConf.temperature"><code class="docutils literal notranslate"><span class="pre">DefaultSimConf.temperature</span></code></a></li>
+</ul>
+</li>
+<li class="toc-h2 nav-item toc-entry"><a class="reference internal nav-link" href="#arbdmodel.sim_config.SimConf"><code class="docutils literal notranslate"><span class="pre">SimConf</span></code></a><ul class="nav section-nav flex-column">
+<li class="toc-h3 nav-item toc-entry"><a class="reference internal nav-link" href="#arbdmodel.sim_config.SimConf.combine"><code class="docutils literal notranslate"><span class="pre">SimConf.combine()</span></code></a></li>
+<li class="toc-h3 nav-item toc-entry"><a class="reference internal nav-link" href="#arbdmodel.sim_config.SimConf.get_binary"><code class="docutils literal notranslate"><span class="pre">SimConf.get_binary()</span></code></a></li>
+<li class="toc-h3 nav-item toc-entry"><a class="reference internal nav-link" href="#arbdmodel.sim_config.SimConf.items"><code class="docutils literal notranslate"><span class="pre">SimConf.items()</span></code></a></li>
+<li class="toc-h3 nav-item toc-entry"><a class="reference internal nav-link" href="#arbdmodel.sim_config.SimConf.set_binary"><code class="docutils literal notranslate"><span class="pre">SimConf.set_binary()</span></code></a></li>
+<li class="toc-h3 nav-item toc-entry"><a class="reference internal nav-link" href="#arbdmodel.sim_config.SimConf.temperature"><code class="docutils literal notranslate"><span class="pre">SimConf.temperature</span></code></a></li>
+</ul>
+</li>
+</ul>
+ </nav></div>
+
+</div></div>
+
</div>
<footer class="bd-footer-content">
diff --git a/_build/html/api/index.html b/_build/html/api/index.html
index 362e8a4d7ab380fa6e05152d80b48054c0615ba0..1fa2ea59524b1f75a2c4cc623ba731e2d4d45073 100644
--- a/_build/html/api/index.html
+++ b/_build/html/api/index.html
@@ -32,19 +32,19 @@
<link rel="stylesheet" type="text/css" href="../_static/styles/sphinx-book-theme.css?v=eba8b062" />
<link rel="stylesheet" type="text/css" href="../_static/togglebutton.css?v=13237357" />
<link rel="stylesheet" type="text/css" href="../_static/copybutton.css?v=76b2166b" />
- <link rel="stylesheet" type="text/css" href="../_static/mystnb.4510f1fc1dee50b3e5859aac5469c37c29e427902b24a333a5f9fcb2f0b3ac41.css" />
+ <link rel="stylesheet" type="text/css" href="../_static/mystnb.4510f1fc1dee50b3e5859aac5469c37c29e427902b24a333a5f9fcb2f0b3ac41.css?v=be8a1c11" />
<link rel="stylesheet" type="text/css" href="../_static/sphinx-thebe.css?v=4fa983c6" />
<link rel="stylesheet" type="text/css" href="../_static/tabs.css?v=4c969af8" />
- <link rel="stylesheet" type="text/css" href="../_static/proof.css" />
+ <link rel="stylesheet" type="text/css" href="../_static/proof.css?v=b4b7a797" />
<link rel="stylesheet" type="text/css" href="../_static/styles/sphinx-examples.css?v=e236af4b" />
- <link rel="stylesheet" type="text/css" href="../_static/css/tooltipster.custom.css" />
- <link rel="stylesheet" type="text/css" href="../_static/css/tooltipster.bundle.min.css" />
- <link rel="stylesheet" type="text/css" href="../_static/css/tooltipster-sideTip-shadow.min.css" />
- <link rel="stylesheet" type="text/css" href="../_static/css/tooltipster-sideTip-punk.min.css" />
- <link rel="stylesheet" type="text/css" href="../_static/css/tooltipster-sideTip-noir.min.css" />
- <link rel="stylesheet" type="text/css" href="../_static/css/tooltipster-sideTip-light.min.css" />
- <link rel="stylesheet" type="text/css" href="../_static/css/tooltipster-sideTip-borderless.min.css" />
- <link rel="stylesheet" type="text/css" href="../_static/css/micromodal.css" />
+ <link rel="stylesheet" type="text/css" href="../_static/css/tooltipster.custom.css?v=7bc2f056" />
+ <link rel="stylesheet" type="text/css" href="../_static/css/tooltipster.bundle.min.css?v=37217874" />
+ <link rel="stylesheet" type="text/css" href="../_static/css/tooltipster-sideTip-shadow.min.css?v=6227e517" />
+ <link rel="stylesheet" type="text/css" href="../_static/css/tooltipster-sideTip-punk.min.css?v=94669e23" />
+ <link rel="stylesheet" type="text/css" href="../_static/css/tooltipster-sideTip-noir.min.css?v=21a39f42" />
+ <link rel="stylesheet" type="text/css" href="../_static/css/tooltipster-sideTip-light.min.css?v=a18b2449" />
+ <link rel="stylesheet" type="text/css" href="../_static/css/tooltipster-sideTip-borderless.min.css?v=dbff53e4" />
+ <link rel="stylesheet" type="text/css" href="../_static/css/micromodal.css?v=d7bf34ee" />
<link rel="stylesheet" type="text/css" href="../_static/sphinx-design.min.css?v=95c83b7e" />
<!-- Pre-loaded scripts that we'll load fully later -->
@@ -61,9 +61,9 @@
<script src="../_static/copybutton.js?v=f281be69"></script>
<script src="../_static/scripts/sphinx-book-theme.js?v=887ef09a"></script>
<script src="../_static/tabs.js?v=3ee01567"></script>
- <script src="../_static/js/hoverxref.js"></script>
- <script src="../_static/js/tooltipster.bundle.min.js"></script>
- <script src="../_static/js/micromodal.min.js"></script>
+ <script src="../_static/js/hoverxref.js?v=c95ade4f"></script>
+ <script src="../_static/js/tooltipster.bundle.min.js?v=18bf091b"></script>
+ <script src="../_static/js/micromodal.min.js?v=04d6302d"></script>
<script>let toggleHintShow = 'Click to show';</script>
<script>let toggleHintHide = 'Click to hide';</script>
<script>let toggleOpenOnPrint = 'true';</script>
diff --git a/_build/html/api/interaction_potentials/ibi.html b/_build/html/api/interaction_potentials/ibi.html
index 3801754a9bf06b682a9998e61df3f2084c58908a..2b68869596205923953f5ca90b6cb5f9e69fd35d 100644
--- a/_build/html/api/interaction_potentials/ibi.html
+++ b/_build/html/api/interaction_potentials/ibi.html
@@ -32,19 +32,19 @@
<link rel="stylesheet" type="text/css" href="../../_static/styles/sphinx-book-theme.css?v=eba8b062" />
<link rel="stylesheet" type="text/css" href="../../_static/togglebutton.css?v=13237357" />
<link rel="stylesheet" type="text/css" href="../../_static/copybutton.css?v=76b2166b" />
- <link rel="stylesheet" type="text/css" href="../../_static/mystnb.4510f1fc1dee50b3e5859aac5469c37c29e427902b24a333a5f9fcb2f0b3ac41.css" />
+ <link rel="stylesheet" type="text/css" href="../../_static/mystnb.4510f1fc1dee50b3e5859aac5469c37c29e427902b24a333a5f9fcb2f0b3ac41.css?v=be8a1c11" />
<link rel="stylesheet" type="text/css" href="../../_static/sphinx-thebe.css?v=4fa983c6" />
<link rel="stylesheet" type="text/css" href="../../_static/tabs.css?v=4c969af8" />
- <link rel="stylesheet" type="text/css" href="../../_static/proof.css" />
+ <link rel="stylesheet" type="text/css" href="../../_static/proof.css?v=b4b7a797" />
<link rel="stylesheet" type="text/css" href="../../_static/styles/sphinx-examples.css?v=e236af4b" />
- <link rel="stylesheet" type="text/css" href="../../_static/css/tooltipster.custom.css" />
- <link rel="stylesheet" type="text/css" href="../../_static/css/tooltipster.bundle.min.css" />
- <link rel="stylesheet" type="text/css" href="../../_static/css/tooltipster-sideTip-shadow.min.css" />
- <link rel="stylesheet" type="text/css" href="../../_static/css/tooltipster-sideTip-punk.min.css" />
- <link rel="stylesheet" type="text/css" href="../../_static/css/tooltipster-sideTip-noir.min.css" />
- <link rel="stylesheet" type="text/css" href="../../_static/css/tooltipster-sideTip-light.min.css" />
- <link rel="stylesheet" type="text/css" href="../../_static/css/tooltipster-sideTip-borderless.min.css" />
- <link rel="stylesheet" type="text/css" href="../../_static/css/micromodal.css" />
+ <link rel="stylesheet" type="text/css" href="../../_static/css/tooltipster.custom.css?v=7bc2f056" />
+ <link rel="stylesheet" type="text/css" href="../../_static/css/tooltipster.bundle.min.css?v=37217874" />
+ <link rel="stylesheet" type="text/css" href="../../_static/css/tooltipster-sideTip-shadow.min.css?v=6227e517" />
+ <link rel="stylesheet" type="text/css" href="../../_static/css/tooltipster-sideTip-punk.min.css?v=94669e23" />
+ <link rel="stylesheet" type="text/css" href="../../_static/css/tooltipster-sideTip-noir.min.css?v=21a39f42" />
+ <link rel="stylesheet" type="text/css" href="../../_static/css/tooltipster-sideTip-light.min.css?v=a18b2449" />
+ <link rel="stylesheet" type="text/css" href="../../_static/css/tooltipster-sideTip-borderless.min.css?v=dbff53e4" />
+ <link rel="stylesheet" type="text/css" href="../../_static/css/micromodal.css?v=d7bf34ee" />
<link rel="stylesheet" type="text/css" href="../../_static/sphinx-design.min.css?v=95c83b7e" />
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@@ -61,9 +61,9 @@
<script src="../../_static/copybutton.js?v=f281be69"></script>
<script src="../../_static/scripts/sphinx-book-theme.js?v=887ef09a"></script>
<script src="../../_static/tabs.js?v=3ee01567"></script>
- <script src="../../_static/js/hoverxref.js"></script>
- <script src="../../_static/js/tooltipster.bundle.min.js"></script>
- <script src="../../_static/js/micromodal.min.js"></script>
+ <script src="../../_static/js/hoverxref.js?v=c95ade4f"></script>
+ <script src="../../_static/js/tooltipster.bundle.min.js?v=18bf091b"></script>
+ <script src="../../_static/js/micromodal.min.js?v=04d6302d"></script>
<script>let toggleHintShow = 'Click to show';</script>
<script>let toggleHintHide = 'Click to hide';</script>
<script>let toggleOpenOnPrint = 'true';</script>
diff --git a/_build/html/api/interaction_potentials/index.html b/_build/html/api/interaction_potentials/index.html
index a113e418c96adac24300a50ad0867e68dd1f8d22..48ad74db3b1a3307b629d5285d928c56dd79acb9 100644
--- a/_build/html/api/interaction_potentials/index.html
+++ b/_build/html/api/interaction_potentials/index.html
@@ -32,19 +32,19 @@
<link rel="stylesheet" type="text/css" href="../../_static/styles/sphinx-book-theme.css?v=eba8b062" />
<link rel="stylesheet" type="text/css" href="../../_static/togglebutton.css?v=13237357" />
<link rel="stylesheet" type="text/css" href="../../_static/copybutton.css?v=76b2166b" />
- <link rel="stylesheet" type="text/css" href="../../_static/mystnb.4510f1fc1dee50b3e5859aac5469c37c29e427902b24a333a5f9fcb2f0b3ac41.css" />
+ <link rel="stylesheet" type="text/css" href="../../_static/mystnb.4510f1fc1dee50b3e5859aac5469c37c29e427902b24a333a5f9fcb2f0b3ac41.css?v=be8a1c11" />
<link rel="stylesheet" type="text/css" href="../../_static/sphinx-thebe.css?v=4fa983c6" />
<link rel="stylesheet" type="text/css" href="../../_static/tabs.css?v=4c969af8" />
- <link rel="stylesheet" type="text/css" href="../../_static/proof.css" />
+ <link rel="stylesheet" type="text/css" href="../../_static/proof.css?v=b4b7a797" />
<link rel="stylesheet" type="text/css" href="../../_static/styles/sphinx-examples.css?v=e236af4b" />
- <link rel="stylesheet" type="text/css" href="../../_static/css/tooltipster.custom.css" />
- <link rel="stylesheet" type="text/css" href="../../_static/css/tooltipster.bundle.min.css" />
- <link rel="stylesheet" type="text/css" href="../../_static/css/tooltipster-sideTip-shadow.min.css" />
- <link rel="stylesheet" type="text/css" href="../../_static/css/tooltipster-sideTip-punk.min.css" />
- <link rel="stylesheet" type="text/css" href="../../_static/css/tooltipster-sideTip-noir.min.css" />
- <link rel="stylesheet" type="text/css" href="../../_static/css/tooltipster-sideTip-light.min.css" />
- <link rel="stylesheet" type="text/css" href="../../_static/css/tooltipster-sideTip-borderless.min.css" />
- <link rel="stylesheet" type="text/css" href="../../_static/css/micromodal.css" />
+ <link rel="stylesheet" type="text/css" href="../../_static/css/tooltipster.custom.css?v=7bc2f056" />
+ <link rel="stylesheet" type="text/css" href="../../_static/css/tooltipster.bundle.min.css?v=37217874" />
+ <link rel="stylesheet" type="text/css" href="../../_static/css/tooltipster-sideTip-shadow.min.css?v=6227e517" />
+ <link rel="stylesheet" type="text/css" href="../../_static/css/tooltipster-sideTip-punk.min.css?v=94669e23" />
+ <link rel="stylesheet" type="text/css" href="../../_static/css/tooltipster-sideTip-noir.min.css?v=21a39f42" />
+ <link rel="stylesheet" type="text/css" href="../../_static/css/tooltipster-sideTip-light.min.css?v=a18b2449" />
+ <link rel="stylesheet" type="text/css" href="../../_static/css/tooltipster-sideTip-borderless.min.css?v=dbff53e4" />
+ <link rel="stylesheet" type="text/css" href="../../_static/css/micromodal.css?v=d7bf34ee" />
<link rel="stylesheet" type="text/css" href="../../_static/sphinx-design.min.css?v=95c83b7e" />
<!-- Pre-loaded scripts that we'll load fully later -->
@@ -61,9 +61,9 @@
<script src="../../_static/copybutton.js?v=f281be69"></script>
<script src="../../_static/scripts/sphinx-book-theme.js?v=887ef09a"></script>
<script src="../../_static/tabs.js?v=3ee01567"></script>
- <script src="../../_static/js/hoverxref.js"></script>
- <script src="../../_static/js/tooltipster.bundle.min.js"></script>
- <script src="../../_static/js/micromodal.min.js"></script>
+ <script src="../../_static/js/hoverxref.js?v=c95ade4f"></script>
+ <script src="../../_static/js/tooltipster.bundle.min.js?v=18bf091b"></script>
+ <script src="../../_static/js/micromodal.min.js?v=04d6302d"></script>
<script>let toggleHintShow = 'Click to show';</script>
<script>let toggleHintHide = 'Click to hide';</script>
<script>let toggleOpenOnPrint = 'true';</script>
diff --git a/_build/html/api/interaction_potentials/interactions.html b/_build/html/api/interaction_potentials/interactions.html
index bd633f9d1322f1b1836fab7292a05c089d7eae64..537d965a5c68341edcd4ae0e4ad0fd55f2e1974e 100644
--- a/_build/html/api/interaction_potentials/interactions.html
+++ b/_build/html/api/interaction_potentials/interactions.html
@@ -32,19 +32,19 @@
<link rel="stylesheet" type="text/css" href="../../_static/styles/sphinx-book-theme.css?v=eba8b062" />
<link rel="stylesheet" type="text/css" href="../../_static/togglebutton.css?v=13237357" />
<link rel="stylesheet" type="text/css" href="../../_static/copybutton.css?v=76b2166b" />
- <link rel="stylesheet" type="text/css" href="../../_static/mystnb.4510f1fc1dee50b3e5859aac5469c37c29e427902b24a333a5f9fcb2f0b3ac41.css" />
+ <link rel="stylesheet" type="text/css" href="../../_static/mystnb.4510f1fc1dee50b3e5859aac5469c37c29e427902b24a333a5f9fcb2f0b3ac41.css?v=be8a1c11" />
<link rel="stylesheet" type="text/css" href="../../_static/sphinx-thebe.css?v=4fa983c6" />
<link rel="stylesheet" type="text/css" href="../../_static/tabs.css?v=4c969af8" />
- <link rel="stylesheet" type="text/css" href="../../_static/proof.css" />
+ <link rel="stylesheet" type="text/css" href="../../_static/proof.css?v=b4b7a797" />
<link rel="stylesheet" type="text/css" href="../../_static/styles/sphinx-examples.css?v=e236af4b" />
- <link rel="stylesheet" type="text/css" href="../../_static/css/tooltipster.custom.css" />
- <link rel="stylesheet" type="text/css" href="../../_static/css/tooltipster.bundle.min.css" />
- <link rel="stylesheet" type="text/css" href="../../_static/css/tooltipster-sideTip-shadow.min.css" />
- <link rel="stylesheet" type="text/css" href="../../_static/css/tooltipster-sideTip-punk.min.css" />
- <link rel="stylesheet" type="text/css" href="../../_static/css/tooltipster-sideTip-noir.min.css" />
- <link rel="stylesheet" type="text/css" href="../../_static/css/tooltipster-sideTip-light.min.css" />
- <link rel="stylesheet" type="text/css" href="../../_static/css/tooltipster-sideTip-borderless.min.css" />
- <link rel="stylesheet" type="text/css" href="../../_static/css/micromodal.css" />
+ <link rel="stylesheet" type="text/css" href="../../_static/css/tooltipster.custom.css?v=7bc2f056" />
+ <link rel="stylesheet" type="text/css" href="../../_static/css/tooltipster.bundle.min.css?v=37217874" />
+ <link rel="stylesheet" type="text/css" href="../../_static/css/tooltipster-sideTip-shadow.min.css?v=6227e517" />
+ <link rel="stylesheet" type="text/css" href="../../_static/css/tooltipster-sideTip-punk.min.css?v=94669e23" />
+ <link rel="stylesheet" type="text/css" href="../../_static/css/tooltipster-sideTip-noir.min.css?v=21a39f42" />
+ <link rel="stylesheet" type="text/css" href="../../_static/css/tooltipster-sideTip-light.min.css?v=a18b2449" />
+ <link rel="stylesheet" type="text/css" href="../../_static/css/tooltipster-sideTip-borderless.min.css?v=dbff53e4" />
+ <link rel="stylesheet" type="text/css" href="../../_static/css/micromodal.css?v=d7bf34ee" />
<link rel="stylesheet" type="text/css" href="../../_static/sphinx-design.min.css?v=95c83b7e" />
<!-- Pre-loaded scripts that we'll load fully later -->
@@ -61,9 +61,9 @@
<script src="../../_static/copybutton.js?v=f281be69"></script>
<script src="../../_static/scripts/sphinx-book-theme.js?v=887ef09a"></script>
<script src="../../_static/tabs.js?v=3ee01567"></script>
- <script src="../../_static/js/hoverxref.js"></script>
- <script src="../../_static/js/tooltipster.bundle.min.js"></script>
- <script src="../../_static/js/micromodal.min.js"></script>
+ <script src="../../_static/js/hoverxref.js?v=c95ade4f"></script>
+ <script src="../../_static/js/tooltipster.bundle.min.js?v=18bf091b"></script>
+ <script src="../../_static/js/micromodal.min.js?v=04d6302d"></script>
<script>let toggleHintShow = 'Click to show';</script>
<script>let toggleHintHide = 'Click to hide';</script>
<script>let toggleOpenOnPrint = 'true';</script>
@@ -354,6 +354,11 @@ document.write(`
<li class="toc-h3 nav-item toc-entry"><a class="reference internal nav-link" href="#arbdmodel.interactions.AbstractPotential.write_file"><code class="docutils literal notranslate"><span class="pre">AbstractPotential.write_file()</span></code></a></li>
</ul>
</li>
+<li class="toc-h2 nav-item toc-entry"><a class="reference internal nav-link" href="#arbdmodel.interactions.BoundaryPotential"><code class="docutils literal notranslate"><span class="pre">BoundaryPotential</span></code></a><ul class="nav section-nav flex-column">
+<li class="toc-h3 nav-item toc-entry"><a class="reference internal nav-link" href="#arbdmodel.interactions.BoundaryPotential.potential"><code class="docutils literal notranslate"><span class="pre">BoundaryPotential.potential()</span></code></a></li>
+<li class="toc-h3 nav-item toc-entry"><a class="reference internal nav-link" href="#arbdmodel.interactions.BoundaryPotential.write_file"><code class="docutils literal notranslate"><span class="pre">BoundaryPotential.write_file()</span></code></a></li>
+</ul>
+</li>
<li class="toc-h2 nav-item toc-entry"><a class="reference internal nav-link" href="#arbdmodel.interactions.HalfHarmonic"><code class="docutils literal notranslate"><span class="pre">HalfHarmonic</span></code></a><ul class="nav section-nav flex-column">
<li class="toc-h3 nav-item toc-entry"><a class="reference internal nav-link" href="#arbdmodel.interactions.HalfHarmonic.potential"><code class="docutils literal notranslate"><span class="pre">HalfHarmonic.potential()</span></code></a></li>
</ul>
@@ -461,6 +466,27 @@ document.write(`
</dd></dl>
+<dl class="py class">
+<dt class="sig sig-object py" id="arbdmodel.interactions.BoundaryPotential">
+<em class="property"><span class="pre">class</span><span class="w"> </span></em><span class="sig-name descname"><span class="pre">BoundaryPotential</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">cell_vectors</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">cell_origin</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">well_depth</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">1.0</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">resolution</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">2.0</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">blur</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">5.0</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">filename</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">'boundary.dx'</span></span></em>, <em class="sig-param"><span class="o"><span class="pre">**</span></span><span class="n"><span class="pre">kwargs</span></span></em><span class="sig-paren">)</span><a class="reference internal" href="../../_modules/arbdmodel/interactions.html#BoundaryPotential"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#arbdmodel.interactions.BoundaryPotential" title="Link to this definition">#</a></dt>
+<dd><p>Bases: <a class="reference internal" href="#arbdmodel.interactions.AbstractPotential" title="arbdmodel.interactions.AbstractPotential"><code class="xref py py-class docutils literal notranslate"><span class="pre">AbstractPotential</span></code></a></p>
+<p>Boundary potential for confining simulations.</p>
+<dl class="py method">
+<dt class="sig sig-object py" id="arbdmodel.interactions.BoundaryPotential.potential">
+<span class="sig-name descname"><span class="pre">potential</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">r</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">types</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em><span class="sig-paren">)</span><a class="reference internal" href="../../_modules/arbdmodel/interactions.html#BoundaryPotential.potential"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#arbdmodel.interactions.BoundaryPotential.potential" title="Link to this definition">#</a></dt>
+<dd><p>Calculate potential at positions.</p>
+<p>This isn’t used directly for grid potentials in ARBD, but implemented
+for consistency with the AbstractPotential interface.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="arbdmodel.interactions.BoundaryPotential.write_file">
+<span class="sig-name descname"><span class="pre">write_file</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">filename</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">types</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em><span class="sig-paren">)</span><a class="reference internal" href="../../_modules/arbdmodel/interactions.html#BoundaryPotential.write_file"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#arbdmodel.interactions.BoundaryPotential.write_file" title="Link to this definition">#</a></dt>
+<dd><p>Write boundary potential to grid file.</p>
+</dd></dl>
+
+</dd></dl>
+
<dl class="py class">
<dt class="sig sig-object py" id="arbdmodel.interactions.HalfHarmonic">
<em class="property"><span class="pre">class</span><span class="w"> </span></em><span class="sig-name descname"><span class="pre">HalfHarmonic</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">range_</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">(0,</span> <span class="pre">None)</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">resolution</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">0.1</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">max_force</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">max_potential</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">zero</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">'last'</span></span></em><span class="sig-paren">)</span><a class="reference internal" href="../../_modules/arbdmodel/interactions.html#HalfHarmonic"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#arbdmodel.interactions.HalfHarmonic" title="Link to this definition">#</a></dt>
@@ -717,6 +743,11 @@ document.write(`
<li class="toc-h3 nav-item toc-entry"><a class="reference internal nav-link" href="#arbdmodel.interactions.AbstractPotential.write_file"><code class="docutils literal notranslate"><span class="pre">AbstractPotential.write_file()</span></code></a></li>
</ul>
</li>
+<li class="toc-h2 nav-item toc-entry"><a class="reference internal nav-link" href="#arbdmodel.interactions.BoundaryPotential"><code class="docutils literal notranslate"><span class="pre">BoundaryPotential</span></code></a><ul class="nav section-nav flex-column">
+<li class="toc-h3 nav-item toc-entry"><a class="reference internal nav-link" href="#arbdmodel.interactions.BoundaryPotential.potential"><code class="docutils literal notranslate"><span class="pre">BoundaryPotential.potential()</span></code></a></li>
+<li class="toc-h3 nav-item toc-entry"><a class="reference internal nav-link" href="#arbdmodel.interactions.BoundaryPotential.write_file"><code class="docutils literal notranslate"><span class="pre">BoundaryPotential.write_file()</span></code></a></li>
+</ul>
+</li>
<li class="toc-h2 nav-item toc-entry"><a class="reference internal nav-link" href="#arbdmodel.interactions.HalfHarmonic"><code class="docutils literal notranslate"><span class="pre">HalfHarmonic</span></code></a><ul class="nav section-nav flex-column">
<li class="toc-h3 nav-item toc-entry"><a class="reference internal nav-link" href="#arbdmodel.interactions.HalfHarmonic.potential"><code class="docutils literal notranslate"><span class="pre">HalfHarmonic.potential()</span></code></a></li>
</ul>
diff --git a/_build/html/api/polymer_modeling/fjc_polymer_model.html b/_build/html/api/polymer_modeling/fjc_polymer_model.html
index 8babd4b9dd5d1df29c6510559c0ea606bb7b501b..64a5b45512e8fc57f5690e8a14876faf2e8a8c0f 100644
--- a/_build/html/api/polymer_modeling/fjc_polymer_model.html
+++ b/_build/html/api/polymer_modeling/fjc_polymer_model.html
@@ -32,19 +32,19 @@
<link rel="stylesheet" type="text/css" href="../../_static/styles/sphinx-book-theme.css?v=eba8b062" />
<link rel="stylesheet" type="text/css" href="../../_static/togglebutton.css?v=13237357" />
<link rel="stylesheet" type="text/css" href="../../_static/copybutton.css?v=76b2166b" />
- <link rel="stylesheet" type="text/css" href="../../_static/mystnb.4510f1fc1dee50b3e5859aac5469c37c29e427902b24a333a5f9fcb2f0b3ac41.css" />
+ <link rel="stylesheet" type="text/css" href="../../_static/mystnb.4510f1fc1dee50b3e5859aac5469c37c29e427902b24a333a5f9fcb2f0b3ac41.css?v=be8a1c11" />
<link rel="stylesheet" type="text/css" href="../../_static/sphinx-thebe.css?v=4fa983c6" />
<link rel="stylesheet" type="text/css" href="../../_static/tabs.css?v=4c969af8" />
- <link rel="stylesheet" type="text/css" href="../../_static/proof.css" />
+ <link rel="stylesheet" type="text/css" href="../../_static/proof.css?v=b4b7a797" />
<link rel="stylesheet" type="text/css" href="../../_static/styles/sphinx-examples.css?v=e236af4b" />
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- <link rel="stylesheet" type="text/css" href="../../_static/css/tooltipster.bundle.min.css" />
- <link rel="stylesheet" type="text/css" href="../../_static/css/tooltipster-sideTip-shadow.min.css" />
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- <link rel="stylesheet" type="text/css" href="../../_static/css/tooltipster-sideTip-borderless.min.css" />
- <link rel="stylesheet" type="text/css" href="../../_static/css/micromodal.css" />
+ <link rel="stylesheet" type="text/css" href="../../_static/css/tooltipster.custom.css?v=7bc2f056" />
+ <link rel="stylesheet" type="text/css" href="../../_static/css/tooltipster.bundle.min.css?v=37217874" />
+ <link rel="stylesheet" type="text/css" href="../../_static/css/tooltipster-sideTip-shadow.min.css?v=6227e517" />
+ <link rel="stylesheet" type="text/css" href="../../_static/css/tooltipster-sideTip-punk.min.css?v=94669e23" />
+ <link rel="stylesheet" type="text/css" href="../../_static/css/tooltipster-sideTip-noir.min.css?v=21a39f42" />
+ <link rel="stylesheet" type="text/css" href="../../_static/css/tooltipster-sideTip-light.min.css?v=a18b2449" />
+ <link rel="stylesheet" type="text/css" href="../../_static/css/tooltipster-sideTip-borderless.min.css?v=dbff53e4" />
+ <link rel="stylesheet" type="text/css" href="../../_static/css/micromodal.css?v=d7bf34ee" />
<link rel="stylesheet" type="text/css" href="../../_static/sphinx-design.min.css?v=95c83b7e" />
<!-- Pre-loaded scripts that we'll load fully later -->
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<script src="../../_static/copybutton.js?v=f281be69"></script>
<script src="../../_static/scripts/sphinx-book-theme.js?v=887ef09a"></script>
<script src="../../_static/tabs.js?v=3ee01567"></script>
- <script src="../../_static/js/hoverxref.js"></script>
- <script src="../../_static/js/tooltipster.bundle.min.js"></script>
- <script src="../../_static/js/micromodal.min.js"></script>
+ <script src="../../_static/js/hoverxref.js?v=c95ade4f"></script>
+ <script src="../../_static/js/tooltipster.bundle.min.js?v=18bf091b"></script>
+ <script src="../../_static/js/micromodal.min.js?v=04d6302d"></script>
<script>let toggleHintShow = 'Click to show';</script>
<script>let toggleHintHide = 'Click to hide';</script>
<script>let toggleOpenOnPrint = 'true';</script>
diff --git a/_build/html/api/polymer_modeling/hps_polymer_model.html b/_build/html/api/polymer_modeling/hps_polymer_model.html
index 5f13b6fd7d98625a9b64da9c39476bb81e4a0999..8b1e2842379dc66b94d65b2501673ffb0bf94366 100644
--- a/_build/html/api/polymer_modeling/hps_polymer_model.html
+++ b/_build/html/api/polymer_modeling/hps_polymer_model.html
@@ -32,19 +32,19 @@
<link rel="stylesheet" type="text/css" href="../../_static/styles/sphinx-book-theme.css?v=eba8b062" />
<link rel="stylesheet" type="text/css" href="../../_static/togglebutton.css?v=13237357" />
<link rel="stylesheet" type="text/css" href="../../_static/copybutton.css?v=76b2166b" />
- <link rel="stylesheet" type="text/css" href="../../_static/mystnb.4510f1fc1dee50b3e5859aac5469c37c29e427902b24a333a5f9fcb2f0b3ac41.css" />
+ <link rel="stylesheet" type="text/css" href="../../_static/mystnb.4510f1fc1dee50b3e5859aac5469c37c29e427902b24a333a5f9fcb2f0b3ac41.css?v=be8a1c11" />
<link rel="stylesheet" type="text/css" href="../../_static/sphinx-thebe.css?v=4fa983c6" />
<link rel="stylesheet" type="text/css" href="../../_static/tabs.css?v=4c969af8" />
- <link rel="stylesheet" type="text/css" href="../../_static/proof.css" />
+ <link rel="stylesheet" type="text/css" href="../../_static/proof.css?v=b4b7a797" />
<link rel="stylesheet" type="text/css" href="../../_static/styles/sphinx-examples.css?v=e236af4b" />
- <link rel="stylesheet" type="text/css" href="../../_static/css/tooltipster.custom.css" />
- <link rel="stylesheet" type="text/css" href="../../_static/css/tooltipster.bundle.min.css" />
- <link rel="stylesheet" type="text/css" href="../../_static/css/tooltipster-sideTip-shadow.min.css" />
- <link rel="stylesheet" type="text/css" href="../../_static/css/tooltipster-sideTip-punk.min.css" />
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- <link rel="stylesheet" type="text/css" href="../../_static/css/tooltipster-sideTip-light.min.css" />
- <link rel="stylesheet" type="text/css" href="../../_static/css/tooltipster-sideTip-borderless.min.css" />
- <link rel="stylesheet" type="text/css" href="../../_static/css/micromodal.css" />
+ <link rel="stylesheet" type="text/css" href="../../_static/css/tooltipster.custom.css?v=7bc2f056" />
+ <link rel="stylesheet" type="text/css" href="../../_static/css/tooltipster.bundle.min.css?v=37217874" />
+ <link rel="stylesheet" type="text/css" href="../../_static/css/tooltipster-sideTip-shadow.min.css?v=6227e517" />
+ <link rel="stylesheet" type="text/css" href="../../_static/css/tooltipster-sideTip-punk.min.css?v=94669e23" />
+ <link rel="stylesheet" type="text/css" href="../../_static/css/tooltipster-sideTip-noir.min.css?v=21a39f42" />
+ <link rel="stylesheet" type="text/css" href="../../_static/css/tooltipster-sideTip-light.min.css?v=a18b2449" />
+ <link rel="stylesheet" type="text/css" href="../../_static/css/tooltipster-sideTip-borderless.min.css?v=dbff53e4" />
+ <link rel="stylesheet" type="text/css" href="../../_static/css/micromodal.css?v=d7bf34ee" />
<link rel="stylesheet" type="text/css" href="../../_static/sphinx-design.min.css?v=95c83b7e" />
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@@ -61,9 +61,9 @@
<script src="../../_static/copybutton.js?v=f281be69"></script>
<script src="../../_static/scripts/sphinx-book-theme.js?v=887ef09a"></script>
<script src="../../_static/tabs.js?v=3ee01567"></script>
- <script src="../../_static/js/hoverxref.js"></script>
- <script src="../../_static/js/tooltipster.bundle.min.js"></script>
- <script src="../../_static/js/micromodal.min.js"></script>
+ <script src="../../_static/js/hoverxref.js?v=c95ade4f"></script>
+ <script src="../../_static/js/tooltipster.bundle.min.js?v=18bf091b"></script>
+ <script src="../../_static/js/micromodal.min.js?v=04d6302d"></script>
<script>let toggleHintShow = 'Click to show';</script>
<script>let toggleHintHide = 'Click to hide';</script>
<script>let toggleOpenOnPrint = 'true';</script>
diff --git a/_build/html/api/polymer_modeling/index.html b/_build/html/api/polymer_modeling/index.html
index d64c0d2c13d32e4ebf0b48f7eaf388ebad1cf96c..aff54d1930cca49815ea5fec3f84749d5f135a99 100644
--- a/_build/html/api/polymer_modeling/index.html
+++ b/_build/html/api/polymer_modeling/index.html
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<link rel="stylesheet" type="text/css" href="../../_static/styles/sphinx-book-theme.css?v=eba8b062" />
<link rel="stylesheet" type="text/css" href="../../_static/togglebutton.css?v=13237357" />
<link rel="stylesheet" type="text/css" href="../../_static/copybutton.css?v=76b2166b" />
- <link rel="stylesheet" type="text/css" href="../../_static/mystnb.4510f1fc1dee50b3e5859aac5469c37c29e427902b24a333a5f9fcb2f0b3ac41.css" />
+ <link rel="stylesheet" type="text/css" href="../../_static/mystnb.4510f1fc1dee50b3e5859aac5469c37c29e427902b24a333a5f9fcb2f0b3ac41.css?v=be8a1c11" />
<link rel="stylesheet" type="text/css" href="../../_static/sphinx-thebe.css?v=4fa983c6" />
<link rel="stylesheet" type="text/css" href="../../_static/tabs.css?v=4c969af8" />
- <link rel="stylesheet" type="text/css" href="../../_static/proof.css" />
+ <link rel="stylesheet" type="text/css" href="../../_static/proof.css?v=b4b7a797" />
<link rel="stylesheet" type="text/css" href="../../_static/styles/sphinx-examples.css?v=e236af4b" />
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- <link rel="stylesheet" type="text/css" href="../../_static/css/micromodal.css" />
+ <link rel="stylesheet" type="text/css" href="../../_static/css/tooltipster.custom.css?v=7bc2f056" />
+ <link rel="stylesheet" type="text/css" href="../../_static/css/tooltipster.bundle.min.css?v=37217874" />
+ <link rel="stylesheet" type="text/css" href="../../_static/css/tooltipster-sideTip-shadow.min.css?v=6227e517" />
+ <link rel="stylesheet" type="text/css" href="../../_static/css/tooltipster-sideTip-punk.min.css?v=94669e23" />
+ <link rel="stylesheet" type="text/css" href="../../_static/css/tooltipster-sideTip-noir.min.css?v=21a39f42" />
+ <link rel="stylesheet" type="text/css" href="../../_static/css/tooltipster-sideTip-light.min.css?v=a18b2449" />
+ <link rel="stylesheet" type="text/css" href="../../_static/css/tooltipster-sideTip-borderless.min.css?v=dbff53e4" />
+ <link rel="stylesheet" type="text/css" href="../../_static/css/micromodal.css?v=d7bf34ee" />
<link rel="stylesheet" type="text/css" href="../../_static/sphinx-design.min.css?v=95c83b7e" />
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@@ -61,9 +61,9 @@
<script src="../../_static/copybutton.js?v=f281be69"></script>
<script src="../../_static/scripts/sphinx-book-theme.js?v=887ef09a"></script>
<script src="../../_static/tabs.js?v=3ee01567"></script>
- <script src="../../_static/js/hoverxref.js"></script>
- <script src="../../_static/js/tooltipster.bundle.min.js"></script>
- <script src="../../_static/js/micromodal.min.js"></script>
+ <script src="../../_static/js/hoverxref.js?v=c95ade4f"></script>
+ <script src="../../_static/js/tooltipster.bundle.min.js?v=18bf091b"></script>
+ <script src="../../_static/js/micromodal.min.js?v=04d6302d"></script>
<script>let toggleHintShow = 'Click to show';</script>
<script>let toggleHintHide = 'Click to hide';</script>
<script>let toggleOpenOnPrint = 'true';</script>
diff --git a/_build/html/api/polymer_modeling/kh_polymer_model.html b/_build/html/api/polymer_modeling/kh_polymer_model.html
index 362ac003db232545b823677f4b26192fc60af5e4..7da886fc925c29b37aeaa7e7efcf1a05c3d33604 100644
--- a/_build/html/api/polymer_modeling/kh_polymer_model.html
+++ b/_build/html/api/polymer_modeling/kh_polymer_model.html
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<link rel="stylesheet" type="text/css" href="../../_static/togglebutton.css?v=13237357" />
<link rel="stylesheet" type="text/css" href="../../_static/copybutton.css?v=76b2166b" />
- <link rel="stylesheet" type="text/css" href="../../_static/mystnb.4510f1fc1dee50b3e5859aac5469c37c29e427902b24a333a5f9fcb2f0b3ac41.css" />
+ <link rel="stylesheet" type="text/css" href="../../_static/mystnb.4510f1fc1dee50b3e5859aac5469c37c29e427902b24a333a5f9fcb2f0b3ac41.css?v=be8a1c11" />
<link rel="stylesheet" type="text/css" href="../../_static/sphinx-thebe.css?v=4fa983c6" />
<link rel="stylesheet" type="text/css" href="../../_static/tabs.css?v=4c969af8" />
- <link rel="stylesheet" type="text/css" href="../../_static/proof.css" />
+ <link rel="stylesheet" type="text/css" href="../../_static/proof.css?v=b4b7a797" />
<link rel="stylesheet" type="text/css" href="../../_static/styles/sphinx-examples.css?v=e236af4b" />
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- <link rel="stylesheet" type="text/css" href="../../_static/css/tooltipster-sideTip-noir.min.css" />
- <link rel="stylesheet" type="text/css" href="../../_static/css/tooltipster-sideTip-light.min.css" />
- <link rel="stylesheet" type="text/css" href="../../_static/css/tooltipster-sideTip-borderless.min.css" />
- <link rel="stylesheet" type="text/css" href="../../_static/css/micromodal.css" />
+ <link rel="stylesheet" type="text/css" href="../../_static/css/tooltipster.custom.css?v=7bc2f056" />
+ <link rel="stylesheet" type="text/css" href="../../_static/css/tooltipster.bundle.min.css?v=37217874" />
+ <link rel="stylesheet" type="text/css" href="../../_static/css/tooltipster-sideTip-shadow.min.css?v=6227e517" />
+ <link rel="stylesheet" type="text/css" href="../../_static/css/tooltipster-sideTip-punk.min.css?v=94669e23" />
+ <link rel="stylesheet" type="text/css" href="../../_static/css/tooltipster-sideTip-noir.min.css?v=21a39f42" />
+ <link rel="stylesheet" type="text/css" href="../../_static/css/tooltipster-sideTip-light.min.css?v=a18b2449" />
+ <link rel="stylesheet" type="text/css" href="../../_static/css/tooltipster-sideTip-borderless.min.css?v=dbff53e4" />
+ <link rel="stylesheet" type="text/css" href="../../_static/css/micromodal.css?v=d7bf34ee" />
<link rel="stylesheet" type="text/css" href="../../_static/sphinx-design.min.css?v=95c83b7e" />
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<script src="../../_static/copybutton.js?v=f281be69"></script>
<script src="../../_static/scripts/sphinx-book-theme.js?v=887ef09a"></script>
<script src="../../_static/tabs.js?v=3ee01567"></script>
- <script src="../../_static/js/hoverxref.js"></script>
- <script src="../../_static/js/tooltipster.bundle.min.js"></script>
- <script src="../../_static/js/micromodal.min.js"></script>
+ <script src="../../_static/js/hoverxref.js?v=c95ade4f"></script>
+ <script src="../../_static/js/tooltipster.bundle.min.js?v=18bf091b"></script>
+ <script src="../../_static/js/micromodal.min.js?v=04d6302d"></script>
<script>let toggleHintShow = 'Click to show';</script>
<script>let toggleHintHide = 'Click to hide';</script>
<script>let toggleOpenOnPrint = 'true';</script>
diff --git a/_build/html/api/polymer_modeling/mpipi_polymer.html b/_build/html/api/polymer_modeling/mpipi_polymer.html
index 7e755840719e5a7a621949ccd0dfb64ca25e903d..5dad403b28fad6c0c0a234d3e5b3d42480ec5dca 100644
--- a/_build/html/api/polymer_modeling/mpipi_polymer.html
+++ b/_build/html/api/polymer_modeling/mpipi_polymer.html
@@ -32,19 +32,19 @@
<link rel="stylesheet" type="text/css" href="../../_static/styles/sphinx-book-theme.css?v=eba8b062" />
<link rel="stylesheet" type="text/css" href="../../_static/togglebutton.css?v=13237357" />
<link rel="stylesheet" type="text/css" href="../../_static/copybutton.css?v=76b2166b" />
- <link rel="stylesheet" type="text/css" href="../../_static/mystnb.4510f1fc1dee50b3e5859aac5469c37c29e427902b24a333a5f9fcb2f0b3ac41.css" />
+ <link rel="stylesheet" type="text/css" href="../../_static/mystnb.4510f1fc1dee50b3e5859aac5469c37c29e427902b24a333a5f9fcb2f0b3ac41.css?v=be8a1c11" />
<link rel="stylesheet" type="text/css" href="../../_static/sphinx-thebe.css?v=4fa983c6" />
<link rel="stylesheet" type="text/css" href="../../_static/tabs.css?v=4c969af8" />
- <link rel="stylesheet" type="text/css" href="../../_static/proof.css" />
+ <link rel="stylesheet" type="text/css" href="../../_static/proof.css?v=b4b7a797" />
<link rel="stylesheet" type="text/css" href="../../_static/styles/sphinx-examples.css?v=e236af4b" />
- <link rel="stylesheet" type="text/css" href="../../_static/css/tooltipster.custom.css" />
- <link rel="stylesheet" type="text/css" href="../../_static/css/tooltipster.bundle.min.css" />
- <link rel="stylesheet" type="text/css" href="../../_static/css/tooltipster-sideTip-shadow.min.css" />
- <link rel="stylesheet" type="text/css" href="../../_static/css/tooltipster-sideTip-punk.min.css" />
- <link rel="stylesheet" type="text/css" href="../../_static/css/tooltipster-sideTip-noir.min.css" />
- <link rel="stylesheet" type="text/css" href="../../_static/css/tooltipster-sideTip-light.min.css" />
- <link rel="stylesheet" type="text/css" href="../../_static/css/tooltipster-sideTip-borderless.min.css" />
- <link rel="stylesheet" type="text/css" href="../../_static/css/micromodal.css" />
+ <link rel="stylesheet" type="text/css" href="../../_static/css/tooltipster.custom.css?v=7bc2f056" />
+ <link rel="stylesheet" type="text/css" href="../../_static/css/tooltipster.bundle.min.css?v=37217874" />
+ <link rel="stylesheet" type="text/css" href="../../_static/css/tooltipster-sideTip-shadow.min.css?v=6227e517" />
+ <link rel="stylesheet" type="text/css" href="../../_static/css/tooltipster-sideTip-punk.min.css?v=94669e23" />
+ <link rel="stylesheet" type="text/css" href="../../_static/css/tooltipster-sideTip-noir.min.css?v=21a39f42" />
+ <link rel="stylesheet" type="text/css" href="../../_static/css/tooltipster-sideTip-light.min.css?v=a18b2449" />
+ <link rel="stylesheet" type="text/css" href="../../_static/css/tooltipster-sideTip-borderless.min.css?v=dbff53e4" />
+ <link rel="stylesheet" type="text/css" href="../../_static/css/micromodal.css?v=d7bf34ee" />
<link rel="stylesheet" type="text/css" href="../../_static/sphinx-design.min.css?v=95c83b7e" />
<!-- Pre-loaded scripts that we'll load fully later -->
@@ -61,9 +61,9 @@
<script src="../../_static/copybutton.js?v=f281be69"></script>
<script src="../../_static/scripts/sphinx-book-theme.js?v=887ef09a"></script>
<script src="../../_static/tabs.js?v=3ee01567"></script>
- <script src="../../_static/js/hoverxref.js"></script>
- <script src="../../_static/js/tooltipster.bundle.min.js"></script>
- <script src="../../_static/js/micromodal.min.js"></script>
+ <script src="../../_static/js/hoverxref.js?v=c95ade4f"></script>
+ <script src="../../_static/js/tooltipster.bundle.min.js?v=18bf091b"></script>
+ <script src="../../_static/js/micromodal.min.js?v=04d6302d"></script>
<script>let toggleHintShow = 'Click to show';</script>
<script>let toggleHintHide = 'Click to hide';</script>
<script>let toggleOpenOnPrint = 'true';</script>
diff --git a/_build/html/api/polymer_modeling/onck_polymer_model.html b/_build/html/api/polymer_modeling/onck_polymer_model.html
index 12b4a00ba5137314698b43e62f177860a1063ba8..4cbc83c3ccba60db0cb36e1f3f9e851b3cd0e28e 100644
--- a/_build/html/api/polymer_modeling/onck_polymer_model.html
+++ b/_build/html/api/polymer_modeling/onck_polymer_model.html
@@ -32,19 +32,19 @@
<link rel="stylesheet" type="text/css" href="../../_static/styles/sphinx-book-theme.css?v=eba8b062" />
<link rel="stylesheet" type="text/css" href="../../_static/togglebutton.css?v=13237357" />
<link rel="stylesheet" type="text/css" href="../../_static/copybutton.css?v=76b2166b" />
- <link rel="stylesheet" type="text/css" href="../../_static/mystnb.4510f1fc1dee50b3e5859aac5469c37c29e427902b24a333a5f9fcb2f0b3ac41.css" />
+ <link rel="stylesheet" type="text/css" href="../../_static/mystnb.4510f1fc1dee50b3e5859aac5469c37c29e427902b24a333a5f9fcb2f0b3ac41.css?v=be8a1c11" />
<link rel="stylesheet" type="text/css" href="../../_static/sphinx-thebe.css?v=4fa983c6" />
<link rel="stylesheet" type="text/css" href="../../_static/tabs.css?v=4c969af8" />
- <link rel="stylesheet" type="text/css" href="../../_static/proof.css" />
+ <link rel="stylesheet" type="text/css" href="../../_static/proof.css?v=b4b7a797" />
<link rel="stylesheet" type="text/css" href="../../_static/styles/sphinx-examples.css?v=e236af4b" />
- <link rel="stylesheet" type="text/css" href="../../_static/css/tooltipster.custom.css" />
- <link rel="stylesheet" type="text/css" href="../../_static/css/tooltipster.bundle.min.css" />
- <link rel="stylesheet" type="text/css" href="../../_static/css/tooltipster-sideTip-shadow.min.css" />
- <link rel="stylesheet" type="text/css" href="../../_static/css/tooltipster-sideTip-punk.min.css" />
- <link rel="stylesheet" type="text/css" href="../../_static/css/tooltipster-sideTip-noir.min.css" />
- <link rel="stylesheet" type="text/css" href="../../_static/css/tooltipster-sideTip-light.min.css" />
- <link rel="stylesheet" type="text/css" href="../../_static/css/tooltipster-sideTip-borderless.min.css" />
- <link rel="stylesheet" type="text/css" href="../../_static/css/micromodal.css" />
+ <link rel="stylesheet" type="text/css" href="../../_static/css/tooltipster.custom.css?v=7bc2f056" />
+ <link rel="stylesheet" type="text/css" href="../../_static/css/tooltipster.bundle.min.css?v=37217874" />
+ <link rel="stylesheet" type="text/css" href="../../_static/css/tooltipster-sideTip-shadow.min.css?v=6227e517" />
+ <link rel="stylesheet" type="text/css" href="../../_static/css/tooltipster-sideTip-punk.min.css?v=94669e23" />
+ <link rel="stylesheet" type="text/css" href="../../_static/css/tooltipster-sideTip-noir.min.css?v=21a39f42" />
+ <link rel="stylesheet" type="text/css" href="../../_static/css/tooltipster-sideTip-light.min.css?v=a18b2449" />
+ <link rel="stylesheet" type="text/css" href="../../_static/css/tooltipster-sideTip-borderless.min.css?v=dbff53e4" />
+ <link rel="stylesheet" type="text/css" href="../../_static/css/micromodal.css?v=d7bf34ee" />
<link rel="stylesheet" type="text/css" href="../../_static/sphinx-design.min.css?v=95c83b7e" />
<!-- Pre-loaded scripts that we'll load fully later -->
@@ -61,9 +61,9 @@
<script src="../../_static/copybutton.js?v=f281be69"></script>
<script src="../../_static/scripts/sphinx-book-theme.js?v=887ef09a"></script>
<script src="../../_static/tabs.js?v=3ee01567"></script>
- <script src="../../_static/js/hoverxref.js"></script>
- <script src="../../_static/js/tooltipster.bundle.min.js"></script>
- <script src="../../_static/js/micromodal.min.js"></script>
+ <script src="../../_static/js/hoverxref.js?v=c95ade4f"></script>
+ <script src="../../_static/js/tooltipster.bundle.min.js?v=18bf091b"></script>
+ <script src="../../_static/js/micromodal.min.js?v=04d6302d"></script>
<script>let toggleHintShow = 'Click to show';</script>
<script>let toggleHintHide = 'Click to hide';</script>
<script>let toggleOpenOnPrint = 'true';</script>
diff --git a/_build/html/api/polymer_modeling/polymer.html b/_build/html/api/polymer_modeling/polymer.html
index e613c5a705bee456898b074293747f76941cff78..3c00dc073280c440ff894ff1fa43a90b20414af3 100644
--- a/_build/html/api/polymer_modeling/polymer.html
+++ b/_build/html/api/polymer_modeling/polymer.html
@@ -32,19 +32,19 @@
<link rel="stylesheet" type="text/css" href="../../_static/styles/sphinx-book-theme.css?v=eba8b062" />
<link rel="stylesheet" type="text/css" href="../../_static/togglebutton.css?v=13237357" />
<link rel="stylesheet" type="text/css" href="../../_static/copybutton.css?v=76b2166b" />
- <link rel="stylesheet" type="text/css" href="../../_static/mystnb.4510f1fc1dee50b3e5859aac5469c37c29e427902b24a333a5f9fcb2f0b3ac41.css" />
+ <link rel="stylesheet" type="text/css" href="../../_static/mystnb.4510f1fc1dee50b3e5859aac5469c37c29e427902b24a333a5f9fcb2f0b3ac41.css?v=be8a1c11" />
<link rel="stylesheet" type="text/css" href="../../_static/sphinx-thebe.css?v=4fa983c6" />
<link rel="stylesheet" type="text/css" href="../../_static/tabs.css?v=4c969af8" />
- <link rel="stylesheet" type="text/css" href="../../_static/proof.css" />
+ <link rel="stylesheet" type="text/css" href="../../_static/proof.css?v=b4b7a797" />
<link rel="stylesheet" type="text/css" href="../../_static/styles/sphinx-examples.css?v=e236af4b" />
- <link rel="stylesheet" type="text/css" href="../../_static/css/tooltipster.custom.css" />
- <link rel="stylesheet" type="text/css" href="../../_static/css/tooltipster.bundle.min.css" />
- <link rel="stylesheet" type="text/css" href="../../_static/css/tooltipster-sideTip-shadow.min.css" />
- <link rel="stylesheet" type="text/css" href="../../_static/css/tooltipster-sideTip-punk.min.css" />
- <link rel="stylesheet" type="text/css" href="../../_static/css/tooltipster-sideTip-noir.min.css" />
- <link rel="stylesheet" type="text/css" href="../../_static/css/tooltipster-sideTip-light.min.css" />
- <link rel="stylesheet" type="text/css" href="../../_static/css/tooltipster-sideTip-borderless.min.css" />
- <link rel="stylesheet" type="text/css" href="../../_static/css/micromodal.css" />
+ <link rel="stylesheet" type="text/css" href="../../_static/css/tooltipster.custom.css?v=7bc2f056" />
+ <link rel="stylesheet" type="text/css" href="../../_static/css/tooltipster.bundle.min.css?v=37217874" />
+ <link rel="stylesheet" type="text/css" href="../../_static/css/tooltipster-sideTip-shadow.min.css?v=6227e517" />
+ <link rel="stylesheet" type="text/css" href="../../_static/css/tooltipster-sideTip-punk.min.css?v=94669e23" />
+ <link rel="stylesheet" type="text/css" href="../../_static/css/tooltipster-sideTip-noir.min.css?v=21a39f42" />
+ <link rel="stylesheet" type="text/css" href="../../_static/css/tooltipster-sideTip-light.min.css?v=a18b2449" />
+ <link rel="stylesheet" type="text/css" href="../../_static/css/tooltipster-sideTip-borderless.min.css?v=dbff53e4" />
+ <link rel="stylesheet" type="text/css" href="../../_static/css/micromodal.css?v=d7bf34ee" />
<link rel="stylesheet" type="text/css" href="../../_static/sphinx-design.min.css?v=95c83b7e" />
<!-- Pre-loaded scripts that we'll load fully later -->
@@ -61,9 +61,9 @@
<script src="../../_static/copybutton.js?v=f281be69"></script>
<script src="../../_static/scripts/sphinx-book-theme.js?v=887ef09a"></script>
<script src="../../_static/tabs.js?v=3ee01567"></script>
- <script src="../../_static/js/hoverxref.js"></script>
- <script src="../../_static/js/tooltipster.bundle.min.js"></script>
- <script src="../../_static/js/micromodal.min.js"></script>
+ <script src="../../_static/js/hoverxref.js?v=c95ade4f"></script>
+ <script src="../../_static/js/tooltipster.bundle.min.js?v=18bf091b"></script>
+ <script src="../../_static/js/micromodal.min.js?v=04d6302d"></script>
<script>let toggleHintShow = 'Click to show';</script>
<script>let toggleHintHide = 'Click to hide';</script>
<script>let toggleOpenOnPrint = 'true';</script>
@@ -484,7 +484,7 @@ connection, location_in_self, location_in_other</p>
<dl class="py class">
<dt class="sig sig-object py" id="arbdmodel.polymer.PolymerBeads">
<em class="property"><span class="pre">class</span><span class="w"> </span></em><span class="sig-name descname"><span class="pre">PolymerBeads</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">polymer</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">sequence</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">monomers_per_bead_group</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">1</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">rest_length</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="o"><span class="pre">**</span></span><span class="n"><span class="pre">kwargs</span></span></em><span class="sig-paren">)</span><a class="reference internal" href="../../_modules/arbdmodel/polymer.html#PolymerBeads"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#arbdmodel.polymer.PolymerBeads" title="Link to this definition">#</a></dt>
-<dd><p>Bases: <code class="xref py py-class docutils literal notranslate"><span class="pre">Group</span></code></p>
+<dd><p>Bases: <a class="reference internal" href="../core/core_objects.html#arbdmodel.core_objects.Group" title="arbdmodel.core_objects.Group"><code class="xref py py-class docutils literal notranslate"><span class="pre">Group</span></code></a></p>
<p>Abstract class for bead-based models that are built from Polymer objects</p>
<dl class="py property">
<dt class="sig sig-object py" id="arbdmodel.polymer.PolymerBeads.monomers_per_bead_group">
@@ -558,7 +558,7 @@ connection, location_in_self, location_in_other</p>
<dl class="py class">
<dt class="sig sig-object py" id="arbdmodel.polymer.PolymerModel">
<em class="property"><span class="pre">class</span><span class="w"> </span></em><span class="sig-name descname"><span class="pre">PolymerModel</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">polymers</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">sequences</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">monomers_per_bead_group</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">1</span></span></em>, <em class="sig-param"><span class="o"><span class="pre">**</span></span><span class="n"><span class="pre">kwargs</span></span></em><span class="sig-paren">)</span><a class="reference internal" href="../../_modules/arbdmodel/polymer.html#PolymerModel"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#arbdmodel.polymer.PolymerModel" title="Link to this definition">#</a></dt>
-<dd><p>Bases: <code class="xref py py-class docutils literal notranslate"><span class="pre">ArbdModel</span></code></p>
+<dd><p>Bases: <a class="reference internal" href="../core/model.html#arbdmodel.model.ArbdModel" title="arbdmodel.model.ArbdModel"><code class="xref py py-class docutils literal notranslate"><span class="pre">ArbdModel</span></code></a></p>
<dl class="py method">
<dt class="sig sig-object py" id="arbdmodel.polymer.PolymerModel.generate_beads">
<span class="sig-name descname"><span class="pre">generate_beads</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="reference internal" href="../../_modules/arbdmodel/polymer.html#PolymerModel.generate_beads"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#arbdmodel.polymer.PolymerModel.generate_beads" title="Link to this definition">#</a></dt>
diff --git a/_build/html/api/polymer_modeling/sali_polymer_model.html b/_build/html/api/polymer_modeling/sali_polymer_model.html
index 89061134341234ab0e1c5ed26e1a4b627eafd750..1feeb534e607b5fcf5ee9fb59232955ecbc29cb2 100644
--- a/_build/html/api/polymer_modeling/sali_polymer_model.html
+++ b/_build/html/api/polymer_modeling/sali_polymer_model.html
@@ -32,19 +32,19 @@
<link rel="stylesheet" type="text/css" href="../../_static/styles/sphinx-book-theme.css?v=eba8b062" />
<link rel="stylesheet" type="text/css" href="../../_static/togglebutton.css?v=13237357" />
<link rel="stylesheet" type="text/css" href="../../_static/copybutton.css?v=76b2166b" />
- <link rel="stylesheet" type="text/css" href="../../_static/mystnb.4510f1fc1dee50b3e5859aac5469c37c29e427902b24a333a5f9fcb2f0b3ac41.css" />
+ <link rel="stylesheet" type="text/css" href="../../_static/mystnb.4510f1fc1dee50b3e5859aac5469c37c29e427902b24a333a5f9fcb2f0b3ac41.css?v=be8a1c11" />
<link rel="stylesheet" type="text/css" href="../../_static/sphinx-thebe.css?v=4fa983c6" />
<link rel="stylesheet" type="text/css" href="../../_static/tabs.css?v=4c969af8" />
- <link rel="stylesheet" type="text/css" href="../../_static/proof.css" />
+ <link rel="stylesheet" type="text/css" href="../../_static/proof.css?v=b4b7a797" />
<link rel="stylesheet" type="text/css" href="../../_static/styles/sphinx-examples.css?v=e236af4b" />
- <link rel="stylesheet" type="text/css" href="../../_static/css/tooltipster.custom.css" />
- <link rel="stylesheet" type="text/css" href="../../_static/css/tooltipster.bundle.min.css" />
- <link rel="stylesheet" type="text/css" href="../../_static/css/tooltipster-sideTip-shadow.min.css" />
- <link rel="stylesheet" type="text/css" href="../../_static/css/tooltipster-sideTip-punk.min.css" />
- <link rel="stylesheet" type="text/css" href="../../_static/css/tooltipster-sideTip-noir.min.css" />
- <link rel="stylesheet" type="text/css" href="../../_static/css/tooltipster-sideTip-light.min.css" />
- <link rel="stylesheet" type="text/css" href="../../_static/css/tooltipster-sideTip-borderless.min.css" />
- <link rel="stylesheet" type="text/css" href="../../_static/css/micromodal.css" />
+ <link rel="stylesheet" type="text/css" href="../../_static/css/tooltipster.custom.css?v=7bc2f056" />
+ <link rel="stylesheet" type="text/css" href="../../_static/css/tooltipster.bundle.min.css?v=37217874" />
+ <link rel="stylesheet" type="text/css" href="../../_static/css/tooltipster-sideTip-shadow.min.css?v=6227e517" />
+ <link rel="stylesheet" type="text/css" href="../../_static/css/tooltipster-sideTip-punk.min.css?v=94669e23" />
+ <link rel="stylesheet" type="text/css" href="../../_static/css/tooltipster-sideTip-noir.min.css?v=21a39f42" />
+ <link rel="stylesheet" type="text/css" href="../../_static/css/tooltipster-sideTip-light.min.css?v=a18b2449" />
+ <link rel="stylesheet" type="text/css" href="../../_static/css/tooltipster-sideTip-borderless.min.css?v=dbff53e4" />
+ <link rel="stylesheet" type="text/css" href="../../_static/css/micromodal.css?v=d7bf34ee" />
<link rel="stylesheet" type="text/css" href="../../_static/sphinx-design.min.css?v=95c83b7e" />
<!-- Pre-loaded scripts that we'll load fully later -->
@@ -61,9 +61,9 @@
<script src="../../_static/copybutton.js?v=f281be69"></script>
<script src="../../_static/scripts/sphinx-book-theme.js?v=887ef09a"></script>
<script src="../../_static/tabs.js?v=3ee01567"></script>
- <script src="../../_static/js/hoverxref.js"></script>
- <script src="../../_static/js/tooltipster.bundle.min.js"></script>
- <script src="../../_static/js/micromodal.min.js"></script>
+ <script src="../../_static/js/hoverxref.js?v=c95ade4f"></script>
+ <script src="../../_static/js/tooltipster.bundle.min.js?v=18bf091b"></script>
+ <script src="../../_static/js/micromodal.min.js?v=04d6302d"></script>
<script>let toggleHintShow = 'Click to show';</script>
<script>let toggleHintHide = 'Click to hide';</script>
<script>let toggleOpenOnPrint = 'true';</script>
@@ -323,7 +323,9 @@ document.write(`
</button>
`);
</script>
-
+<button class="sidebar-toggle secondary-toggle btn btn-sm" title="Toggle secondary sidebar" data-bs-placement="bottom" data-bs-toggle="tooltip">
+ <span class="fa-solid fa-list"></span>
+</button>
</div></div>
</div>
@@ -339,6 +341,27 @@ document.write(`
<div id="print-main-content">
<div id="jb-print-toc">
+ <div>
+ <h2> Contents </h2>
+ </div>
+ <nav aria-label="Page">
+ <ul class="visible nav section-nav flex-column">
+<li class="toc-h2 nav-item toc-entry"><a class="reference internal nav-link" href="#arbdmodel.sali_polymer_model.LinearBond"><code class="docutils literal notranslate"><span class="pre">LinearBond</span></code></a><ul class="nav section-nav flex-column">
+<li class="toc-h3 nav-item toc-entry"><a class="reference internal nav-link" href="#arbdmodel.sali_polymer_model.LinearBond.potential"><code class="docutils literal notranslate"><span class="pre">LinearBond.potential()</span></code></a></li>
+</ul>
+</li>
+<li class="toc-h2 nav-item toc-entry"><a class="reference internal nav-link" href="#arbdmodel.sali_polymer_model.SaliBeadsFromPolymer"><code class="docutils literal notranslate"><span class="pre">SaliBeadsFromPolymer</span></code></a></li>
+<li class="toc-h2 nav-item toc-entry"><a class="reference internal nav-link" href="#arbdmodel.sali_polymer_model.SaliModel"><code class="docutils literal notranslate"><span class="pre">SaliModel</span></code></a><ul class="nav section-nav flex-column">
+<li class="toc-h3 nav-item toc-entry"><a class="reference internal nav-link" href="#arbdmodel.sali_polymer_model.SaliModel.generate_beads"><code class="docutils literal notranslate"><span class="pre">SaliModel.generate_beads()</span></code></a></li>
+<li class="toc-h3 nav-item toc-entry"><a class="reference internal nav-link" href="#arbdmodel.sali_polymer_model.SaliModel.update_splines"><code class="docutils literal notranslate"><span class="pre">SaliModel.update_splines()</span></code></a></li>
+</ul>
+</li>
+<li class="toc-h2 nav-item toc-entry"><a class="reference internal nav-link" href="#arbdmodel.sali_polymer_model.SaliNonbonded"><code class="docutils literal notranslate"><span class="pre">SaliNonbonded</span></code></a><ul class="nav section-nav flex-column">
+<li class="toc-h3 nav-item toc-entry"><a class="reference internal nav-link" href="#arbdmodel.sali_polymer_model.SaliNonbonded.potential"><code class="docutils literal notranslate"><span class="pre">SaliNonbonded.potential()</span></code></a></li>
+</ul>
+</li>
+</ul>
+ </nav>
</div>
</div>
</div>
@@ -351,6 +374,51 @@ document.write(`
<section class="tex2jax_ignore mathjax_ignore" id="sali-polymer-model">
<h1>sali_polymer_model<a class="headerlink" href="#sali-polymer-model" title="Link to this heading">#</a></h1>
<p>Module documentation for <code class="docutils literal notranslate"><span class="pre">arbdmodel.sali_polymer_model</span></code>.</p>
+<dl class="py class" id="module-arbdmodel.sali_polymer_model">
+<dt class="sig sig-object py" id="arbdmodel.sali_polymer_model.LinearBond">
+<em class="property"><span class="pre">class</span><span class="w"> </span></em><span class="sig-name descname"><span class="pre">LinearBond</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">k</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">r0</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">rRange</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">(0,</span> <span class="pre">50)</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">resolution</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">0.1</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">maxForce</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">max_potential</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">prefix</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">'potentials/'</span></span></em><span class="sig-paren">)</span><a class="reference internal" href="../../_modules/arbdmodel/sali_polymer_model.html#LinearBond"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#arbdmodel.sali_polymer_model.LinearBond" title="Link to this definition">#</a></dt>
+<dd><p>Bases: <a class="reference internal" href="../interaction_potentials/interactions.html#arbdmodel.interactions.HarmonicBond" title="arbdmodel.interactions.HarmonicBond"><code class="xref py py-class docutils literal notranslate"><span class="pre">HarmonicBond</span></code></a></p>
+<dl class="py method">
+<dt class="sig sig-object py" id="arbdmodel.sali_polymer_model.LinearBond.potential">
+<span class="sig-name descname"><span class="pre">potential</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">dr</span></span></em><span class="sig-paren">)</span><a class="reference internal" href="../../_modules/arbdmodel/sali_polymer_model.html#LinearBond.potential"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#arbdmodel.sali_polymer_model.LinearBond.potential" title="Link to this definition">#</a></dt>
+<dd></dd></dl>
+
+</dd></dl>
+
+<dl class="py class">
+<dt class="sig sig-object py" id="arbdmodel.sali_polymer_model.SaliBeadsFromPolymer">
+<em class="property"><span class="pre">class</span><span class="w"> </span></em><span class="sig-name descname"><span class="pre">SaliBeadsFromPolymer</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">polymer</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">sequence</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="o"><span class="pre">**</span></span><span class="n"><span class="pre">kwargs</span></span></em><span class="sig-paren">)</span><a class="reference internal" href="../../_modules/arbdmodel/sali_polymer_model.html#SaliBeadsFromPolymer"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#arbdmodel.sali_polymer_model.SaliBeadsFromPolymer" title="Link to this definition">#</a></dt>
+<dd><p>Bases: <a class="reference internal" href="../core/core_objects.html#arbdmodel.core_objects.Group" title="arbdmodel.core_objects.Group"><code class="xref py py-class docutils literal notranslate"><span class="pre">Group</span></code></a></p>
+</dd></dl>
+
+<dl class="py class">
+<dt class="sig sig-object py" id="arbdmodel.sali_polymer_model.SaliModel">
+<em class="property"><span class="pre">class</span><span class="w"> </span></em><span class="sig-name descname"><span class="pre">SaliModel</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">polymers</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">sequences</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">debye_length</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">10</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">damping_coefficient</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">10</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">DEBUG</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">False</span></span></em>, <em class="sig-param"><span class="o"><span class="pre">**</span></span><span class="n"><span class="pre">kwargs</span></span></em><span class="sig-paren">)</span><a class="reference internal" href="../../_modules/arbdmodel/sali_polymer_model.html#SaliModel"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#arbdmodel.sali_polymer_model.SaliModel" title="Link to this definition">#</a></dt>
+<dd><p>Bases: <a class="reference internal" href="../core/model.html#arbdmodel.model.ArbdModel" title="arbdmodel.model.ArbdModel"><code class="xref py py-class docutils literal notranslate"><span class="pre">ArbdModel</span></code></a></p>
+<dl class="py method">
+<dt class="sig sig-object py" id="arbdmodel.sali_polymer_model.SaliModel.generate_beads">
+<span class="sig-name descname"><span class="pre">generate_beads</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="reference internal" href="../../_modules/arbdmodel/sali_polymer_model.html#SaliModel.generate_beads"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#arbdmodel.sali_polymer_model.SaliModel.generate_beads" title="Link to this definition">#</a></dt>
+<dd></dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="arbdmodel.sali_polymer_model.SaliModel.update_splines">
+<span class="sig-name descname"><span class="pre">update_splines</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">coords</span></span></em><span class="sig-paren">)</span><a class="reference internal" href="../../_modules/arbdmodel/sali_polymer_model.html#SaliModel.update_splines"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#arbdmodel.sali_polymer_model.SaliModel.update_splines" title="Link to this definition">#</a></dt>
+<dd></dd></dl>
+
+</dd></dl>
+
+<dl class="py class">
+<dt class="sig sig-object py" id="arbdmodel.sali_polymer_model.SaliNonbonded">
+<em class="property"><span class="pre">class</span><span class="w"> </span></em><span class="sig-name descname"><span class="pre">SaliNonbonded</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">resolution</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">0.1</span></span></em><span class="sig-paren">)</span><a class="reference internal" href="../../_modules/arbdmodel/sali_polymer_model.html#SaliNonbonded"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#arbdmodel.sali_polymer_model.SaliNonbonded" title="Link to this definition">#</a></dt>
+<dd><p>Bases: <a class="reference internal" href="../interaction_potentials/interactions.html#arbdmodel.interactions.AbstractPotential" title="arbdmodel.interactions.AbstractPotential"><code class="xref py py-class docutils literal notranslate"><span class="pre">AbstractPotential</span></code></a></p>
+<dl class="py method">
+<dt class="sig sig-object py" id="arbdmodel.sali_polymer_model.SaliNonbonded.potential">
+<span class="sig-name descname"><span class="pre">potential</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">r</span></span></em><span class="sig-paren">)</span><a class="reference internal" href="../../_modules/arbdmodel/sali_polymer_model.html#SaliNonbonded.potential"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#arbdmodel.sali_polymer_model.SaliNonbonded.potential" title="Link to this definition">#</a></dt>
+<dd><p>Constant force excluded volume</p>
+</dd></dl>
+
+</dd></dl>
+
</section>
<script type="text/x-thebe-config">
@@ -390,6 +458,34 @@ document.write(`
+ <div class="bd-sidebar-secondary bd-toc"><div class="sidebar-secondary-items sidebar-secondary__inner">
+
+
+ <div class="sidebar-secondary-item">
+ <div class="page-toc tocsection onthispage">
+ <i class="fa-solid fa-list"></i> Contents
+ </div>
+ <nav class="bd-toc-nav page-toc">
+ <ul class="visible nav section-nav flex-column">
+<li class="toc-h2 nav-item toc-entry"><a class="reference internal nav-link" href="#arbdmodel.sali_polymer_model.LinearBond"><code class="docutils literal notranslate"><span class="pre">LinearBond</span></code></a><ul class="nav section-nav flex-column">
+<li class="toc-h3 nav-item toc-entry"><a class="reference internal nav-link" href="#arbdmodel.sali_polymer_model.LinearBond.potential"><code class="docutils literal notranslate"><span class="pre">LinearBond.potential()</span></code></a></li>
+</ul>
+</li>
+<li class="toc-h2 nav-item toc-entry"><a class="reference internal nav-link" href="#arbdmodel.sali_polymer_model.SaliBeadsFromPolymer"><code class="docutils literal notranslate"><span class="pre">SaliBeadsFromPolymer</span></code></a></li>
+<li class="toc-h2 nav-item toc-entry"><a class="reference internal nav-link" href="#arbdmodel.sali_polymer_model.SaliModel"><code class="docutils literal notranslate"><span class="pre">SaliModel</span></code></a><ul class="nav section-nav flex-column">
+<li class="toc-h3 nav-item toc-entry"><a class="reference internal nav-link" href="#arbdmodel.sali_polymer_model.SaliModel.generate_beads"><code class="docutils literal notranslate"><span class="pre">SaliModel.generate_beads()</span></code></a></li>
+<li class="toc-h3 nav-item toc-entry"><a class="reference internal nav-link" href="#arbdmodel.sali_polymer_model.SaliModel.update_splines"><code class="docutils literal notranslate"><span class="pre">SaliModel.update_splines()</span></code></a></li>
+</ul>
+</li>
+<li class="toc-h2 nav-item toc-entry"><a class="reference internal nav-link" href="#arbdmodel.sali_polymer_model.SaliNonbonded"><code class="docutils literal notranslate"><span class="pre">SaliNonbonded</span></code></a><ul class="nav section-nav flex-column">
+<li class="toc-h3 nav-item toc-entry"><a class="reference internal nav-link" href="#arbdmodel.sali_polymer_model.SaliNonbonded.potential"><code class="docutils literal notranslate"><span class="pre">SaliNonbonded.potential()</span></code></a></li>
+</ul>
+</li>
+</ul>
+ </nav></div>
+
+</div></div>
+
</div>
<footer class="bd-footer-content">
diff --git a/_build/html/api/polymer_modeling/ssdna_two_bead.html b/_build/html/api/polymer_modeling/ssdna_two_bead.html
index 59c77b01cd5324cbecafa14385591ecff8db10df..9cddcd48dc13841fd0d52475835e442c07c62e30 100644
--- a/_build/html/api/polymer_modeling/ssdna_two_bead.html
+++ b/_build/html/api/polymer_modeling/ssdna_two_bead.html
@@ -32,19 +32,19 @@
<link rel="stylesheet" type="text/css" href="../../_static/styles/sphinx-book-theme.css?v=eba8b062" />
<link rel="stylesheet" type="text/css" href="../../_static/togglebutton.css?v=13237357" />
<link rel="stylesheet" type="text/css" href="../../_static/copybutton.css?v=76b2166b" />
- <link rel="stylesheet" type="text/css" href="../../_static/mystnb.4510f1fc1dee50b3e5859aac5469c37c29e427902b24a333a5f9fcb2f0b3ac41.css" />
+ <link rel="stylesheet" type="text/css" href="../../_static/mystnb.4510f1fc1dee50b3e5859aac5469c37c29e427902b24a333a5f9fcb2f0b3ac41.css?v=be8a1c11" />
<link rel="stylesheet" type="text/css" href="../../_static/sphinx-thebe.css?v=4fa983c6" />
<link rel="stylesheet" type="text/css" href="../../_static/tabs.css?v=4c969af8" />
- <link rel="stylesheet" type="text/css" href="../../_static/proof.css" />
+ <link rel="stylesheet" type="text/css" href="../../_static/proof.css?v=b4b7a797" />
<link rel="stylesheet" type="text/css" href="../../_static/styles/sphinx-examples.css?v=e236af4b" />
- <link rel="stylesheet" type="text/css" href="../../_static/css/tooltipster.custom.css" />
- <link rel="stylesheet" type="text/css" href="../../_static/css/tooltipster.bundle.min.css" />
- <link rel="stylesheet" type="text/css" href="../../_static/css/tooltipster-sideTip-shadow.min.css" />
- <link rel="stylesheet" type="text/css" href="../../_static/css/tooltipster-sideTip-punk.min.css" />
- <link rel="stylesheet" type="text/css" href="../../_static/css/tooltipster-sideTip-noir.min.css" />
- <link rel="stylesheet" type="text/css" href="../../_static/css/tooltipster-sideTip-light.min.css" />
- <link rel="stylesheet" type="text/css" href="../../_static/css/tooltipster-sideTip-borderless.min.css" />
- <link rel="stylesheet" type="text/css" href="../../_static/css/micromodal.css" />
+ <link rel="stylesheet" type="text/css" href="../../_static/css/tooltipster.custom.css?v=7bc2f056" />
+ <link rel="stylesheet" type="text/css" href="../../_static/css/tooltipster.bundle.min.css?v=37217874" />
+ <link rel="stylesheet" type="text/css" href="../../_static/css/tooltipster-sideTip-shadow.min.css?v=6227e517" />
+ <link rel="stylesheet" type="text/css" href="../../_static/css/tooltipster-sideTip-punk.min.css?v=94669e23" />
+ <link rel="stylesheet" type="text/css" href="../../_static/css/tooltipster-sideTip-noir.min.css?v=21a39f42" />
+ <link rel="stylesheet" type="text/css" href="../../_static/css/tooltipster-sideTip-light.min.css?v=a18b2449" />
+ <link rel="stylesheet" type="text/css" href="../../_static/css/tooltipster-sideTip-borderless.min.css?v=dbff53e4" />
+ <link rel="stylesheet" type="text/css" href="../../_static/css/micromodal.css?v=d7bf34ee" />
<link rel="stylesheet" type="text/css" href="../../_static/sphinx-design.min.css?v=95c83b7e" />
<!-- Pre-loaded scripts that we'll load fully later -->
@@ -61,9 +61,9 @@
<script src="../../_static/copybutton.js?v=f281be69"></script>
<script src="../../_static/scripts/sphinx-book-theme.js?v=887ef09a"></script>
<script src="../../_static/tabs.js?v=3ee01567"></script>
- <script src="../../_static/js/hoverxref.js"></script>
- <script src="../../_static/js/tooltipster.bundle.min.js"></script>
- <script src="../../_static/js/micromodal.min.js"></script>
+ <script src="../../_static/js/hoverxref.js?v=c95ade4f"></script>
+ <script src="../../_static/js/tooltipster.bundle.min.js?v=18bf091b"></script>
+ <script src="../../_static/js/micromodal.min.js?v=04d6302d"></script>
<script>let toggleHintShow = 'Click to show';</script>
<script>let toggleHintHide = 'Click to hide';</script>
<script>let toggleOpenOnPrint = 'true';</script>
@@ -379,17 +379,17 @@ document.write(`
<dd><p>Bases: <a class="reference internal" href="polymer.html#arbdmodel.polymer.PolymerBeads" title="arbdmodel.polymer.PolymerBeads"><code class="xref py py-class docutils literal notranslate"><span class="pre">PolymerBeads</span></code></a></p>
<dl class="py attribute">
<dt class="sig sig-object py" id="arbdmodel.ssdna_two_bead.DnaStrandBeads.b">
-<span class="sig-name descname"><span class="pre">b</span></span><em class="property"><span class="w"> </span><span class="p"><span class="pre">=</span></span><span class="w"> </span><span class="pre"><arbdmodel.PointParticle</span> <span class="pre">"B"</span> <span class="pre">of</span> <span class="pre"><<class</span> <span class="pre">'arbdmodel.ParticleType'></span> <span class="pre">B>></span></em><a class="headerlink" href="#arbdmodel.ssdna_two_bead.DnaStrandBeads.b" title="Link to this definition">#</a></dt>
+<span class="sig-name descname"><span class="pre">b</span></span><em class="property"><span class="w"> </span><span class="p"><span class="pre">=</span></span><span class="w"> </span><span class="pre"><arbdmodel.core_objects.PointParticle</span> <span class="pre">"B"</span> <span class="pre">of</span> <span class="pre"><<class</span> <span class="pre">'arbdmodel.core_objects.ParticleType'></span> <span class="pre">B>></span></em><a class="headerlink" href="#arbdmodel.ssdna_two_bead.DnaStrandBeads.b" title="Link to this definition">#</a></dt>
<dd></dd></dl>
<dl class="py attribute">
<dt class="sig sig-object py" id="arbdmodel.ssdna_two_bead.DnaStrandBeads.nt">
-<span class="sig-name descname"><span class="pre">nt</span></span><em class="property"><span class="w"> </span><span class="p"><span class="pre">=</span></span><span class="w"> </span><span class="pre"><arbdmodel.Group</span> <span class="pre">object></span></em><a class="headerlink" href="#arbdmodel.ssdna_two_bead.DnaStrandBeads.nt" title="Link to this definition">#</a></dt>
+<span class="sig-name descname"><span class="pre">nt</span></span><em class="property"><span class="w"> </span><span class="p"><span class="pre">=</span></span><span class="w"> </span><span class="pre"><arbdmodel.core_objects.Group</span> <span class="pre">object></span></em><a class="headerlink" href="#arbdmodel.ssdna_two_bead.DnaStrandBeads.nt" title="Link to this definition">#</a></dt>
<dd></dd></dl>
<dl class="py attribute">
<dt class="sig sig-object py" id="arbdmodel.ssdna_two_bead.DnaStrandBeads.p">
-<span class="sig-name descname"><span class="pre">p</span></span><em class="property"><span class="w"> </span><span class="p"><span class="pre">=</span></span><span class="w"> </span><span class="pre"><arbdmodel.PointParticle</span> <span class="pre">"P"</span> <span class="pre">of</span> <span class="pre"><<class</span> <span class="pre">'arbdmodel.ParticleType'></span> <span class="pre">P>></span></em><a class="headerlink" href="#arbdmodel.ssdna_two_bead.DnaStrandBeads.p" title="Link to this definition">#</a></dt>
+<span class="sig-name descname"><span class="pre">p</span></span><em class="property"><span class="w"> </span><span class="p"><span class="pre">=</span></span><span class="w"> </span><span class="pre"><arbdmodel.core_objects.PointParticle</span> <span class="pre">"P"</span> <span class="pre">of</span> <span class="pre"><<class</span> <span class="pre">'arbdmodel.core_objects.ParticleType'></span> <span class="pre">P>></span></em><a class="headerlink" href="#arbdmodel.ssdna_two_bead.DnaStrandBeads.p" title="Link to this definition">#</a></dt>
<dd></dd></dl>
</dd></dl>
diff --git a/_build/html/api/rigidbody_models/index.html b/_build/html/api/rigidbody_models/index.html
index 1bb772d34fe8dbbe9e45090a8fc2ac5baaf874fc..05bb82ed4904227335e1ef61f7b875738b2f6496 100644
--- a/_build/html/api/rigidbody_models/index.html
+++ b/_build/html/api/rigidbody_models/index.html
@@ -32,19 +32,19 @@
<link rel="stylesheet" type="text/css" href="../../_static/styles/sphinx-book-theme.css?v=eba8b062" />
<link rel="stylesheet" type="text/css" href="../../_static/togglebutton.css?v=13237357" />
<link rel="stylesheet" type="text/css" href="../../_static/copybutton.css?v=76b2166b" />
- <link rel="stylesheet" type="text/css" href="../../_static/mystnb.4510f1fc1dee50b3e5859aac5469c37c29e427902b24a333a5f9fcb2f0b3ac41.css" />
+ <link rel="stylesheet" type="text/css" href="../../_static/mystnb.4510f1fc1dee50b3e5859aac5469c37c29e427902b24a333a5f9fcb2f0b3ac41.css?v=be8a1c11" />
<link rel="stylesheet" type="text/css" href="../../_static/sphinx-thebe.css?v=4fa983c6" />
<link rel="stylesheet" type="text/css" href="../../_static/tabs.css?v=4c969af8" />
- <link rel="stylesheet" type="text/css" href="../../_static/proof.css" />
+ <link rel="stylesheet" type="text/css" href="../../_static/proof.css?v=b4b7a797" />
<link rel="stylesheet" type="text/css" href="../../_static/styles/sphinx-examples.css?v=e236af4b" />
- <link rel="stylesheet" type="text/css" href="../../_static/css/tooltipster.custom.css" />
- <link rel="stylesheet" type="text/css" href="../../_static/css/tooltipster.bundle.min.css" />
- <link rel="stylesheet" type="text/css" href="../../_static/css/tooltipster-sideTip-shadow.min.css" />
- <link rel="stylesheet" type="text/css" href="../../_static/css/tooltipster-sideTip-punk.min.css" />
- <link rel="stylesheet" type="text/css" href="../../_static/css/tooltipster-sideTip-noir.min.css" />
- <link rel="stylesheet" type="text/css" href="../../_static/css/tooltipster-sideTip-light.min.css" />
- <link rel="stylesheet" type="text/css" href="../../_static/css/tooltipster-sideTip-borderless.min.css" />
- <link rel="stylesheet" type="text/css" href="../../_static/css/micromodal.css" />
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diff --git a/_build/html/api/rigidbody_models/mesh_process_surface.html b/_build/html/api/rigidbody_models/mesh_process_surface.html
index 5655316cbbfd1fb49c737938d0e5c701d9322bf0..7a72f906f33d6121c29559b523c71109ef3ad646 100644
--- a/_build/html/api/rigidbody_models/mesh_process_surface.html
+++ b/_build/html/api/rigidbody_models/mesh_process_surface.html
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+ <link rel="stylesheet" type="text/css" href="../../_static/mystnb.4510f1fc1dee50b3e5859aac5469c37c29e427902b24a333a5f9fcb2f0b3ac41.css?v=be8a1c11" />
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@@ -323,7 +323,9 @@ document.write(`
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</script>
-
+<button class="sidebar-toggle secondary-toggle btn btn-sm" title="Toggle secondary sidebar" data-bs-placement="bottom" data-bs-toggle="tooltip">
+ <span class="fa-solid fa-list"></span>
+</button>
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@@ -339,6 +341,25 @@ document.write(`
<div id="print-main-content">
<div id="jb-print-toc">
+ <div>
+ <h2> Contents </h2>
+ </div>
+ <nav aria-label="Page">
+ <ul class="visible nav section-nav flex-column">
+<li class="toc-h2 nav-item toc-entry"><a class="reference internal nav-link" href="#arbdmodel.mesh_process_surface.SurfaceMeshProcessor"><code class="docutils literal notranslate"><span class="pre">SurfaceMeshProcessor</span></code></a><ul class="nav section-nav flex-column">
+<li class="toc-h3 nav-item toc-entry"><a class="reference internal nav-link" href="#arbdmodel.mesh_process_surface.SurfaceMeshProcessor.MICRON_TO_ANGSTROM"><code class="docutils literal notranslate"><span class="pre">SurfaceMeshProcessor.MICRON_TO_ANGSTROM</span></code></a></li>
+<li class="toc-h3 nav-item toc-entry"><a class="reference internal nav-link" href="#arbdmodel.mesh_process_surface.SurfaceMeshProcessor.calculate_damping"><code class="docutils literal notranslate"><span class="pre">SurfaceMeshProcessor.calculate_damping()</span></code></a></li>
+<li class="toc-h3 nav-item toc-entry"><a class="reference internal nav-link" href="#arbdmodel.mesh_process_surface.SurfaceMeshProcessor.generate_potential_grid"><code class="docutils literal notranslate"><span class="pre">SurfaceMeshProcessor.generate_potential_grid()</span></code></a></li>
+<li class="toc-h3 nav-item toc-entry"><a class="reference internal nav-link" href="#arbdmodel.mesh_process_surface.SurfaceMeshProcessor.get_attached_particles"><code class="docutils literal notranslate"><span class="pre">SurfaceMeshProcessor.get_attached_particles()</span></code></a></li>
+<li class="toc-h3 nav-item toc-entry"><a class="reference internal nav-link" href="#arbdmodel.mesh_process_surface.SurfaceMeshProcessor.save_aligned_mesh"><code class="docutils literal notranslate"><span class="pre">SurfaceMeshProcessor.save_aligned_mesh()</span></code></a></li>
+<li class="toc-h3 nav-item toc-entry"><a class="reference internal nav-link" href="#arbdmodel.mesh_process_surface.SurfaceMeshProcessor.save_aligned_mesh_both_formats"><code class="docutils literal notranslate"><span class="pre">SurfaceMeshProcessor.save_aligned_mesh_both_formats()</span></code></a></li>
+<li class="toc-h3 nav-item toc-entry"><a class="reference internal nav-link" href="#arbdmodel.mesh_process_surface.SurfaceMeshProcessor.save_as_pdb"><code class="docutils literal notranslate"><span class="pre">SurfaceMeshProcessor.save_as_pdb()</span></code></a></li>
+<li class="toc-h3 nav-item toc-entry"><a class="reference internal nav-link" href="#arbdmodel.mesh_process_surface.SurfaceMeshProcessor.write_no_enter_potential_dx"><code class="docutils literal notranslate"><span class="pre">SurfaceMeshProcessor.write_no_enter_potential_dx()</span></code></a></li>
+</ul>
+</li>
+<li class="toc-h2 nav-item toc-entry"><a class="reference internal nav-link" href="#arbdmodel.mesh_process_surface.process_surface_mesh"><code class="docutils literal notranslate"><span class="pre">process_surface_mesh()</span></code></a></li>
+</ul>
+ </nav>
</div>
</div>
</div>
@@ -351,6 +372,81 @@ document.write(`
<section class="tex2jax_ignore mathjax_ignore" id="mesh-process-surface">
<h1>mesh_process_surface<a class="headerlink" href="#mesh-process-surface" title="Link to this heading">#</a></h1>
<p>Module documentation for <code class="docutils literal notranslate"><span class="pre">arbdmodel.mesh_process_surface</span></code>.</p>
+<dl class="py class" id="module-arbdmodel.mesh_process_surface">
+<dt class="sig sig-object py" id="arbdmodel.mesh_process_surface.SurfaceMeshProcessor">
+<em class="property"><span class="pre">class</span><span class="w"> </span></em><span class="sig-name descname"><span class="pre">SurfaceMeshProcessor</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">mesh_file</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">density</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">19.3</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">simconf</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">unit_scale</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">10000</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">work_dir</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em><span class="sig-paren">)</span><a class="reference internal" href="../../_modules/arbdmodel/mesh_process_surface.html#SurfaceMeshProcessor"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#arbdmodel.mesh_process_surface.SurfaceMeshProcessor" title="Link to this definition">#</a></dt>
+<dd><p>Bases: <a class="hxr-hoverxref hxr-tooltip reference external" href="https://docs.python.org/3/library/functions.html#object" title="(in Python v3.13)"><code class="xref py py-class docutils literal notranslate"><span class="pre">object</span></code></a></p>
+<p>Process surface meshes to calculate inertia, hydrodynamics and generate potential fields</p>
+<dl class="py attribute">
+<dt class="sig sig-object py" id="arbdmodel.mesh_process_surface.SurfaceMeshProcessor.MICRON_TO_ANGSTROM">
+<span class="sig-name descname"><span class="pre">MICRON_TO_ANGSTROM</span></span><em class="property"><span class="w"> </span><span class="p"><span class="pre">=</span></span><span class="w"> </span><span class="pre">10000</span></em><a class="headerlink" href="#arbdmodel.mesh_process_surface.SurfaceMeshProcessor.MICRON_TO_ANGSTROM" title="Link to this definition">#</a></dt>
+<dd></dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="arbdmodel.mesh_process_surface.SurfaceMeshProcessor.calculate_damping">
+<span class="sig-name descname"><span class="pre">calculate_damping</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">work_dir</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em><span class="sig-paren">)</span><a class="reference internal" href="../../_modules/arbdmodel/mesh_process_surface.html#SurfaceMeshProcessor.calculate_damping"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#arbdmodel.mesh_process_surface.SurfaceMeshProcessor.calculate_damping" title="Link to this definition">#</a></dt>
+<dd><p>Calculate hydrodynamic properties using HydroPro</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="arbdmodel.mesh_process_surface.SurfaceMeshProcessor.generate_potential_grid">
+<span class="sig-name descname"><span class="pre">generate_potential_grid</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">spacing</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">2.0</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">buffer</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">20.0</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">k</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">1.0</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">cutoff</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">10.0</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">max_potential</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">1000.0</span></span></em><span class="sig-paren">)</span><a class="reference internal" href="../../_modules/arbdmodel/mesh_process_surface.html#SurfaceMeshProcessor.generate_potential_grid"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#arbdmodel.mesh_process_surface.SurfaceMeshProcessor.generate_potential_grid" title="Link to this definition">#</a></dt>
+<dd><p>Generate potential grid for ARBD</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="arbdmodel.mesh_process_surface.SurfaceMeshProcessor.get_attached_particles">
+<span class="sig-name descname"><span class="pre">get_attached_particles</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="reference internal" href="../../_modules/arbdmodel/mesh_process_surface.html#SurfaceMeshProcessor.get_attached_particles"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#arbdmodel.mesh_process_surface.SurfaceMeshProcessor.get_attached_particles" title="Link to this definition">#</a></dt>
+<dd></dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="arbdmodel.mesh_process_surface.SurfaceMeshProcessor.save_aligned_mesh">
+<span class="sig-name descname"><span class="pre">save_aligned_mesh</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">output_file</span></span></em><span class="sig-paren">)</span><a class="reference internal" href="../../_modules/arbdmodel/mesh_process_surface.html#SurfaceMeshProcessor.save_aligned_mesh"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#arbdmodel.mesh_process_surface.SurfaceMeshProcessor.save_aligned_mesh" title="Link to this definition">#</a></dt>
+<dd><p>Save the aligned mesh to a new .msh file</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="arbdmodel.mesh_process_surface.SurfaceMeshProcessor.save_aligned_mesh_both_formats">
+<span class="sig-name descname"><span class="pre">save_aligned_mesh_both_formats</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">base_filename</span></span></em><span class="sig-paren">)</span><a class="reference internal" href="../../_modules/arbdmodel/mesh_process_surface.html#SurfaceMeshProcessor.save_aligned_mesh_both_formats"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#arbdmodel.mesh_process_surface.SurfaceMeshProcessor.save_aligned_mesh_both_formats" title="Link to this definition">#</a></dt>
+<dd><p>Save the aligned mesh in both MSH and PDB formats</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="arbdmodel.mesh_process_surface.SurfaceMeshProcessor.save_as_pdb">
+<span class="sig-name descname"><span class="pre">save_as_pdb</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">output_file</span></span></em><span class="sig-paren">)</span><a class="reference internal" href="../../_modules/arbdmodel/mesh_process_surface.html#SurfaceMeshProcessor.save_as_pdb"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#arbdmodel.mesh_process_surface.SurfaceMeshProcessor.save_as_pdb" title="Link to this definition">#</a></dt>
+<dd><p>Save the aligned mesh as a PDB file (coordinates in Ã…)</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="arbdmodel.mesh_process_surface.SurfaceMeshProcessor.write_no_enter_potential_dx">
+<span class="sig-name descname"><span class="pre">write_no_enter_potential_dx</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">output_file</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="o"><span class="pre">**</span></span><span class="n"><span class="pre">kwargs</span></span></em><span class="sig-paren">)</span><a class="reference internal" href="../../_modules/arbdmodel/mesh_process_surface.html#SurfaceMeshProcessor.write_no_enter_potential_dx"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#arbdmodel.mesh_process_surface.SurfaceMeshProcessor.write_no_enter_potential_dx" title="Link to this definition">#</a></dt>
+<dd></dd></dl>
+
+</dd></dl>
+
+<dl class="py function">
+<dt class="sig sig-object py" id="arbdmodel.mesh_process_surface.process_surface_mesh">
+<span class="sig-name descname"><span class="pre">process_surface_mesh</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">mesh_file</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">density</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">19.3</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">temperature</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">303</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">viscosity</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">0.01</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">solvent_density</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">1.0</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">output_dx</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">'surface_potential.dx'</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">output_mesh</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">'aligned_surface.msh'</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">binary_path</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="o"><span class="pre">**</span></span><span class="n"><span class="pre">kwargs</span></span></em><span class="sig-paren">)</span><a class="reference internal" href="../../_modules/arbdmodel/mesh_process_surface.html#process_surface_mesh"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#arbdmodel.mesh_process_surface.process_surface_mesh" title="Link to this definition">#</a></dt>
+<dd><p>Process surface mesh file and calculate all properties</p>
+<dl class="field-list simple">
+<dt class="field-odd">Parameters<span class="colon">:</span></dt>
+<dd class="field-odd"><ul class="simple">
+<li><p><strong>mesh_file</strong> – Path to .msh file containing surface triangles</p></li>
+<li><p><strong>density</strong> – Material density in g/cm³</p></li>
+<li><p><strong>temperature</strong> – Temperature in Kelvin</p></li>
+<li><p><strong>viscosity</strong> – Solvent viscosity in poise</p></li>
+<li><p><strong>solvent_density</strong> – Solvent density in g/cm³</p></li>
+<li><p><strong>output_dx</strong> – Optional path to output potential DX file</p></li>
+<li><p><strong>output_mesh</strong> – Optional path to save aligned mesh</p></li>
+<li><p><strong>binary_path</strong> – Path to HydroPro executable</p></li>
+<li><p><strong>expected_mass</strong> – Optional expected mass in amu to calibrate calculations</p></li>
+<li><p><strong>expected_aspect_ratio</strong> – Optional expected aspect ratio to calibrate inertia</p></li>
+<li><p><strong>**kwargs</strong> – Additional arguments for potential generation</p></li>
+</ul>
+</dd>
+</dl>
+</dd></dl>
+
</section>
<script type="text/x-thebe-config">
@@ -390,6 +486,32 @@ document.write(`
+ <div class="bd-sidebar-secondary bd-toc"><div class="sidebar-secondary-items sidebar-secondary__inner">
+
+
+ <div class="sidebar-secondary-item">
+ <div class="page-toc tocsection onthispage">
+ <i class="fa-solid fa-list"></i> Contents
+ </div>
+ <nav class="bd-toc-nav page-toc">
+ <ul class="visible nav section-nav flex-column">
+<li class="toc-h2 nav-item toc-entry"><a class="reference internal nav-link" href="#arbdmodel.mesh_process_surface.SurfaceMeshProcessor"><code class="docutils literal notranslate"><span class="pre">SurfaceMeshProcessor</span></code></a><ul class="nav section-nav flex-column">
+<li class="toc-h3 nav-item toc-entry"><a class="reference internal nav-link" href="#arbdmodel.mesh_process_surface.SurfaceMeshProcessor.MICRON_TO_ANGSTROM"><code class="docutils literal notranslate"><span class="pre">SurfaceMeshProcessor.MICRON_TO_ANGSTROM</span></code></a></li>
+<li class="toc-h3 nav-item toc-entry"><a class="reference internal nav-link" href="#arbdmodel.mesh_process_surface.SurfaceMeshProcessor.calculate_damping"><code class="docutils literal notranslate"><span class="pre">SurfaceMeshProcessor.calculate_damping()</span></code></a></li>
+<li class="toc-h3 nav-item toc-entry"><a class="reference internal nav-link" href="#arbdmodel.mesh_process_surface.SurfaceMeshProcessor.generate_potential_grid"><code class="docutils literal notranslate"><span class="pre">SurfaceMeshProcessor.generate_potential_grid()</span></code></a></li>
+<li class="toc-h3 nav-item toc-entry"><a class="reference internal nav-link" href="#arbdmodel.mesh_process_surface.SurfaceMeshProcessor.get_attached_particles"><code class="docutils literal notranslate"><span class="pre">SurfaceMeshProcessor.get_attached_particles()</span></code></a></li>
+<li class="toc-h3 nav-item toc-entry"><a class="reference internal nav-link" href="#arbdmodel.mesh_process_surface.SurfaceMeshProcessor.save_aligned_mesh"><code class="docutils literal notranslate"><span class="pre">SurfaceMeshProcessor.save_aligned_mesh()</span></code></a></li>
+<li class="toc-h3 nav-item toc-entry"><a class="reference internal nav-link" href="#arbdmodel.mesh_process_surface.SurfaceMeshProcessor.save_aligned_mesh_both_formats"><code class="docutils literal notranslate"><span class="pre">SurfaceMeshProcessor.save_aligned_mesh_both_formats()</span></code></a></li>
+<li class="toc-h3 nav-item toc-entry"><a class="reference internal nav-link" href="#arbdmodel.mesh_process_surface.SurfaceMeshProcessor.save_as_pdb"><code class="docutils literal notranslate"><span class="pre">SurfaceMeshProcessor.save_as_pdb()</span></code></a></li>
+<li class="toc-h3 nav-item toc-entry"><a class="reference internal nav-link" href="#arbdmodel.mesh_process_surface.SurfaceMeshProcessor.write_no_enter_potential_dx"><code class="docutils literal notranslate"><span class="pre">SurfaceMeshProcessor.write_no_enter_potential_dx()</span></code></a></li>
+</ul>
+</li>
+<li class="toc-h2 nav-item toc-entry"><a class="reference internal nav-link" href="#arbdmodel.mesh_process_surface.process_surface_mesh"><code class="docutils literal notranslate"><span class="pre">process_surface_mesh()</span></code></a></li>
+</ul>
+ </nav></div>
+
+</div></div>
+
</div>
<footer class="bd-footer-content">
diff --git a/_build/html/api/rigidbody_models/mesh_process_volume.html b/_build/html/api/rigidbody_models/mesh_process_volume.html
index 86590eeab15f031c0599d07677c4f0114b594e1a..1487ed12a0ab8f7f869c60d3bb39083c534dbe21 100644
--- a/_build/html/api/rigidbody_models/mesh_process_volume.html
+++ b/_build/html/api/rigidbody_models/mesh_process_volume.html
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@@ -339,6 +341,24 @@ document.write(`
<div id="print-main-content">
<div id="jb-print-toc">
+ <div>
+ <h2> Contents </h2>
+ </div>
+ <nav aria-label="Page">
+ <ul class="visible nav section-nav flex-column">
+<li class="toc-h2 nav-item toc-entry"><a class="reference internal nav-link" href="#arbdmodel.mesh_process_volume.MeshProcessor"><code class="docutils literal notranslate"><span class="pre">MeshProcessor</span></code></a><ul class="nav section-nav flex-column">
+<li class="toc-h3 nav-item toc-entry"><a class="reference internal nav-link" href="#arbdmodel.mesh_process_volume.MeshProcessor.MICRON_TO_ANGSTROM"><code class="docutils literal notranslate"><span class="pre">MeshProcessor.MICRON_TO_ANGSTROM</span></code></a></li>
+<li class="toc-h3 nav-item toc-entry"><a class="reference internal nav-link" href="#arbdmodel.mesh_process_volume.MeshProcessor.calculate_damping"><code class="docutils literal notranslate"><span class="pre">MeshProcessor.calculate_damping()</span></code></a></li>
+<li class="toc-h3 nav-item toc-entry"><a class="reference internal nav-link" href="#arbdmodel.mesh_process_volume.MeshProcessor.generate_potential_grid"><code class="docutils literal notranslate"><span class="pre">MeshProcessor.generate_potential_grid()</span></code></a></li>
+<li class="toc-h3 nav-item toc-entry"><a class="reference internal nav-link" href="#arbdmodel.mesh_process_volume.MeshProcessor.get_attached_particles"><code class="docutils literal notranslate"><span class="pre">MeshProcessor.get_attached_particles()</span></code></a></li>
+<li class="toc-h3 nav-item toc-entry"><a class="reference internal nav-link" href="#arbdmodel.mesh_process_volume.MeshProcessor.save_aligned_mesh"><code class="docutils literal notranslate"><span class="pre">MeshProcessor.save_aligned_mesh()</span></code></a></li>
+<li class="toc-h3 nav-item toc-entry"><a class="reference internal nav-link" href="#arbdmodel.mesh_process_volume.MeshProcessor.save_as_pdb"><code class="docutils literal notranslate"><span class="pre">MeshProcessor.save_as_pdb()</span></code></a></li>
+<li class="toc-h3 nav-item toc-entry"><a class="reference internal nav-link" href="#arbdmodel.mesh_process_volume.MeshProcessor.write_no_enter_potential"><code class="docutils literal notranslate"><span class="pre">MeshProcessor.write_no_enter_potential()</span></code></a></li>
+</ul>
+</li>
+<li class="toc-h2 nav-item toc-entry"><a class="reference internal nav-link" href="#arbdmodel.mesh_process_volume.process_mesh_file"><code class="docutils literal notranslate"><span class="pre">process_mesh_file()</span></code></a></li>
+</ul>
+ </nav>
</div>
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@@ -351,6 +371,75 @@ document.write(`
<section class="tex2jax_ignore mathjax_ignore" id="mesh-process-volume">
<h1>mesh_process_volume<a class="headerlink" href="#mesh-process-volume" title="Link to this heading">#</a></h1>
<p>Module documentation for <code class="docutils literal notranslate"><span class="pre">arbdmodel.mesh_process_volume</span></code>.</p>
+<dl class="py class" id="module-arbdmodel.mesh_process_volume">
+<dt class="sig sig-object py" id="arbdmodel.mesh_process_volume.MeshProcessor">
+<em class="property"><span class="pre">class</span><span class="w"> </span></em><span class="sig-name descname"><span class="pre">MeshProcessor</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">mesh_file</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">density</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">19.3</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">simconf</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">unit_scale</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">10000</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">work_dir</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">expected_mass</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em><span class="sig-paren">)</span><a class="reference internal" href="../../_modules/arbdmodel/mesh_process_volume.html#MeshProcessor"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#arbdmodel.mesh_process_volume.MeshProcessor" title="Link to this definition">#</a></dt>
+<dd><p>Bases: <a class="hxr-hoverxref hxr-tooltip reference external" href="https://docs.python.org/3/library/functions.html#object" title="(in Python v3.13)"><code class="xref py py-class docutils literal notranslate"><span class="pre">object</span></code></a></p>
+<p>Process gmsh files to calculate inertia, hydrodynamics and generate potential fields</p>
+<dl class="py attribute">
+<dt class="sig sig-object py" id="arbdmodel.mesh_process_volume.MeshProcessor.MICRON_TO_ANGSTROM">
+<span class="sig-name descname"><span class="pre">MICRON_TO_ANGSTROM</span></span><em class="property"><span class="w"> </span><span class="p"><span class="pre">=</span></span><span class="w"> </span><span class="pre">10000</span></em><a class="headerlink" href="#arbdmodel.mesh_process_volume.MeshProcessor.MICRON_TO_ANGSTROM" title="Link to this definition">#</a></dt>
+<dd></dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="arbdmodel.mesh_process_volume.MeshProcessor.calculate_damping">
+<span class="sig-name descname"><span class="pre">calculate_damping</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="reference internal" href="../../_modules/arbdmodel/mesh_process_volume.html#MeshProcessor.calculate_damping"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#arbdmodel.mesh_process_volume.MeshProcessor.calculate_damping" title="Link to this definition">#</a></dt>
+<dd><p>Calculate hydrodynamic properties using HydroPro</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="arbdmodel.mesh_process_volume.MeshProcessor.generate_potential_grid">
+<span class="sig-name descname"><span class="pre">generate_potential_grid</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">spacing</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">2.0</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">buffer</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">20.0</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">k</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">1.0</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">cutoff</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">10.0</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">max_potential</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">1000.0</span></span></em><span class="sig-paren">)</span><a class="reference internal" href="../../_modules/arbdmodel/mesh_process_volume.html#MeshProcessor.generate_potential_grid"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#arbdmodel.mesh_process_volume.MeshProcessor.generate_potential_grid" title="Link to this definition">#</a></dt>
+<dd><p>Generate potential grid for ARBD</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="arbdmodel.mesh_process_volume.MeshProcessor.get_attached_particles">
+<span class="sig-name descname"><span class="pre">get_attached_particles</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="reference internal" href="../../_modules/arbdmodel/mesh_process_volume.html#MeshProcessor.get_attached_particles"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#arbdmodel.mesh_process_volume.MeshProcessor.get_attached_particles" title="Link to this definition">#</a></dt>
+<dd></dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="arbdmodel.mesh_process_volume.MeshProcessor.save_aligned_mesh">
+<span class="sig-name descname"><span class="pre">save_aligned_mesh</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">output_file</span></span></em><span class="sig-paren">)</span><a class="reference internal" href="../../_modules/arbdmodel/mesh_process_volume.html#MeshProcessor.save_aligned_mesh"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#arbdmodel.mesh_process_volume.MeshProcessor.save_aligned_mesh" title="Link to this definition">#</a></dt>
+<dd></dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="arbdmodel.mesh_process_volume.MeshProcessor.save_as_pdb">
+<span class="sig-name descname"><span class="pre">save_as_pdb</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">output_file</span></span></em><span class="sig-paren">)</span><a class="reference internal" href="../../_modules/arbdmodel/mesh_process_volume.html#MeshProcessor.save_as_pdb"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#arbdmodel.mesh_process_volume.MeshProcessor.save_as_pdb" title="Link to this definition">#</a></dt>
+<dd><p>Save the aligned mesh as a PDB file (coordinates in Ã…)</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="arbdmodel.mesh_process_volume.MeshProcessor.write_no_enter_potential">
+<span class="sig-name descname"><span class="pre">write_no_enter_potential</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">output_file</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="o"><span class="pre">**</span></span><span class="n"><span class="pre">kwargs</span></span></em><span class="sig-paren">)</span><a class="reference internal" href="../../_modules/arbdmodel/mesh_process_volume.html#MeshProcessor.write_no_enter_potential"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#arbdmodel.mesh_process_volume.MeshProcessor.write_no_enter_potential" title="Link to this definition">#</a></dt>
+<dd><p>Generate and write potential field to DX file so particles do not fall inside rigidbody.</p>
+</dd></dl>
+
+</dd></dl>
+
+<dl class="py function">
+<dt class="sig sig-object py" id="arbdmodel.mesh_process_volume.process_mesh_file">
+<span class="sig-name descname"><span class="pre">process_mesh_file</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">mesh_file</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">density</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">19.3</span></span></em>, <em class="sig-param"><span class="o"><span class="pre">**</span></span><span class="n"><span class="pre">kwargs</span></span></em><span class="sig-paren">)</span><a class="reference internal" href="../../_modules/arbdmodel/mesh_process_volume.html#process_mesh_file"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#arbdmodel.mesh_process_volume.process_mesh_file" title="Link to this definition">#</a></dt>
+<dd><p>Process mesh file and calculate all properties</p>
+<dl class="field-list simple">
+<dt class="field-odd">Parameters<span class="colon">:</span></dt>
+<dd class="field-odd"><ul class="simple">
+<li><p><strong>mesh_file</strong> – Path to .msh file</p></li>
+<li><p><strong>density</strong> – Material density in g/cm³</p></li>
+<li><p><strong>temperature</strong> – Temperature in Kelvin</p></li>
+<li><p><strong>viscosity</strong> – Solvent viscosity in poise</p></li>
+<li><p><strong>solvent_density</strong> – Solvent density in g/cm³</p></li>
+<li><p><strong>output_dx</strong> – Optional path to output potential DX file</p></li>
+<li><p><strong>output_mesh</strong> – Optional path to save aligned mesh</p></li>
+<li><p><strong>binary_path</strong> – Path to HydroPro executable</p></li>
+<li><p><strong>expected_mass</strong> – Optional expected mass in amu to calibrate calculations</p></li>
+<li><p><strong>expected_aspect_ratio</strong> – Optional expected aspect ratio to calibrate inertia</p></li>
+<li><p><strong>**kwargs</strong> – Additional arguments for potential generation</p></li>
+</ul>
+</dd>
+</dl>
+</dd></dl>
+
</section>
<script type="text/x-thebe-config">
@@ -390,6 +479,31 @@ document.write(`
+ <div class="bd-sidebar-secondary bd-toc"><div class="sidebar-secondary-items sidebar-secondary__inner">
+
+
+ <div class="sidebar-secondary-item">
+ <div class="page-toc tocsection onthispage">
+ <i class="fa-solid fa-list"></i> Contents
+ </div>
+ <nav class="bd-toc-nav page-toc">
+ <ul class="visible nav section-nav flex-column">
+<li class="toc-h2 nav-item toc-entry"><a class="reference internal nav-link" href="#arbdmodel.mesh_process_volume.MeshProcessor"><code class="docutils literal notranslate"><span class="pre">MeshProcessor</span></code></a><ul class="nav section-nav flex-column">
+<li class="toc-h3 nav-item toc-entry"><a class="reference internal nav-link" href="#arbdmodel.mesh_process_volume.MeshProcessor.MICRON_TO_ANGSTROM"><code class="docutils literal notranslate"><span class="pre">MeshProcessor.MICRON_TO_ANGSTROM</span></code></a></li>
+<li class="toc-h3 nav-item toc-entry"><a class="reference internal nav-link" href="#arbdmodel.mesh_process_volume.MeshProcessor.calculate_damping"><code class="docutils literal notranslate"><span class="pre">MeshProcessor.calculate_damping()</span></code></a></li>
+<li class="toc-h3 nav-item toc-entry"><a class="reference internal nav-link" href="#arbdmodel.mesh_process_volume.MeshProcessor.generate_potential_grid"><code class="docutils literal notranslate"><span class="pre">MeshProcessor.generate_potential_grid()</span></code></a></li>
+<li class="toc-h3 nav-item toc-entry"><a class="reference internal nav-link" href="#arbdmodel.mesh_process_volume.MeshProcessor.get_attached_particles"><code class="docutils literal notranslate"><span class="pre">MeshProcessor.get_attached_particles()</span></code></a></li>
+<li class="toc-h3 nav-item toc-entry"><a class="reference internal nav-link" href="#arbdmodel.mesh_process_volume.MeshProcessor.save_aligned_mesh"><code class="docutils literal notranslate"><span class="pre">MeshProcessor.save_aligned_mesh()</span></code></a></li>
+<li class="toc-h3 nav-item toc-entry"><a class="reference internal nav-link" href="#arbdmodel.mesh_process_volume.MeshProcessor.save_as_pdb"><code class="docutils literal notranslate"><span class="pre">MeshProcessor.save_as_pdb()</span></code></a></li>
+<li class="toc-h3 nav-item toc-entry"><a class="reference internal nav-link" href="#arbdmodel.mesh_process_volume.MeshProcessor.write_no_enter_potential"><code class="docutils literal notranslate"><span class="pre">MeshProcessor.write_no_enter_potential()</span></code></a></li>
+</ul>
+</li>
+<li class="toc-h2 nav-item toc-entry"><a class="reference internal nav-link" href="#arbdmodel.mesh_process_volume.process_mesh_file"><code class="docutils literal notranslate"><span class="pre">process_mesh_file()</span></code></a></li>
+</ul>
+ </nav></div>
+
+</div></div>
+
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diff --git a/_build/html/api/rigidbody_models/mesh_rigidbody.html b/_build/html/api/rigidbody_models/mesh_rigidbody.html
index 027e61043554d60af7c51285ef2c2a16477a8f8d..e7fabf249dc9adf83ad1d677dbdb9048176d46c9 100644
--- a/_build/html/api/rigidbody_models/mesh_rigidbody.html
+++ b/_build/html/api/rigidbody_models/mesh_rigidbody.html
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- <link rel="stylesheet" type="text/css" href="../../_static/css/tooltipster-sideTip-light.min.css" />
- <link rel="stylesheet" type="text/css" href="../../_static/css/tooltipster-sideTip-borderless.min.css" />
- <link rel="stylesheet" type="text/css" href="../../_static/css/micromodal.css" />
+ <link rel="stylesheet" type="text/css" href="../../_static/css/tooltipster.custom.css?v=7bc2f056" />
+ <link rel="stylesheet" type="text/css" href="../../_static/css/tooltipster.bundle.min.css?v=37217874" />
+ <link rel="stylesheet" type="text/css" href="../../_static/css/tooltipster-sideTip-shadow.min.css?v=6227e517" />
+ <link rel="stylesheet" type="text/css" href="../../_static/css/tooltipster-sideTip-punk.min.css?v=94669e23" />
+ <link rel="stylesheet" type="text/css" href="../../_static/css/tooltipster-sideTip-noir.min.css?v=21a39f42" />
+ <link rel="stylesheet" type="text/css" href="../../_static/css/tooltipster-sideTip-light.min.css?v=a18b2449" />
+ <link rel="stylesheet" type="text/css" href="../../_static/css/tooltipster-sideTip-borderless.min.css?v=dbff53e4" />
+ <link rel="stylesheet" type="text/css" href="../../_static/css/micromodal.css?v=d7bf34ee" />
<link rel="stylesheet" type="text/css" href="../../_static/sphinx-design.min.css?v=95c83b7e" />
<!-- Pre-loaded scripts that we'll load fully later -->
@@ -61,9 +61,9 @@
<script src="../../_static/copybutton.js?v=f281be69"></script>
<script src="../../_static/scripts/sphinx-book-theme.js?v=887ef09a"></script>
<script src="../../_static/tabs.js?v=3ee01567"></script>
- <script src="../../_static/js/hoverxref.js"></script>
- <script src="../../_static/js/tooltipster.bundle.min.js"></script>
- <script src="../../_static/js/micromodal.min.js"></script>
+ <script src="../../_static/js/hoverxref.js?v=c95ade4f"></script>
+ <script src="../../_static/js/tooltipster.bundle.min.js?v=18bf091b"></script>
+ <script src="../../_static/js/micromodal.min.js?v=04d6302d"></script>
<script>let toggleHintShow = 'Click to show';</script>
<script>let toggleHintHide = 'Click to hide';</script>
<script>let toggleOpenOnPrint = 'true';</script>
@@ -323,7 +323,9 @@ document.write(`
</button>
`);
</script>
-
+<button class="sidebar-toggle secondary-toggle btn btn-sm" title="Toggle secondary sidebar" data-bs-placement="bottom" data-bs-toggle="tooltip">
+ <span class="fa-solid fa-list"></span>
+</button>
</div></div>
</div>
@@ -339,6 +341,14 @@ document.write(`
<div id="print-main-content">
<div id="jb-print-toc">
+ <div>
+ <h2> Contents </h2>
+ </div>
+ <nav aria-label="Page">
+ <ul class="visible nav section-nav flex-column">
+<li class="toc-h2 nav-item toc-entry"><a class="reference internal nav-link" href="#arbdmodel.mesh_rigidbody.MeshRigidBodyType"><code class="docutils literal notranslate"><span class="pre">MeshRigidBodyType</span></code></a></li>
+</ul>
+ </nav>
</div>
</div>
</div>
@@ -351,6 +361,13 @@ document.write(`
<section class="tex2jax_ignore mathjax_ignore" id="mesh-rigidbody">
<h1>mesh_rigidbody<a class="headerlink" href="#mesh-rigidbody" title="Link to this heading">#</a></h1>
<p>Module documentation for <code class="docutils literal notranslate"><span class="pre">arbdmodel.mesh_rigidbody</span></code>.</p>
+<dl class="py class" id="module-arbdmodel.mesh_rigidbody">
+<dt class="sig sig-object py" id="arbdmodel.mesh_rigidbody.MeshRigidBodyType">
+<em class="property"><span class="pre">class</span><span class="w"> </span></em><span class="sig-name descname"><span class="pre">MeshRigidBodyType</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">name</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">mesh_file</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">density</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">19.3</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">simconf</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">unit_scale</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">10000.0</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">use_surface</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">False</span></span></em>, <em class="sig-param"><span class="o"><span class="pre">**</span></span><span class="n"><span class="pre">kwargs</span></span></em><span class="sig-paren">)</span><a class="reference internal" href="../../_modules/arbdmodel/mesh_rigidbody.html#MeshRigidBodyType"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#arbdmodel.mesh_rigidbody.MeshRigidBodyType" title="Link to this definition">#</a></dt>
+<dd><p>Bases: <a class="reference internal" href="../core/core_objects.html#arbdmodel.core_objects.RigidBodyType" title="arbdmodel.core_objects.RigidBodyType"><code class="xref py py-class docutils literal notranslate"><span class="pre">RigidBodyType</span></code></a></p>
+<p>RigidBodyType subclass for shape rigid body objects</p>
+</dd></dl>
+
</section>
<script type="text/x-thebe-config">
@@ -390,6 +407,21 @@ document.write(`
+ <div class="bd-sidebar-secondary bd-toc"><div class="sidebar-secondary-items sidebar-secondary__inner">
+
+
+ <div class="sidebar-secondary-item">
+ <div class="page-toc tocsection onthispage">
+ <i class="fa-solid fa-list"></i> Contents
+ </div>
+ <nav class="bd-toc-nav page-toc">
+ <ul class="visible nav section-nav flex-column">
+<li class="toc-h2 nav-item toc-entry"><a class="reference internal nav-link" href="#arbdmodel.mesh_rigidbody.MeshRigidBodyType"><code class="docutils literal notranslate"><span class="pre">MeshRigidBodyType</span></code></a></li>
+</ul>
+ </nav></div>
+
+</div></div>
+
</div>
<footer class="bd-footer-content">
diff --git a/_build/html/api/rigidbody_models/simplearbd.html b/_build/html/api/rigidbody_models/simplearbd.html
index a4c675714717cad3bb96225f8cf291ea9ddd31e5..33270f143dceef2ee07c18436fe0bba8fee2372d 100644
--- a/_build/html/api/rigidbody_models/simplearbd.html
+++ b/_build/html/api/rigidbody_models/simplearbd.html
@@ -32,19 +32,19 @@
<link rel="stylesheet" type="text/css" href="../../_static/styles/sphinx-book-theme.css?v=eba8b062" />
<link rel="stylesheet" type="text/css" href="../../_static/togglebutton.css?v=13237357" />
<link rel="stylesheet" type="text/css" href="../../_static/copybutton.css?v=76b2166b" />
- <link rel="stylesheet" type="text/css" href="../../_static/mystnb.4510f1fc1dee50b3e5859aac5469c37c29e427902b24a333a5f9fcb2f0b3ac41.css" />
+ <link rel="stylesheet" type="text/css" href="../../_static/mystnb.4510f1fc1dee50b3e5859aac5469c37c29e427902b24a333a5f9fcb2f0b3ac41.css?v=be8a1c11" />
<link rel="stylesheet" type="text/css" href="../../_static/sphinx-thebe.css?v=4fa983c6" />
<link rel="stylesheet" type="text/css" href="../../_static/tabs.css?v=4c969af8" />
- <link rel="stylesheet" type="text/css" href="../../_static/proof.css" />
+ <link rel="stylesheet" type="text/css" href="../../_static/proof.css?v=b4b7a797" />
<link rel="stylesheet" type="text/css" href="../../_static/styles/sphinx-examples.css?v=e236af4b" />
- <link rel="stylesheet" type="text/css" href="../../_static/css/tooltipster.custom.css" />
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- <link rel="stylesheet" type="text/css" href="../../_static/css/tooltipster-sideTip-shadow.min.css" />
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- <link rel="stylesheet" type="text/css" href="../../_static/css/tooltipster-sideTip-noir.min.css" />
- <link rel="stylesheet" type="text/css" href="../../_static/css/tooltipster-sideTip-light.min.css" />
- <link rel="stylesheet" type="text/css" href="../../_static/css/tooltipster-sideTip-borderless.min.css" />
- <link rel="stylesheet" type="text/css" href="../../_static/css/micromodal.css" />
+ <link rel="stylesheet" type="text/css" href="../../_static/css/tooltipster.custom.css?v=7bc2f056" />
+ <link rel="stylesheet" type="text/css" href="../../_static/css/tooltipster.bundle.min.css?v=37217874" />
+ <link rel="stylesheet" type="text/css" href="../../_static/css/tooltipster-sideTip-shadow.min.css?v=6227e517" />
+ <link rel="stylesheet" type="text/css" href="../../_static/css/tooltipster-sideTip-punk.min.css?v=94669e23" />
+ <link rel="stylesheet" type="text/css" href="../../_static/css/tooltipster-sideTip-noir.min.css?v=21a39f42" />
+ <link rel="stylesheet" type="text/css" href="../../_static/css/tooltipster-sideTip-light.min.css?v=a18b2449" />
+ <link rel="stylesheet" type="text/css" href="../../_static/css/tooltipster-sideTip-borderless.min.css?v=dbff53e4" />
+ <link rel="stylesheet" type="text/css" href="../../_static/css/micromodal.css?v=d7bf34ee" />
<link rel="stylesheet" type="text/css" href="../../_static/sphinx-design.min.css?v=95c83b7e" />
<!-- Pre-loaded scripts that we'll load fully later -->
@@ -61,9 +61,9 @@
<script src="../../_static/copybutton.js?v=f281be69"></script>
<script src="../../_static/scripts/sphinx-book-theme.js?v=887ef09a"></script>
<script src="../../_static/tabs.js?v=3ee01567"></script>
- <script src="../../_static/js/hoverxref.js"></script>
- <script src="../../_static/js/tooltipster.bundle.min.js"></script>
- <script src="../../_static/js/micromodal.min.js"></script>
+ <script src="../../_static/js/hoverxref.js?v=c95ade4f"></script>
+ <script src="../../_static/js/tooltipster.bundle.min.js?v=18bf091b"></script>
+ <script src="../../_static/js/micromodal.min.js?v=04d6302d"></script>
<script>let toggleHintShow = 'Click to show';</script>
<script>let toggleHintHide = 'Click to hide';</script>
<script>let toggleOpenOnPrint = 'true';</script>
@@ -323,7 +323,9 @@ document.write(`
</button>
`);
</script>
-
+<button class="sidebar-toggle secondary-toggle btn btn-sm" title="Toggle secondary sidebar" data-bs-placement="bottom" data-bs-toggle="tooltip">
+ <span class="fa-solid fa-list"></span>
+</button>
</div></div>
</div>
@@ -339,6 +341,22 @@ document.write(`
<div id="print-main-content">
<div id="jb-print-toc">
+ <div>
+ <h2> Contents </h2>
+ </div>
+ <nav aria-label="Page">
+ <ul class="visible nav section-nav flex-column">
+<li class="toc-h2 nav-item toc-entry"><a class="reference internal nav-link" href="#arbdmodel.simplearbd.SimpleArbdConfig"><code class="docutils literal notranslate"><span class="pre">SimpleArbdConfig</span></code></a><ul class="nav section-nav flex-column">
+<li class="toc-h3 nav-item toc-entry"><a class="reference internal nav-link" href="#arbdmodel.simplearbd.SimpleArbdConfig.create_engine"><code class="docutils literal notranslate"><span class="pre">SimpleArbdConfig.create_engine()</span></code></a></li>
+<li class="toc-h3 nav-item toc-entry"><a class="reference internal nav-link" href="#arbdmodel.simplearbd.SimpleArbdConfig.create_model"><code class="docutils literal notranslate"><span class="pre">SimpleArbdConfig.create_model()</span></code></a></li>
+<li class="toc-h3 nav-item toc-entry"><a class="reference internal nav-link" href="#arbdmodel.simplearbd.SimpleArbdConfig.run_simulation"><code class="docutils literal notranslate"><span class="pre">SimpleArbdConfig.run_simulation()</span></code></a></li>
+<li class="toc-h3 nav-item toc-entry"><a class="reference internal nav-link" href="#arbdmodel.simplearbd.SimpleArbdConfig.setup_diffusible_objects"><code class="docutils literal notranslate"><span class="pre">SimpleArbdConfig.setup_diffusible_objects()</span></code></a></li>
+<li class="toc-h3 nav-item toc-entry"><a class="reference internal nav-link" href="#arbdmodel.simplearbd.SimpleArbdConfig.setup_static_objects"><code class="docutils literal notranslate"><span class="pre">SimpleArbdConfig.setup_static_objects()</span></code></a></li>
+</ul>
+</li>
+<li class="toc-h2 nav-item toc-entry"><a class="reference internal nav-link" href="#arbdmodel.simplearbd.main"><code class="docutils literal notranslate"><span class="pre">main()</span></code></a></li>
+</ul>
+ </nav>
</div>
</div>
</div>
@@ -351,6 +369,85 @@ document.write(`
<section class="tex2jax_ignore mathjax_ignore" id="simplearbd">
<h1>simplearbd<a class="headerlink" href="#simplearbd" title="Link to this heading">#</a></h1>
<p>Module documentation for <code class="docutils literal notranslate"><span class="pre">arbdmodel.simplearbd</span></code>.</p>
+<dl class="py class" id="module-arbdmodel.simplearbd">
+<dt class="sig sig-object py" id="arbdmodel.simplearbd.SimpleArbdConfig">
+<em class="property"><span class="pre">class</span><span class="w"> </span></em><span class="sig-name descname"><span class="pre">SimpleArbdConfig</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">config_path</span></span></em><span class="sig-paren">)</span><a class="reference internal" href="../../_modules/arbdmodel/simplearbd.html#SimpleArbdConfig"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#arbdmodel.simplearbd.SimpleArbdConfig" title="Link to this definition">#</a></dt>
+<dd><p>Bases: <a class="hxr-hoverxref hxr-tooltip reference external" href="https://docs.python.org/3/library/functions.html#object" title="(in Python v3.13)"><code class="xref py py-class docutils literal notranslate"><span class="pre">object</span></code></a></p>
+<p>Parse and manage SimpleARBD configuration file.</p>
+<p>This class provides a modern, clean interface for reading SimpleARBD
+configuration files and setting up the simulation.</p>
+<dl class="py method">
+<dt class="sig sig-object py" id="arbdmodel.simplearbd.SimpleArbdConfig.create_engine">
+<span class="sig-name descname"><span class="pre">create_engine</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="reference internal" href="../../_modules/arbdmodel/simplearbd.html#SimpleArbdConfig.create_engine"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#arbdmodel.simplearbd.SimpleArbdConfig.create_engine" title="Link to this definition">#</a></dt>
+<dd><p>Create a SimpleArbdEngine from the configuration.</p>
+<dl class="field-list simple">
+<dt class="field-odd">Returns<span class="colon">:</span></dt>
+<dd class="field-odd"><p>SimpleArbdEngine instance</p>
+</dd>
+<dt class="field-even">Return type<span class="colon">:</span></dt>
+<dd class="field-even"><p><a class="reference internal" href="structure_rigidbody.html#arbdmodel.structure_rigidbody.SimpleArbdEngine" title="arbdmodel.structure_rigidbody.SimpleArbdEngine"><em>SimpleArbdEngine</em></a></p>
+</dd>
+</dl>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="arbdmodel.simplearbd.SimpleArbdConfig.create_model">
+<span class="sig-name descname"><span class="pre">create_model</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="reference internal" href="../../_modules/arbdmodel/simplearbd.html#SimpleArbdConfig.create_model"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#arbdmodel.simplearbd.SimpleArbdConfig.create_model" title="Link to this definition">#</a></dt>
+<dd><p>Create a StructureRigidBodyModel from the configuration.</p>
+<dl class="field-list simple">
+<dt class="field-odd">Returns<span class="colon">:</span></dt>
+<dd class="field-odd"><p>StructureRigidBodyModel instance</p>
+</dd>
+<dt class="field-even">Return type<span class="colon">:</span></dt>
+<dd class="field-even"><p><a class="reference internal" href="structure_rigidbody.html#arbdmodel.structure_rigidbody.StructureRigidBodyModel" title="arbdmodel.structure_rigidbody.StructureRigidBodyModel"><em>StructureRigidBodyModel</em></a></p>
+</dd>
+</dl>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="arbdmodel.simplearbd.SimpleArbdConfig.run_simulation">
+<span class="sig-name descname"><span class="pre">run_simulation</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">model</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">engine</span></span></em><span class="sig-paren">)</span><a class="reference internal" href="../../_modules/arbdmodel/simplearbd.html#SimpleArbdConfig.run_simulation"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#arbdmodel.simplearbd.SimpleArbdConfig.run_simulation" title="Link to this definition">#</a></dt>
+<dd><p>Run the simulation.</p>
+<dl class="field-list simple">
+<dt class="field-odd">Parameters<span class="colon">:</span></dt>
+<dd class="field-odd"><ul class="simple">
+<li><p><strong>model</strong> (<a class="reference internal" href="structure_rigidbody.html#arbdmodel.structure_rigidbody.StructureRigidBodyModel" title="arbdmodel.structure_rigidbody.StructureRigidBodyModel"><em>StructureRigidBodyModel</em></a>) – StructureRigidBodyModel to simulate</p></li>
+<li><p><strong>engine</strong> (<a class="reference internal" href="structure_rigidbody.html#arbdmodel.structure_rigidbody.SimpleArbdEngine" title="arbdmodel.structure_rigidbody.SimpleArbdEngine"><em>SimpleArbdEngine</em></a>) – SimpleArbdEngine to use for simulation</p></li>
+</ul>
+</dd>
+</dl>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="arbdmodel.simplearbd.SimpleArbdConfig.setup_diffusible_objects">
+<span class="sig-name descname"><span class="pre">setup_diffusible_objects</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">model</span></span></em><span class="sig-paren">)</span><a class="reference internal" href="../../_modules/arbdmodel/simplearbd.html#SimpleArbdConfig.setup_diffusible_objects"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#arbdmodel.simplearbd.SimpleArbdConfig.setup_diffusible_objects" title="Link to this definition">#</a></dt>
+<dd><p>Set up diffusible objects in the model.</p>
+<dl class="field-list simple">
+<dt class="field-odd">Parameters<span class="colon">:</span></dt>
+<dd class="field-odd"><p><strong>model</strong> (<a class="reference internal" href="structure_rigidbody.html#arbdmodel.structure_rigidbody.StructureRigidBodyModel" title="arbdmodel.structure_rigidbody.StructureRigidBodyModel"><em>StructureRigidBodyModel</em></a>) – StructureRigidBodyModel to add diffusible objects to</p>
+</dd>
+</dl>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="arbdmodel.simplearbd.SimpleArbdConfig.setup_static_objects">
+<span class="sig-name descname"><span class="pre">setup_static_objects</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">model</span></span></em><span class="sig-paren">)</span><a class="reference internal" href="../../_modules/arbdmodel/simplearbd.html#SimpleArbdConfig.setup_static_objects"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#arbdmodel.simplearbd.SimpleArbdConfig.setup_static_objects" title="Link to this definition">#</a></dt>
+<dd><p>Set up static objects in the model.</p>
+<dl class="field-list simple">
+<dt class="field-odd">Parameters<span class="colon">:</span></dt>
+<dd class="field-odd"><p><strong>model</strong> (<a class="reference internal" href="structure_rigidbody.html#arbdmodel.structure_rigidbody.StructureRigidBodyModel" title="arbdmodel.structure_rigidbody.StructureRigidBodyModel"><em>StructureRigidBodyModel</em></a>) – StructureRigidBodyModel to add static objects to</p>
+</dd>
+</dl>
+</dd></dl>
+
+</dd></dl>
+
+<dl class="py function">
+<dt class="sig sig-object py" id="arbdmodel.simplearbd.main">
+<span class="sig-name descname"><span class="pre">main</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="reference internal" href="../../_modules/arbdmodel/simplearbd.html#main"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#arbdmodel.simplearbd.main" title="Link to this definition">#</a></dt>
+<dd><p>Main function to process SimpleARBD configuration file and run simulation.</p>
+</dd></dl>
+
</section>
<script type="text/x-thebe-config">
@@ -390,6 +487,29 @@ document.write(`
+ <div class="bd-sidebar-secondary bd-toc"><div class="sidebar-secondary-items sidebar-secondary__inner">
+
+
+ <div class="sidebar-secondary-item">
+ <div class="page-toc tocsection onthispage">
+ <i class="fa-solid fa-list"></i> Contents
+ </div>
+ <nav class="bd-toc-nav page-toc">
+ <ul class="visible nav section-nav flex-column">
+<li class="toc-h2 nav-item toc-entry"><a class="reference internal nav-link" href="#arbdmodel.simplearbd.SimpleArbdConfig"><code class="docutils literal notranslate"><span class="pre">SimpleArbdConfig</span></code></a><ul class="nav section-nav flex-column">
+<li class="toc-h3 nav-item toc-entry"><a class="reference internal nav-link" href="#arbdmodel.simplearbd.SimpleArbdConfig.create_engine"><code class="docutils literal notranslate"><span class="pre">SimpleArbdConfig.create_engine()</span></code></a></li>
+<li class="toc-h3 nav-item toc-entry"><a class="reference internal nav-link" href="#arbdmodel.simplearbd.SimpleArbdConfig.create_model"><code class="docutils literal notranslate"><span class="pre">SimpleArbdConfig.create_model()</span></code></a></li>
+<li class="toc-h3 nav-item toc-entry"><a class="reference internal nav-link" href="#arbdmodel.simplearbd.SimpleArbdConfig.run_simulation"><code class="docutils literal notranslate"><span class="pre">SimpleArbdConfig.run_simulation()</span></code></a></li>
+<li class="toc-h3 nav-item toc-entry"><a class="reference internal nav-link" href="#arbdmodel.simplearbd.SimpleArbdConfig.setup_diffusible_objects"><code class="docutils literal notranslate"><span class="pre">SimpleArbdConfig.setup_diffusible_objects()</span></code></a></li>
+<li class="toc-h3 nav-item toc-entry"><a class="reference internal nav-link" href="#arbdmodel.simplearbd.SimpleArbdConfig.setup_static_objects"><code class="docutils literal notranslate"><span class="pre">SimpleArbdConfig.setup_static_objects()</span></code></a></li>
+</ul>
+</li>
+<li class="toc-h2 nav-item toc-entry"><a class="reference internal nav-link" href="#arbdmodel.simplearbd.main"><code class="docutils literal notranslate"><span class="pre">main()</span></code></a></li>
+</ul>
+ </nav></div>
+
+</div></div>
+
</div>
<footer class="bd-footer-content">
diff --git a/_build/html/api/rigidbody_models/structure_from_pdb.html b/_build/html/api/rigidbody_models/structure_from_pdb.html
index be472a34fc1f9a7e4eed109e0515a0924629cfa6..0c5538e4dc25170b20c63bef858b9086e006bc00 100644
--- a/_build/html/api/rigidbody_models/structure_from_pdb.html
+++ b/_build/html/api/rigidbody_models/structure_from_pdb.html
@@ -32,19 +32,19 @@
<link rel="stylesheet" type="text/css" href="../../_static/styles/sphinx-book-theme.css?v=eba8b062" />
<link rel="stylesheet" type="text/css" href="../../_static/togglebutton.css?v=13237357" />
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- <link rel="stylesheet" type="text/css" href="../../_static/mystnb.4510f1fc1dee50b3e5859aac5469c37c29e427902b24a333a5f9fcb2f0b3ac41.css" />
+ <link rel="stylesheet" type="text/css" href="../../_static/mystnb.4510f1fc1dee50b3e5859aac5469c37c29e427902b24a333a5f9fcb2f0b3ac41.css?v=be8a1c11" />
<link rel="stylesheet" type="text/css" href="../../_static/sphinx-thebe.css?v=4fa983c6" />
<link rel="stylesheet" type="text/css" href="../../_static/tabs.css?v=4c969af8" />
- <link rel="stylesheet" type="text/css" href="../../_static/proof.css" />
+ <link rel="stylesheet" type="text/css" href="../../_static/proof.css?v=b4b7a797" />
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- <link rel="stylesheet" type="text/css" href="../../_static/css/tooltipster-sideTip-borderless.min.css" />
- <link rel="stylesheet" type="text/css" href="../../_static/css/micromodal.css" />
+ <link rel="stylesheet" type="text/css" href="../../_static/css/tooltipster.custom.css?v=7bc2f056" />
+ <link rel="stylesheet" type="text/css" href="../../_static/css/tooltipster.bundle.min.css?v=37217874" />
+ <link rel="stylesheet" type="text/css" href="../../_static/css/tooltipster-sideTip-shadow.min.css?v=6227e517" />
+ <link rel="stylesheet" type="text/css" href="../../_static/css/tooltipster-sideTip-punk.min.css?v=94669e23" />
+ <link rel="stylesheet" type="text/css" href="../../_static/css/tooltipster-sideTip-noir.min.css?v=21a39f42" />
+ <link rel="stylesheet" type="text/css" href="../../_static/css/tooltipster-sideTip-light.min.css?v=a18b2449" />
+ <link rel="stylesheet" type="text/css" href="../../_static/css/tooltipster-sideTip-borderless.min.css?v=dbff53e4" />
+ <link rel="stylesheet" type="text/css" href="../../_static/css/micromodal.css?v=d7bf34ee" />
<link rel="stylesheet" type="text/css" href="../../_static/sphinx-design.min.css?v=95c83b7e" />
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@@ -61,9 +61,9 @@
<script src="../../_static/copybutton.js?v=f281be69"></script>
<script src="../../_static/scripts/sphinx-book-theme.js?v=887ef09a"></script>
<script src="../../_static/tabs.js?v=3ee01567"></script>
- <script src="../../_static/js/hoverxref.js"></script>
- <script src="../../_static/js/tooltipster.bundle.min.js"></script>
- <script src="../../_static/js/micromodal.min.js"></script>
+ <script src="../../_static/js/hoverxref.js?v=c95ade4f"></script>
+ <script src="../../_static/js/tooltipster.bundle.min.js?v=18bf091b"></script>
+ <script src="../../_static/js/micromodal.min.js?v=04d6302d"></script>
<script>let toggleHintShow = 'Click to show';</script>
<script>let toggleHintHide = 'Click to hide';</script>
<script>let toggleOpenOnPrint = 'true';</script>
@@ -323,7 +323,9 @@ document.write(`
</button>
`);
</script>
-
+<button class="sidebar-toggle secondary-toggle btn btn-sm" title="Toggle secondary sidebar" data-bs-placement="bottom" data-bs-toggle="tooltip">
+ <span class="fa-solid fa-list"></span>
+</button>
</div></div>
</div>
@@ -339,6 +341,24 @@ document.write(`
<div id="print-main-content">
<div id="jb-print-toc">
+ <div>
+ <h2> Contents </h2>
+ </div>
+ <nav aria-label="Page">
+ <ul class="visible nav section-nav flex-column">
+<li class="toc-h2 nav-item toc-entry"><a class="reference internal nav-link" href="#arbdmodel.structure_from_pdb.StructureProcessor"><code class="docutils literal notranslate"><span class="pre">StructureProcessor</span></code></a><ul class="nav section-nav flex-column">
+<li class="toc-h3 nav-item toc-entry"><a class="reference internal nav-link" href="#arbdmodel.structure_from_pdb.StructureProcessor.align_structure"><code class="docutils literal notranslate"><span class="pre">StructureProcessor.align_structure()</span></code></a></li>
+<li class="toc-h3 nav-item toc-entry"><a class="reference internal nav-link" href="#arbdmodel.structure_from_pdb.StructureProcessor.apply_gaussian_smoothing"><code class="docutils literal notranslate"><span class="pre">StructureProcessor.apply_gaussian_smoothing()</span></code></a></li>
+<li class="toc-h3 nav-item toc-entry"><a class="reference internal nav-link" href="#arbdmodel.structure_from_pdb.StructureProcessor.calculate_hydrodynamic_properties"><code class="docutils literal notranslate"><span class="pre">StructureProcessor.calculate_hydrodynamic_properties()</span></code></a></li>
+<li class="toc-h3 nav-item toc-entry"><a class="reference internal nav-link" href="#arbdmodel.structure_from_pdb.StructureProcessor.generate_charge_distribution"><code class="docutils literal notranslate"><span class="pre">StructureProcessor.generate_charge_distribution()</span></code></a></li>
+<li class="toc-h3 nav-item toc-entry"><a class="reference internal nav-link" href="#arbdmodel.structure_from_pdb.StructureProcessor.generate_electrostatic_map"><code class="docutils literal notranslate"><span class="pre">StructureProcessor.generate_electrostatic_map()</span></code></a></li>
+<li class="toc-h3 nav-item toc-entry"><a class="reference internal nav-link" href="#arbdmodel.structure_from_pdb.StructureProcessor.generate_vdw_maps"><code class="docutils literal notranslate"><span class="pre">StructureProcessor.generate_vdw_maps()</span></code></a></li>
+<li class="toc-h3 nav-item toc-entry"><a class="reference internal nav-link" href="#arbdmodel.structure_from_pdb.StructureProcessor.get_grid_files"><code class="docutils literal notranslate"><span class="pre">StructureProcessor.get_grid_files()</span></code></a></li>
+<li class="toc-h3 nav-item toc-entry"><a class="reference internal nav-link" href="#arbdmodel.structure_from_pdb.StructureProcessor.process_structure"><code class="docutils literal notranslate"><span class="pre">StructureProcessor.process_structure()</span></code></a></li>
+</ul>
+</li>
+</ul>
+ </nav>
</div>
</div>
</div>
@@ -351,6 +371,61 @@ document.write(`
<section class="tex2jax_ignore mathjax_ignore" id="structure-from-pdb">
<h1>structure_from_pdb<a class="headerlink" href="#structure-from-pdb" title="Link to this heading">#</a></h1>
<p>Module documentation for <code class="docutils literal notranslate"><span class="pre">arbdmodel.structure_from_pdb</span></code>.</p>
+<dl class="py class" id="module-arbdmodel.structure_from_pdb">
+<dt class="sig sig-object py" id="arbdmodel.structure_from_pdb.StructureProcessor">
+<em class="property"><span class="pre">class</span><span class="w"> </span></em><span class="sig-name descname"><span class="pre">StructureProcessor</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">structure_path</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">simconf</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">num_heavy_cluster</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">3</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">parameters_folder</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">'./parameters'</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">work_dir</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em><span class="sig-paren">)</span><a class="reference internal" href="../../_modules/arbdmodel/structure_from_pdb.html#StructureProcessor"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#arbdmodel.structure_from_pdb.StructureProcessor" title="Link to this definition">#</a></dt>
+<dd><p>Bases: <a class="hxr-hoverxref hxr-tooltip reference external" href="https://docs.python.org/3/library/functions.html#object" title="(in Python v3.13)"><code class="xref py py-class docutils literal notranslate"><span class="pre">object</span></code></a></p>
+<p>Process molecular structure files to calculate properties and generate maps for ARBD</p>
+<dl class="py method">
+<dt class="sig sig-object py" id="arbdmodel.structure_from_pdb.StructureProcessor.align_structure">
+<span class="sig-name descname"><span class="pre">align_structure</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="reference internal" href="../../_modules/arbdmodel/structure_from_pdb.html#StructureProcessor.align_structure"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#arbdmodel.structure_from_pdb.StructureProcessor.align_structure" title="Link to this definition">#</a></dt>
+<dd><p>Align structure to principal axes using VMD.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="arbdmodel.structure_from_pdb.StructureProcessor.apply_gaussian_smoothing">
+<span class="sig-name descname"><span class="pre">apply_gaussian_smoothing</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">gaussianWidth</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">2.5</span></span></em><span class="sig-paren">)</span><a class="reference internal" href="../../_modules/arbdmodel/structure_from_pdb.html#StructureProcessor.apply_gaussian_smoothing"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#arbdmodel.structure_from_pdb.StructureProcessor.apply_gaussian_smoothing" title="Link to this definition">#</a></dt>
+<dd><p>Apply Gaussian smoothing to all potential maps.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="arbdmodel.structure_from_pdb.StructureProcessor.calculate_hydrodynamic_properties">
+<span class="sig-name descname"><span class="pre">calculate_hydrodynamic_properties</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="reference internal" href="../../_modules/arbdmodel/structure_from_pdb.html#StructureProcessor.calculate_hydrodynamic_properties"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#arbdmodel.structure_from_pdb.StructureProcessor.calculate_hydrodynamic_properties" title="Link to this definition">#</a></dt>
+<dd><p>Calculate hydrodynamic properties using HydroPro.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="arbdmodel.structure_from_pdb.StructureProcessor.generate_charge_distribution">
+<span class="sig-name descname"><span class="pre">generate_charge_distribution</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">resolution</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">2.0</span></span></em><span class="sig-paren">)</span><a class="reference internal" href="../../_modules/arbdmodel/structure_from_pdb.html#StructureProcessor.generate_charge_distribution"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#arbdmodel.structure_from_pdb.StructureProcessor.generate_charge_distribution" title="Link to this definition">#</a></dt>
+<dd><p>Generate charge distribution using VMD.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="arbdmodel.structure_from_pdb.StructureProcessor.generate_electrostatic_map">
+<span class="sig-name descname"><span class="pre">generate_electrostatic_map</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">buffer</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">50</span></span></em><span class="sig-paren">)</span><a class="reference internal" href="../../_modules/arbdmodel/structure_from_pdb.html#StructureProcessor.generate_electrostatic_map"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#arbdmodel.structure_from_pdb.StructureProcessor.generate_electrostatic_map" title="Link to this definition">#</a></dt>
+<dd><p>Generate electrostatic potential map using APBS.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="arbdmodel.structure_from_pdb.StructureProcessor.generate_vdw_maps">
+<span class="sig-name descname"><span class="pre">generate_vdw_maps</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">potResolution</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">1</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">denResolution</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">2</span></span></em><span class="sig-paren">)</span><a class="reference internal" href="../../_modules/arbdmodel/structure_from_pdb.html#StructureProcessor.generate_vdw_maps"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#arbdmodel.structure_from_pdb.StructureProcessor.generate_vdw_maps" title="Link to this definition">#</a></dt>
+<dd><p>Generate VDW maps using VMD.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="arbdmodel.structure_from_pdb.StructureProcessor.get_grid_files">
+<span class="sig-name descname"><span class="pre">get_grid_files</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="reference internal" href="../../_modules/arbdmodel/structure_from_pdb.html#StructureProcessor.get_grid_files"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#arbdmodel.structure_from_pdb.StructureProcessor.get_grid_files" title="Link to this definition">#</a></dt>
+<dd><p>Get dictionary of grid files for use in RigidBodyType.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="arbdmodel.structure_from_pdb.StructureProcessor.process_structure">
+<span class="sig-name descname"><span class="pre">process_structure</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="reference internal" href="../../_modules/arbdmodel/structure_from_pdb.html#StructureProcessor.process_structure"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#arbdmodel.structure_from_pdb.StructureProcessor.process_structure" title="Link to this definition">#</a></dt>
+<dd><p>Process structure to get all properties and potential maps</p>
+</dd></dl>
+
+</dd></dl>
+
</section>
<script type="text/x-thebe-config">
@@ -390,6 +465,31 @@ document.write(`
+ <div class="bd-sidebar-secondary bd-toc"><div class="sidebar-secondary-items sidebar-secondary__inner">
+
+
+ <div class="sidebar-secondary-item">
+ <div class="page-toc tocsection onthispage">
+ <i class="fa-solid fa-list"></i> Contents
+ </div>
+ <nav class="bd-toc-nav page-toc">
+ <ul class="visible nav section-nav flex-column">
+<li class="toc-h2 nav-item toc-entry"><a class="reference internal nav-link" href="#arbdmodel.structure_from_pdb.StructureProcessor"><code class="docutils literal notranslate"><span class="pre">StructureProcessor</span></code></a><ul class="nav section-nav flex-column">
+<li class="toc-h3 nav-item toc-entry"><a class="reference internal nav-link" href="#arbdmodel.structure_from_pdb.StructureProcessor.align_structure"><code class="docutils literal notranslate"><span class="pre">StructureProcessor.align_structure()</span></code></a></li>
+<li class="toc-h3 nav-item toc-entry"><a class="reference internal nav-link" href="#arbdmodel.structure_from_pdb.StructureProcessor.apply_gaussian_smoothing"><code class="docutils literal notranslate"><span class="pre">StructureProcessor.apply_gaussian_smoothing()</span></code></a></li>
+<li class="toc-h3 nav-item toc-entry"><a class="reference internal nav-link" href="#arbdmodel.structure_from_pdb.StructureProcessor.calculate_hydrodynamic_properties"><code class="docutils literal notranslate"><span class="pre">StructureProcessor.calculate_hydrodynamic_properties()</span></code></a></li>
+<li class="toc-h3 nav-item toc-entry"><a class="reference internal nav-link" href="#arbdmodel.structure_from_pdb.StructureProcessor.generate_charge_distribution"><code class="docutils literal notranslate"><span class="pre">StructureProcessor.generate_charge_distribution()</span></code></a></li>
+<li class="toc-h3 nav-item toc-entry"><a class="reference internal nav-link" href="#arbdmodel.structure_from_pdb.StructureProcessor.generate_electrostatic_map"><code class="docutils literal notranslate"><span class="pre">StructureProcessor.generate_electrostatic_map()</span></code></a></li>
+<li class="toc-h3 nav-item toc-entry"><a class="reference internal nav-link" href="#arbdmodel.structure_from_pdb.StructureProcessor.generate_vdw_maps"><code class="docutils literal notranslate"><span class="pre">StructureProcessor.generate_vdw_maps()</span></code></a></li>
+<li class="toc-h3 nav-item toc-entry"><a class="reference internal nav-link" href="#arbdmodel.structure_from_pdb.StructureProcessor.get_grid_files"><code class="docutils literal notranslate"><span class="pre">StructureProcessor.get_grid_files()</span></code></a></li>
+<li class="toc-h3 nav-item toc-entry"><a class="reference internal nav-link" href="#arbdmodel.structure_from_pdb.StructureProcessor.process_structure"><code class="docutils literal notranslate"><span class="pre">StructureProcessor.process_structure()</span></code></a></li>
+</ul>
+</li>
+</ul>
+ </nav></div>
+
+</div></div>
+
</div>
<footer class="bd-footer-content">
diff --git a/_build/html/api/rigidbody_models/structure_rigidbody.html b/_build/html/api/rigidbody_models/structure_rigidbody.html
index f45c9795d28a9dff48cebae4147d6e8009f7a0bd..67ab6610aa9ffa085fe79e6be64ae3e1c1ccaf20 100644
--- a/_build/html/api/rigidbody_models/structure_rigidbody.html
+++ b/_build/html/api/rigidbody_models/structure_rigidbody.html
@@ -32,19 +32,19 @@
<link rel="stylesheet" type="text/css" href="../../_static/styles/sphinx-book-theme.css?v=eba8b062" />
<link rel="stylesheet" type="text/css" href="../../_static/togglebutton.css?v=13237357" />
<link rel="stylesheet" type="text/css" href="../../_static/copybutton.css?v=76b2166b" />
- <link rel="stylesheet" type="text/css" href="../../_static/mystnb.4510f1fc1dee50b3e5859aac5469c37c29e427902b24a333a5f9fcb2f0b3ac41.css" />
+ <link rel="stylesheet" type="text/css" href="../../_static/mystnb.4510f1fc1dee50b3e5859aac5469c37c29e427902b24a333a5f9fcb2f0b3ac41.css?v=be8a1c11" />
<link rel="stylesheet" type="text/css" href="../../_static/sphinx-thebe.css?v=4fa983c6" />
<link rel="stylesheet" type="text/css" href="../../_static/tabs.css?v=4c969af8" />
- <link rel="stylesheet" type="text/css" href="../../_static/proof.css" />
+ <link rel="stylesheet" type="text/css" href="../../_static/proof.css?v=b4b7a797" />
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- <link rel="stylesheet" type="text/css" href="../../_static/css/micromodal.css" />
+ <link rel="stylesheet" type="text/css" href="../../_static/css/tooltipster.custom.css?v=7bc2f056" />
+ <link rel="stylesheet" type="text/css" href="../../_static/css/tooltipster.bundle.min.css?v=37217874" />
+ <link rel="stylesheet" type="text/css" href="../../_static/css/tooltipster-sideTip-shadow.min.css?v=6227e517" />
+ <link rel="stylesheet" type="text/css" href="../../_static/css/tooltipster-sideTip-punk.min.css?v=94669e23" />
+ <link rel="stylesheet" type="text/css" href="../../_static/css/tooltipster-sideTip-noir.min.css?v=21a39f42" />
+ <link rel="stylesheet" type="text/css" href="../../_static/css/tooltipster-sideTip-light.min.css?v=a18b2449" />
+ <link rel="stylesheet" type="text/css" href="../../_static/css/tooltipster-sideTip-borderless.min.css?v=dbff53e4" />
+ <link rel="stylesheet" type="text/css" href="../../_static/css/micromodal.css?v=d7bf34ee" />
<link rel="stylesheet" type="text/css" href="../../_static/sphinx-design.min.css?v=95c83b7e" />
<!-- Pre-loaded scripts that we'll load fully later -->
@@ -61,9 +61,9 @@
<script src="../../_static/copybutton.js?v=f281be69"></script>
<script src="../../_static/scripts/sphinx-book-theme.js?v=887ef09a"></script>
<script src="../../_static/tabs.js?v=3ee01567"></script>
- <script src="../../_static/js/hoverxref.js"></script>
- <script src="../../_static/js/tooltipster.bundle.min.js"></script>
- <script src="../../_static/js/micromodal.min.js"></script>
+ <script src="../../_static/js/hoverxref.js?v=c95ade4f"></script>
+ <script src="../../_static/js/tooltipster.bundle.min.js?v=18bf091b"></script>
+ <script src="../../_static/js/micromodal.min.js?v=04d6302d"></script>
<script>let toggleHintShow = 'Click to show';</script>
<script>let toggleHintHide = 'Click to hide';</script>
<script>let toggleOpenOnPrint = 'true';</script>
@@ -323,7 +323,9 @@ document.write(`
</button>
`);
</script>
-
+<button class="sidebar-toggle secondary-toggle btn btn-sm" title="Toggle secondary sidebar" data-bs-placement="bottom" data-bs-toggle="tooltip">
+ <span class="fa-solid fa-list"></span>
+</button>
</div></div>
</div>
@@ -339,6 +341,28 @@ document.write(`
<div id="print-main-content">
<div id="jb-print-toc">
+ <div>
+ <h2> Contents </h2>
+ </div>
+ <nav aria-label="Page">
+ <ul class="visible nav section-nav flex-column">
+<li class="toc-h2 nav-item toc-entry"><a class="reference internal nav-link" href="#arbdmodel.structure_rigidbody.DiffusiveRigidBodyType"><code class="docutils literal notranslate"><span class="pre">DiffusiveRigidBodyType</span></code></a></li>
+<li class="toc-h2 nav-item toc-entry"><a class="reference internal nav-link" href="#arbdmodel.structure_rigidbody.SimpleArbdEngine"><code class="docutils literal notranslate"><span class="pre">SimpleArbdEngine</span></code></a><ul class="nav section-nav flex-column">
+<li class="toc-h3 nav-item toc-entry"><a class="reference internal nav-link" href="#arbdmodel.structure_rigidbody.SimpleArbdEngine.run_simulation"><code class="docutils literal notranslate"><span class="pre">SimpleArbdEngine.run_simulation()</span></code></a></li>
+<li class="toc-h3 nav-item toc-entry"><a class="reference internal nav-link" href="#arbdmodel.structure_rigidbody.SimpleArbdEngine.write_simulation_files"><code class="docutils literal notranslate"><span class="pre">SimpleArbdEngine.write_simulation_files()</span></code></a></li>
+</ul>
+</li>
+<li class="toc-h2 nav-item toc-entry"><a class="reference internal nav-link" href="#arbdmodel.structure_rigidbody.StaticObject"><code class="docutils literal notranslate"><span class="pre">StaticObject</span></code></a><ul class="nav section-nav flex-column">
+<li class="toc-h3 nav-item toc-entry"><a class="reference internal nav-link" href="#arbdmodel.structure_rigidbody.StaticObject.process"><code class="docutils literal notranslate"><span class="pre">StaticObject.process()</span></code></a></li>
+</ul>
+</li>
+<li class="toc-h2 nav-item toc-entry"><a class="reference internal nav-link" href="#arbdmodel.structure_rigidbody.StructureRigidBodyModel"><code class="docutils literal notranslate"><span class="pre">StructureRigidBodyModel</span></code></a><ul class="nav section-nav flex-column">
+<li class="toc-h3 nav-item toc-entry"><a class="reference internal nav-link" href="#arbdmodel.structure_rigidbody.StructureRigidBodyModel.add_diffusible_object"><code class="docutils literal notranslate"><span class="pre">StructureRigidBodyModel.add_diffusible_object()</span></code></a></li>
+<li class="toc-h3 nav-item toc-entry"><a class="reference internal nav-link" href="#arbdmodel.structure_rigidbody.StructureRigidBodyModel.add_static_object"><code class="docutils literal notranslate"><span class="pre">StructureRigidBodyModel.add_static_object()</span></code></a></li>
+</ul>
+</li>
+</ul>
+ </nav>
</div>
</div>
</div>
@@ -351,6 +375,108 @@ document.write(`
<section class="tex2jax_ignore mathjax_ignore" id="structure-rigidbody">
<h1>structure_rigidbody<a class="headerlink" href="#structure-rigidbody" title="Link to this heading">#</a></h1>
<p>Module documentation for <code class="docutils literal notranslate"><span class="pre">arbdmodel.structure_rigidbody</span></code>.</p>
+<dl class="py class" id="module-arbdmodel.structure_rigidbody">
+<dt class="sig sig-object py" id="arbdmodel.structure_rigidbody.DiffusiveRigidBodyType">
+<em class="property"><span class="pre">class</span><span class="w"> </span></em><span class="sig-name descname"><span class="pre">DiffusiveRigidBodyType</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">name</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">structure_path</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">simconf</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">work_dir</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="o"><span class="pre">**</span></span><span class="n"><span class="pre">kwargs</span></span></em><span class="sig-paren">)</span><a class="reference internal" href="../../_modules/arbdmodel/structure_rigidbody.html#DiffusiveRigidBodyType"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#arbdmodel.structure_rigidbody.DiffusiveRigidBodyType" title="Link to this definition">#</a></dt>
+<dd><p>Bases: <a class="reference internal" href="../core/core_objects.html#arbdmodel.core_objects.RigidBodyType" title="arbdmodel.core_objects.RigidBodyType"><code class="xref py py-class docutils literal notranslate"><span class="pre">RigidBodyType</span></code></a></p>
+<p>RigidBodyType subclass for structure-based rigid body objects</p>
+</dd></dl>
+
+<dl class="py class">
+<dt class="sig sig-object py" id="arbdmodel.structure_rigidbody.SimpleArbdEngine">
+<em class="property"><span class="pre">class</span><span class="w"> </span></em><span class="sig-name descname"><span class="pre">SimpleArbdEngine</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">extra_bd_file_lines</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">''</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">configuration</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="o"><span class="pre">**</span></span><span class="n"><span class="pre">conf_params</span></span></em><span class="sig-paren">)</span><a class="reference internal" href="../../_modules/arbdmodel/structure_rigidbody.html#SimpleArbdEngine"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#arbdmodel.structure_rigidbody.SimpleArbdEngine" title="Link to this definition">#</a></dt>
+<dd><p>Bases: <a class="reference internal" href="../simulation_engines/engine.html#arbdmodel.engine.ArbdEngine" title="arbdmodel.engine.ArbdEngine"><code class="xref py py-class docutils literal notranslate"><span class="pre">ArbdEngine</span></code></a></p>
+<p>Enhanced ARBD engine with additional functionality for structure simulations</p>
+<dl class="py method">
+<dt class="sig sig-object py" id="arbdmodel.structure_rigidbody.SimpleArbdEngine.run_simulation">
+<span class="sig-name descname"><span class="pre">run_simulation</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">model</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">output_name</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">replicas</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">1</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">gpu</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">0</span></span></em>, <em class="sig-param"><span class="o"><span class="pre">**</span></span><span class="n"><span class="pre">kwargs</span></span></em><span class="sig-paren">)</span><a class="reference internal" href="../../_modules/arbdmodel/structure_rigidbody.html#SimpleArbdEngine.run_simulation"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#arbdmodel.structure_rigidbody.SimpleArbdEngine.run_simulation" title="Link to this definition">#</a></dt>
+<dd><p>Run ARBD simulation.</p>
+<dl class="field-list simple">
+<dt class="field-odd">Parameters<span class="colon">:</span></dt>
+<dd class="field-odd"><ul class="simple">
+<li><p><strong>model</strong> – ArbdModel to simulate</p></li>
+<li><p><strong>output_name</strong> – Base name for output files</p></li>
+<li><p><strong>replicas</strong> – Number of replicas to run</p></li>
+<li><p><strong>gpu</strong> – GPU index to use</p></li>
+<li><p><strong>**kwargs</strong> – Additional arguments for simulate method</p></li>
+</ul>
+</dd>
+</dl>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="arbdmodel.structure_rigidbody.SimpleArbdEngine.write_simulation_files">
+<span class="sig-name descname"><span class="pre">write_simulation_files</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">model</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">output_name</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">configuration</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="o"><span class="pre">**</span></span><span class="n"><span class="pre">conf_params</span></span></em><span class="sig-paren">)</span><a class="reference internal" href="../../_modules/arbdmodel/structure_rigidbody.html#SimpleArbdEngine.write_simulation_files"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#arbdmodel.structure_rigidbody.SimpleArbdEngine.write_simulation_files" title="Link to this definition">#</a></dt>
+<dd><p>Write all simulation files.</p>
+<dl class="field-list simple">
+<dt class="field-odd">Parameters<span class="colon">:</span></dt>
+<dd class="field-odd"><ul class="simple">
+<li><p><strong>model</strong> – ArbdModel to simulate</p></li>
+<li><p><strong>output_name</strong> – Base name for output files</p></li>
+<li><p><strong>configuration</strong> – SimConf object</p></li>
+<li><p><strong>**conf_params</strong> – Additional configuration parameters</p></li>
+</ul>
+</dd>
+</dl>
+</dd></dl>
+
+</dd></dl>
+
+<dl class="py class">
+<dt class="sig sig-object py" id="arbdmodel.structure_rigidbody.StaticObject">
+<em class="property"><span class="pre">class</span><span class="w"> </span></em><span class="sig-name descname"><span class="pre">StaticObject</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">structure_path</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">name</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">simconf</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">work_dir</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">is_gigantic</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">False</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">threshold</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">300</span></span></em><span class="sig-paren">)</span><a class="reference internal" href="../../_modules/arbdmodel/structure_rigidbody.html#StaticObject"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#arbdmodel.structure_rigidbody.StaticObject" title="Link to this definition">#</a></dt>
+<dd><p>Bases: <a class="hxr-hoverxref hxr-tooltip reference external" href="https://docs.python.org/3/library/functions.html#object" title="(in Python v3.13)"><code class="xref py py-class docutils literal notranslate"><span class="pre">object</span></code></a></p>
+<p>Class representing a static (immobile) object in the simulation</p>
+<dl class="py method">
+<dt class="sig sig-object py" id="arbdmodel.structure_rigidbody.StaticObject.process">
+<span class="sig-name descname"><span class="pre">process</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="reference internal" href="../../_modules/arbdmodel/structure_rigidbody.html#StaticObject.process"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#arbdmodel.structure_rigidbody.StaticObject.process" title="Link to this definition">#</a></dt>
+<dd><p>Process the structure file to create potential and density grids</p>
+</dd></dl>
+
+</dd></dl>
+
+<dl class="py class">
+<dt class="sig sig-object py" id="arbdmodel.structure_rigidbody.StructureRigidBodyModel">
+<em class="property"><span class="pre">class</span><span class="w"> </span></em><span class="sig-name descname"><span class="pre">StructureRigidBodyModel</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">cell_vectors</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">cell_origin</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">dimensions</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">buffer_factor</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">1.2</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">configuration</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">use_boundary</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">True</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">boundary_params</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="o"><span class="pre">**</span></span><span class="n"><span class="pre">kwargs</span></span></em><span class="sig-paren">)</span><a class="reference internal" href="../../_modules/arbdmodel/structure_rigidbody.html#StructureRigidBodyModel"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#arbdmodel.structure_rigidbody.StructureRigidBodyModel" title="Link to this definition">#</a></dt>
+<dd><p>Bases: <a class="reference internal" href="../core/model.html#arbdmodel.model.ArbdModel" title="arbdmodel.model.ArbdModel"><code class="xref py py-class docutils literal notranslate"><span class="pre">ArbdModel</span></code></a></p>
+<p>Model class for structure-based rigid body simulations</p>
+<dl class="py method">
+<dt class="sig sig-object py" id="arbdmodel.structure_rigidbody.StructureRigidBodyModel.add_diffusible_object">
+<span class="sig-name descname"><span class="pre">add_diffusible_object</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">structure_path</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">rb_type</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">copies</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">1</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">positions</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">orientations</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">name</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">initial_region</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">random_seed</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">work_dir</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em><span class="sig-paren">)</span><a class="reference internal" href="../../_modules/arbdmodel/structure_rigidbody.html#StructureRigidBodyModel.add_diffusible_object"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#arbdmodel.structure_rigidbody.StructureRigidBodyModel.add_diffusible_object" title="Link to this definition">#</a></dt>
+<dd><p>Add a diffusible (mobile) rigid body type to the model.</p>
+<dl class="field-list simple">
+<dt class="field-odd">Parameters<span class="colon">:</span></dt>
+<dd class="field-odd"><ul class="simple">
+<li><p><strong>structure_path</strong> – Path to structure files (.psf/.pdb) to create a StructureRigidBodyType</p></li>
+<li><p><strong>rb_type</strong> – Existing RigidBodyType instance (if structure_path not provided)</p></li>
+<li><p><strong>copies</strong> – Number of copies to add</p></li>
+<li><p><strong>positions</strong> – Optional list of positions for each copy</p></li>
+<li><p><strong>orientations</strong> – Optional list of orientations for each copy</p></li>
+<li><p><strong>name</strong> – Optional base name for the rigid bodies</p></li>
+<li><p><strong>initial_region</strong> – Optional dict with vectors defining initial region</p></li>
+<li><p><strong>random_seed</strong> – Optional seed for random number generator</p></li>
+<li><p><strong>work_dir</strong> – Optional working directory for structure processing</p></li>
+</ul>
+</dd>
+<dt class="field-even">Returns<span class="colon">:</span></dt>
+<dd class="field-even"><p>List of created RigidBody instances</p>
+</dd>
+</dl>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="arbdmodel.structure_rigidbody.StructureRigidBodyModel.add_static_object">
+<span class="sig-name descname"><span class="pre">add_static_object</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">structure_path</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">work_dir</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">is_gigantic</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">False</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">threshold</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">300</span></span></em><span class="sig-paren">)</span><a class="reference internal" href="../../_modules/arbdmodel/structure_rigidbody.html#StructureRigidBodyModel.add_static_object"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#arbdmodel.structure_rigidbody.StructureRigidBodyModel.add_static_object" title="Link to this definition">#</a></dt>
+<dd><p>Add this static object to an ARBD model.</p>
+<dl class="field-list simple">
+<dt class="field-odd">Parameters<span class="colon">:</span></dt>
+<dd class="field-odd"><p><strong>model</strong> – ArbdModel to add this static object to</p>
+</dd>
+</dl>
+</dd></dl>
+
+</dd></dl>
+
</section>
<script type="text/x-thebe-config">
@@ -390,6 +516,35 @@ document.write(`
+ <div class="bd-sidebar-secondary bd-toc"><div class="sidebar-secondary-items sidebar-secondary__inner">
+
+
+ <div class="sidebar-secondary-item">
+ <div class="page-toc tocsection onthispage">
+ <i class="fa-solid fa-list"></i> Contents
+ </div>
+ <nav class="bd-toc-nav page-toc">
+ <ul class="visible nav section-nav flex-column">
+<li class="toc-h2 nav-item toc-entry"><a class="reference internal nav-link" href="#arbdmodel.structure_rigidbody.DiffusiveRigidBodyType"><code class="docutils literal notranslate"><span class="pre">DiffusiveRigidBodyType</span></code></a></li>
+<li class="toc-h2 nav-item toc-entry"><a class="reference internal nav-link" href="#arbdmodel.structure_rigidbody.SimpleArbdEngine"><code class="docutils literal notranslate"><span class="pre">SimpleArbdEngine</span></code></a><ul class="nav section-nav flex-column">
+<li class="toc-h3 nav-item toc-entry"><a class="reference internal nav-link" href="#arbdmodel.structure_rigidbody.SimpleArbdEngine.run_simulation"><code class="docutils literal notranslate"><span class="pre">SimpleArbdEngine.run_simulation()</span></code></a></li>
+<li class="toc-h3 nav-item toc-entry"><a class="reference internal nav-link" href="#arbdmodel.structure_rigidbody.SimpleArbdEngine.write_simulation_files"><code class="docutils literal notranslate"><span class="pre">SimpleArbdEngine.write_simulation_files()</span></code></a></li>
+</ul>
+</li>
+<li class="toc-h2 nav-item toc-entry"><a class="reference internal nav-link" href="#arbdmodel.structure_rigidbody.StaticObject"><code class="docutils literal notranslate"><span class="pre">StaticObject</span></code></a><ul class="nav section-nav flex-column">
+<li class="toc-h3 nav-item toc-entry"><a class="reference internal nav-link" href="#arbdmodel.structure_rigidbody.StaticObject.process"><code class="docutils literal notranslate"><span class="pre">StaticObject.process()</span></code></a></li>
+</ul>
+</li>
+<li class="toc-h2 nav-item toc-entry"><a class="reference internal nav-link" href="#arbdmodel.structure_rigidbody.StructureRigidBodyModel"><code class="docutils literal notranslate"><span class="pre">StructureRigidBodyModel</span></code></a><ul class="nav section-nav flex-column">
+<li class="toc-h3 nav-item toc-entry"><a class="reference internal nav-link" href="#arbdmodel.structure_rigidbody.StructureRigidBodyModel.add_diffusible_object"><code class="docutils literal notranslate"><span class="pre">StructureRigidBodyModel.add_diffusible_object()</span></code></a></li>
+<li class="toc-h3 nav-item toc-entry"><a class="reference internal nav-link" href="#arbdmodel.structure_rigidbody.StructureRigidBodyModel.add_static_object"><code class="docutils literal notranslate"><span class="pre">StructureRigidBodyModel.add_static_object()</span></code></a></li>
+</ul>
+</li>
+</ul>
+ </nav></div>
+
+</div></div>
+
</div>
<footer class="bd-footer-content">
diff --git a/_build/html/api/shape-based_models/index.html b/_build/html/api/shape-based_models/index.html
index 3f9b017dbb97e7b516840f97e7a61f6a267b71e6..ef2d81fb859653795956daca1c5ac55c60dc1b93 100644
--- a/_build/html/api/shape-based_models/index.html
+++ b/_build/html/api/shape-based_models/index.html
@@ -32,19 +32,19 @@
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+ <link rel="stylesheet" type="text/css" href="../../_static/mystnb.4510f1fc1dee50b3e5859aac5469c37c29e427902b24a333a5f9fcb2f0b3ac41.css?v=be8a1c11" />
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diff --git a/_build/html/api/shape-based_models/shape_cg.html b/_build/html/api/shape-based_models/shape_cg.html
index 195482f350900b2fc7c39a17f5430047490d50de..45673d830a4a8a6ef3f67045769590d59e9bdfb9 100644
--- a/_build/html/api/shape-based_models/shape_cg.html
+++ b/_build/html/api/shape-based_models/shape_cg.html
@@ -32,19 +32,19 @@
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<script>let toggleHintHide = 'Click to hide';</script>
<script>let toggleOpenOnPrint = 'true';</script>
@@ -346,8 +346,35 @@ document.write(`
</div>
<nav aria-label="Page">
<ul class="visible nav section-nav flex-column">
+<li class="toc-h2 nav-item toc-entry"><a class="reference internal nav-link" href="#arbdmodel.shape_cg.ShapeCGFactory"><code class="docutils literal notranslate"><span class="pre">ShapeCGFactory</span></code></a><ul class="nav section-nav flex-column">
+<li class="toc-h3 nav-item toc-entry"><a class="reference internal nav-link" href="#arbdmodel.shape_cg.ShapeCGFactory.calc_atom_sasa"><code class="docutils literal notranslate"><span class="pre">ShapeCGFactory.calc_atom_sasa()</span></code></a></li>
+<li class="toc-h3 nav-item toc-entry"><a class="reference internal nav-link" href="#arbdmodel.shape_cg.ShapeCGFactory.generate_protein"><code class="docutils literal notranslate"><span class="pre">ShapeCGFactory.generate_protein()</span></code></a></li>
+<li class="toc-h3 nav-item toc-entry"><a class="reference internal nav-link" href="#arbdmodel.shape_cg.ShapeCGFactory.get_coarse_protein"><code class="docutils literal notranslate"><span class="pre">ShapeCGFactory.get_coarse_protein()</span></code></a></li>
+<li class="toc-h3 nav-item toc-entry"><a class="reference internal nav-link" href="#arbdmodel.shape_cg.ShapeCGFactory.get_coarse_types"><code class="docutils literal notranslate"><span class="pre">ShapeCGFactory.get_coarse_types()</span></code></a></li>
+</ul>
+</li>
+<li class="toc-h2 nav-item toc-entry"><a class="reference internal nav-link" href="#arbdmodel.shape_cg.ShapeCGModel"><code class="docutils literal notranslate"><span class="pre">ShapeCGModel</span></code></a><ul class="nav section-nav flex-column">
+<li class="toc-h3 nav-item toc-entry"><a class="reference internal nav-link" href="#arbdmodel.shape_cg.ShapeCGModel.add_confinement"><code class="docutils literal notranslate"><span class="pre">ShapeCGModel.add_confinement()</span></code></a></li>
+<li class="toc-h3 nav-item toc-entry"><a class="reference internal nav-link" href="#arbdmodel.shape_cg.ShapeCGModel.add_protein_nb_interactions"><code class="docutils literal notranslate"><span class="pre">ShapeCGModel.add_protein_nb_interactions()</span></code></a></li>
+<li class="toc-h3 nav-item toc-entry"><a class="reference internal nav-link" href="#arbdmodel.shape_cg.ShapeCGModel.add_proteins"><code class="docutils literal notranslate"><span class="pre">ShapeCGModel.add_proteins()</span></code></a></li>
+<li class="toc-h3 nav-item toc-entry"><a class="reference internal nav-link" href="#arbdmodel.shape_cg.ShapeCGModel.calculate_total_mass"><code class="docutils literal notranslate"><span class="pre">ShapeCGModel.calculate_total_mass()</span></code></a></li>
+<li class="toc-h3 nav-item toc-entry"><a class="reference internal nav-link" href="#arbdmodel.shape_cg.ShapeCGModel.concentration_to_debye_length"><code class="docutils literal notranslate"><span class="pre">ShapeCGModel.concentration_to_debye_length()</span></code></a></li>
+<li class="toc-h3 nav-item toc-entry"><a class="reference internal nav-link" href="#arbdmodel.shape_cg.ShapeCGModel.from_protein_list"><code class="docutils literal notranslate"><span class="pre">ShapeCGModel.from_protein_list()</span></code></a></li>
+<li class="toc-h3 nav-item toc-entry"><a class="reference internal nav-link" href="#arbdmodel.shape_cg.ShapeCGModel.generate_random_protein_positions"><code class="docutils literal notranslate"><span class="pre">ShapeCGModel.generate_random_protein_positions()</span></code></a></li>
+<li class="toc-h3 nav-item toc-entry"><a class="reference internal nav-link" href="#arbdmodel.shape_cg.ShapeCGModel.get_protein_types"><code class="docutils literal notranslate"><span class="pre">ShapeCGModel.get_protein_types()</span></code></a></li>
+<li class="toc-h3 nav-item toc-entry"><a class="reference internal nav-link" href="#arbdmodel.shape_cg.ShapeCGModel.run_from_minimized"><code class="docutils literal notranslate"><span class="pre">ShapeCGModel.run_from_minimized()</span></code></a></li>
+<li class="toc-h3 nav-item toc-entry"><a class="reference internal nav-link" href="#arbdmodel.shape_cg.ShapeCGModel.run_minimization"><code class="docutils literal notranslate"><span class="pre">ShapeCGModel.run_minimization()</span></code></a></li>
+<li class="toc-h3 nav-item toc-entry"><a class="reference internal nav-link" href="#arbdmodel.shape_cg.ShapeCGModel.setup_and_run"><code class="docutils literal notranslate"><span class="pre">ShapeCGModel.setup_and_run()</span></code></a></li>
+</ul>
+</li>
+<li class="toc-h2 nav-item toc-entry"><a class="reference internal nav-link" href="#arbdmodel.shape_cg.ShapeCGNonbonded"><code class="docutils literal notranslate"><span class="pre">ShapeCGNonbonded</span></code></a><ul class="nav section-nav flex-column">
+<li class="toc-h3 nav-item toc-entry"><a class="reference internal nav-link" href="#arbdmodel.shape_cg.ShapeCGNonbonded.filename"><code class="docutils literal notranslate"><span class="pre">ShapeCGNonbonded.filename()</span></code></a></li>
+<li class="toc-h3 nav-item toc-entry"><a class="reference internal nav-link" href="#arbdmodel.shape_cg.ShapeCGNonbonded.potential"><code class="docutils literal notranslate"><span class="pre">ShapeCGNonbonded.potential()</span></code></a></li>
+</ul>
+</li>
<li class="toc-h2 nav-item toc-entry"><a class="reference internal nav-link" href="#arbdmodel.shape_cg.find_shape_based_sites"><code class="docutils literal notranslate"><span class="pre">find_shape_based_sites()</span></code></a></li>
<li class="toc-h2 nav-item toc-entry"><a class="reference internal nav-link" href="#arbdmodel.shape_cg.get_particle_assignments"><code class="docutils literal notranslate"><span class="pre">get_particle_assignments()</span></code></a></li>
+<li class="toc-h2 nav-item toc-entry"><a class="reference internal nav-link" href="#arbdmodel.shape_cg.read_files"><code class="docutils literal notranslate"><span class="pre">read_files()</span></code></a></li>
</ul>
</nav>
</div>
@@ -364,14 +391,379 @@ document.write(`
<p>Shape-based coarse-grained modeling module for protein simulations.</p>
<p>This module provides classes for creating shape-based coarse-grained models
of proteins for use in molecular dynamics simulations.</p>
-<dl class="py function" id="module-arbdmodel.shape_cg">
+<p id="module-arbdmodel.shape_cg">Shape-based coarse-grained modeling module for protein simulations.</p>
+<p>This module provides classes for creating shape-based coarse-grained models
+of proteins for use in molecular dynamics simulations.</p>
+<dl class="py class">
+<dt class="sig sig-object py" id="arbdmodel.shape_cg.ShapeCGFactory">
+<em class="property"><span class="pre">class</span><span class="w"> </span></em><span class="sig-name descname"><span class="pre">ShapeCGFactory</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">psf</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">pdb</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">disordered_residues</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">name</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">'SHCG'</span></span></em><span class="sig-paren">)</span><a class="reference internal" href="../../_modules/arbdmodel/shape_cg.html#ShapeCGFactory"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#arbdmodel.shape_cg.ShapeCGFactory" title="Link to this definition">#</a></dt>
+<dd><p>Bases: <a class="hxr-hoverxref hxr-tooltip reference external" href="https://docs.python.org/3/library/functions.html#object" title="(in Python v3.13)"><code class="xref py py-class docutils literal notranslate"><span class="pre">object</span></code></a></p>
+<p>Factory class for creating coarse-grained protein models.</p>
+<p>This class creates reduced-resolution models of proteins based on
+their shape, with customizable resolution and properties.</p>
+<dl class="py method">
+<dt class="sig sig-object py" id="arbdmodel.shape_cg.ShapeCGFactory.calc_atom_sasa">
+<span class="sig-name descname"><span class="pre">calc_atom_sasa</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">atom_slice</span></span></em><span class="sig-paren">)</span><a class="reference internal" href="../../_modules/arbdmodel/shape_cg.html#ShapeCGFactory.calc_atom_sasa"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#arbdmodel.shape_cg.ShapeCGFactory.calc_atom_sasa" title="Link to this definition">#</a></dt>
+<dd><p>Calculate solvent accessible surface area for atoms.</p>
+<dl class="field-list simple">
+<dt class="field-odd">Parameters<span class="colon">:</span></dt>
+<dd class="field-odd"><p><strong>atom_slice</strong> – Slice or indices for atoms to calculate SASA</p>
+</dd>
+<dt class="field-even">Returns<span class="colon">:</span></dt>
+<dd class="field-even"><p>Tuple of (normalized SASA, atomic radii)</p>
+</dd>
+</dl>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="arbdmodel.shape_cg.ShapeCGFactory.generate_protein">
+<span class="sig-name descname"><span class="pre">generate_protein</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">position</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">orientation</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">index</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">0</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">num_CG_sites</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em><span class="sig-paren">)</span><a class="reference internal" href="../../_modules/arbdmodel/shape_cg.html#ShapeCGFactory.generate_protein"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#arbdmodel.shape_cg.ShapeCGFactory.generate_protein" title="Link to this definition">#</a></dt>
+<dd><p>Generate a new protein instance at the specified position and orientation.</p>
+<dl class="field-list simple">
+<dt class="field-odd">Parameters<span class="colon">:</span></dt>
+<dd class="field-odd"><ul class="simple">
+<li><p><strong>position</strong> – 3D position for the protein</p></li>
+<li><p><strong>orientation</strong> – Optional orientation matrix</p></li>
+<li><p><strong>index</strong> – Unique index for this protein instance</p></li>
+<li><p><strong>num_CG_sites</strong> – Number of CG sites to use</p></li>
+</ul>
+</dd>
+<dt class="field-even">Returns<span class="colon">:</span></dt>
+<dd class="field-even"><p>Group containing the positioned protein</p>
+</dd>
+</dl>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="arbdmodel.shape_cg.ShapeCGFactory.get_coarse_protein">
+<span class="sig-name descname"><span class="pre">get_coarse_protein</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">num_CG_sites</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em><span class="sig-paren">)</span><a class="reference internal" href="../../_modules/arbdmodel/shape_cg.html#ShapeCGFactory.get_coarse_protein"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#arbdmodel.shape_cg.ShapeCGFactory.get_coarse_protein" title="Link to this definition">#</a></dt>
+<dd><p>Generate a coarse-grained protein model.</p>
+<dl class="field-list simple">
+<dt class="field-odd">Parameters<span class="colon">:</span></dt>
+<dd class="field-odd"><p><strong>num_CG_sites</strong> – Number of sites to represent the protein (default: based on mass)</p>
+</dd>
+<dt class="field-even">Returns<span class="colon">:</span></dt>
+<dd class="field-even"><p>Group containing the coarse-grained protein</p>
+</dd>
+</dl>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="arbdmodel.shape_cg.ShapeCGFactory.get_coarse_types">
+<span class="sig-name descname"><span class="pre">get_coarse_types</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">num_CG_sites</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em><span class="sig-paren">)</span><a class="reference internal" href="../../_modules/arbdmodel/shape_cg.html#ShapeCGFactory.get_coarse_types"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#arbdmodel.shape_cg.ShapeCGFactory.get_coarse_types" title="Link to this definition">#</a></dt>
+<dd><p>Get particle types used in the coarse-grained model.</p>
+<dl class="field-list simple">
+<dt class="field-odd">Parameters<span class="colon">:</span></dt>
+<dd class="field-odd"><p><strong>num_CG_sites</strong> – Number of sites to represent the protein</p>
+</dd>
+<dt class="field-even">Returns<span class="colon">:</span></dt>
+<dd class="field-even"><p>List of ParticleType objects</p>
+</dd>
+</dl>
+</dd></dl>
+
+</dd></dl>
+
+<dl class="py class">
+<dt class="sig sig-object py" id="arbdmodel.shape_cg.ShapeCGModel">
+<em class="property"><span class="pre">class</span><span class="w"> </span></em><span class="sig-name descname"><span class="pre">ShapeCGModel</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">protein_factories</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">box_size</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="o"><span class="pre">**</span></span><span class="n"><span class="pre">kwargs</span></span></em><span class="sig-paren">)</span><a class="reference internal" href="../../_modules/arbdmodel/shape_cg.html#ShapeCGModel"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#arbdmodel.shape_cg.ShapeCGModel" title="Link to this definition">#</a></dt>
+<dd><p>Bases: <a class="reference internal" href="../core/model.html#arbdmodel.model.ArbdModel" title="arbdmodel.model.ArbdModel"><code class="xref py py-class docutils literal notranslate"><span class="pre">ArbdModel</span></code></a></p>
+<p>Model class for shape-based coarse-grained protein simulations.</p>
+<p>This class handles creating and simulating systems with multiple
+shape-based coarse-grained proteins.</p>
+<dl class="py method">
+<dt class="sig sig-object py" id="arbdmodel.shape_cg.ShapeCGModel.add_confinement">
+<span class="sig-name descname"><span class="pre">add_confinement</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">protein_group</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">radius</span></span></em><span class="sig-paren">)</span><a class="reference internal" href="../../_modules/arbdmodel/shape_cg.html#ShapeCGModel.add_confinement"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#arbdmodel.shape_cg.ShapeCGModel.add_confinement" title="Link to this definition">#</a></dt>
+<dd><p>Add spherical confinement to all protein particles.</p>
+<dl class="field-list simple">
+<dt class="field-odd">Parameters<span class="colon">:</span></dt>
+<dd class="field-odd"><ul class="simple">
+<li><p><strong>protein_group</strong> – Group containing proteins</p></li>
+<li><p><strong>radius</strong> – Confinement radius</p></li>
+</ul>
+</dd>
+</dl>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="arbdmodel.shape_cg.ShapeCGModel.add_protein_nb_interactions">
+<span class="sig-name descname"><span class="pre">add_protein_nb_interactions</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">prot_types</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">nt_sigma</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">10</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">debye_length</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em><span class="sig-paren">)</span><a class="reference internal" href="../../_modules/arbdmodel/shape_cg.html#ShapeCGModel.add_protein_nb_interactions"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#arbdmodel.shape_cg.ShapeCGModel.add_protein_nb_interactions" title="Link to this definition">#</a></dt>
+<dd><p>Add nonbonded interactions between protein particles.</p>
+<dl class="field-list simple">
+<dt class="field-odd">Parameters<span class="colon">:</span></dt>
+<dd class="field-odd"><ul class="simple">
+<li><p><strong>prot_types</strong> – List of protein particle types</p></li>
+<li><p><strong>nt_sigma</strong> – Sigma parameter for nucleic acid interactions</p></li>
+<li><p><strong>debye_length</strong> – Debye length for electrostatics (default: calculated from 150 mM)</p></li>
+</ul>
+</dd>
+</dl>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="arbdmodel.shape_cg.ShapeCGModel.add_proteins">
+<span class="sig-name descname"><span class="pre">add_proteins</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">protein_counts</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">protein_positions</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">num_CG_sites</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">nt_sigma</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">10</span></span></em><span class="sig-paren">)</span><a class="reference internal" href="../../_modules/arbdmodel/shape_cg.html#ShapeCGModel.add_proteins"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#arbdmodel.shape_cg.ShapeCGModel.add_proteins" title="Link to this definition">#</a></dt>
+<dd><p>Add proteins to the simulation model.</p>
+<dl class="field-list simple">
+<dt class="field-odd">Parameters<span class="colon">:</span></dt>
+<dd class="field-odd"><ul class="simple">
+<li><p><strong>protein_counts</strong> – Dictionary mapping protein names to counts</p></li>
+<li><p><strong>protein_positions</strong> – List of positions for all proteins</p></li>
+<li><p><strong>num_CG_sites</strong> – Number of CG sites per protein</p></li>
+<li><p><strong>nt_sigma</strong> – Sigma parameter for nucleic acid interactions</p></li>
+</ul>
+</dd>
+<dt class="field-even">Returns<span class="colon">:</span></dt>
+<dd class="field-even"><p>Group containing all added proteins</p>
+</dd>
+</dl>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="arbdmodel.shape_cg.ShapeCGModel.calculate_total_mass">
+<span class="sig-name descname"><span class="pre">calculate_total_mass</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">protein_counts</span></span></em><span class="sig-paren">)</span><a class="reference internal" href="../../_modules/arbdmodel/shape_cg.html#ShapeCGModel.calculate_total_mass"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#arbdmodel.shape_cg.ShapeCGModel.calculate_total_mass" title="Link to this definition">#</a></dt>
+<dd><p>Calculate total mass of proteins.</p>
+<dl class="field-list simple">
+<dt class="field-odd">Parameters<span class="colon">:</span></dt>
+<dd class="field-odd"><p><strong>protein_counts</strong> – Dictionary mapping protein names to counts</p>
+</dd>
+<dt class="field-even">Returns<span class="colon">:</span></dt>
+<dd class="field-even"><p>Total mass in daltons</p>
+</dd>
+</dl>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="arbdmodel.shape_cg.ShapeCGModel.concentration_to_debye_length">
+<span class="sig-name descname"><span class="pre">concentration_to_debye_length</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">c</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">temperature</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">295</span></span></em><span class="sig-paren">)</span><a class="reference internal" href="../../_modules/arbdmodel/shape_cg.html#ShapeCGModel.concentration_to_debye_length"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#arbdmodel.shape_cg.ShapeCGModel.concentration_to_debye_length" title="Link to this definition">#</a></dt>
+<dd><p>Convert salt concentration to Debye length.</p>
+<dl class="field-list simple">
+<dt class="field-odd">Parameters<span class="colon">:</span></dt>
+<dd class="field-odd"><ul class="simple">
+<li><p><strong>c</strong> – Salt concentration in mM</p></li>
+<li><p><strong>temperature</strong> – Temperature in K</p></li>
+</ul>
+</dd>
+<dt class="field-even">Returns<span class="colon">:</span></dt>
+<dd class="field-even"><p>Debye length in Angstroms</p>
+</dd>
+</dl>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="arbdmodel.shape_cg.ShapeCGModel.from_protein_list">
+<em class="property"><span class="pre">classmethod</span><span class="w"> </span></em><span class="sig-name descname"><span class="pre">from_protein_list</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">pdb_list</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">pdb_paths</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="o"><span class="pre">**</span></span><span class="n"><span class="pre">kwargs</span></span></em><span class="sig-paren">)</span><a class="reference internal" href="../../_modules/arbdmodel/shape_cg.html#ShapeCGModel.from_protein_list"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#arbdmodel.shape_cg.ShapeCGModel.from_protein_list" title="Link to this definition">#</a></dt>
+<dd><p>Create a model from a list of protein PDB IDs.</p>
+<dl class="field-list simple">
+<dt class="field-odd">Parameters<span class="colon">:</span></dt>
+<dd class="field-odd"><ul class="simple">
+<li><p><strong>pdb_list</strong> – List of protein PDB IDs</p></li>
+<li><p><strong>pdb_paths</strong> – Optional dictionary mapping PDB IDs to PSF/PDB file paths</p></li>
+<li><p><strong>**kwargs</strong> – Additional arguments for the ShapeCGModel constructor</p></li>
+</ul>
+</dd>
+<dt class="field-even">Returns<span class="colon">:</span></dt>
+<dd class="field-even"><p>ShapeCGModel instance</p>
+</dd>
+</dl>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="arbdmodel.shape_cg.ShapeCGModel.generate_random_protein_positions">
+<span class="sig-name descname"><span class="pre">generate_random_protein_positions</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">protein_counts</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">radius</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">seed</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em><span class="sig-paren">)</span><a class="reference internal" href="../../_modules/arbdmodel/shape_cg.html#ShapeCGModel.generate_random_protein_positions"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#arbdmodel.shape_cg.ShapeCGModel.generate_random_protein_positions" title="Link to this definition">#</a></dt>
+<dd><p>Generate random positions for proteins within a spherical volume.</p>
+<dl class="field-list simple">
+<dt class="field-odd">Parameters<span class="colon">:</span></dt>
+<dd class="field-odd"><ul class="simple">
+<li><p><strong>protein_counts</strong> – Dictionary mapping protein names to counts</p></li>
+<li><p><strong>radius</strong> – Radius of the sphere</p></li>
+<li><p><strong>seed</strong> – Random seed (default: None)</p></li>
+</ul>
+</dd>
+<dt class="field-even">Returns<span class="colon">:</span></dt>
+<dd class="field-even"><p>List of 3D positions</p>
+</dd>
+</dl>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="arbdmodel.shape_cg.ShapeCGModel.get_protein_types">
+<span class="sig-name descname"><span class="pre">get_protein_types</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">protein_counts</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">num_CG_sites</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em><span class="sig-paren">)</span><a class="reference internal" href="../../_modules/arbdmodel/shape_cg.html#ShapeCGModel.get_protein_types"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#arbdmodel.shape_cg.ShapeCGModel.get_protein_types" title="Link to this definition">#</a></dt>
+<dd><p>Get all protein types for the given protein counts.</p>
+<dl class="field-list simple">
+<dt class="field-odd">Parameters<span class="colon">:</span></dt>
+<dd class="field-odd"><ul class="simple">
+<li><p><strong>protein_counts</strong> – Dictionary mapping protein names to counts</p></li>
+<li><p><strong>num_CG_sites</strong> – Number of CG sites per protein</p></li>
+</ul>
+</dd>
+<dt class="field-even">Returns<span class="colon">:</span></dt>
+<dd class="field-even"><p>List of all protein particle types</p>
+</dd>
+</dl>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="arbdmodel.shape_cg.ShapeCGModel.run_from_minimized">
+<span class="sig-name descname"><span class="pre">run_from_minimized</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">protein_counts</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">radius</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">200</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">num_CG_sites</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">salt_concentration</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">150</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">gpu</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">0</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">dry_run</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">True</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">num_steps</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">100000000.0</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">output_period</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">10000.0</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">timestep</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">0.0002</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">minimization_file</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em><span class="sig-paren">)</span><a class="reference internal" href="../../_modules/arbdmodel/shape_cg.html#ShapeCGModel.run_from_minimized"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#arbdmodel.shape_cg.ShapeCGModel.run_from_minimized" title="Link to this definition">#</a></dt>
+<dd><p>Run a full simulation starting from a minimized configuration.</p>
+<dl class="field-list simple">
+<dt class="field-odd">Parameters<span class="colon">:</span></dt>
+<dd class="field-odd"><ul class="simple">
+<li><p><strong>protein_counts</strong> – Dictionary mapping protein names to counts</p></li>
+<li><p><strong>radius</strong> – Confinement radius</p></li>
+<li><p><strong>num_CG_sites</strong> – Number of CG sites per protein</p></li>
+<li><p><strong>salt_concentration</strong> – Salt concentration in mM</p></li>
+<li><p><strong>gpu</strong> – GPU index to use</p></li>
+<li><p><strong>dry_run</strong> – If True, don’t actually run the simulation</p></li>
+<li><p><strong>num_steps</strong> – Number of simulation steps</p></li>
+<li><p><strong>output_period</strong> – Steps between outputs</p></li>
+<li><p><strong>timestep</strong> – Simulation timestep</p></li>
+<li><p><strong>minimization_file</strong> – Path to minimization restart file</p></li>
+</ul>
+</dd>
+<dt class="field-even">Returns<span class="colon">:</span></dt>
+<dd class="field-even"><p>Final simulation state</p>
+</dd>
+</dl>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="arbdmodel.shape_cg.ShapeCGModel.run_minimization">
+<span class="sig-name descname"><span class="pre">run_minimization</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">protein_counts</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">radius</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">200</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">gpu</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">0</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">num_steps</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">100000.0</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">output_period</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">10000.0</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">timestep</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">0.0002</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">directory</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">'run_1'</span></span></em><span class="sig-paren">)</span><a class="reference internal" href="../../_modules/arbdmodel/shape_cg.html#ShapeCGModel.run_minimization"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#arbdmodel.shape_cg.ShapeCGModel.run_minimization" title="Link to this definition">#</a></dt>
+<dd><p>Run a minimization simulation with minimal CG sites.</p>
+<dl class="field-list simple">
+<dt class="field-odd">Parameters<span class="colon">:</span></dt>
+<dd class="field-odd"><ul class="simple">
+<li><p><strong>protein_counts</strong> – Dictionary mapping protein names to counts</p></li>
+<li><p><strong>radius</strong> – Confinement radius</p></li>
+<li><p><strong>gpu</strong> – GPU index to use</p></li>
+<li><p><strong>num_steps</strong> – Number of minimization steps</p></li>
+<li><p><strong>output_period</strong> – Steps between outputs</p></li>
+<li><p><strong>timestep</strong> – Simulation timestep</p></li>
+<li><p><strong>directory</strong> – Output directory</p></li>
+</ul>
+</dd>
+<dt class="field-even">Returns<span class="colon">:</span></dt>
+<dd class="field-even"><p>Path to restart file</p>
+</dd>
+</dl>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="arbdmodel.shape_cg.ShapeCGModel.setup_and_run">
+<span class="sig-name descname"><span class="pre">setup_and_run</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">protein_counts</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">radius</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">200</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">num_CG_sites</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">salt_concentration</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">150</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">gpu</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">0</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">dry_run</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">True</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">num_steps</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">100000000.0</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">output_period</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">10000.0</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">timestep</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">0.0002</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">positions</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">restart_file</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em><span class="sig-paren">)</span><a class="reference internal" href="../../_modules/arbdmodel/shape_cg.html#ShapeCGModel.setup_and_run"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#arbdmodel.shape_cg.ShapeCGModel.setup_and_run" title="Link to this definition">#</a></dt>
+<dd><p>Set up and run a simulation with the specified parameters.</p>
+<dl class="field-list simple">
+<dt class="field-odd">Parameters<span class="colon">:</span></dt>
+<dd class="field-odd"><ul class="simple">
+<li><p><strong>protein_counts</strong> – Dictionary mapping protein names to counts</p></li>
+<li><p><strong>radius</strong> – Confinement radius</p></li>
+<li><p><strong>num_CG_sites</strong> – Number of CG sites per protein</p></li>
+<li><p><strong>salt_concentration</strong> – Salt concentration in mM</p></li>
+<li><p><strong>gpu</strong> – GPU index to use</p></li>
+<li><p><strong>dry_run</strong> – If True, don’t actually run the simulation</p></li>
+<li><p><strong>num_steps</strong> – Number of simulation steps</p></li>
+<li><p><strong>output_period</strong> – Steps between outputs</p></li>
+<li><p><strong>timestep</strong> – Simulation timestep</p></li>
+<li><p><strong>positions</strong> – Optional pre-defined positions for proteins</p></li>
+<li><p><strong>restart_file</strong> – Optional restart file path</p></li>
+</ul>
+</dd>
+<dt class="field-even">Returns<span class="colon">:</span></dt>
+<dd class="field-even"><p>Final simulation state</p>
+</dd>
+</dl>
+</dd></dl>
+
+</dd></dl>
+
+<dl class="py class">
+<dt class="sig sig-object py" id="arbdmodel.shape_cg.ShapeCGNonbonded">
+<em class="property"><span class="pre">class</span><span class="w"> </span></em><span class="sig-name descname"><span class="pre">ShapeCGNonbonded</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">debye_length</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">10</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">resolution</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">0.3</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">rMin</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">5</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">range_</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">(0,</span> <span class="pre">50)</span></span></em>, <em class="sig-param"><span class="o"><span class="pre">**</span></span><span class="n"><span class="pre">kwargs</span></span></em><span class="sig-paren">)</span><a class="reference internal" href="../../_modules/arbdmodel/shape_cg.html#ShapeCGNonbonded"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#arbdmodel.shape_cg.ShapeCGNonbonded" title="Link to this definition">#</a></dt>
+<dd><p>Bases: <a class="reference internal" href="../interaction_potentials/interactions.html#arbdmodel.interactions.AbstractPotential" title="arbdmodel.interactions.AbstractPotential"><code class="xref py py-class docutils literal notranslate"><span class="pre">AbstractPotential</span></code></a></p>
+<p>Nonbonded potential for shape-based coarse grained models.</p>
+<p>The potential includes electrostatic and Lennard-Jones components.</p>
+<dl class="py method">
+<dt class="sig sig-object py" id="arbdmodel.shape_cg.ShapeCGNonbonded.filename">
+<span class="sig-name descname"><span class="pre">filename</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">types</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em><span class="sig-paren">)</span><a class="reference internal" href="../../_modules/arbdmodel/shape_cg.html#ShapeCGNonbonded.filename"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#arbdmodel.shape_cg.ShapeCGNonbonded.filename" title="Link to this definition">#</a></dt>
+<dd><p>Get filename for potential lookup table.</p>
+<dl class="field-list simple">
+<dt class="field-odd">Parameters<span class="colon">:</span></dt>
+<dd class="field-odd"><p><strong>types</strong> – Tuple of particle types</p>
+</dd>
+<dt class="field-even">Returns<span class="colon">:</span></dt>
+<dd class="field-even"><p>Filename string</p>
+</dd>
+</dl>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="arbdmodel.shape_cg.ShapeCGNonbonded.potential">
+<span class="sig-name descname"><span class="pre">potential</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">r</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">types</span></span></em><span class="sig-paren">)</span><a class="reference internal" href="../../_modules/arbdmodel/shape_cg.html#ShapeCGNonbonded.potential"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#arbdmodel.shape_cg.ShapeCGNonbonded.potential" title="Link to this definition">#</a></dt>
+<dd><p>Calculate the potential energy at distance r.</p>
+<dl class="field-list simple">
+<dt class="field-odd">Parameters<span class="colon">:</span></dt>
+<dd class="field-odd"><ul class="simple">
+<li><p><strong>r</strong> – Array of distances</p></li>
+<li><p><strong>types</strong> – Tuple of (typeA, typeB) particle types</p></li>
+</ul>
+</dd>
+<dt class="field-even">Returns<span class="colon">:</span></dt>
+<dd class="field-even"><p>Array of potential energies</p>
+</dd>
+</dl>
+</dd></dl>
+
+</dd></dl>
+
+<dl class="py function">
<dt class="sig sig-object py" id="arbdmodel.shape_cg.find_shape_based_sites">
<span class="sig-name descname"><span class="pre">find_shape_based_sites</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">fine_positions</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">N_cg</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">num_steps</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">learning_schedule</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">weights</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">seed</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">1234</span></span></em><span class="sig-paren">)</span><a class="reference internal" href="../../_modules/arbdmodel/shape_cg.html#find_shape_based_sites"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#arbdmodel.shape_cg.find_shape_based_sites" title="Link to this definition">#</a></dt>
-<dd></dd></dl>
+<dd><p>Find optimal placement of coarse-grained sites based on structure shape.</p>
+<p>This function uses a competitive learning algorithm to determine optimal
+placement of coarse-grained sites within a molecular structure, considering
+both geometry and optional weights (like atom masses).</p>
+<dl class="field-list simple">
+<dt class="field-odd">Parameters<span class="colon">:</span></dt>
+<dd class="field-odd"><ul class="simple">
+<li><p><strong>fine_positions</strong> – Array of atomic positions, shape (n_atoms, 3)</p></li>
+<li><p><strong>N_cg</strong> – Number of coarse-grained sites to create</p></li>
+<li><p><strong>num_steps</strong> – Number of learning steps (default: 400*N_cg)</p></li>
+<li><p><strong>learning_schedule</strong> – Custom schedule for learning parameters (default: None)</p></li>
+<li><p><strong>weights</strong> – Optional weights for each atom (default: uniform)</p></li>
+<li><p><strong>seed</strong> – Random seed for reproducibility</p></li>
+</ul>
+</dd>
+<dt class="field-even">Returns<span class="colon">:</span></dt>
+<dd class="field-even"><p>Array of positions for coarse-grained sites, shape (N_cg, 3)</p>
+</dd>
+</dl>
+</dd></dl>
<dl class="py function">
<dt class="sig sig-object py" id="arbdmodel.shape_cg.get_particle_assignments">
<span class="sig-name descname"><span class="pre">get_particle_assignments</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">fine_sites</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">coarse_sites</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">max_distance</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">20</span></span></em><span class="sig-paren">)</span><a class="reference internal" href="../../_modules/arbdmodel/shape_cg.html#get_particle_assignments"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#arbdmodel.shape_cg.get_particle_assignments" title="Link to this definition">#</a></dt>
+<dd><p>Assign fine-grained particles to coarse-grained sites.</p>
+<p>This function maps each atom to its closest coarse-grained site,
+using a KD-tree for efficient distance calculations.</p>
+<dl class="field-list simple">
+<dt class="field-odd">Parameters<span class="colon">:</span></dt>
+<dd class="field-odd"><ul class="simple">
+<li><p><strong>fine_sites</strong> – Array of atomic positions, shape (n_atoms, 3)</p></li>
+<li><p><strong>coarse_sites</strong> – Array of coarse-grained site positions, shape (n_cg, 3)</p></li>
+<li><p><strong>max_distance</strong> – Maximum distance to consider for assignments</p></li>
+</ul>
+</dd>
+<dt class="field-even">Returns<span class="colon">:</span></dt>
+<dd class="field-even"><p>Array of assignments, indicating which CG site each atom belongs to</p>
+</dd>
+</dl>
+</dd></dl>
+
+<dl class="py function">
+<dt class="sig sig-object py" id="arbdmodel.shape_cg.read_files">
+<span class="sig-name descname"><span class="pre">read_files</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">psf</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">pdb</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">parameter_files</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">system_type</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">'charmm'</span></span></em><span class="sig-paren">)</span><a class="reference internal" href="../../_modules/arbdmodel/shape_cg.html#read_files"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#arbdmodel.shape_cg.read_files" title="Link to this definition">#</a></dt>
<dd></dd></dl>
</section>
@@ -422,8 +814,35 @@ of proteins for use in molecular dynamics simulations.</p>
</div>
<nav class="bd-toc-nav page-toc">
<ul class="visible nav section-nav flex-column">
+<li class="toc-h2 nav-item toc-entry"><a class="reference internal nav-link" href="#arbdmodel.shape_cg.ShapeCGFactory"><code class="docutils literal notranslate"><span class="pre">ShapeCGFactory</span></code></a><ul class="nav section-nav flex-column">
+<li class="toc-h3 nav-item toc-entry"><a class="reference internal nav-link" href="#arbdmodel.shape_cg.ShapeCGFactory.calc_atom_sasa"><code class="docutils literal notranslate"><span class="pre">ShapeCGFactory.calc_atom_sasa()</span></code></a></li>
+<li class="toc-h3 nav-item toc-entry"><a class="reference internal nav-link" href="#arbdmodel.shape_cg.ShapeCGFactory.generate_protein"><code class="docutils literal notranslate"><span class="pre">ShapeCGFactory.generate_protein()</span></code></a></li>
+<li class="toc-h3 nav-item toc-entry"><a class="reference internal nav-link" href="#arbdmodel.shape_cg.ShapeCGFactory.get_coarse_protein"><code class="docutils literal notranslate"><span class="pre">ShapeCGFactory.get_coarse_protein()</span></code></a></li>
+<li class="toc-h3 nav-item toc-entry"><a class="reference internal nav-link" href="#arbdmodel.shape_cg.ShapeCGFactory.get_coarse_types"><code class="docutils literal notranslate"><span class="pre">ShapeCGFactory.get_coarse_types()</span></code></a></li>
+</ul>
+</li>
+<li class="toc-h2 nav-item toc-entry"><a class="reference internal nav-link" href="#arbdmodel.shape_cg.ShapeCGModel"><code class="docutils literal notranslate"><span class="pre">ShapeCGModel</span></code></a><ul class="nav section-nav flex-column">
+<li class="toc-h3 nav-item toc-entry"><a class="reference internal nav-link" href="#arbdmodel.shape_cg.ShapeCGModel.add_confinement"><code class="docutils literal notranslate"><span class="pre">ShapeCGModel.add_confinement()</span></code></a></li>
+<li class="toc-h3 nav-item toc-entry"><a class="reference internal nav-link" href="#arbdmodel.shape_cg.ShapeCGModel.add_protein_nb_interactions"><code class="docutils literal notranslate"><span class="pre">ShapeCGModel.add_protein_nb_interactions()</span></code></a></li>
+<li class="toc-h3 nav-item toc-entry"><a class="reference internal nav-link" href="#arbdmodel.shape_cg.ShapeCGModel.add_proteins"><code class="docutils literal notranslate"><span class="pre">ShapeCGModel.add_proteins()</span></code></a></li>
+<li class="toc-h3 nav-item toc-entry"><a class="reference internal nav-link" href="#arbdmodel.shape_cg.ShapeCGModel.calculate_total_mass"><code class="docutils literal notranslate"><span class="pre">ShapeCGModel.calculate_total_mass()</span></code></a></li>
+<li class="toc-h3 nav-item toc-entry"><a class="reference internal nav-link" href="#arbdmodel.shape_cg.ShapeCGModel.concentration_to_debye_length"><code class="docutils literal notranslate"><span class="pre">ShapeCGModel.concentration_to_debye_length()</span></code></a></li>
+<li class="toc-h3 nav-item toc-entry"><a class="reference internal nav-link" href="#arbdmodel.shape_cg.ShapeCGModel.from_protein_list"><code class="docutils literal notranslate"><span class="pre">ShapeCGModel.from_protein_list()</span></code></a></li>
+<li class="toc-h3 nav-item toc-entry"><a class="reference internal nav-link" href="#arbdmodel.shape_cg.ShapeCGModel.generate_random_protein_positions"><code class="docutils literal notranslate"><span class="pre">ShapeCGModel.generate_random_protein_positions()</span></code></a></li>
+<li class="toc-h3 nav-item toc-entry"><a class="reference internal nav-link" href="#arbdmodel.shape_cg.ShapeCGModel.get_protein_types"><code class="docutils literal notranslate"><span class="pre">ShapeCGModel.get_protein_types()</span></code></a></li>
+<li class="toc-h3 nav-item toc-entry"><a class="reference internal nav-link" href="#arbdmodel.shape_cg.ShapeCGModel.run_from_minimized"><code class="docutils literal notranslate"><span class="pre">ShapeCGModel.run_from_minimized()</span></code></a></li>
+<li class="toc-h3 nav-item toc-entry"><a class="reference internal nav-link" href="#arbdmodel.shape_cg.ShapeCGModel.run_minimization"><code class="docutils literal notranslate"><span class="pre">ShapeCGModel.run_minimization()</span></code></a></li>
+<li class="toc-h3 nav-item toc-entry"><a class="reference internal nav-link" href="#arbdmodel.shape_cg.ShapeCGModel.setup_and_run"><code class="docutils literal notranslate"><span class="pre">ShapeCGModel.setup_and_run()</span></code></a></li>
+</ul>
+</li>
+<li class="toc-h2 nav-item toc-entry"><a class="reference internal nav-link" href="#arbdmodel.shape_cg.ShapeCGNonbonded"><code class="docutils literal notranslate"><span class="pre">ShapeCGNonbonded</span></code></a><ul class="nav section-nav flex-column">
+<li class="toc-h3 nav-item toc-entry"><a class="reference internal nav-link" href="#arbdmodel.shape_cg.ShapeCGNonbonded.filename"><code class="docutils literal notranslate"><span class="pre">ShapeCGNonbonded.filename()</span></code></a></li>
+<li class="toc-h3 nav-item toc-entry"><a class="reference internal nav-link" href="#arbdmodel.shape_cg.ShapeCGNonbonded.potential"><code class="docutils literal notranslate"><span class="pre">ShapeCGNonbonded.potential()</span></code></a></li>
+</ul>
+</li>
<li class="toc-h2 nav-item toc-entry"><a class="reference internal nav-link" href="#arbdmodel.shape_cg.find_shape_based_sites"><code class="docutils literal notranslate"><span class="pre">find_shape_based_sites()</span></code></a></li>
<li class="toc-h2 nav-item toc-entry"><a class="reference internal nav-link" href="#arbdmodel.shape_cg.get_particle_assignments"><code class="docutils literal notranslate"><span class="pre">get_particle_assignments()</span></code></a></li>
+<li class="toc-h2 nav-item toc-entry"><a class="reference internal nav-link" href="#arbdmodel.shape_cg.read_files"><code class="docutils literal notranslate"><span class="pre">read_files()</span></code></a></li>
</ul>
</nav></div>
diff --git a/_build/html/api/simulation_engines/engine.html b/_build/html/api/simulation_engines/engine.html
index 44f15561f3a4cde819dc9ec62ac2142b14e9ba73..b963931b11a8ba59cffe1329d112f0f273c932cb 100644
--- a/_build/html/api/simulation_engines/engine.html
+++ b/_build/html/api/simulation_engines/engine.html
@@ -32,19 +32,19 @@
<link rel="stylesheet" type="text/css" href="../../_static/styles/sphinx-book-theme.css?v=eba8b062" />
<link rel="stylesheet" type="text/css" href="../../_static/togglebutton.css?v=13237357" />
<link rel="stylesheet" type="text/css" href="../../_static/copybutton.css?v=76b2166b" />
- <link rel="stylesheet" type="text/css" href="../../_static/mystnb.4510f1fc1dee50b3e5859aac5469c37c29e427902b24a333a5f9fcb2f0b3ac41.css" />
+ <link rel="stylesheet" type="text/css" href="../../_static/mystnb.4510f1fc1dee50b3e5859aac5469c37c29e427902b24a333a5f9fcb2f0b3ac41.css?v=be8a1c11" />
<link rel="stylesheet" type="text/css" href="../../_static/sphinx-thebe.css?v=4fa983c6" />
<link rel="stylesheet" type="text/css" href="../../_static/tabs.css?v=4c969af8" />
- <link rel="stylesheet" type="text/css" href="../../_static/proof.css" />
+ <link rel="stylesheet" type="text/css" href="../../_static/proof.css?v=b4b7a797" />
<link rel="stylesheet" type="text/css" href="../../_static/styles/sphinx-examples.css?v=e236af4b" />
- <link rel="stylesheet" type="text/css" href="../../_static/css/tooltipster.custom.css" />
- <link rel="stylesheet" type="text/css" href="../../_static/css/tooltipster.bundle.min.css" />
- <link rel="stylesheet" type="text/css" href="../../_static/css/tooltipster-sideTip-shadow.min.css" />
- <link rel="stylesheet" type="text/css" href="../../_static/css/tooltipster-sideTip-punk.min.css" />
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- <link rel="stylesheet" type="text/css" href="../../_static/css/tooltipster-sideTip-light.min.css" />
- <link rel="stylesheet" type="text/css" href="../../_static/css/tooltipster-sideTip-borderless.min.css" />
- <link rel="stylesheet" type="text/css" href="../../_static/css/micromodal.css" />
+ <link rel="stylesheet" type="text/css" href="../../_static/css/tooltipster.custom.css?v=7bc2f056" />
+ <link rel="stylesheet" type="text/css" href="../../_static/css/tooltipster.bundle.min.css?v=37217874" />
+ <link rel="stylesheet" type="text/css" href="../../_static/css/tooltipster-sideTip-shadow.min.css?v=6227e517" />
+ <link rel="stylesheet" type="text/css" href="../../_static/css/tooltipster-sideTip-punk.min.css?v=94669e23" />
+ <link rel="stylesheet" type="text/css" href="../../_static/css/tooltipster-sideTip-noir.min.css?v=21a39f42" />
+ <link rel="stylesheet" type="text/css" href="../../_static/css/tooltipster-sideTip-light.min.css?v=a18b2449" />
+ <link rel="stylesheet" type="text/css" href="../../_static/css/tooltipster-sideTip-borderless.min.css?v=dbff53e4" />
+ <link rel="stylesheet" type="text/css" href="../../_static/css/micromodal.css?v=d7bf34ee" />
<link rel="stylesheet" type="text/css" href="../../_static/sphinx-design.min.css?v=95c83b7e" />
<!-- Pre-loaded scripts that we'll load fully later -->
@@ -61,9 +61,9 @@
<script src="../../_static/copybutton.js?v=f281be69"></script>
<script src="../../_static/scripts/sphinx-book-theme.js?v=887ef09a"></script>
<script src="../../_static/tabs.js?v=3ee01567"></script>
- <script src="../../_static/js/hoverxref.js"></script>
- <script src="../../_static/js/tooltipster.bundle.min.js"></script>
- <script src="../../_static/js/micromodal.min.js"></script>
+ <script src="../../_static/js/hoverxref.js?v=c95ade4f"></script>
+ <script src="../../_static/js/tooltipster.bundle.min.js?v=18bf091b"></script>
+ <script src="../../_static/js/micromodal.min.js?v=04d6302d"></script>
<script>let toggleHintShow = 'Click to show';</script>
<script>let toggleHintHide = 'Click to hide';</script>
<script>let toggleOpenOnPrint = 'true';</script>
@@ -323,7 +323,9 @@ document.write(`
</button>
`);
</script>
-
+<button class="sidebar-toggle secondary-toggle btn btn-sm" title="Toggle secondary sidebar" data-bs-placement="bottom" data-bs-toggle="tooltip">
+ <span class="fa-solid fa-list"></span>
+</button>
</div></div>
</div>
@@ -339,6 +341,44 @@ document.write(`
<div id="print-main-content">
<div id="jb-print-toc">
+ <div>
+ <h2> Contents </h2>
+ </div>
+ <nav aria-label="Page">
+ <ul class="visible nav section-nav flex-column">
+<li class="toc-h2 nav-item toc-entry"><a class="reference internal nav-link" href="#arbdmodel.engine.APBSRunner"><code class="docutils literal notranslate"><span class="pre">APBSRunner</span></code></a><ul class="nav section-nav flex-column">
+<li class="toc-h3 nav-item toc-entry"><a class="reference internal nav-link" href="#arbdmodel.engine.APBSRunner.run_calculation"><code class="docutils literal notranslate"><span class="pre">APBSRunner.run_calculation()</span></code></a></li>
+<li class="toc-h3 nav-item toc-entry"><a class="reference internal nav-link" href="#arbdmodel.engine.APBSRunner.write_config"><code class="docutils literal notranslate"><span class="pre">APBSRunner.write_config()</span></code></a></li>
+</ul>
+</li>
+<li class="toc-h2 nav-item toc-entry"><a class="reference internal nav-link" href="#arbdmodel.engine.ArbdEngine"><code class="docutils literal notranslate"><span class="pre">ArbdEngine</span></code></a><ul class="nav section-nav flex-column">
+<li class="toc-h3 nav-item toc-entry"><a class="reference internal nav-link" href="#arbdmodel.engine.ArbdEngine.default_binary"><code class="docutils literal notranslate"><span class="pre">ArbdEngine.default_binary</span></code></a></li>
+<li class="toc-h3 nav-item toc-entry"><a class="reference internal nav-link" href="#arbdmodel.engine.ArbdEngine.get_default_conf"><code class="docutils literal notranslate"><span class="pre">ArbdEngine.get_default_conf()</span></code></a></li>
+<li class="toc-h3 nav-item toc-entry"><a class="reference internal nav-link" href="#arbdmodel.engine.ArbdEngine.write_simulation_files"><code class="docutils literal notranslate"><span class="pre">ArbdEngine.write_simulation_files()</span></code></a></li>
+</ul>
+</li>
+<li class="toc-h2 nav-item toc-entry"><a class="reference internal nav-link" href="#arbdmodel.engine.HydroProRunner"><code class="docutils literal notranslate"><span class="pre">HydroProRunner</span></code></a><ul class="nav section-nav flex-column">
+<li class="toc-h3 nav-item toc-entry"><a class="reference internal nav-link" href="#arbdmodel.engine.HydroProRunner.parse_output"><code class="docutils literal notranslate"><span class="pre">HydroProRunner.parse_output()</span></code></a></li>
+<li class="toc-h3 nav-item toc-entry"><a class="reference internal nav-link" href="#arbdmodel.engine.HydroProRunner.run_calculation"><code class="docutils literal notranslate"><span class="pre">HydroProRunner.run_calculation()</span></code></a></li>
+<li class="toc-h3 nav-item toc-entry"><a class="reference internal nav-link" href="#arbdmodel.engine.HydroProRunner.write_config"><code class="docutils literal notranslate"><span class="pre">HydroProRunner.write_config()</span></code></a></li>
+</ul>
+</li>
+<li class="toc-h2 nav-item toc-entry"><a class="reference internal nav-link" href="#arbdmodel.engine.NamdEngine"><code class="docutils literal notranslate"><span class="pre">NamdEngine</span></code></a><ul class="nav section-nav flex-column">
+<li class="toc-h3 nav-item toc-entry"><a class="reference internal nav-link" href="#arbdmodel.engine.NamdEngine.default_binary"><code class="docutils literal notranslate"><span class="pre">NamdEngine.default_binary</span></code></a></li>
+<li class="toc-h3 nav-item toc-entry"><a class="reference internal nav-link" href="#arbdmodel.engine.NamdEngine.get_default_conf"><code class="docutils literal notranslate"><span class="pre">NamdEngine.get_default_conf()</span></code></a></li>
+<li class="toc-h3 nav-item toc-entry"><a class="reference internal nav-link" href="#arbdmodel.engine.NamdEngine.write_conf"><code class="docutils literal notranslate"><span class="pre">NamdEngine.write_conf()</span></code></a></li>
+<li class="toc-h3 nav-item toc-entry"><a class="reference internal nav-link" href="#arbdmodel.engine.NamdEngine.write_simulation_files"><code class="docutils literal notranslate"><span class="pre">NamdEngine.write_simulation_files()</span></code></a></li>
+</ul>
+</li>
+<li class="toc-h2 nav-item toc-entry"><a class="reference internal nav-link" href="#arbdmodel.engine.SimEngine"><code class="docutils literal notranslate"><span class="pre">SimEngine</span></code></a><ul class="nav section-nav flex-column">
+<li class="toc-h3 nav-item toc-entry"><a class="reference internal nav-link" href="#arbdmodel.engine.SimEngine.default_binary"><code class="docutils literal notranslate"><span class="pre">SimEngine.default_binary</span></code></a></li>
+<li class="toc-h3 nav-item toc-entry"><a class="reference internal nav-link" href="#arbdmodel.engine.SimEngine.get_default_conf"><code class="docutils literal notranslate"><span class="pre">SimEngine.get_default_conf()</span></code></a></li>
+<li class="toc-h3 nav-item toc-entry"><a class="reference internal nav-link" href="#arbdmodel.engine.SimEngine.simulate"><code class="docutils literal notranslate"><span class="pre">SimEngine.simulate()</span></code></a></li>
+<li class="toc-h3 nav-item toc-entry"><a class="reference internal nav-link" href="#arbdmodel.engine.SimEngine.write_simulation_files"><code class="docutils literal notranslate"><span class="pre">SimEngine.write_simulation_files()</span></code></a></li>
+</ul>
+</li>
+</ul>
+ </nav>
</div>
</div>
</div>
@@ -351,6 +391,186 @@ document.write(`
<section class="tex2jax_ignore mathjax_ignore" id="engine">
<h1>engine<a class="headerlink" href="#engine" title="Link to this heading">#</a></h1>
<p>Module documentation for <code class="docutils literal notranslate"><span class="pre">arbdmodel.engine</span></code>.</p>
+<dl class="py class" id="module-arbdmodel.engine">
+<dt class="sig sig-object py" id="arbdmodel.engine.APBSRunner">
+<em class="property"><span class="pre">class</span><span class="w"> </span></em><span class="sig-name descname"><span class="pre">APBSRunner</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">simconf</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">binary_path</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">psize_script</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em><span class="sig-paren">)</span><a class="reference internal" href="../../_modules/arbdmodel/engine.html#APBSRunner"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#arbdmodel.engine.APBSRunner" title="Link to this definition">#</a></dt>
+<dd><p>Bases: <a class="hxr-hoverxref hxr-tooltip reference external" href="https://docs.python.org/3/library/functions.html#object" title="(in Python v3.13)"><code class="xref py py-class docutils literal notranslate"><span class="pre">object</span></code></a></p>
+<p>Interface to APBS for electrostatics calculations</p>
+<dl class="py method">
+<dt class="sig sig-object py" id="arbdmodel.engine.APBSRunner.run_calculation">
+<span class="sig-name descname"><span class="pre">run_calculation</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">structure_name</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">xyz_dims</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">work_dir</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">'.'</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">salt_conc</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">0.15</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">temperature</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">300</span></span></em><span class="sig-paren">)</span><a class="reference internal" href="../../_modules/arbdmodel/engine.html#APBSRunner.run_calculation"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#arbdmodel.engine.APBSRunner.run_calculation" title="Link to this definition">#</a></dt>
+<dd><p>Run APBS calculation.</p>
+<dl class="field-list simple">
+<dt class="field-odd">Parameters<span class="colon">:</span></dt>
+<dd class="field-odd"><ul class="simple">
+<li><p><strong>structure_name</strong> – Base name of structure files</p></li>
+<li><p><strong>xyz_dims</strong> – [x, y, z] dimensions</p></li>
+<li><p><strong>work_dir</strong> – Working directory</p></li>
+<li><p><strong>salt_conc</strong> – Salt concentration in M</p></li>
+<li><p><strong>temperature</strong> – Temperature in K</p></li>
+</ul>
+</dd>
+<dt class="field-even">Returns<span class="colon">:</span></dt>
+<dd class="field-even"><p>Path to output potential file</p>
+</dd>
+</dl>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="arbdmodel.engine.APBSRunner.write_config">
+<span class="sig-name descname"><span class="pre">write_config</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">structure_name</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">xyz_dims</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">salt_conc</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">0.15</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">temperature</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">300</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">buffer</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">50</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">large_system</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">'Off'</span></span></em><span class="sig-paren">)</span><a class="reference internal" href="../../_modules/arbdmodel/engine.html#APBSRunner.write_config"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#arbdmodel.engine.APBSRunner.write_config" title="Link to this definition">#</a></dt>
+<dd><p>Write APBS configuration file.</p>
+<dl class="field-list simple">
+<dt class="field-odd">Parameters<span class="colon">:</span></dt>
+<dd class="field-odd"><ul class="simple">
+<li><p><strong>structure_name</strong> – Base name of structure files</p></li>
+<li><p><strong>xyz_dims</strong> – [x, y, z] dimensions</p></li>
+<li><p><strong>salt_conc</strong> – Salt concentration in M</p></li>
+<li><p><strong>temperature</strong> – Temperature in K</p></li>
+<li><p><strong>buffer</strong> – Grid buffer size in Å</p></li>
+<li><p><strong>large_system</strong> – ‘On’ or ‘Off’ for large system mode</p></li>
+</ul>
+</dd>
+</dl>
+</dd></dl>
+
+</dd></dl>
+
+<dl class="py class">
+<dt class="sig sig-object py" id="arbdmodel.engine.ArbdEngine">
+<em class="property"><span class="pre">class</span><span class="w"> </span></em><span class="sig-name descname"><span class="pre">ArbdEngine</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">extra_bd_file_lines</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">''</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">configuration</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="o"><span class="pre">**</span></span><span class="n"><span class="pre">conf_params</span></span></em><span class="sig-paren">)</span><a class="reference internal" href="../../_modules/arbdmodel/engine.html#ArbdEngine"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#arbdmodel.engine.ArbdEngine" title="Link to this definition">#</a></dt>
+<dd><p>Bases: <a class="reference internal" href="#arbdmodel.engine.SimEngine" title="arbdmodel.engine.SimEngine"><code class="xref py py-class docutils literal notranslate"><span class="pre">SimEngine</span></code></a></p>
+<p>Interface to ARBD simulation engine</p>
+<dl class="py property">
+<dt class="sig sig-object py" id="arbdmodel.engine.ArbdEngine.default_binary">
+<em class="property"><span class="pre">property</span><span class="w"> </span></em><span class="sig-name descname"><span class="pre">default_binary</span></span><a class="headerlink" href="#arbdmodel.engine.ArbdEngine.default_binary" title="Link to this definition">#</a></dt>
+<dd></dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="arbdmodel.engine.ArbdEngine.get_default_conf">
+<span class="sig-name descname"><span class="pre">get_default_conf</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="reference internal" href="../../_modules/arbdmodel/engine.html#ArbdEngine.get_default_conf"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#arbdmodel.engine.ArbdEngine.get_default_conf" title="Link to this definition">#</a></dt>
+<dd></dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="arbdmodel.engine.ArbdEngine.write_simulation_files">
+<span class="sig-name descname"><span class="pre">write_simulation_files</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">model</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">output_name</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">configuration</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="o"><span class="pre">**</span></span><span class="n"><span class="pre">conf_params</span></span></em><span class="sig-paren">)</span><a class="reference internal" href="../../_modules/arbdmodel/engine.html#ArbdEngine.write_simulation_files"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#arbdmodel.engine.ArbdEngine.write_simulation_files" title="Link to this definition">#</a></dt>
+<dd></dd></dl>
+
+</dd></dl>
+
+<dl class="py class">
+<dt class="sig sig-object py" id="arbdmodel.engine.HydroProRunner">
+<em class="property"><span class="pre">class</span><span class="w"> </span></em><span class="sig-name descname"><span class="pre">HydroProRunner</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">mass</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">simconf</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">structure_name</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">'hydrocal'</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">cal_type</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">'shape'</span></span></em><span class="sig-paren">)</span><a class="reference internal" href="../../_modules/arbdmodel/engine.html#HydroProRunner"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#arbdmodel.engine.HydroProRunner" title="Link to this definition">#</a></dt>
+<dd><p>Bases: <a class="hxr-hoverxref hxr-tooltip reference external" href="https://docs.python.org/3/library/functions.html#object" title="(in Python v3.13)"><code class="xref py py-class docutils literal notranslate"><span class="pre">object</span></code></a></p>
+<p>Interface to HydroPro for hydrodynamic calculations</p>
+<dl class="py method">
+<dt class="sig sig-object py" id="arbdmodel.engine.HydroProRunner.parse_output">
+<span class="sig-name descname"><span class="pre">parse_output</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">output_file</span></span></em><span class="sig-paren">)</span><a class="reference internal" href="../../_modules/arbdmodel/engine.html#HydroProRunner.parse_output"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#arbdmodel.engine.HydroProRunner.parse_output" title="Link to this definition">#</a></dt>
+<dd></dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="arbdmodel.engine.HydroProRunner.run_calculation">
+<span class="sig-name descname"><span class="pre">run_calculation</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">work_dir</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">'.'</span></span></em><span class="sig-paren">)</span><a class="reference internal" href="../../_modules/arbdmodel/engine.html#HydroProRunner.run_calculation"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#arbdmodel.engine.HydroProRunner.run_calculation" title="Link to this definition">#</a></dt>
+<dd><p>Run HydroPro calculation.</p>
+<dl class="field-list simple">
+<dt class="field-odd">Parameters<span class="colon">:</span></dt>
+<dd class="field-odd"><ul class="simple">
+<li><p><strong>structure_name</strong> – Base name of structure files</p></li>
+<li><p><strong>mass</strong> – Mass in AMU</p></li>
+<li><p><strong>work_dir</strong> – Working directory for calculation</p></li>
+</ul>
+</dd>
+<dt class="field-even">Returns<span class="colon">:</span></dt>
+<dd class="field-even"><p><ul class="simple">
+<li><p>translation_damping: [Dx, Dy, Dz]</p></li>
+<li><p>rotation_damping: [Rx, Ry, Rz]</p></li>
+</ul>
+</p>
+</dd>
+<dt class="field-odd">Return type<span class="colon">:</span></dt>
+<dd class="field-odd"><p>Dictionary containing</p>
+</dd>
+</dl>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="arbdmodel.engine.HydroProRunner.write_config">
+<span class="sig-name descname"><span class="pre">write_config</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">output_path</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">'hydropro.dat'</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">aer</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">2.9</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">nsig</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">6</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">sig_min</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">1</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">sig_max</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">2</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">specific_volume</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">0.702</span></span></em><span class="sig-paren">)</span><a class="reference internal" href="../../_modules/arbdmodel/engine.html#HydroProRunner.write_config"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#arbdmodel.engine.HydroProRunner.write_config" title="Link to this definition">#</a></dt>
+<dd><p>Write HydroPro configuration file with explicit parameters.</p>
+<dl class="field-list simple">
+<dt class="field-odd">Parameters<span class="colon">:</span></dt>
+<dd class="field-odd"><ul class="simple">
+<li><p><strong>output_path</strong> – Path to write config file</p></li>
+<li><p><strong>cal_type</strong> – shape(0) or mesh(1)</p></li>
+<li><p><strong>structure_name</strong> – Name of the molecule/structure</p></li>
+<li><p><strong>mass</strong> – Molecular weight in Daltons (amu)</p></li>
+<li><p><strong>aer</strong> – Atomic Element Radius in Angstroms</p></li>
+<li><p><strong>nsig</strong> – Number of values of the shell thickness</p></li>
+<li><p><strong>sig_min</strong> – Minimum radius of beads in the shell (Angstroms)</p></li>
+<li><p><strong>sig_max</strong> – Maximum radius of beads in the shell (Angstroms)</p></li>
+<li><p><strong>specific_volume</strong> – Partial specific volume in cm³/g</p></li>
+</ul>
+</dd>
+</dl>
+</dd></dl>
+
+</dd></dl>
+
+<dl class="py class">
+<dt class="sig sig-object py" id="arbdmodel.engine.NamdEngine">
+<em class="property"><span class="pre">class</span><span class="w"> </span></em><span class="sig-name descname"><span class="pre">NamdEngine</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">configuration</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="o"><span class="pre">**</span></span><span class="n"><span class="pre">conf_params</span></span></em><span class="sig-paren">)</span><a class="reference internal" href="../../_modules/arbdmodel/engine.html#NamdEngine"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#arbdmodel.engine.NamdEngine" title="Link to this definition">#</a></dt>
+<dd><p>Bases: <a class="reference internal" href="#arbdmodel.engine.SimEngine" title="arbdmodel.engine.SimEngine"><code class="xref py py-class docutils literal notranslate"><span class="pre">SimEngine</span></code></a></p>
+<p>Partial interface to NAMD simulation engine</p>
+<dl class="py property">
+<dt class="sig sig-object py" id="arbdmodel.engine.NamdEngine.default_binary">
+<em class="property"><span class="pre">property</span><span class="w"> </span></em><span class="sig-name descname"><span class="pre">default_binary</span></span><a class="headerlink" href="#arbdmodel.engine.NamdEngine.default_binary" title="Link to this definition">#</a></dt>
+<dd></dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="arbdmodel.engine.NamdEngine.get_default_conf">
+<span class="sig-name descname"><span class="pre">get_default_conf</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="reference internal" href="../../_modules/arbdmodel/engine.html#NamdEngine.get_default_conf"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#arbdmodel.engine.NamdEngine.get_default_conf" title="Link to this definition">#</a></dt>
+<dd></dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="arbdmodel.engine.NamdEngine.write_conf">
+<span class="sig-name descname"><span class="pre">write_conf</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">model</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">output_name</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">minimization_steps</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">4800</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">num_steps</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">1000000.0</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">output_directory</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">'output'</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">update_dimensions</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">True</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">extrabonds</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">True</span></span></em><span class="sig-paren">)</span><a class="reference internal" href="../../_modules/arbdmodel/engine.html#NamdEngine.write_conf"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#arbdmodel.engine.NamdEngine.write_conf" title="Link to this definition">#</a></dt>
+<dd><p>Write a NAMD configuration file (developed for the mrdna package)</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="arbdmodel.engine.NamdEngine.write_simulation_files">
+<span class="sig-name descname"><span class="pre">write_simulation_files</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">model</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">output_name</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">configuration</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">write_pqr</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">False</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">copy_ff_from</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">PosixPath('/Users/pinyili/Documents/research/arbdmodel-simple/arbdmodel/resources/charmm36.nbfix')</span></span></em>, <em class="sig-param"><span class="o"><span class="pre">**</span></span><span class="n"><span class="pre">conf_params</span></span></em><span class="sig-paren">)</span><a class="reference internal" href="../../_modules/arbdmodel/engine.html#NamdEngine.write_simulation_files"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#arbdmodel.engine.NamdEngine.write_simulation_files" title="Link to this definition">#</a></dt>
+<dd></dd></dl>
+
+</dd></dl>
+
+<dl class="py class">
+<dt class="sig sig-object py" id="arbdmodel.engine.SimEngine">
+<em class="property"><span class="pre">class</span><span class="w"> </span></em><span class="sig-name descname"><span class="pre">SimEngine</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">configuration</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em><span class="sig-paren">)</span><a class="reference internal" href="../../_modules/arbdmodel/engine.html#SimEngine"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#arbdmodel.engine.SimEngine" title="Link to this definition">#</a></dt>
+<dd><p>Bases: <a class="hxr-hoverxref hxr-tooltip reference external" href="https://docs.python.org/3/library/functions.html#object" title="(in Python v3.13)"><code class="xref py py-class docutils literal notranslate"><span class="pre">object</span></code></a></p>
+<p>Abstract class for running a simulation of a model</p>
+<dl class="py property">
+<dt class="sig sig-object py" id="arbdmodel.engine.SimEngine.default_binary">
+<em class="property"><span class="pre">abstract</span><span class="w"> </span><span class="pre">property</span><span class="w"> </span></em><span class="sig-name descname"><span class="pre">default_binary</span></span><a class="headerlink" href="#arbdmodel.engine.SimEngine.default_binary" title="Link to this definition">#</a></dt>
+<dd></dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="arbdmodel.engine.SimEngine.get_default_conf">
+<em class="property"><span class="pre">abstract</span><span class="w"> </span></em><span class="sig-name descname"><span class="pre">get_default_conf</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="reference internal" href="../../_modules/arbdmodel/engine.html#SimEngine.get_default_conf"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#arbdmodel.engine.SimEngine.get_default_conf" title="Link to this definition">#</a></dt>
+<dd></dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="arbdmodel.engine.SimEngine.simulate">
+<span class="sig-name descname"><span class="pre">simulate</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">model</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">output_name</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">output_directory</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">'output'</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">directory</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">'.'</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">log_file</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">binary</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">num_procs</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">dry_run</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">False</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">configuration</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">replicas</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">1</span></span></em>, <em class="sig-param"><span class="o"><span class="pre">**</span></span><span class="n"><span class="pre">conf_params</span></span></em><span class="sig-paren">)</span><a class="reference internal" href="../../_modules/arbdmodel/engine.html#SimEngine.simulate"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#arbdmodel.engine.SimEngine.simulate" title="Link to this definition">#</a></dt>
+<dd></dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="arbdmodel.engine.SimEngine.write_simulation_files">
+<em class="property"><span class="pre">abstract</span><span class="w"> </span></em><span class="sig-name descname"><span class="pre">write_simulation_files</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">model</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">output_name</span></span></em><span class="sig-paren">)</span><a class="reference internal" href="../../_modules/arbdmodel/engine.html#SimEngine.write_simulation_files"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#arbdmodel.engine.SimEngine.write_simulation_files" title="Link to this definition">#</a></dt>
+<dd></dd></dl>
+
+</dd></dl>
+
</section>
<script type="text/x-thebe-config">
@@ -390,6 +610,51 @@ document.write(`
+ <div class="bd-sidebar-secondary bd-toc"><div class="sidebar-secondary-items sidebar-secondary__inner">
+
+
+ <div class="sidebar-secondary-item">
+ <div class="page-toc tocsection onthispage">
+ <i class="fa-solid fa-list"></i> Contents
+ </div>
+ <nav class="bd-toc-nav page-toc">
+ <ul class="visible nav section-nav flex-column">
+<li class="toc-h2 nav-item toc-entry"><a class="reference internal nav-link" href="#arbdmodel.engine.APBSRunner"><code class="docutils literal notranslate"><span class="pre">APBSRunner</span></code></a><ul class="nav section-nav flex-column">
+<li class="toc-h3 nav-item toc-entry"><a class="reference internal nav-link" href="#arbdmodel.engine.APBSRunner.run_calculation"><code class="docutils literal notranslate"><span class="pre">APBSRunner.run_calculation()</span></code></a></li>
+<li class="toc-h3 nav-item toc-entry"><a class="reference internal nav-link" href="#arbdmodel.engine.APBSRunner.write_config"><code class="docutils literal notranslate"><span class="pre">APBSRunner.write_config()</span></code></a></li>
+</ul>
+</li>
+<li class="toc-h2 nav-item toc-entry"><a class="reference internal nav-link" href="#arbdmodel.engine.ArbdEngine"><code class="docutils literal notranslate"><span class="pre">ArbdEngine</span></code></a><ul class="nav section-nav flex-column">
+<li class="toc-h3 nav-item toc-entry"><a class="reference internal nav-link" href="#arbdmodel.engine.ArbdEngine.default_binary"><code class="docutils literal notranslate"><span class="pre">ArbdEngine.default_binary</span></code></a></li>
+<li class="toc-h3 nav-item toc-entry"><a class="reference internal nav-link" href="#arbdmodel.engine.ArbdEngine.get_default_conf"><code class="docutils literal notranslate"><span class="pre">ArbdEngine.get_default_conf()</span></code></a></li>
+<li class="toc-h3 nav-item toc-entry"><a class="reference internal nav-link" href="#arbdmodel.engine.ArbdEngine.write_simulation_files"><code class="docutils literal notranslate"><span class="pre">ArbdEngine.write_simulation_files()</span></code></a></li>
+</ul>
+</li>
+<li class="toc-h2 nav-item toc-entry"><a class="reference internal nav-link" href="#arbdmodel.engine.HydroProRunner"><code class="docutils literal notranslate"><span class="pre">HydroProRunner</span></code></a><ul class="nav section-nav flex-column">
+<li class="toc-h3 nav-item toc-entry"><a class="reference internal nav-link" href="#arbdmodel.engine.HydroProRunner.parse_output"><code class="docutils literal notranslate"><span class="pre">HydroProRunner.parse_output()</span></code></a></li>
+<li class="toc-h3 nav-item toc-entry"><a class="reference internal nav-link" href="#arbdmodel.engine.HydroProRunner.run_calculation"><code class="docutils literal notranslate"><span class="pre">HydroProRunner.run_calculation()</span></code></a></li>
+<li class="toc-h3 nav-item toc-entry"><a class="reference internal nav-link" href="#arbdmodel.engine.HydroProRunner.write_config"><code class="docutils literal notranslate"><span class="pre">HydroProRunner.write_config()</span></code></a></li>
+</ul>
+</li>
+<li class="toc-h2 nav-item toc-entry"><a class="reference internal nav-link" href="#arbdmodel.engine.NamdEngine"><code class="docutils literal notranslate"><span class="pre">NamdEngine</span></code></a><ul class="nav section-nav flex-column">
+<li class="toc-h3 nav-item toc-entry"><a class="reference internal nav-link" href="#arbdmodel.engine.NamdEngine.default_binary"><code class="docutils literal notranslate"><span class="pre">NamdEngine.default_binary</span></code></a></li>
+<li class="toc-h3 nav-item toc-entry"><a class="reference internal nav-link" href="#arbdmodel.engine.NamdEngine.get_default_conf"><code class="docutils literal notranslate"><span class="pre">NamdEngine.get_default_conf()</span></code></a></li>
+<li class="toc-h3 nav-item toc-entry"><a class="reference internal nav-link" href="#arbdmodel.engine.NamdEngine.write_conf"><code class="docutils literal notranslate"><span class="pre">NamdEngine.write_conf()</span></code></a></li>
+<li class="toc-h3 nav-item toc-entry"><a class="reference internal nav-link" href="#arbdmodel.engine.NamdEngine.write_simulation_files"><code class="docutils literal notranslate"><span class="pre">NamdEngine.write_simulation_files()</span></code></a></li>
+</ul>
+</li>
+<li class="toc-h2 nav-item toc-entry"><a class="reference internal nav-link" href="#arbdmodel.engine.SimEngine"><code class="docutils literal notranslate"><span class="pre">SimEngine</span></code></a><ul class="nav section-nav flex-column">
+<li class="toc-h3 nav-item toc-entry"><a class="reference internal nav-link" href="#arbdmodel.engine.SimEngine.default_binary"><code class="docutils literal notranslate"><span class="pre">SimEngine.default_binary</span></code></a></li>
+<li class="toc-h3 nav-item toc-entry"><a class="reference internal nav-link" href="#arbdmodel.engine.SimEngine.get_default_conf"><code class="docutils literal notranslate"><span class="pre">SimEngine.get_default_conf()</span></code></a></li>
+<li class="toc-h3 nav-item toc-entry"><a class="reference internal nav-link" href="#arbdmodel.engine.SimEngine.simulate"><code class="docutils literal notranslate"><span class="pre">SimEngine.simulate()</span></code></a></li>
+<li class="toc-h3 nav-item toc-entry"><a class="reference internal nav-link" href="#arbdmodel.engine.SimEngine.write_simulation_files"><code class="docutils literal notranslate"><span class="pre">SimEngine.write_simulation_files()</span></code></a></li>
+</ul>
+</li>
+</ul>
+ </nav></div>
+
+</div></div>
+
</div>
<footer class="bd-footer-content">
diff --git a/_build/html/api/simulation_engines/index.html b/_build/html/api/simulation_engines/index.html
index 550c28923e8b14d77c07b9c1f5decccc78cdd46b..2dec772f8a93eed9e1686cd7f157d8db0dcdff31 100644
--- a/_build/html/api/simulation_engines/index.html
+++ b/_build/html/api/simulation_engines/index.html
@@ -32,19 +32,19 @@
<link rel="stylesheet" type="text/css" href="../../_static/styles/sphinx-book-theme.css?v=eba8b062" />
<link rel="stylesheet" type="text/css" href="../../_static/togglebutton.css?v=13237357" />
<link rel="stylesheet" type="text/css" href="../../_static/copybutton.css?v=76b2166b" />
- <link rel="stylesheet" type="text/css" href="../../_static/mystnb.4510f1fc1dee50b3e5859aac5469c37c29e427902b24a333a5f9fcb2f0b3ac41.css" />
+ <link rel="stylesheet" type="text/css" href="../../_static/mystnb.4510f1fc1dee50b3e5859aac5469c37c29e427902b24a333a5f9fcb2f0b3ac41.css?v=be8a1c11" />
<link rel="stylesheet" type="text/css" href="../../_static/sphinx-thebe.css?v=4fa983c6" />
<link rel="stylesheet" type="text/css" href="../../_static/tabs.css?v=4c969af8" />
- <link rel="stylesheet" type="text/css" href="../../_static/proof.css" />
+ <link rel="stylesheet" type="text/css" href="../../_static/proof.css?v=b4b7a797" />
<link rel="stylesheet" type="text/css" href="../../_static/styles/sphinx-examples.css?v=e236af4b" />
- <link rel="stylesheet" type="text/css" href="../../_static/css/tooltipster.custom.css" />
- <link rel="stylesheet" type="text/css" href="../../_static/css/tooltipster.bundle.min.css" />
- <link rel="stylesheet" type="text/css" href="../../_static/css/tooltipster-sideTip-shadow.min.css" />
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- <link rel="stylesheet" type="text/css" href="../../_static/css/tooltipster-sideTip-noir.min.css" />
- <link rel="stylesheet" type="text/css" href="../../_static/css/tooltipster-sideTip-light.min.css" />
- <link rel="stylesheet" type="text/css" href="../../_static/css/tooltipster-sideTip-borderless.min.css" />
- <link rel="stylesheet" type="text/css" href="../../_static/css/micromodal.css" />
+ <link rel="stylesheet" type="text/css" href="../../_static/css/tooltipster.custom.css?v=7bc2f056" />
+ <link rel="stylesheet" type="text/css" href="../../_static/css/tooltipster.bundle.min.css?v=37217874" />
+ <link rel="stylesheet" type="text/css" href="../../_static/css/tooltipster-sideTip-shadow.min.css?v=6227e517" />
+ <link rel="stylesheet" type="text/css" href="../../_static/css/tooltipster-sideTip-punk.min.css?v=94669e23" />
+ <link rel="stylesheet" type="text/css" href="../../_static/css/tooltipster-sideTip-noir.min.css?v=21a39f42" />
+ <link rel="stylesheet" type="text/css" href="../../_static/css/tooltipster-sideTip-light.min.css?v=a18b2449" />
+ <link rel="stylesheet" type="text/css" href="../../_static/css/tooltipster-sideTip-borderless.min.css?v=dbff53e4" />
+ <link rel="stylesheet" type="text/css" href="../../_static/css/micromodal.css?v=d7bf34ee" />
<link rel="stylesheet" type="text/css" href="../../_static/sphinx-design.min.css?v=95c83b7e" />
<!-- Pre-loaded scripts that we'll load fully later -->
@@ -61,9 +61,9 @@
<script src="../../_static/copybutton.js?v=f281be69"></script>
<script src="../../_static/scripts/sphinx-book-theme.js?v=887ef09a"></script>
<script src="../../_static/tabs.js?v=3ee01567"></script>
- <script src="../../_static/js/hoverxref.js"></script>
- <script src="../../_static/js/tooltipster.bundle.min.js"></script>
- <script src="../../_static/js/micromodal.min.js"></script>
+ <script src="../../_static/js/hoverxref.js?v=c95ade4f"></script>
+ <script src="../../_static/js/tooltipster.bundle.min.js?v=18bf091b"></script>
+ <script src="../../_static/js/micromodal.min.js?v=04d6302d"></script>
<script>let toggleHintShow = 'Click to show';</script>
<script>let toggleHintHide = 'Click to hide';</script>
<script>let toggleOpenOnPrint = 'true';</script>
diff --git a/_build/html/api/simulation_engines/parmed_bd.html b/_build/html/api/simulation_engines/parmed_bd.html
index 055e44c41ba80f4d945bd5aabada302f17bbfeec..c99edfd8f447345fac7e5e3226c42f3f934362ee 100644
--- a/_build/html/api/simulation_engines/parmed_bd.html
+++ b/_build/html/api/simulation_engines/parmed_bd.html
@@ -32,19 +32,19 @@
<link rel="stylesheet" type="text/css" href="../../_static/styles/sphinx-book-theme.css?v=eba8b062" />
<link rel="stylesheet" type="text/css" href="../../_static/togglebutton.css?v=13237357" />
<link rel="stylesheet" type="text/css" href="../../_static/copybutton.css?v=76b2166b" />
- <link rel="stylesheet" type="text/css" href="../../_static/mystnb.4510f1fc1dee50b3e5859aac5469c37c29e427902b24a333a5f9fcb2f0b3ac41.css" />
+ <link rel="stylesheet" type="text/css" href="../../_static/mystnb.4510f1fc1dee50b3e5859aac5469c37c29e427902b24a333a5f9fcb2f0b3ac41.css?v=be8a1c11" />
<link rel="stylesheet" type="text/css" href="../../_static/sphinx-thebe.css?v=4fa983c6" />
<link rel="stylesheet" type="text/css" href="../../_static/tabs.css?v=4c969af8" />
- <link rel="stylesheet" type="text/css" href="../../_static/proof.css" />
+ <link rel="stylesheet" type="text/css" href="../../_static/proof.css?v=b4b7a797" />
<link rel="stylesheet" type="text/css" href="../../_static/styles/sphinx-examples.css?v=e236af4b" />
- <link rel="stylesheet" type="text/css" href="../../_static/css/tooltipster.custom.css" />
- <link rel="stylesheet" type="text/css" href="../../_static/css/tooltipster.bundle.min.css" />
- <link rel="stylesheet" type="text/css" href="../../_static/css/tooltipster-sideTip-shadow.min.css" />
- <link rel="stylesheet" type="text/css" href="../../_static/css/tooltipster-sideTip-punk.min.css" />
- <link rel="stylesheet" type="text/css" href="../../_static/css/tooltipster-sideTip-noir.min.css" />
- <link rel="stylesheet" type="text/css" href="../../_static/css/tooltipster-sideTip-light.min.css" />
- <link rel="stylesheet" type="text/css" href="../../_static/css/tooltipster-sideTip-borderless.min.css" />
- <link rel="stylesheet" type="text/css" href="../../_static/css/micromodal.css" />
+ <link rel="stylesheet" type="text/css" href="../../_static/css/tooltipster.custom.css?v=7bc2f056" />
+ <link rel="stylesheet" type="text/css" href="../../_static/css/tooltipster.bundle.min.css?v=37217874" />
+ <link rel="stylesheet" type="text/css" href="../../_static/css/tooltipster-sideTip-shadow.min.css?v=6227e517" />
+ <link rel="stylesheet" type="text/css" href="../../_static/css/tooltipster-sideTip-punk.min.css?v=94669e23" />
+ <link rel="stylesheet" type="text/css" href="../../_static/css/tooltipster-sideTip-noir.min.css?v=21a39f42" />
+ <link rel="stylesheet" type="text/css" href="../../_static/css/tooltipster-sideTip-light.min.css?v=a18b2449" />
+ <link rel="stylesheet" type="text/css" href="../../_static/css/tooltipster-sideTip-borderless.min.css?v=dbff53e4" />
+ <link rel="stylesheet" type="text/css" href="../../_static/css/micromodal.css?v=d7bf34ee" />
<link rel="stylesheet" type="text/css" href="../../_static/sphinx-design.min.css?v=95c83b7e" />
<!-- Pre-loaded scripts that we'll load fully later -->
@@ -61,9 +61,9 @@
<script src="../../_static/copybutton.js?v=f281be69"></script>
<script src="../../_static/scripts/sphinx-book-theme.js?v=887ef09a"></script>
<script src="../../_static/tabs.js?v=3ee01567"></script>
- <script src="../../_static/js/hoverxref.js"></script>
- <script src="../../_static/js/tooltipster.bundle.min.js"></script>
- <script src="../../_static/js/micromodal.min.js"></script>
+ <script src="../../_static/js/hoverxref.js?v=c95ade4f"></script>
+ <script src="../../_static/js/tooltipster.bundle.min.js?v=18bf091b"></script>
+ <script src="../../_static/js/micromodal.min.js?v=04d6302d"></script>
<script>let toggleHintShow = 'Click to show';</script>
<script>let toggleHintHide = 'Click to hide';</script>
<script>let toggleOpenOnPrint = 'true';</script>
@@ -323,7 +323,9 @@ document.write(`
</button>
`);
</script>
-
+<button class="sidebar-toggle secondary-toggle btn btn-sm" title="Toggle secondary sidebar" data-bs-placement="bottom" data-bs-toggle="tooltip">
+ <span class="fa-solid fa-list"></span>
+</button>
</div></div>
</div>
@@ -339,6 +341,25 @@ document.write(`
<div id="print-main-content">
<div id="jb-print-toc">
+ <div>
+ <h2> Contents </h2>
+ </div>
+ <nav aria-label="Page">
+ <ul class="visible nav section-nav flex-column">
+<li class="toc-h2 nav-item toc-entry"><a class="reference internal nav-link" href="#arbdmodel.parmed_bd.ParmedArbd"><code class="docutils literal notranslate"><span class="pre">ParmedArbd</span></code></a><ul class="nav section-nav flex-column">
+<li class="toc-h3 nav-item toc-entry"><a class="reference internal nav-link" href="#arbdmodel.parmed_bd.ParmedArbd.parmed_structure"><code class="docutils literal notranslate"><span class="pre">ParmedArbd.parmed_structure</span></code></a></li>
+<li class="toc-h3 nav-item toc-entry"><a class="reference internal nav-link" href="#arbdmodel.parmed_bd.ParmedArbd.atom_types"><code class="docutils literal notranslate"><span class="pre">ParmedArbd.atom_types</span></code></a></li>
+<li class="toc-h3 nav-item toc-entry"><a class="reference internal nav-link" href="#arbdmodel.parmed_bd.ParmedArbd.atoms_map"><code class="docutils literal notranslate"><span class="pre">ParmedArbd.atoms_map</span></code></a></li>
+<li class="toc-h3 nav-item toc-entry"><a class="reference internal nav-link" href="#arbdmodel.parmed_bd.ParmedArbd.convert_sod_to_mg"><code class="docutils literal notranslate"><span class="pre">ParmedArbd.convert_sod_to_mg()</span></code></a></li>
+<li class="toc-h3 nav-item toc-entry"><a class="reference internal nav-link" href="#arbdmodel.parmed_bd.ParmedArbd.create_dual_topology"><code class="docutils literal notranslate"><span class="pre">ParmedArbd.create_dual_topology()</span></code></a></li>
+<li class="toc-h3 nav-item toc-entry"><a class="reference internal nav-link" href="#arbdmodel.parmed_bd.ParmedArbd.create_dual_topology_model"><code class="docutils literal notranslate"><span class="pre">ParmedArbd.create_dual_topology_model()</span></code></a></li>
+<li class="toc-h3 nav-item toc-entry"><a class="reference internal nav-link" href="#arbdmodel.parmed_bd.ParmedArbd.load_structure"><code class="docutils literal notranslate"><span class="pre">ParmedArbd.load_structure()</span></code></a></li>
+<li class="toc-h3 nav-item toc-entry"><a class="reference internal nav-link" href="#arbdmodel.parmed_bd.ParmedArbd.simulate"><code class="docutils literal notranslate"><span class="pre">ParmedArbd.simulate()</span></code></a></li>
+<li class="toc-h3 nav-item toc-entry"><a class="reference internal nav-link" href="#arbdmodel.parmed_bd.ParmedArbd.write_restraint_files"><code class="docutils literal notranslate"><span class="pre">ParmedArbd.write_restraint_files()</span></code></a></li>
+</ul>
+</li>
+</ul>
+ </nav>
</div>
</div>
</div>
@@ -351,6 +372,145 @@ document.write(`
<section class="tex2jax_ignore mathjax_ignore" id="parmed-bd">
<h1>parmed_bd<a class="headerlink" href="#parmed-bd" title="Link to this heading">#</a></h1>
<p>Module documentation for <code class="docutils literal notranslate"><span class="pre">arbdmodel.parmed_bd</span></code>.</p>
+<dl class="py class" id="module-arbdmodel.parmed_bd">
+<dt class="sig sig-object py" id="arbdmodel.parmed_bd.ParmedArbd">
+<em class="property"><span class="pre">class</span><span class="w"> </span></em><span class="sig-name descname"><span class="pre">ParmedArbd</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">parmed_structure</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">psf</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">pdb</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">parameter_files</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">system_type</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">'charmm'</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">integrator</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">'MD'</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">cutoff</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">12</span></span></em>, <em class="sig-param"><span class="o"><span class="pre">**</span></span><span class="n"><span class="pre">kwargs</span></span></em><span class="sig-paren">)</span><a class="reference internal" href="../../_modules/arbdmodel/parmed_bd.html#ParmedArbd"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#arbdmodel.parmed_bd.ParmedArbd" title="Link to this definition">#</a></dt>
+<dd><p>Bases: <a class="reference internal" href="../core/model.html#arbdmodel.model.ArbdModel" title="arbdmodel.model.ArbdModel"><code class="xref py py-class docutils literal notranslate"><span class="pre">ArbdModel</span></code></a></p>
+<p>Class for converting ParmEd structures to ARBD models for simulation.</p>
+<p>This class facilitates the conversion of molecular structures loaded with ParmEd
+into ARBD simulation models, preserving bonded and non-bonded interactions.
+It also supports creating dual topology models for free energy calculations.</p>
+<dl class="py attribute">
+<dt class="sig sig-object py" id="arbdmodel.parmed_bd.ParmedArbd.parmed_structure">
+<span class="sig-name descname"><span class="pre">parmed_structure</span></span><a class="headerlink" href="#arbdmodel.parmed_bd.ParmedArbd.parmed_structure" title="Link to this definition">#</a></dt>
+<dd><p>The original ParmEd structure</p>
+</dd></dl>
+
+<dl class="py attribute">
+<dt class="sig sig-object py" id="arbdmodel.parmed_bd.ParmedArbd.atom_types">
+<span class="sig-name descname"><span class="pre">atom_types</span></span><a class="headerlink" href="#arbdmodel.parmed_bd.ParmedArbd.atom_types" title="Link to this definition">#</a></dt>
+<dd><p>Dictionary mapping atom type names to ParticleType objects</p>
+</dd></dl>
+
+<dl class="py attribute">
+<dt class="sig sig-object py" id="arbdmodel.parmed_bd.ParmedArbd.atoms_map">
+<span class="sig-name descname"><span class="pre">atoms_map</span></span><a class="headerlink" href="#arbdmodel.parmed_bd.ParmedArbd.atoms_map" title="Link to this definition">#</a></dt>
+<dd><p>Mapping from ParmEd atoms to ARBD atoms</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="arbdmodel.parmed_bd.ParmedArbd.convert_sod_to_mg">
+<em class="property"><span class="pre">static</span><span class="w"> </span></em><span class="sig-name descname"><span class="pre">convert_sod_to_mg</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">structure</span></span></em><span class="sig-paren">)</span><a class="reference internal" href="../../_modules/arbdmodel/parmed_bd.html#ParmedArbd.convert_sod_to_mg"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#arbdmodel.parmed_bd.ParmedArbd.convert_sod_to_mg" title="Link to this definition">#</a></dt>
+<dd><p>Convert sodium ions to magnesium ions in a structure.</p>
+<dl class="field-list simple">
+<dt class="field-odd">Parameters<span class="colon">:</span></dt>
+<dd class="field-odd"><p><strong>structure</strong> – ParmEd structure to modify</p>
+</dd>
+<dt class="field-even">Returns<span class="colon">:</span></dt>
+<dd class="field-even"><p>Modified structure</p>
+</dd>
+</dl>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="arbdmodel.parmed_bd.ParmedArbd.create_dual_topology">
+<em class="property"><span class="pre">static</span><span class="w"> </span></em><span class="sig-name descname"><span class="pre">create_dual_topology</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">p1</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">p2</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">u1</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">u2</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em><span class="sig-paren">)</span><a class="reference internal" href="../../_modules/arbdmodel/parmed_bd.html#ParmedArbd.create_dual_topology"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#arbdmodel.parmed_bd.ParmedArbd.create_dual_topology" title="Link to this definition">#</a></dt>
+<dd><p>Create a dual topology structure from two ParmEd structures.</p>
+<dl class="field-list simple">
+<dt class="field-odd">Parameters<span class="colon">:</span></dt>
+<dd class="field-odd"><ul class="simple">
+<li><p><strong>p1</strong> – First ParmEd structure</p></li>
+<li><p><strong>p2</strong> – Second ParmEd structure</p></li>
+<li><p><strong>u1</strong> – Optional MDAnalysis universe for p1</p></li>
+<li><p><strong>u2</strong> – Optional MDAnalysis universe for p2</p></li>
+</ul>
+</dd>
+<dt class="field-even">Returns<span class="colon">:</span></dt>
+<dd class="field-even"><p>Tuple of (combined structure, restraint pairs, base pair bonds)</p>
+</dd>
+</dl>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="arbdmodel.parmed_bd.ParmedArbd.create_dual_topology_model">
+<em class="property"><span class="pre">classmethod</span><span class="w"> </span></em><span class="sig-name descname"><span class="pre">create_dual_topology_model</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">p1</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">p2</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">u1</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">u2</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="o"><span class="pre">**</span></span><span class="n"><span class="pre">kwargs</span></span></em><span class="sig-paren">)</span><a class="reference internal" href="../../_modules/arbdmodel/parmed_bd.html#ParmedArbd.create_dual_topology_model"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#arbdmodel.parmed_bd.ParmedArbd.create_dual_topology_model" title="Link to this definition">#</a></dt>
+<dd><p>Create a dual topology ARBD model from two ParmEd structures.</p>
+<dl class="field-list simple">
+<dt class="field-odd">Parameters<span class="colon">:</span></dt>
+<dd class="field-odd"><ul class="simple">
+<li><p><strong>p1</strong> – First ParmEd structure</p></li>
+<li><p><strong>p2</strong> – Second ParmEd structure</p></li>
+<li><p><strong>u1</strong> – Optional MDAnalysis universe for p1</p></li>
+<li><p><strong>u2</strong> – Optional MDAnalysis universe for p2</p></li>
+<li><p><strong>**kwargs</strong> – Additional arguments for ParmedArbd</p></li>
+</ul>
+</dd>
+<dt class="field-even">Returns<span class="colon">:</span></dt>
+<dd class="field-even"><p>ParmedArbd model with dual topology</p>
+</dd>
+</dl>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="arbdmodel.parmed_bd.ParmedArbd.load_structure">
+<span class="sig-name descname"><span class="pre">load_structure</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">parmed_structure</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">psf</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">pdb</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">parameter_files</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">system_type</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">'charmm'</span></span></em><span class="sig-paren">)</span><a class="reference internal" href="../../_modules/arbdmodel/parmed_bd.html#ParmedArbd.load_structure"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#arbdmodel.parmed_bd.ParmedArbd.load_structure" title="Link to this definition">#</a></dt>
+<dd><p>Load a ParmEd structure or read from PSF/PDB files.</p>
+<dl class="field-list simple">
+<dt class="field-odd">Parameters<span class="colon">:</span></dt>
+<dd class="field-odd"><ul class="simple">
+<li><p><strong>parmed_structure</strong> – Existing ParmEd structure object (optional)</p></li>
+<li><p><strong>psf</strong> – Path to PSF file (optional if parmed_structure is provided)</p></li>
+<li><p><strong>pdb</strong> – Path to PDB file (optional if parmed_structure is provided)</p></li>
+<li><p><strong>parameter_files</strong> – List of parameter files (optional)</p></li>
+<li><p><strong>system_type</strong> – Type of system (‘charmm’, etc.)</p></li>
+</ul>
+</dd>
+<dt class="field-even">Returns<span class="colon">:</span></dt>
+<dd class="field-even"><p>self for method chaining</p>
+</dd>
+</dl>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="arbdmodel.parmed_bd.ParmedArbd.simulate">
+<span class="sig-name descname"><span class="pre">simulate</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">output_name</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">output_directory</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">'output'</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">log_file</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">directory</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">'.'</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">binary</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">num_procs</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">dry_run</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">False</span></span></em>, <em class="sig-param"><span class="o"><span class="pre">**</span></span><span class="n"><span class="pre">conf_params</span></span></em><span class="sig-paren">)</span><a class="reference internal" href="../../_modules/arbdmodel/parmed_bd.html#ParmedArbd.simulate"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#arbdmodel.parmed_bd.ParmedArbd.simulate" title="Link to this definition">#</a></dt>
+<dd><p>Run simulation with the ARBD model.</p>
+<dl class="field-list simple">
+<dt class="field-odd">Parameters<span class="colon">:</span></dt>
+<dd class="field-odd"><ul class="simple">
+<li><p><strong>output_name</strong> – Base name for output files</p></li>
+<li><p><strong>output_directory</strong> – Directory for output files</p></li>
+<li><p><strong>log_file</strong> – File for logging</p></li>
+<li><p><strong>directory</strong> – Working directory</p></li>
+<li><p><strong>binary</strong> – Path to simulation binary</p></li>
+<li><p><strong>num_procs</strong> – Number of processors to use</p></li>
+<li><p><strong>dry_run</strong> – If True, don’t actually run</p></li>
+<li><p><strong>**conf_params</strong> – Additional configuration parameters</p></li>
+</ul>
+</dd>
+<dt class="field-even">Returns<span class="colon">:</span></dt>
+<dd class="field-even"><p>Result of the simulation</p>
+</dd>
+</dl>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="arbdmodel.parmed_bd.ParmedArbd.write_restraint_files">
+<span class="sig-name descname"><span class="pre">write_restraint_files</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">fep_file</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">'dual.fep.exb'</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">min_fep_file</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">'dual.min.fep.exb'</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">bp_file</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">'dual.bp.exb'</span></span></em><span class="sig-paren">)</span><a class="reference internal" href="../../_modules/arbdmodel/parmed_bd.html#ParmedArbd.write_restraint_files"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#arbdmodel.parmed_bd.ParmedArbd.write_restraint_files" title="Link to this definition">#</a></dt>
+<dd><p>Write restraint files for dual topology simulations.</p>
+<dl class="field-list simple">
+<dt class="field-odd">Parameters<span class="colon">:</span></dt>
+<dd class="field-odd"><ul class="simple">
+<li><p><strong>fep_file</strong> – Output file for FEP restraints</p></li>
+<li><p><strong>min_fep_file</strong> – Output file for minimization FEP restraints</p></li>
+<li><p><strong>bp_file</strong> – Output file for base pair restraints</p></li>
+</ul>
+</dd>
+</dl>
+</dd></dl>
+
+</dd></dl>
+
</section>
<script type="text/x-thebe-config">
@@ -390,6 +550,32 @@ document.write(`
+ <div class="bd-sidebar-secondary bd-toc"><div class="sidebar-secondary-items sidebar-secondary__inner">
+
+
+ <div class="sidebar-secondary-item">
+ <div class="page-toc tocsection onthispage">
+ <i class="fa-solid fa-list"></i> Contents
+ </div>
+ <nav class="bd-toc-nav page-toc">
+ <ul class="visible nav section-nav flex-column">
+<li class="toc-h2 nav-item toc-entry"><a class="reference internal nav-link" href="#arbdmodel.parmed_bd.ParmedArbd"><code class="docutils literal notranslate"><span class="pre">ParmedArbd</span></code></a><ul class="nav section-nav flex-column">
+<li class="toc-h3 nav-item toc-entry"><a class="reference internal nav-link" href="#arbdmodel.parmed_bd.ParmedArbd.parmed_structure"><code class="docutils literal notranslate"><span class="pre">ParmedArbd.parmed_structure</span></code></a></li>
+<li class="toc-h3 nav-item toc-entry"><a class="reference internal nav-link" href="#arbdmodel.parmed_bd.ParmedArbd.atom_types"><code class="docutils literal notranslate"><span class="pre">ParmedArbd.atom_types</span></code></a></li>
+<li class="toc-h3 nav-item toc-entry"><a class="reference internal nav-link" href="#arbdmodel.parmed_bd.ParmedArbd.atoms_map"><code class="docutils literal notranslate"><span class="pre">ParmedArbd.atoms_map</span></code></a></li>
+<li class="toc-h3 nav-item toc-entry"><a class="reference internal nav-link" href="#arbdmodel.parmed_bd.ParmedArbd.convert_sod_to_mg"><code class="docutils literal notranslate"><span class="pre">ParmedArbd.convert_sod_to_mg()</span></code></a></li>
+<li class="toc-h3 nav-item toc-entry"><a class="reference internal nav-link" href="#arbdmodel.parmed_bd.ParmedArbd.create_dual_topology"><code class="docutils literal notranslate"><span class="pre">ParmedArbd.create_dual_topology()</span></code></a></li>
+<li class="toc-h3 nav-item toc-entry"><a class="reference internal nav-link" href="#arbdmodel.parmed_bd.ParmedArbd.create_dual_topology_model"><code class="docutils literal notranslate"><span class="pre">ParmedArbd.create_dual_topology_model()</span></code></a></li>
+<li class="toc-h3 nav-item toc-entry"><a class="reference internal nav-link" href="#arbdmodel.parmed_bd.ParmedArbd.load_structure"><code class="docutils literal notranslate"><span class="pre">ParmedArbd.load_structure()</span></code></a></li>
+<li class="toc-h3 nav-item toc-entry"><a class="reference internal nav-link" href="#arbdmodel.parmed_bd.ParmedArbd.simulate"><code class="docutils literal notranslate"><span class="pre">ParmedArbd.simulate()</span></code></a></li>
+<li class="toc-h3 nav-item toc-entry"><a class="reference internal nav-link" href="#arbdmodel.parmed_bd.ParmedArbd.write_restraint_files"><code class="docutils literal notranslate"><span class="pre">ParmedArbd.write_restraint_files()</span></code></a></li>
+</ul>
+</li>
+</ul>
+ </nav></div>
+
+</div></div>
+
</div>
<footer class="bd-footer-content">
diff --git a/_build/html/api/utilities/binary_manager.html b/_build/html/api/utilities/binary_manager.html
index 494db2d1d7217f9889750a32a8ac015ae0792356..cdf5ceaef2b137d1fba3e181ec878f861559b782 100644
--- a/_build/html/api/utilities/binary_manager.html
+++ b/_build/html/api/utilities/binary_manager.html
@@ -32,19 +32,19 @@
<link rel="stylesheet" type="text/css" href="../../_static/styles/sphinx-book-theme.css?v=eba8b062" />
<link rel="stylesheet" type="text/css" href="../../_static/togglebutton.css?v=13237357" />
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- <link rel="stylesheet" type="text/css" href="../../_static/mystnb.4510f1fc1dee50b3e5859aac5469c37c29e427902b24a333a5f9fcb2f0b3ac41.css" />
+ <link rel="stylesheet" type="text/css" href="../../_static/mystnb.4510f1fc1dee50b3e5859aac5469c37c29e427902b24a333a5f9fcb2f0b3ac41.css?v=be8a1c11" />
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+ <link rel="stylesheet" type="text/css" href="../../_static/proof.css?v=b4b7a797" />
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+ <link rel="stylesheet" type="text/css" href="../../_static/css/tooltipster.custom.css?v=7bc2f056" />
+ <link rel="stylesheet" type="text/css" href="../../_static/css/tooltipster.bundle.min.css?v=37217874" />
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+ <link rel="stylesheet" type="text/css" href="../../_static/css/tooltipster-sideTip-noir.min.css?v=21a39f42" />
+ <link rel="stylesheet" type="text/css" href="../../_static/css/tooltipster-sideTip-light.min.css?v=a18b2449" />
+ <link rel="stylesheet" type="text/css" href="../../_static/css/tooltipster-sideTip-borderless.min.css?v=dbff53e4" />
+ <link rel="stylesheet" type="text/css" href="../../_static/css/micromodal.css?v=d7bf34ee" />
<link rel="stylesheet" type="text/css" href="../../_static/sphinx-design.min.css?v=95c83b7e" />
<!-- Pre-loaded scripts that we'll load fully later -->
@@ -61,9 +61,9 @@
<script src="../../_static/copybutton.js?v=f281be69"></script>
<script src="../../_static/scripts/sphinx-book-theme.js?v=887ef09a"></script>
<script src="../../_static/tabs.js?v=3ee01567"></script>
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- <script src="../../_static/js/tooltipster.bundle.min.js"></script>
- <script src="../../_static/js/micromodal.min.js"></script>
+ <script src="../../_static/js/hoverxref.js?v=c95ade4f"></script>
+ <script src="../../_static/js/tooltipster.bundle.min.js?v=18bf091b"></script>
+ <script src="../../_static/js/micromodal.min.js?v=04d6302d"></script>
<script>let toggleHintShow = 'Click to show';</script>
<script>let toggleHintHide = 'Click to hide';</script>
<script>let toggleOpenOnPrint = 'true';</script>
@@ -323,7 +323,9 @@ document.write(`
</button>
`);
</script>
-
+<button class="sidebar-toggle secondary-toggle btn btn-sm" title="Toggle secondary sidebar" data-bs-placement="bottom" data-bs-toggle="tooltip">
+ <span class="fa-solid fa-list"></span>
+</button>
</div></div>
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@@ -339,6 +341,14 @@ document.write(`
<div id="print-main-content">
<div id="jb-print-toc">
+ <div>
+ <h2> Contents </h2>
+ </div>
+ <nav aria-label="Page">
+ <ul class="visible nav section-nav flex-column">
+<li class="toc-h2 nav-item toc-entry"><a class="reference internal nav-link" href="#arbdmodel.binary_manager.initialize_binary_paths"><code class="docutils literal notranslate"><span class="pre">initialize_binary_paths()</span></code></a></li>
+</ul>
+ </nav>
</div>
</div>
</div>
@@ -352,6 +362,15 @@ document.write(`
<h1>binary_manager<a class="headerlink" href="#binary-manager" title="Link to this heading">#</a></h1>
<p>Binary path management module for simulation engines and processors.
This module provides a singleton object to manage paths to external binaries.</p>
+<p id="module-arbdmodel.binary_manager">Binary path management module for simulation engines and processors.
+This module provides a singleton object to manage paths to external binaries.</p>
+<dl class="py function">
+<dt class="sig sig-object py" id="arbdmodel.binary_manager.initialize_binary_paths">
+<span class="sig-name descname"><span class="pre">initialize_binary_paths</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="reference internal" href="../../_modules/arbdmodel/binary_manager.html#initialize_binary_paths"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#arbdmodel.binary_manager.initialize_binary_paths" title="Link to this definition">#</a></dt>
+<dd><p>Initialize binary paths from environment variables.
+This function should be called during package initialization.</p>
+</dd></dl>
+
</section>
<script type="text/x-thebe-config">
@@ -391,6 +410,21 @@ This module provides a singleton object to manage paths to external binaries.</p
+ <div class="bd-sidebar-secondary bd-toc"><div class="sidebar-secondary-items sidebar-secondary__inner">
+
+
+ <div class="sidebar-secondary-item">
+ <div class="page-toc tocsection onthispage">
+ <i class="fa-solid fa-list"></i> Contents
+ </div>
+ <nav class="bd-toc-nav page-toc">
+ <ul class="visible nav section-nav flex-column">
+<li class="toc-h2 nav-item toc-entry"><a class="reference internal nav-link" href="#arbdmodel.binary_manager.initialize_binary_paths"><code class="docutils literal notranslate"><span class="pre">initialize_binary_paths()</span></code></a></li>
+</ul>
+ </nav></div>
+
+</div></div>
+
</div>
<footer class="bd-footer-content">
diff --git a/_build/html/api/utilities/coords.html b/_build/html/api/utilities/coords.html
index 4dbcefa903896e1b490235a1784205de325e3888..1e2da889a84bd5f1f6a30235ba76c176297186e4 100644
--- a/_build/html/api/utilities/coords.html
+++ b/_build/html/api/utilities/coords.html
@@ -32,19 +32,19 @@
<link rel="stylesheet" type="text/css" href="../../_static/styles/sphinx-book-theme.css?v=eba8b062" />
<link rel="stylesheet" type="text/css" href="../../_static/togglebutton.css?v=13237357" />
<link rel="stylesheet" type="text/css" href="../../_static/copybutton.css?v=76b2166b" />
- <link rel="stylesheet" type="text/css" href="../../_static/mystnb.4510f1fc1dee50b3e5859aac5469c37c29e427902b24a333a5f9fcb2f0b3ac41.css" />
+ <link rel="stylesheet" type="text/css" href="../../_static/mystnb.4510f1fc1dee50b3e5859aac5469c37c29e427902b24a333a5f9fcb2f0b3ac41.css?v=be8a1c11" />
<link rel="stylesheet" type="text/css" href="../../_static/sphinx-thebe.css?v=4fa983c6" />
<link rel="stylesheet" type="text/css" href="../../_static/tabs.css?v=4c969af8" />
- <link rel="stylesheet" type="text/css" href="../../_static/proof.css" />
+ <link rel="stylesheet" type="text/css" href="../../_static/proof.css?v=b4b7a797" />
<link rel="stylesheet" type="text/css" href="../../_static/styles/sphinx-examples.css?v=e236af4b" />
- <link rel="stylesheet" type="text/css" href="../../_static/css/tooltipster.custom.css" />
- <link rel="stylesheet" type="text/css" href="../../_static/css/tooltipster.bundle.min.css" />
- <link rel="stylesheet" type="text/css" href="../../_static/css/tooltipster-sideTip-shadow.min.css" />
- <link rel="stylesheet" type="text/css" href="../../_static/css/tooltipster-sideTip-punk.min.css" />
- <link rel="stylesheet" type="text/css" href="../../_static/css/tooltipster-sideTip-noir.min.css" />
- <link rel="stylesheet" type="text/css" href="../../_static/css/tooltipster-sideTip-light.min.css" />
- <link rel="stylesheet" type="text/css" href="../../_static/css/tooltipster-sideTip-borderless.min.css" />
- <link rel="stylesheet" type="text/css" href="../../_static/css/micromodal.css" />
+ <link rel="stylesheet" type="text/css" href="../../_static/css/tooltipster.custom.css?v=7bc2f056" />
+ <link rel="stylesheet" type="text/css" href="../../_static/css/tooltipster.bundle.min.css?v=37217874" />
+ <link rel="stylesheet" type="text/css" href="../../_static/css/tooltipster-sideTip-shadow.min.css?v=6227e517" />
+ <link rel="stylesheet" type="text/css" href="../../_static/css/tooltipster-sideTip-punk.min.css?v=94669e23" />
+ <link rel="stylesheet" type="text/css" href="../../_static/css/tooltipster-sideTip-noir.min.css?v=21a39f42" />
+ <link rel="stylesheet" type="text/css" href="../../_static/css/tooltipster-sideTip-light.min.css?v=a18b2449" />
+ <link rel="stylesheet" type="text/css" href="../../_static/css/tooltipster-sideTip-borderless.min.css?v=dbff53e4" />
+ <link rel="stylesheet" type="text/css" href="../../_static/css/micromodal.css?v=d7bf34ee" />
<link rel="stylesheet" type="text/css" href="../../_static/sphinx-design.min.css?v=95c83b7e" />
<!-- Pre-loaded scripts that we'll load fully later -->
@@ -61,9 +61,9 @@
<script src="../../_static/copybutton.js?v=f281be69"></script>
<script src="../../_static/scripts/sphinx-book-theme.js?v=887ef09a"></script>
<script src="../../_static/tabs.js?v=3ee01567"></script>
- <script src="../../_static/js/hoverxref.js"></script>
- <script src="../../_static/js/tooltipster.bundle.min.js"></script>
- <script src="../../_static/js/micromodal.min.js"></script>
+ <script src="../../_static/js/hoverxref.js?v=c95ade4f"></script>
+ <script src="../../_static/js/tooltipster.bundle.min.js?v=18bf091b"></script>
+ <script src="../../_static/js/micromodal.min.js?v=04d6302d"></script>
<script>let toggleHintShow = 'Click to show';</script>
<script>let toggleHintHide = 'Click to hide';</script>
<script>let toggleOpenOnPrint = 'true';</script>
@@ -346,6 +346,9 @@ document.write(`
</div>
<nav aria-label="Page">
<ul class="visible nav section-nav flex-column">
+<li class="toc-h2 nav-item toc-entry"><a class="reference internal nav-link" href="#arbdmodel.coords.Generate_coordinates"><code class="docutils literal notranslate"><span class="pre">Generate_coordinates()</span></code></a></li>
+<li class="toc-h2 nav-item toc-entry"><a class="reference internal nav-link" href="#arbdmodel.coords.Generate_spanning_vectors"><code class="docutils literal notranslate"><span class="pre">Generate_spanning_vectors()</span></code></a></li>
+<li class="toc-h2 nav-item toc-entry"><a class="reference internal nav-link" href="#arbdmodel.coords.calculate_dimensions_from_cell_vectors"><code class="docutils literal notranslate"><span class="pre">calculate_dimensions_from_cell_vectors()</span></code></a></li>
<li class="toc-h2 nav-item toc-entry"><a class="reference internal nav-link" href="#arbdmodel.coords.minimizeRmsd"><code class="docutils literal notranslate"><span class="pre">minimizeRmsd()</span></code></a></li>
<li class="toc-h2 nav-item toc-entry"><a class="reference internal nav-link" href="#arbdmodel.coords.quaternion_exp"><code class="docutils literal notranslate"><span class="pre">quaternion_exp()</span></code></a></li>
<li class="toc-h2 nav-item toc-entry"><a class="reference internal nav-link" href="#arbdmodel.coords.quaternion_from_matrix"><code class="docutils literal notranslate"><span class="pre">quaternion_from_matrix()</span></code></a></li>
@@ -374,6 +377,37 @@ document.write(`
<h1>coords<a class="headerlink" href="#coords" title="Link to this heading">#</a></h1>
<p>Module documentation for <code class="docutils literal notranslate"><span class="pre">arbdmodel.coords</span></code>.</p>
<dl class="py function" id="module-arbdmodel.coords">
+<dt class="sig sig-object py" id="arbdmodel.coords.Generate_coordinates">
+<span class="sig-name descname"><span class="pre">Generate_coordinates</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">bv1</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">bv2</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">bv3</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">n1</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">n2</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">n3</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">num_copy</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">origin</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">replica_index</span></span></em><span class="sig-paren">)</span><a class="reference internal" href="../../_modules/arbdmodel/coords.html#Generate_coordinates"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#arbdmodel.coords.Generate_coordinates" title="Link to this definition">#</a></dt>
+<dd></dd></dl>
+
+<dl class="py function">
+<dt class="sig sig-object py" id="arbdmodel.coords.Generate_spanning_vectors">
+<span class="sig-name descname"><span class="pre">Generate_spanning_vectors</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">bv1</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">bv2</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">bv3</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">dimensions</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">buff</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">5</span></span></em><span class="sig-paren">)</span><a class="reference internal" href="../../_modules/arbdmodel/coords.html#Generate_spanning_vectors"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#arbdmodel.coords.Generate_spanning_vectors" title="Link to this definition">#</a></dt>
+<dd></dd></dl>
+
+<dl class="py function">
+<dt class="sig sig-object py" id="arbdmodel.coords.calculate_dimensions_from_cell_vectors">
+<span class="sig-name descname"><span class="pre">calculate_dimensions_from_cell_vectors</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">cell_vectors</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">cell_origin</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">buffer_factor</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">1.2</span></span></em><span class="sig-paren">)</span><a class="reference internal" href="../../_modules/arbdmodel/coords.html#calculate_dimensions_from_cell_vectors"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#arbdmodel.coords.calculate_dimensions_from_cell_vectors" title="Link to this definition">#</a></dt>
+<dd><p>Calculate simulation box dimensions from cell basis vectors with buffer.</p>
+<dl class="field-list simple">
+<dt class="field-odd">Parameters<span class="colon">:</span></dt>
+<dd class="field-odd"><ul class="simple">
+<li><p><strong>cell_vectors</strong> – List of 3 cell basis vectors [[x1,y1,z1], [x2,y2,z2], [x3,y3,z3]]</p></li>
+<li><p><strong>cell_origin</strong> – Cell origin coordinates [x,y,z], defaults to [0,0,0]</p></li>
+<li><p><strong>buffer_factor</strong> – Factor to scale the dimensions for additional buffer space</p></li>
+</ul>
+</dd>
+<dt class="field-even">Returns<span class="colon">:</span></dt>
+<dd class="field-even"><p>3D box dimensions as a tuple (x_dim, y_dim, z_dim)</p>
+</dd>
+<dt class="field-odd">Return type<span class="colon">:</span></dt>
+<dd class="field-odd"><p>dimensions</p>
+</dd>
+</dl>
+</dd></dl>
+
+<dl class="py function">
<dt class="sig sig-object py" id="arbdmodel.coords.minimizeRmsd">
<span class="sig-name descname"><span class="pre">minimizeRmsd</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">coordsB</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">coordsA</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">weights</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em><span class="sig-paren">)</span><a class="reference internal" href="../../_modules/arbdmodel/coords.html#minimizeRmsd"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#arbdmodel.coords.minimizeRmsd" title="Link to this definition">#</a></dt>
<dd></dd></dl>
@@ -486,6 +520,9 @@ document.write(`
</div>
<nav class="bd-toc-nav page-toc">
<ul class="visible nav section-nav flex-column">
+<li class="toc-h2 nav-item toc-entry"><a class="reference internal nav-link" href="#arbdmodel.coords.Generate_coordinates"><code class="docutils literal notranslate"><span class="pre">Generate_coordinates()</span></code></a></li>
+<li class="toc-h2 nav-item toc-entry"><a class="reference internal nav-link" href="#arbdmodel.coords.Generate_spanning_vectors"><code class="docutils literal notranslate"><span class="pre">Generate_spanning_vectors()</span></code></a></li>
+<li class="toc-h2 nav-item toc-entry"><a class="reference internal nav-link" href="#arbdmodel.coords.calculate_dimensions_from_cell_vectors"><code class="docutils literal notranslate"><span class="pre">calculate_dimensions_from_cell_vectors()</span></code></a></li>
<li class="toc-h2 nav-item toc-entry"><a class="reference internal nav-link" href="#arbdmodel.coords.minimizeRmsd"><code class="docutils literal notranslate"><span class="pre">minimizeRmsd()</span></code></a></li>
<li class="toc-h2 nav-item toc-entry"><a class="reference internal nav-link" href="#arbdmodel.coords.quaternion_exp"><code class="docutils literal notranslate"><span class="pre">quaternion_exp()</span></code></a></li>
<li class="toc-h2 nav-item toc-entry"><a class="reference internal nav-link" href="#arbdmodel.coords.quaternion_from_matrix"><code class="docutils literal notranslate"><span class="pre">quaternion_from_matrix()</span></code></a></li>
diff --git a/_build/html/api/utilities/grid.html b/_build/html/api/utilities/grid.html
index e8780d4a7736a8b83625c299e94cb0106d5b5b22..6916b5a51aaf50cbef038be38d22438a0f5bada1 100644
--- a/_build/html/api/utilities/grid.html
+++ b/_build/html/api/utilities/grid.html
@@ -32,19 +32,19 @@
<link rel="stylesheet" type="text/css" href="../../_static/styles/sphinx-book-theme.css?v=eba8b062" />
<link rel="stylesheet" type="text/css" href="../../_static/togglebutton.css?v=13237357" />
<link rel="stylesheet" type="text/css" href="../../_static/copybutton.css?v=76b2166b" />
- <link rel="stylesheet" type="text/css" href="../../_static/mystnb.4510f1fc1dee50b3e5859aac5469c37c29e427902b24a333a5f9fcb2f0b3ac41.css" />
+ <link rel="stylesheet" type="text/css" href="../../_static/mystnb.4510f1fc1dee50b3e5859aac5469c37c29e427902b24a333a5f9fcb2f0b3ac41.css?v=be8a1c11" />
<link rel="stylesheet" type="text/css" href="../../_static/sphinx-thebe.css?v=4fa983c6" />
<link rel="stylesheet" type="text/css" href="../../_static/tabs.css?v=4c969af8" />
- <link rel="stylesheet" type="text/css" href="../../_static/proof.css" />
+ <link rel="stylesheet" type="text/css" href="../../_static/proof.css?v=b4b7a797" />
<link rel="stylesheet" type="text/css" href="../../_static/styles/sphinx-examples.css?v=e236af4b" />
- <link rel="stylesheet" type="text/css" href="../../_static/css/tooltipster.custom.css" />
- <link rel="stylesheet" type="text/css" href="../../_static/css/tooltipster.bundle.min.css" />
- <link rel="stylesheet" type="text/css" href="../../_static/css/tooltipster-sideTip-shadow.min.css" />
- <link rel="stylesheet" type="text/css" href="../../_static/css/tooltipster-sideTip-punk.min.css" />
- <link rel="stylesheet" type="text/css" href="../../_static/css/tooltipster-sideTip-noir.min.css" />
- <link rel="stylesheet" type="text/css" href="../../_static/css/tooltipster-sideTip-light.min.css" />
- <link rel="stylesheet" type="text/css" href="../../_static/css/tooltipster-sideTip-borderless.min.css" />
- <link rel="stylesheet" type="text/css" href="../../_static/css/micromodal.css" />
+ <link rel="stylesheet" type="text/css" href="../../_static/css/tooltipster.custom.css?v=7bc2f056" />
+ <link rel="stylesheet" type="text/css" href="../../_static/css/tooltipster.bundle.min.css?v=37217874" />
+ <link rel="stylesheet" type="text/css" href="../../_static/css/tooltipster-sideTip-shadow.min.css?v=6227e517" />
+ <link rel="stylesheet" type="text/css" href="../../_static/css/tooltipster-sideTip-punk.min.css?v=94669e23" />
+ <link rel="stylesheet" type="text/css" href="../../_static/css/tooltipster-sideTip-noir.min.css?v=21a39f42" />
+ <link rel="stylesheet" type="text/css" href="../../_static/css/tooltipster-sideTip-light.min.css?v=a18b2449" />
+ <link rel="stylesheet" type="text/css" href="../../_static/css/tooltipster-sideTip-borderless.min.css?v=dbff53e4" />
+ <link rel="stylesheet" type="text/css" href="../../_static/css/micromodal.css?v=d7bf34ee" />
<link rel="stylesheet" type="text/css" href="../../_static/sphinx-design.min.css?v=95c83b7e" />
<!-- Pre-loaded scripts that we'll load fully later -->
@@ -61,9 +61,9 @@
<script src="../../_static/copybutton.js?v=f281be69"></script>
<script src="../../_static/scripts/sphinx-book-theme.js?v=887ef09a"></script>
<script src="../../_static/tabs.js?v=3ee01567"></script>
- <script src="../../_static/js/hoverxref.js"></script>
- <script src="../../_static/js/tooltipster.bundle.min.js"></script>
- <script src="../../_static/js/micromodal.min.js"></script>
+ <script src="../../_static/js/hoverxref.js?v=c95ade4f"></script>
+ <script src="../../_static/js/tooltipster.bundle.min.js?v=18bf091b"></script>
+ <script src="../../_static/js/micromodal.min.js?v=04d6302d"></script>
<script>let toggleHintShow = 'Click to show';</script>
<script>let toggleHintHide = 'Click to hide';</script>
<script>let toggleOpenOnPrint = 'true';</script>
@@ -346,6 +346,8 @@ document.write(`
</div>
<nav aria-label="Page">
<ul class="visible nav section-nav flex-column">
+<li class="toc-h2 nav-item toc-entry"><a class="reference internal nav-link" href="#arbdmodel.grid.Bound_grid"><code class="docutils literal notranslate"><span class="pre">Bound_grid()</span></code></a></li>
+<li class="toc-h2 nav-item toc-entry"><a class="reference internal nav-link" href="#arbdmodel.grid.Create_null"><code class="docutils literal notranslate"><span class="pre">Create_null()</span></code></a></li>
<li class="toc-h2 nav-item toc-entry"><a class="reference internal nav-link" href="#arbdmodel.grid.TestAverageGrids"><code class="docutils literal notranslate"><span class="pre">TestAverageGrids</span></code></a><ul class="nav section-nav flex-column">
<li class="toc-h3 nav-item toc-entry"><a class="reference internal nav-link" href="#arbdmodel.grid.TestAverageGrids.test_average_grids"><code class="docutils literal notranslate"><span class="pre">TestAverageGrids.test_average_grids()</span></code></a></li>
</ul>
@@ -359,11 +361,13 @@ document.write(`
<li class="toc-h2 nav-item toc-entry"><a class="reference internal nav-link" href="#arbdmodel.grid.gaussian_kernel"><code class="docutils literal notranslate"><span class="pre">gaussian_kernel()</span></code></a></li>
<li class="toc-h2 nav-item toc-entry"><a class="reference internal nav-link" href="#arbdmodel.grid.get_slice_enclosing_smaller_grid"><code class="docutils literal notranslate"><span class="pre">get_slice_enclosing_smaller_grid()</span></code></a></li>
<li class="toc-h2 nav-item toc-entry"><a class="reference internal nav-link" href="#arbdmodel.grid.isotropic_kernel"><code class="docutils literal notranslate"><span class="pre">isotropic_kernel()</span></code></a></li>
+<li class="toc-h2 nav-item toc-entry"><a class="reference internal nav-link" href="#arbdmodel.grid.loadGrid"><code class="docutils literal notranslate"><span class="pre">loadGrid()</span></code></a></li>
<li class="toc-h2 nav-item toc-entry"><a class="reference internal nav-link" href="#arbdmodel.grid.neighborhood_average"><code class="docutils literal notranslate"><span class="pre">neighborhood_average()</span></code></a></li>
<li class="toc-h2 nav-item toc-entry"><a class="reference internal nav-link" href="#arbdmodel.grid.replace_false_with_distance"><code class="docutils literal notranslate"><span class="pre">replace_false_with_distance()</span></code></a></li>
<li class="toc-h2 nav-item toc-entry"><a class="reference internal nav-link" href="#arbdmodel.grid.slab_potential_z"><code class="docutils literal notranslate"><span class="pre">slab_potential_z()</span></code></a></li>
<li class="toc-h2 nav-item toc-entry"><a class="reference internal nav-link" href="#arbdmodel.grid.spherical_confinement"><code class="docutils literal notranslate"><span class="pre">spherical_confinement()</span></code></a></li>
<li class="toc-h2 nav-item toc-entry"><a class="reference internal nav-link" href="#arbdmodel.grid.writeDx"><code class="docutils literal notranslate"><span class="pre">writeDx()</span></code></a></li>
+<li class="toc-h2 nav-item toc-entry"><a class="reference internal nav-link" href="#arbdmodel.grid.write_confine_dx"><code class="docutils literal notranslate"><span class="pre">write_confine_dx()</span></code></a></li>
</ul>
</nav>
</div>
@@ -378,7 +382,19 @@ document.write(`
<section class="tex2jax_ignore mathjax_ignore" id="grid">
<h1>grid<a class="headerlink" href="#grid" title="Link to this heading">#</a></h1>
<p>Module documentation for <code class="docutils literal notranslate"><span class="pre">arbdmodel.grid</span></code>.</p>
-<dl class="py class" id="module-arbdmodel.grid">
+<dl class="py function" id="module-arbdmodel.grid">
+<dt class="sig sig-object py" id="arbdmodel.grid.Bound_grid">
+<span class="sig-name descname"><span class="pre">Bound_grid</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">inFile</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">outFile</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">lowerBound</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">upperBound</span></span></em><span class="sig-paren">)</span><a class="reference internal" href="../../_modules/arbdmodel/grid.html#Bound_grid"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#arbdmodel.grid.Bound_grid" title="Link to this definition">#</a></dt>
+<dd><p>Apply bounds to grid values</p>
+</dd></dl>
+
+<dl class="py function">
+<dt class="sig sig-object py" id="arbdmodel.grid.Create_null">
+<span class="sig-name descname"><span class="pre">Create_null</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">grid_path</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">'null.dx'</span></span></em><span class="sig-paren">)</span><a class="reference internal" href="../../_modules/arbdmodel/grid.html#Create_null"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#arbdmodel.grid.Create_null" title="Link to this definition">#</a></dt>
+<dd><p>Create null potential grid</p>
+</dd></dl>
+
+<dl class="py class">
<dt class="sig sig-object py" id="arbdmodel.grid.TestAverageGrids">
<em class="property"><span class="pre">class</span><span class="w"> </span></em><span class="sig-name descname"><span class="pre">TestAverageGrids</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">methodName</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">'runTest'</span></span></em><span class="sig-paren">)</span><a class="reference internal" href="../../_modules/arbdmodel/grid.html#TestAverageGrids"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#arbdmodel.grid.TestAverageGrids" title="Link to this definition">#</a></dt>
<dd><p>Bases: <code class="xref py py-class docutils literal notranslate"><span class="pre">TestCase</span></code></p>
@@ -552,6 +568,12 @@ It should accept a scalar or an array-like object and return a scalar or an arra
</div>
</dd></dl>
+<dl class="py function">
+<dt class="sig sig-object py" id="arbdmodel.grid.loadGrid">
+<span class="sig-name descname"><span class="pre">loadGrid</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">file</span></span></em>, <em class="sig-param"><span class="o"><span class="pre">**</span></span><span class="n"><span class="pre">kwargs</span></span></em><span class="sig-paren">)</span><a class="reference internal" href="../../_modules/arbdmodel/grid.html#loadGrid"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#arbdmodel.grid.loadGrid" title="Link to this definition">#</a></dt>
+<dd><p>Load grid data from DX file</p>
+</dd></dl>
+
<dl class="py function">
<dt class="sig sig-object py" id="arbdmodel.grid.neighborhood_average">
<span class="sig-name descname"><span class="pre">neighborhood_average</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">grid</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">neighborhood</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">1</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">fill_value</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">'mirror'</span></span></em><span class="sig-paren">)</span><a class="reference internal" href="../../_modules/arbdmodel/grid.html#neighborhood_average"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#arbdmodel.grid.neighborhood_average" title="Link to this definition">#</a></dt>
@@ -604,6 +626,11 @@ It should accept a scalar or an array-like object and return a scalar or an arra
<span class="sig-name descname"><span class="pre">writeDx</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">outfile</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">data</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">origin</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">delta</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">fmt</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">'%.12f'</span></span></em><span class="sig-paren">)</span><a class="reference internal" href="../../_modules/arbdmodel/grid.html#writeDx"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#arbdmodel.grid.writeDx" title="Link to this definition">#</a></dt>
<dd></dd></dl>
+<dl class="py function">
+<dt class="sig sig-object py" id="arbdmodel.grid.write_confine_dx">
+<span class="sig-name descname"><span class="pre">write_confine_dx</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">radius</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">100</span></span></em><span class="sig-paren">)</span><a class="reference internal" href="../../_modules/arbdmodel/grid.html#write_confine_dx"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#arbdmodel.grid.write_confine_dx" title="Link to this definition">#</a></dt>
+<dd></dd></dl>
+
</section>
<script type="text/x-thebe-config">
@@ -652,6 +679,8 @@ It should accept a scalar or an array-like object and return a scalar or an arra
</div>
<nav class="bd-toc-nav page-toc">
<ul class="visible nav section-nav flex-column">
+<li class="toc-h2 nav-item toc-entry"><a class="reference internal nav-link" href="#arbdmodel.grid.Bound_grid"><code class="docutils literal notranslate"><span class="pre">Bound_grid()</span></code></a></li>
+<li class="toc-h2 nav-item toc-entry"><a class="reference internal nav-link" href="#arbdmodel.grid.Create_null"><code class="docutils literal notranslate"><span class="pre">Create_null()</span></code></a></li>
<li class="toc-h2 nav-item toc-entry"><a class="reference internal nav-link" href="#arbdmodel.grid.TestAverageGrids"><code class="docutils literal notranslate"><span class="pre">TestAverageGrids</span></code></a><ul class="nav section-nav flex-column">
<li class="toc-h3 nav-item toc-entry"><a class="reference internal nav-link" href="#arbdmodel.grid.TestAverageGrids.test_average_grids"><code class="docutils literal notranslate"><span class="pre">TestAverageGrids.test_average_grids()</span></code></a></li>
</ul>
@@ -665,11 +694,13 @@ It should accept a scalar or an array-like object and return a scalar or an arra
<li class="toc-h2 nav-item toc-entry"><a class="reference internal nav-link" href="#arbdmodel.grid.gaussian_kernel"><code class="docutils literal notranslate"><span class="pre">gaussian_kernel()</span></code></a></li>
<li class="toc-h2 nav-item toc-entry"><a class="reference internal nav-link" href="#arbdmodel.grid.get_slice_enclosing_smaller_grid"><code class="docutils literal notranslate"><span class="pre">get_slice_enclosing_smaller_grid()</span></code></a></li>
<li class="toc-h2 nav-item toc-entry"><a class="reference internal nav-link" href="#arbdmodel.grid.isotropic_kernel"><code class="docutils literal notranslate"><span class="pre">isotropic_kernel()</span></code></a></li>
+<li class="toc-h2 nav-item toc-entry"><a class="reference internal nav-link" href="#arbdmodel.grid.loadGrid"><code class="docutils literal notranslate"><span class="pre">loadGrid()</span></code></a></li>
<li class="toc-h2 nav-item toc-entry"><a class="reference internal nav-link" href="#arbdmodel.grid.neighborhood_average"><code class="docutils literal notranslate"><span class="pre">neighborhood_average()</span></code></a></li>
<li class="toc-h2 nav-item toc-entry"><a class="reference internal nav-link" href="#arbdmodel.grid.replace_false_with_distance"><code class="docutils literal notranslate"><span class="pre">replace_false_with_distance()</span></code></a></li>
<li class="toc-h2 nav-item toc-entry"><a class="reference internal nav-link" href="#arbdmodel.grid.slab_potential_z"><code class="docutils literal notranslate"><span class="pre">slab_potential_z()</span></code></a></li>
<li class="toc-h2 nav-item toc-entry"><a class="reference internal nav-link" href="#arbdmodel.grid.spherical_confinement"><code class="docutils literal notranslate"><span class="pre">spherical_confinement()</span></code></a></li>
<li class="toc-h2 nav-item toc-entry"><a class="reference internal nav-link" href="#arbdmodel.grid.writeDx"><code class="docutils literal notranslate"><span class="pre">writeDx()</span></code></a></li>
+<li class="toc-h2 nav-item toc-entry"><a class="reference internal nav-link" href="#arbdmodel.grid.write_confine_dx"><code class="docutils literal notranslate"><span class="pre">write_confine_dx()</span></code></a></li>
</ul>
</nav></div>
diff --git a/_build/html/api/utilities/index.html b/_build/html/api/utilities/index.html
index 7690f4ecec8585895f2f9317710f6ff41fd76545..4ce4aa5d8948d249a1cfeb912f46af5b89c85dd4 100644
--- a/_build/html/api/utilities/index.html
+++ b/_build/html/api/utilities/index.html
@@ -32,19 +32,19 @@
<link rel="stylesheet" type="text/css" href="../../_static/styles/sphinx-book-theme.css?v=eba8b062" />
<link rel="stylesheet" type="text/css" href="../../_static/togglebutton.css?v=13237357" />
<link rel="stylesheet" type="text/css" href="../../_static/copybutton.css?v=76b2166b" />
- <link rel="stylesheet" type="text/css" href="../../_static/mystnb.4510f1fc1dee50b3e5859aac5469c37c29e427902b24a333a5f9fcb2f0b3ac41.css" />
+ <link rel="stylesheet" type="text/css" href="../../_static/mystnb.4510f1fc1dee50b3e5859aac5469c37c29e427902b24a333a5f9fcb2f0b3ac41.css?v=be8a1c11" />
<link rel="stylesheet" type="text/css" href="../../_static/sphinx-thebe.css?v=4fa983c6" />
<link rel="stylesheet" type="text/css" href="../../_static/tabs.css?v=4c969af8" />
- <link rel="stylesheet" type="text/css" href="../../_static/proof.css" />
+ <link rel="stylesheet" type="text/css" href="../../_static/proof.css?v=b4b7a797" />
<link rel="stylesheet" type="text/css" href="../../_static/styles/sphinx-examples.css?v=e236af4b" />
- <link rel="stylesheet" type="text/css" href="../../_static/css/tooltipster.custom.css" />
- <link rel="stylesheet" type="text/css" href="../../_static/css/tooltipster.bundle.min.css" />
- <link rel="stylesheet" type="text/css" href="../../_static/css/tooltipster-sideTip-shadow.min.css" />
- <link rel="stylesheet" type="text/css" href="../../_static/css/tooltipster-sideTip-punk.min.css" />
- <link rel="stylesheet" type="text/css" href="../../_static/css/tooltipster-sideTip-noir.min.css" />
- <link rel="stylesheet" type="text/css" href="../../_static/css/tooltipster-sideTip-light.min.css" />
- <link rel="stylesheet" type="text/css" href="../../_static/css/tooltipster-sideTip-borderless.min.css" />
- <link rel="stylesheet" type="text/css" href="../../_static/css/micromodal.css" />
+ <link rel="stylesheet" type="text/css" href="../../_static/css/tooltipster.custom.css?v=7bc2f056" />
+ <link rel="stylesheet" type="text/css" href="../../_static/css/tooltipster.bundle.min.css?v=37217874" />
+ <link rel="stylesheet" type="text/css" href="../../_static/css/tooltipster-sideTip-shadow.min.css?v=6227e517" />
+ <link rel="stylesheet" type="text/css" href="../../_static/css/tooltipster-sideTip-punk.min.css?v=94669e23" />
+ <link rel="stylesheet" type="text/css" href="../../_static/css/tooltipster-sideTip-noir.min.css?v=21a39f42" />
+ <link rel="stylesheet" type="text/css" href="../../_static/css/tooltipster-sideTip-light.min.css?v=a18b2449" />
+ <link rel="stylesheet" type="text/css" href="../../_static/css/tooltipster-sideTip-borderless.min.css?v=dbff53e4" />
+ <link rel="stylesheet" type="text/css" href="../../_static/css/micromodal.css?v=d7bf34ee" />
<link rel="stylesheet" type="text/css" href="../../_static/sphinx-design.min.css?v=95c83b7e" />
<!-- Pre-loaded scripts that we'll load fully later -->
@@ -61,9 +61,9 @@
<script src="../../_static/copybutton.js?v=f281be69"></script>
<script src="../../_static/scripts/sphinx-book-theme.js?v=887ef09a"></script>
<script src="../../_static/tabs.js?v=3ee01567"></script>
- <script src="../../_static/js/hoverxref.js"></script>
- <script src="../../_static/js/tooltipster.bundle.min.js"></script>
- <script src="../../_static/js/micromodal.min.js"></script>
+ <script src="../../_static/js/hoverxref.js?v=c95ade4f"></script>
+ <script src="../../_static/js/tooltipster.bundle.min.js?v=18bf091b"></script>
+ <script src="../../_static/js/micromodal.min.js?v=04d6302d"></script>
<script>let toggleHintShow = 'Click to show';</script>
<script>let toggleHintHide = 'Click to hide';</script>
<script>let toggleOpenOnPrint = 'true';</script>
diff --git a/_build/html/api/utilities/logger.html b/_build/html/api/utilities/logger.html
index 96466df61ded6b5f350c2c0bc9e9ecbd26fb2ff3..b2019818b85ebaa370635bf6ed2d0b831a843568 100644
--- a/_build/html/api/utilities/logger.html
+++ b/_build/html/api/utilities/logger.html
@@ -32,19 +32,19 @@
<link rel="stylesheet" type="text/css" href="../../_static/styles/sphinx-book-theme.css?v=eba8b062" />
<link rel="stylesheet" type="text/css" href="../../_static/togglebutton.css?v=13237357" />
<link rel="stylesheet" type="text/css" href="../../_static/copybutton.css?v=76b2166b" />
- <link rel="stylesheet" type="text/css" href="../../_static/mystnb.4510f1fc1dee50b3e5859aac5469c37c29e427902b24a333a5f9fcb2f0b3ac41.css" />
+ <link rel="stylesheet" type="text/css" href="../../_static/mystnb.4510f1fc1dee50b3e5859aac5469c37c29e427902b24a333a5f9fcb2f0b3ac41.css?v=be8a1c11" />
<link rel="stylesheet" type="text/css" href="../../_static/sphinx-thebe.css?v=4fa983c6" />
<link rel="stylesheet" type="text/css" href="../../_static/tabs.css?v=4c969af8" />
- <link rel="stylesheet" type="text/css" href="../../_static/proof.css" />
+ <link rel="stylesheet" type="text/css" href="../../_static/proof.css?v=b4b7a797" />
<link rel="stylesheet" type="text/css" href="../../_static/styles/sphinx-examples.css?v=e236af4b" />
- <link rel="stylesheet" type="text/css" href="../../_static/css/tooltipster.custom.css" />
- <link rel="stylesheet" type="text/css" href="../../_static/css/tooltipster.bundle.min.css" />
- <link rel="stylesheet" type="text/css" href="../../_static/css/tooltipster-sideTip-shadow.min.css" />
- <link rel="stylesheet" type="text/css" href="../../_static/css/tooltipster-sideTip-punk.min.css" />
- <link rel="stylesheet" type="text/css" href="../../_static/css/tooltipster-sideTip-noir.min.css" />
- <link rel="stylesheet" type="text/css" href="../../_static/css/tooltipster-sideTip-light.min.css" />
- <link rel="stylesheet" type="text/css" href="../../_static/css/tooltipster-sideTip-borderless.min.css" />
- <link rel="stylesheet" type="text/css" href="../../_static/css/micromodal.css" />
+ <link rel="stylesheet" type="text/css" href="../../_static/css/tooltipster.custom.css?v=7bc2f056" />
+ <link rel="stylesheet" type="text/css" href="../../_static/css/tooltipster.bundle.min.css?v=37217874" />
+ <link rel="stylesheet" type="text/css" href="../../_static/css/tooltipster-sideTip-shadow.min.css?v=6227e517" />
+ <link rel="stylesheet" type="text/css" href="../../_static/css/tooltipster-sideTip-punk.min.css?v=94669e23" />
+ <link rel="stylesheet" type="text/css" href="../../_static/css/tooltipster-sideTip-noir.min.css?v=21a39f42" />
+ <link rel="stylesheet" type="text/css" href="../../_static/css/tooltipster-sideTip-light.min.css?v=a18b2449" />
+ <link rel="stylesheet" type="text/css" href="../../_static/css/tooltipster-sideTip-borderless.min.css?v=dbff53e4" />
+ <link rel="stylesheet" type="text/css" href="../../_static/css/micromodal.css?v=d7bf34ee" />
<link rel="stylesheet" type="text/css" href="../../_static/sphinx-design.min.css?v=95c83b7e" />
<!-- Pre-loaded scripts that we'll load fully later -->
@@ -61,9 +61,9 @@
<script src="../../_static/copybutton.js?v=f281be69"></script>
<script src="../../_static/scripts/sphinx-book-theme.js?v=887ef09a"></script>
<script src="../../_static/tabs.js?v=3ee01567"></script>
- <script src="../../_static/js/hoverxref.js"></script>
- <script src="../../_static/js/tooltipster.bundle.min.js"></script>
- <script src="../../_static/js/micromodal.min.js"></script>
+ <script src="../../_static/js/hoverxref.js?v=c95ade4f"></script>
+ <script src="../../_static/js/tooltipster.bundle.min.js?v=18bf091b"></script>
+ <script src="../../_static/js/micromodal.min.js?v=04d6302d"></script>
<script>let toggleHintShow = 'Click to show';</script>
<script>let toggleHintHide = 'Click to hide';</script>
<script>let toggleOpenOnPrint = 'true';</script>
@@ -323,7 +323,9 @@ document.write(`
</button>
`);
</script>
-
+<button class="sidebar-toggle secondary-toggle btn btn-sm" title="Toggle secondary sidebar" data-bs-placement="bottom" data-bs-toggle="tooltip">
+ <span class="fa-solid fa-list"></span>
+</button>
</div></div>
</div>
@@ -339,6 +341,14 @@ document.write(`
<div id="print-main-content">
<div id="jb-print-toc">
+ <div>
+ <h2> Contents </h2>
+ </div>
+ <nav aria-label="Page">
+ <ul class="visible nav section-nav flex-column">
+<li class="toc-h2 nav-item toc-entry"><a class="reference internal nav-link" href="#arbdmodel.logger.get_resource_path"><code class="docutils literal notranslate"><span class="pre">get_resource_path()</span></code></a></li>
+</ul>
+ </nav>
</div>
</div>
</div>
@@ -351,18 +361,11 @@ document.write(`
<section class="tex2jax_ignore mathjax_ignore" id="logger">
<h1>logger<a class="headerlink" href="#logger" title="Link to this heading">#</a></h1>
<p>Module documentation for <code class="docutils literal notranslate"><span class="pre">arbdmodel.logger</span></code>.</p>
-<p id="module-arbdmodel.logger">Instances of the Logger class represent a single logging channel. A
-“logging channel†indicates an area of an application. Exactly how an
-“area†is defined is up to the application developer. Since an
-application can have any number of areas, logging channels are identified
-by a unique string. Application areas can be nested (e.g. an area
-of “input processing†might include sub-areas “read CSV filesâ€, “read
-XLS files†and “read Gnumeric filesâ€). To cater for this natural nesting,
-channel names are organized into a namespace hierarchy where levels are
-separated by periods, much like the Java or Python package namespace. So
-in the instance given above, channel names might be “input†for the upper
-level, and “input.csvâ€, “input.xls†and “input.gnu†for the sub-levels.
-There is no arbitrary limit to the depth of nesting.</p>
+<dl class="py function" id="module-arbdmodel.logger">
+<dt class="sig sig-object py" id="arbdmodel.logger.get_resource_path">
+<span class="sig-name descname"><span class="pre">get_resource_path</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">relative_path</span></span></em><span class="sig-paren">)</span><a class="reference internal" href="../../_modules/arbdmodel/logger.html#get_resource_path"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#arbdmodel.logger.get_resource_path" title="Link to this definition">#</a></dt>
+<dd></dd></dl>
+
</section>
<script type="text/x-thebe-config">
@@ -402,6 +405,21 @@ There is no arbitrary limit to the depth of nesting.</p>
+ <div class="bd-sidebar-secondary bd-toc"><div class="sidebar-secondary-items sidebar-secondary__inner">
+
+
+ <div class="sidebar-secondary-item">
+ <div class="page-toc tocsection onthispage">
+ <i class="fa-solid fa-list"></i> Contents
+ </div>
+ <nav class="bd-toc-nav page-toc">
+ <ul class="visible nav section-nav flex-column">
+<li class="toc-h2 nav-item toc-entry"><a class="reference internal nav-link" href="#arbdmodel.logger.get_resource_path"><code class="docutils literal notranslate"><span class="pre">get_resource_path()</span></code></a></li>
+</ul>
+ </nav></div>
+
+</div></div>
+
</div>
<footer class="bd-footer-content">
diff --git a/_build/html/api/utilities/version.html b/_build/html/api/utilities/version.html
index 63b2cdfefc749166d64c1dfc04f91aa4ffd9e879..4ffe2535c2cd64764a3bda79974f171e5bea75d5 100644
--- a/_build/html/api/utilities/version.html
+++ b/_build/html/api/utilities/version.html
@@ -32,19 +32,19 @@
<link rel="stylesheet" type="text/css" href="../../_static/styles/sphinx-book-theme.css?v=eba8b062" />
<link rel="stylesheet" type="text/css" href="../../_static/togglebutton.css?v=13237357" />
<link rel="stylesheet" type="text/css" href="../../_static/copybutton.css?v=76b2166b" />
- <link rel="stylesheet" type="text/css" href="../../_static/mystnb.4510f1fc1dee50b3e5859aac5469c37c29e427902b24a333a5f9fcb2f0b3ac41.css" />
+ <link rel="stylesheet" type="text/css" href="../../_static/mystnb.4510f1fc1dee50b3e5859aac5469c37c29e427902b24a333a5f9fcb2f0b3ac41.css?v=be8a1c11" />
<link rel="stylesheet" type="text/css" href="../../_static/sphinx-thebe.css?v=4fa983c6" />
<link rel="stylesheet" type="text/css" href="../../_static/tabs.css?v=4c969af8" />
- <link rel="stylesheet" type="text/css" href="../../_static/proof.css" />
+ <link rel="stylesheet" type="text/css" href="../../_static/proof.css?v=b4b7a797" />
<link rel="stylesheet" type="text/css" href="../../_static/styles/sphinx-examples.css?v=e236af4b" />
- <link rel="stylesheet" type="text/css" href="../../_static/css/tooltipster.custom.css" />
- <link rel="stylesheet" type="text/css" href="../../_static/css/tooltipster.bundle.min.css" />
- <link rel="stylesheet" type="text/css" href="../../_static/css/tooltipster-sideTip-shadow.min.css" />
- <link rel="stylesheet" type="text/css" href="../../_static/css/tooltipster-sideTip-punk.min.css" />
- <link rel="stylesheet" type="text/css" href="../../_static/css/tooltipster-sideTip-noir.min.css" />
- <link rel="stylesheet" type="text/css" href="../../_static/css/tooltipster-sideTip-light.min.css" />
- <link rel="stylesheet" type="text/css" href="../../_static/css/tooltipster-sideTip-borderless.min.css" />
- <link rel="stylesheet" type="text/css" href="../../_static/css/micromodal.css" />
+ <link rel="stylesheet" type="text/css" href="../../_static/css/tooltipster.custom.css?v=7bc2f056" />
+ <link rel="stylesheet" type="text/css" href="../../_static/css/tooltipster.bundle.min.css?v=37217874" />
+ <link rel="stylesheet" type="text/css" href="../../_static/css/tooltipster-sideTip-shadow.min.css?v=6227e517" />
+ <link rel="stylesheet" type="text/css" href="../../_static/css/tooltipster-sideTip-punk.min.css?v=94669e23" />
+ <link rel="stylesheet" type="text/css" href="../../_static/css/tooltipster-sideTip-noir.min.css?v=21a39f42" />
+ <link rel="stylesheet" type="text/css" href="../../_static/css/tooltipster-sideTip-light.min.css?v=a18b2449" />
+ <link rel="stylesheet" type="text/css" href="../../_static/css/tooltipster-sideTip-borderless.min.css?v=dbff53e4" />
+ <link rel="stylesheet" type="text/css" href="../../_static/css/micromodal.css?v=d7bf34ee" />
<link rel="stylesheet" type="text/css" href="../../_static/sphinx-design.min.css?v=95c83b7e" />
<!-- Pre-loaded scripts that we'll load fully later -->
@@ -61,9 +61,9 @@
<script src="../../_static/copybutton.js?v=f281be69"></script>
<script src="../../_static/scripts/sphinx-book-theme.js?v=887ef09a"></script>
<script src="../../_static/tabs.js?v=3ee01567"></script>
- <script src="../../_static/js/hoverxref.js"></script>
- <script src="../../_static/js/tooltipster.bundle.min.js"></script>
- <script src="../../_static/js/micromodal.min.js"></script>
+ <script src="../../_static/js/hoverxref.js?v=c95ade4f"></script>
+ <script src="../../_static/js/tooltipster.bundle.min.js?v=18bf091b"></script>
+ <script src="../../_static/js/micromodal.min.js?v=04d6302d"></script>
<script>let toggleHintShow = 'Click to show';</script>
<script>let toggleHintHide = 'Click to hide';</script>
<script>let toggleOpenOnPrint = 'true';</script>
diff --git a/_build/html/genindex.html b/_build/html/genindex.html
index 7da555ba2814bac5428d56fe564a41564223f9a6..de0f0c4473dd11545e1e9c02370e3894d8dd9632 100644
--- a/_build/html/genindex.html
+++ b/_build/html/genindex.html
@@ -31,19 +31,19 @@
<link rel="stylesheet" type="text/css" href="_static/styles/sphinx-book-theme.css?v=eba8b062" />
<link rel="stylesheet" type="text/css" href="_static/togglebutton.css?v=13237357" />
<link rel="stylesheet" type="text/css" href="_static/copybutton.css?v=76b2166b" />
- <link rel="stylesheet" type="text/css" href="_static/mystnb.4510f1fc1dee50b3e5859aac5469c37c29e427902b24a333a5f9fcb2f0b3ac41.css" />
+ <link rel="stylesheet" type="text/css" href="_static/mystnb.4510f1fc1dee50b3e5859aac5469c37c29e427902b24a333a5f9fcb2f0b3ac41.css?v=be8a1c11" />
<link rel="stylesheet" type="text/css" href="_static/sphinx-thebe.css?v=4fa983c6" />
<link rel="stylesheet" type="text/css" href="_static/tabs.css?v=4c969af8" />
- <link rel="stylesheet" type="text/css" href="_static/proof.css" />
+ <link rel="stylesheet" type="text/css" href="_static/proof.css?v=b4b7a797" />
<link rel="stylesheet" type="text/css" href="_static/styles/sphinx-examples.css?v=e236af4b" />
- <link rel="stylesheet" type="text/css" href="_static/css/tooltipster.custom.css" />
- <link rel="stylesheet" type="text/css" href="_static/css/tooltipster.bundle.min.css" />
- <link rel="stylesheet" type="text/css" href="_static/css/tooltipster-sideTip-shadow.min.css" />
- <link rel="stylesheet" type="text/css" href="_static/css/tooltipster-sideTip-punk.min.css" />
- <link rel="stylesheet" type="text/css" href="_static/css/tooltipster-sideTip-noir.min.css" />
- <link rel="stylesheet" type="text/css" href="_static/css/tooltipster-sideTip-light.min.css" />
- <link rel="stylesheet" type="text/css" href="_static/css/tooltipster-sideTip-borderless.min.css" />
- <link rel="stylesheet" type="text/css" href="_static/css/micromodal.css" />
+ <link rel="stylesheet" type="text/css" href="_static/css/tooltipster.custom.css?v=7bc2f056" />
+ <link rel="stylesheet" type="text/css" href="_static/css/tooltipster.bundle.min.css?v=37217874" />
+ <link rel="stylesheet" type="text/css" href="_static/css/tooltipster-sideTip-shadow.min.css?v=6227e517" />
+ <link rel="stylesheet" type="text/css" href="_static/css/tooltipster-sideTip-punk.min.css?v=94669e23" />
+ <link rel="stylesheet" type="text/css" href="_static/css/tooltipster-sideTip-noir.min.css?v=21a39f42" />
+ <link rel="stylesheet" type="text/css" href="_static/css/tooltipster-sideTip-light.min.css?v=a18b2449" />
+ <link rel="stylesheet" type="text/css" href="_static/css/tooltipster-sideTip-borderless.min.css?v=dbff53e4" />
+ <link rel="stylesheet" type="text/css" href="_static/css/micromodal.css?v=d7bf34ee" />
<link rel="stylesheet" type="text/css" href="_static/sphinx-design.min.css?v=95c83b7e" />
<!-- Pre-loaded scripts that we'll load fully later -->
@@ -60,9 +60,9 @@
<script src="_static/copybutton.js?v=f281be69"></script>
<script src="_static/scripts/sphinx-book-theme.js?v=887ef09a"></script>
<script src="_static/tabs.js?v=3ee01567"></script>
- <script src="_static/js/hoverxref.js"></script>
- <script src="_static/js/tooltipster.bundle.min.js"></script>
- <script src="_static/js/micromodal.min.js"></script>
+ <script src="_static/js/hoverxref.js?v=c95ade4f"></script>
+ <script src="_static/js/tooltipster.bundle.min.js?v=18bf091b"></script>
+ <script src="_static/js/micromodal.min.js?v=04d6302d"></script>
<script>let toggleHintShow = 'Click to show';</script>
<script>let toggleHintHide = 'Click to hide';</script>
<script>let toggleOpenOnPrint = 'true';</script>
@@ -334,19 +334,102 @@ document.write(`
</li>
<li><a href="api/interaction_potentials/interactions.html#arbdmodel.interactions.AbstractPotential">AbstractPotential (class in arbdmodel.interactions)</a>
</li>
- <li><a href="api/polymer_modeling/polymer.html#arbdmodel.polymer.PolymerGroup.add_grid_potential">add_grid_potential() (PolymerGroup method)</a>
+ <li><a href="api/core/model.html#arbdmodel.model.ArbdModel.add">add() (ArbdModel method)</a>
+
+ <ul>
+ <li><a href="api/core/core_objects.html#arbdmodel.core_objects.Parent.add">(Parent method)</a>
+</li>
+ </ul></li>
+ <li><a href="api/core/core_objects.html#arbdmodel.core_objects.Parent.add_angle">add_angle() (Parent method)</a>
+</li>
+ <li><a href="api/core/core_objects.html#arbdmodel.core_objects.Parent.add_bond">add_bond() (Parent method)</a>
+</li>
+ <li><a href="api/core/core_objects.html#arbdmodel.core_objects.Parent.add_bond_angle">add_bond_angle() (Parent method)</a>
+</li>
+ <li><a href="api/shape-based_models/shape_cg.html#arbdmodel.shape_cg.ShapeCGModel.add_confinement">add_confinement() (ShapeCGModel method)</a>
+</li>
+ <li><a href="api/rigidbody_models/structure_rigidbody.html#arbdmodel.structure_rigidbody.StructureRigidBodyModel.add_diffusible_object">add_diffusible_object() (StructureRigidBodyModel method)</a>
+</li>
+ <li><a href="api/core/core_objects.html#arbdmodel.core_objects.Parent.add_dihedral">add_dihedral() (Parent method)</a>
+</li>
+ <li><a href="api/core/core_objects.html#arbdmodel.core_objects.Parent.add_exclusion">add_exclusion() (Parent method)</a>
+</li>
+ <li><a href="api/core/core_objects.html#arbdmodel.core_objects.ParticleType.add_grid_potential">add_grid_potential() (ParticleType method)</a>
+
+ <ul>
+ <li><a href="api/core/core_objects.html#arbdmodel.core_objects.PointParticle.add_grid_potential">(PointParticle method)</a>
+</li>
+ <li><a href="api/polymer_modeling/polymer.html#arbdmodel.polymer.PolymerGroup.add_grid_potential">(PolymerGroup method)</a>
+</li>
+ </ul></li>
+ <li><a href="api/core/model.html#arbdmodel.model.ArbdModel.add_group_site">add_group_site() (ArbdModel method)</a>
+</li>
+ <li><a href="api/core/core_objects.html#arbdmodel.core_objects.Parent.add_improper">add_improper() (Parent method)</a>
</li>
<li><a href="api/polymer_modeling/polymer.html#arbdmodel.polymer.PolymerSection.add_location">add_location() (PolymerSection method)</a>
</li>
+ <li><a href="api/core/model.html#arbdmodel.model.ArbdModel.add_nonbonded_interaction">add_nonbonded_interaction() (ArbdModel method)</a>
+</li>
+ <li><a href="api/core/core_objects.html#arbdmodel.core_objects.Parent.add_product_potential">add_product_potential() (Parent method)</a>
+</li>
+ <li><a href="api/shape-based_models/shape_cg.html#arbdmodel.shape_cg.ShapeCGModel.add_protein_nb_interactions">add_protein_nb_interactions() (ShapeCGModel method)</a>
+</li>
+ <li><a href="api/shape-based_models/shape_cg.html#arbdmodel.shape_cg.ShapeCGModel.add_proteins">add_proteins() (ShapeCGModel method)</a>
+</li>
+ <li><a href="api/core/core_objects.html#arbdmodel.core_objects.GroupSite.add_restraint">add_restraint() (GroupSite method)</a>
+
+ <ul>
+ <li><a href="api/core/core_objects.html#arbdmodel.core_objects.PointParticle.add_restraint">(PointParticle method)</a>
+</li>
+ <li><a href="api/core/core_objects.html#arbdmodel.core_objects.RigidBody.add_restraint">(RigidBody method)</a>
+</li>
+ </ul></li>
<li><a href="api/utilities/grid.html#arbdmodel.grid.add_smaller_grid">add_smaller_grid() (in module arbdmodel.grid)</a>
+</li>
+ <li><a href="api/rigidbody_models/structure_rigidbody.html#arbdmodel.structure_rigidbody.StructureRigidBodyModel.add_static_object">add_static_object() (StructureRigidBodyModel method)</a>
+</li>
+ <li><a href="api/core/core_objects.html#arbdmodel.core_objects.Parent.add_vector_angle">add_vector_angle() (Parent method)</a>
+</li>
+ <li><a href="api/rigidbody_models/structure_from_pdb.html#arbdmodel.structure_from_pdb.StructureProcessor.align_structure">align_structure() (StructureProcessor method)</a>
</li>
<li><a href="api/interaction_potentials/ibi.html#arbdmodel.ibi.AngleDof">AngleDof (class in arbdmodel.ibi)</a>
+</li>
+ <li><a href="api/simulation_engines/engine.html#arbdmodel.engine.APBSRunner">APBSRunner (class in arbdmodel.engine)</a>
+</li>
+ <li><a href="api/rigidbody_models/structure_from_pdb.html#arbdmodel.structure_from_pdb.StructureProcessor.apply_gaussian_smoothing">apply_gaussian_smoothing() (StructureProcessor method)</a>
+</li>
+ <li><a href="api/core/core_objects.html#arbdmodel.core_objects.Transformable.applyOrientation">applyOrientation() (Transformable method)</a>
+</li>
+ <li><a href="api/simulation_engines/engine.html#arbdmodel.engine.ArbdEngine">ArbdEngine (class in arbdmodel.engine)</a>
+</li>
+ <li><a href="api/core/model.html#arbdmodel.model.ArbdModel">ArbdModel (class in arbdmodel.model)</a>
</li>
<li>
+ arbdmodel.binary_manager
+
+ <ul>
+ <li><a href="api/utilities/binary_manager.html#module-arbdmodel.binary_manager">module</a>
+</li>
+ </ul></li>
+ <li>
arbdmodel.coords
<ul>
<li><a href="api/utilities/coords.html#module-arbdmodel.coords">module</a>
+</li>
+ </ul></li>
+ <li>
+ arbdmodel.core_objects
+
+ <ul>
+ <li><a href="api/core/core_objects.html#module-arbdmodel.core_objects">module</a>
+</li>
+ </ul></li>
+ <li>
+ arbdmodel.engine
+
+ <ul>
+ <li><a href="api/simulation_engines/engine.html#module-arbdmodel.engine">module</a>
</li>
</ul></li>
<li>
@@ -363,6 +446,8 @@ document.write(`
<li><a href="api/utilities/grid.html#module-arbdmodel.grid">module</a>
</li>
</ul></li>
+ </ul></td>
+ <td style="width: 33%; vertical-align: top;"><ul>
<li>
arbdmodel.hps_polymer_model
@@ -384,8 +469,6 @@ document.write(`
<li><a href="api/interaction_potentials/interactions.html#module-arbdmodel.interactions">module</a>
</li>
</ul></li>
- </ul></td>
- <td style="width: 33%; vertical-align: top;"><ul>
<li>
arbdmodel.kh_polymer_model
@@ -398,6 +481,34 @@ document.write(`
<ul>
<li><a href="api/utilities/logger.html#module-arbdmodel.logger">module</a>
+</li>
+ </ul></li>
+ <li>
+ arbdmodel.mesh_process_surface
+
+ <ul>
+ <li><a href="api/rigidbody_models/mesh_process_surface.html#module-arbdmodel.mesh_process_surface">module</a>
+</li>
+ </ul></li>
+ <li>
+ arbdmodel.mesh_process_volume
+
+ <ul>
+ <li><a href="api/rigidbody_models/mesh_process_volume.html#module-arbdmodel.mesh_process_volume">module</a>
+</li>
+ </ul></li>
+ <li>
+ arbdmodel.mesh_rigidbody
+
+ <ul>
+ <li><a href="api/rigidbody_models/mesh_rigidbody.html#module-arbdmodel.mesh_rigidbody">module</a>
+</li>
+ </ul></li>
+ <li>
+ arbdmodel.model
+
+ <ul>
+ <li><a href="api/core/model.html#module-arbdmodel.model">module</a>
</li>
</ul></li>
<li>
@@ -412,6 +523,13 @@ document.write(`
<ul>
<li><a href="api/polymer_modeling/onck_polymer_model.html#module-arbdmodel.onck_polymer_model">module</a>
+</li>
+ </ul></li>
+ <li>
+ arbdmodel.parmed_bd
+
+ <ul>
+ <li><a href="api/simulation_engines/parmed_bd.html#module-arbdmodel.parmed_bd">module</a>
</li>
</ul></li>
<li>
@@ -419,6 +537,13 @@ document.write(`
<ul>
<li><a href="api/polymer_modeling/polymer.html#module-arbdmodel.polymer">module</a>
+</li>
+ </ul></li>
+ <li>
+ arbdmodel.sali_polymer_model
+
+ <ul>
+ <li><a href="api/polymer_modeling/sali_polymer_model.html#module-arbdmodel.sali_polymer_model">module</a>
</li>
</ul></li>
<li>
@@ -426,6 +551,20 @@ document.write(`
<ul>
<li><a href="api/shape-based_models/shape_cg.html#module-arbdmodel.shape_cg">module</a>
+</li>
+ </ul></li>
+ <li>
+ arbdmodel.sim_config
+
+ <ul>
+ <li><a href="api/core/sim_config.html#module-arbdmodel.sim_config">module</a>
+</li>
+ </ul></li>
+ <li>
+ arbdmodel.simplearbd
+
+ <ul>
+ <li><a href="api/rigidbody_models/simplearbd.html#module-arbdmodel.simplearbd">module</a>
</li>
</ul></li>
<li>
@@ -433,6 +572,20 @@ document.write(`
<ul>
<li><a href="api/polymer_modeling/ssdna_two_bead.html#module-arbdmodel.ssdna_two_bead">module</a>
+</li>
+ </ul></li>
+ <li>
+ arbdmodel.structure_from_pdb
+
+ <ul>
+ <li><a href="api/rigidbody_models/structure_from_pdb.html#module-arbdmodel.structure_from_pdb">module</a>
+</li>
+ </ul></li>
+ <li>
+ arbdmodel.structure_rigidbody
+
+ <ul>
+ <li><a href="api/rigidbody_models/structure_rigidbody.html#module-arbdmodel.structure_rigidbody">module</a>
</li>
</ul></li>
<li>
@@ -442,6 +595,14 @@ document.write(`
<li><a href="api/utilities/version.html#module-arbdmodel.version">module</a>
</li>
</ul></li>
+ <li><a href="api/core/model.html#arbdmodel.model.ArbdModel.assign_IBI_degrees_of_freedom">assign_IBI_degrees_of_freedom() (ArbdModel method)</a>
+</li>
+ <li><a href="api/simulation_engines/parmed_bd.html#arbdmodel.parmed_bd.ParmedArbd.atom_types">atom_types (ParmedArbd attribute)</a>
+</li>
+ <li><a href="api/simulation_engines/parmed_bd.html#arbdmodel.parmed_bd.ParmedArbd.atoms_map">atoms_map (ParmedArbd attribute)</a>
+</li>
+ <li><a href="api/core/core_objects.html#arbdmodel.core_objects.RigidBodyType.attach_particle">attach_particle() (RigidBodyType method)</a>
+</li>
<li><a href="api/utilities/grid.html#arbdmodel.grid.average_grids">average_grids() (in module arbdmodel.grid)</a>
</li>
</ul></td>
@@ -452,11 +613,15 @@ document.write(`
<td style="width: 33%; vertical-align: top;"><ul>
<li><a href="api/polymer_modeling/ssdna_two_bead.html#arbdmodel.ssdna_two_bead.DnaStrandBeads.b">b (DnaStrandBeads attribute)</a>
</li>
- </ul></td>
- <td style="width: 33%; vertical-align: top;"><ul>
<li><a href="api/interaction_potentials/ibi.html#arbdmodel.ibi.BondAngleDof">BondAngleDof (class in arbdmodel.ibi)</a>
</li>
+ </ul></td>
+ <td style="width: 33%; vertical-align: top;"><ul>
<li><a href="api/interaction_potentials/ibi.html#arbdmodel.ibi.BondDof">BondDof (class in arbdmodel.ibi)</a>
+</li>
+ <li><a href="api/utilities/grid.html#arbdmodel.grid.Bound_grid">Bound_grid() (in module arbdmodel.grid)</a>
+</li>
+ <li><a href="api/interaction_potentials/interactions.html#arbdmodel.interactions.BoundaryPotential">BoundaryPotential (class in arbdmodel.interactions)</a>
</li>
</ul></td>
</tr></table>
@@ -464,11 +629,39 @@ document.write(`
<h2 id="C">C</h2>
<table style="width: 100%" class="indextable genindextable"><tr>
<td style="width: 33%; vertical-align: top;"><ul>
+ <li><a href="api/shape-based_models/shape_cg.html#arbdmodel.shape_cg.ShapeCGFactory.calc_atom_sasa">calc_atom_sasa() (ShapeCGFactory method)</a>
+</li>
+ <li><a href="api/rigidbody_models/mesh_process_volume.html#arbdmodel.mesh_process_volume.MeshProcessor.calculate_damping">calculate_damping() (MeshProcessor method)</a>
+
+ <ul>
+ <li><a href="api/rigidbody_models/mesh_process_surface.html#arbdmodel.mesh_process_surface.SurfaceMeshProcessor.calculate_damping">(SurfaceMeshProcessor method)</a>
+</li>
+ </ul></li>
+ <li><a href="api/utilities/coords.html#arbdmodel.coords.calculate_dimensions_from_cell_vectors">calculate_dimensions_from_cell_vectors() (in module arbdmodel.coords)</a>
+</li>
+ <li><a href="api/rigidbody_models/structure_from_pdb.html#arbdmodel.structure_from_pdb.StructureProcessor.calculate_hydrodynamic_properties">calculate_hydrodynamic_properties() (StructureProcessor method)</a>
+</li>
+ <li><a href="api/shape-based_models/shape_cg.html#arbdmodel.shape_cg.ShapeCGModel.calculate_total_mass">calculate_total_mass() (ShapeCGModel method)</a>
+</li>
<li><a href="api/utilities/version.html#arbdmodel.version.call_git_describe">call_git_describe() (in module arbdmodel.version)</a>
</li>
<li><a href="api/utilities/version.html#arbdmodel.version.check_git_repository">check_git_repository() (in module arbdmodel.version)</a>
+</li>
+ <li><a href="api/core/core_objects.html#arbdmodel.core_objects.Child">Child (class in arbdmodel.core_objects)</a>
</li>
<li><a href="api/utilities/version.html#arbdmodel.version.Citation">Citation (class in arbdmodel.version)</a>
+</li>
+ <li><a href="api/core/model.html#arbdmodel.model.ArbdModel.clear_all">clear_all() (ArbdModel method)</a>
+
+ <ul>
+ <li><a href="api/core/core_objects.html#arbdmodel.core_objects.Parent.clear_all">(Parent method)</a>
+</li>
+ </ul></li>
+ <li><a href="api/core/core_objects.html#arbdmodel.core_objects.Clone">Clone (class in arbdmodel.core_objects)</a>
+</li>
+ <li><a href="api/core/core_objects.html#arbdmodel.core_objects.Group.clone">clone() (Group method)</a>
+</li>
+ <li><a href="api/core/sim_config.html#arbdmodel.sim_config.SimConf.combine">combine() (SimConf method)</a>
</li>
<li><a href="api/interaction_potentials/ibi.html#arbdmodel.ibi.AngleDof.compute_volume">compute_volume() (AngleDof method)</a>
@@ -484,6 +677,8 @@ document.write(`
</ul></li>
</ul></td>
<td style="width: 33%; vertical-align: top;"><ul>
+ <li><a href="api/shape-based_models/shape_cg.html#arbdmodel.shape_cg.ShapeCGModel.concentration_to_debye_length">concentration_to_debye_length() (ShapeCGModel method)</a>
+</li>
<li><a href="api/polymer_modeling/polymer.html#arbdmodel.polymer.ConnectableElement">ConnectableElement (class in arbdmodel.polymer)</a>
</li>
<li><a href="api/polymer_modeling/polymer.html#arbdmodel.polymer.Connection">Connection (class in arbdmodel.polymer)</a>
@@ -497,10 +692,22 @@ document.write(`
<li><a href="api/polymer_modeling/polymer.html#arbdmodel.polymer.PolymerSection.contour_to_position">contour_to_position() (PolymerSection method)</a>
</li>
<li><a href="api/polymer_modeling/polymer.html#arbdmodel.polymer.PolymerSection.contour_to_tangent">contour_to_tangent() (PolymerSection method)</a>
+</li>
+ <li><a href="api/simulation_engines/parmed_bd.html#arbdmodel.parmed_bd.ParmedArbd.convert_sod_to_mg">convert_sod_to_mg() (ParmedArbd static method)</a>
</li>
<li><a href="api/utilities/grid.html#arbdmodel.grid.convolve_kernel_truncate">convolve_kernel_truncate() (in module arbdmodel.grid)</a>
</li>
<li><a href="api/utilities/grid.html#arbdmodel.grid.create_bounding_grid">create_bounding_grid() (in module arbdmodel.grid)</a>
+</li>
+ <li><a href="api/simulation_engines/parmed_bd.html#arbdmodel.parmed_bd.ParmedArbd.create_dual_topology">create_dual_topology() (ParmedArbd static method)</a>
+</li>
+ <li><a href="api/simulation_engines/parmed_bd.html#arbdmodel.parmed_bd.ParmedArbd.create_dual_topology_model">create_dual_topology_model() (ParmedArbd class method)</a>
+</li>
+ <li><a href="api/rigidbody_models/simplearbd.html#arbdmodel.simplearbd.SimpleArbdConfig.create_engine">create_engine() (SimpleArbdConfig method)</a>
+</li>
+ <li><a href="api/rigidbody_models/simplearbd.html#arbdmodel.simplearbd.SimpleArbdConfig.create_model">create_model() (SimpleArbdConfig method)</a>
+</li>
+ <li><a href="api/utilities/grid.html#arbdmodel.grid.Create_null">Create_null() (in module arbdmodel.grid)</a>
</li>
</ul></td>
</tr></table>
@@ -508,31 +715,63 @@ document.write(`
<h2 id="D">D</h2>
<table style="width: 100%" class="indextable genindextable"><tr>
<td style="width: 33%; vertical-align: top;"><ul>
+ <li><a href="api/simulation_engines/engine.html#arbdmodel.engine.ArbdEngine.default_binary">default_binary (ArbdEngine property)</a>
+
+ <ul>
+ <li><a href="api/simulation_engines/engine.html#arbdmodel.engine.NamdEngine.default_binary">(NamdEngine property)</a>
+</li>
+ <li><a href="api/simulation_engines/engine.html#arbdmodel.engine.SimEngine.default_binary">(SimEngine property)</a>
+</li>
+ </ul></li>
+ <li><a href="api/core/sim_config.html#arbdmodel.sim_config.DefaultSimConf">DefaultSimConf (class in arbdmodel.sim_config)</a>
+</li>
<li><a href="api/interaction_potentials/ibi.html#arbdmodel.ibi.DegreeOfFreedom">DegreeOfFreedom (class in arbdmodel.ibi)</a>
</li>
<li><a href="api/polymer_modeling/polymer.html#arbdmodel.polymer.Connection.delete">delete() (Connection method)</a>
+</li>
+ <li><a href="api/rigidbody_models/structure_rigidbody.html#arbdmodel.structure_rigidbody.DiffusiveRigidBodyType">DiffusiveRigidBodyType (class in arbdmodel.structure_rigidbody)</a>
</li>
<li><a href="api/interaction_potentials/ibi.html#arbdmodel.ibi.DihedralDof">DihedralDof (class in arbdmodel.ibi)</a>
</li>
</ul></td>
<td style="width: 33%; vertical-align: top;"><ul>
- <li><a href="api/polymer_modeling/polymer.html#arbdmodel.polymer.PolymerGroup.dimensions_from_structure">dimensions_from_structure() (PolymerGroup method)</a>
+ <li><a href="api/core/model.html#arbdmodel.model.ArbdModel.dimensions_from_structure">dimensions_from_structure() (ArbdModel method)</a>
+
+ <ul>
+ <li><a href="api/polymer_modeling/polymer.html#arbdmodel.polymer.PolymerGroup.dimensions_from_structure">(PolymerGroup method)</a>
</li>
+ </ul></li>
<li><a href="api/utilities/version.html#arbdmodel.version.Citation.display">display() (Citation method)</a>
</li>
<li><a href="api/polymer_modeling/ssdna_two_bead.html#arbdmodel.ssdna_two_bead.DnaModel">DnaModel (class in arbdmodel.ssdna_two_bead)</a>
</li>
<li><a href="api/polymer_modeling/ssdna_two_bead.html#arbdmodel.ssdna_two_bead.DnaStrandBeads">DnaStrandBeads (class in arbdmodel.ssdna_two_bead)</a>
</li>
+ <li><a href="api/core/core_objects.html#arbdmodel.core_objects.Group.duplicate">duplicate() (Group method)</a>
+
+ <ul>
+ <li><a href="api/core/core_objects.html#arbdmodel.core_objects.PointParticle.duplicate">(PointParticle method)</a>
+</li>
+ <li><a href="api/core/core_objects.html#arbdmodel.core_objects.RigidBody.duplicate">(RigidBody method)</a>
+</li>
+ </ul></li>
</ul></td>
</tr></table>
<h2 id="E">E</h2>
<table style="width: 100%" class="indextable genindextable"><tr>
<td style="width: 33%; vertical-align: top;"><ul>
- <li><a href="api/polymer_modeling/polymer.html#arbdmodel.polymer.PolymerGroup.extend">extend() (PolymerGroup method)</a>
+ <li><a href="api/core/core_objects.html#arbdmodel.core_objects.ParticleType.excludedAttributes">excludedAttributes (ParticleType attribute)</a>
</li>
</ul></td>
+ <td style="width: 33%; vertical-align: top;"><ul>
+ <li><a href="api/core/model.html#arbdmodel.model.ArbdModel.extend">extend() (ArbdModel method)</a>
+
+ <ul>
+ <li><a href="api/polymer_modeling/polymer.html#arbdmodel.polymer.PolymerGroup.extend">(PolymerGroup method)</a>
+</li>
+ </ul></li>
+ </ul></td>
</tr></table>
<h2 id="F">F</h2>
@@ -546,6 +785,8 @@ document.write(`
<li><a href="api/interaction_potentials/interactions.html#arbdmodel.interactions.HarmonicBondedPotential.filename">(HarmonicBondedPotential method)</a>
</li>
<li><a href="api/interaction_potentials/interactions.html#arbdmodel.interactions.NullPotential.filename">(NullPotential method)</a>
+</li>
+ <li><a href="api/shape-based_models/shape_cg.html#arbdmodel.shape_cg.ShapeCGNonbonded.filename">(ShapeCGNonbonded method)</a>
</li>
<li><a href="api/interaction_potentials/interactions.html#arbdmodel.interactions.WLCSKPotential.filename">(WLCSKPotential method)</a>
</li>
@@ -559,6 +800,8 @@ document.write(`
<li><a href="api/polymer_modeling/fjc_polymer_model.html#arbdmodel.fjc_polymer_model.FjcBeadsFromPolymer">FjcBeadsFromPolymer (class in arbdmodel.fjc_polymer_model)</a>
</li>
<li><a href="api/polymer_modeling/fjc_polymer_model.html#arbdmodel.fjc_polymer_model.FjcModel">FjcModel (class in arbdmodel.fjc_polymer_model)</a>
+</li>
+ <li><a href="api/shape-based_models/shape_cg.html#arbdmodel.shape_cg.ShapeCGModel.from_protein_list">from_protein_list() (ShapeCGModel class method)</a>
</li>
</ul></td>
</tr></table>
@@ -569,33 +812,115 @@ document.write(`
<li><a href="api/utilities/grid.html#arbdmodel.grid.gaussian_kernel">gaussian_kernel() (in module arbdmodel.grid)</a>
</li>
<li><a href="api/polymer_modeling/polymer.html#arbdmodel.polymer.PolymerModel.generate_beads">generate_beads() (PolymerModel method)</a>
+
+ <ul>
+ <li><a href="api/polymer_modeling/sali_polymer_model.html#arbdmodel.sali_polymer_model.SaliModel.generate_beads">(SaliModel method)</a>
</li>
- <li><a href="api/polymer_modeling/polymer.html#arbdmodel.polymer.PolymerGroup.get_center">get_center() (PolymerGroup method)</a>
+ </ul></li>
+ <li><a href="api/rigidbody_models/structure_from_pdb.html#arbdmodel.structure_from_pdb.StructureProcessor.generate_charge_distribution">generate_charge_distribution() (StructureProcessor method)</a>
+</li>
+ <li><a href="api/utilities/coords.html#arbdmodel.coords.Generate_coordinates">Generate_coordinates() (in module arbdmodel.coords)</a>
+</li>
+ <li><a href="api/rigidbody_models/structure_from_pdb.html#arbdmodel.structure_from_pdb.StructureProcessor.generate_electrostatic_map">generate_electrostatic_map() (StructureProcessor method)</a>
+</li>
+ <li><a href="api/rigidbody_models/mesh_process_volume.html#arbdmodel.mesh_process_volume.MeshProcessor.generate_potential_grid">generate_potential_grid() (MeshProcessor method)</a>
<ul>
+ <li><a href="api/rigidbody_models/mesh_process_surface.html#arbdmodel.mesh_process_surface.SurfaceMeshProcessor.generate_potential_grid">(SurfaceMeshProcessor method)</a>
+</li>
+ </ul></li>
+ <li><a href="api/shape-based_models/shape_cg.html#arbdmodel.shape_cg.ShapeCGFactory.generate_protein">generate_protein() (ShapeCGFactory method)</a>
+</li>
+ <li><a href="api/shape-based_models/shape_cg.html#arbdmodel.shape_cg.ShapeCGModel.generate_random_protein_positions">generate_random_protein_positions() (ShapeCGModel method)</a>
+</li>
+ <li><a href="api/utilities/coords.html#arbdmodel.coords.Generate_spanning_vectors">Generate_spanning_vectors() (in module arbdmodel.coords)</a>
+</li>
+ <li><a href="api/rigidbody_models/structure_from_pdb.html#arbdmodel.structure_from_pdb.StructureProcessor.generate_vdw_maps">generate_vdw_maps() (StructureProcessor method)</a>
+</li>
+ <li><a href="api/core/core_objects.html#arbdmodel.core_objects.Parent.get_angles">get_angles() (Parent method)</a>
+</li>
+ <li><a href="api/rigidbody_models/mesh_process_volume.html#arbdmodel.mesh_process_volume.MeshProcessor.get_attached_particles">get_attached_particles() (MeshProcessor method)</a>
+
+ <ul>
+ <li><a href="api/rigidbody_models/mesh_process_surface.html#arbdmodel.mesh_process_surface.SurfaceMeshProcessor.get_attached_particles">(SurfaceMeshProcessor method)</a>
+</li>
+ </ul></li>
+ <li><a href="api/core/sim_config.html#arbdmodel.sim_config.SimConf.get_binary">get_binary() (SimConf method)</a>
+</li>
+ <li><a href="api/core/core_objects.html#arbdmodel.core_objects.Parent.get_bond_angles">get_bond_angles() (Parent method)</a>
+</li>
+ <li><a href="api/core/core_objects.html#arbdmodel.core_objects.Parent.get_bonds">get_bonds() (Parent method)</a>
+</li>
+ <li><a href="api/core/core_objects.html#arbdmodel.core_objects.GroupSite.get_center">get_center() (GroupSite method)</a>
+
+ <ul>
+ <li><a href="api/core/core_objects.html#arbdmodel.core_objects.Parent.get_center">(Parent method)</a>
+</li>
+ <li><a href="api/polymer_modeling/polymer.html#arbdmodel.polymer.PolymerGroup.get_center">(PolymerGroup method)</a>
+</li>
<li><a href="api/polymer_modeling/polymer.html#arbdmodel.polymer.PolymerSection.get_center">(PolymerSection method)</a>
</li>
</ul></li>
<li><a href="api/interaction_potentials/ibi.html#arbdmodel.ibi.AbstractIBIpotential.get_cg_distribution">get_cg_distribution() (AbstractIBIpotential method)</a>
+</li>
+ <li><a href="api/shape-based_models/shape_cg.html#arbdmodel.shape_cg.ShapeCGFactory.get_coarse_protein">get_coarse_protein() (ShapeCGFactory method)</a>
+</li>
+ <li><a href="api/shape-based_models/shape_cg.html#arbdmodel.shape_cg.ShapeCGFactory.get_coarse_types">get_coarse_types() (ShapeCGFactory method)</a>
+</li>
+ <li><a href="api/core/core_objects.html#arbdmodel.core_objects.Transformable.get_collapsed_position">get_collapsed_position() (Transformable method)</a>
</li>
<li><a href="api/polymer_modeling/polymer.html#arbdmodel.polymer.Location.get_connected_location">get_connected_location() (Location method)</a>
</li>
<li><a href="api/polymer_modeling/polymer.html#arbdmodel.polymer.PolymerGroup.get_connections">get_connections() (PolymerGroup method)</a>
</li>
<li><a href="api/polymer_modeling/polymer.html#arbdmodel.polymer.ConnectableElement.get_connections_and_locations">get_connections_and_locations() (ConnectableElement method)</a>
-</li>
- <li><a href="api/polymer_modeling/polymer.html#arbdmodel.polymer.PolymerSection.get_contour_sorted_connections_and_locations">get_contour_sorted_connections_and_locations() (PolymerSection method)</a>
</li>
</ul></td>
<td style="width: 33%; vertical-align: top;"><ul>
+ <li><a href="api/polymer_modeling/polymer.html#arbdmodel.polymer.PolymerSection.get_contour_sorted_connections_and_locations">get_contour_sorted_connections_and_locations() (PolymerSection method)</a>
+</li>
+ <li><a href="api/simulation_engines/engine.html#arbdmodel.engine.ArbdEngine.get_default_conf">get_default_conf() (ArbdEngine method)</a>
+
+ <ul>
+ <li><a href="api/simulation_engines/engine.html#arbdmodel.engine.NamdEngine.get_default_conf">(NamdEngine method)</a>
+</li>
+ <li><a href="api/simulation_engines/engine.html#arbdmodel.engine.SimEngine.get_default_conf">(SimEngine method)</a>
+</li>
+ </ul></li>
+ <li><a href="api/core/core_objects.html#arbdmodel.core_objects.Parent.get_dihedrals">get_dihedrals() (Parent method)</a>
+</li>
+ <li><a href="api/core/core_objects.html#arbdmodel.core_objects.Parent.get_exclusions">get_exclusions() (Parent method)</a>
+</li>
+ <li><a href="api/rigidbody_models/structure_from_pdb.html#arbdmodel.structure_from_pdb.StructureProcessor.get_grid_files">get_grid_files() (StructureProcessor method)</a>
+</li>
+ <li><a href="api/core/core_objects.html#arbdmodel.core_objects.Parent.get_impropers">get_impropers() (Parent method)</a>
+</li>
<li><a href="api/polymer_modeling/polymer.html#arbdmodel.polymer.ConnectableElement.get_location_at">get_location_at() (ConnectableElement method)</a>
</li>
<li><a href="api/polymer_modeling/polymer.html#arbdmodel.polymer.ConnectableElement.get_locations">get_locations() (ConnectableElement method)</a>
</li>
<li><a href="api/polymer_modeling/polymer.html#arbdmodel.polymer.Location.get_monomer_index">get_monomer_index() (Location method)</a>
+</li>
+ <li><a href="api/core/core_objects.html#arbdmodel.core_objects.Clone.get_original_recursively">get_original_recursively() (Clone method)</a>
</li>
<li><a href="api/shape-based_models/shape_cg.html#arbdmodel.shape_cg.get_particle_assignments">get_particle_assignments() (in module arbdmodel.shape_cg)</a>
</li>
+ <li><a href="api/core/core_objects.html#arbdmodel.core_objects.Parent.get_product_potentials">get_product_potentials() (Parent method)</a>
+</li>
+ <li><a href="api/shape-based_models/shape_cg.html#arbdmodel.shape_cg.ShapeCGModel.get_protein_types">get_protein_types() (ShapeCGModel method)</a>
+</li>
+ <li><a href="api/utilities/logger.html#arbdmodel.logger.get_resource_path">get_resource_path() (in module arbdmodel.logger)</a>
+</li>
+ <li><a href="api/core/core_objects.html#arbdmodel.core_objects.GroupSite.get_restraints">get_restraints() (GroupSite method)</a>
+
+ <ul>
+ <li><a href="api/core/core_objects.html#arbdmodel.core_objects.Parent.get_restraints">(Parent method)</a>
+</li>
+ <li><a href="api/core/core_objects.html#arbdmodel.core_objects.PointParticle.get_restraints">(PointParticle method)</a>
+</li>
+ <li><a href="api/core/core_objects.html#arbdmodel.core_objects.RigidBody.get_restraints">(RigidBody method)</a>
+</li>
+ </ul></li>
<li><a href="api/utilities/grid.html#arbdmodel.grid.get_slice_enclosing_smaller_grid">get_slice_enclosing_smaller_grid() (in module arbdmodel.grid)</a>
</li>
<li><a href="api/interaction_potentials/ibi.html#arbdmodel.ibi.AbstractIBIpotential.get_target_distribution">get_target_distribution() (AbstractIBIpotential method)</a>
@@ -606,7 +931,15 @@ document.write(`
<li><a href="api/interaction_potentials/ibi.html#arbdmodel.ibi.PairDistributionDof.get_values">(PairDistributionDof method)</a>
</li>
</ul></li>
+ <li><a href="api/core/core_objects.html#arbdmodel.core_objects.Parent.get_vector_angles">get_vector_angles() (Parent method)</a>
+</li>
<li><a href="api/utilities/version.html#arbdmodel.version.get_version">get_version() (in module arbdmodel.version)</a>
+</li>
+ <li><a href="api/core/model.html#arbdmodel.model.ArbdModel.getParticleTypesAndCounts">getParticleTypesAndCounts() (ArbdModel method)</a>
+</li>
+ <li><a href="api/core/core_objects.html#arbdmodel.core_objects.Group">Group (class in arbdmodel.core_objects)</a>
+</li>
+ <li><a href="api/core/core_objects.html#arbdmodel.core_objects.GroupSite">GroupSite (class in arbdmodel.core_objects)</a>
</li>
</ul></td>
</tr></table>
@@ -622,10 +955,10 @@ document.write(`
</li>
<li><a href="api/interaction_potentials/interactions.html#arbdmodel.interactions.HarmonicBondedPotential">HarmonicBondedPotential (class in arbdmodel.interactions)</a>
</li>
- </ul></td>
- <td style="width: 33%; vertical-align: top;"><ul>
<li><a href="api/interaction_potentials/interactions.html#arbdmodel.interactions.HarmonicDihedral">HarmonicDihedral (class in arbdmodel.interactions)</a>
</li>
+ </ul></td>
+ <td style="width: 33%; vertical-align: top;"><ul>
<li><a href="api/interaction_potentials/interactions.html#arbdmodel.interactions.HarmonicVectorAngle">HarmonicVectorAngle (class in arbdmodel.interactions)</a>
</li>
<li><a href="api/polymer_modeling/hps_polymer_model.html#arbdmodel.hps_polymer_model.HpsBeads">HpsBeads (class in arbdmodel.hps_polymer_model)</a>
@@ -633,6 +966,8 @@ document.write(`
<li><a href="api/polymer_modeling/hps_polymer_model.html#arbdmodel.hps_polymer_model.HpsModel">HpsModel (class in arbdmodel.hps_polymer_model)</a>
</li>
<li><a href="api/polymer_modeling/hps_polymer_model.html#arbdmodel.hps_polymer_model.HpsNonbonded">HpsNonbonded (class in arbdmodel.hps_polymer_model)</a>
+</li>
+ <li><a href="api/simulation_engines/engine.html#arbdmodel.engine.HydroProRunner">HydroProRunner (class in arbdmodel.engine)</a>
</li>
</ul></td>
</tr></table>
@@ -647,14 +982,24 @@ document.write(`
<li><a href="api/interaction_potentials/ibi.html#arbdmodel.ibi.IBIDihedral">IBIDihedral (class in arbdmodel.ibi)</a>
</li>
<li><a href="api/interaction_potentials/ibi.html#arbdmodel.ibi.IBINonbonded">IBINonbonded (class in arbdmodel.ibi)</a>
+</li>
+ <li><a href="api/core/core_objects.html#arbdmodel.core_objects.Parent.index">index() (Parent method)</a>
+</li>
+ <li><a href="api/utilities/binary_manager.html#arbdmodel.binary_manager.initialize_binary_paths">initialize_binary_paths() (in module arbdmodel.binary_manager)</a>
</li>
</ul></td>
<td style="width: 33%; vertical-align: top;"><ul>
+ <li><a href="api/core/core_objects.html#arbdmodel.core_objects.Parent.insert">insert() (Parent method)</a>
+</li>
<li><a href="api/polymer_modeling/polymer.html#arbdmodel.polymer.PolymerSection.insert_monomers">insert_monomers() (PolymerSection method)</a>
</li>
<li><a href="api/utilities/version.html#arbdmodel.version.is_dirty">is_dirty() (in module arbdmodel.version)</a>
+</li>
+ <li><a href="api/core/core_objects.html#arbdmodel.core_objects.ParticleType.is_same_type">is_same_type() (ParticleType method)</a>
</li>
<li><a href="api/utilities/grid.html#arbdmodel.grid.isotropic_kernel">isotropic_kernel() (in module arbdmodel.grid)</a>
+</li>
+ <li><a href="api/core/sim_config.html#arbdmodel.sim_config.SimConf.items">items() (SimConf method)</a>
</li>
<li><a href="api/polymer_modeling/polymer.html#arbdmodel.polymer.PolymerSection.iterate_connections_and_locations">iterate_connections_and_locations() (PolymerSection method)</a>
</li>
@@ -689,9 +1034,17 @@ document.write(`
<table style="width: 100%" class="indextable genindextable"><tr>
<td style="width: 33%; vertical-align: top;"><ul>
<li><a href="api/interaction_potentials/interactions.html#arbdmodel.interactions.LennardJones">LennardJones (class in arbdmodel.interactions)</a>
+</li>
+ <li><a href="api/polymer_modeling/sali_polymer_model.html#arbdmodel.sali_polymer_model.LinearBond">LinearBond (class in arbdmodel.sali_polymer_model)</a>
+</li>
+ <li><a href="api/simulation_engines/parmed_bd.html#arbdmodel.parmed_bd.ParmedArbd.load_structure">load_structure() (ParmedArbd method)</a>
</li>
</ul></td>
<td style="width: 33%; vertical-align: top;"><ul>
+ <li><a href="api/core/model.html#arbdmodel.model.ArbdModel.load_target_IBI_distributions">load_target_IBI_distributions() (ArbdModel method)</a>
+</li>
+ <li><a href="api/utilities/grid.html#arbdmodel.grid.loadGrid">loadGrid() (in module arbdmodel.grid)</a>
+</li>
<li><a href="api/polymer_modeling/polymer.html#arbdmodel.polymer.Location">Location (class in arbdmodel.polymer)</a>
</li>
</ul></td>
@@ -700,13 +1053,31 @@ document.write(`
<h2 id="M">M</h2>
<table style="width: 100%" class="indextable genindextable"><tr>
<td style="width: 33%; vertical-align: top;"><ul>
+ <li><a href="api/rigidbody_models/simplearbd.html#arbdmodel.simplearbd.main">main() (in module arbdmodel.simplearbd)</a>
+</li>
+ <li><a href="api/rigidbody_models/mesh_process_volume.html#arbdmodel.mesh_process_volume.MeshProcessor">MeshProcessor (class in arbdmodel.mesh_process_volume)</a>
+</li>
+ <li><a href="api/rigidbody_models/mesh_rigidbody.html#arbdmodel.mesh_rigidbody.MeshRigidBodyType">MeshRigidBodyType (class in arbdmodel.mesh_rigidbody)</a>
+</li>
+ <li><a href="api/rigidbody_models/mesh_process_volume.html#arbdmodel.mesh_process_volume.MeshProcessor.MICRON_TO_ANGSTROM">MICRON_TO_ANGSTROM (MeshProcessor attribute)</a>
+
+ <ul>
+ <li><a href="api/rigidbody_models/mesh_process_surface.html#arbdmodel.mesh_process_surface.SurfaceMeshProcessor.MICRON_TO_ANGSTROM">(SurfaceMeshProcessor attribute)</a>
+</li>
+ </ul></li>
<li><a href="api/utilities/coords.html#arbdmodel.coords.minimizeRmsd">minimizeRmsd() (in module arbdmodel.coords)</a>
</li>
<li>
module
<ul>
+ <li><a href="api/utilities/binary_manager.html#module-arbdmodel.binary_manager">arbdmodel.binary_manager</a>
+</li>
<li><a href="api/utilities/coords.html#module-arbdmodel.coords">arbdmodel.coords</a>
+</li>
+ <li><a href="api/core/core_objects.html#module-arbdmodel.core_objects">arbdmodel.core_objects</a>
+</li>
+ <li><a href="api/simulation_engines/engine.html#module-arbdmodel.engine">arbdmodel.engine</a>
</li>
<li><a href="api/polymer_modeling/fjc_polymer_model.html#module-arbdmodel.fjc_polymer_model">arbdmodel.fjc_polymer_model</a>
</li>
@@ -721,16 +1092,36 @@ document.write(`
<li><a href="api/polymer_modeling/kh_polymer_model.html#module-arbdmodel.kh_polymer_model">arbdmodel.kh_polymer_model</a>
</li>
<li><a href="api/utilities/logger.html#module-arbdmodel.logger">arbdmodel.logger</a>
+</li>
+ <li><a href="api/rigidbody_models/mesh_process_surface.html#module-arbdmodel.mesh_process_surface">arbdmodel.mesh_process_surface</a>
+</li>
+ <li><a href="api/rigidbody_models/mesh_process_volume.html#module-arbdmodel.mesh_process_volume">arbdmodel.mesh_process_volume</a>
+</li>
+ <li><a href="api/rigidbody_models/mesh_rigidbody.html#module-arbdmodel.mesh_rigidbody">arbdmodel.mesh_rigidbody</a>
+</li>
+ <li><a href="api/core/model.html#module-arbdmodel.model">arbdmodel.model</a>
</li>
<li><a href="api/polymer_modeling/mpipi_polymer.html#module-arbdmodel.mpipi_polymer">arbdmodel.mpipi_polymer</a>
</li>
<li><a href="api/polymer_modeling/onck_polymer_model.html#module-arbdmodel.onck_polymer_model">arbdmodel.onck_polymer_model</a>
+</li>
+ <li><a href="api/simulation_engines/parmed_bd.html#module-arbdmodel.parmed_bd">arbdmodel.parmed_bd</a>
</li>
<li><a href="api/polymer_modeling/polymer.html#module-arbdmodel.polymer">arbdmodel.polymer</a>
+</li>
+ <li><a href="api/polymer_modeling/sali_polymer_model.html#module-arbdmodel.sali_polymer_model">arbdmodel.sali_polymer_model</a>
</li>
<li><a href="api/shape-based_models/shape_cg.html#module-arbdmodel.shape_cg">arbdmodel.shape_cg</a>
+</li>
+ <li><a href="api/core/sim_config.html#module-arbdmodel.sim_config">arbdmodel.sim_config</a>
+</li>
+ <li><a href="api/rigidbody_models/simplearbd.html#module-arbdmodel.simplearbd">arbdmodel.simplearbd</a>
</li>
<li><a href="api/polymer_modeling/ssdna_two_bead.html#module-arbdmodel.ssdna_two_bead">arbdmodel.ssdna_two_bead</a>
+</li>
+ <li><a href="api/rigidbody_models/structure_from_pdb.html#module-arbdmodel.structure_from_pdb">arbdmodel.structure_from_pdb</a>
+</li>
+ <li><a href="api/rigidbody_models/structure_rigidbody.html#module-arbdmodel.structure_rigidbody">arbdmodel.structure_rigidbody</a>
</li>
<li><a href="api/utilities/version.html#module-arbdmodel.version">arbdmodel.version</a>
</li>
@@ -753,12 +1144,14 @@ document.write(`
<h2 id="N">N</h2>
<table style="width: 100%" class="indextable genindextable"><tr>
<td style="width: 33%; vertical-align: top;"><ul>
- <li><a href="api/utilities/grid.html#arbdmodel.grid.neighborhood_average">neighborhood_average() (in module arbdmodel.grid)</a>
+ <li><a href="api/simulation_engines/engine.html#arbdmodel.engine.NamdEngine">NamdEngine (class in arbdmodel.engine)</a>
</li>
- <li><a href="api/polymer_modeling/ssdna_two_bead.html#arbdmodel.ssdna_two_bead.DnaStrandBeads.nt">nt (DnaStrandBeads attribute)</a>
+ <li><a href="api/utilities/grid.html#arbdmodel.grid.neighborhood_average">neighborhood_average() (in module arbdmodel.grid)</a>
</li>
</ul></td>
<td style="width: 33%; vertical-align: top;"><ul>
+ <li><a href="api/polymer_modeling/ssdna_two_bead.html#arbdmodel.ssdna_two_bead.DnaStrandBeads.nt">nt (DnaStrandBeads attribute)</a>
+</li>
<li><a href="api/interaction_potentials/interactions.html#arbdmodel.interactions.NullPotential">NullPotential (class in arbdmodel.interactions)</a>
</li>
<li><a href="api/polymer_modeling/polymer.html#arbdmodel.polymer.PolymerBeads.num_bead_groups">num_bead_groups (PolymerBeads property)</a>
@@ -788,6 +1181,18 @@ document.write(`
<li><a href="api/polymer_modeling/ssdna_two_bead.html#arbdmodel.ssdna_two_bead.DnaStrandBeads.p">p (DnaStrandBeads attribute)</a>
</li>
<li><a href="api/interaction_potentials/ibi.html#arbdmodel.ibi.PairDistributionDof">PairDistributionDof (class in arbdmodel.ibi)</a>
+</li>
+ <li><a href="api/core/core_objects.html#arbdmodel.core_objects.Parent">Parent (class in arbdmodel.core_objects)</a>
+</li>
+ <li><a href="api/simulation_engines/parmed_bd.html#arbdmodel.parmed_bd.ParmedArbd.parmed_structure">parmed_structure (ParmedArbd attribute)</a>
+</li>
+ <li><a href="api/simulation_engines/parmed_bd.html#arbdmodel.parmed_bd.ParmedArbd">ParmedArbd (class in arbdmodel.parmed_bd)</a>
+</li>
+ <li><a href="api/simulation_engines/engine.html#arbdmodel.engine.HydroProRunner.parse_output">parse_output() (HydroProRunner method)</a>
+</li>
+ <li><a href="api/core/core_objects.html#arbdmodel.core_objects.ParticleType">ParticleType (class in arbdmodel.core_objects)</a>
+</li>
+ <li><a href="api/core/model.html#arbdmodel.model.PdbModel">PdbModel (class in arbdmodel.model)</a>
</li>
<li><a href="api/interaction_potentials/interactions.html#arbdmodel.interactions.AbstractPotential.periodic">periodic (AbstractPotential property)</a>
@@ -797,6 +1202,8 @@ document.write(`
<li><a href="api/interaction_potentials/ibi.html#arbdmodel.ibi.IBIDihedral.periodic">(IBIDihedral property)</a>
</li>
</ul></li>
+ <li><a href="api/core/core_objects.html#arbdmodel.core_objects.PointParticle">PointParticle (class in arbdmodel.core_objects)</a>
+</li>
<li><a href="api/polymer_modeling/polymer.html#arbdmodel.polymer.PolymerBeads">PolymerBeads (class in arbdmodel.polymer)</a>
</li>
<li><a href="api/polymer_modeling/polymer.html#arbdmodel.polymer.PolymerGroup">PolymerGroup (class in arbdmodel.polymer)</a>
@@ -809,6 +1216,8 @@ document.write(`
<ul>
<li><a href="api/interaction_potentials/interactions.html#arbdmodel.interactions.AbstractPotential.potential">(AbstractPotential method)</a>
+</li>
+ <li><a href="api/interaction_potentials/interactions.html#arbdmodel.interactions.BoundaryPotential.potential">(BoundaryPotential method)</a>
</li>
<li><a href="api/interaction_potentials/interactions.html#arbdmodel.interactions.HalfHarmonic.potential">(HalfHarmonic method)</a>
</li>
@@ -821,12 +1230,18 @@ document.write(`
<li><a href="api/polymer_modeling/kh_polymer_model.html#arbdmodel.kh_polymer_model.KhNonbonded.potential">(KhNonbonded method)</a>
</li>
<li><a href="api/interaction_potentials/interactions.html#arbdmodel.interactions.LennardJones.potential">(LennardJones method)</a>
+</li>
+ <li><a href="api/polymer_modeling/sali_polymer_model.html#arbdmodel.sali_polymer_model.LinearBond.potential">(LinearBond method)</a>
</li>
<li><a href="api/polymer_modeling/mpipi_polymer.html#arbdmodel.mpipi_polymer.MpipiNonbonded.potential">(MpipiNonbonded method)</a>
</li>
<li><a href="api/interaction_potentials/interactions.html#arbdmodel.interactions.NullPotential.potential">(NullPotential method)</a>
</li>
<li><a href="api/polymer_modeling/onck_polymer_model.html#arbdmodel.onck_polymer_model.OnckNonbonded.potential">(OnckNonbonded method)</a>
+</li>
+ <li><a href="api/polymer_modeling/sali_polymer_model.html#arbdmodel.sali_polymer_model.SaliNonbonded.potential">(SaliNonbonded method)</a>
+</li>
+ <li><a href="api/shape-based_models/shape_cg.html#arbdmodel.shape_cg.ShapeCGNonbonded.potential">(ShapeCGNonbonded method)</a>
</li>
<li><a href="api/interaction_potentials/interactions.html#arbdmodel.interactions.TabulatedNonbonded.potential">(TabulatedNonbonded method)</a>
</li>
@@ -836,6 +1251,18 @@ document.write(`
</li>
</ul></li>
</ul></td>
+ <td style="width: 33%; vertical-align: top;"><ul>
+ <li><a href="api/core/model.html#arbdmodel.model.ArbdModel.prepare_for_simulation">prepare_for_simulation() (ArbdModel method)</a>
+</li>
+ <li><a href="api/rigidbody_models/structure_rigidbody.html#arbdmodel.structure_rigidbody.StaticObject.process">process() (StaticObject method)</a>
+</li>
+ <li><a href="api/rigidbody_models/mesh_process_volume.html#arbdmodel.mesh_process_volume.process_mesh_file">process_mesh_file() (in module arbdmodel.mesh_process_volume)</a>
+</li>
+ <li><a href="api/rigidbody_models/structure_from_pdb.html#arbdmodel.structure_from_pdb.StructureProcessor.process_structure">process_structure() (StructureProcessor method)</a>
+</li>
+ <li><a href="api/rigidbody_models/mesh_process_surface.html#arbdmodel.mesh_process_surface.process_surface_mesh">process_surface_mesh() (in module arbdmodel.mesh_process_surface)</a>
+</li>
+ </ul></td>
</tr></table>
<h2 id="Q">Q</h2>
@@ -870,35 +1297,85 @@ document.write(`
<li><a href="api/utilities/coords.html#arbdmodel.coords.read_average_arbd_coordinates">read_average_arbd_coordinates() (in module arbdmodel.coords)</a>
</li>
<li><a href="api/interaction_potentials/ibi.html#arbdmodel.ibi.AbstractIBIpotential.read_cg_potential">read_cg_potential() (AbstractIBIpotential method)</a>
+</li>
+ <li><a href="api/shape-based_models/shape_cg.html#arbdmodel.shape_cg.read_files">read_files() (in module arbdmodel.shape_cg)</a>
</li>
<li><a href="api/utilities/version.html#arbdmodel.version.read_release_version">read_release_version() (in module arbdmodel.version)</a>
</li>
<li><a href="api/utilities/version.html#arbdmodel.version.read_version_file">read_version_file() (in module arbdmodel.version)</a>
</li>
- </ul></td>
- <td style="width: 33%; vertical-align: top;"><ul>
<li><a href="api/utilities/coords.html#arbdmodel.coords.readArbdCoords">readArbdCoords() (in module arbdmodel.coords)</a>
</li>
<li><a href="api/utilities/coords.html#arbdmodel.coords.readAvgArbdCoords">readAvgArbdCoords() (in module arbdmodel.coords)</a>
+</li>
+ <li><a href="api/core/core_objects.html#arbdmodel.core_objects.Parent.remove">remove() (Parent method)</a>
</li>
<li><a href="api/polymer_modeling/polymer.html#arbdmodel.polymer.PolymerSection.remove_monomers">remove_monomers() (PolymerSection method)</a>
</li>
<li><a href="api/utilities/grid.html#arbdmodel.grid.replace_false_with_distance">replace_false_with_distance() (in module arbdmodel.grid)</a>
+</li>
+ </ul></td>
+ <td style="width: 33%; vertical-align: top;"><ul>
+ <li><a href="api/core/core_objects.html#arbdmodel.core_objects.RigidBody">RigidBody (class in arbdmodel.core_objects)</a>
+</li>
+ <li><a href="api/core/core_objects.html#arbdmodel.core_objects.RigidBodyType">RigidBodyType (class in arbdmodel.core_objects)</a>
</li>
<li><a href="api/polymer_modeling/polymer.html#arbdmodel.polymer.PolymerGroup.rotate">rotate() (PolymerGroup method)</a>
<ul>
<li><a href="api/polymer_modeling/polymer.html#arbdmodel.polymer.PolymerSection.rotate">(PolymerSection method)</a>
+</li>
+ <li><a href="api/core/core_objects.html#arbdmodel.core_objects.Transformable.rotate">(Transformable method)</a>
</li>
</ul></li>
<li><a href="api/utilities/coords.html#arbdmodel.coords.rotationAboutAxis">rotationAboutAxis() (in module arbdmodel.coords)</a>
</li>
+ <li><a href="api/simulation_engines/engine.html#arbdmodel.engine.APBSRunner.run_calculation">run_calculation() (APBSRunner method)</a>
+
+ <ul>
+ <li><a href="api/simulation_engines/engine.html#arbdmodel.engine.HydroProRunner.run_calculation">(HydroProRunner method)</a>
+</li>
+ </ul></li>
+ <li><a href="api/shape-based_models/shape_cg.html#arbdmodel.shape_cg.ShapeCGModel.run_from_minimized">run_from_minimized() (ShapeCGModel method)</a>
+</li>
+ <li><a href="api/core/model.html#arbdmodel.model.ArbdModel.run_IBI">run_IBI() (ArbdModel method)</a>
+</li>
+ <li><a href="api/shape-based_models/shape_cg.html#arbdmodel.shape_cg.ShapeCGModel.run_minimization">run_minimization() (ShapeCGModel method)</a>
+</li>
+ <li><a href="api/rigidbody_models/simplearbd.html#arbdmodel.simplearbd.SimpleArbdConfig.run_simulation">run_simulation() (SimpleArbdConfig method)</a>
+
+ <ul>
+ <li><a href="api/rigidbody_models/structure_rigidbody.html#arbdmodel.structure_rigidbody.SimpleArbdEngine.run_simulation">(SimpleArbdEngine method)</a>
+</li>
+ </ul></li>
</ul></td>
</tr></table>
<h2 id="S">S</h2>
<table style="width: 100%" class="indextable genindextable"><tr>
<td style="width: 33%; vertical-align: top;"><ul>
+ <li><a href="api/polymer_modeling/sali_polymer_model.html#arbdmodel.sali_polymer_model.SaliBeadsFromPolymer">SaliBeadsFromPolymer (class in arbdmodel.sali_polymer_model)</a>
+</li>
+ <li><a href="api/polymer_modeling/sali_polymer_model.html#arbdmodel.sali_polymer_model.SaliModel">SaliModel (class in arbdmodel.sali_polymer_model)</a>
+</li>
+ <li><a href="api/polymer_modeling/sali_polymer_model.html#arbdmodel.sali_polymer_model.SaliNonbonded">SaliNonbonded (class in arbdmodel.sali_polymer_model)</a>
+</li>
+ <li><a href="api/rigidbody_models/mesh_process_volume.html#arbdmodel.mesh_process_volume.MeshProcessor.save_aligned_mesh">save_aligned_mesh() (MeshProcessor method)</a>
+
+ <ul>
+ <li><a href="api/rigidbody_models/mesh_process_surface.html#arbdmodel.mesh_process_surface.SurfaceMeshProcessor.save_aligned_mesh">(SurfaceMeshProcessor method)</a>
+</li>
+ </ul></li>
+ <li><a href="api/rigidbody_models/mesh_process_surface.html#arbdmodel.mesh_process_surface.SurfaceMeshProcessor.save_aligned_mesh_both_formats">save_aligned_mesh_both_formats() (SurfaceMeshProcessor method)</a>
+</li>
+ <li><a href="api/rigidbody_models/mesh_process_volume.html#arbdmodel.mesh_process_volume.MeshProcessor.save_as_pdb">save_as_pdb() (MeshProcessor method)</a>
+
+ <ul>
+ <li><a href="api/rigidbody_models/mesh_process_surface.html#arbdmodel.mesh_process_surface.SurfaceMeshProcessor.save_as_pdb">(SurfaceMeshProcessor method)</a>
+</li>
+ </ul></li>
+ <li><a href="api/core/sim_config.html#arbdmodel.sim_config.SimConf.set_binary">set_binary() (SimConf method)</a>
+</li>
<li><a href="api/polymer_modeling/polymer.html#arbdmodel.polymer.Location.set_connection">set_connection() (Location method)</a>
</li>
<li><a href="api/polymer_modeling/fjc_polymer_model.html#arbdmodel.fjc_polymer_model.FjcModel.set_damping_coefficient">set_damping_coefficient() (FjcModel method)</a>
@@ -913,12 +1390,40 @@ document.write(`
<li><a href="api/polymer_modeling/onck_polymer_model.html#arbdmodel.onck_polymer_model.OnckModel.set_damping_coefficient">(OnckModel method)</a>
</li>
</ul></li>
- </ul></td>
- <td style="width: 33%; vertical-align: top;"><ul>
<li><a href="api/polymer_modeling/polymer.html#arbdmodel.polymer.PolymerSection.set_orientation_splines">set_orientation_splines() (PolymerSection method)</a>
</li>
<li><a href="api/polymer_modeling/polymer.html#arbdmodel.polymer.PolymerSection.set_splines">set_splines() (PolymerSection method)</a>
</li>
+ <li><a href="api/shape-based_models/shape_cg.html#arbdmodel.shape_cg.ShapeCGModel.setup_and_run">setup_and_run() (ShapeCGModel method)</a>
+</li>
+ <li><a href="api/rigidbody_models/simplearbd.html#arbdmodel.simplearbd.SimpleArbdConfig.setup_diffusible_objects">setup_diffusible_objects() (SimpleArbdConfig method)</a>
+</li>
+ </ul></td>
+ <td style="width: 33%; vertical-align: top;"><ul>
+ <li><a href="api/rigidbody_models/simplearbd.html#arbdmodel.simplearbd.SimpleArbdConfig.setup_static_objects">setup_static_objects() (SimpleArbdConfig method)</a>
+</li>
+ <li><a href="api/shape-based_models/shape_cg.html#arbdmodel.shape_cg.ShapeCGFactory">ShapeCGFactory (class in arbdmodel.shape_cg)</a>
+</li>
+ <li><a href="api/shape-based_models/shape_cg.html#arbdmodel.shape_cg.ShapeCGModel">ShapeCGModel (class in arbdmodel.shape_cg)</a>
+</li>
+ <li><a href="api/shape-based_models/shape_cg.html#arbdmodel.shape_cg.ShapeCGNonbonded">ShapeCGNonbonded (class in arbdmodel.shape_cg)</a>
+</li>
+ <li><a href="api/core/sim_config.html#arbdmodel.sim_config.SimConf">SimConf (class in arbdmodel.sim_config)</a>
+</li>
+ <li><a href="api/simulation_engines/engine.html#arbdmodel.engine.SimEngine">SimEngine (class in arbdmodel.engine)</a>
+</li>
+ <li><a href="api/rigidbody_models/simplearbd.html#arbdmodel.simplearbd.SimpleArbdConfig">SimpleArbdConfig (class in arbdmodel.simplearbd)</a>
+</li>
+ <li><a href="api/rigidbody_models/structure_rigidbody.html#arbdmodel.structure_rigidbody.SimpleArbdEngine">SimpleArbdEngine (class in arbdmodel.structure_rigidbody)</a>
+</li>
+ <li><a href="api/core/model.html#arbdmodel.model.ArbdModel.simulate">simulate() (ArbdModel method)</a>
+
+ <ul>
+ <li><a href="api/simulation_engines/parmed_bd.html#arbdmodel.parmed_bd.ParmedArbd.simulate">(ParmedArbd method)</a>
+</li>
+ <li><a href="api/simulation_engines/engine.html#arbdmodel.engine.SimEngine.simulate">(SimEngine method)</a>
+</li>
+ </ul></li>
<li><a href="api/utilities/grid.html#arbdmodel.grid.slab_potential_z">slab_potential_z() (in module arbdmodel.grid)</a>
</li>
<li><a href="api/utilities/grid.html#arbdmodel.grid.spherical_confinement">spherical_confinement() (in module arbdmodel.grid)</a>
@@ -931,6 +1436,14 @@ document.write(`
<li><a href="api/polymer_modeling/mpipi_polymer.html#arbdmodel.mpipi_polymer.MpipiModel.spring_constant">(MpipiModel attribute)</a>
</li>
</ul></li>
+ <li><a href="api/rigidbody_models/structure_rigidbody.html#arbdmodel.structure_rigidbody.StaticObject">StaticObject (class in arbdmodel.structure_rigidbody)</a>
+</li>
+ <li><a href="api/rigidbody_models/structure_from_pdb.html#arbdmodel.structure_from_pdb.StructureProcessor">StructureProcessor (class in arbdmodel.structure_from_pdb)</a>
+</li>
+ <li><a href="api/rigidbody_models/structure_rigidbody.html#arbdmodel.structure_rigidbody.StructureRigidBodyModel">StructureRigidBodyModel (class in arbdmodel.structure_rigidbody)</a>
+</li>
+ <li><a href="api/rigidbody_models/mesh_process_surface.html#arbdmodel.mesh_process_surface.SurfaceMeshProcessor">SurfaceMeshProcessor (class in arbdmodel.mesh_process_surface)</a>
+</li>
</ul></td>
</tr></table>
@@ -939,16 +1452,30 @@ document.write(`
<td style="width: 33%; vertical-align: top;"><ul>
<li><a href="api/interaction_potentials/interactions.html#arbdmodel.interactions.TabulatedNonbonded">TabulatedNonbonded (class in arbdmodel.interactions)</a>
</li>
+ <li><a href="api/core/sim_config.html#arbdmodel.sim_config.DefaultSimConf.temperature">temperature (DefaultSimConf property)</a>
+
+ <ul>
+ <li><a href="api/core/sim_config.html#arbdmodel.sim_config.SimConf.temperature">(SimConf property)</a>
+</li>
+ </ul></li>
<li><a href="api/utilities/grid.html#arbdmodel.grid.TestAverageGrids.test_average_grids">test_average_grids() (TestAverageGrids method)</a>
</li>
<li><a href="api/utilities/grid.html#arbdmodel.grid.TestAverageGrids">TestAverageGrids (class in arbdmodel.grid)</a>
+</li>
+ <li><a href="api/core/core_objects.html#arbdmodel.core_objects.Transformable.transform">transform() (Transformable method)</a>
+</li>
+ <li><a href="api/core/core_objects.html#arbdmodel.core_objects.Transformable">Transformable (class in arbdmodel.core_objects)</a>
</li>
<li><a href="api/polymer_modeling/polymer.html#arbdmodel.polymer.PolymerGroup.translate">translate() (PolymerGroup method)</a>
<ul>
<li><a href="api/polymer_modeling/polymer.html#arbdmodel.polymer.PolymerSection.translate">(PolymerSection method)</a>
+</li>
+ <li><a href="api/core/core_objects.html#arbdmodel.core_objects.Transformable.translate">(Transformable method)</a>
</li>
</ul></li>
+ </ul></td>
+ <td style="width: 33%; vertical-align: top;"><ul>
<li><a href="api/interaction_potentials/interactions.html#arbdmodel.interactions.HarmonicAngle.type_">type_ (HarmonicAngle property)</a>
<ul>
@@ -973,11 +1500,21 @@ document.write(`
<td style="width: 33%; vertical-align: top;"><ul>
<li><a href="api/utilities/coords.html#arbdmodel.coords.unit_quat_conversions">unit_quat_conversions() (in module arbdmodel.coords)</a>
</li>
+ <li><a href="api/core/model.html#arbdmodel.model.ArbdModel.update">update() (ArbdModel method)</a>
+
+ <ul>
+ <li><a href="api/polymer_modeling/polymer.html#arbdmodel.polymer.PolymerGroup.update">(PolymerGroup method)</a>
+</li>
+ </ul></li>
</ul></td>
<td style="width: 33%; vertical-align: top;"><ul>
- <li><a href="api/polymer_modeling/polymer.html#arbdmodel.polymer.PolymerGroup.update">update() (PolymerGroup method)</a>
-</li>
<li><a href="api/polymer_modeling/polymer.html#arbdmodel.polymer.PolymerModel.update_splines">update_splines() (PolymerModel method)</a>
+
+ <ul>
+ <li><a href="api/polymer_modeling/sali_polymer_model.html#arbdmodel.sali_polymer_model.SaliModel.update_splines">(SaliModel method)</a>
+</li>
+ </ul></li>
+ <li><a href="api/core/model.html#arbdmodel.model.ArbdModel.useNonbondedScheme">useNonbondedScheme() (ArbdModel method)</a>
</li>
</ul></td>
</tr></table>
@@ -1007,20 +1544,54 @@ document.write(`
</li>
<li><a href="api/interaction_potentials/ibi.html#arbdmodel.ibi.AbstractIBIpotential.write_cg_potential">write_cg_potential() (AbstractIBIpotential method)</a>
</li>
- </ul></td>
- <td style="width: 33%; vertical-align: top;"><ul>
+ <li><a href="api/simulation_engines/engine.html#arbdmodel.engine.NamdEngine.write_conf">write_conf() (NamdEngine method)</a>
+</li>
+ <li><a href="api/simulation_engines/engine.html#arbdmodel.engine.APBSRunner.write_config">write_config() (APBSRunner method)</a>
+
+ <ul>
+ <li><a href="api/simulation_engines/engine.html#arbdmodel.engine.HydroProRunner.write_config">(HydroProRunner method)</a>
+</li>
+ </ul></li>
+ <li><a href="api/utilities/grid.html#arbdmodel.grid.write_confine_dx">write_confine_dx() (in module arbdmodel.grid)</a>
+</li>
<li><a href="api/interaction_potentials/ibi.html#arbdmodel.ibi.AbstractIBIpotential.write_file">write_file() (AbstractIBIpotential method)</a>
<ul>
<li><a href="api/interaction_potentials/interactions.html#arbdmodel.interactions.AbstractPotential.write_file">(AbstractPotential method)</a>
+</li>
+ <li><a href="api/interaction_potentials/interactions.html#arbdmodel.interactions.BoundaryPotential.write_file">(BoundaryPotential method)</a>
</li>
<li><a href="api/interaction_potentials/ibi.html#arbdmodel.ibi.IBINonbonded.write_file">(IBINonbonded method)</a>
</li>
<li><a href="api/interaction_potentials/interactions.html#arbdmodel.interactions.TabulatedNonbonded.write_file">(TabulatedNonbonded method)</a>
</li>
</ul></li>
+ </ul></td>
+ <td style="width: 33%; vertical-align: top;"><ul>
+ <li><a href="api/rigidbody_models/mesh_process_volume.html#arbdmodel.mesh_process_volume.MeshProcessor.write_no_enter_potential">write_no_enter_potential() (MeshProcessor method)</a>
+</li>
+ <li><a href="api/rigidbody_models/mesh_process_surface.html#arbdmodel.mesh_process_surface.SurfaceMeshProcessor.write_no_enter_potential_dx">write_no_enter_potential_dx() (SurfaceMeshProcessor method)</a>
+</li>
+ <li><a href="api/core/model.html#arbdmodel.model.PdbModel.write_pdb">write_pdb() (PdbModel method)</a>
+</li>
+ <li><a href="api/core/model.html#arbdmodel.model.PdbModel.write_pqr">write_pqr() (PdbModel method)</a>
+</li>
+ <li><a href="api/core/model.html#arbdmodel.model.PdbModel.write_psf">write_psf() (PdbModel method)</a>
+</li>
<li><a href="api/utilities/version.html#arbdmodel.version.write_release_version">write_release_version() (in module arbdmodel.version)</a>
</li>
+ <li><a href="api/simulation_engines/parmed_bd.html#arbdmodel.parmed_bd.ParmedArbd.write_restraint_files">write_restraint_files() (ParmedArbd method)</a>
+</li>
+ <li><a href="api/simulation_engines/engine.html#arbdmodel.engine.ArbdEngine.write_simulation_files">write_simulation_files() (ArbdEngine method)</a>
+
+ <ul>
+ <li><a href="api/simulation_engines/engine.html#arbdmodel.engine.NamdEngine.write_simulation_files">(NamdEngine method)</a>
+</li>
+ <li><a href="api/simulation_engines/engine.html#arbdmodel.engine.SimEngine.write_simulation_files">(SimEngine method)</a>
+</li>
+ <li><a href="api/rigidbody_models/structure_rigidbody.html#arbdmodel.structure_rigidbody.SimpleArbdEngine.write_simulation_files">(SimpleArbdEngine method)</a>
+</li>
+ </ul></li>
<li><a href="api/utilities/grid.html#arbdmodel.grid.writeDx">writeDx() (in module arbdmodel.grid)</a>
</li>
</ul></td>
diff --git a/_build/html/intro.html b/_build/html/intro.html
index 204712db74a591400bb9cc0a1d4c937880774fc5..753237cd058dac596899227ba10636e2407315b6 100644
--- a/_build/html/intro.html
+++ b/_build/html/intro.html
@@ -32,19 +32,19 @@
<link rel="stylesheet" type="text/css" href="_static/styles/sphinx-book-theme.css?v=eba8b062" />
<link rel="stylesheet" type="text/css" href="_static/togglebutton.css?v=13237357" />
<link rel="stylesheet" type="text/css" href="_static/copybutton.css?v=76b2166b" />
- <link rel="stylesheet" type="text/css" href="_static/mystnb.4510f1fc1dee50b3e5859aac5469c37c29e427902b24a333a5f9fcb2f0b3ac41.css" />
+ <link rel="stylesheet" type="text/css" href="_static/mystnb.4510f1fc1dee50b3e5859aac5469c37c29e427902b24a333a5f9fcb2f0b3ac41.css?v=be8a1c11" />
<link rel="stylesheet" type="text/css" href="_static/sphinx-thebe.css?v=4fa983c6" />
<link rel="stylesheet" type="text/css" href="_static/tabs.css?v=4c969af8" />
- <link rel="stylesheet" type="text/css" href="_static/proof.css" />
+ <link rel="stylesheet" type="text/css" href="_static/proof.css?v=b4b7a797" />
<link rel="stylesheet" type="text/css" href="_static/styles/sphinx-examples.css?v=e236af4b" />
- <link rel="stylesheet" type="text/css" href="_static/css/tooltipster.custom.css" />
- <link rel="stylesheet" type="text/css" href="_static/css/tooltipster.bundle.min.css" />
- <link rel="stylesheet" type="text/css" href="_static/css/tooltipster-sideTip-shadow.min.css" />
- <link rel="stylesheet" type="text/css" href="_static/css/tooltipster-sideTip-punk.min.css" />
- <link rel="stylesheet" type="text/css" href="_static/css/tooltipster-sideTip-noir.min.css" />
- <link rel="stylesheet" type="text/css" href="_static/css/tooltipster-sideTip-light.min.css" />
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<td>
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+ <td>   
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+ <td></td>
+ <td>   
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+ <td></td>
+ <td>   
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+ <em></em></td></tr>
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<em></em></td></tr>
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+ <td></td>
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+ <td>   
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+ <td></td>
+ <td>   
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+ <td></td>
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+ <td>   
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[[1, "arbdmodel.core_objects.RigidBody.get_restraints", false]], "get_slice_enclosing_smaller_grid() (in module arbdmodel.grid)": [[32, "arbdmodel.grid.get_slice_enclosing_smaller_grid", false]], "get_target_distribution() (abstractibipotential method)": [[6, "arbdmodel.ibi.AbstractIBIpotential.get_target_distribution", false]], "get_values() (degreeoffreedom method)": [[6, "arbdmodel.ibi.DegreeOfFreedom.get_values", false]], "get_values() (pairdistributiondof method)": [[6, "arbdmodel.ibi.PairDistributionDof.get_values", false]], "get_vector_angles() (parent method)": [[1, "arbdmodel.core_objects.Parent.get_vector_angles", false]], "get_version() (in module arbdmodel.version)": [[35, "arbdmodel.version.get_version", false]], "getparticletypesandcounts() (arbdmodel method)": [[3, "arbdmodel.model.ArbdModel.getParticleTypesAndCounts", false]], "group (class in arbdmodel.core_objects)": [[1, "arbdmodel.core_objects.Group", false]], "groupsite (class in arbdmodel.core_objects)": [[1, "arbdmodel.core_objects.GroupSite", false]], "halfharmonic (class in arbdmodel.interactions)": [[8, "arbdmodel.interactions.HalfHarmonic", false]], "harmonicangle (class in arbdmodel.interactions)": [[8, "arbdmodel.interactions.HarmonicAngle", false]], "harmonicbond (class in arbdmodel.interactions)": [[8, "arbdmodel.interactions.HarmonicBond", false]], "harmonicbondedpotential (class in arbdmodel.interactions)": [[8, "arbdmodel.interactions.HarmonicBondedPotential", false]], "harmonicdihedral (class in arbdmodel.interactions)": [[8, "arbdmodel.interactions.HarmonicDihedral", false]], "harmonicvectorangle (class in arbdmodel.interactions)": [[8, "arbdmodel.interactions.HarmonicVectorAngle", false]], "hpsbeads (class in arbdmodel.hps_polymer_model)": [[10, "arbdmodel.hps_polymer_model.HpsBeads", false]], "hpsmodel (class in arbdmodel.hps_polymer_model)": [[10, "arbdmodel.hps_polymer_model.HpsModel", false]], "hpsnonbonded (class in arbdmodel.hps_polymer_model)": [[10, "arbdmodel.hps_polymer_model.HpsNonbonded", false]], "hydroprorunner (class in arbdmodel.engine)": [[27, "arbdmodel.engine.HydroProRunner", false]], "ibiangle (class in arbdmodel.ibi)": [[6, "arbdmodel.ibi.IBIAngle", false]], "ibibond (class in arbdmodel.ibi)": [[6, "arbdmodel.ibi.IBIBond", false]], "ibidihedral (class in arbdmodel.ibi)": [[6, "arbdmodel.ibi.IBIDihedral", false]], "ibinonbonded (class in arbdmodel.ibi)": [[6, "arbdmodel.ibi.IBINonbonded", false]], "index() (parent method)": [[1, "arbdmodel.core_objects.Parent.index", false]], "initialize_binary_paths() (in module arbdmodel.binary_manager)": [[30, "arbdmodel.binary_manager.initialize_binary_paths", false]], "insert() (parent method)": [[1, "arbdmodel.core_objects.Parent.insert", false]], "insert_monomers() (polymersection method)": [[15, "arbdmodel.polymer.PolymerSection.insert_monomers", false]], "is_dirty() (in module arbdmodel.version)": [[35, "arbdmodel.version.is_dirty", false]], "is_same_type() (particletype method)": [[1, "arbdmodel.core_objects.ParticleType.is_same_type", false]], "isotropic_kernel() (in module arbdmodel.grid)": [[32, "arbdmodel.grid.isotropic_kernel", false]], "items() (simconf method)": [[4, "arbdmodel.sim_config.SimConf.items", false]], "iterate_connections_and_locations() (polymersection method)": [[15, "arbdmodel.polymer.PolymerSection.iterate_connections_and_locations", false]], "khbeads (class in arbdmodel.kh_polymer_model)": [[12, "arbdmodel.kh_polymer_model.KhBeads", false]], "khmodel (class in arbdmodel.kh_polymer_model)": [[12, "arbdmodel.kh_polymer_model.KhModel", false]], "khnonbonded (class in arbdmodel.kh_polymer_model)": [[12, "arbdmodel.kh_polymer_model.KhNonbonded", false]], "kscale (harmonicangle property)": [[8, "arbdmodel.interactions.HarmonicAngle.kscale", false]], "kscale (harmonicbond property)": [[8, "arbdmodel.interactions.HarmonicBond.kscale", false]], "kscale (harmonicbondedpotential property)": [[8, "arbdmodel.interactions.HarmonicBondedPotential.kscale", false]], "kscale (harmonicdihedral property)": [[8, "arbdmodel.interactions.HarmonicDihedral.kscale", false]], "kscale (harmonicvectorangle property)": [[8, "arbdmodel.interactions.HarmonicVectorAngle.kscale", false]], "lennardjones (class in arbdmodel.interactions)": [[8, "arbdmodel.interactions.LennardJones", false]], "linearbond (class in arbdmodel.sali_polymer_model)": [[16, "arbdmodel.sali_polymer_model.LinearBond", false]], "load_structure() (parmedarbd method)": [[29, "arbdmodel.parmed_bd.ParmedArbd.load_structure", false]], "load_target_ibi_distributions() (arbdmodel method)": [[3, "arbdmodel.model.ArbdModel.load_target_IBI_distributions", false]], "loadgrid() (in module arbdmodel.grid)": [[32, "arbdmodel.grid.loadGrid", false]], "location (class in arbdmodel.polymer)": [[15, "arbdmodel.polymer.Location", false]], "main() (in module arbdmodel.simplearbd)": [[22, "arbdmodel.simplearbd.main", false]], "meshprocessor (class in arbdmodel.mesh_process_volume)": [[20, "arbdmodel.mesh_process_volume.MeshProcessor", false]], "meshrigidbodytype (class in arbdmodel.mesh_rigidbody)": [[21, "arbdmodel.mesh_rigidbody.MeshRigidBodyType", false]], "micron_to_angstrom (meshprocessor attribute)": [[20, "arbdmodel.mesh_process_volume.MeshProcessor.MICRON_TO_ANGSTROM", false]], "micron_to_angstrom (surfacemeshprocessor attribute)": [[19, "arbdmodel.mesh_process_surface.SurfaceMeshProcessor.MICRON_TO_ANGSTROM", false]], "minimizermsd() (in module arbdmodel.coords)": [[31, "arbdmodel.coords.minimizeRmsd", false]], "module": [[1, "module-arbdmodel.core_objects", false], [3, "module-arbdmodel.model", false], [4, "module-arbdmodel.sim_config", false], [6, "module-arbdmodel.ibi", false], [8, "module-arbdmodel.interactions", false], [9, "module-arbdmodel.fjc_polymer_model", false], [10, "module-arbdmodel.hps_polymer_model", false], [12, "module-arbdmodel.kh_polymer_model", false], [13, "module-arbdmodel.mpipi_polymer", false], [14, "module-arbdmodel.onck_polymer_model", false], [15, "module-arbdmodel.polymer", false], [16, "module-arbdmodel.sali_polymer_model", false], [17, "module-arbdmodel.ssdna_two_bead", false], [19, "module-arbdmodel.mesh_process_surface", false], [20, "module-arbdmodel.mesh_process_volume", false], [21, "module-arbdmodel.mesh_rigidbody", false], [22, "module-arbdmodel.simplearbd", false], [23, "module-arbdmodel.structure_from_pdb", false], [24, "module-arbdmodel.structure_rigidbody", false], [26, "module-arbdmodel.shape_cg", false], [27, "module-arbdmodel.engine", false], [29, "module-arbdmodel.parmed_bd", false], [30, "module-arbdmodel.binary_manager", false], [31, "module-arbdmodel.coords", false], [32, "module-arbdmodel.grid", false], [34, "module-arbdmodel.logger", false], [35, "module-arbdmodel.version", false]], "monomer_index_to_contour() (polymersection method)": [[15, "arbdmodel.polymer.PolymerSection.monomer_index_to_contour", false]], "monomers_per_bead_group (polymerbeads property)": [[15, "arbdmodel.polymer.PolymerBeads.monomers_per_bead_group", false]], "mpipibeads (class in arbdmodel.mpipi_polymer)": [[13, "arbdmodel.mpipi_polymer.MpipiBeads", false]], "mpipimodel (class in arbdmodel.mpipi_polymer)": [[13, "arbdmodel.mpipi_polymer.MpipiModel", false]], "mpipinonbonded (class in arbdmodel.mpipi_polymer)": [[13, "arbdmodel.mpipi_polymer.MpipiNonbonded", false]], "namdengine (class in arbdmodel.engine)": [[27, "arbdmodel.engine.NamdEngine", false]], "neighborhood_average() (in module arbdmodel.grid)": [[32, "arbdmodel.grid.neighborhood_average", false]], "nt (dnastrandbeads attribute)": [[17, "arbdmodel.ssdna_two_bead.DnaStrandBeads.nt", false]], "nullpotential (class in arbdmodel.interactions)": [[8, "arbdmodel.interactions.NullPotential", false]], "num_bead_groups (polymerbeads property)": [[15, "arbdmodel.polymer.PolymerBeads.num_bead_groups", false]], "onckbeads (class in arbdmodel.onck_polymer_model)": [[14, "arbdmodel.onck_polymer_model.OnckBeads", false]], "onckmodel (class in arbdmodel.onck_polymer_model)": [[14, "arbdmodel.onck_polymer_model.OnckModel", false]], "oncknonbonded (class in arbdmodel.onck_polymer_model)": [[14, "arbdmodel.onck_polymer_model.OnckNonbonded", false]], "other() (connection method)": [[15, "arbdmodel.polymer.Connection.other", false]], "p (dnastrandbeads attribute)": [[17, "arbdmodel.ssdna_two_bead.DnaStrandBeads.p", false]], "pairdistributiondof (class in arbdmodel.ibi)": [[6, "arbdmodel.ibi.PairDistributionDof", false]], "parent (class in arbdmodel.core_objects)": [[1, "arbdmodel.core_objects.Parent", false]], "parmed_structure (parmedarbd attribute)": [[29, "arbdmodel.parmed_bd.ParmedArbd.parmed_structure", false]], "parmedarbd (class in arbdmodel.parmed_bd)": [[29, "arbdmodel.parmed_bd.ParmedArbd", false]], "parse_output() (hydroprorunner method)": [[27, "arbdmodel.engine.HydroProRunner.parse_output", false]], "particletype (class in arbdmodel.core_objects)": [[1, "arbdmodel.core_objects.ParticleType", false]], "pdbmodel (class in arbdmodel.model)": [[3, "arbdmodel.model.PdbModel", false]], "periodic (abstractpotential property)": [[8, "arbdmodel.interactions.AbstractPotential.periodic", false]], "periodic (harmonicdihedral property)": [[8, "arbdmodel.interactions.HarmonicDihedral.periodic", false]], "periodic (ibidihedral property)": [[6, "arbdmodel.ibi.IBIDihedral.periodic", false]], "pointparticle (class in arbdmodel.core_objects)": [[1, "arbdmodel.core_objects.PointParticle", false]], "polymerbeads (class in arbdmodel.polymer)": [[15, "arbdmodel.polymer.PolymerBeads", false]], "polymergroup (class in arbdmodel.polymer)": [[15, "arbdmodel.polymer.PolymerGroup", false]], "polymermodel (class in arbdmodel.polymer)": [[15, "arbdmodel.polymer.PolymerModel", false]], "polymersection (class in arbdmodel.polymer)": [[15, "arbdmodel.polymer.PolymerSection", false]], "potential() (abstractibipotential method)": [[6, "arbdmodel.ibi.AbstractIBIpotential.potential", false]], "potential() (abstractpotential method)": [[8, "arbdmodel.interactions.AbstractPotential.potential", false]], "potential() (boundarypotential method)": [[8, "arbdmodel.interactions.BoundaryPotential.potential", false]], "potential() (halfharmonic method)": [[8, "arbdmodel.interactions.HalfHarmonic.potential", false]], "potential() (harmonicbond method)": [[8, "arbdmodel.interactions.HarmonicBond.potential", false]], "potential() (harmonicbondedpotential method)": [[8, "arbdmodel.interactions.HarmonicBondedPotential.potential", false]], "potential() (hpsnonbonded method)": [[10, "arbdmodel.hps_polymer_model.HpsNonbonded.potential", false]], "potential() (khnonbonded method)": [[12, "arbdmodel.kh_polymer_model.KhNonbonded.potential", false]], "potential() (lennardjones method)": [[8, "arbdmodel.interactions.LennardJones.potential", false]], "potential() (linearbond method)": [[16, "arbdmodel.sali_polymer_model.LinearBond.potential", false]], "potential() (mpipinonbonded method)": [[13, "arbdmodel.mpipi_polymer.MpipiNonbonded.potential", false]], "potential() (nullpotential method)": [[8, "arbdmodel.interactions.NullPotential.potential", false]], "potential() (oncknonbonded method)": [[14, "arbdmodel.onck_polymer_model.OnckNonbonded.potential", false]], "potential() (salinonbonded method)": [[16, "arbdmodel.sali_polymer_model.SaliNonbonded.potential", false]], "potential() (shapecgnonbonded method)": [[26, "arbdmodel.shape_cg.ShapeCGNonbonded.potential", false]], "potential() (tabulatednonbonded method)": [[8, "arbdmodel.interactions.TabulatedNonbonded.potential", false]], "potential() (wlcskangle method)": [[8, "arbdmodel.interactions.WLCSKAngle.potential", false]], "potential() (wlcskbond method)": [[8, "arbdmodel.interactions.WLCSKBond.potential", false]], "prepare_for_simulation() (arbdmodel method)": [[3, "arbdmodel.model.ArbdModel.prepare_for_simulation", false]], "process() (staticobject method)": [[24, "arbdmodel.structure_rigidbody.StaticObject.process", false]], "process_mesh_file() (in module arbdmodel.mesh_process_volume)": [[20, "arbdmodel.mesh_process_volume.process_mesh_file", false]], "process_structure() (structureprocessor method)": [[23, "arbdmodel.structure_from_pdb.StructureProcessor.process_structure", false]], "process_surface_mesh() (in module arbdmodel.mesh_process_surface)": [[19, "arbdmodel.mesh_process_surface.process_surface_mesh", false]], "quaternion_exp() (in module arbdmodel.coords)": [[31, "arbdmodel.coords.quaternion_exp", false]], "quaternion_from_matrix() (in module arbdmodel.coords)": [[31, "arbdmodel.coords.quaternion_from_matrix", false]], "quaternion_inverse() (in module arbdmodel.coords)": [[31, "arbdmodel.coords.quaternion_inverse", false]], "quaternion_product() (in module arbdmodel.coords)": [[31, "arbdmodel.coords.quaternion_product", false]], "quaternion_slerp() (in module arbdmodel.coords)": [[31, "arbdmodel.coords.quaternion_slerp", false]], "quaternion_to_matrix() (in module arbdmodel.coords)": [[31, "arbdmodel.coords.quaternion_to_matrix", false]], "radiusdof (class in arbdmodel.ibi)": [[6, "arbdmodel.ibi.RadiusDof", false]], "range_ (abstractpotential property)": [[8, "arbdmodel.interactions.AbstractPotential.range_", false]], "read_arbd_coordinates() (in module arbdmodel.coords)": [[31, "arbdmodel.coords.read_arbd_coordinates", false]], "read_average_arbd_coordinates() (in module arbdmodel.coords)": [[31, "arbdmodel.coords.read_average_arbd_coordinates", false]], "read_cg_potential() (abstractibipotential method)": [[6, "arbdmodel.ibi.AbstractIBIpotential.read_cg_potential", false]], "read_files() (in module arbdmodel.shape_cg)": [[26, "arbdmodel.shape_cg.read_files", false]], "read_release_version() (in module arbdmodel.version)": [[35, "arbdmodel.version.read_release_version", false]], "read_version_file() (in module arbdmodel.version)": [[35, "arbdmodel.version.read_version_file", false]], "readarbdcoords() (in module arbdmodel.coords)": [[31, "arbdmodel.coords.readArbdCoords", false]], "readavgarbdcoords() (in module arbdmodel.coords)": [[31, "arbdmodel.coords.readAvgArbdCoords", false]], "remove() (parent method)": [[1, "arbdmodel.core_objects.Parent.remove", false]], "remove_monomers() (polymersection method)": [[15, "arbdmodel.polymer.PolymerSection.remove_monomers", false]], "replace_false_with_distance() (in module arbdmodel.grid)": [[32, "arbdmodel.grid.replace_false_with_distance", false]], "rigidbody (class in arbdmodel.core_objects)": [[1, "arbdmodel.core_objects.RigidBody", false]], "rigidbodytype (class in arbdmodel.core_objects)": [[1, "arbdmodel.core_objects.RigidBodyType", false]], "rotate() (polymergroup method)": [[15, "arbdmodel.polymer.PolymerGroup.rotate", false]], "rotate() (polymersection method)": [[15, "arbdmodel.polymer.PolymerSection.rotate", false]], "rotate() (transformable method)": [[1, "arbdmodel.core_objects.Transformable.rotate", false]], "rotationaboutaxis() (in module arbdmodel.coords)": [[31, "arbdmodel.coords.rotationAboutAxis", false]], "run_calculation() (apbsrunner method)": [[27, "arbdmodel.engine.APBSRunner.run_calculation", false]], "run_calculation() (hydroprorunner method)": [[27, "arbdmodel.engine.HydroProRunner.run_calculation", false]], "run_from_minimized() (shapecgmodel method)": [[26, "arbdmodel.shape_cg.ShapeCGModel.run_from_minimized", false]], "run_ibi() (arbdmodel method)": [[3, "arbdmodel.model.ArbdModel.run_IBI", false]], "run_minimization() (shapecgmodel method)": [[26, "arbdmodel.shape_cg.ShapeCGModel.run_minimization", false]], "run_simulation() (simplearbdconfig method)": [[22, "arbdmodel.simplearbd.SimpleArbdConfig.run_simulation", false]], "run_simulation() (simplearbdengine method)": [[24, "arbdmodel.structure_rigidbody.SimpleArbdEngine.run_simulation", false]], "salibeadsfrompolymer (class in arbdmodel.sali_polymer_model)": [[16, "arbdmodel.sali_polymer_model.SaliBeadsFromPolymer", false]], "salimodel (class in arbdmodel.sali_polymer_model)": [[16, "arbdmodel.sali_polymer_model.SaliModel", false]], "salinonbonded (class in arbdmodel.sali_polymer_model)": [[16, "arbdmodel.sali_polymer_model.SaliNonbonded", false]], "save_aligned_mesh() (meshprocessor method)": [[20, "arbdmodel.mesh_process_volume.MeshProcessor.save_aligned_mesh", false]], "save_aligned_mesh() (surfacemeshprocessor method)": [[19, "arbdmodel.mesh_process_surface.SurfaceMeshProcessor.save_aligned_mesh", false]], "save_aligned_mesh_both_formats() (surfacemeshprocessor method)": [[19, "arbdmodel.mesh_process_surface.SurfaceMeshProcessor.save_aligned_mesh_both_formats", false]], "save_as_pdb() (meshprocessor method)": [[20, "arbdmodel.mesh_process_volume.MeshProcessor.save_as_pdb", false]], "save_as_pdb() (surfacemeshprocessor method)": [[19, "arbdmodel.mesh_process_surface.SurfaceMeshProcessor.save_as_pdb", false]], "set_binary() (simconf method)": [[4, "arbdmodel.sim_config.SimConf.set_binary", false]], "set_connection() (location method)": [[15, "arbdmodel.polymer.Location.set_connection", false]], "set_damping_coefficient() (fjcmodel method)": [[9, "arbdmodel.fjc_polymer_model.FjcModel.set_damping_coefficient", false]], "set_damping_coefficient() (hpsmodel method)": [[10, "arbdmodel.hps_polymer_model.HpsModel.set_damping_coefficient", false]], "set_damping_coefficient() (khmodel method)": [[12, "arbdmodel.kh_polymer_model.KhModel.set_damping_coefficient", false]], "set_damping_coefficient() (mpipimodel method)": [[13, "arbdmodel.mpipi_polymer.MpipiModel.set_damping_coefficient", false]], "set_damping_coefficient() (onckmodel method)": [[14, "arbdmodel.onck_polymer_model.OnckModel.set_damping_coefficient", false]], "set_orientation_splines() (polymersection method)": [[15, "arbdmodel.polymer.PolymerSection.set_orientation_splines", false]], "set_splines() (polymersection method)": [[15, "arbdmodel.polymer.PolymerSection.set_splines", false]], "setup_and_run() (shapecgmodel method)": [[26, "arbdmodel.shape_cg.ShapeCGModel.setup_and_run", false]], "setup_diffusible_objects() (simplearbdconfig method)": [[22, "arbdmodel.simplearbd.SimpleArbdConfig.setup_diffusible_objects", false]], "setup_static_objects() (simplearbdconfig method)": [[22, "arbdmodel.simplearbd.SimpleArbdConfig.setup_static_objects", false]], "shapecgfactory (class in arbdmodel.shape_cg)": [[26, "arbdmodel.shape_cg.ShapeCGFactory", false]], "shapecgmodel (class in arbdmodel.shape_cg)": [[26, "arbdmodel.shape_cg.ShapeCGModel", false]], "shapecgnonbonded (class in arbdmodel.shape_cg)": [[26, "arbdmodel.shape_cg.ShapeCGNonbonded", false]], "simconf (class in arbdmodel.sim_config)": [[4, "arbdmodel.sim_config.SimConf", false]], "simengine (class in arbdmodel.engine)": [[27, "arbdmodel.engine.SimEngine", false]], "simplearbdconfig (class in arbdmodel.simplearbd)": [[22, "arbdmodel.simplearbd.SimpleArbdConfig", false]], "simplearbdengine (class in arbdmodel.structure_rigidbody)": [[24, "arbdmodel.structure_rigidbody.SimpleArbdEngine", false]], "simulate() (arbdmodel method)": [[3, "arbdmodel.model.ArbdModel.simulate", false]], "simulate() (parmedarbd method)": [[29, "arbdmodel.parmed_bd.ParmedArbd.simulate", false]], "simulate() (simengine method)": [[27, "arbdmodel.engine.SimEngine.simulate", false]], "slab_potential_z() (in module arbdmodel.grid)": [[32, "arbdmodel.grid.slab_potential_z", false]], "spherical_confinement() (in module arbdmodel.grid)": [[32, "arbdmodel.grid.spherical_confinement", false]], "spring_constant (hpsmodel attribute)": [[10, "arbdmodel.hps_polymer_model.HpsModel.spring_constant", false]], "spring_constant (khmodel attribute)": [[12, "arbdmodel.kh_polymer_model.KhModel.spring_constant", false]], "spring_constant (mpipimodel attribute)": [[13, "arbdmodel.mpipi_polymer.MpipiModel.spring_constant", false]], "staticobject (class 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diff --git a/_build/html/tutorials/index.html b/_build/html/tutorials/index.html
index d1638632b95a53b50060f7981ee21f90bfb963ae..e5e6773fd178236b1fe6afd4811a0f83dc9404a1 100644
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- <link rel="stylesheet" type="text/css" href="../_static/proof.css" />
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+ <link rel="stylesheet" type="text/css" href="../_static/css/tooltipster.custom.css?v=7bc2f056" />
+ <link rel="stylesheet" type="text/css" href="../_static/css/tooltipster.bundle.min.css?v=37217874" />
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<script>let toggleOpenOnPrint = 'true';</script>
@@ -347,8 +347,6 @@ document.write(`
<nav aria-label="Page">
<ul class="visible nav section-nav flex-column">
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-<li class="toc-h3 nav-item toc-entry"><a class="reference internal nav-link" href="#polymer-objects">2-polymer_objects</a></li>
<li class="toc-h3 nav-item toc-entry"><a class="reference internal nav-link" href="#iterative-boltzmann-inversion">3-iterative-boltzmann-inversion</a></li>
<li class="toc-h3 nav-item toc-entry"><a class="reference internal nav-link" href="#rigid-bodies">4-rigid-bodies</a></li>
</ul>
@@ -369,18 +367,6 @@ document.write(`
<p>This section contains tutorials and examples for working with the arbdmodel package.</p>
<section id="available-tutorials">
<h2>Available Tutorials<a class="headerlink" href="#available-tutorials" title="Link to this heading">#</a></h2>
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-<h3>1- basics<a class="headerlink" href="#basics" title="Link to this heading">#</a></h3>
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-</section>
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-<h3>2-polymer_objects<a class="headerlink" href="#polymer-objects" title="Link to this heading">#</a></h3>
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-<li><p><a class="reference internal" href="2-polymer-objects.html"><span class="std std-doc">2 Polymer Objects</span></a></p></li>
-</ul>
-</section>
<section id="iterative-boltzmann-inversion">
<h3>3-iterative-boltzmann-inversion<a class="headerlink" href="#iterative-boltzmann-inversion" title="Link to this heading">#</a></h3>
<ul class="simple">
@@ -391,6 +377,8 @@ document.write(`
<h3>4-rigid-bodies<a class="headerlink" href="#rigid-bodies" title="Link to this heading">#</a></h3>
<ul class="simple">
<li><p><a class="reference internal" href="4-rigid-bodies/4-rigid-bodies.html"><span class="std std-doc">4 Rigid Bodies</span></a></p></li>
+<li><p><a class="reference internal" href="1-basics.html"><span class="std std-doc">1 Basics</span></a></p></li>
+<li><p><a class="reference internal" href="2-polymer-objects.html"><span class="std std-doc">2 Polymer Objects</span></a></p></li>
</ul>
</section>
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@@ -461,8 +449,6 @@ document.write(`
<nav class="bd-toc-nav page-toc">
<ul class="visible nav section-nav flex-column">
<li class="toc-h2 nav-item toc-entry"><a class="reference internal nav-link" href="#available-tutorials">Available Tutorials</a><ul class="nav section-nav flex-column">
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-<li class="toc-h3 nav-item toc-entry"><a class="reference internal nav-link" href="#polymer-objects">2-polymer_objects</a></li>
<li class="toc-h3 nav-item toc-entry"><a class="reference internal nav-link" href="#iterative-boltzmann-inversion">3-iterative-boltzmann-inversion</a></li>
<li class="toc-h3 nav-item toc-entry"><a class="reference internal nav-link" href="#rigid-bodies">4-rigid-bodies</a></li>
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diff --git a/tutorials/index.md b/tutorials/index.md
index 9e0793fdac81501680e3399a8ec159606bd73e52..ae7fdbe821d5571dda7e2a7e5444f63f208cc63b 100644
--- a/tutorials/index.md
+++ b/tutorials/index.md
@@ -4,12 +4,6 @@ This section contains tutorials and examples for working with the arbdmodel pack
## Available Tutorials
-### 1- basics
-- [1 Basics](1-basics.ipynb)
-
-### 2-polymer_objects
-- [2 Polymer Objects](2-polymer-objects.ipynb)
-
### 3-iterative-boltzmann-inversion
- [3 Ibi](3-iterative-boltzmann-inversion/3-ibi.ipynb)
@@ -18,4 +12,5 @@ This section contains tutorials and examples for working with the arbdmodel pack
- [4 Rigid Bodies](4-rigid-bodies/4-rigid-bodies.ipynb)
-
+- [1 Basics](1-basics.ipynb)
+- [2 Polymer Objects](2-polymer-objects.ipynb)