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href="../../_static/mystnb.4510f1fc1dee50b3e5859aac5469c37c29e427902b24a333a5f9fcb2f0b3ac41.css?v=be8a1c11" /> + <link rel="stylesheet" type="text/css" href="../../_static/mystnb.4510f1fc1dee50b3e5859aac5469c37c29e427902b24a333a5f9fcb2f0b3ac41.css" /> <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?v=b4b7a797" /> + <link rel="stylesheet" type="text/css" href="../../_static/proof.css" /> <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?v=7bc2f056" /> - <link rel="stylesheet" type="text/css" href="../../_static/css/tooltipster.bundle.min.css?v=37217874" /> - <link rel="stylesheet" type="text/css" 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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/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?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 src="../../_static/js/hoverxref.js"></script> + <script src="../../_static/js/tooltipster.bundle.min.js"></script> + <script src="../../_static/js/micromodal.min.js"></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/_modules/arbdmodel/coords.html b/_build/html/_modules/arbdmodel/coords.html index 0ce389b55003d09724192748d8950fa33a7f4990..66cd0352cc270bcdc08eb42f83f970620984b258 100644 --- a/_build/html/_modules/arbdmodel/coords.html +++ b/_build/html/_modules/arbdmodel/coords.html @@ -300,9 +300,8 @@ document.write(` <article class="bd-article"> <h1>Source code for arbdmodel.coords</h1><div class="highlight"><pre> -<span></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">logger</span> +<span></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">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">scipy.optimize</span><span class="w"> </span><span class="kn">import</span> <span class="n">newton</span> <span class="k">def</span><span class="w"> </span><span class="nf">minimizeRmsd</span><span class="p">(</span><span class="n">coordsB</span><span class="p">,</span> <span class="n">coordsA</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">maxIter</span><span class="o">=</span><span class="mi">100</span><span class="p">):</span> <span class="c1">## Going through many iterations wasn't really needed</span> @@ -562,6 +561,63 @@ document.write(` <span class="k">return</span> <span class="n">quaternion_to_matrix</span><span class="p">(</span><span class="n">q</span><span class="p">)</span></div> +<span class="c1"># By Chun</span> +<div class="viewcode-block" id="Generate_spanning_vectors"> +<a class="viewcode-back" href="../../api/utilities/coords.html#arbdmodel.coords.Generate_spanning_vectors">[docs]</a> +<span class="k">def</span><span class="w"> </span><span class="nf">Generate_spanning_vectors</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">dimensions</span><span class="p">,</span> <span class="n">buff</span><span class="o">=</span><span class="mi">5</span><span class="p">):</span> + <span class="n">dd</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="o">+</span> <span class="mi">2</span> <span class="o">*</span> <span class="n">buff</span> + + <span class="n">n1</span> <span class="o">=</span> <span class="nb">round</span><span class="p">(</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">bv1</span><span class="p">)</span><span class="o">/</span><span class="n">dd</span><span class="p">)</span> <span class="o">+</span> <span class="mi">1</span> + <span class="n">n2</span> <span class="o">=</span> <span class="nb">round</span><span class="p">(</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">bv2</span><span class="p">)</span><span class="o">/</span><span class="n">dd</span><span class="p">)</span> <span class="o">+</span> <span class="mi">1</span> + <span class="n">n3</span> <span class="o">=</span> <span class="nb">round</span><span class="p">(</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">bv3</span><span class="p">)</span><span class="o">/</span><span class="n">dd</span><span class="p">)</span> <span class="o">+</span> <span class="mi">1</span> + + <span class="n">v1</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">bv1</span><span class="p">)</span> <span class="o">/</span><span class="n">n1</span> + <span class="n">v2</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">bv2</span><span class="p">)</span> <span class="o">/</span><span class="n">n2</span> + <span class="n">v3</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">bv3</span><span class="p">)</span> <span class="o">/</span><span class="n">n3</span> + + <span class="k">return</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="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></div> + + +<div class="viewcode-block" id="Generate_coordinates"> +<a class="viewcode-back" href="../../api/utilities/coords.html#arbdmodel.coords.Generate_coordinates">[docs]</a> +<span class="k">def</span><span class="w"> </span><span class="nf">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">num_copy</span><span class="p">,</span> <span class="n">origin</span><span class="p">,</span> <span class="n">replica_index</span><span class="p">):</span> + <span class="n">ori_vec</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">origin</span><span class="p">)</span> + + <span class="k">if</span> <span class="n">n1</span> <span class="o">*</span> <span class="n">n2</span> <span class="o">*</span> <span class="n">n3</span> <span class="o">></span> <span class="n">num_copy</span><span class="p">:</span> + <span class="n">check</span> <span class="o">=</span> <span class="kc">True</span> + <span class="k">else</span><span class="p">:</span> + <span class="n">check</span> <span class="o">=</span> <span class="kc">False</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="mi">42</span> <span class="o">+</span> <span class="n">replica_index</span><span class="p">)</span> + + <span class="n">count</span> <span class="o">=</span> <span class="mi">0</span> + <span class="n">inds</span> <span class="o">=</span> <span class="p">[]</span> + <span class="k">while</span> <span class="n">count</span> <span class="o"><</span> <span class="n">num_copy</span><span class="p">:</span> + <span class="n">ind</span> <span class="o">=</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">randint</span><span class="p">(</span><span class="mi">0</span><span class="p">,</span> <span class="n">n1</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">randint</span><span class="p">(</span><span class="mi">0</span><span class="p">,</span> <span class="n">n2</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">randint</span><span class="p">(</span><span class="mi">0</span><span class="p">,</span> <span class="n">n3</span><span class="p">))</span> + <span class="k">if</span> <span class="ow">not</span> <span class="n">check</span><span class="p">:</span> + <span class="n">inds</span><span class="o">.</span><span class="n">append</span><span class="p">(</span><span class="n">ind</span><span class="p">)</span> + <span class="n">count</span> <span class="o">+=</span> <span class="mi">1</span> + <span class="k">elif</span> <span class="n">check</span><span class="p">:</span> + <span class="k">if</span> <span class="ow">not</span> <span class="n">ind</span> <span class="ow">in</span> <span class="n">inds</span><span class="p">:</span> + <span class="n">inds</span><span class="o">.</span><span class="n">append</span><span class="p">(</span><span class="n">ind</span><span class="p">)</span> + <span class="n">count</span> <span class="o">+=</span> <span class="mi">1</span> + <span class="k">else</span><span class="p">:</span> + <span class="k">while</span> <span class="n">ind</span> <span class="ow">in</span> <span class="n">inds</span><span class="p">:</span> + <span class="n">ind</span> <span class="o">=</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">randint</span><span class="p">(</span><span class="mi">0</span><span class="p">,</span> <span class="n">n1</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">randint</span><span class="p">(</span><span class="mi">0</span><span class="p">,</span> <span class="n">n2</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">randint</span><span class="p">(</span><span class="mi">0</span><span class="p">,</span> <span class="n">n3</span><span class="p">))</span> + <span class="n">inds</span><span class="o">.</span><span class="n">append</span><span class="p">(</span><span class="n">ind</span><span class="p">)</span> + <span class="n">count</span> <span class="o">+=</span> <span class="mi">1</span> + + <span class="n">coors</span> <span class="o">=</span> <span class="p">[]</span> + <span class="k">for</span> <span class="n">ind</span> <span class="ow">in</span> <span class="n">inds</span><span class="p">:</span> + <span class="n">r1</span> <span class="o">=</span> <span class="p">(</span><span class="n">ind</span><span class="p">[</span><span class="mi">0</span><span class="p">]</span> <span class="o">-</span> <span class="p">(</span><span class="n">n1</span> <span class="o">-</span> <span class="mi">1</span><span class="p">)</span> <span class="o">*</span> <span class="mf">0.5</span><span class="p">)</span> <span class="o">*</span> <span class="n">bv1</span> + <span class="n">r2</span> <span class="o">=</span> <span class="p">(</span><span class="n">ind</span><span class="p">[</span><span class="mi">1</span><span class="p">]</span> <span class="o">-</span> <span class="p">(</span><span class="n">n2</span> <span class="o">-</span> <span class="mi">1</span><span class="p">)</span> <span class="o">*</span> <span class="mf">0.5</span><span class="p">)</span> <span class="o">*</span> <span class="n">bv2</span> + <span class="n">r3</span> <span class="o">=</span> <span class="p">(</span><span class="n">ind</span><span class="p">[</span><span class="mi">2</span><span class="p">]</span> <span class="o">-</span> <span class="p">(</span><span class="n">n3</span> <span class="o">-</span> <span class="mi">1</span><span class="p">)</span> <span class="o">*</span> <span class="mf">0.5</span><span class="p">)</span> <span class="o">*</span> <span class="n">bv3</span> + <span class="n">coors</span><span class="o">.</span><span class="n">append</span><span class="p">((</span><span class="n">r1</span> <span class="o">+</span> <span class="n">r2</span> <span class="o">+</span> <span class="n">r3</span> <span class="o">+</span> <span class="n">ori_vec</span><span class="p">)</span><span class="o">.</span><span class="n">tolist</span><span class="p">())</span> + + <span class="k">return</span> <span class="n">coors</span></div> + +<span class="c1">#Code to here from simplearbd</span> + <div class="viewcode-block" id="readArbdCoords"> <a class="viewcode-back" href="../../api/utilities/coords.html#arbdmodel.coords.readArbdCoords">[docs]</a> <span class="k">def</span><span class="w"> </span><span class="nf">readArbdCoords</span><span class="p">(</span><span class="n">fname</span><span class="p">):</span> @@ -608,12 +664,49 @@ document.write(` <span class="k">if</span> <span class="n">rmsd</span> <span class="o">></span> <span class="n">rmsd_threshold</span><span class="o">**</span><span class="mi">2</span><span class="p">:</span> <span class="k">break</span> <span class="n">t0</span><span class="o">=</span><span class="n">t</span><span class="o">+</span><span class="mi">1</span> - <span class="n">logger</span><span class="o">.</span><span class="n">info</span><span class="p">(</span><span class="s2">"Averaging coordinates in </span><span class="si">%s</span><span class="s2"> after frame </span><span class="si">%d</span><span class="s2">"</span> <span class="o">%</span> <span class="p">(</span><span class="n">dcd</span><span class="p">,</span> <span class="n">t0</span><span class="p">)</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">"Averaging coordinates in </span><span class="si">{</span><span class="n">dcd</span><span class="si">}</span><span class="s2"> after frame </span><span class="si">{</span><span class="n">t0</span><span class="si">}</span><span class="s2">"</span><span class="p">)</span> <span class="n">pos</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">pos</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">return</span> <span class="n">pos</span></div> + +<div class="viewcode-block" id="calculate_dimensions_from_cell_vectors"> +<a class="viewcode-back" href="../../api/utilities/coords.html#arbdmodel.coords.calculate_dimensions_from_cell_vectors">[docs]</a> +<span class="k">def</span><span class="w"> </span><span class="nf">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="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="w"> </span><span class="sd">"""</span> +<span class="sd"> Calculate simulation box dimensions from cell basis vectors with buffer.</span> +<span class="sd"> </span> +<span class="sd"> Args:</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], defaults to [0,0,0]</span> +<span class="sd"> buffer_factor: Factor to scale the dimensions for additional buffer space</span> +<span class="sd"> </span> +<span class="sd"> Returns:</span> +<span class="sd"> dimensions: 3D box dimensions as a tuple (x_dim, y_dim, z_dim)</span> +<span class="sd"> """</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="k">return</span> <span class="kc">None</span> + + <span class="c1"># Make sure we have proper cell vectors</span> + <span class="k">if</span> <span class="nb">len</span><span class="p">(</span><span class="n">cell_vectors</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="s2">"Expected 3 cell basis vectors, got </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">len</span><span class="p">(</span><span class="n">cell_vectors</span><span class="p">)))</span> + + <span class="c1"># Convert to numpy arrays for easier manipulation</span> + <span class="n">vectors</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">v</span><span class="p">)</span> <span class="k">for</span> <span class="n">v</span> <span class="ow">in</span> <span class="n">cell_vectors</span><span class="p">]</span> + + <span class="c1"># Calculate maximum extent along each dimension</span> + <span class="n">dimensions</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="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">for</span> <span class="n">v</span> <span class="ow">in</span> <span class="n">vectors</span><span class="p">:</span> + <span class="n">dimensions</span><span class="p">[</span><span class="n">i</span><span class="p">]</span> <span class="o">+=</span> <span class="nb">abs</span><span class="p">(</span><span class="n">v</span><span class="p">[</span><span class="n">i</span><span class="p">])</span> + + <span class="c1"># Apply buffer factor</span> + <span class="n">dimensions</span> <span class="o">=</span> <span class="p">[</span><span class="n">dim</span> <span class="o">*</span> <span class="n">buffer_factor</span> <span class="k">for</span> <span class="n">dim</span> <span class="ow">in</span> <span class="n">dimensions</span><span class="p">]</span> + + <span class="k">return</span> <span class="nb">tuple</span><span class="p">(</span><span class="n">dimensions</span><span class="p">)</span></div> + + <div class="viewcode-block" id="unit_quat_conversions"> <a class="viewcode-back" href="../../api/utilities/coords.html#arbdmodel.coords.unit_quat_conversions">[docs]</a> <span class="k">def</span><span class="w"> </span><span class="nf">unit_quat_conversions</span><span class="p">():</span> diff --git a/_build/html/_modules/arbdmodel/core_objects.html b/_build/html/_modules/arbdmodel/core_objects.html index 477f08cd4f932444ff74417eed1c7a01d3e918ec..a5bd644d3a46624008907373c41be191d4c50907 100644 --- a/_build/html/_modules/arbdmodel/core_objects.html +++ b/_build/html/_modules/arbdmodel/core_objects.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?v=be8a1c11" /> + <link rel="stylesheet" type="text/css" href="../../_static/mystnb.4510f1fc1dee50b3e5859aac5469c37c29e427902b24a333a5f9fcb2f0b3ac41.css" /> <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?v=b4b7a797" /> + <link rel="stylesheet" type="text/css" href="../../_static/proof.css" /> <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?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/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/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?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 src="../../_static/js/hoverxref.js"></script> + <script src="../../_static/js/tooltipster.bundle.min.js"></script> + <script src="../../_static/js/micromodal.min.js"></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/_modules/arbdmodel/engine.html b/_build/html/_modules/arbdmodel/engine.html index d6ee79f69a2270a038e340148eb6ee7c874a8cd4..0e96a9ba36d38fcecf61cf023a801c5eeea2c957 100644 --- a/_build/html/_modules/arbdmodel/engine.html +++ b/_build/html/_modules/arbdmodel/engine.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?v=be8a1c11" /> + <link rel="stylesheet" type="text/css" href="../../_static/mystnb.4510f1fc1dee50b3e5859aac5469c37c29e427902b24a333a5f9fcb2f0b3ac41.css" /> <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?v=b4b7a797" /> + <link rel="stylesheet" type="text/css" href="../../_static/proof.css" /> <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?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/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/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?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 src="../../_static/js/hoverxref.js"></script> + <script src="../../_static/js/tooltipster.bundle.min.js"></script> + <script src="../../_static/js/micromodal.min.js"></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/_modules/arbdmodel/fjc_polymer_model.html b/_build/html/_modules/arbdmodel/fjc_polymer_model.html index a593295481f11ec14c3c8926f488de6f2212da1b..12c67ccf3ca1ad42bbe9e35558d3eedd2967c4ef 100644 --- a/_build/html/_modules/arbdmodel/fjc_polymer_model.html +++ b/_build/html/_modules/arbdmodel/fjc_polymer_model.html @@ -304,12 +304,12 @@ document.write(` <span class="c1">## Test with `python -m arbdmodel.fjc_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">logger</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">.</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="kn">from</span><span class="w"> </span><span class="nn">.polymer</span><span class="w"> </span><span class="kn">import</span> <span class="n">PolymerBeads</span><span class="p">,</span> <span class="n">PolymerModel</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="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">"""Define particle types"""</span> @@ -318,15 +318,6 @@ document.write(` <span class="n">mass</span><span class="o">=</span><span class="mi">120</span> <span class="p">)</span> -<span class="c1"># ## Bonded potentials</span> -<span class="c1"># class FjcNonbonded(AbstractPotential):</span> -<span class="c1"># """ This potential should apply zero force; however, it is required for the arbd engine """</span> -<span class="c1"># def __init__(self, resolution=0.1, range_=(0,1)):</span> -<span class="c1"># AbstractPotential.__init__(self, resolution=resolution, range_=range_)</span> - -<span class="c1"># def potential(self, r, types):</span> -<span class="c1"># u = np.zeros(r.shape)</span> -<span class="c1"># return u</span> <div class="viewcode-block" id="FjcBeadsFromPolymer"> <a class="viewcode-back" href="../../api/polymer_modeling/fjc_polymer_model.html#arbdmodel.fjc_polymer_model.FjcBeadsFromPolymer">[docs]</a> diff --git a/_build/html/_modules/arbdmodel/grid.html b/_build/html/_modules/arbdmodel/grid.html index 23e9ecbd3f9f4dd289d59d3214b212b504fee889..2b14aafa4a05033331261939a88d7f5ebfc97523 100644 --- a/_build/html/_modules/arbdmodel/grid.html +++ b/_build/html/_modules/arbdmodel/grid.html @@ -300,8 +300,91 @@ document.write(` <article class="bd-article"> <h1>Source code for arbdmodel.grid</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></span><span class="kn">from</span><span class="w"> </span><span class="nn">__future__</span><span class="w"> </span><span class="kn">import</span> <span class="n">absolute_import</span><span class="p">,</span> <span class="n">print_function</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">scipy</span><span class="w"> </span><span class="kn">import</span> <span class="n">signal</span> +<span class="kn">import</span><span class="w"> </span><span class="nn">os</span><span class="o">,</span><span class="nn">sys</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">import</span><span class="w"> </span><span class="nn">unittest</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> + + +<div class="viewcode-block" id="writeDx"> +<a class="viewcode-back" href="../../api/utilities/grid.html#arbdmodel.grid.writeDx">[docs]</a> +<span class="k">def</span><span class="w"> </span><span class="nf">writeDx</span><span class="p">(</span><span class="n">outfile</span><span class="p">,</span> <span class="n">data</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="n">fmt</span><span class="o">=</span><span class="s2">"</span><span class="si">%.12f</span><span class="s2">"</span><span class="p">):</span> +<span class="w"> </span><span class="sd">"""Write 3D grid data to an OpenDX format file.</span> +<span class="sd"> Write 3D grid data to an OpenDX format file.</span> +<span class="sd"> </span> +<span class="sd"> OpenDX is a visualization software format that can be used to visualize </span> +<span class="sd"> volumetric data.</span> +<span class="sd"> </span> +<span class="sd"> Parameters</span> +<span class="sd"> ----------</span> +<span class="sd"> outfile : str or file-like object</span> +<span class="sd"> The path to the output file or a file-like object.</span> +<span class="sd"> data : numpy.ndarray</span> +<span class="sd"> 3D array containing the grid data to be written.</span> +<span class="sd"> origin : list or tuple</span> +<span class="sd"> The (x, y, z) coordinates of the origin of the grid.</span> +<span class="sd"> delta : list or tuple</span> +<span class="sd"> The grid spacing in the (x, y, z) directions.</span> +<span class="sd"> fmt : str, optional</span> +<span class="sd"> Format string for the data values. Default is "%.12f".</span> +<span class="sd"> </span> +<span class="sd"> Notes</span> +<span class="sd"> -----</span> +<span class="sd"> The output file follows the OpenDX format specification:</span> +<span class="sd"> http://opendx.sdsc.edu/docs/html/pages/usrgu068.htm#HDREDF</span> +<span class="sd"> </span> +<span class="sd"> The data is written in a way that is compatible with visualization software</span> +<span class="sd"> that accepts OpenDX format.</span> +<span class="sd"> </span> +<span class="sd"> Raises</span> +<span class="sd"> ------</span> +<span class="sd"> AssertionError</span> +<span class="sd"> If data is not a 3D array or if origin or delta do not have length 3.</span> +<span class="sd"> """</span> + + <span class="n">shape</span> <span class="o">=</span> <span class="n">np</span><span class="o">.</span><span class="n">shape</span><span class="p">(</span><span class="n">data</span><span class="p">)</span> + <span class="n">num</span> <span class="o">=</span> <span class="n">np</span><span class="o">.</span><span class="n">prod</span><span class="p">(</span><span class="n">shape</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">shape</span><span class="p">)</span> <span class="o">==</span> <span class="mi">3</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">origin</span><span class="p">)</span> <span class="o">==</span> <span class="mi">3</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">delta</span><span class="p">)</span> <span class="o">==</span> <span class="mi">3</span> <span class="p">)</span> + <span class="n">headerInfo</span> <span class="o">=</span> <span class="nb">dict</span><span class="p">(</span> <span class="n">nx</span><span class="o">=</span><span class="n">shape</span><span class="p">[</span><span class="mi">0</span><span class="p">],</span> <span class="n">ny</span><span class="o">=</span><span class="n">shape</span><span class="p">[</span><span class="mi">1</span><span class="p">],</span> <span class="n">nz</span><span class="o">=</span><span class="n">shape</span><span class="p">[</span><span class="mi">2</span><span class="p">],</span> + <span class="n">ox</span><span class="o">=</span><span class="n">origin</span><span class="p">[</span><span class="mi">0</span><span class="p">],</span> <span class="n">oy</span><span class="o">=</span><span class="n">origin</span><span class="p">[</span><span class="mi">1</span><span class="p">],</span> <span class="n">oz</span><span class="o">=</span><span class="n">origin</span><span class="p">[</span><span class="mi">2</span><span class="p">],</span> + <span class="n">dx</span><span class="o">=</span><span class="n">delta</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="n">delta</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="n">delta</span><span class="p">[</span><span class="mi">2</span><span class="p">],</span> + <span class="n">num</span><span class="o">=</span><span class="n">num</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">flatten</span><span class="p">(</span><span class="n">order</span><span class="o">=</span><span class="s1">'C'</span><span class="p">)</span> + <span class="n">header</span> <span class="o">=</span> <span class="s2">"""# OpenDX density file</span> +<span class="s2"># File format: http://opendx.sdsc.edu/docs/html/pages/usrgu068.htm#HDREDF</span> +<span class="s2">object 1 class gridpositions counts </span><span class="si">{nx}</span><span class="s2"> </span><span class="si">{ny}</span><span class="s2"> </span><span class="si">{nz}</span> +<span class="s2">origin </span><span class="si">{ox}</span><span class="s2"> </span><span class="si">{oy}</span><span class="s2"> </span><span class="si">{oz}</span> +<span class="s2">delta </span><span class="si">{dx}</span><span class="s2"> 0.000000 0.000000</span> +<span class="s2">delta 0.000000 </span><span class="si">{dy}</span><span class="s2"> 0.000000</span> +<span class="s2">delta 0.000000 0.000000 </span><span class="si">{dz}</span> +<span class="s2">object 2 class gridconnections counts </span><span class="si">{nx}</span><span class="s2"> </span><span class="si">{ny}</span><span class="s2"> </span><span class="si">{nz}</span> +<span class="s2">object 3 class array type double rank 0 items </span><span class="si">{num}</span><span class="s2"> data follows"""</span><span class="o">.</span><span class="n">format</span><span class="p">(</span><span class="o">**</span><span class="n">headerInfo</span><span class="p">)</span> + <span class="nb">len</span><span class="p">(</span><span class="n">data</span><span class="p">)</span> + + <span class="k">if</span> <span class="n">num</span> <span class="o">==</span> <span class="mi">3</span><span class="o">*</span><span class="p">(</span><span class="n">num</span><span class="o">//</span><span class="mi">3</span><span class="p">):</span> + <span class="n">footer</span> <span class="o">=</span> <span class="s2">""</span> + <span class="k">else</span><span class="p">:</span> + <span class="n">footer</span> <span class="o">=</span> <span class="s2">" "</span><span class="o">.</span><span class="n">join</span><span class="p">([</span><span class="n">fmt</span> <span class="o">%</span> <span class="n">x</span> <span class="k">for</span> <span class="n">x</span> <span class="ow">in</span> <span class="n">data</span><span class="p">[</span><span class="mi">3</span><span class="o">*</span><span class="p">(</span><span class="n">num</span><span class="o">//</span><span class="mi">3</span><span class="p">):]])</span> <span class="c1"># last line of data</span> + <span class="n">footer</span> <span class="o">+=</span> <span class="s2">"</span><span class="se">\n</span><span class="s2">"</span> + + <span class="n">footer</span> <span class="o">+=</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="n">np</span><span class="o">.</span><span class="n">savetxt</span><span class="p">(</span> <span class="n">outfile</span><span class="p">,</span> <span class="n">np</span><span class="o">.</span><span class="n">reshape</span><span class="p">(</span><span class="n">data</span><span class="p">[:</span><span class="mi">3</span><span class="o">*</span><span class="p">(</span><span class="n">num</span><span class="o">//</span><span class="mi">3</span><span class="p">)],</span> <span class="p">(</span><span class="n">num</span><span class="o">//</span><span class="mi">3</span><span class="p">,</span><span class="mi">3</span><span class="p">),</span> <span class="n">order</span><span class="o">=</span><span class="s1">'C'</span><span class="p">),</span> + <span class="n">fmt</span><span class="o">=</span><span class="n">fmt</span><span class="p">,</span> + <span class="n">header</span><span class="o">=</span><span class="n">header</span><span class="p">,</span> <span class="n">comments</span><span class="o">=</span><span class="s1">''</span><span class="p">,</span> <span class="n">footer</span><span class="o">=</span><span class="n">footer</span> <span class="p">)</span></div> + + <div class="viewcode-block" id="add_smaller_grid"> <a class="viewcode-back" href="../../api/utilities/grid.html#arbdmodel.grid.add_smaller_grid">[docs]</a> @@ -310,7 +393,6 @@ document.write(` <span class="n">grid</span><span class="o">.</span><span class="n">grid</span><span class="p">[</span><span class="n">slices</span><span class="p">]</span> <span class="o">=</span> <span class="n">grid</span><span class="o">.</span><span class="n">grid</span><span class="p">[</span><span class="n">slices</span><span class="p">]</span> <span class="o">+</span> <span class="n">smaller_grid</span><span class="o">.</span><span class="n">grid</span></div> - <div class="viewcode-block" id="average_grids"> <a class="viewcode-back" href="../../api/utilities/grid.html#arbdmodel.grid.average_grids">[docs]</a> <span class="k">def</span><span class="w"> </span><span class="nf">average_grids</span><span class="p">(</span><span class="n">grids</span><span class="p">,</span> <span class="n">mask</span><span class="o">=</span><span class="s1">'nan'</span><span class="p">):</span> @@ -353,6 +435,79 @@ document.write(` <span class="k">return</span> <span class="n">average</span></div> +<div class="viewcode-block" id="loadGrid"> +<a class="viewcode-back" href="../../api/utilities/grid.html#arbdmodel.grid.loadGrid">[docs]</a> +<span class="k">def</span><span class="w"> </span><span class="nf">loadGrid</span><span class="p">(</span><span class="n">file</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">"""Load grid data from DX file"""</span> + <span class="c1"># Read DX file header to get dimensions and metadata</span> + <span class="k">with</span> <span class="nb">open</span><span class="p">(</span><span class="n">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">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="c1"># Parse header</span> + <span class="k">for</span> <span class="n">line</span> <span class="ow">in</span> <span class="n">lines</span><span class="p">:</span> + <span class="k">if</span> <span class="s1">'counts'</span> <span class="ow">in</span> <span class="n">line</span><span class="p">:</span> + <span class="n">dims</span> <span class="o">=</span> <span class="p">[</span><span class="nb">int</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">line</span><span class="o">.</span><span class="n">split</span><span class="p">()[</span><span class="o">-</span><span class="mi">3</span><span class="p">:]]</span> + <span class="k">break</span> + + <span class="k">for</span> <span class="n">line</span> <span class="ow">in</span> <span class="n">lines</span><span class="p">:</span> + <span class="k">if</span> <span class="s1">'origin'</span> <span class="ow">in</span> <span class="n">line</span><span class="p">:</span> + <span class="n">origin</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">line</span><span class="o">.</span><span class="n">split</span><span class="p">()[</span><span class="o">-</span><span class="mi">3</span><span class="p">:]]</span> + <span class="k">break</span> + + <span class="k">for</span> <span class="n">line</span> <span class="ow">in</span> <span class="n">lines</span><span class="p">:</span> + <span class="k">if</span> <span class="s1">'delta'</span> <span class="ow">in</span> <span class="n">line</span><span class="p">:</span> + <span class="n">delta</span> <span class="o">=</span> <span class="nb">float</span><span class="p">(</span><span class="n">line</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="k">break</span> + + <span class="c1"># Read data values</span> + <span class="n">data</span> <span class="o">=</span> <span class="p">[]</span> + <span class="k">for</span> <span class="n">line</span> <span class="ow">in</span> <span class="n">lines</span><span class="p">:</span> + <span class="k">try</span><span class="p">:</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">line</span><span class="o">.</span><span class="n">split</span><span class="p">()]</span> + <span class="n">data</span><span class="o">.</span><span class="n">extend</span><span class="p">(</span><span class="n">values</span><span class="p">)</span> + <span class="k">except</span> <span class="ne">ValueError</span><span class="p">:</span> + <span class="k">continue</span> + + <span class="c1"># Reshape into 3D array</span> + <span class="n">grid</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">data</span><span class="p">)</span><span class="o">.</span><span class="n">reshape</span><span class="p">(</span><span class="n">dims</span><span class="p">)</span> + <span class="k">return</span> <span class="n">grid</span><span class="p">,</span> <span class="n">origin</span><span class="p">,</span> <span class="n">delta</span></div> + + +<div class="viewcode-block" id="Bound_grid"> +<a class="viewcode-back" href="../../api/utilities/grid.html#arbdmodel.grid.Bound_grid">[docs]</a> +<span class="k">def</span><span class="w"> </span><span class="nf">Bound_grid</span><span class="p">(</span><span class="n">inFile</span><span class="p">,</span> <span class="n">outFile</span><span class="p">,</span> <span class="n">lowerBound</span><span class="p">,</span> <span class="n">upperBound</span><span class="p">):</span> +<span class="w"> </span><span class="sd">"""Apply bounds to grid values"""</span> + <span class="c1"># Fix scientific notation</span> + <span class="n">cmd_in</span> <span class="o">=</span> <span class="s2">"sed -r 's/^([0-9]+)e/</span><span class="se">\1</span><span class="s2">.0e/g; s/ ([0-9]+)e/ </span><span class="se">\1</span><span class="s2">.0e/' "</span> <span class="o">+</span> <span class="n">inFile</span> <span class="o">+</span> <span class="s2">" > bound_grid_temp0.dx"</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="s2">"sed -r 's/^(-[0-9]+)e/</span><span class="se">\1</span><span class="s2">.0e/g; s/ (-[0-9]+)e/ </span><span class="se">\1</span><span class="s2">.0e/' bound_grid_temp0.dx > bound_grid_temp1.dx"</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="k">assert</span><span class="p">(</span><span class="n">lowerBound</span> <span class="o"><</span> <span class="n">upperBound</span><span class="p">)</span> + + <span class="c1"># Load 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="s1">'bound_grid_temp1.dx'</span><span class="p">)</span> + + <span class="c1"># Apply bounds</span> + <span class="n">grid</span><span class="p">[</span><span class="n">grid</span> <span class="o">></span> <span class="n">upperBound</span><span class="p">]</span> <span class="o">=</span> <span class="n">upperBound</span> + <span class="n">grid</span><span class="p">[</span><span class="n">grid</span> <span class="o"><</span> <span class="n">lowerBound</span><span class="p">]</span> <span class="o">=</span> <span class="n">lowerBound</span> + + <span class="c1"># Write output</span> + <span class="n">writeDx</span><span class="p">(</span><span class="n">outFile</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></div> + + + + +<div class="viewcode-block" id="Create_null"> +<a class="viewcode-back" href="../../api/utilities/grid.html#arbdmodel.grid.Create_null">[docs]</a> +<span class="k">def</span><span class="w"> </span><span class="nf">Create_null</span><span class="p">(</span><span class="n">grid_path</span><span class="o">=</span><span class="s1">'null.dx'</span><span class="p">):</span> +<span class="w"> </span><span class="sd">"""Create null potential grid"""</span> + <span class="n">zeros</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">2</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="n">origin</span> <span class="o">=</span> <span class="o">-</span><span class="mi">1500</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">1</span><span class="p">,</span><span class="mi">1</span><span class="p">))</span> + <span class="n">delta</span> <span class="o">=</span> <span class="p">[</span><span class="mi">3000</span><span class="p">,</span> <span class="mi">3000</span><span class="p">,</span> <span class="mi">3000</span><span class="p">]</span> + <span class="n">writeDx</span><span class="p">(</span><span class="n">grid_path</span><span class="p">,</span> <span class="n">zeros</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="TestAverageGrids"> <a class="viewcode-back" href="../../api/utilities/grid.html#arbdmodel.grid.TestAverageGrids">[docs]</a> <span class="k">class</span><span class="w"> </span><span class="nc">TestAverageGrids</span><span class="p">(</span><span class="n">unittest</span><span class="o">.</span><span class="n">TestCase</span><span class="p">):</span> @@ -668,6 +823,30 @@ document.write(` <div class="viewcode-block" id="slab_potential_z"> <a class="viewcode-back" href="../../api/utilities/grid.html#arbdmodel.grid.slab_potential_z">[docs]</a> <span class="k">def</span><span class="w"> </span><span class="nf">slab_potential_z</span><span class="p">(</span><span class="n">force_constant</span><span class="p">,</span> <span class="n">center</span><span class="p">,</span> <span class="n">dimensions</span><span class="p">,</span> <span class="n">resolution</span><span class="p">,</span> <span class="n">exponent</span><span class="o">=</span><span class="mi">2</span><span class="p">):</span> +<span class="w"> </span><span class="sd">"""</span> +<span class="sd"> Generate a potential energy field that depends only on the z-coordinate, creating a slab-like potential.</span> +<span class="sd"> Parameters</span> +<span class="sd"> ----------</span> +<span class="sd"> force_constant : float</span> +<span class="sd"> The strength of the potential (energy per unit distance^exponent).</span> +<span class="sd"> center : list or tuple</span> +<span class="sd"> The (x, y, z) coordinates of the center of the potential.</span> +<span class="sd"> dimensions : list or tuple</span> +<span class="sd"> The (x, y, z) dimensions of the grid in length units.</span> +<span class="sd"> resolution : float or list or tuple</span> +<span class="sd"> The grid spacing in length units. If a single value is provided, it's used for all dimensions.</span> +<span class="sd"> exponent : int, optional</span> +<span class="sd"> The exponent determining the shape of the potential. Default is 2 (harmonic potential).</span> +<span class="sd"> Returns</span> +<span class="sd"> -------</span> +<span class="sd"> numpy.ndarray</span> +<span class="sd"> A 3D array representing the potential energy field, where the energy depends only</span> +<span class="sd"> on the distance from the z-center raised to the specified exponent.</span> +<span class="sd"> Notes</span> +<span class="sd"> -----</span> +<span class="sd"> The potential U at each point is calculated as:</span> +<span class="sd"> U = (force_constant/exponent) * |z - center_z|^exponent</span> +<span class="sd"> """</span> <span class="k">try</span><span class="p">:</span> <span class="n">resolution</span><span class="p">[</span><span class="mi">0</span><span class="p">]</span> <span class="k">except</span><span class="p">:</span> @@ -729,49 +908,51 @@ document.write(` <span class="k">return</span> <span class="n">U</span></div> - -<div class="viewcode-block" id="writeDx"> -<a class="viewcode-back" href="../../api/utilities/grid.html#arbdmodel.grid.writeDx">[docs]</a> -<span class="k">def</span><span class="w"> </span><span class="nf">writeDx</span><span class="p">(</span><span class="n">outfile</span><span class="p">,</span> <span class="n">data</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="n">fmt</span><span class="o">=</span><span class="s2">"</span><span class="si">%.12f</span><span class="s2">"</span><span class="p">):</span> - <span class="n">shape</span> <span class="o">=</span> <span class="n">np</span><span class="o">.</span><span class="n">shape</span><span class="p">(</span><span class="n">data</span><span class="p">)</span> - <span class="n">num</span> <span class="o">=</span> <span class="n">np</span><span class="o">.</span><span class="n">prod</span><span class="p">(</span><span class="n">shape</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">shape</span><span class="p">)</span> <span class="o">==</span> <span class="mi">3</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">origin</span><span class="p">)</span> <span class="o">==</span> <span class="mi">3</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">delta</span><span class="p">)</span> <span class="o">==</span> <span class="mi">3</span> <span class="p">)</span> - <span class="n">headerInfo</span> <span class="o">=</span> <span class="nb">dict</span><span class="p">(</span> <span class="n">nx</span><span class="o">=</span><span class="n">shape</span><span class="p">[</span><span class="mi">0</span><span class="p">],</span> <span class="n">ny</span><span class="o">=</span><span class="n">shape</span><span class="p">[</span><span class="mi">1</span><span class="p">],</span> <span class="n">nz</span><span class="o">=</span><span class="n">shape</span><span class="p">[</span><span class="mi">2</span><span class="p">],</span> - <span class="n">ox</span><span class="o">=</span><span class="n">origin</span><span class="p">[</span><span class="mi">0</span><span class="p">],</span> <span class="n">oy</span><span class="o">=</span><span class="n">origin</span><span class="p">[</span><span class="mi">1</span><span class="p">],</span> <span class="n">oz</span><span class="o">=</span><span class="n">origin</span><span class="p">[</span><span class="mi">2</span><span class="p">],</span> - <span class="n">dx</span><span class="o">=</span><span class="n">delta</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="n">delta</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="n">delta</span><span class="p">[</span><span class="mi">2</span><span class="p">],</span> - <span class="n">num</span><span class="o">=</span><span class="n">num</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">flatten</span><span class="p">(</span><span class="n">order</span><span class="o">=</span><span class="s1">'C'</span><span class="p">)</span> - <span class="n">header</span> <span class="o">=</span> <span class="s2">"""# OpenDX density file</span> -<span class="s2"># File format: http://opendx.sdsc.edu/docs/html/pages/usrgu068.htm#HDREDF</span> -<span class="s2">object 1 class gridpositions counts </span><span class="si">{nx}</span><span class="s2"> </span><span class="si">{ny}</span><span class="s2"> </span><span class="si">{nz}</span> -<span class="s2">origin </span><span class="si">{ox}</span><span class="s2"> </span><span class="si">{oy}</span><span class="s2"> </span><span class="si">{oz}</span> -<span class="s2">delta </span><span class="si">{dx}</span><span class="s2"> 0.000000 0.000000</span> -<span class="s2">delta 0.000000 </span><span class="si">{dy}</span><span class="s2"> 0.000000</span> -<span class="s2">delta 0.000000 0.000000 </span><span class="si">{dz}</span> -<span class="s2">object 2 class gridconnections counts </span><span class="si">{nx}</span><span class="s2"> </span><span class="si">{ny}</span><span class="s2"> </span><span class="si">{nz}</span> -<span class="s2">object 3 class array type double rank 0 items </span><span class="si">{num}</span><span class="s2"> data follows"""</span><span class="o">.</span><span class="n">format</span><span class="p">(</span><span class="o">**</span><span class="n">headerInfo</span><span class="p">)</span> - <span class="nb">len</span><span class="p">(</span><span class="n">data</span><span class="p">)</span> +<div class="viewcode-block" id="write_confine_dx"> +<a class="viewcode-back" href="../../api/utilities/grid.html#arbdmodel.grid.write_confine_dx">[docs]</a> +<span class="k">def</span><span class="w"> </span><span class="nf">write_confine_dx</span><span class="p">(</span><span class="n">radius</span><span class="o">=</span><span class="mi">100</span> <span class="p">):</span> <span class="c1">#Might merge with spherical confinement? </span> - <span class="k">if</span> <span class="n">num</span> <span class="o">==</span> <span class="mi">3</span><span class="o">*</span><span class="p">(</span><span class="n">num</span><span class="o">//</span><span class="mi">3</span><span class="p">):</span> - <span class="n">footer</span> <span class="o">=</span> <span class="s2">""</span> - <span class="k">else</span><span class="p">:</span> - <span class="n">footer</span> <span class="o">=</span> <span class="s2">" "</span><span class="o">.</span><span class="n">join</span><span class="p">([</span><span class="n">fmt</span> <span class="o">%</span> <span class="n">x</span> <span class="k">for</span> <span class="n">x</span> <span class="ow">in</span> <span class="n">data</span><span class="p">[</span><span class="mi">3</span><span class="o">*</span><span class="p">(</span><span class="n">num</span><span class="o">//</span><span class="mi">3</span><span class="p">):]])</span> <span class="c1"># last line of data</span> - <span class="n">footer</span> <span class="o">+=</span> <span class="s2">"</span><span class="se">\n</span><span class="s2">"</span> + <span class="n">outfile</span><span class="o">=</span><span class="sa">f</span><span class="s1">'confine-</span><span class="si">{</span><span class="n">radius</span><span class="si">}</span><span class="s1">.dx'</span> + <span class="k">if</span> <span class="n">Path</span><span class="p">(</span><span class="n">outfile</span><span class="p">)</span><span class="o">.</span><span class="n">exists</span><span class="p">():</span> <span class="k">return</span> - <span class="n">footer</span> <span class="o">+=</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="n">np</span><span class="o">.</span><span class="n">savetxt</span><span class="p">(</span> <span class="n">outfile</span><span class="p">,</span> <span class="n">np</span><span class="o">.</span><span class="n">reshape</span><span class="p">(</span><span class="n">data</span><span class="p">[:</span><span class="mi">3</span><span class="o">*</span><span class="p">(</span><span class="n">num</span><span class="o">//</span><span class="mi">3</span><span class="p">)],</span> <span class="p">(</span><span class="n">num</span><span class="o">//</span><span class="mi">3</span><span class="p">,</span><span class="mi">3</span><span class="p">),</span> <span class="n">order</span><span class="o">=</span><span class="s1">'C'</span><span class="p">),</span> - <span class="n">fmt</span><span class="o">=</span><span class="n">fmt</span><span class="p">,</span> - <span class="n">header</span><span class="o">=</span><span class="n">header</span><span class="p">,</span> <span class="n">comments</span><span class="o">=</span><span class="s1">''</span><span class="p">,</span> <span class="n">footer</span><span class="o">=</span><span class="n">footer</span> <span class="p">)</span></div> + <span class="n">k</span> <span class="o">=</span> <span class="mi">1</span> <span class="c1"># Spring constant [kcal/mol/AA^2]</span> + <span class="c1"># radius=800</span> + + <span class="n">x0</span> <span class="o">=</span> <span class="n">y0</span> <span class="o">=</span> <span class="o">-</span><span class="n">radius</span> <span class="o">-</span> <span class="mi">50</span> + <span class="n">x1</span> <span class="o">=</span> <span class="n">y1</span> <span class="o">=</span> <span class="o">-</span><span class="n">x0</span> + <span class="n">z0</span><span class="p">,</span><span class="n">z1</span> <span class="o">=</span> <span class="n">x0</span><span class="p">,</span><span class="n">x1</span> + + <span class="n">dx</span> <span class="o">=</span> <span class="n">dy</span> <span class="o">=</span> <span class="n">dz</span> <span class="o">=</span> <span class="mi">2</span> + + <span class="k">assert</span><span class="p">(</span> <span class="n">x1</span> <span class="o">></span> <span class="n">x0</span> <span class="p">)</span> + <span class="k">assert</span><span class="p">(</span> <span class="n">y1</span> <span class="o">></span> <span class="n">y0</span> <span class="p">)</span> + <span class="k">assert</span><span class="p">(</span> <span class="n">z1</span> <span class="o">></span> <span class="n">z0</span> <span class="p">)</span> + +<span class="w"> </span><span class="sd">""" Create grid axes """</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">np</span><span class="o">.</span><span class="n">arange</span><span class="p">(</span> <span class="n">a</span><span class="o">-</span><span class="n">res</span><span class="o">/</span><span class="mi">2</span><span class="p">,</span> <span class="n">b</span><span class="o">+</span><span class="n">res</span><span class="o">/</span><span class="mi">2</span><span class="p">,</span> <span class="n">res</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="p">,</span><span class="n">res</span> <span class="ow">in</span> <span class="nb">zip</span><span class="p">((</span><span class="n">x0</span><span class="p">,</span><span class="n">y0</span><span class="p">,</span><span class="n">z0</span><span class="p">),(</span><span class="n">x1</span><span class="p">,</span><span class="n">y1</span><span class="p">,</span><span class="n">z1</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"># x = np.arange( -100, 100, dx ) # alternatively, be explicit</span> + + <span class="c1"># assert( x[0] == -x[-1] )</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 meshgrid for making potential</span> + <span class="n">R</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">X</span><span class="o">**</span><span class="mi">2</span> <span class="o">+</span> <span class="n">Y</span><span class="o">**</span><span class="mi">2</span> <span class="o">+</span> <span class="n">Z</span><span class="o">**</span><span class="mi">2</span><span class="p">)</span> + + +<span class="w"> </span><span class="sd">""" Create the potential, adding 0.5 k deltaX**2 for each half plane """</span> + <span class="n">pot</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">X</span><span class="o">.</span><span class="n">shape</span> <span class="p">)</span> + + + <span class="n">ids</span> <span class="o">=</span> <span class="n">R</span> <span class="o">></span> <span class="n">radius</span> + <span class="n">pot</span><span class="p">[</span><span class="n">ids</span><span class="p">]</span> <span class="o">=</span> <span class="mf">0.5</span><span class="o">*</span><span class="n">k</span><span class="o">*</span><span class="p">(</span><span class="n">R</span><span class="p">[</span><span class="n">ids</span><span class="p">]</span><span class="o">-</span><span class="n">radius</span><span class="p">)</span><span class="o">**</span><span class="mi">2</span> + <span class="n">ids</span> <span class="o">=</span> <span class="n">R</span> <span class="o">></span> <span class="n">radius</span> <span class="o">+</span> <span class="mi">25</span> + <span class="n">pot</span><span class="p">[</span><span class="n">ids</span><span class="p">]</span> <span class="o">=</span> <span class="mf">0.5</span><span class="o">*</span><span class="n">k</span><span class="o">*</span><span class="mi">25</span><span class="o">**</span><span class="mi">2</span> <span class="o">+</span> <span class="mf">0.5</span><span class="o">*</span><span class="n">k</span><span class="o">*</span><span class="mi">25</span><span class="o">**</span><span class="mi">2</span><span class="o">*</span><span class="p">(</span><span class="n">R</span><span class="p">[</span><span class="n">ids</span><span class="p">]</span><span class="o">-</span><span class="n">radius</span><span class="o">-</span><span class="mi">25</span><span class="p">)</span> <span class="c1"># switch to linear potential</span> +<span class="w"> </span><span class="sd">""" Write the dx file """</span> + <span class="n">writeDx</span><span class="p">(</span><span class="n">outfile</span><span class="p">,</span> <span class="n">pot</span><span class="p">,</span> + <span class="n">delta</span><span class="o">=</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="n">origin</span><span class="o">=</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="n">y</span><span class="p">[</span><span class="mi">0</span><span class="p">],</span><span class="n">z</span><span class="p">[</span><span class="mi">0</span><span class="p">]))</span></div> <span class="c1">## Utility functions</span> diff --git a/_build/html/_modules/arbdmodel/hps_polymer_model.html b/_build/html/_modules/arbdmodel/hps_polymer_model.html index 71106f64e6290b34f8972fba5a1b0903428081d2..d20df1ec998f8a83785c2a318d06238955e3440c 100644 --- a/_build/html/_modules/arbdmodel/hps_polymer_model.html +++ b/_build/html/_modules/arbdmodel/hps_polymer_model.html @@ -304,11 +304,10 @@ document.write(` <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">logger</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">.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">ParticleType</span><span class="p">,</span> <span class="n">PointParticle</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">PolymerBeads</span><span class="p">,</span> <span class="n">PolymerModel</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> diff --git a/_build/html/_modules/arbdmodel/ibi.html b/_build/html/_modules/arbdmodel/ibi.html index 0a3dea8e91eb9e61738983fff3cd210cad5557ff..28cd332671391c0f8851e477ed36415916daaf69 100644 --- a/_build/html/_modules/arbdmodel/ibi.html +++ b/_build/html/_modules/arbdmodel/ibi.html @@ -304,7 +304,8 @@ document.write(` <span class="kn">from</span><span class="w"> </span><span class="nn">scipy.signal</span><span class="w"> </span><span class="kn">import</span> <span class="n">savgol_filter</span> <span class="k">as</span> <span class="n">savgol</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">.</span><span class="w"> </span><span class="kn">import</span> <span class="n">ArbdModel</span><span class="p">,</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">ArbdModel</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">logger</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="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> @@ -591,6 +592,74 @@ document.write(` <div class="viewcode-block" id="AbstractIBIpotential"> <a class="viewcode-back" href="../../api/interaction_potentials/ibi.html#arbdmodel.ibi.AbstractIBIpotential">[docs]</a> <span class="k">class</span><span class="w"> </span><span class="nc">AbstractIBIpotential</span><span class="p">(</span><span class="n">AbstractPotential</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">"""</span> +<span class="sd"> A class that implements the Iterative Boltzmann Inversion method for generating potentials.</span> + +<span class="sd"> This abstract class provides the foundation for creating IBI potentials that are derived</span> +<span class="sd"> from target distributions. IBI is a method to derive effective pair potentials from radial</span> +<span class="sd"> distribution functions in molecular systems.</span> + +<span class="sd"> Parameters</span> +<span class="sd"> ----------</span> +<span class="sd"> name : str</span> +<span class="sd"> Name of the potential, used for file naming.</span> +<span class="sd"> degrees_of_freedom : list</span> +<span class="sd"> List of degrees of freedom to consider in the potential.</span> +<span class="sd"> range_ : tuple, optional</span> +<span class="sd"> Range of distances to consider (min, max), default is (0, 30).</span> +<span class="sd"> resolution : float, optional</span> +<span class="sd"> Resolution of the binning for the distribution, default is 0.1.</span> +<span class="sd"> max_force : float, optional</span> +<span class="sd"> Maximum force allowed in the potential.</span> +<span class="sd"> max_potential : float, optional</span> +<span class="sd"> Maximum potential value allowed.</span> +<span class="sd"> out_of_bounds_force : str or float, optional</span> +<span class="sd"> Force to apply outside the well-defined density region, default is 'max_force'.</span> +<span class="sd"> zero : str, optional</span> +<span class="sd"> Method to set the zero point of the potential, default is 'last'.</span> +<span class="sd"> smooth : int or None, optional</span> +<span class="sd"> Window size for Savitzky-Golay filter, if None will be calculated automatically.</span> +<span class="sd"> learning_rate : float or callable, optional</span> +<span class="sd"> Learning rate for potential updates, default is 0.9.</span> +<span class="sd"> iteration : int, optional</span> +<span class="sd"> Current iteration number, default is 1.</span> +<span class="sd"> filename_prefix : str, optional</span> +<span class="sd"> Path prefix for saving potentials, default is 'IBIPotentials/'.</span> + +<span class="sd"> Attributes</span> +<span class="sd"> ----------</span> +<span class="sd"> bins : numpy.ndarray</span> +<span class="sd"> Bin edges for the distribution.</span> +<span class="sd"> potential : numpy.ndarray</span> +<span class="sd"> Current potential values.</span> + +<span class="sd"> Methods</span> +<span class="sd"> -------</span> +<span class="sd"> potential(r)</span> +<span class="sd"> Abstract method to calculate potential at distance r.</span> +<span class="sd"> filename(types=None, iteration=None, smoothed=True)</span> +<span class="sd"> Generate filename for the potential.</span> +<span class="sd"> write_file()</span> +<span class="sd"> Write the potential to a file.</span> +<span class="sd"> get_target_distribution(universe=None, trajectory=None, recalculate=False)</span> +<span class="sd"> Get or calculate the target distribution.</span> +<span class="sd"> get_cg_distribution(universe, trajectory=None, box=None, recalculate=False)</span> +<span class="sd"> Get or calculate the coarse-grained distribution.</span> +<span class="sd"> read_cg_potential(iteration=None)</span> +<span class="sd"> Read a potential from a file.</span> +<span class="sd"> write_cg_potential(universe=None, scaling_factor=None, temperature=295, tol=None, clean_edges=True, box=None)</span> +<span class="sd"> Calculate and save the potential based on distributions.</span> + +<span class="sd"> Notes</span> +<span class="sd"> -----</span> +<span class="sd"> IBI is an iterative method that refines potentials to match target distributions.</span> +<span class="sd"> The process involves:</span> +<span class="sd"> 1. Starting with an initial guess (usually Boltzmann inversion of the target)</span> +<span class="sd"> 2. Running simulations with the current potential</span> +<span class="sd"> 3. Comparing resulting distributions with the target</span> +<span class="sd"> 4. Updating the potential based on the difference</span> +<span class="sd"> 5. Repeating until convergence</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">name</span><span class="p">,</span> <span class="n">degrees_of_freedom</span><span class="o">=</span><span class="p">[],</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="mi">30</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">max_force</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">out_of_bounds_force</span><span class="o">=</span><span class="s1">'max_force'</span><span class="p">,</span> <span class="n">zero</span><span class="o">=</span><span class="s1">'last'</span><span class="p">,</span> <span class="n">smooth</span><span class="o">=</span><span class="kc">None</span><span class="p">,</span> <span class="n">learning_rate</span><span class="o">=</span><span class="mf">0.9</span><span class="p">,</span> <span class="n">iteration</span><span class="o">=</span><span class="mi">1</span><span class="p">,</span> <span class="n">filename_prefix</span><span class="o">=</span><span class="s1">'IBIPotentials/'</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">degrees_of_freedom</span> <span class="o">=</span> <span class="n">degrees_of_freedom</span> diff --git a/_build/html/_modules/arbdmodel/interactions.html b/_build/html/_modules/arbdmodel/interactions.html index 69aec89cfc441c0b1cc75c1497408b79a1311975..7f0d8df5d5cbc40ac546d6bf58b2f3ebafb19caf 100644 --- a/_build/html/_modules/arbdmodel/interactions.html +++ b/_build/html/_modules/arbdmodel/interactions.html @@ -305,7 +305,7 @@ document.write(` <span class="kn">import</span><span class="w"> </span><span class="nn">scipy</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">shutil</span><span class="w"> </span><span class="kn">import</span> <span class="n">copyfile</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="sd">""" Module providing classes used to describe potentials in ARBD """</span> @@ -313,6 +313,55 @@ document.write(` <div class="viewcode-block" id="AbstractPotential"> <a class="viewcode-back" href="../../api/interaction_potentials/interactions.html#arbdmodel.interactions.AbstractPotential">[docs]</a> <span class="k">class</span><span class="w"> </span><span class="nc">AbstractPotential</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">"""</span> +<span class="sd"> Abstract base class for implementing interaction potentials.</span> +<span class="sd"> This class defines the basic structure for creating and managing interaction potential</span> +<span class="sd"> functions that can be written to files and used in simulations.</span> +<span class="sd"> Parameters</span> +<span class="sd"> ----------</span> +<span class="sd"> range_ : tuple of (float, float or None)</span> +<span class="sd"> The range of distances for the potential (min, max).</span> +<span class="sd"> If max is None, potential extends to infinity.</span> +<span class="sd"> resolution : float, optional</span> +<span class="sd"> The spacing between points in the discretized potential. Default is 0.1.</span> +<span class="sd"> max_force : float or None, optional</span> +<span class="sd"> Maximum allowed force magnitude. If provided, forces exceeding this value will be capped.</span> +<span class="sd"> max_potential : float or None, optional</span> +<span class="sd"> Maximum allowed potential energy. If provided, the potential will be modified</span> +<span class="sd"> to ensure it doesn't exceed this value.</span> +<span class="sd"> zero : str, optional</span> +<span class="sd"> Method to set the zero of the potential. Options are:</span> +<span class="sd"> - 'min': Zero is at the minimum value</span> +<span class="sd"> - 'first': Zero is at the first point</span> +<span class="sd"> - 'last': Zero is at the last point</span> +<span class="sd"> Attributes</span> +<span class="sd"> ----------</span> +<span class="sd"> range_ : tuple of (float, float or None)</span> +<span class="sd"> The range of distances for the potential.</span> +<span class="sd"> resolution : float</span> +<span class="sd"> The spacing between points in the discretized potential.</span> +<span class="sd"> max_force : float or None</span> +<span class="sd"> Maximum allowed force magnitude.</span> +<span class="sd"> max_potential : float or None</span> +<span class="sd"> Maximum allowed potential energy.</span> +<span class="sd"> zero : str</span> +<span class="sd"> Method to set the zero of the potential.</span> +<span class="sd"> periodic : bool</span> +<span class="sd"> Whether the potential is periodic (False by default).</span> +<span class="sd"> Methods</span> +<span class="sd"> -------</span> +<span class="sd"> potential(r, types=None)</span> +<span class="sd"> Abstract method that must be implemented by subclasses.</span> +<span class="sd"> Calculates the potential value at distance r.</span> +<span class="sd"> write_file(filename=None, types=None)</span> +<span class="sd"> Writes the potential to a file.</span> +<span class="sd"> filename(types=None)</span> +<span class="sd"> Abstract method that should be implemented by subclasses.</span> +<span class="sd"> Returns a filename for the potential.</span> +<span class="sd"> Notes</span> +<span class="sd"> -----</span> +<span class="sd"> Subclasses must implement at minimum the `potential` and `filename` methods.</span> +<span class="sd"> """</span> <span class="w"> </span><span class="sd">""" Abstract class for writing potentials """</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">range_</span><span class="o">=</span><span class="p">(</span><span class="mi">0</span><span class="p">,</span><span class="kc">None</span><span class="p">),</span> <span class="n">resolution</span><span class="o">=</span><span class="mf">0.1</span><span class="p">,</span> @@ -490,6 +539,215 @@ document.write(` </div> +<div class="viewcode-block" id="BoundaryPotential"> +<a class="viewcode-back" href="../../api/interaction_potentials/interactions.html#arbdmodel.interactions.BoundaryPotential">[docs]</a> +<span class="k">class</span><span class="w"> </span><span class="nc">BoundaryPotential</span><span class="p">(</span><span class="n">AbstractPotential</span><span class="p">):</span> +<span class="w"> </span><span class="sd">"""Boundary potential for confining 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="p">,</span> <span class="n">cell_origin</span><span class="o">=</span><span class="kc">None</span><span class="p">,</span> <span class="n">well_depth</span><span class="o">=</span><span class="mf">1.0</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="n">blur</span><span class="o">=</span><span class="mf">5.0</span><span class="p">,</span><span class="n">filename</span><span class="o">=</span><span class="s2">"boundary.dx"</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 boundary potential.</span> +<span class="sd"> </span> +<span class="sd"> Args:</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"> well_depth: Depth of potential well</span> +<span class="sd"> resolution: Grid resolution</span> +<span class="sd"> blur: Smoothing parameter</span> +<span class="sd"> **kwargs: Additional parameters for AbstractPotential</span> +<span class="sd"> """</span> + <span class="n">default_range</span> <span class="o">=</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">max</span><span class="p">([</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">v</span><span class="p">)</span> <span class="k">for</span> <span class="n">v</span> <span class="ow">in</span> <span class="n">cell_vectors</span><span class="p">]))</span> + <span class="k">if</span> <span class="s1">'range_'</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">'range_'</span><span class="p">]</span> <span class="o">=</span> <span class="n">default_range</span> + <span class="k">if</span> <span class="s1">'resolution'</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">'resolution'</span><span class="p">]</span> <span class="o">=</span> <span class="n">resolution</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="o">**</span><span class="n">kwargs</span><span class="p">)</span> + + <span class="bp">self</span><span class="o">.</span><span class="n">cell_vectors</span> <span class="o">=</span> <span class="n">cell_vectors</span> + <span class="bp">self</span><span class="o">.</span><span class="n">cell_origin</span> <span class="o">=</span> <span class="n">cell_origin</span> <span class="ow">or</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">well_depth</span> <span class="o">=</span> <span class="n">well_depth</span> + <span class="bp">self</span><span class="o">.</span><span class="n">blur</span> <span class="o">=</span> <span class="n">blur</span> + <span class="bp">self</span><span class="o">.</span><span class="n">grid_cache</span> <span class="o">=</span> <span class="kc">None</span> + <span class="bp">self</span><span class="o">.</span><span class="n">filename</span><span class="o">=</span><span class="n">filename</span> + + <span class="k">def</span><span class="w"> </span><span class="nf">_find_boundary_resolution</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span> +<span class="w"> </span><span class="sd">"""Find appropriate boundary resolution for the cell vectors."""</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">cell_vectors</span> + <span class="n">min_PBC_length</span> <span class="o">=</span> <span class="nb">min</span><span class="p">([</span><span class="nb">max</span><span class="p">(</span><span class="n">v1</span><span class="p">),</span> <span class="nb">max</span><span class="p">(</span><span class="n">v2</span><span class="p">),</span> <span class="nb">max</span><span class="p">(</span><span class="n">v3</span><span class="p">)])</span> + + <span class="k">if</span> <span class="n">min_PBC_length</span> <span class="o"><</span> <span class="bp">self</span><span class="o">.</span><span class="n">resolution</span><span class="p">:</span> + <span class="n">dd</span> <span class="o">=</span> <span class="nb">round</span><span class="p">(</span><span class="n">min_PBC_length</span> <span class="o">/</span> <span class="mi">2</span><span class="p">)</span> + <span class="k">else</span><span class="p">:</span> + <span class="n">dd</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">resolution</span> + + <span class="n">n1</span> <span class="o">=</span> <span class="nb">round</span><span class="p">(</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">v1</span><span class="p">)</span><span class="o">/</span><span class="n">dd</span><span class="p">)</span> + <span class="n">n2</span> <span class="o">=</span> <span class="nb">round</span><span class="p">(</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">v2</span><span class="p">)</span><span class="o">/</span><span class="n">dd</span><span class="p">)</span> + <span class="n">n3</span> <span class="o">=</span> <span class="nb">round</span><span class="p">(</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">v3</span><span class="p">)</span><span class="o">/</span><span class="n">dd</span><span class="p">)</span> + + <span class="k">return</span> <span class="n">dd</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="k">def</span><span class="w"> </span><span class="nf">_find_boundary_end_points</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span> +<span class="w"> </span><span class="sd">"""Find boundary endpoints from cell vectors and origin."""</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">cell_vectors</span> + + <span class="n">xyz_travel</span> <span class="o">=</span> <span class="p">[</span><span class="nb">sum</span><span class="p">([</span><span class="n">v1</span><span class="p">[</span><span class="n">ind</span><span class="p">],</span> <span class="n">v2</span><span class="p">[</span><span class="n">ind</span><span class="p">],</span> <span class="n">v3</span><span class="p">[</span><span class="n">ind</span><span class="p">]])</span> <span class="k">for</span> <span class="n">ind</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="n">xyz_min</span> <span class="o">=</span> <span class="p">[</span><span class="bp">self</span><span class="o">.</span><span class="n">cell_origin</span><span class="p">[</span><span class="n">ind</span><span class="p">]</span> <span class="o">-</span> <span class="n">xyz_travel</span><span class="p">[</span><span class="n">ind</span><span class="p">]</span> <span class="o">*</span> <span class="mf">0.5</span> <span class="k">for</span> <span class="n">ind</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="n">xyz_max</span> <span class="o">=</span> <span class="p">[</span><span class="bp">self</span><span class="o">.</span><span class="n">cell_origin</span><span class="p">[</span><span class="n">ind</span><span class="p">]</span> <span class="o">+</span> <span class="n">xyz_travel</span><span class="p">[</span><span class="n">ind</span><span class="p">]</span> <span class="o">*</span> <span class="mf">0.5</span> <span class="k">for</span> <span class="n">ind</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">return</span> <span class="p">(</span><span class="n">xyz_min</span><span class="p">[</span><span class="mi">0</span><span class="p">],</span> <span class="n">xyz_min</span><span class="p">[</span><span class="mi">1</span><span class="p">],</span> <span class="n">xyz_min</span><span class="p">[</span><span class="mi">2</span><span class="p">],</span> <span class="n">xyz_max</span><span class="p">[</span><span class="mi">0</span><span class="p">],</span> <span class="n">xyz_max</span><span class="p">[</span><span class="mi">1</span><span class="p">],</span> <span class="n">xyz_max</span><span class="p">[</span><span class="mi">2</span><span class="p">])</span> + + <span class="k">def</span><span class="w"> </span><span class="nf">_create_boundary_region</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">mx</span><span class="p">,</span> <span class="n">my</span><span class="p">,</span> <span class="n">mz</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="w"> </span><span class="sd">"""Create boundary region points for the cell."""</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">cell_vectors</span> + <span class="n">v1_scaled</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">v1</span><span class="p">)</span> <span class="o">/</span> <span class="n">n1</span> + <span class="n">v2_scaled</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">v2</span><span class="p">)</span> <span class="o">/</span> <span class="n">n2</span> + <span class="n">v3_scaled</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">v3</span><span class="p">)</span> <span class="o">/</span> <span class="n">n3</span> + + <span class="n">region_pts</span> <span class="o">=</span> <span class="p">[]</span> + <span class="n">start_pt</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">mx</span><span class="p">,</span> <span class="n">my</span><span class="p">,</span> <span class="n">mz</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">n1</span> <span class="o">+</span> <span class="mi">1</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="n">n2</span> <span class="o">+</span> <span class="mi">1</span><span class="p">):</span> + <span class="k">for</span> <span class="n">k</span> <span class="ow">in</span> <span class="nb">range</span><span class="p">(</span><span class="n">n3</span> <span class="o">+</span> <span class="mi">1</span><span class="p">):</span> + <span class="n">region_pts</span><span class="o">.</span><span class="n">append</span><span class="p">(</span><span class="n">start_pt</span> <span class="o">+</span> <span class="n">i</span> <span class="o">*</span> <span class="n">v1_scaled</span> <span class="o">+</span> <span class="n">j</span> <span class="o">*</span> <span class="n">v2_scaled</span> <span class="o">+</span> <span class="n">k</span> <span class="o">*</span> <span class="n">v3_scaled</span><span class="p">)</span> + + <span class="k">return</span> <span class="n">region_pts</span> + + <span class="k">def</span><span class="w"> </span><span class="nf">_convert_to_mesh_points</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">region_pts</span><span class="p">,</span> <span class="n">min_wallX</span><span class="p">,</span> <span class="n">min_wallY</span><span class="p">,</span> <span class="n">min_wallZ</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="n">grid_shape</span><span class="p">):</span> +<span class="w"> </span><span class="sd">"""Convert region points to grid indices."""</span> + <span class="n">mesh_pts</span> <span class="o">=</span> <span class="p">[]</span> + <span class="k">for</span> <span class="n">pt</span> <span class="ow">in</span> <span class="n">region_pts</span><span class="p">:</span> + <span class="n">indx</span> <span class="o">=</span> <span class="nb">round</span><span class="p">((</span><span class="n">pt</span><span class="p">[</span><span class="mi">0</span><span class="p">]</span> <span class="o">-</span> <span class="n">min_wallX</span><span class="p">)</span> <span class="o">/</span> <span class="n">dx</span><span class="p">)</span> + <span class="n">indy</span> <span class="o">=</span> <span class="nb">round</span><span class="p">((</span><span class="n">pt</span><span class="p">[</span><span class="mi">1</span><span class="p">]</span> <span class="o">-</span> <span class="n">min_wallY</span><span class="p">)</span> <span class="o">/</span> <span class="n">dy</span><span class="p">)</span> + <span class="n">indz</span> <span class="o">=</span> <span class="nb">round</span><span class="p">((</span><span class="n">pt</span><span class="p">[</span><span class="mi">2</span><span class="p">]</span> <span class="o">-</span> <span class="n">min_wallZ</span><span class="p">)</span> <span class="o">/</span> <span class="n">dz</span><span class="p">)</span> + <span class="k">if</span> <span class="p">(</span><span class="mi">0</span> <span class="o"><=</span> <span class="n">indx</span> <span class="o"><</span> <span class="n">grid_shape</span><span class="p">[</span><span class="mi">0</span><span class="p">]</span> <span class="ow">and</span> <span class="mi">0</span> <span class="o"><=</span> <span class="n">indy</span> <span class="o"><</span> <span class="n">grid_shape</span><span class="p">[</span><span class="mi">1</span><span class="p">]</span> <span class="ow">and</span> <span class="mi">0</span> <span class="o"><=</span> <span class="n">indz</span> <span class="o"><</span> <span class="n">grid_shape</span><span class="p">[</span><span class="mi">2</span><span class="p">]):</span> + <span class="n">mesh_pts</span><span class="o">.</span><span class="n">append</span><span class="p">((</span><span class="n">indx</span><span class="p">,</span> <span class="n">indy</span><span class="p">,</span> <span class="n">indz</span><span class="p">))</span> + <span class="k">return</span> <span class="n">mesh_pts</span> + + <span class="k">def</span><span class="w"> </span><span class="nf">_create_rectangular_mesh</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">wall_range_x</span><span class="p">,</span> <span class="n">wall_range_y</span><span class="p">,</span> <span class="n">wall_range_z</span><span class="p">,</span> <span class="n">dd</span><span class="p">):</span> +<span class="w"> </span><span class="sd">"""Create a rectangular mesh grid."""</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">wall_range_x</span><span class="p">[</span><span class="mi">0</span><span class="p">],</span> <span class="n">wall_range_x</span><span class="p">[</span><span class="mi">1</span><span class="p">],</span> <span class="nb">int</span><span class="p">((</span><span class="n">wall_range_x</span><span class="p">[</span><span class="mi">1</span><span class="p">]</span><span class="o">-</span><span class="n">wall_range_x</span><span class="p">[</span><span class="mi">0</span><span class="p">])</span><span class="o">/</span><span class="n">dd</span><span class="p">)</span> <span class="o">+</span> <span class="mi">1</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">wall_range_y</span><span class="p">[</span><span class="mi">0</span><span class="p">],</span> <span class="n">wall_range_y</span><span class="p">[</span><span class="mi">1</span><span class="p">],</span> <span class="nb">int</span><span class="p">((</span><span class="n">wall_range_y</span><span class="p">[</span><span class="mi">1</span><span class="p">]</span><span class="o">-</span><span class="n">wall_range_y</span><span class="p">[</span><span class="mi">0</span><span class="p">])</span><span class="o">/</span><span class="n">dd</span><span class="p">)</span> <span class="o">+</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">wall_range_z</span><span class="p">[</span><span class="mi">0</span><span class="p">],</span> <span class="n">wall_range_z</span><span class="p">[</span><span class="mi">1</span><span class="p">],</span> <span class="nb">int</span><span class="p">((</span><span class="n">wall_range_z</span><span class="p">[</span><span class="mi">1</span><span class="p">]</span><span class="o">-</span><span class="n">wall_range_z</span><span class="p">[</span><span class="mi">0</span><span class="p">])</span><span class="o">/</span><span class="n">dd</span><span class="p">)</span> <span class="o">+</span> <span class="mi">1</span><span class="p">)</span> + + <span class="n">dx</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">np</span><span class="o">.</span><span class="n">diff</span><span class="p">(</span><span class="n">x</span><span class="p">))</span> + <span class="n">dy</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">np</span><span class="o">.</span><span class="n">diff</span><span class="p">(</span><span class="n">y</span><span class="p">))</span> + <span class="n">dz</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">np</span><span class="o">.</span><span class="n">diff</span><span class="p">(</span><span class="n">z</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="k">return</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">dx</span><span class="p">,</span> <span class="n">dy</span><span class="p">,</span> <span class="n">dz</span> + + <span class="k">def</span><span class="w"> </span><span class="nf">_blur_3d_grid</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">grid</span><span class="p">,</span> <span class="n">blur_size</span><span class="p">,</span> <span class="n">dd</span><span class="p">):</span> +<span class="w"> </span><span class="sd">"""Apply 3D Gaussian blur to a grid."""</span> + <span class="c1"># Create Gaussian kernel</span> + <span class="n">sideLen</span> <span class="o">=</span> <span class="mi">2</span><span class="o">*</span><span class="nb">int</span><span class="p">(</span><span class="n">blur_size</span><span class="o">*</span><span class="mi">3</span><span class="p">)</span><span class="o">+</span><span class="mi">1</span> + <span class="n">gauss</span> <span class="o">=</span> <span class="n">scipy</span><span class="o">.</span><span class="n">signal</span><span class="o">.</span><span class="n">gaussian</span><span class="p">(</span><span class="n">sideLen</span><span class="p">,</span> <span class="n">blur_size</span><span class="o">/</span><span class="n">dd</span><span class="p">)</span> + <span class="n">i</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="n">sideLen</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="o">=</span> <span class="n">np</span><span class="o">.</span><span class="n">meshgrid</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="n">i</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="n">kernel</span> <span class="o">=</span> <span class="n">gauss</span><span class="p">[</span><span class="n">i</span><span class="p">]</span><span class="o">*</span><span class="n">gauss</span><span class="p">[</span><span class="n">j</span><span class="p">]</span><span class="o">*</span><span class="n">gauss</span><span class="p">[</span><span class="n">k</span><span class="p">]</span> + <span class="n">kernel</span> <span class="o">=</span> <span class="n">kernel</span><span class="o">/</span><span class="n">kernel</span><span class="o">.</span><span class="n">sum</span><span class="p">()</span> + + <span class="c1"># Apply convolution</span> + <span class="k">return</span> <span class="n">scipy</span><span class="o">.</span><span class="n">signal</span><span class="o">.</span><span class="n">fftconvolve</span><span class="p">(</span><span class="n">grid</span><span class="p">,</span> <span class="n">kernel</span><span class="p">,</span> <span class="n">mode</span><span class="o">=</span><span class="s1">'same'</span><span class="p">)</span> + +<div class="viewcode-block" id="BoundaryPotential.potential"> +<a class="viewcode-back" href="../../api/interaction_potentials/interactions.html#arbdmodel.interactions.BoundaryPotential.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="n">types</span><span class="o">=</span><span class="kc">None</span><span class="p">):</span> +<span class="w"> </span><span class="sd">"""Calculate potential at positions.</span> +<span class="sd"> </span> +<span class="sd"> This isn't used directly for grid potentials in ARBD, but implemented </span> +<span class="sd"> for consistency with the AbstractPotential interface.</span> +<span class="sd"> """</span> + <span class="c1"># Calculate distance from boundary</span> + <span class="n">max_dist</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">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">v</span><span class="p">)</span> <span class="k">for</span> <span class="n">v</span> <span class="ow">in</span> <span class="bp">self</span><span class="o">.</span><span class="n">cell_vectors</span><span class="p">])</span> <span class="o">/</span> <span class="mi">2</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">r</span><span class="p">)</span> + <span class="k">for</span> <span class="n">i</span><span class="p">,</span> <span class="n">ri</span> <span class="ow">in</span> <span class="nb">enumerate</span><span class="p">(</span><span class="n">r</span><span class="p">):</span> + <span class="c1"># Simplified: calculate distance from origin in normalized coordinates</span> + <span class="n">dist_vec</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">ri</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="bp">self</span><span class="o">.</span><span class="n">cell_vectors</span><span class="p">[</span><span class="mi">0</span><span class="p">]),</span> + <span class="n">ri</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="bp">self</span><span class="o">.</span><span class="n">cell_vectors</span><span class="p">[</span><span class="mi">1</span><span class="p">]),</span> + <span class="n">ri</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="bp">self</span><span class="o">.</span><span class="n">cell_vectors</span><span class="p">[</span><span class="mi">2</span><span class="p">])</span> + <span class="p">])</span> + + <span class="c1"># Distance from boundary (simplified)</span> + <span class="n">dist_from_boundary</span> <span class="o">=</span> <span class="n">max_dist</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">np</span><span class="o">.</span><span class="n">abs</span><span class="p">(</span><span class="n">dist_vec</span><span class="p">))</span> + + <span class="k">if</span> <span class="n">dist_from_boundary</span> <span class="o"><</span> <span class="mi">0</span><span class="p">:</span> + <span class="n">potential</span><span class="p">[</span><span class="n">i</span><span class="p">]</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">well_depth</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="n">dist_from_boundary</span><span class="o">/</span><span class="bp">self</span><span class="o">.</span><span class="n">blur</span><span class="p">))</span> + + <span class="k">return</span> <span class="n">potential</span></div> + + +<div class="viewcode-block" id="BoundaryPotential.write_file"> +<a class="viewcode-back" href="../../api/interaction_potentials/interactions.html#arbdmodel.interactions.BoundaryPotential.write_file">[docs]</a> + <span class="k">def</span><span class="w"> </span><span class="nf">write_file</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">filename</span><span class="o">=</span><span class="kc">None</span><span class="p">,</span> <span class="n">types</span><span class="o">=</span><span class="kc">None</span><span class="p">):</span> +<span class="w"> </span><span class="sd">"""Write boundary potential to grid file."""</span> + + <span class="c1"># Find optimal resolution</span> + <span class="n">dd</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="bp">self</span><span class="o">.</span><span class="n">_find_boundary_resolution</span><span class="p">()</span> + + <span class="c1"># Find boundary endpoints</span> + <span class="n">mx</span><span class="p">,</span> <span class="n">my</span><span class="p">,</span> <span class="n">mz</span><span class="p">,</span> <span class="n">Mx</span><span class="p">,</span> <span class="n">My</span><span class="p">,</span> <span class="n">Mz</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">_find_boundary_end_points</span><span class="p">()</span> + + <span class="c1"># Set up wall ranges with buffer</span> + <span class="n">scale</span> <span class="o">=</span> <span class="mf">1.5</span> <span class="c1"># Scale factor for wall range</span> + <span class="n">wall_range_x</span> <span class="o">=</span> <span class="p">(</span><span class="n">scale</span><span class="o">*</span><span class="p">(</span><span class="n">mx</span><span class="o">-</span><span class="mi">2</span><span class="o">*</span><span class="bp">self</span><span class="o">.</span><span class="n">blur</span><span class="p">),</span> <span class="n">scale</span><span class="o">*</span><span class="p">(</span><span class="n">Mx</span><span class="o">+</span><span class="mi">2</span><span class="o">*</span><span class="bp">self</span><span class="o">.</span><span class="n">blur</span><span class="p">))</span> + <span class="n">wall_range_y</span> <span class="o">=</span> <span class="p">(</span><span class="n">scale</span><span class="o">*</span><span class="p">(</span><span class="n">my</span><span class="o">-</span><span class="mi">2</span><span class="o">*</span><span class="bp">self</span><span class="o">.</span><span class="n">blur</span><span class="p">),</span> <span class="n">scale</span><span class="o">*</span><span class="p">(</span><span class="n">My</span><span class="o">+</span><span class="mi">2</span><span class="o">*</span><span class="bp">self</span><span class="o">.</span><span class="n">blur</span><span class="p">))</span> + <span class="n">wall_range_z</span> <span class="o">=</span> <span class="p">(</span><span class="n">scale</span><span class="o">*</span><span class="p">(</span><span class="n">mz</span><span class="o">-</span><span class="mi">2</span><span class="o">*</span><span class="bp">self</span><span class="o">.</span><span class="n">blur</span><span class="p">),</span> <span class="n">scale</span><span class="o">*</span><span class="p">(</span><span class="n">Mz</span><span class="o">+</span><span class="mi">2</span><span class="o">*</span><span class="bp">self</span><span class="o">.</span><span class="n">blur</span><span class="p">))</span> + + <span class="c1"># Create mesh</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">dx</span><span class="p">,</span> <span class="n">dy</span><span class="p">,</span> <span class="n">dz</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">_create_rectangular_mesh</span><span class="p">(</span> + <span class="n">wall_range_x</span><span class="p">,</span> <span class="n">wall_range_y</span><span class="p">,</span> <span class="n">wall_range_z</span><span class="p">,</span> <span class="n">dd</span><span class="p">)</span> + + <span class="c1"># Create boundary points</span> + <span class="n">region_pts</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">_create_boundary_region</span><span class="p">(</span> + <span class="n">mx</span><span class="p">,</span> <span class="n">my</span><span class="p">,</span> <span class="n">mz</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="c1"># Convert to mesh points</span> + <span class="n">mesh_pts</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">_convert_to_mesh_points</span><span class="p">(</span> + <span class="n">region_pts</span><span class="p">,</span> <span class="n">wall_range_x</span><span class="p">[</span><span class="mi">0</span><span class="p">],</span> <span class="n">wall_range_y</span><span class="p">[</span><span class="mi">0</span><span class="p">],</span> <span class="n">wall_range_z</span><span class="p">[</span><span class="mi">0</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="n">X</span><span class="o">.</span><span class="n">shape</span><span class="p">)</span> + + <span class="c1"># Create potential</span> + <span class="n">pot</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">np</span><span class="o">.</span><span class="n">shape</span><span class="p">(</span><span class="n">X</span><span class="p">))</span> + <span class="k">for</span> <span class="n">pt</span> <span class="ow">in</span> <span class="n">mesh_pts</span><span class="p">:</span> + <span class="n">pot</span><span class="p">[</span><span class="n">pt</span><span class="p">[</span><span class="mi">0</span><span class="p">],</span> <span class="n">pt</span><span class="p">[</span><span class="mi">1</span><span class="p">],</span> <span class="n">pt</span><span class="p">[</span><span class="mi">2</span><span class="p">]]</span> <span class="o">=</span> <span class="o">-</span><span class="bp">self</span><span class="o">.</span><span class="n">well_depth</span> <span class="c1"># Negative for attraction</span> + + <span class="c1"># Apply Gaussian blur</span> + <span class="n">pot_blur</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">_blur_3d_grid</span><span class="p">(</span><span class="n">pot</span><span class="p">,</span> <span class="bp">self</span><span class="o">.</span><span class="n">blur</span><span class="p">,</span> <span class="n">dd</span><span class="p">)</span> + + <span class="c1"># Write to DX file</span> + <span class="n">origin_out</span> <span class="o">=</span> <span class="p">[</span><span class="n">wall_range_x</span><span class="p">[</span><span class="mi">0</span><span class="p">],</span> <span class="n">wall_range_y</span><span class="p">[</span><span class="mi">0</span><span class="p">],</span> <span class="n">wall_range_z</span><span class="p">[</span><span class="mi">0</span><span class="p">]]</span> + <span class="n">delta</span> <span class="o">=</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="n">writeDx</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">filename</span><span class="p">,</span> <span class="n">pot_blur</span><span class="p">,</span> <span class="n">origin_out</span><span class="p">,</span> <span class="n">delta</span><span class="p">)</span> + + <span class="k">return</span> <span class="bp">self</span><span class="o">.</span><span class="n">filename</span></div> +</div> + + +<div class="viewcode-block" id="NullPotential"> +<a class="viewcode-back" href="../../api/interaction_potentials/interactions.html#arbdmodel.interactions.NullPotential">[docs]</a> +<span class="k">class</span><span class="w"> </span><span class="nc">NullPotential</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">range_</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="n">resolution</span><span class="o">=</span><span class="mf">0.5</span><span class="p">,</span> <span class="n">filename_prefix</span><span class="o">=</span><span class="s1">'./potentials/'</span><span class="p">,</span> <span class="o">*</span><span class="n">args</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">filename_prefix</span> <span class="o">=</span> <span class="n">filename_prefix</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">range_</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">resolution</span><span class="p">,</span> <span class="o">*</span><span class="n">args</span><span class="p">,</span><span class="o">**</span><span class="n">kwargs</span><span class="p">)</span> + +<div class="viewcode-block" id="NullPotential.potential"> +<a class="viewcode-back" href="../../api/interaction_potentials/interactions.html#arbdmodel.interactions.NullPotential.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="n">types</span><span class="p">):</span> + <span class="k">return</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></div> + + +<div class="viewcode-block" id="NullPotential.filename"> +<a class="viewcode-back" href="../../api/interaction_potentials/interactions.html#arbdmodel.interactions.NullPotential.filename">[docs]</a> + <span class="k">def</span><span class="w"> </span><span class="nf">filename</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">types</span><span class="o">=</span><span class="kc">None</span><span class="p">):</span> + <span class="k">return</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">filename_prefix</span><span class="si">}</span><span class="s2">nullpot.dat"</span></div> +</div> + + <span class="c1">## Bonded potentials </span> <div class="viewcode-block" id="HarmonicBondedPotential"> <a class="viewcode-back" href="../../api/interaction_potentials/interactions.html#arbdmodel.interactions.HarmonicBondedPotential">[docs]</a> @@ -707,25 +965,6 @@ document.write(` </div> -<div class="viewcode-block" id="NullPotential"> -<a class="viewcode-back" href="../../api/interaction_potentials/interactions.html#arbdmodel.interactions.NullPotential">[docs]</a> -<span class="k">class</span><span class="w"> </span><span class="nc">NullPotential</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">range_</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="n">resolution</span><span class="o">=</span><span class="mf">0.5</span><span class="p">,</span> <span class="n">filename_prefix</span><span class="o">=</span><span class="s1">'./potentials/'</span><span class="p">,</span> <span class="o">*</span><span class="n">args</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">filename_prefix</span> <span class="o">=</span> <span class="n">filename_prefix</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">range_</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">resolution</span><span class="p">,</span> <span class="o">*</span><span class="n">args</span><span class="p">,</span><span class="o">**</span><span class="n">kwargs</span><span class="p">)</span> - -<div class="viewcode-block" id="NullPotential.potential"> -<a class="viewcode-back" href="../../api/interaction_potentials/interactions.html#arbdmodel.interactions.NullPotential.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="n">types</span><span class="p">):</span> - <span class="k">return</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></div> - - -<div class="viewcode-block" id="NullPotential.filename"> -<a class="viewcode-back" href="../../api/interaction_potentials/interactions.html#arbdmodel.interactions.NullPotential.filename">[docs]</a> - <span class="k">def</span><span class="w"> </span><span class="nf">filename</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">types</span><span class="o">=</span><span class="kc">None</span><span class="p">):</span> - <span class="k">return</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">filename_prefix</span><span class="si">}</span><span class="s2">nullpot.dat"</span></div> -</div> - </pre></div> </article> diff --git a/_build/html/_modules/arbdmodel/kh_polymer_model.html b/_build/html/_modules/arbdmodel/kh_polymer_model.html index ae7e94d17dcf07eeac073f974df8e49584aa5fbb..36a120ecce365f1edc66d4b94f0830b88e79ce81 100644 --- a/_build/html/_modules/arbdmodel/kh_polymer_model.html +++ b/_build/html/_modules/arbdmodel/kh_polymer_model.html @@ -304,13 +304,12 @@ document.write(` <span class="c1">## Test with `python -m arbdmodel.kh_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">logger</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">.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">.</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="kn">from</span><span class="w"> </span><span class="nn">.polymer</span><span class="w"> </span><span class="kn">import</span> <span class="n">PolymerBeads</span><span class="p">,</span> <span class="n">PolymerModel</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="kn">from</span><span class="w"> </span><span class="nn">.kh_polymer_model_pair_epsilon</span><span class="w"> </span><span class="kn">import</span> <span class="n">epsilon_mj</span> <span class="sd">"""Define particle types"""</span> <span class="n">_types</span> <span class="o">=</span> <span class="nb">dict</span><span class="p">(</span> @@ -423,10 +422,61 @@ document.write(` <span class="c1">## Add types for IDPs</span> <span class="n">_types</span><span class="p">[</span><span class="n">k</span><span class="o">+</span><span class="s1">'IDP'</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="o">+</span><span class="s1">'IDP'</span><span class="p">,</span> <span class="n">mass</span><span class="o">=</span><span class="n">t</span><span class="o">.</span><span class="n">mass</span><span class="p">,</span> <span class="n">charge</span><span class="o">=</span><span class="n">t</span><span class="o">.</span><span class="n">charge</span><span class="p">,</span> <span class="n">sigma</span><span class="o">=</span><span class="n">t</span><span class="o">.</span><span class="n">sigma</span><span class="p">,</span> <span class="n">is_idp</span><span class="o">=</span><span class="kc">True</span><span class="p">,</span> <span class="n">resname</span><span class="o">=</span><span class="n">t</span><span class="o">.</span><span class="n">resname</span><span class="p">)</span> + +<span class="n">data</span><span class="o">=</span> <span class="n">np</span><span class="o">.</span><span class="n">loadtxt</span><span class="p">(</span><span class="n">get_resource_path</span><span class="p">(</span><span class="s2">"kh_pairwise_epsilon.csv"</span><span class="p">),</span> <span class="n">dtype</span><span class="o">=</span><span class="nb">str</span><span class="p">)</span> +<span class="n">epsilon_mj</span> <span class="o">=</span> <span class="nb">dict</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="p">,</span><span class="n">v</span> <span class="ow">in</span> <span class="n">data</span><span class="p">:</span> + <span class="n">v</span> <span class="o">=</span> <span class="nb">float</span><span class="p">(</span><span class="n">v</span><span class="p">)</span> + <span class="n">epsilon_mj</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="o">=</span> <span class="n">v</span> + <span class="n">epsilon_mj</span><span class="p">[(</span><span class="n">n2</span><span class="p">,</span><span class="n">n1</span><span class="p">)]</span> <span class="o">=</span> <span class="n">v</span> + <span class="n">epsilon_mj</span><span class="p">[(</span><span class="n">n1</span><span class="o">+</span><span class="s1">'IDP'</span><span class="p">,</span><span class="n">n2</span><span class="p">)]</span><span class="o">=</span><span class="n">v</span> + <span class="n">epsilon_mj</span><span class="p">[(</span><span class="n">n2</span><span class="p">,</span><span class="n">n1</span><span class="o">+</span><span class="s1">'IDP'</span><span class="p">)]</span><span class="o">=</span><span class="n">v</span> + <span class="n">epsilon_mj</span><span class="p">[(</span><span class="n">n2</span><span class="o">+</span><span class="s1">'IDP'</span><span class="p">,</span><span class="n">n1</span><span class="p">)]</span><span class="o">=</span><span class="n">v</span> + <span class="n">epsilon_mj</span><span class="p">[(</span><span class="n">n1</span><span class="p">,</span><span class="n">n2</span><span class="o">+</span><span class="s1">'IDP'</span><span class="p">)]</span><span class="o">=</span><span class="n">v</span> + <span class="n">epsilon_mj</span><span class="p">[(</span><span class="n">n2</span><span class="o">+</span><span class="s1">'IDP'</span><span class="p">,</span><span class="n">n1</span><span class="o">+</span><span class="s1">'IDP'</span><span class="p">)]</span><span class="o">=</span><span class="n">v</span> + <span class="n">epsilon_mj</span><span class="p">[(</span><span class="n">n1</span><span class="o">+</span><span class="s1">'IDP'</span><span class="p">,</span><span class="n">n2</span><span class="o">+</span><span class="s1">'IDP'</span><span class="p">)]</span><span class="o">=</span><span class="n">v</span> + + <div class="viewcode-block" id="KhNonbonded"> <a class="viewcode-back" href="../../api/polymer_modeling/kh_polymer_model.html#arbdmodel.kh_polymer_model.KhNonbonded">[docs]</a> <span class="k">class</span><span class="w"> </span><span class="nc">KhNonbonded</span><span class="p">(</span><span class="n">AbstractPotential</span><span class="p">):</span> +<span class="w"> </span><span class="sd">"""</span> +<span class="sd"> A class implementing the Kim-Hummer nonbonded potential energy model for protein interactions.</span> +<span class="sd"> This model combines electrostatic interactions with a modified Lennard-Jones potential</span> +<span class="sd"> that accounts for hydrophobic effects using the KH (Kim-Hummer) scaling approach.</span> +<span class="sd"> The potential is particularly useful for modeling interactions between intrinsically</span> +<span class="sd"> disordered proteins (IDPs) and folded proteins.</span> + +<span class="sd"> Parameters</span> +<span class="sd"> ----------</span> +<span class="sd"> debye_length : float, optional</span> +<span class="sd"> The Debye screening length in Angstroms, default is 10Ã…</span> +<span class="sd"> resolution : float, optional</span> +<span class="sd"> The spatial resolution for potential calculations, default is 0.1Ã…</span> +<span class="sd"> range_ : tuple, optional</span> +<span class="sd"> The range of distances (min, max) over which to compute the potential,</span> +<span class="sd"> default is (0, None) where None means no upper limit</span> + +<span class="sd"> Attributes</span> +<span class="sd"> ----------</span> +<span class="sd"> debye_length : float</span> +<span class="sd"> The Debye screening length in Angstroms</span> +<span class="sd"> max_force : float</span> +<span class="sd"> Maximum allowed force from this potential, set to 50</span> + +<span class="sd"> Methods</span> +<span class="sd"> -------</span> +<span class="sd"> potential(r, types)</span> +<span class="sd"> Calculates the nonbonded potential energy between two atom types at distance r.</span> +<span class="sd"> Combines electrostatic interactions with a modified Lennard-Jones potential.</span> +<span class="sd"> </span> +<span class="sd"> References</span> +<span class="sd"> ----------</span> +<span class="sd"> Kim, Y. C., & Hummer, G. (2008). Coarse-grained models for simulations of </span> +<span class="sd"> multiprotein complexes: application to ubiquitin binding. Journal of molecular </span> +<span class="sd"> biology, 375(5), 1416-1433.</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">debye_length</span><span class="o">=</span><span class="mi">10</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">range_</span><span class="o">=</span><span class="p">(</span><span class="mi">0</span><span class="p">,</span><span class="kc">None</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> <span class="n">range_</span><span class="o">=</span><span class="n">range_</span><span class="p">)</span> <span class="bp">self</span><span class="o">.</span><span class="n">debye_length</span> <span class="o">=</span> <span class="n">debye_length</span> diff --git a/_build/html/_modules/arbdmodel/logger.html b/_build/html/_modules/arbdmodel/logger.html index f75f469f82f3456df6dace30d28470996dc94502..11b7b3f2c6dbe1140571b52fb072064b76d8e1c4 100644 --- a/_build/html/_modules/arbdmodel/logger.html +++ b/_build/html/_modules/arbdmodel/logger.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?v=be8a1c11" /> + <link rel="stylesheet" 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<script src="../../_static/js/tooltipster.bundle.min.js?v=18bf091b"></script> - <script src="../../_static/js/micromodal.min.js?v=04d6302d"></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>let toggleHintShow = 'Click to show';</script> <script>let toggleHintHide = 'Click to hide';</script> <script>let toggleOpenOnPrint = 'true';</script> diff --git a/_build/html/_modules/arbdmodel/mesh_rigidbody.html b/_build/html/_modules/arbdmodel/mesh_rigidbody.html index 3b3cb20f8aacbb54aad5e8de8e2b4f00684a02d3..3646e22af78f285a3c1e89ebcd21a66add731327 100644 --- a/_build/html/_modules/arbdmodel/mesh_rigidbody.html +++ b/_build/html/_modules/arbdmodel/mesh_rigidbody.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?v=be8a1c11" /> + <link rel="stylesheet" type="text/css" href="../../_static/mystnb.4510f1fc1dee50b3e5859aac5469c37c29e427902b24a333a5f9fcb2f0b3ac41.css" /> <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?v=b4b7a797" /> + <link rel="stylesheet" type="text/css" href="../../_static/proof.css" /> <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?v=7bc2f056" /> - <link rel="stylesheet" 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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/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?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 src="../../_static/js/hoverxref.js"></script> + <script src="../../_static/js/tooltipster.bundle.min.js"></script> + <script src="../../_static/js/micromodal.min.js"></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/_modules/arbdmodel/model.html b/_build/html/_modules/arbdmodel/model.html index 6e89ccb5434c29f023dbe42d7522dc9e3947926e..cebae80423bcabc55acefc141307ba10548d707c 100644 --- a/_build/html/_modules/arbdmodel/model.html +++ b/_build/html/_modules/arbdmodel/model.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" /> 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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/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/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?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 src="../../_static/js/hoverxref.js"></script> + <script src="../../_static/js/tooltipster.bundle.min.js"></script> + <script src="../../_static/js/micromodal.min.js"></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/_modules/arbdmodel/mpipi_polymer.html b/_build/html/_modules/arbdmodel/mpipi_polymer.html index 514a01214847f18525715058835820b73b85989b..8ed099e8bb1a66403efcabe3860f2fda0fb4c319 100644 --- a/_build/html/_modules/arbdmodel/mpipi_polymer.html +++ b/_build/html/_modules/arbdmodel/mpipi_polymer.html @@ -306,7 +306,9 @@ document.write(` <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">pandas</span><span class="w"> </span><span class="k">as</span><span class="w"> </span><span class="nn">pd</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">logger</span><span class="p">,</span> <span class="n">ParticleType</span><span class="p">,</span> <span class="n">PointParticle</span><span class="p">,</span> <span class="n">get_resource_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="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="kn">from</span><span class="w"> </span><span class="nn">.polymer</span><span class="w"> </span><span class="kn">import</span> <span class="n">PolymerBeads</span><span class="p">,</span> <span class="n">PolymerModel</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> diff --git a/_build/html/_modules/arbdmodel/onck_polymer_model.html b/_build/html/_modules/arbdmodel/onck_polymer_model.html index 86941c699c625e4491a5b5af8655a2436d7f6fca..cddbbb3efa7ac55b2312d4a2eca7c02b6cca22dd 100644 --- a/_build/html/_modules/arbdmodel/onck_polymer_model.html +++ b/_build/html/_modules/arbdmodel/onck_polymer_model.html @@ -307,7 +307,8 @@ document.write(` <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">devlogger</span><span class="p">,</span> <span class="n">logger</span><span class="p">,</span> <span class="n">ParticleType</span><span class="p">,</span> <span class="n">PointParticle</span><span class="p">,</span> <span class="n">get_resource_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">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">.core_objects</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="kn">from</span><span class="w"> </span><span class="nn">.polymer</span><span class="w"> </span><span class="kn">import</span> <span class="n">PolymerBeads</span><span class="p">,</span> <span class="n">PolymerModel</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="kn">from</span><span class="w"> </span><span class="nn">.version</span><span class="w"> </span><span class="kn">import</span> <span class="n">Citation</span> @@ -514,7 +515,44 @@ document.write(` <div class="viewcode-block" id="OnckNonbonded"> <a class="viewcode-back" href="../../api/polymer_modeling/onck_polymer_model.html#arbdmodel.onck_polymer_model.OnckNonbonded">[docs]</a> <span class="k">class</span><span class="w"> </span><span class="nc">OnckNonbonded</span><span class="p">(</span><span class="n">AbstractPotential</span><span class="p">):</span> -<span class="w"> </span><span class="sd">""" Nonbonded interaction for 1BPA and 1BPA-1.1 """</span> +<span class="w"> </span><span class="sd">"""</span> +<span class="sd"> Nonbonded interaction potential for 1BPA and 1BPA-1.1.</span> + +<span class="sd"> This class implements nonbonded interactions including electrostatics with</span> +<span class="sd"> distance-dependent dielectric and Lennard-Jones type potentials.</span> + +<span class="sd"> Parameters</span> +<span class="sd"> ----------</span> +<span class="sd"> debye_length : float, optional</span> +<span class="sd"> The Debye-Hückel screening length in angstroms. Default is 12.7 Ã….</span> +<span class="sd"> resolution : float, optional</span> +<span class="sd"> The spatial resolution for potential calculation. Default is 0.1 Ã….</span> +<span class="sd"> range_ : tuple, optional</span> +<span class="sd"> The range of distances for which to calculate the potential. Default is (0, None).</span> + +<span class="sd"> Attributes</span> +<span class="sd"> ----------</span> +<span class="sd"> debye_length : float</span> +<span class="sd"> The Debye-Hückel screening length in angstroms.</span> +<span class="sd"> max_force : float</span> +<span class="sd"> Maximum allowed force in the system, used as a cap for stability.</span> + +<span class="sd"> Methods</span> +<span class="sd"> -------</span> +<span class="sd"> potential(r, types)</span> +<span class="sd"> Calculate the nonbonded potential energy between two residue types at distance r.</span> + +<span class="sd"> Notes</span> +<span class="sd"> -----</span> +<span class="sd"> The potential includes:</span> +<span class="sd"> 1. Electrostatic interactions with distance-dependent dielectric constant</span> +<span class="sd"> 2. Modified Lennard-Jones interactions that depend on residue types:</span> +<span class="sd"> - Special 8-6 LJ potential for cationic-aromatic interactions in 1.0cp/1.1 versions</span> +<span class="sd"> - General LJ-type potential for other interactions</span> + +<span class="sd"> The effective dielectric D decreases with distance according to a specific formula.</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">debye_length</span><span class="o">=</span><span class="mf">12.7</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">range_</span><span class="o">=</span><span class="p">(</span><span class="mi">0</span><span class="p">,</span><span class="kc">None</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> <span class="n">range_</span><span class="o">=</span><span class="n">range_</span><span class="p">)</span> <span class="bp">self</span><span class="o">.</span><span class="n">debye_length</span> <span class="o">=</span> <span class="n">debye_length</span> @@ -574,6 +612,56 @@ document.write(` <div class="viewcode-block" id="OnckBeads"> <a class="viewcode-back" href="../../api/polymer_modeling/onck_polymer_model.html#arbdmodel.onck_polymer_model.OnckBeads">[docs]</a> <span class="k">class</span><span class="w"> </span><span class="nc">OnckBeads</span><span class="p">(</span><span class="n">PolymerBeads</span><span class="p">):</span> +<span class="w"> </span><span class="sd">"""</span> +<span class="sd"> A class that represents polymer beads in the Onck model.</span> + +<span class="sd"> The Onck model is a coarse-grained model for proteins where each amino acid is represented</span> +<span class="sd"> by a single bead. The model includes specific bonded interactions (bonds, angles, dihedrals)</span> +<span class="sd"> based on the amino acid types in the sequence.</span> + +<span class="sd"> Parameters</span> +<span class="sd"> ----------</span> +<span class="sd"> polymer : Polymer</span> +<span class="sd"> The parent polymer object to which these beads belong.</span> +<span class="sd"> sequence : list, optional</span> +<span class="sd"> The sequence of amino acid types for each bead, must match polymer length.</span> +<span class="sd"> spring_constant : float, default=38.422562</span> +<span class="sd"> Spring constant for peptide bonds in units of 8038 kJ/(N_A nm^2) or 0.5 kcal_mol/AA^2.</span> +<span class="sd"> rest_length : float, default=3.8</span> +<span class="sd"> Equilibrium length of peptide bonds.</span> +<span class="sd"> version : float, optional</span> +<span class="sd"> Version of the Onck model to use. Defaults to 1.1 if not specified.</span> +<span class="sd"> **kwargs</span> +<span class="sd"> Additional keyword arguments passed to the parent PolymerBeads constructor.</span> + +<span class="sd"> Attributes</span> +<span class="sd"> ----------</span> +<span class="sd"> version : float</span> +<span class="sd"> The version of the Onck model being used.</span> +<span class="sd"> types_dict : dict</span> +<span class="sd"> Mapping between amino acid codes and bead types.</span> +<span class="sd"> peptide_bond : HarmonicBond</span> +<span class="sd"> Bond potential used for peptide bonds between adjacent beads.</span> +<span class="sd"> polymer : Polymer</span> +<span class="sd"> Reference to the parent polymer object.</span> +<span class="sd"> sequence : list</span> +<span class="sd"> The amino acid sequence.</span> +<span class="sd"> spring_constant : float</span> +<span class="sd"> The spring constant used for peptide bonds.</span> + +<span class="sd"> Raises</span> +<span class="sd"> ------</span> +<span class="sd"> ValueError</span> +<span class="sd"> If the version is not supported or if the sequence length doesn't match the polymer length.</span> +<span class="sd"> NotImplementedError</span> +<span class="sd"> If sequence is None (random sequence generation not implemented).</span> + +<span class="sd"> Notes</span> +<span class="sd"> -----</span> +<span class="sd"> The Onck model distinguishes between proline (P), glycine (G), and all other amino acids (X)</span> +<span class="sd"> for certain bonded interactions. Special potentials are loaded from files for angle and </span> +<span class="sd"> dihedral interactions based on this classification.</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">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="n">spring_constant</span> <span class="o">=</span> <span class="mf">38.422562</span><span class="p">,</span> <span class="c1"># units "8038 kJ / (N_A nm**2)" "0.5 * kcal_mol/AA**2"</span> <span class="n">rest_length</span><span class="o">=</span><span class="mf">3.8</span><span class="p">,</span> <span class="n">version</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> diff --git a/_build/html/_modules/arbdmodel/parmed_bd.html b/_build/html/_modules/arbdmodel/parmed_bd.html index 078a3934901fc053dec12f37d4b4ed9af5b124db..e23804d479c4be09223187ddc6d70fcd7c05c57e 100644 --- a/_build/html/_modules/arbdmodel/parmed_bd.html +++ b/_build/html/_modules/arbdmodel/parmed_bd.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?v=be8a1c11" /> + <link rel="stylesheet" type="text/css" href="../../_static/mystnb.4510f1fc1dee50b3e5859aac5469c37c29e427902b24a333a5f9fcb2f0b3ac41.css" /> <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?v=b4b7a797" /> + <link rel="stylesheet" type="text/css" href="../../_static/proof.css" /> <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?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/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/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?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 src="../../_static/js/hoverxref.js"></script> + <script src="../../_static/js/tooltipster.bundle.min.js"></script> + <script src="../../_static/js/micromodal.min.js"></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/_modules/arbdmodel/polymer.html b/_build/html/_modules/arbdmodel/polymer.html index b3c5982152b4547765636500d102af521e9ae9ab..f355ff74947ad7abb74aac1a539e7e703ce75f0b 100644 --- a/_build/html/_modules/arbdmodel/polymer.html +++ b/_build/html/_modules/arbdmodel/polymer.html @@ -302,16 +302,17 @@ document.write(` <h1>Source code for arbdmodel.polymer</h1><div class="highlight"><pre> <span></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">from</span><span class="w"> </span><span class="nn">.</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">.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">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">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">copy</span><span class="w"> </span><span class="kn">import</span> <span class="n">deepcopy</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">scipy</span><span class="w"> </span><span class="kn">import</span> <span class="n">interpolate</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">Group</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">.coords</span><span class="w"> </span><span class="kn">import</span> <span class="n">rotationAboutAxis</span><span class="p">,</span> <span class="n">quaternion_from_matrix</span><span class="p">,</span> <span class="n">quaternion_to_matrix</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">Group</span><span class="p">,</span> <span class="n">PointParticle</span> <span class="sd">"""</span> <span class="sd">TODO:</span> diff --git a/_build/html/_modules/arbdmodel/sali_polymer_model.html b/_build/html/_modules/arbdmodel/sali_polymer_model.html index 8ea3233d04d919f61e7fb0d79ae56dadcb61c012..434f43fcb154745fba5cc15cfe019063f9260799 100644 --- a/_build/html/_modules/arbdmodel/sali_polymer_model.html +++ b/_build/html/_modules/arbdmodel/sali_polymer_model.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?v=be8a1c11" /> + <link rel="stylesheet" type="text/css" href="../../_static/mystnb.4510f1fc1dee50b3e5859aac5469c37c29e427902b24a333a5f9fcb2f0b3ac41.css" /> <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?v=b4b7a797" /> + <link rel="stylesheet" type="text/css" href="../../_static/proof.css" /> <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?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/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/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?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 src="../../_static/js/hoverxref.js"></script> + <script src="../../_static/js/tooltipster.bundle.min.js"></script> + <script src="../../_static/js/micromodal.min.js"></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/_modules/arbdmodel/shape_cg.html b/_build/html/_modules/arbdmodel/shape_cg.html index 03b7b126aaa15e2706aad6cba0ea98c1afd6098a..04a1c6fbe4f752b1a042a0ef948bfdb2bf67e893 100644 --- a/_build/html/_modules/arbdmodel/shape_cg.html +++ b/_build/html/_modules/arbdmodel/shape_cg.html @@ -300,18 +300,72 @@ document.write(` <article class="bd-article"> <h1>Source code for arbdmodel.shape_cg</h1><div class="highlight"><pre> -<span></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></span><span class="sd">"""</span> +<span class="sd">Shape-based coarse-grained modeling module for protein simulations.</span> + +<span class="sd">This module provides classes for creating shape-based coarse-grained models</span> +<span class="sd">of proteins for use in molecular dynamics simulations.</span> +<span class="sd">"""</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">scipy.spatial</span><span class="w"> </span><span class="kn">import</span> <span class="n">KDTree</span> + +<span class="kn">import</span><span class="w"> </span><span class="nn">parmed</span> +<span class="kn">import</span><span class="w"> </span><span class="nn">freesasa</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">.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">AbstractPotential</span><span class="p">,</span> <span class="n">HarmonicBond</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">.coords</span><span class="w"> </span><span class="kn">import</span> <span class="n">rotationAboutAxis</span><span class="p">,</span> <span class="n">read_arbd_coordinates</span> + +<div class="viewcode-block" id="read_files"> +<a class="viewcode-back" href="../../api/shape-based_models/shape_cg.html#arbdmodel.shape_cg.read_files">[docs]</a> +<span class="k">def</span><span class="w"> </span><span class="nf">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="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="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="c1"># import ipdb; ipdb.set_trace()</span> + <span class="c1"># params = parmed.charmm.CharmmParameterSet(parameter_files[-1])</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> -<span class="c1">## I'm not convinced this is that great</span> <div class="viewcode-block" id="find_shape_based_sites"> <a class="viewcode-back" href="../../api/shape-based_models/shape_cg.html#arbdmodel.shape_cg.find_shape_based_sites">[docs]</a> <span class="k">def</span><span class="w"> </span><span class="nf">find_shape_based_sites</span><span class="p">(</span><span class="n">fine_positions</span><span class="p">,</span> <span class="n">N_cg</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">learning_schedule</span><span class="o">=</span><span class="kc">None</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">seed</span> <span class="o">=</span> <span class="mi">1234</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">learning_schedule</span><span class="o">=</span><span class="kc">None</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">seed</span><span class="o">=</span><span class="mi">1234</span><span class="p">):</span> +<span class="w"> </span><span class="sd">"""Find optimal placement of coarse-grained sites based on structure shape.</span> +<span class="sd"> </span> +<span class="sd"> This function uses a competitive learning algorithm to determine optimal</span> +<span class="sd"> placement of coarse-grained sites within a molecular structure, considering</span> +<span class="sd"> both geometry and optional weights (like atom masses).</span> +<span class="sd"> </span> +<span class="sd"> Args:</span> +<span class="sd"> fine_positions: Array of atomic positions, shape (n_atoms, 3)</span> +<span class="sd"> N_cg: Number of coarse-grained sites to create</span> +<span class="sd"> num_steps: Number of learning steps (default: 400*N_cg)</span> +<span class="sd"> learning_schedule: Custom schedule for learning parameters (default: None)</span> +<span class="sd"> weights: Optional weights for each atom (default: uniform)</span> +<span class="sd"> seed: Random seed for reproducibility</span> +<span class="sd"> </span> +<span class="sd"> Returns:</span> +<span class="sd"> Array of positions for coarse-grained sites, shape (N_cg, 3)</span> +<span class="sd"> """</span> <span class="n">rng</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">default_rng</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">n_fg</span> <span class="o">=</span> <span class="nb">len</span><span class="p">(</span><span class="n">fine_positions</span><span class="p">)</span> @@ -322,75 +376,864 @@ document.write(` <span class="n">weights</span> <span class="o">=</span> <span class="n">weights</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">weights</span><span class="p">)</span> <span class="k">if</span> <span class="n">num_steps</span> <span class="ow">is</span> <span class="kc">None</span><span class="p">:</span> - <span class="n">num_steps</span> <span class="o">=</span> <span class="mi">400</span><span class="o">*</span><span class="n">N_cg</span> + <span class="n">num_steps</span> <span class="o">=</span> <span class="mi">400</span> <span class="o">*</span> <span class="n">N_cg</span> - <span class="c1"># p.collapsedPosition()</span> - <span class="c1"># r_fg = [p.position for p in fine]</span> <span class="n">r_fg</span> <span class="o">=</span> <span class="n">fine_positions</span> - <span class="c1">## Initialize CG sites</span> - <span class="n">r_cg</span> <span class="o">=</span> <span class="n">r_fg</span><span class="p">[</span><span class="n">rng</span><span class="o">.</span><span class="n">choice</span><span class="p">(</span> <span class="n">n_fg</span><span class="p">,</span> <span class="n">size</span><span class="o">=</span><span class="n">N_cg</span><span class="p">,</span> <span class="n">replace</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">weights</span> <span class="p">)]</span> + <span class="c1"># Initialize CG sites by selecting random atoms, weighted by provided weights</span> + <span class="n">r_cg</span> <span class="o">=</span> <span class="n">r_fg</span><span class="p">[</span><span class="n">rng</span><span class="o">.</span><span class="n">choice</span><span class="p">(</span><span class="n">n_fg</span><span class="p">,</span> <span class="n">size</span><span class="o">=</span><span class="n">N_cg</span><span class="p">,</span> <span class="n">replace</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">weights</span><span class="p">)]</span> <span class="k">if</span> <span class="ow">not</span> <span class="n">np</span><span class="o">.</span><span class="n">all</span><span class="p">(</span><span class="n">np</span><span class="o">.</span><span class="n">isfinite</span><span class="p">(</span><span class="n">r_cg</span><span class="p">)):</span> - <span class="k">raise</span> <span class="ne">Exception</span> + <span class="k">raise</span> <span class="ne">ValueError</span><span class="p">(</span><span class="s2">"Initial CG positions contain non-finite values"</span><span class="p">)</span> + <span class="c1"># Define learning schedule if not provided</span> <span class="k">if</span> <span class="n">learning_schedule</span> <span class="ow">is</span> <span class="kc">None</span><span class="p">:</span> - <span class="n">e0</span><span class="p">,</span><span class="n">e1</span> <span class="o">=</span> <span class="mf">0.3</span><span class="p">,</span><span class="mf">0.05</span> - <span class="n">l0</span><span class="p">,</span><span class="n">l1</span> <span class="o">=</span> <span class="mf">0.2</span><span class="o">*</span><span class="n">N_cg</span><span class="p">,</span><span class="mf">0.01</span> + <span class="n">e0</span><span class="p">,</span> <span class="n">e1</span> <span class="o">=</span> <span class="mf">0.3</span><span class="p">,</span> <span class="mf">0.05</span> <span class="c1"># Initial and final learning rates</span> + <span class="n">l0</span><span class="p">,</span> <span class="n">l1</span> <span class="o">=</span> <span class="mf">0.2</span> <span class="o">*</span> <span class="n">N_cg</span><span class="p">,</span> <span class="mf">0.01</span> <span class="c1"># Initial and final neighborhood parameters</span> - <span class="n">epsilon</span> <span class="o">=</span> <span class="k">lambda</span> <span class="n">s</span><span class="p">:</span> <span class="n">e0</span><span class="o">*</span><span class="p">(</span><span class="n">e1</span><span class="o">/</span><span class="n">e0</span><span class="p">)</span><span class="o">**</span><span class="p">(</span><span class="n">s</span><span class="o">/</span><span class="n">num_steps</span><span class="p">)</span> - <span class="n">lambda_</span> <span class="o">=</span> <span class="k">lambda</span> <span class="n">s</span><span class="p">:</span> <span class="n">l0</span><span class="o">*</span><span class="p">(</span><span class="n">l1</span><span class="o">/</span><span class="n">l0</span><span class="p">)</span><span class="o">**</span><span class="p">(</span><span class="n">s</span><span class="o">/</span><span class="n">num_steps</span><span class="p">)</span> + <span class="n">epsilon</span> <span class="o">=</span> <span class="k">lambda</span> <span class="n">s</span><span class="p">:</span> <span class="n">e0</span> <span class="o">*</span> <span class="p">(</span><span class="n">e1</span><span class="o">/</span><span class="n">e0</span><span class="p">)</span><span class="o">**</span><span class="p">(</span><span class="n">s</span><span class="o">/</span><span class="n">num_steps</span><span class="p">)</span> + <span class="n">lambda_</span> <span class="o">=</span> <span class="k">lambda</span> <span class="n">s</span><span class="p">:</span> <span class="n">l0</span> <span class="o">*</span> <span class="p">(</span><span class="n">l1</span><span class="o">/</span><span class="n">l0</span><span class="p">)</span><span class="o">**</span><span class="p">(</span><span class="n">s</span><span class="o">/</span><span class="n">num_steps</span><span class="p">)</span> - <span class="c1">## choose random fine particle for each step</span> - <span class="n">rs</span> <span class="o">=</span> <span class="n">r_fg</span><span class="p">[</span><span class="n">rng</span><span class="o">.</span><span class="n">choice</span><span class="p">(</span> <span class="n">n_fg</span><span class="p">,</span> <span class="n">size</span><span class="o">=</span><span class="n">num_steps</span><span class="p">,</span> <span class="n">p</span><span class="o">=</span><span class="n">weights</span> <span class="p">)]</span> + <span class="c1"># Choose random fine particles for each step, weighted by provided weights</span> + <span class="n">rs</span> <span class="o">=</span> <span class="n">r_fg</span><span class="p">[</span><span class="n">rng</span><span class="o">.</span><span class="n">choice</span><span class="p">(</span><span class="n">n_fg</span><span class="p">,</span> <span class="n">size</span><span class="o">=</span><span class="n">num_steps</span><span class="p">,</span> <span class="n">p</span><span class="o">=</span><span class="n">weights</span><span class="p">)]</span> - <span class="k">for</span> <span class="n">step</span><span class="p">,</span><span class="n">r</span> <span class="ow">in</span> <span class="nb">enumerate</span><span class="p">(</span><span class="n">rs</span><span class="p">,</span><span class="mi">1</span><span class="p">):</span> - <span class="n">dr0</span> <span class="o">=</span> <span class="p">(</span><span class="n">r</span><span class="p">[</span><span class="kc">None</span><span class="p">,:]</span><span class="o">-</span><span class="n">r_cg</span><span class="p">)</span> + <span class="c1"># Competitive learning algorithm</span> + <span class="k">for</span> <span class="n">step</span><span class="p">,</span> <span class="n">r</span> <span class="ow">in</span> <span class="nb">enumerate</span><span class="p">(</span><span class="n">rs</span><span class="p">,</span> <span class="mi">1</span><span class="p">):</span> + <span class="c1"># Calculate distances to all CG sites</span> + <span class="n">dr0</span> <span class="o">=</span> <span class="p">(</span><span class="n">r</span><span class="p">[</span><span class="kc">None</span><span class="p">,</span> <span class="p">:]</span> <span class="o">-</span> <span class="n">r_cg</span><span class="p">)</span> <span class="n">dr0_sq</span> <span class="o">=</span> <span class="p">(</span><span class="n">dr0</span><span class="o">**</span><span class="mi">2</span><span class="p">)</span><span class="o">.</span><span class="n">sum</span><span class="p">(</span><span class="n">axis</span><span class="o">=-</span><span class="mi">1</span><span class="p">)</span> - <span class="c1">## number of CG sites closer to FG site</span> + <span class="c1"># Calculate k parameter (number of CG sites closer than each site)</span> <span class="n">k</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">dr0_sq</span> <span class="o"><</span> <span class="n">x</span><span class="p">)</span><span class="o">.</span><span class="n">sum</span><span class="p">()</span> <span class="k">for</span> <span class="n">x</span> <span class="ow">in</span> <span class="n">dr0_sq</span><span class="p">])</span> <span class="k">if</span> <span class="ow">not</span> <span class="n">np</span><span class="o">.</span><span class="n">all</span><span class="p">(</span><span class="n">np</span><span class="o">.</span><span class="n">isfinite</span><span class="p">(</span><span class="n">k</span><span class="p">)):</span> - <span class="k">raise</span> <span class="ne">Exception</span> + <span class="k">raise</span> <span class="ne">ValueError</span><span class="p">(</span><span class="s2">"Non-finite values in k array during learning"</span><span class="p">)</span> + <span class="c1"># Calculate learning rate for each CG site</span> <span class="n">learn_rate</span> <span class="o">=</span> <span class="n">epsilon</span><span class="p">(</span><span class="n">step</span><span class="p">)</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">lambda_</span><span class="p">(</span><span class="n">step</span><span class="p">))</span> <span class="k">if</span> <span class="ow">not</span> <span class="n">np</span><span class="o">.</span><span class="n">all</span><span class="p">(</span><span class="n">np</span><span class="o">.</span><span class="n">isfinite</span><span class="p">(</span><span class="n">learn_rate</span><span class="p">)):</span> - <span class="k">raise</span> <span class="ne">Exception</span> + <span class="k">raise</span> <span class="ne">ValueError</span><span class="p">(</span><span class="s2">"Non-finite values in learning rate during learning"</span><span class="p">)</span> - <span class="n">r_cg</span> <span class="o">=</span> <span class="n">r_cg</span> <span class="o">+</span> <span class="n">learn_rate</span><span class="p">[:,</span><span class="kc">None</span><span class="p">]</span> <span class="o">*</span> <span class="n">dr0</span> + <span class="c1"># Update CG site positions</span> + <span class="n">r_cg</span> <span class="o">=</span> <span class="n">r_cg</span> <span class="o">+</span> <span class="n">learn_rate</span><span class="p">[:,</span> <span class="kc">None</span><span class="p">]</span> <span class="o">*</span> <span class="n">dr0</span> <span class="k">return</span> <span class="n">r_cg</span></div> - <div class="viewcode-block" id="get_particle_assignments"> <a class="viewcode-back" href="../../api/shape-based_models/shape_cg.html#arbdmodel.shape_cg.get_particle_assignments">[docs]</a> -<span class="k">def</span><span class="w"> </span><span class="nf">get_particle_assignments</span><span class="p">(</span> <span class="n">fine_sites</span><span class="p">,</span> <span class="n">coarse_sites</span><span class="p">,</span> <span class="n">max_distance</span><span class="o">=</span><span class="mi">20</span> <span class="p">):</span> - - <span class="n">t_fg</span> <span class="o">=</span> <span class="n">KDTree</span><span class="p">(</span> <span class="n">fine_sites</span> <span class="p">)</span> - <span class="n">t_cg</span> <span class="o">=</span> <span class="n">KDTree</span><span class="p">(</span> <span class="n">coarse_sites</span> <span class="p">)</span> - - <span class="n">coo</span> <span class="o">=</span> <span class="n">t_fg</span><span class="o">.</span><span class="n">sparse_distance_matrix</span><span class="p">(</span> <span class="n">t_cg</span><span class="p">,</span> <span class="n">output_type</span><span class="o">=</span><span class="s1">'coo_matrix'</span><span class="p">,</span> <span class="n">max_distance</span><span class="o">=</span><span class="n">max_distance</span> <span class="p">)</span> +<span class="k">def</span><span class="w"> </span><span class="nf">get_particle_assignments</span><span class="p">(</span><span class="n">fine_sites</span><span class="p">,</span> <span class="n">coarse_sites</span><span class="p">,</span> <span class="n">max_distance</span><span class="o">=</span><span class="mi">20</span><span class="p">):</span> +<span class="w"> </span><span class="sd">"""Assign fine-grained particles to coarse-grained sites.</span> +<span class="sd"> </span> +<span class="sd"> This function maps each atom to its closest coarse-grained site,</span> +<span class="sd"> using a KD-tree for efficient distance calculations.</span> +<span class="sd"> </span> +<span class="sd"> Args:</span> +<span class="sd"> fine_sites: Array of atomic positions, shape (n_atoms, 3)</span> +<span class="sd"> coarse_sites: Array of coarse-grained site positions, shape (n_cg, 3)</span> +<span class="sd"> max_distance: Maximum distance to consider for assignments</span> +<span class="sd"> </span> +<span class="sd"> Returns:</span> +<span class="sd"> Array of assignments, indicating which CG site each atom belongs to</span> +<span class="sd"> """</span> + <span class="n">t_fg</span> <span class="o">=</span> <span class="n">KDTree</span><span class="p">(</span><span class="n">fine_sites</span><span class="p">)</span> + <span class="n">t_cg</span> <span class="o">=</span> <span class="n">KDTree</span><span class="p">(</span><span class="n">coarse_sites</span><span class="p">)</span> + <span class="c1"># Build sparse distance matrix between fine and coarse sites</span> + <span class="n">coo</span> <span class="o">=</span> <span class="n">t_fg</span><span class="o">.</span><span class="n">sparse_distance_matrix</span><span class="p">(</span><span class="n">t_cg</span><span class="p">,</span> <span class="n">output_type</span><span class="o">=</span><span class="s1">'coo_matrix'</span><span class="p">,</span> <span class="n">max_distance</span><span class="o">=</span><span class="n">max_distance</span><span class="p">)</span> <span class="n">csr</span> <span class="o">=</span> <span class="n">coo</span><span class="o">.</span><span class="n">tocsr</span><span class="p">()</span> - <span class="k">def</span><span class="w"> </span><span class="nf">_nonzero_row_argmin</span><span class="p">(</span> <span class="n">csr</span> <span class="p">):</span> + <span class="k">def</span><span class="w"> </span><span class="nf">_nonzero_row_argmin</span><span class="p">(</span><span class="n">csr</span><span class="p">):</span> +<span class="w"> </span><span class="sd">"""Find indices of minimum values in each row of sparse matrix."""</span> <span class="n">result</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="n">csr</span><span class="o">.</span><span class="n">shape</span><span class="p">[</span><span class="mi">0</span><span class="p">]):</span> <span class="n">sl</span> <span class="o">=</span> <span class="nb">slice</span><span class="p">(</span><span class="n">csr</span><span class="o">.</span><span class="n">indptr</span><span class="p">[</span><span class="n">i</span><span class="p">],</span> <span class="n">csr</span><span class="o">.</span><span class="n">indptr</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="k">if</span> <span class="nb">len</span><span class="p">(</span><span class="n">csr</span><span class="o">.</span><span class="n">data</span><span class="p">[</span><span class="n">sl</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">Exception</span><span class="p">(</span><span class="s2">"Some fine particles too far from coarse sites to assign"</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="s2">"Fine particle </span><span class="si">{</span><span class="n">i</span><span class="si">}</span><span class="s2"> is too far from all coarse sites to assign"</span><span class="p">)</span> <span class="k">else</span><span class="p">:</span> <span class="n">idx</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">csr</span><span class="o">.</span><span class="n">data</span><span class="p">[</span><span class="n">sl</span><span class="p">])</span> - <span class="n">j</span> <span class="o">=</span> <span class="n">csr</span><span class="o">.</span><span class="n">indices</span><span class="p">[</span><span class="n">sl</span><span class="p">][</span><span class="n">idx</span><span class="p">]</span> <span class="c1"># column index</span> + <span class="n">j</span> <span class="o">=</span> <span class="n">csr</span><span class="o">.</span><span class="n">indices</span><span class="p">[</span><span class="n">sl</span><span class="p">][</span><span class="n">idx</span><span class="p">]</span> <span class="c1"># column index</span> <span class="n">result</span><span class="o">.</span><span class="n">append</span><span class="p">(</span><span class="n">j</span><span class="p">)</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="n">result</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">assignments</span> <span class="o">=</span> <span class="n">_nonzero_row_argmin</span><span class="p">(</span><span class="n">csr</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">assignments</span><span class="p">)</span> <span class="o">==</span> <span class="nb">len</span><span class="p">(</span><span class="n">fine_sites</span><span class="p">))</span> <span class="k">return</span> <span class="n">assignments</span></div> + + +<div class="viewcode-block" id="ShapeCGNonbonded"> +<a class="viewcode-back" href="../../api/shape-based_models/shape_cg.html#arbdmodel.shape_cg.ShapeCGNonbonded">[docs]</a> +<span class="k">class</span><span class="w"> </span><span class="nc">ShapeCGNonbonded</span><span class="p">(</span><span class="n">AbstractPotential</span><span class="p">):</span> +<span class="w"> </span><span class="sd">"""Nonbonded potential for shape-based coarse grained models.</span> +<span class="sd"> </span> +<span class="sd"> The potential includes electrostatic and Lennard-Jones components.</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">debye_length</span><span class="o">=</span><span class="mi">10</span><span class="p">,</span> <span class="n">resolution</span><span class="o">=</span><span class="mf">0.3</span><span class="p">,</span> <span class="n">rMin</span><span class="o">=</span><span class="mi">5</span><span class="p">,</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="mi">50</span><span class="p">),</span> <span class="o">**</span><span class="n">kwargs</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> <span class="n">range_</span><span class="o">=</span><span class="n">range_</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">debye_length</span> <span class="o">=</span> <span class="n">debye_length</span> + <span class="bp">self</span><span class="o">.</span><span class="n">maxForce</span> <span class="o">=</span> <span class="mi">50</span> + <span class="bp">self</span><span class="o">.</span><span class="n">rMin</span> <span class="o">=</span> <span class="n">rMin</span> + +<div class="viewcode-block" id="ShapeCGNonbonded.potential"> +<a class="viewcode-back" href="../../api/shape-based_models/shape_cg.html#arbdmodel.shape_cg.ShapeCGNonbonded.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="n">types</span><span class="p">):</span> +<span class="w"> </span><span class="sd">"""Calculate the potential energy at distance r.</span> +<span class="sd"> </span> +<span class="sd"> Args:</span> +<span class="sd"> r: Array of distances</span> +<span class="sd"> types: Tuple of (typeA, typeB) particle types</span> +<span class="sd"> </span> +<span class="sd"> Returns:</span> +<span class="sd"> Array of potential energies</span> +<span class="sd"> """</span> + <span class="n">typeA</span><span class="p">,</span> <span class="n">typeB</span> <span class="o">=</span> <span class="n">types</span> + + <span class="c1"># Electrostatics</span> + <span class="n">ld</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">debye_length</span> + <span class="n">q1</span> <span class="o">=</span> <span class="n">typeA</span><span class="o">.</span><span class="n">charge</span> + <span class="n">q2</span> <span class="o">=</span> <span class="n">typeB</span><span class="o">.</span><span class="n">charge</span> + <span class="n">D</span> <span class="o">=</span> <span class="mi">80</span> <span class="c1"># dielectric of water</span> + <span class="c1"># units "e**2 / (4 * pi * epsilon0 AA)" kcal_mol</span> + <span class="n">A</span> <span class="o">=</span> <span class="mf">332.06371</span> + <span class="n">u_elec</span> <span class="o">=</span> <span class="p">(</span><span class="n">A</span> <span class="o">*</span> <span class="n">q1</span> <span class="o">*</span> <span class="n">q2</span> <span class="o">/</span> <span class="n">D</span><span class="p">)</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">r</span> <span class="o">/</span> <span class="n">ld</span><span class="p">)</span> <span class="o">/</span> <span class="n">r</span> + + <span class="c1"># Lennard-Jones</span> + <span class="n">epsilon</span> <span class="o">=</span> <span class="mf">0.5</span> + <span class="k">if</span> <span class="nb">hasattr</span><span class="p">(</span><span class="n">typeA</span><span class="p">,</span> <span class="s1">'nts'</span><span class="p">)</span> <span class="ow">or</span> <span class="nb">hasattr</span><span class="p">(</span><span class="n">typeB</span><span class="p">,</span> <span class="s1">'nts'</span><span class="p">):</span> + <span class="n">epsilon</span> <span class="o">=</span> <span class="mf">1.0</span> + + <span class="n">sigma</span> <span class="o">=</span> <span class="mf">0.5</span> <span class="o">*</span> <span class="p">(</span><span class="n">typeA</span><span class="o">.</span><span class="n">sigma</span> <span class="o">+</span> <span class="n">typeB</span><span class="o">.</span><span class="n">sigma</span><span class="p">)</span> + <span class="n">r6</span> <span class="o">=</span> <span class="p">(</span><span class="n">sigma</span> <span class="o">/</span> <span class="n">r</span><span class="p">)</span> <span class="o">**</span> <span class="mi">6</span> + <span class="n">r12</span> <span class="o">=</span> <span class="n">r6</span> <span class="o">**</span> <span class="mi">2</span> + <span class="n">u_lj</span> <span class="o">=</span> <span class="mi">4</span> <span class="o">*</span> <span class="n">epsilon</span> <span class="o">*</span> <span class="p">(</span><span class="n">r12</span> <span class="o">-</span> <span class="n">r6</span><span class="p">)</span> + + <span class="c1"># Modified to be repulsive</span> + <span class="n">rmin</span> <span class="o">=</span> <span class="n">sigma</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="mi">6</span><span class="p">)</span> + <span class="k">try</span><span class="p">:</span> + <span class="n">i</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">r</span> <span class="o">>=</span> <span class="n">rmin</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">u_lj</span> <span class="o">=</span> <span class="n">u_lj</span> <span class="o">-</span> <span class="n">u_lj</span><span class="p">[</span><span class="n">i</span><span class="p">]</span> + <span class="n">u_lj</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="o">=</span> <span class="mi">0</span> + <span class="k">except</span> <span class="ne">IndexError</span><span class="p">:</span> + <span class="c1"># Handle case where r doesn't contain values >= rmin</span> + <span class="n">u_lj</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">r</span><span class="p">)</span> + + <span class="c1"># Combine potentials</span> + <span class="n">u</span> <span class="o">=</span> <span class="n">u_elec</span> <span class="o">+</span> <span class="n">u_lj</span> + <span class="n">u</span><span class="p">[</span><span class="mi">0</span><span class="p">]</span> <span class="o">=</span> <span class="n">u</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="n">u</span><span class="p">)</span> <span class="o">></span> <span class="mi">1</span> <span class="k">else</span> <span class="mi">0</span> <span class="c1"># Remove NaN</span> + + <span class="c1"># Cap the maximum force</span> + <span class="n">maxForce</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">maxForce</span> + <span class="k">if</span> <span class="n">maxForce</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">r</span><span class="p">)</span> <span class="o">></span> <span class="mi">1</span><span class="p">:</span> + <span class="k">assert</span><span class="p">(</span><span class="n">maxForce</span> <span class="o">></span> <span class="mi">0</span><span class="p">)</span> + <span class="n">f</span> <span class="o">=</span> <span class="n">np</span><span class="o">.</span><span class="n">diff</span><span class="p">(</span><span class="n">u</span><span class="p">)</span> <span class="o">/</span> <span class="n">np</span><span class="o">.</span><span class="n">diff</span><span class="p">(</span><span class="n">r</span><span class="p">)</span> + <span class="n">f</span><span class="p">[</span><span class="n">f</span> <span class="o">></span> <span class="n">maxForce</span><span class="p">]</span> <span class="o">=</span> <span class="n">maxForce</span> + <span class="n">f</span><span class="p">[</span><span class="n">f</span> <span class="o"><</span> <span class="o">-</span><span class="n">maxForce</span><span class="p">]</span> <span class="o">=</span> <span class="o">-</span><span class="n">maxForce</span> + <span class="n">u</span><span class="p">[</span><span class="mi">0</span><span class="p">]</span> <span class="o">=</span> <span class="mi">0</span> + <span class="n">u</span><span class="p">[</span><span class="mi">1</span><span class="p">:]</span> <span class="o">=</span> <span class="n">np</span><span class="o">.</span><span class="n">cumsum</span><span class="p">(</span><span class="n">f</span> <span class="o">*</span> <span class="n">np</span><span class="o">.</span><span class="n">diff</span><span class="p">(</span><span class="n">r</span><span class="p">))</span> + + <span class="n">u</span> <span class="o">=</span> <span class="n">u</span> <span class="o">-</span> <span class="n">u</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">u</span><span class="p">)</span> <span class="o">></span> <span class="mi">0</span> <span class="k">else</span> <span class="n">u</span> + <span class="k">return</span> <span class="n">u</span></div> + + +<div class="viewcode-block" id="ShapeCGNonbonded.filename"> +<a class="viewcode-back" href="../../api/shape-based_models/shape_cg.html#arbdmodel.shape_cg.ShapeCGNonbonded.filename">[docs]</a> + <span class="k">def</span><span class="w"> </span><span class="nf">filename</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">types</span><span class="o">=</span><span class="kc">None</span><span class="p">):</span> +<span class="w"> </span><span class="sd">"""Get filename for potential lookup table.</span> +<span class="sd"> </span> +<span class="sd"> Args:</span> +<span class="sd"> types: Tuple of particle types</span> +<span class="sd"> </span> +<span class="sd"> Returns:</span> +<span class="sd"> Filename string</span> +<span class="sd"> """</span> + <span class="n">typeA</span><span class="p">,</span> <span class="n">typeB</span> <span class="o">=</span> <span class="n">types</span> + <span class="k">return</span> <span class="sa">f</span><span class="s2">"potentials/shapecg_</span><span class="si">{</span><span class="n">typeA</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">typeB</span><span class="o">.</span><span class="n">name</span><span class="si">}</span><span class="s2">.dat"</span></div> +</div> + + + +<div class="viewcode-block" id="ShapeCGFactory"> +<a class="viewcode-back" href="../../api/shape-based_models/shape_cg.html#arbdmodel.shape_cg.ShapeCGFactory">[docs]</a> +<span class="k">class</span><span class="w"> </span><span class="nc">ShapeCGFactory</span><span class="p">:</span> +<span class="w"> </span><span class="sd">"""Factory class for creating coarse-grained protein models.</span> +<span class="sd"> </span> +<span class="sd"> This class creates reduced-resolution models of proteins based on</span> +<span class="sd"> their shape, with customizable resolution and properties.</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">psf</span><span class="p">,</span> <span class="n">pdb</span><span class="p">,</span> <span class="n">disordered_residues</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="s1">'SHCG'</span><span class="p">):</span> +<span class="w"> </span><span class="sd">"""Initialize the factory.</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"> disordered_residues: List of residue indices considered disordered</span> +<span class="sd"> name: Name prefix for generated particles</span> +<span class="sd"> """</span> + <span class="bp">self</span><span class="o">.</span><span class="n">psf</span> <span class="o">=</span> <span class="n">psf</span> + <span class="bp">self</span><span class="o">.</span><span class="n">pdb</span> <span class="o">=</span> <span class="n">pdb</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="k">if</span> <span class="n">disordered_residues</span> <span class="ow">is</span> <span class="kc">None</span><span class="p">:</span> + <span class="n">disordered_residues</span> <span class="o">=</span> <span class="p">[]</span> + + <span class="c1"># Using parmed because MDA sometimes misreads psf attributes</span> + <span class="bp">self</span><span class="o">.</span><span class="n">_fine</span> <span class="o">=</span> <span class="n">_fine</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="bp">self</span><span class="o">.</span><span class="n">_fine_positions</span> <span class="o">=</span> <span class="n">_fine</span><span class="o">.</span><span class="n">coordinates</span> + <span class="bp">self</span><span class="o">.</span><span class="n">_fine_masses</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">mass</span> <span class="k">for</span> <span class="n">a</span> <span class="ow">in</span> <span class="n">_fine</span><span class="p">])</span> + <span class="bp">self</span><span class="o">.</span><span class="n">_fine_charges</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">charge</span> <span class="k">for</span> <span class="n">a</span> <span class="ow">in</span> <span class="n">_fine</span><span class="p">])</span> + <span class="bp">self</span><span class="o">.</span><span class="n">_fine_names</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">name</span> <span class="k">for</span> <span class="n">a</span> <span class="ow">in</span> <span class="n">_fine</span><span class="p">])</span> + <span class="bp">self</span><span class="o">.</span><span class="n">_fine_resnames</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">residue</span><span class="o">.</span><span class="n">name</span> <span class="k">for</span> <span class="n">a</span> <span class="ow">in</span> <span class="n">_fine</span><span class="p">])</span> + <span class="bp">self</span><span class="o">.</span><span class="n">_fine_idp</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="k">if</span> <span class="n">a</span><span class="o">.</span><span class="n">residue</span><span class="o">.</span><span class="n">idx</span> <span class="ow">in</span> <span class="n">disordered_residues</span> <span class="k">else</span> <span class="mi">0</span> <span class="k">for</span> <span class="n">a</span> <span class="ow">in</span> <span class="n">_fine</span><span class="p">])</span> + <span class="bp">self</span><span class="o">.</span><span class="n">_fine_resid</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">residue</span><span class="o">.</span><span class="n">idx</span> <span class="k">for</span> <span class="n">a</span> <span class="ow">in</span> <span class="n">_fine</span><span class="p">])</span> + <span class="bp">self</span><span class="o">.</span><span class="n">_fine_total_mass</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">_fine_masses</span><span class="o">.</span><span class="n">sum</span><span class="p">()</span> + <span class="bp">self</span><span class="o">.</span><span class="n">_coarse_dict</span> <span class="o">=</span> <span class="p">{}</span> <span class="c1"># dictionary that caches shape-CG model with number of beads as key</span> + +<div class="viewcode-block" id="ShapeCGFactory.calc_atom_sasa"> +<a class="viewcode-back" href="../../api/shape-based_models/shape_cg.html#arbdmodel.shape_cg.ShapeCGFactory.calc_atom_sasa">[docs]</a> + <span class="k">def</span><span class="w"> </span><span class="nf">calc_atom_sasa</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">atom_slice</span><span class="p">):</span> +<span class="w"> </span><span class="sd">"""Calculate solvent accessible surface area for atoms.</span> +<span class="sd"> </span> +<span class="sd"> Args:</span> +<span class="sd"> atom_slice: Slice or indices for atoms to calculate SASA</span> +<span class="sd"> </span> +<span class="sd"> Returns:</span> +<span class="sd"> Tuple of (normalized SASA, atomic radii)</span> +<span class="sd"> """</span> + <span class="n">sl</span> <span class="o">=</span> <span class="n">atom_slice</span> + <span class="k">try</span><span class="p">:</span> + <span class="bp">self</span><span class="o">.</span><span class="n">atom_radii</span> + <span class="k">except</span> <span class="ne">AttributeError</span><span class="p">:</span> + <span class="n">structure</span> <span class="o">=</span> <span class="n">freesasa</span><span class="o">.</span><span class="n">Structure</span><span class="p">()</span> + <span class="n">structure</span><span class="o">.</span><span class="n">addAtoms</span><span class="p">(</span> + <span class="bp">self</span><span class="o">.</span><span class="n">_fine_names</span><span class="p">,</span> + <span class="bp">self</span><span class="o">.</span><span class="n">_fine_resnames</span><span class="p">,</span> + <span class="p">[</span><span class="nb">int</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="bp">self</span><span class="o">.</span><span class="n">_fine_resid</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">_fine_positions</span><span class="p">)</span> <span class="o">*</span> <span class="s1">'A'</span><span class="p">,</span> + <span class="o">*</span><span class="p">[</span><span class="bp">self</span><span class="o">.</span><span class="n">_fine_positions</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="ow">in</span> <span class="nb">range</span><span class="p">(</span><span class="mi">3</span><span class="p">)]</span> + <span class="p">)</span> + + <span class="n">res</span> <span class="o">=</span> <span class="n">freesasa</span><span class="o">.</span><span class="n">calc</span><span class="p">(</span><span class="n">structure</span><span class="p">)</span> + + <span class="bp">self</span><span class="o">.</span><span class="n">atom_radii</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">structure</span><span class="o">.</span><span class="n">radius</span><span class="p">(</span><span class="n">i</span><span class="p">)</span> <span class="o">+</span> <span class="mf">1.4</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">res</span><span class="o">.</span><span class="n">nAtoms</span><span class="p">())])</span> + <span class="bp">self</span><span class="o">.</span><span class="n">atom_sasa</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">res</span><span class="o">.</span><span class="n">atomArea</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="ow">in</span> <span class="nb">range</span><span class="p">(</span><span class="n">res</span><span class="o">.</span><span class="n">nAtoms</span><span class="p">())])</span> + <span class="bp">self</span><span class="o">.</span><span class="n">atom_area</span> <span class="o">=</span> <span class="mi">4</span> <span class="o">*</span> <span class="n">np</span><span class="o">.</span><span class="n">pi</span> <span class="o">*</span> <span class="bp">self</span><span class="o">.</span><span class="n">atom_radii</span><span class="o">**</span><span class="mi">2</span> + + <span class="n">w</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">atom_sasa</span><span class="p">[</span><span class="n">sl</span><span class="p">]</span> <span class="o">/</span> <span class="bp">self</span><span class="o">.</span><span class="n">atom_area</span><span class="p">[</span><span class="n">sl</span><span class="p">]</span> + <span class="k">return</span> <span class="n">w</span><span class="p">,</span> <span class="bp">self</span><span class="o">.</span><span class="n">atom_radii</span><span class="p">[</span><span class="n">sl</span><span class="p">]</span></div> + + +<div class="viewcode-block" id="ShapeCGFactory.get_coarse_protein"> +<a class="viewcode-back" href="../../api/shape-based_models/shape_cg.html#arbdmodel.shape_cg.ShapeCGFactory.get_coarse_protein">[docs]</a> + <span class="k">def</span><span class="w"> </span><span class="nf">get_coarse_protein</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">num_CG_sites</span><span class="o">=</span><span class="kc">None</span><span class="p">):</span> +<span class="w"> </span><span class="sd">"""Generate a coarse-grained protein model.</span> +<span class="sd"> </span> +<span class="sd"> Args:</span> +<span class="sd"> num_CG_sites: Number of sites to represent the protein (default: based on mass)</span> +<span class="sd"> </span> +<span class="sd"> Returns:</span> +<span class="sd"> Group containing the coarse-grained protein</span> +<span class="sd"> """</span> + <span class="k">if</span> <span class="n">num_CG_sites</span> <span class="ow">is</span> <span class="kc">None</span><span class="p">:</span> + <span class="c1"># Default to ~5000 dalton/site</span> + <span class="n">num_CG_sites</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">round</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">_fine_total_mass</span> <span class="o">/</span> <span class="mi">5000</span><span class="p">))</span> + + <span class="k">if</span> <span class="n">num_CG_sites</span> <span class="ow">not</span> <span class="ow">in</span> <span class="bp">self</span><span class="o">.</span><span class="n">_coarse_dict</span><span class="p">:</span> + <span class="c1"># Find optimal placement of CG sites based on shape</span> + <span class="n">r_cg</span> <span class="o">=</span> <span class="n">find_shape_based_sites</span><span class="p">(</span> + <span class="bp">self</span><span class="o">.</span><span class="n">_fine_positions</span><span class="p">,</span> + <span class="n">N_cg</span><span class="o">=</span><span class="n">num_CG_sites</span><span class="p">,</span> + <span class="n">weights</span><span class="o">=</span><span class="bp">self</span><span class="o">.</span><span class="n">_fine_masses</span> + <span class="p">)</span> + + <span class="c1"># Assign atoms to CG sites</span> + <span class="n">mapping</span> <span class="o">=</span> <span class="n">get_particle_assignments</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">_fine_positions</span><span class="p">,</span> <span class="n">r_cg</span><span class="p">,</span> <span class="n">max_distance</span><span class="o">=</span><span class="mi">80</span><span class="p">)</span> + <span class="bp">self</span><span class="o">.</span><span class="n">mapping</span> <span class="o">=</span> <span class="n">mapping</span> + + <span class="n">types</span> <span class="o">=</span> <span class="p">[]</span> + <span class="n">parts</span> <span class="o">=</span> <span class="p">[]</span> + + <span class="c1"># Calculate average residue ID for each CG site for consistent numbering</span> + <span class="n">cg_fine_resids</span> <span class="o">=</span> <span class="p">[</span><span class="bp">self</span><span class="o">.</span><span class="n">_fine_resid</span><span class="p">[</span><span class="n">mapping</span> <span class="o">==</span> <span class="n">i</span><span class="p">]</span><span class="o">.</span><span class="n">mean</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">num_CG_sites</span><span class="p">)]</span> + <span class="n">cg_resids</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">np</span><span class="o">.</span><span class="n">argsort</span><span class="p">(</span><span class="n">cg_fine_resids</span><span class="p">))</span> <span class="o">+</span> <span class="mi">1</span> + + <span class="n">part_by_resid</span> <span class="o">=</span> <span class="nb">dict</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">r</span><span class="p">,</span> <span class="n">rid</span><span class="p">)</span> <span class="ow">in</span> <span class="nb">sorted</span><span class="p">(</span><span class="nb">enumerate</span><span class="p">(</span><span class="nb">zip</span><span class="p">(</span><span class="n">r_cg</span><span class="p">,</span> <span class="n">cg_resids</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">1</span><span class="p">][</span><span class="mi">1</span><span class="p">]):</span> + <span class="n">sl</span> <span class="o">=</span> <span class="p">(</span><span class="n">mapping</span> <span class="o">==</span> <span class="n">i</span><span class="p">)</span> + <span class="n">rad_gyr0</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">mean</span><span class="p">(((</span><span class="bp">self</span><span class="o">.</span><span class="n">_fine_positions</span><span class="p">[</span><span class="n">sl</span><span class="p">]</span> <span class="o">-</span> <span class="n">r_cg</span><span class="p">[</span><span class="n">i</span><span class="p">])</span><span class="o">**</span><span class="mi">2</span><span class="p">)</span><span class="o">.</span><span class="n">sum</span><span class="p">(</span><span class="n">axis</span><span class="o">=-</span><span class="mi">1</span><span class="p">)))</span> + + <span class="c1"># Calculate effective radius using SASA-weighted approach</span> + <span class="k">def</span><span class="w"> </span><span class="nf">_calc_sasa_rad</span><span class="p">():</span> + <span class="n">w</span><span class="p">,</span> <span class="n">radii</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">calc_atom_sasa</span><span class="p">(</span><span class="n">sl</span><span class="p">)</span> + <span class="n">w</span> <span class="o">=</span> <span class="n">w</span> <span class="o">/</span> <span class="n">w</span><span class="o">.</span><span class="n">sum</span><span class="p">()</span> <span class="c1"># normalized</span> + <span class="n">r_sq</span> <span class="o">=</span> <span class="p">((</span><span class="bp">self</span><span class="o">.</span><span class="n">_fine_positions</span><span class="p">[</span><span class="n">sl</span><span class="p">]</span> <span class="o">-</span> <span class="n">r_cg</span><span class="p">[</span><span class="n">i</span><span class="p">])</span><span class="o">**</span><span class="mi">2</span><span class="p">)</span><span class="o">.</span><span class="n">sum</span><span class="p">(</span><span class="n">axis</span><span class="o">=-</span><span class="mi">1</span><span class="p">)</span> <span class="o">+</span> <span class="n">radii</span><span class="o">**</span><span class="mi">2</span> + <span class="n">alpha</span> <span class="o">=</span> <span class="mi">1</span> + <span class="k">return</span> <span class="n">np</span><span class="o">.</span><span class="n">sqrt</span><span class="p">((</span><span class="n">r_sq</span><span class="o">**</span><span class="n">alpha</span> <span class="o">*</span> <span class="n">w</span><span class="p">)</span><span class="o">.</span><span class="n">sum</span><span class="p">())</span><span class="o">**</span><span class="p">(</span><span class="mf">1.0</span><span class="o">/</span><span class="n">alpha</span><span class="p">)</span> + + <span class="n">_alpha</span> <span class="o">=</span> <span class="mf">1.1</span> + <span class="n">_eps</span> <span class="o">=</span> <span class="mf">0.8</span> <span class="o">*</span> <span class="mf">12.78</span><span class="o">**</span><span class="p">(</span><span class="mf">1.2</span> <span class="o">-</span> <span class="n">_alpha</span><span class="p">)</span> + <span class="n">rad_gyr</span> <span class="o">=</span> <span class="n">_eps</span> <span class="o">*</span> <span class="n">_calc_sasa_rad</span><span class="p">()</span><span class="o">**</span><span class="n">_alpha</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">'CG residue </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">num_CG_sites</span><span class="si">}</span><span class="s1">: rgyr = </span><span class="si">{</span><span class="n">rad_gyr0</span><span class="si">}</span><span class="s1">; rgyr_sasa = </span><span class="si">{</span><span class="n">rad_gyr</span><span class="si">}</span><span class="s1">'</span><span class="p">)</span> + + <span class="n">rad</span> <span class="o">=</span> <span class="n">rad_gyr</span> + <span class="n">mass</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">_fine_masses</span><span class="p">[</span><span class="n">sl</span><span class="p">]</span><span class="o">.</span><span class="n">sum</span><span class="p">()</span> + <span class="n">charge</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">_fine_charges</span><span class="p">[</span><span class="n">sl</span><span class="p">]</span><span class="o">.</span><span class="n">sum</span><span class="p">()</span> + <span class="n">idp</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">_fine_idp</span><span class="p">[</span><span class="n">sl</span><span class="p">]</span><span class="o">.</span><span class="n">sum</span><span class="p">()</span> + + <span class="c1"># Scale diffusivity based on mass</span> + <span class="n">a</span> <span class="o">=</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">_fine_total_mass</span><span class="p">)</span><span class="o">**</span><span class="p">(</span><span class="mi">1</span><span class="o">/</span><span class="mi">3</span><span class="p">)</span> + <span class="n">D</span> <span class="o">=</span> <span class="n">num_CG_sites</span> <span class="o">/</span> <span class="n">a</span> <span class="c1"># heuristic with correct scaling</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="bp">self</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">num_CG_sites</span><span class="si">:</span><span class="s1">02d</span><span class="si">}</span><span class="s1">_</span><span class="si">{</span><span class="n">i</span><span class="si">:</span><span class="s1">02d</span><span class="si">}</span><span class="s1">'</span> + <span class="n">t</span> <span class="o">=</span> <span class="n">ParticleType</span><span class="p">(</span> + <span class="n">name</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">sigma</span><span class="o">=</span><span class="mi">2</span> <span class="o">*</span> <span class="n">rad</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="mi">6</span><span class="p">),</span> + <span class="n">charge</span><span class="o">=</span><span class="n">charge</span><span class="p">,</span> + <span class="n">idp</span><span class="o">=</span><span class="n">idp</span><span class="p">,</span> + <span class="n">diffusivity</span><span class="o">=</span><span class="n">D</span><span class="p">,</span> + <span class="p">)</span> + <span class="n">p</span> <span class="o">=</span> <span class="n">PointParticle</span><span class="p">(</span><span class="n">t</span><span class="p">,</span> <span class="n">r</span><span class="p">,</span> <span class="n">name</span><span class="p">,</span> <span class="n">resid</span><span class="o">=</span><span class="n">rid</span><span class="p">,</span> <span class="n">residue</span><span class="o">=</span><span class="n">rid</span><span class="p">)</span> + <span class="n">types</span><span class="o">.</span><span class="n">append</span><span class="p">(</span><span class="n">t</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="n">part_by_resid</span><span class="p">[</span><span class="n">rid</span><span class="p">]</span> <span class="o">=</span> <span class="n">p</span> + + <span class="n">g</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="bp">self</span><span class="o">.</span><span class="n">name</span><span class="p">,</span> <span class="n">segname</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">children</span><span class="o">=</span><span class="n">parts</span><span class="p">)</span> + + <span class="c1"># Add all-to-all elastic network for structured region</span> + <span class="n">num_idp</span> <span class="o">=</span> <span class="nb">sum</span><span class="p">([</span><span class="n">p</span><span class="o">.</span><span class="n">idp</span> <span class="o">></span> <span class="mf">0.5</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="k">for</span> <span class="n">i</span><span class="p">,</span> <span class="n">p1</span> <span class="ow">in</span> <span class="nb">enumerate</span><span class="p">(</span><span class="n">parts</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="n">p1</span><span class="o">.</span><span class="n">idp</span> <span class="o">></span> <span class="mf">0.5</span><span class="p">:</span> + <span class="k">continue</span> + <span class="k">for</span> <span class="n">j</span><span class="p">,</span> <span class="n">p2</span> <span class="ow">in</span> <span class="nb">enumerate</span><span class="p">(</span><span class="n">parts</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="n">i</span><span class="o">+</span><span class="mi">1</span><span class="p">):</span> + <span class="k">if</span> <span class="n">p2</span><span class="o">.</span><span class="n">idp</span> <span class="o">></span> <span class="mf">0.5</span><span class="p">:</span> + <span class="k">continue</span> + <span class="n">r0</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">p2</span><span class="o">.</span><span class="n">position</span> <span class="o">-</span> <span class="n">p1</span><span class="o">.</span><span class="n">position</span><span class="p">))</span> + <span class="n">g</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">p1</span><span class="p">,</span> + <span class="n">j</span><span class="o">=</span><span class="n">p2</span><span class="p">,</span> + <span class="n">bond</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="mi">50</span><span class="o">/</span><span class="p">(</span><span class="n">num_CG_sites</span><span class="o">-</span><span class="n">num_idp</span><span class="p">)</span><span class="o">**</span><span class="mi">2</span><span class="p">,</span> <span class="n">r0</span><span class="o">=</span><span class="n">r0</span><span class="p">),</span> + <span class="n">exclude</span><span class="o">=</span><span class="kc">True</span> + <span class="p">)</span> + + <span class="c1"># Add bonds to nearest beads for idp regions</span> + <span class="n">idp_parts</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">parts</span> <span class="k">if</span> <span class="n">p</span><span class="o">.</span><span class="n">idp</span> <span class="o">></span> <span class="mf">0.5</span><span class="p">]</span> + <span class="n">_idp_bonds</span> <span class="o">=</span> <span class="nb">set</span><span class="p">()</span> + <span class="k">for</span> <span class="n">p1</span> <span class="ow">in</span> <span class="n">idp_parts</span><span class="p">:</span> + <span class="k">try</span><span class="p">:</span> + <span class="n">p2</span> <span class="o">=</span> <span class="n">part_by_resid</span><span class="p">[</span><span class="n">p1</span><span class="o">.</span><span class="n">resid</span><span class="o">+</span><span class="mi">1</span><span class="p">]</span> + <span class="n">_idp_bonds</span><span class="o">.</span><span class="n">add</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="k">except</span> <span class="ne">KeyError</span><span class="p">:</span> + <span class="k">pass</span> + <span class="k">try</span><span class="p">:</span> + <span class="n">p2</span> <span class="o">=</span> <span class="n">part_by_resid</span><span class="p">[</span><span class="n">p1</span><span class="o">.</span><span class="n">resid</span><span class="o">-</span><span class="mi">1</span><span class="p">]</span> + <span class="n">_idp_bonds</span><span class="o">.</span><span class="n">add</span><span class="p">((</span><span class="n">p2</span><span class="p">,</span> <span class="n">p1</span><span class="p">))</span> + <span class="k">except</span> <span class="ne">KeyError</span><span class="p">:</span> + <span class="k">pass</span> + + <span class="k">for</span> <span class="n">p1</span><span class="p">,</span> <span class="n">p2</span> <span class="ow">in</span> <span class="n">_idp_bonds</span><span class="p">:</span> + <span class="n">r0</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">p2</span><span class="o">.</span><span class="n">position</span> <span class="o">-</span> <span class="n">p1</span><span class="o">.</span><span class="n">position</span><span class="p">))</span> + <span class="n">g</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">p1</span><span class="p">,</span> <span class="n">j</span><span class="o">=</span><span class="n">p2</span><span class="p">,</span> <span class="n">bond</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="mi">1</span><span class="p">,</span> <span class="n">r0</span><span class="o">=</span><span class="n">r0</span><span class="p">),</span> <span class="n">exclude</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">_coarse_dict</span><span class="p">[</span><span class="n">num_CG_sites</span><span class="p">]</span> <span class="o">=</span> <span class="p">(</span><span class="n">g</span><span class="p">,</span> <span class="n">types</span><span class="p">)</span> + + <span class="k">return</span> <span class="bp">self</span><span class="o">.</span><span class="n">_coarse_dict</span><span class="p">[</span><span class="n">num_CG_sites</span><span class="p">][</span><span class="mi">0</span><span class="p">]</span></div> + + +<div class="viewcode-block" id="ShapeCGFactory.get_coarse_types"> +<a class="viewcode-back" href="../../api/shape-based_models/shape_cg.html#arbdmodel.shape_cg.ShapeCGFactory.get_coarse_types">[docs]</a> + <span class="k">def</span><span class="w"> </span><span class="nf">get_coarse_types</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">num_CG_sites</span><span class="o">=</span><span class="kc">None</span><span class="p">):</span> +<span class="w"> </span><span class="sd">"""Get particle types used in the coarse-grained model.</span> +<span class="sd"> </span> +<span class="sd"> Args:</span> +<span class="sd"> num_CG_sites: Number of sites to represent the protein</span> +<span class="sd"> </span> +<span class="sd"> Returns:</span> +<span class="sd"> List of ParticleType objects</span> +<span class="sd"> """</span> + <span class="k">if</span> <span class="n">num_CG_sites</span> <span class="ow">is</span> <span class="kc">None</span><span class="p">:</span> + <span class="c1"># Default to ~5000 dalton/site</span> + <span class="n">num_CG_sites</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">round</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">_fine_total_mass</span> <span class="o">/</span> <span class="mi">5000</span><span class="p">))</span> + + <span class="k">if</span> <span class="n">num_CG_sites</span> <span class="ow">not</span> <span class="ow">in</span> <span class="bp">self</span><span class="o">.</span><span class="n">_coarse_dict</span><span class="p">:</span> + <span class="bp">self</span><span class="o">.</span><span class="n">get_coarse_protein</span><span class="p">(</span><span class="n">num_CG_sites</span><span class="p">)</span> + + <span class="k">return</span> <span class="bp">self</span><span class="o">.</span><span class="n">_coarse_dict</span><span class="p">[</span><span class="n">num_CG_sites</span><span class="p">][</span><span class="mi">1</span><span class="p">]</span></div> + + +<div class="viewcode-block" id="ShapeCGFactory.generate_protein"> +<a class="viewcode-back" href="../../api/shape-based_models/shape_cg.html#arbdmodel.shape_cg.ShapeCGFactory.generate_protein">[docs]</a> + <span class="k">def</span><span class="w"> </span><span class="nf">generate_protein</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="n">index</span><span class="o">=</span><span class="mi">0</span><span class="p">,</span> <span class="n">num_CG_sites</span><span class="o">=</span><span class="kc">None</span><span class="p">):</span> +<span class="w"> </span><span class="sd">"""Generate a new protein instance at the specified position and orientation.</span> +<span class="sd"> </span> +<span class="sd"> Args:</span> +<span class="sd"> position: 3D position for the protein</span> +<span class="sd"> orientation: Optional orientation matrix</span> +<span class="sd"> index: Unique index for this protein instance</span> +<span class="sd"> num_CG_sites: Number of CG sites to use</span> +<span class="sd"> </span> +<span class="sd"> Returns:</span> +<span class="sd"> Group containing the positioned protein</span> +<span class="sd"> """</span> + <span class="n">new</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">get_coarse_protein</span><span class="p">(</span><span class="n">num_CG_sites</span><span class="p">)</span><span class="o">.</span><span class="n">duplicate</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">new</span><span class="o">.</span><span class="n">orientation</span> <span class="o">=</span> <span class="n">orientation</span> + <span class="n">new</span><span class="o">.</span><span class="n">position</span> <span class="o">=</span> <span class="n">position</span> + + <span class="n">new</span><span class="o">.</span><span class="n">segname</span> <span class="o">=</span> <span class="sa">f</span><span class="s1">'</span><span class="si">{</span><span class="n">new</span><span class="o">.</span><span class="n">name</span><span class="si">}{</span><span class="n">index</span><span class="si">:</span><span class="s1">03d</span><span class="si">}</span><span class="s1">'</span> + <span class="n">new</span><span class="o">.</span><span class="n">name</span> <span class="o">=</span> <span class="n">new</span><span class="o">.</span><span class="n">segname</span> + <span class="k">return</span> <span class="n">new</span></div> +</div> + + + +<div class="viewcode-block" id="ShapeCGModel"> +<a class="viewcode-back" href="../../api/shape-based_models/shape_cg.html#arbdmodel.shape_cg.ShapeCGModel">[docs]</a> +<span class="k">class</span><span class="w"> </span><span class="nc">ShapeCGModel</span><span class="p">(</span><span class="n">ArbdModel</span><span class="p">):</span> +<span class="w"> </span><span class="sd">"""Model class for shape-based coarse-grained protein simulations.</span> +<span class="sd"> </span> +<span class="sd"> This class handles creating and simulating systems with multiple</span> +<span class="sd"> shape-based coarse-grained proteins.</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">protein_factories</span><span class="o">=</span><span class="kc">None</span><span class="p">,</span> <span class="n">box_size</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 the model.</span> +<span class="sd"> </span> +<span class="sd"> Args:</span> +<span class="sd"> protein_factories: Dictionary mapping protein names to ShapeCGFactory objects</span> +<span class="sd"> box_size: Size of simulation box (default: None for automatic sizing)</span> +<span class="sd"> **kwargs: Additional arguments for ArbdModel</span> +<span class="sd"> """</span> + <span class="n">dimensions</span> <span class="o">=</span> <span class="p">[</span><span class="n">box_size</span><span class="p">,</span> <span class="n">box_size</span><span class="p">,</span> <span class="n">box_size</span><span class="p">]</span> <span class="k">if</span> <span class="n">box_size</span> <span class="k">else</span> <span class="kc">None</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">dimensions</span><span class="o">=</span><span class="n">dimensions</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">protein_factories</span> <span class="o">=</span> <span class="n">protein_factories</span> <span class="ow">or</span> <span class="p">{}</span> + <span class="bp">self</span><span class="o">.</span><span class="n">protein_types_cache</span> <span class="o">=</span> <span class="p">{}</span> <span class="c1"># Cache for protein types</span> + +<div class="viewcode-block" id="ShapeCGModel.concentration_to_debye_length"> +<a class="viewcode-back" href="../../api/shape-based_models/shape_cg.html#arbdmodel.shape_cg.ShapeCGModel.concentration_to_debye_length">[docs]</a> + <span class="k">def</span><span class="w"> </span><span class="nf">concentration_to_debye_length</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">c</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="w"> </span><span class="sd">"""Convert salt concentration to Debye length.</span> +<span class="sd"> </span> +<span class="sd"> Args:</span> +<span class="sd"> c: Salt concentration in mM</span> +<span class="sd"> temperature: Temperature in K</span> +<span class="sd"> </span> +<span class="sd"> Returns:</span> +<span class="sd"> Debye length in Angstroms</span> +<span class="sd"> """</span> + <span class="c1"># sqrt(80 * epsilon0 * 295 K / ((150 mM) * e**2/particle))</span> + <span class="k">return</span> <span class="mf">11.154259</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="mi">150</span><span class="o">/</span><span class="n">c</span><span class="p">)</span> <span class="o">*</span> <span class="p">(</span><span class="mi">295</span><span class="o">/</span><span class="n">temperature</span><span class="p">))</span></div> + + +<div class="viewcode-block" id="ShapeCGModel.add_protein_nb_interactions"> +<a class="viewcode-back" href="../../api/shape-based_models/shape_cg.html#arbdmodel.shape_cg.ShapeCGModel.add_protein_nb_interactions">[docs]</a> + <span class="k">def</span><span class="w"> </span><span class="nf">add_protein_nb_interactions</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">prot_types</span><span class="p">,</span> <span class="n">nt_sigma</span><span class="o">=</span><span class="mi">10</span><span class="p">,</span> <span class="n">debye_length</span><span class="o">=</span><span class="kc">None</span><span class="p">):</span> +<span class="w"> </span><span class="sd">"""Add nonbonded interactions between protein particles.</span> +<span class="sd"> </span> +<span class="sd"> Args:</span> +<span class="sd"> prot_types: List of protein particle types</span> +<span class="sd"> nt_sigma: Sigma parameter for nucleic acid interactions</span> +<span class="sd"> debye_length: Debye length for electrostatics (default: calculated from 150 mM)</span> +<span class="sd"> """</span> + <span class="k">if</span> <span class="n">debye_length</span> <span class="ow">is</span> <span class="kc">None</span><span class="p">:</span> + <span class="n">debye_length</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">concentration_to_debye_length</span><span class="p">(</span><span class="mi">150</span><span class="p">)</span> + + <span class="n">prot_nb</span> <span class="o">=</span> <span class="n">ShapeCGNonbonded</span><span class="p">(</span><span class="n">debye_length</span><span class="o">=</span><span class="n">debye_length</span><span class="p">)</span> + <span class="n">old_interactions</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">nbSchemes</span> + <span class="bp">self</span><span class="o">.</span><span class="n">nbSchemes</span> <span class="o">=</span> <span class="p">[]</span> + + <span class="c1"># Add protein-protein interactions</span> + <span class="k">for</span> <span class="n">i</span><span class="p">,</span> <span class="n">prot_t1</span> <span class="ow">in</span> <span class="nb">enumerate</span><span class="p">(</span><span class="n">prot_types</span><span class="p">):</span> + <span class="k">for</span> <span class="n">j</span><span class="p">,</span> <span class="n">prot_t2</span> <span class="ow">in</span> <span class="nb">enumerate</span><span class="p">(</span><span class="n">prot_types</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="bp">self</span><span class="o">.</span><span class="n">useNonbondedScheme</span><span class="p">(</span><span class="n">prot_nb</span><span class="p">,</span> <span class="n">typeA</span><span class="o">=</span><span class="n">prot_t1</span><span class="p">,</span> <span class="n">typeB</span><span class="o">=</span><span class="n">prot_t2</span><span class="p">)</span> + + <span class="c1"># Add protein-nucleic acid interactions if present</span> + <span class="k">try</span><span class="p">:</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">nucleic_types</span><span class="p">:</span> + <span class="k">if</span> <span class="n">t</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">'O'</span><span class="p">:</span> + <span class="k">continue</span> + <span class="n">t</span><span class="o">.</span><span class="n">charge</span> <span class="o">=</span> <span class="o">-</span><span class="mi">1</span> <span class="o">*</span> <span class="n">t</span><span class="o">.</span><span class="n">nts</span> + <span class="n">t</span><span class="o">.</span><span class="n">sigma</span> <span class="o">=</span> <span class="n">nt_sigma</span> + <span class="bp">self</span><span class="o">.</span><span class="n">useNonbondedScheme</span><span class="p">(</span><span class="n">prot_nb</span><span class="p">,</span> <span class="n">typeA</span><span class="o">=</span><span class="n">t</span><span class="p">,</span> <span class="n">typeB</span><span class="o">=</span><span class="n">prot_t1</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="c1"># Restore previous interactions</span> + <span class="bp">self</span><span class="o">.</span><span class="n">nbSchemes</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">nbSchemes</span> <span class="o">+</span> <span class="n">old_interactions</span></div> + + +<div class="viewcode-block" id="ShapeCGModel.get_protein_types"> +<a class="viewcode-back" href="../../api/shape-based_models/shape_cg.html#arbdmodel.shape_cg.ShapeCGModel.get_protein_types">[docs]</a> + <span class="k">def</span><span class="w"> </span><span class="nf">get_protein_types</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">protein_counts</span><span class="p">,</span> <span class="n">num_CG_sites</span><span class="o">=</span><span class="kc">None</span><span class="p">):</span> +<span class="w"> </span><span class="sd">"""Get all protein types for the given protein counts.</span> +<span class="sd"> </span> +<span class="sd"> Args:</span> +<span class="sd"> protein_counts: Dictionary mapping protein names to counts</span> +<span class="sd"> num_CG_sites: Number of CG sites per protein</span> +<span class="sd"> </span> +<span class="sd"> Returns:</span> +<span class="sd"> List of all protein particle types</span> +<span class="sd"> """</span> + <span class="n">cache_key</span> <span class="o">=</span> <span class="p">(</span><span class="nb">tuple</span><span class="p">(</span><span class="nb">sorted</span><span class="p">(</span><span class="n">protein_counts</span><span class="o">.</span><span class="n">items</span><span class="p">())),</span> <span class="n">num_CG_sites</span><span class="p">)</span> + <span class="k">if</span> <span class="n">cache_key</span> <span class="ow">in</span> <span class="bp">self</span><span class="o">.</span><span class="n">protein_types_cache</span><span class="p">:</span> + <span class="k">return</span> <span class="bp">self</span><span class="o">.</span><span class="n">protein_types_cache</span><span class="p">[</span><span class="n">cache_key</span><span class="p">]</span> + + <span class="n">prot_types</span> <span class="o">=</span> <span class="p">[]</span> + <span class="k">for</span> <span class="n">k</span><span class="p">,</span> <span class="n">count</span> <span class="ow">in</span> <span class="n">protein_counts</span><span class="o">.</span><span class="n">items</span><span class="p">():</span> + <span class="k">if</span> <span class="n">count</span> <span class="o">==</span> <span class="mi">0</span> <span class="ow">or</span> <span class="n">k</span> <span class="ow">not</span> <span class="ow">in</span> <span class="bp">self</span><span class="o">.</span><span class="n">protein_factories</span><span class="p">:</span> + <span class="k">continue</span> + <span class="n">prot_types</span><span class="o">.</span><span class="n">extend</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">protein_factories</span><span class="p">[</span><span class="n">k</span><span class="p">]</span><span class="o">.</span><span class="n">get_coarse_types</span><span class="p">(</span><span class="n">num_CG_sites</span><span class="p">))</span> + + <span class="bp">self</span><span class="o">.</span><span class="n">protein_types_cache</span><span class="p">[</span><span class="n">cache_key</span><span class="p">]</span> <span class="o">=</span> <span class="n">prot_types</span> + <span class="k">return</span> <span class="n">prot_types</span></div> + + +<div class="viewcode-block" id="ShapeCGModel.add_proteins"> +<a class="viewcode-back" href="../../api/shape-based_models/shape_cg.html#arbdmodel.shape_cg.ShapeCGModel.add_proteins">[docs]</a> + <span class="k">def</span><span class="w"> </span><span class="nf">add_proteins</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">protein_counts</span><span class="p">,</span> <span class="n">protein_positions</span><span class="p">,</span> <span class="n">num_CG_sites</span><span class="o">=</span><span class="kc">None</span><span class="p">,</span> <span class="n">nt_sigma</span><span class="o">=</span><span class="mi">10</span><span class="p">):</span> +<span class="w"> </span><span class="sd">"""Add proteins to the simulation model.</span> +<span class="sd"> </span> +<span class="sd"> Args:</span> +<span class="sd"> protein_counts: Dictionary mapping protein names to counts</span> +<span class="sd"> protein_positions: List of positions for all proteins</span> +<span class="sd"> num_CG_sites: Number of CG sites per protein</span> +<span class="sd"> nt_sigma: Sigma parameter for nucleic acid interactions</span> +<span class="sd"> </span> +<span class="sd"> Returns:</span> +<span class="sd"> Group containing all added proteins</span> +<span class="sd"> """</span> + <span class="n">all_pro</span> <span class="o">=</span> <span class="p">[]</span> + <span class="n">start</span> <span class="o">=</span> <span class="mi">0</span> + + <span class="c1"># Create proteins and add them to the model</span> + <span class="k">for</span> <span class="n">k</span><span class="p">,</span> <span class="n">count</span> <span class="ow">in</span> <span class="n">protein_counts</span><span class="o">.</span><span class="n">items</span><span class="p">():</span> + <span class="k">if</span> <span class="n">count</span> <span class="o">==</span> <span class="mi">0</span> <span class="ow">or</span> <span class="n">k</span> <span class="ow">not</span> <span class="ow">in</span> <span class="bp">self</span><span class="o">.</span><span class="n">protein_factories</span><span class="p">:</span> + <span class="k">continue</span> + + <span class="n">pro_parts</span> <span class="o">=</span> <span class="p">[</span> + <span class="bp">self</span><span class="o">.</span><span class="n">protein_factories</span><span class="p">[</span><span class="n">k</span><span class="p">]</span><span class="o">.</span><span class="n">generate_protein</span><span class="p">(</span> + <span class="n">protein_positions</span><span class="p">[</span><span class="n">start</span> <span class="o">+</span> <span class="n">i</span><span class="p">],</span> + <span class="n">index</span><span class="o">=</span><span class="n">i</span><span class="p">,</span> + <span class="n">num_CG_sites</span><span class="o">=</span><span class="n">num_CG_sites</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">count</span><span class="p">)</span> + <span class="p">]</span> + + <span class="n">g</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="sa">f</span><span class="s1">'all_</span><span class="si">{</span><span class="n">k</span><span class="si">}</span><span class="s1">'</span><span class="p">,</span> <span class="n">children</span><span class="o">=</span><span class="n">pro_parts</span><span class="p">)</span> + <span class="n">all_pro</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="n">start</span> <span class="o">+=</span> <span class="n">count</span> + + <span class="c1"># Create a group containing all proteins</span> + <span class="n">protein_group</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">'cytosol'</span><span class="p">,</span> <span class="n">children</span><span class="o">=</span><span class="n">all_pro</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">protein_group</span><span class="p">)</span> + + <span class="c1"># Add nonbonded interactions</span> + <span class="n">prot_types</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">get_protein_types</span><span class="p">(</span><span class="n">protein_counts</span><span class="p">,</span> <span class="n">num_CG_sites</span><span class="p">)</span> + <span class="bp">self</span><span class="o">.</span><span class="n">add_protein_nb_interactions</span><span class="p">(</span><span class="n">prot_types</span><span class="p">,</span> <span class="n">nt_sigma</span><span class="o">=</span><span class="n">nt_sigma</span><span class="p">)</span> + + <span class="k">return</span> <span class="n">protein_group</span></div> + + +<div class="viewcode-block" id="ShapeCGModel.generate_random_protein_positions"> +<a class="viewcode-back" href="../../api/shape-based_models/shape_cg.html#arbdmodel.shape_cg.ShapeCGModel.generate_random_protein_positions">[docs]</a> + <span class="k">def</span><span class="w"> </span><span class="nf">generate_random_protein_positions</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">protein_counts</span><span class="p">,</span> <span class="n">radius</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="w"> </span><span class="sd">"""Generate random positions for proteins within a spherical volume.</span> +<span class="sd"> </span> +<span class="sd"> Args:</span> +<span class="sd"> protein_counts: Dictionary mapping protein names to counts</span> +<span class="sd"> radius: Radius of the sphere</span> +<span class="sd"> seed: Random seed (default: None)</span> +<span class="sd"> </span> +<span class="sd"> Returns:</span> +<span class="sd"> List of 3D positions</span> +<span class="sd"> """</span> + <span class="k">if</span> <span class="n">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">seed</span><span class="p">(</span><span class="n">seed</span><span class="p">)</span> + + <span class="n">total_proteins</span> <span class="o">=</span> <span class="nb">sum</span><span class="p">(</span><span class="n">protein_counts</span><span class="o">.</span><span class="n">values</span><span class="p">())</span> + + <span class="c1"># Generate random positions on a sphere with random radii</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">eye</span><span class="p">(</span><span class="mi">3</span><span class="p">)</span> + + <span class="n">angles</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">random</span><span class="p">((</span><span class="n">total_proteins</span><span class="p">,</span> <span class="mi">2</span><span class="p">))</span> + <span class="n">angles</span><span class="p">[:,</span> <span class="mi">0</span><span class="p">]</span> <span class="o">=</span> <span class="n">angles</span><span class="p">[:,</span> <span class="mi">0</span><span class="p">]</span> <span class="o">*</span> <span class="mi">360</span> <span class="c1"># Azimuthal angle</span> + <span class="n">angles</span><span class="p">[:,</span> <span class="mi">1</span><span class="p">]</span> <span class="o">=</span> <span class="n">np</span><span class="o">.</span><span class="n">arccos</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="n">angles</span><span class="p">[:,</span> <span class="mi">1</span><span class="p">])</span> <span class="o">*</span> <span class="mi">180</span><span class="o">/</span><span class="n">np</span><span class="o">.</span><span class="n">pi</span> <span class="c1"># Polar angle</span> + + <span class="c1"># Create rotation matrices</span> + <span class="n">pro_rots</span> <span class="o">=</span> <span class="p">[</span> + <span class="n">rotationAboutAxis</span><span class="p">(</span><span class="n">_z</span><span class="p">,</span> <span class="n">a0</span><span class="p">)</span><span class="o">.</span><span class="n">dot</span><span class="p">(</span><span class="n">rotationAboutAxis</span><span class="p">(</span><span class="n">_x</span><span class="p">,</span> <span class="n">a1</span><span class="p">))</span> + <span class="k">for</span> <span class="n">a0</span><span class="p">,</span> <span class="n">a1</span> <span class="ow">in</span> <span class="n">angles</span> + <span class="p">]</span> + + <span class="c1"># Generate radii with cubic distribution for uniform volume sampling</span> + <span class="n">radii</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">random</span><span class="p">((</span><span class="n">total_proteins</span><span class="p">,</span> <span class="mi">1</span><span class="p">))</span><span class="o">**</span><span class="p">(</span><span class="mi">1</span><span class="o">/</span><span class="mi">3</span><span class="p">)</span> <span class="o">*</span> <span class="n">radius</span> + + <span class="c1"># Final positions</span> + <span class="n">pro_centers</span> <span class="o">=</span> <span class="p">[</span><span class="n">R</span><span class="p">[:,</span> <span class="mi">2</span><span class="p">]</span> <span class="o">*</span> <span class="n">r</span> <span class="k">for</span> <span class="n">R</span><span class="p">,</span> <span class="n">r</span> <span class="ow">in</span> <span class="nb">zip</span><span class="p">(</span><span class="n">pro_rots</span><span class="p">,</span> <span class="n">radii</span><span class="p">)]</span> + + <span class="k">return</span> <span class="n">pro_centers</span></div> + + +<div class="viewcode-block" id="ShapeCGModel.setup_and_run"> +<a class="viewcode-back" href="../../api/shape-based_models/shape_cg.html#arbdmodel.shape_cg.ShapeCGModel.setup_and_run">[docs]</a> + <span class="k">def</span><span class="w"> </span><span class="nf">setup_and_run</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">protein_counts</span><span class="p">,</span> <span class="n">radius</span><span class="o">=</span><span class="mi">200</span><span class="p">,</span> <span class="n">num_CG_sites</span><span class="o">=</span><span class="kc">None</span><span class="p">,</span> + <span class="n">salt_concentration</span><span class="o">=</span><span class="mi">150</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">dry_run</span><span class="o">=</span><span class="kc">True</span><span class="p">,</span> + <span class="n">num_steps</span><span class="o">=</span><span class="mf">1e8</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="n">timestep</span><span class="o">=</span><span class="mf">200e-6</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">restart_file</span><span class="o">=</span><span class="kc">None</span><span class="p">):</span> +<span class="w"> </span><span class="sd">"""Set up and run a simulation with the specified parameters.</span> +<span class="sd"> </span> +<span class="sd"> Args:</span> +<span class="sd"> protein_counts: Dictionary mapping protein names to counts</span> +<span class="sd"> radius: Confinement radius</span> +<span class="sd"> num_CG_sites: Number of CG sites per protein</span> +<span class="sd"> salt_concentration: Salt concentration in mM</span> +<span class="sd"> gpu: GPU index to use</span> +<span class="sd"> dry_run: If True, don't actually run the simulation</span> +<span class="sd"> num_steps: Number of simulation steps</span> +<span class="sd"> output_period: Steps between outputs</span> +<span class="sd"> timestep: Simulation timestep</span> +<span class="sd"> positions: Optional pre-defined positions for proteins</span> +<span class="sd"> restart_file: Optional restart file path</span> +<span class="sd"> </span> +<span class="sd"> Returns:</span> +<span class="sd"> Final simulation state</span> +<span class="sd"> """</span> + <span class="c1"># Set up system parameters</span> + <span class="n">debye_length</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">concentration_to_debye_length</span><span class="p">(</span><span class="n">salt_concentration</span><span class="p">)</span> + + <span class="c1"># Get number of proteins</span> + <span class="n">total_proteins</span> <span class="o">=</span> <span class="nb">sum</span><span class="p">(</span><span class="n">protein_counts</span><span class="o">.</span><span class="n">values</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">"Setting up system with </span><span class="si">{</span><span class="n">total_proteins</span><span class="si">}</span><span class="s2"> proteins"</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="p">:</span> + <span class="n">positions</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">generate_random_protein_positions</span><span class="p">(</span><span class="n">protein_counts</span><span class="p">,</span> <span class="n">radius</span><span class="p">)</span> + + <span class="c1"># Set up simulation name and directory</span> + <span class="n">name</span> <span class="o">=</span> <span class="sa">f</span><span class="s1">'CG</span><span class="si">{</span><span class="n">num_CG_sites</span><span class="si">}</span><span class="s1">_r</span><span class="si">{</span><span class="n">radius</span><span class="si">}</span><span class="s1">_salt</span><span class="si">{</span><span class="n">salt_concentration</span><span class="si">}</span><span class="s1">'</span> + <span class="n">directory</span> <span class="o">=</span> <span class="sa">f</span><span class="s1">'run_</span><span class="si">{</span><span class="n">num_CG_sites</span><span class="si">}</span><span class="s1">'</span> + + <span class="c1"># Add proteins to model</span> + <span class="n">protein_group</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">add_proteins</span><span class="p">(</span> + <span class="n">protein_counts</span><span class="p">,</span> + <span class="n">positions</span><span class="p">,</span> + <span class="n">num_CG_sites</span><span class="o">=</span><span class="n">num_CG_sites</span> + <span class="p">)</span> + + <span class="c1"># Add confinement to protein particles</span> + <span class="bp">self</span><span class="o">.</span><span class="n">add_confinement</span><span class="p">(</span><span class="n">protein_group</span><span class="p">,</span> <span class="n">radius</span><span class="p">)</span> + + <span class="c1"># Run the simulation</span> + <span class="bp">self</span><span class="o">.</span><span class="n">simulate</span><span class="p">(</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">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">timestep</span><span class="o">=</span><span class="n">timestep</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">restart_file</span><span class="o">=</span><span class="n">restart_file</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="k">return</span> <span class="bp">self</span></div> + + +<div class="viewcode-block" id="ShapeCGModel.add_confinement"> +<a class="viewcode-back" href="../../api/shape-based_models/shape_cg.html#arbdmodel.shape_cg.ShapeCGModel.add_confinement">[docs]</a> + <span class="k">def</span><span class="w"> </span><span class="nf">add_confinement</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">protein_group</span><span class="p">,</span> <span class="n">radius</span><span class="p">):</span> +<span class="w"> </span><span class="sd">"""Add spherical confinement to all protein particles.</span> +<span class="sd"> </span> +<span class="sd"> Args:</span> +<span class="sd"> protein_group: Group containing proteins</span> +<span class="sd"> radius: Confinement radius</span> +<span class="sd"> """</span> + <span class="c1"># Make sure the confinement file exists</span> + <span class="n">confinement_file</span> <span class="o">=</span> <span class="sa">f</span><span class="s1">'../confine-</span><span class="si">{</span><span class="n">radius</span><span class="si">}</span><span class="s1">.dx'</span> + <span class="k">if</span> <span class="ow">not</span> <span class="n">Path</span><span class="p">(</span><span class="n">confinement_file</span><span class="p">)</span><span class="o">.</span><span class="n">exists</span><span class="p">():</span> + <span class="c1"># Create confinement file</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">write_confine_dx</span> + <span class="n">write_confine_dx</span><span class="p">(</span><span class="n">radius</span><span class="o">=</span><span class="n">radius</span><span class="p">)</span> + + <span class="c1"># Add confinement to all protein particles</span> + <span class="k">for</span> <span class="n">t</span> <span class="ow">in</span> <span class="nb">set</span><span class="p">([</span><span class="n">p</span><span class="o">.</span><span class="n">type_</span> <span class="k">for</span> <span class="n">p</span> <span class="ow">in</span> <span class="n">protein_group</span><span class="p">]):</span> + <span class="n">t</span><span class="o">.</span><span class="n">grid</span> <span class="o">=</span> <span class="p">[(</span><span class="n">confinement_file</span><span class="p">,</span> <span class="mi">1</span><span class="p">)]</span> + + <span class="c1"># Add confinement to all nonbonded scheme particle types</span> + <span class="k">for</span> <span class="n">s</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="bp">self</span><span class="o">.</span><span class="n">nbSchemes</span><span class="p">:</span> + <span class="k">for</span> <span class="n">t</span> <span class="ow">in</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">t</span><span class="o">.</span><span class="n">grid</span> <span class="o">=</span> <span class="p">[(</span><span class="n">confinement_file</span><span class="p">,</span> <span class="mi">1</span><span class="p">)]</span></div> + + +<div class="viewcode-block" id="ShapeCGModel.run_minimization"> +<a class="viewcode-back" href="../../api/shape-based_models/shape_cg.html#arbdmodel.shape_cg.ShapeCGModel.run_minimization">[docs]</a> + <span class="k">def</span><span class="w"> </span><span class="nf">run_minimization</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">protein_counts</span><span class="p">,</span> <span class="n">radius</span><span class="o">=</span><span class="mi">200</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">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">1e4</span><span class="p">,</span> <span class="n">timestep</span><span class="o">=</span><span class="mf">200e-6</span><span class="p">,</span> + <span class="n">directory</span><span class="o">=</span><span class="s1">'run_1'</span><span class="p">):</span> +<span class="w"> </span><span class="sd">"""Run a minimization simulation with minimal CG sites.</span> +<span class="sd"> </span> +<span class="sd"> Args:</span> +<span class="sd"> protein_counts: Dictionary mapping protein names to counts</span> +<span class="sd"> radius: Confinement radius</span> +<span class="sd"> gpu: GPU index to use</span> +<span class="sd"> num_steps: Number of minimization steps</span> +<span class="sd"> output_period: Steps between outputs</span> +<span class="sd"> timestep: Simulation timestep</span> +<span class="sd"> directory: Output directory</span> +<span class="sd"> </span> +<span class="sd"> Returns:</span> +<span class="sd"> Path to restart file</span> +<span class="sd"> """</span> + <span class="c1"># Generate random positions</span> + <span class="n">positions</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">generate_random_protein_positions</span><span class="p">(</span><span class="n">protein_counts</span><span class="p">,</span> <span class="n">radius</span><span class="p">)</span> + + <span class="c1"># Create model with only 1 CG site per protein for quick minimization</span> + <span class="n">protein_group</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">add_proteins</span><span class="p">(</span> + <span class="n">protein_counts</span><span class="p">,</span> + <span class="n">positions</span><span class="p">,</span> + <span class="n">num_CG_sites</span><span class="o">=</span><span class="mi">1</span> + <span class="p">)</span> + + <span class="c1"># Add confinement with stronger parameters for minimization</span> + <span class="k">for</span> <span class="n">t</span> <span class="ow">in</span> <span class="nb">set</span><span class="p">([</span><span class="n">p</span><span class="o">.</span><span class="n">type_</span> <span class="k">for</span> <span class="n">p</span> <span class="ow">in</span> <span class="n">protein_group</span><span class="p">]):</span> + <span class="n">t</span><span class="o">.</span><span class="n">modified</span> <span class="o">=</span> <span class="kc">True</span> + <span class="n">t</span><span class="o">.</span><span class="n">sigma</span> <span class="o">=</span> <span class="mi">2</span> <span class="o">*</span> <span class="n">t</span><span class="o">.</span><span class="n">sigma</span> + <span class="n">t</span><span class="o">.</span><span class="n">grid</span> <span class="o">=</span> <span class="p">[(</span><span class="sa">f</span><span class="s1">'../confine-</span><span class="si">{</span><span class="n">radius</span><span class="si">}</span><span class="s1">.dx'</span><span class="p">,</span> <span class="mi">1</span><span class="p">)]</span> + + <span class="k">for</span> <span class="n">s</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="bp">self</span><span class="o">.</span><span class="n">nbSchemes</span><span class="p">:</span> + <span class="k">for</span> <span class="n">t</span> <span class="ow">in</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">try</span><span class="p">:</span> + <span class="n">t</span><span class="o">.</span><span class="n">modified</span> + <span class="k">except</span> <span class="ne">AttributeError</span><span class="p">:</span> + <span class="n">t</span><span class="o">.</span><span class="n">modified</span> <span class="o">=</span> <span class="kc">True</span> + <span class="n">t</span><span class="o">.</span><span class="n">sigma</span> <span class="o">=</span> <span class="mi">2</span> <span class="o">*</span> <span class="n">t</span><span class="o">.</span><span class="n">sigma</span> + <span class="n">t</span><span class="o">.</span><span class="n">grid</span> <span class="o">=</span> <span class="p">[(</span><span class="sa">f</span><span class="s1">'../confine-</span><span class="si">{</span><span class="n">radius</span><span class="si">}</span><span class="s1">.dx'</span><span class="p">,</span> <span class="mi">1</span><span class="p">)]</span> + + <span class="c1"># Run minimization</span> + <span class="n">minimization_name</span> <span class="o">=</span> <span class="sa">f</span><span class="s1">'min_</span><span class="si">{</span><span class="n">radius</span><span class="si">}</span><span class="s1">'</span> + <span class="bp">self</span><span class="o">.</span><span class="n">simulate</span><span class="p">(</span> + <span class="n">minimization_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">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">timestep</span><span class="o">=</span><span class="n">timestep</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">dry_run</span><span class="o">=</span><span class="kc">False</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="n">directory</span><span class="si">}</span><span class="s1">/output/</span><span class="si">{</span><span class="n">minimization_name</span><span class="si">}</span><span class="s1">.restart'</span></div> + + +<div class="viewcode-block" id="ShapeCGModel.run_from_minimized"> +<a class="viewcode-back" href="../../api/shape-based_models/shape_cg.html#arbdmodel.shape_cg.ShapeCGModel.run_from_minimized">[docs]</a> + <span class="k">def</span><span class="w"> </span><span class="nf">run_from_minimized</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">protein_counts</span><span class="p">,</span> <span class="n">radius</span><span class="o">=</span><span class="mi">200</span><span class="p">,</span> <span class="n">num_CG_sites</span><span class="o">=</span><span class="kc">None</span><span class="p">,</span> + <span class="n">salt_concentration</span><span class="o">=</span><span class="mi">150</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">dry_run</span><span class="o">=</span><span class="kc">True</span><span class="p">,</span> + <span class="n">num_steps</span><span class="o">=</span><span class="mf">1e8</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="n">timestep</span><span class="o">=</span><span class="mf">200e-6</span><span class="p">,</span> + <span class="n">minimization_file</span><span class="o">=</span><span class="kc">None</span><span class="p">):</span> +<span class="w"> </span><span class="sd">"""Run a full simulation starting from a minimized configuration.</span> +<span class="sd"> </span> +<span class="sd"> Args:</span> +<span class="sd"> protein_counts: Dictionary mapping protein names to counts</span> +<span class="sd"> radius: Confinement radius</span> +<span class="sd"> num_CG_sites: Number of CG sites per protein</span> +<span class="sd"> salt_concentration: Salt concentration in mM</span> +<span class="sd"> gpu: GPU index to use</span> +<span class="sd"> dry_run: If True, don't actually run the simulation</span> +<span class="sd"> num_steps: Number of simulation steps</span> +<span class="sd"> output_period: Steps between outputs</span> +<span class="sd"> timestep: Simulation timestep</span> +<span class="sd"> minimization_file: Path to minimization restart file</span> +<span class="sd"> </span> +<span class="sd"> Returns:</span> +<span class="sd"> Final simulation state</span> +<span class="sd"> """</span> + <span class="c1"># Check for restart file or run minimization</span> + <span class="k">if</span> <span class="n">minimization_file</span> <span class="ow">is</span> <span class="kc">None</span> <span class="ow">or</span> <span class="ow">not</span> <span class="n">Path</span><span class="p">(</span><span class="n">minimization_file</span><span class="p">)</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">info</span><span class="p">(</span><span class="s2">"No minimization file found, running minimization first"</span><span class="p">)</span> + <span class="n">minimization_file</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">run_minimization</span><span class="p">(</span><span class="n">protein_counts</span><span class="p">,</span> <span class="n">radius</span><span class="p">,</span> <span class="n">gpu</span><span class="p">)</span> + + <span class="c1"># Clear the model and restart</span> + <span class="bp">self</span><span class="o">.</span><span class="n">clear_all</span><span class="p">()</span> + + <span class="c1"># Read coordinates from restart file</span> + <span class="n">new_protein_coords</span> <span class="o">=</span> <span class="n">read_arbd_coordinates</span><span class="p">(</span><span class="n">minimization_file</span><span class="p">)[</span><span class="nb">len</span><span class="p">(</span><span class="bp">self</span><span class="p">):]</span> + + <span class="c1"># Set up simulation name and directory</span> + <span class="n">name</span> <span class="o">=</span> <span class="sa">f</span><span class="s1">'CG</span><span class="si">{</span><span class="n">num_CG_sites</span><span class="si">}</span><span class="s1">_r</span><span class="si">{</span><span class="n">radius</span><span class="si">}</span><span class="s1">_salt</span><span class="si">{</span><span class="n">salt_concentration</span><span class="si">}</span><span class="s1">'</span> + <span class="n">directory</span> <span class="o">=</span> <span class="sa">f</span><span class="s1">'run_</span><span class="si">{</span><span class="n">num_CG_sites</span><span class="si">}</span><span class="s1">'</span> + + <span class="c1"># Add proteins with proper CG resolution</span> + <span class="n">protein_group</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">add_proteins</span><span class="p">(</span> + <span class="n">protein_counts</span><span class="p">,</span> + <span class="n">new_protein_coords</span><span class="p">,</span> + <span class="n">num_CG_sites</span><span class="o">=</span><span class="n">num_CG_sites</span> + <span class="p">)</span> + + <span class="c1"># Add confinement to protein particles</span> + <span class="bp">self</span><span class="o">.</span><span class="n">add_confinement</span><span class="p">(</span><span class="n">protein_group</span><span class="p">,</span> <span class="n">radius</span><span class="p">)</span> + + <span class="c1"># Run the simulation</span> + <span class="bp">self</span><span class="o">.</span><span class="n">simulate</span><span class="p">(</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">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">timestep</span><span class="o">=</span><span class="n">timestep</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">dry_run</span><span class="o">=</span><span class="n">dry_run</span> + <span class="p">)</span> + + <span class="k">return</span> <span class="bp">self</span></div> + + +<div class="viewcode-block" id="ShapeCGModel.from_protein_list"> +<a class="viewcode-back" href="../../api/shape-based_models/shape_cg.html#arbdmodel.shape_cg.ShapeCGModel.from_protein_list">[docs]</a> + <span class="nd">@classmethod</span> + <span class="k">def</span><span class="w"> </span><span class="nf">from_protein_list</span><span class="p">(</span><span class="bp">cls</span><span class="p">,</span> <span class="n">pdb_list</span><span class="p">,</span> <span class="n">pdb_paths</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">"""Create a model from a list of protein PDB IDs.</span> +<span class="sd"> </span> +<span class="sd"> Args:</span> +<span class="sd"> pdb_list: List of protein PDB IDs</span> +<span class="sd"> pdb_paths: Optional dictionary mapping PDB IDs to PSF/PDB file paths</span> +<span class="sd"> **kwargs: Additional arguments for the ShapeCGModel constructor</span> +<span class="sd"> </span> +<span class="sd"> Returns:</span> +<span class="sd"> ShapeCGModel instance</span> +<span class="sd"> """</span> + <span class="c1"># Create short names for proteins</span> + <span class="n">pdb_name</span> <span class="o">=</span> <span class="p">{</span><span class="n">k</span><span class="p">:</span> <span class="n">k</span><span class="p">[</span><span class="mi">0</span><span class="p">]</span> <span class="o">+</span> <span class="n">k</span><span class="p">[</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="n">pdb_list</span><span class="p">}</span> + + <span class="c1"># Create factory objects for each protein</span> + <span class="n">protein_factories</span> <span class="o">=</span> <span class="p">{}</span> + <span class="k">for</span> <span class="n">k</span> <span class="ow">in</span> <span class="n">pdb_list</span><span class="p">:</span> + <span class="k">if</span> <span class="n">pdb_paths</span> <span class="ow">and</span> <span class="n">k</span> <span class="ow">in</span> <span class="n">pdb_paths</span><span class="p">:</span> + <span class="n">psf</span> <span class="o">=</span> <span class="n">pdb_paths</span><span class="p">[</span><span class="n">k</span><span class="p">][</span><span class="s1">'psf'</span><span class="p">]</span> + <span class="n">pdb</span> <span class="o">=</span> <span class="n">pdb_paths</span><span class="p">[</span><span class="n">k</span><span class="p">][</span><span class="s1">'pdb'</span><span class="p">]</span> + <span class="k">else</span><span class="p">:</span> + <span class="n">psf</span> <span class="o">=</span> <span class="sa">f</span><span class="s1">'</span><span class="si">{</span><span class="n">k</span><span class="si">}</span><span class="s1">_autopsf.psf'</span> + <span class="n">pdb</span> <span class="o">=</span> <span class="sa">f</span><span class="s1">'</span><span class="si">{</span><span class="n">k</span><span class="si">}</span><span class="s1">_autopsf.pdb'</span> + + <span class="n">protein_factories</span><span class="p">[</span><span class="n">k</span><span class="p">]</span> <span class="o">=</span> <span class="n">ShapeCGFactory</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">name</span><span class="o">=</span><span class="n">pdb_name</span><span class="p">[</span><span class="n">k</span><span class="p">])</span> + + <span class="k">return</span> <span class="bp">cls</span><span class="p">(</span><span class="n">protein_factories</span><span class="o">=</span><span class="n">protein_factories</span><span class="p">,</span> <span class="o">**</span><span class="n">kwargs</span><span class="p">)</span></div> + + +<div class="viewcode-block" id="ShapeCGModel.calculate_total_mass"> +<a class="viewcode-back" href="../../api/shape-based_models/shape_cg.html#arbdmodel.shape_cg.ShapeCGModel.calculate_total_mass">[docs]</a> + <span class="k">def</span><span class="w"> </span><span class="nf">calculate_total_mass</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">protein_counts</span><span class="p">):</span> +<span class="w"> </span><span class="sd">"""Calculate total mass of proteins.</span> +<span class="sd"> </span> +<span class="sd"> Args:</span> +<span class="sd"> protein_counts: Dictionary mapping protein names to counts</span> +<span class="sd"> </span> +<span class="sd"> Returns:</span> +<span class="sd"> Total mass in daltons</span> +<span class="sd"> """</span> + <span class="k">return</span> <span class="nb">sum</span><span class="p">([</span> + <span class="bp">self</span><span class="o">.</span><span class="n">protein_factories</span><span class="p">[</span><span class="n">k</span><span class="p">]</span><span class="o">.</span><span class="n">_fine_total_mass</span> <span class="o">*</span> <span class="n">count</span> + <span class="k">for</span> <span class="n">k</span><span class="p">,</span> <span class="n">count</span> <span class="ow">in</span> <span class="n">protein_counts</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">in</span> <span class="bp">self</span><span class="o">.</span><span class="n">protein_factories</span> + <span class="p">])</span></div> +</div> + </pre></div> </article> diff --git a/_build/html/_modules/arbdmodel/sim_config.html b/_build/html/_modules/arbdmodel/sim_config.html index e50e874066de46702bc959e929a04e924a4d44b3..a562b7d55d112ba6ed232af30ae12c691d45b556 100644 --- a/_build/html/_modules/arbdmodel/sim_config.html +++ b/_build/html/_modules/arbdmodel/sim_config.html @@ -31,19 +31,19 @@ <link rel="stylesheet" type="text/css" 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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/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?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 src="../../_static/js/hoverxref.js"></script> + <script src="../../_static/js/tooltipster.bundle.min.js"></script> + <script src="../../_static/js/micromodal.min.js"></script> <script>let toggleHintShow = 'Click to show';</script> <script>let toggleHintHide = 'Click to hide';</script> <script>let toggleOpenOnPrint = 'true';</script> @@ -325,7 +325,40 @@ document.write(` <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="w"> </span><span class="sd">"""</span> +<span class="sd"> Class describing properties for a simulation (ARBD or NAMD).</span> +<span class="sd"> This class stores various simulation parameters, manages binary paths, and provides</span> +<span class="sd"> methods to combine simulation configurations.</span> + +<span class="sd"> Attributes:</span> +<span class="sd"> num_steps (int): Total number of simulation steps.</span> +<span class="sd"> output_period (int): Frequency of output generation.</span> +<span class="sd"> integrator (str): Type of integrator used (e.g., 'MD', 'BD').</span> +<span class="sd"> timestep (float): Simulation time step.</span> +<span class="sd"> thermostat (str): Type of thermostat used.</span> +<span class="sd"> barostat (str): Type of barostat used.</span> +<span class="sd"> temperature (float): Simulation temperature (must be positive).</span> +<span class="sd"> pressure (float): Simulation pressure.</span> +<span class="sd"> cutoff (float): Cutoff distance for interactions.</span> +<span class="sd"> pairlist_distance (float): Distance for generating pair lists.</span> +<span class="sd"> decomp_period (int): Period for decomposition.</span> +<span class="sd"> gpu (bool): Whether to use GPU acceleration.</span> +<span class="sd"> seed (int): Random seed for reproducibility.</span> +<span class="sd"> restart_file (str): Path to restart file.</span> +<span class="sd"> # ARBD-specific parameters</span> +<span class="sd"> rigid_body_integrator (str): Type of rigid body integrator.</span> +<span class="sd"> rigid_body_grid_grid_period (int): Period for rigid body grid updates.</span> +<span class="sd"> # SimpleARBD parameters</span> +<span class="sd"> viscosity (float): Solvent viscosity.</span> +<span class="sd"> solvent_density (float): Solvent density.</span> +<span class="sd"> num_heavy_cluster (int): Number of heavy clusters.</span> + +<span class="sd"> Methods:</span> +<span class="sd"> get_binary(name): Get the path to a specific binary.</span> +<span class="sd"> set_binary(name, path): Set the path to a specific binary.</span> +<span class="sd"> combine(other, policy='override', warn=False): Combine two SimConf objects.</span> +<span class="sd"> items(): Iterate over attribute name-value pairs.</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">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> @@ -475,8 +508,76 @@ document.write(` <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="w"> </span><span class="sd">"""</span> +<span class="sd"> Generic class describing properties for a simulation with default binary paths.</span> +<span class="sd"> This class extends SimConf to provide default binary paths and configuration parameters</span> +<span class="sd"> for molecular dynamics simulations using ARBD.</span> + +<span class="sd"> Parameters</span> +<span class="sd"> ----------</span> +<span class="sd"> num_steps : float, optional</span> +<span class="sd"> Number of simulation steps to run, default 1e5.</span> +<span class="sd"> output_period : float, optional</span> +<span class="sd"> Period for output generation, default 1e3.</span> +<span class="sd"> integrator : str, optional</span> +<span class="sd"> Integration method, default 'MD'.</span> +<span class="sd"> timestep : float, optional</span> +<span class="sd"> Simulation timestep in time units, default 20e-6.</span> +<span class="sd"> thermostat : str, optional</span> +<span class="sd"> Thermostat type, default 'Langevin'.</span> +<span class="sd"> barostat : str or None, optional</span> +<span class="sd"> Barostat type if any, default None.</span> +<span class="sd"> temperature : float, optional</span> +<span class="sd"> Simulation temperature in K, default 295.</span> +<span class="sd"> pressure : float, optional</span> +<span class="sd"> Pressure value for barostat if used, default 1.</span> +<span class="sd"> cutoff : float, optional</span> +<span class="sd"> Interaction cutoff distance, default 50.</span> +<span class="sd"> pairlist_distance : float or None, optional</span> +<span class="sd"> Pairlist buffer distance, default None.</span> +<span class="sd"> decomp_period : int, optional</span> +<span class="sd"> Period for domain decomposition updates, default 40.</span> +<span class="sd"> seed : int or None, optional</span> +<span class="sd"> Random seed for simulation, default None (random).</span> +<span class="sd"> restart_file : str or None, optional</span> +<span class="sd"> Path to restart file if continuing a simulation, default None.</span> +<span class="sd"> gpu : int, optional</span> +<span class="sd"> GPU device index to use, default 0.</span> +<span class="sd"> viscosity : float, optional</span> +<span class="sd"> Solvent viscosity, default 0.01.</span> +<span class="sd"> solvent_density : float, optional</span> +<span class="sd"> Density of the solvent, default 1.0.</span> +<span class="sd"> num_heavy_cluster : int, optional</span> +<span class="sd"> Number of heavy atoms per cluster, default 3.</span> +<span class="sd"> **kwargs</span> +<span class="sd"> Additional keyword arguments to pass to SimConf.</span> + +<span class="sd"> Attributes</span> +<span class="sd"> ----------</span> +<span class="sd"> num_steps : float</span> +<span class="sd"> Number of simulation steps.</span> +<span class="sd"> output_period : float</span> +<span class="sd"> Period for output generation.</span> +<span class="sd"> pressure : float</span> +<span class="sd"> Pressure value for barostat if used.</span> +<span class="sd"> viscosity : float</span> +<span class="sd"> Solvent viscosity.</span> +<span class="sd"> solvent_density : float</span> +<span class="sd"> Density of the solvent.</span> +<span class="sd"> num_heavy_cluster : int</span> +<span class="sd"> Number of heavy atoms per cluster.</span> + +<span class="sd"> Properties</span> +<span class="sd"> ----------</span> +<span class="sd"> temperature : float</span> +<span class="sd"> Simulation temperature with validation (must be positive).</span> +<span class="sd"> </span> +<span class="sd"> Notes</span> +<span class="sd"> -----</span> +<span class="sd"> The class automatically searches for binary dependencies like 'arbd', 'hydropro', 'apbs',</span> +<span class="sd"> 'vmd', and 'namd', and adds their paths to the configuration if found.</span> +<span class="sd"> Essential binaries (currently only 'arbd') will generate warnings if not found.</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">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> diff --git a/_build/html/_modules/arbdmodel/simplearbd.html b/_build/html/_modules/arbdmodel/simplearbd.html index 31a90d2da1ac7196b851cfeb968d620a8326a3d0..9f4a54fd97db07d9ac71a4240925b1abd14f9a4f 100644 --- a/_build/html/_modules/arbdmodel/simplearbd.html +++ b/_build/html/_modules/arbdmodel/simplearbd.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?v=be8a1c11" /> + <link rel="stylesheet" type="text/css" href="../../_static/mystnb.4510f1fc1dee50b3e5859aac5469c37c29e427902b24a333a5f9fcb2f0b3ac41.css" /> <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?v=b4b7a797" /> + <link rel="stylesheet" type="text/css" href="../../_static/proof.css" /> <link 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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/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?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 src="../../_static/js/hoverxref.js"></script> + <script src="../../_static/js/tooltipster.bundle.min.js"></script> + <script src="../../_static/js/micromodal.min.js"></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/_modules/arbdmodel/ssdna_two_bead.html b/_build/html/_modules/arbdmodel/ssdna_two_bead.html index 661adc4d53561713c1bd40d73cb3ee46fa42db9d..cfa16d151bae50c27b252fdf50da2f109d059d65 100644 --- a/_build/html/_modules/arbdmodel/ssdna_two_bead.html +++ b/_build/html/_modules/arbdmodel/ssdna_two_bead.html @@ -305,7 +305,8 @@ document.write(` <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">logger</span><span class="p">,</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="p">,</span> <span class="n">get_resource_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="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">.polymer</span><span class="w"> </span><span class="kn">import</span> <span class="n">PolymerBeads</span><span class="p">,</span> <span class="n">PolymerModel</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">TabulatedNonbonded</span><span class="p">,</span> <span class="n">HarmonicBond</span><span class="p">,</span> <span class="n">HarmonicAngle</span><span class="p">,</span> <span class="n">HarmonicDihedral</span> diff --git a/_build/html/_modules/arbdmodel/structure_from_pdb.html b/_build/html/_modules/arbdmodel/structure_from_pdb.html index 998109a9408d57b05874fc72cff8755c11afcecc..67d0e2619bb0e1ea2cc94cb244cd0a4190185005 100644 --- a/_build/html/_modules/arbdmodel/structure_from_pdb.html +++ b/_build/html/_modules/arbdmodel/structure_from_pdb.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?v=be8a1c11" /> + <link rel="stylesheet" type="text/css" href="../../_static/mystnb.4510f1fc1dee50b3e5859aac5469c37c29e427902b24a333a5f9fcb2f0b3ac41.css" /> <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?v=b4b7a797" /> + <link rel="stylesheet" type="text/css" href="../../_static/proof.css" /> <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?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/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/sphinx-design.min.css?v=95c83b7e" /> <!-- Pre-loaded scripts that we'll load fully later --> @@ 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--- a/_build/html/_modules/arbdmodel/structure_rigidbody.html +++ b/_build/html/_modules/arbdmodel/structure_rigidbody.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?v=be8a1c11" /> + <link rel="stylesheet" type="text/css" href="../../_static/mystnb.4510f1fc1dee50b3e5859aac5469c37c29e427902b24a333a5f9fcb2f0b3ac41.css" /> <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?v=b4b7a797" /> + <link rel="stylesheet" type="text/css" href="../../_static/proof.css" /> <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?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/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/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?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 src="../../_static/js/hoverxref.js"></script> + <script src="../../_static/js/tooltipster.bundle.min.js"></script> + <script src="../../_static/js/micromodal.min.js"></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/_modules/arbdmodel/version.html b/_build/html/_modules/arbdmodel/version.html index e87dea33bbe85522cb588230fed95f45601dd613..907b1dbc326d68d538b7670c3306b154b5462b94 100644 --- a/_build/html/_modules/arbdmodel/version.html +++ b/_build/html/_modules/arbdmodel/version.html @@ -334,13 +334,10 @@ document.write(` <span class="c1">#</span> <span class="c1"># include RELEASE-VERSION</span> -<span class="n">__all__</span> <span class="o">=</span> <span class="p">(</span><span class="s2">"get_version"</span><span class="p">)</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">subprocess</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">Popen</span><span class="p">,</span> <span class="n">PIPE</span> - -<span class="n">_version_file</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="s2">"RELEASE-VERSION"</span> +<span class="c1">## Import packages</span> +<span class="kn">import</span><span class="w"> </span><span class="nn">os</span><span class="o">,</span><span class="nn">subprocess</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">Popen</span><span class="p">,</span> <span class="n">PIPE</span> <span class="c1"># , STDOUT</span> <div class="viewcode-block" id="check_git_repository"> diff --git a/_build/html/_modules/index.html b/_build/html/_modules/index.html index 7add2515093501a5b898d78308f2df16cb5bf2c5..35d2dac22ebaca5c8a359c97dd1cfd17758c3dfd 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?v=be8a1c11" /> + <link rel="stylesheet" type="text/css" href="../_static/mystnb.4510f1fc1dee50b3e5859aac5469c37c29e427902b24a333a5f9fcb2f0b3ac41.css" /> <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?v=b4b7a797" /> + <link rel="stylesheet" type="text/css" href="../_static/proof.css" /> <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?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/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/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?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 src="../_static/js/hoverxref.js"></script> + <script src="../_static/js/tooltipster.bundle.min.js"></script> + <script src="../_static/js/micromodal.min.js"></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/core_objects.html b/_build/html/api/core/core_objects.html index a2dc8819608b9db333e6b3482012074421e88ee0..df28e9fdd3c55e4eb932b0465153f8c59de6bdcc 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?v=be8a1c11" /> + <link rel="stylesheet" type="text/css" href="../../_static/mystnb.4510f1fc1dee50b3e5859aac5469c37c29e427902b24a333a5f9fcb2f0b3ac41.css" /> <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?v=b4b7a797" /> + <link rel="stylesheet" type="text/css" href="../../_static/proof.css" /> <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?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/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/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?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 src="../../_static/js/hoverxref.js"></script> + <script src="../../_static/js/tooltipster.bundle.min.js"></script> + <script src="../../_static/js/micromodal.min.js"></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/index.html b/_build/html/api/core/index.html index 0c02e018ec07b3478c350ebea9df9ced8ec1dcc5..5b3d6093b26f8334221e9702617a68220868b2e6 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?v=be8a1c11" /> + <link rel="stylesheet" type="text/css" href="../../_static/mystnb.4510f1fc1dee50b3e5859aac5469c37c29e427902b24a333a5f9fcb2f0b3ac41.css" /> <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?v=b4b7a797" /> + <link rel="stylesheet" type="text/css" href="../../_static/proof.css" /> <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?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/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/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?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 src="../../_static/js/hoverxref.js"></script> + <script src="../../_static/js/tooltipster.bundle.min.js"></script> + <script src="../../_static/js/micromodal.min.js"></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 39446e2634e455ff61ca937533d114ef03b53d63..91deefdfd700a4541dd935ded4340d9a65165099 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?v=be8a1c11" /> + <link rel="stylesheet" type="text/css" href="../../_static/mystnb.4510f1fc1dee50b3e5859aac5469c37c29e427902b24a333a5f9fcb2f0b3ac41.css" /> <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?v=b4b7a797" /> + <link rel="stylesheet" type="text/css" href="../../_static/proof.css" /> <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?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/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/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?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 src="../../_static/js/hoverxref.js"></script> + <script src="../../_static/js/tooltipster.bundle.min.js"></script> + <script src="../../_static/js/micromodal.min.js"></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/sim_config.html b/_build/html/api/core/sim_config.html index 744c946af50de4b8f313e12ef1cc401099bff1f7..51426d5b0f009390eb4c52c571dd70719acbe3c9 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" /> <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 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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/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?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 src="../../_static/js/hoverxref.js"></script> + <script src="../../_static/js/tooltipster.bundle.min.js"></script> + <script src="../../_static/js/micromodal.min.js"></script> <script>let toggleHintShow = 'Click to show';</script> <script>let toggleHintHide = 'Click to hide';</script> <script>let toggleOpenOnPrint = 'true';</script> @@ -347,15 +347,46 @@ document.write(` <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.num_steps"><code class="docutils literal notranslate"><span class="pre">DefaultSimConf.num_steps</span></code></a></li> +<li class="toc-h3 nav-item toc-entry"><a class="reference internal nav-link" href="#arbdmodel.sim_config.DefaultSimConf.output_period"><code class="docutils literal notranslate"><span class="pre">DefaultSimConf.output_period</span></code></a></li> +<li class="toc-h3 nav-item toc-entry"><a class="reference internal nav-link" href="#arbdmodel.sim_config.DefaultSimConf.pressure"><code class="docutils literal notranslate"><span class="pre">DefaultSimConf.pressure</span></code></a></li> +<li class="toc-h3 nav-item toc-entry"><a class="reference internal nav-link" href="#arbdmodel.sim_config.DefaultSimConf.viscosity"><code class="docutils literal notranslate"><span class="pre">DefaultSimConf.viscosity</span></code></a></li> +<li class="toc-h3 nav-item toc-entry"><a class="reference internal nav-link" href="#arbdmodel.sim_config.DefaultSimConf.solvent_density"><code class="docutils literal notranslate"><span class="pre">DefaultSimConf.solvent_density</span></code></a></li> +<li class="toc-h3 nav-item toc-entry"><a class="reference internal nav-link" href="#arbdmodel.sim_config.DefaultSimConf.num_heavy_cluster"><code class="docutils literal notranslate"><span class="pre">DefaultSimConf.num_heavy_cluster</span></code></a></li> +<li class="toc-h3 nav-item toc-entry"><a class="reference internal nav-link" href="#arbdmodel.sim_config.DefaultSimConf.Properties"><code class="docutils literal notranslate"><span class="pre">DefaultSimConf.Properties</span></code></a></li> <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> +<li class="toc-h3 nav-item toc-entry"><a class="reference internal nav-link" href="#id0"><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.num_steps"><code class="docutils literal notranslate"><span class="pre">SimConf.num_steps</span></code></a></li> +<li class="toc-h3 nav-item toc-entry"><a class="reference internal nav-link" href="#arbdmodel.sim_config.SimConf.output_period"><code class="docutils literal notranslate"><span class="pre">SimConf.output_period</span></code></a></li> +<li class="toc-h3 nav-item toc-entry"><a class="reference internal nav-link" href="#arbdmodel.sim_config.SimConf.integrator"><code class="docutils literal notranslate"><span class="pre">SimConf.integrator</span></code></a></li> +<li class="toc-h3 nav-item toc-entry"><a class="reference internal nav-link" href="#arbdmodel.sim_config.SimConf.timestep"><code class="docutils literal notranslate"><span class="pre">SimConf.timestep</span></code></a></li> +<li class="toc-h3 nav-item toc-entry"><a class="reference internal nav-link" href="#arbdmodel.sim_config.SimConf.thermostat"><code class="docutils literal notranslate"><span class="pre">SimConf.thermostat</span></code></a></li> +<li class="toc-h3 nav-item toc-entry"><a class="reference internal nav-link" href="#arbdmodel.sim_config.SimConf.barostat"><code class="docutils literal notranslate"><span class="pre">SimConf.barostat</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> +<li class="toc-h3 nav-item toc-entry"><a class="reference internal nav-link" href="#arbdmodel.sim_config.SimConf.pressure"><code class="docutils literal notranslate"><span class="pre">SimConf.pressure</span></code></a></li> +<li class="toc-h3 nav-item toc-entry"><a class="reference internal nav-link" href="#arbdmodel.sim_config.SimConf.cutoff"><code class="docutils literal notranslate"><span class="pre">SimConf.cutoff</span></code></a></li> +<li class="toc-h3 nav-item toc-entry"><a class="reference internal nav-link" href="#arbdmodel.sim_config.SimConf.pairlist_distance"><code class="docutils literal notranslate"><span class="pre">SimConf.pairlist_distance</span></code></a></li> +<li class="toc-h3 nav-item toc-entry"><a class="reference internal nav-link" href="#arbdmodel.sim_config.SimConf.decomp_period"><code class="docutils literal notranslate"><span class="pre">SimConf.decomp_period</span></code></a></li> +<li class="toc-h3 nav-item toc-entry"><a class="reference internal nav-link" href="#arbdmodel.sim_config.SimConf.gpu"><code class="docutils literal notranslate"><span class="pre">SimConf.gpu</span></code></a></li> +<li class="toc-h3 nav-item toc-entry"><a class="reference internal nav-link" href="#arbdmodel.sim_config.SimConf.seed"><code class="docutils literal notranslate"><span class="pre">SimConf.seed</span></code></a></li> +<li class="toc-h3 nav-item toc-entry"><a class="reference internal nav-link" href="#arbdmodel.sim_config.SimConf.restart_file"><code class="docutils literal notranslate"><span class="pre">SimConf.restart_file</span></code></a></li> +<li class="toc-h3 nav-item toc-entry"><a class="reference internal nav-link" href="#arbdmodel.sim_config.SimConf.rigid_body_integrator"><code class="docutils literal notranslate"><span class="pre">SimConf.rigid_body_integrator</span></code></a></li> +<li class="toc-h3 nav-item toc-entry"><a class="reference internal nav-link" href="#arbdmodel.sim_config.SimConf.rigid_body_grid_grid_period"><code class="docutils literal notranslate"><span class="pre">SimConf.rigid_body_grid_grid_period</span></code></a></li> +<li class="toc-h3 nav-item toc-entry"><a class="reference internal nav-link" href="#arbdmodel.sim_config.SimConf.viscosity"><code class="docutils literal notranslate"><span class="pre">SimConf.viscosity</span></code></a></li> +<li class="toc-h3 nav-item toc-entry"><a class="reference internal nav-link" href="#arbdmodel.sim_config.SimConf.solvent_density"><code class="docutils literal notranslate"><span class="pre">SimConf.solvent_density</span></code></a></li> +<li class="toc-h3 nav-item toc-entry"><a class="reference internal nav-link" href="#arbdmodel.sim_config.SimConf.num_heavy_cluster"><code class="docutils literal notranslate"><span class="pre">SimConf.num_heavy_cluster</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> +<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.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="#id1"><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="#id2"><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="#id3"><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="#id4"><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="#id5"><code class="docutils literal notranslate"><span class="pre">SimConf.temperature</span></code></a></li> </ul> </li> </ul> @@ -379,10 +410,127 @@ classes for configuring simulation parameters.</p> <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"> +<p>Generic class describing properties for a simulation with default binary paths. +This class extends SimConf to provide default binary paths and configuration parameters +for molecular dynamics simulations using ARBD.</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>num_steps</strong> (<a class="hxr-hoverxref hxr-tooltip reference external" href="https://docs.python.org/3/library/functions.html#float" title="(in Python v3.13)"><em>float</em></a><em>, </em><em>optional</em>) – Number of simulation steps to run, default 1e5.</p></li> +<li><p><strong>output_period</strong> (<a class="hxr-hoverxref hxr-tooltip reference external" href="https://docs.python.org/3/library/functions.html#float" title="(in Python v3.13)"><em>float</em></a><em>, </em><em>optional</em>) – Period for output generation, default 1e3.</p></li> +<li><p><strong>integrator</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>) – Integration method, default ‘MD’.</p></li> +<li><p><strong>timestep</strong> (<a class="hxr-hoverxref hxr-tooltip reference external" href="https://docs.python.org/3/library/functions.html#float" title="(in Python v3.13)"><em>float</em></a><em>, </em><em>optional</em>) – Simulation timestep in time units, default 20e-6.</p></li> +<li><p><strong>thermostat</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>) – Thermostat type, default ‘Langevin’.</p></li> +<li><p><strong>barostat</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><em>None</em><em>, </em><em>optional</em>) – Barostat type if any, default None.</p></li> +<li><p><strong>temperature</strong> (<a class="hxr-hoverxref hxr-tooltip reference external" href="https://docs.python.org/3/library/functions.html#float" title="(in Python v3.13)"><em>float</em></a><em>, </em><em>optional</em>) – Simulation temperature in K, default 295.</p></li> +<li><p><strong>pressure</strong> (<a class="hxr-hoverxref hxr-tooltip reference external" href="https://docs.python.org/3/library/functions.html#float" title="(in Python v3.13)"><em>float</em></a><em>, </em><em>optional</em>) – Pressure value for barostat if used, default 1.</p></li> +<li><p><strong>cutoff</strong> (<a class="hxr-hoverxref hxr-tooltip reference external" href="https://docs.python.org/3/library/functions.html#float" title="(in Python v3.13)"><em>float</em></a><em>, </em><em>optional</em>) – Interaction cutoff distance, default 50.</p></li> +<li><p><strong>pairlist_distance</strong> (<a class="hxr-hoverxref hxr-tooltip reference external" href="https://docs.python.org/3/library/functions.html#float" title="(in Python v3.13)"><em>float</em></a><em> or </em><em>None</em><em>, </em><em>optional</em>) – Pairlist buffer distance, default None.</p></li> +<li><p><strong>decomp_period</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>) – Period for domain decomposition updates, default 40.</p></li> +<li><p><strong>seed</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> or </em><em>None</em><em>, </em><em>optional</em>) – Random seed for simulation, default None (random).</p></li> +<li><p><strong>restart_file</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><em>None</em><em>, </em><em>optional</em>) – Path to restart file if continuing a simulation, default None.</p></li> +<li><p><strong>gpu</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>) – GPU device index to use, default 0.</p></li> +<li><p><strong>viscosity</strong> (<a class="hxr-hoverxref hxr-tooltip reference external" href="https://docs.python.org/3/library/functions.html#float" title="(in Python v3.13)"><em>float</em></a><em>, </em><em>optional</em>) – Solvent viscosity, default 0.01.</p></li> +<li><p><strong>solvent_density</strong> (<a class="hxr-hoverxref hxr-tooltip reference external" href="https://docs.python.org/3/library/functions.html#float" title="(in Python v3.13)"><em>float</em></a><em>, </em><em>optional</em>) – Density of the solvent, default 1.0.</p></li> +<li><p><strong>num_heavy_cluster</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 heavy atoms per cluster, default 3.</p></li> +<li><p><strong>**kwargs</strong> – Additional keyword arguments to pass to SimConf.</p></li> +</ul> +</dd> +</dl> +<dl class="py attribute"> +<dt class="sig sig-object py" id="arbdmodel.sim_config.DefaultSimConf.num_steps"> +<span class="sig-name descname"><span class="pre">num_steps</span></span><a class="headerlink" href="#arbdmodel.sim_config.DefaultSimConf.num_steps" title="Link to this definition">#</a></dt> +<dd><p>Number of simulation steps.</p> +<dl class="field-list simple"> +<dt class="field-odd">Type<span class="colon">:</span></dt> +<dd class="field-odd"><p><a class="hxr-hoverxref hxr-tooltip reference external" href="https://docs.python.org/3/library/functions.html#float" title="(in Python v3.13)">float</a></p> +</dd> +</dl> +</dd></dl> + +<dl class="py attribute"> +<dt class="sig sig-object py" id="arbdmodel.sim_config.DefaultSimConf.output_period"> +<span class="sig-name descname"><span class="pre">output_period</span></span><a class="headerlink" href="#arbdmodel.sim_config.DefaultSimConf.output_period" title="Link to this definition">#</a></dt> +<dd><p>Period for output generation.</p> +<dl class="field-list simple"> +<dt class="field-odd">Type<span class="colon">:</span></dt> +<dd class="field-odd"><p><a class="hxr-hoverxref hxr-tooltip reference external" href="https://docs.python.org/3/library/functions.html#float" title="(in Python v3.13)">float</a></p> +</dd> +</dl> +</dd></dl> + +<dl class="py attribute"> +<dt class="sig sig-object py" id="arbdmodel.sim_config.DefaultSimConf.pressure"> +<span class="sig-name descname"><span class="pre">pressure</span></span><a class="headerlink" href="#arbdmodel.sim_config.DefaultSimConf.pressure" title="Link to this definition">#</a></dt> +<dd><p>Pressure value for barostat if used.</p> +<dl class="field-list simple"> +<dt class="field-odd">Type<span class="colon">:</span></dt> +<dd class="field-odd"><p><a class="hxr-hoverxref hxr-tooltip reference external" href="https://docs.python.org/3/library/functions.html#float" title="(in Python v3.13)">float</a></p> +</dd> +</dl> +</dd></dl> + +<dl class="py attribute"> +<dt class="sig sig-object py" id="arbdmodel.sim_config.DefaultSimConf.viscosity"> +<span class="sig-name descname"><span class="pre">viscosity</span></span><a class="headerlink" href="#arbdmodel.sim_config.DefaultSimConf.viscosity" title="Link to this definition">#</a></dt> +<dd><p>Solvent viscosity.</p> +<dl class="field-list simple"> +<dt class="field-odd">Type<span class="colon">:</span></dt> +<dd class="field-odd"><p><a class="hxr-hoverxref hxr-tooltip reference external" href="https://docs.python.org/3/library/functions.html#float" title="(in Python v3.13)">float</a></p> +</dd> +</dl> +</dd></dl> + +<dl class="py attribute"> +<dt class="sig sig-object py" id="arbdmodel.sim_config.DefaultSimConf.solvent_density"> +<span class="sig-name descname"><span class="pre">solvent_density</span></span><a class="headerlink" href="#arbdmodel.sim_config.DefaultSimConf.solvent_density" title="Link to this definition">#</a></dt> +<dd><p>Density of the solvent.</p> +<dl class="field-list simple"> +<dt class="field-odd">Type<span class="colon">:</span></dt> +<dd class="field-odd"><p><a class="hxr-hoverxref hxr-tooltip reference external" href="https://docs.python.org/3/library/functions.html#float" title="(in Python v3.13)">float</a></p> +</dd> +</dl> +</dd></dl> + +<dl class="py attribute"> +<dt class="sig sig-object py" id="arbdmodel.sim_config.DefaultSimConf.num_heavy_cluster"> +<span class="sig-name descname"><span class="pre">num_heavy_cluster</span></span><a class="headerlink" href="#arbdmodel.sim_config.DefaultSimConf.num_heavy_cluster" title="Link to this definition">#</a></dt> +<dd><p>Number of heavy atoms per cluster.</p> +<dl class="field-list simple"> +<dt class="field-odd">Type<span class="colon">:</span></dt> +<dd class="field-odd"><p><a class="hxr-hoverxref hxr-tooltip reference external" href="https://docs.python.org/3/library/functions.html#int" title="(in Python v3.13)">int</a></p> +</dd> +</dl> +</dd></dl> + +<dl class="py attribute"> +<dt class="sig sig-object py" id="arbdmodel.sim_config.DefaultSimConf.Properties"> +<span class="sig-name descname"><span class="pre">Properties</span></span><a class="headerlink" href="#arbdmodel.sim_config.DefaultSimConf.Properties" title="Link to this definition">#</a></dt> +<dd></dd></dl> + +<dl class="py attribute"> +<dt class="sig sig-object py"> +<span class="sig-name descname"><span class="pre">----------</span></span></dt> +<dd></dd></dl> + +<dl class="py attribute"> <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> +<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><p>Simulation temperature with validation (must be positive).</p> +<dl class="field-list simple"> +<dt class="field-odd">Type<span class="colon">:</span></dt> +<dd class="field-odd"><p><a class="hxr-hoverxref hxr-tooltip reference external" href="https://docs.python.org/3/library/functions.html#float" title="(in Python v3.13)">float</a></p> +</dd> +</dl> +</dd></dl> + +<p class="rubric">Notes</p> +<p>The class automatically searches for binary dependencies like ‘arbd’, ‘hydropro’, ‘apbs’, +‘vmd’, and ‘namd’, and adds their paths to the configuration if found. +Essential binaries (currently only ‘arbd’) will generate warnings if not found.</p> +<dl class="py property"> +<dt class="sig sig-object py" id="id0"> +<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="#id0" title="Link to this definition">#</a></dt> <dd></dd></dl> </dd></dl> @@ -391,18 +539,263 @@ classes for configuring simulation parameters.</p> <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> +<p>Class describing properties for a simulation (ARBD or NAMD). +This class stores various simulation parameters, manages binary paths, and provides +methods to combine simulation configurations.</p> +<dl class="py attribute"> +<dt class="sig sig-object py" id="arbdmodel.sim_config.SimConf.num_steps"> +<span class="sig-name descname"><span class="pre">num_steps</span></span><a class="headerlink" href="#arbdmodel.sim_config.SimConf.num_steps" title="Link to this definition">#</a></dt> +<dd><p>Total number of simulation steps.</p> +<dl class="field-list simple"> +<dt class="field-odd">Type<span class="colon">:</span></dt> +<dd class="field-odd"><p><a class="hxr-hoverxref hxr-tooltip reference external" href="https://docs.python.org/3/library/functions.html#int" title="(in Python v3.13)">int</a></p> +</dd> +</dl> +</dd></dl> + +<dl class="py attribute"> +<dt class="sig sig-object py" id="arbdmodel.sim_config.SimConf.output_period"> +<span class="sig-name descname"><span class="pre">output_period</span></span><a class="headerlink" href="#arbdmodel.sim_config.SimConf.output_period" title="Link to this definition">#</a></dt> +<dd><p>Frequency of output generation.</p> +<dl class="field-list simple"> +<dt class="field-odd">Type<span class="colon">:</span></dt> +<dd class="field-odd"><p><a class="hxr-hoverxref hxr-tooltip reference external" href="https://docs.python.org/3/library/functions.html#int" title="(in Python v3.13)">int</a></p> +</dd> +</dl> +</dd></dl> + +<dl class="py attribute"> +<dt class="sig sig-object py" id="arbdmodel.sim_config.SimConf.integrator"> +<span class="sig-name descname"><span class="pre">integrator</span></span><a class="headerlink" href="#arbdmodel.sim_config.SimConf.integrator" title="Link to this definition">#</a></dt> +<dd><p>Type of integrator used (e.g., ‘MD’, ‘BD’).</p> +<dl class="field-list simple"> +<dt class="field-odd">Type<span class="colon">:</span></dt> +<dd class="field-odd"><p><a class="hxr-hoverxref hxr-tooltip reference external" href="https://docs.python.org/3/library/stdtypes.html#str" title="(in Python v3.13)">str</a></p> +</dd> +</dl> +</dd></dl> + +<dl class="py attribute"> +<dt class="sig sig-object py" id="arbdmodel.sim_config.SimConf.timestep"> +<span class="sig-name descname"><span class="pre">timestep</span></span><a class="headerlink" href="#arbdmodel.sim_config.SimConf.timestep" title="Link to this definition">#</a></dt> +<dd><p>Simulation time step.</p> +<dl class="field-list simple"> +<dt class="field-odd">Type<span class="colon">:</span></dt> +<dd class="field-odd"><p><a class="hxr-hoverxref hxr-tooltip reference external" href="https://docs.python.org/3/library/functions.html#float" title="(in Python v3.13)">float</a></p> +</dd> +</dl> +</dd></dl> + +<dl class="py attribute"> +<dt class="sig sig-object py" id="arbdmodel.sim_config.SimConf.thermostat"> +<span class="sig-name descname"><span class="pre">thermostat</span></span><a class="headerlink" href="#arbdmodel.sim_config.SimConf.thermostat" title="Link to this definition">#</a></dt> +<dd><p>Type of thermostat used.</p> +<dl class="field-list simple"> +<dt class="field-odd">Type<span class="colon">:</span></dt> +<dd class="field-odd"><p><a class="hxr-hoverxref hxr-tooltip reference external" href="https://docs.python.org/3/library/stdtypes.html#str" title="(in Python v3.13)">str</a></p> +</dd> +</dl> +</dd></dl> + +<dl class="py attribute"> +<dt class="sig sig-object py" id="arbdmodel.sim_config.SimConf.barostat"> +<span class="sig-name descname"><span class="pre">barostat</span></span><a class="headerlink" href="#arbdmodel.sim_config.SimConf.barostat" title="Link to this definition">#</a></dt> +<dd><p>Type of barostat used.</p> +<dl class="field-list simple"> +<dt class="field-odd">Type<span class="colon">:</span></dt> +<dd class="field-odd"><p><a class="hxr-hoverxref hxr-tooltip reference external" href="https://docs.python.org/3/library/stdtypes.html#str" title="(in Python v3.13)">str</a></p> +</dd> +</dl> +</dd></dl> + +<dl class="py attribute"> +<dt class="sig sig-object py" id="arbdmodel.sim_config.SimConf.temperature"> +<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><p>Simulation temperature (must be positive).</p> +<dl class="field-list simple"> +<dt class="field-odd">Type<span class="colon">:</span></dt> +<dd class="field-odd"><p><a class="hxr-hoverxref hxr-tooltip reference external" href="https://docs.python.org/3/library/functions.html#float" title="(in Python v3.13)">float</a></p> +</dd> +</dl> +</dd></dl> + +<dl class="py attribute"> +<dt class="sig sig-object py" id="arbdmodel.sim_config.SimConf.pressure"> +<span class="sig-name descname"><span class="pre">pressure</span></span><a class="headerlink" href="#arbdmodel.sim_config.SimConf.pressure" title="Link to this definition">#</a></dt> +<dd><p>Simulation pressure.</p> +<dl class="field-list simple"> +<dt class="field-odd">Type<span class="colon">:</span></dt> +<dd class="field-odd"><p><a class="hxr-hoverxref hxr-tooltip reference external" href="https://docs.python.org/3/library/functions.html#float" title="(in Python v3.13)">float</a></p> +</dd> +</dl> +</dd></dl> + +<dl class="py attribute"> +<dt class="sig sig-object py" id="arbdmodel.sim_config.SimConf.cutoff"> +<span class="sig-name descname"><span class="pre">cutoff</span></span><a class="headerlink" href="#arbdmodel.sim_config.SimConf.cutoff" title="Link to this definition">#</a></dt> +<dd><p>Cutoff distance for interactions.</p> +<dl class="field-list simple"> +<dt class="field-odd">Type<span class="colon">:</span></dt> +<dd class="field-odd"><p><a class="hxr-hoverxref hxr-tooltip reference external" href="https://docs.python.org/3/library/functions.html#float" title="(in Python v3.13)">float</a></p> +</dd> +</dl> +</dd></dl> + +<dl class="py attribute"> +<dt class="sig sig-object py" id="arbdmodel.sim_config.SimConf.pairlist_distance"> +<span class="sig-name descname"><span class="pre">pairlist_distance</span></span><a class="headerlink" href="#arbdmodel.sim_config.SimConf.pairlist_distance" title="Link to this definition">#</a></dt> +<dd><p>Distance for generating pair lists.</p> +<dl class="field-list simple"> +<dt class="field-odd">Type<span class="colon">:</span></dt> +<dd class="field-odd"><p><a class="hxr-hoverxref hxr-tooltip reference external" href="https://docs.python.org/3/library/functions.html#float" title="(in Python v3.13)">float</a></p> +</dd> +</dl> +</dd></dl> + +<dl class="py attribute"> +<dt class="sig sig-object py" id="arbdmodel.sim_config.SimConf.decomp_period"> +<span class="sig-name descname"><span class="pre">decomp_period</span></span><a class="headerlink" href="#arbdmodel.sim_config.SimConf.decomp_period" title="Link to this definition">#</a></dt> +<dd><p>Period for decomposition.</p> +<dl class="field-list simple"> +<dt class="field-odd">Type<span class="colon">:</span></dt> +<dd class="field-odd"><p><a class="hxr-hoverxref hxr-tooltip reference external" href="https://docs.python.org/3/library/functions.html#int" title="(in Python v3.13)">int</a></p> +</dd> +</dl> +</dd></dl> + +<dl class="py attribute"> +<dt class="sig sig-object py" id="arbdmodel.sim_config.SimConf.gpu"> +<span class="sig-name descname"><span class="pre">gpu</span></span><a class="headerlink" href="#arbdmodel.sim_config.SimConf.gpu" title="Link to this definition">#</a></dt> +<dd><p>Whether to use GPU acceleration.</p> +<dl class="field-list simple"> +<dt class="field-odd">Type<span class="colon">:</span></dt> +<dd class="field-odd"><p><a class="hxr-hoverxref hxr-tooltip reference external" href="https://docs.python.org/3/library/functions.html#bool" title="(in Python v3.13)">bool</a></p> +</dd> +</dl> +</dd></dl> + +<dl class="py attribute"> +<dt class="sig sig-object py" id="arbdmodel.sim_config.SimConf.seed"> +<span class="sig-name descname"><span class="pre">seed</span></span><a class="headerlink" href="#arbdmodel.sim_config.SimConf.seed" title="Link to this definition">#</a></dt> +<dd><p>Random seed for reproducibility.</p> +<dl class="field-list simple"> +<dt class="field-odd">Type<span class="colon">:</span></dt> +<dd class="field-odd"><p><a class="hxr-hoverxref hxr-tooltip reference external" href="https://docs.python.org/3/library/functions.html#int" title="(in Python v3.13)">int</a></p> +</dd> +</dl> +</dd></dl> + +<dl class="py attribute"> +<dt class="sig sig-object py" id="arbdmodel.sim_config.SimConf.restart_file"> +<span class="sig-name descname"><span class="pre">restart_file</span></span><a class="headerlink" href="#arbdmodel.sim_config.SimConf.restart_file" title="Link to this definition">#</a></dt> +<dd><p>Path to restart file.</p> +<dl class="field-list simple"> +<dt class="field-odd">Type<span class="colon">:</span></dt> +<dd class="field-odd"><p><a class="hxr-hoverxref hxr-tooltip reference external" href="https://docs.python.org/3/library/stdtypes.html#str" title="(in Python v3.13)">str</a></p> +</dd> +</dl> +</dd></dl> + +<dl class="py attribute"> +<dt class="sig sig-object py"> +<span class="sig-name descname"><span class="pre">#</span> <span class="pre">ARBD-specific</span> <span class="pre">parameters</span></span></dt> +<dd></dd></dl> + +<dl class="py attribute"> +<dt class="sig sig-object py" id="arbdmodel.sim_config.SimConf.rigid_body_integrator"> +<span class="sig-name descname"><span class="pre">rigid_body_integrator</span></span><a class="headerlink" href="#arbdmodel.sim_config.SimConf.rigid_body_integrator" title="Link to this definition">#</a></dt> +<dd><p>Type of rigid body integrator.</p> +<dl class="field-list simple"> +<dt class="field-odd">Type<span class="colon">:</span></dt> +<dd class="field-odd"><p><a class="hxr-hoverxref hxr-tooltip reference external" href="https://docs.python.org/3/library/stdtypes.html#str" title="(in Python v3.13)">str</a></p> +</dd> +</dl> +</dd></dl> + +<dl class="py attribute"> +<dt class="sig sig-object py" id="arbdmodel.sim_config.SimConf.rigid_body_grid_grid_period"> +<span class="sig-name descname"><span class="pre">rigid_body_grid_grid_period</span></span><a class="headerlink" href="#arbdmodel.sim_config.SimConf.rigid_body_grid_grid_period" title="Link to this definition">#</a></dt> +<dd><p>Period for rigid body grid updates.</p> +<dl class="field-list simple"> +<dt class="field-odd">Type<span class="colon">:</span></dt> +<dd class="field-odd"><p><a class="hxr-hoverxref hxr-tooltip reference external" href="https://docs.python.org/3/library/functions.html#int" title="(in Python v3.13)">int</a></p> +</dd> +</dl> +</dd></dl> + +<dl class="py attribute"> +<dt class="sig sig-object py"> +<span class="sig-name descname"><span class="pre">#</span> <span class="pre">SimpleARBD</span> <span class="pre">parameters</span></span></dt> +<dd></dd></dl> + +<dl class="py attribute"> +<dt class="sig sig-object py" id="arbdmodel.sim_config.SimConf.viscosity"> +<span class="sig-name descname"><span class="pre">viscosity</span></span><a class="headerlink" href="#arbdmodel.sim_config.SimConf.viscosity" title="Link to this definition">#</a></dt> +<dd><p>Solvent viscosity.</p> +<dl class="field-list simple"> +<dt class="field-odd">Type<span class="colon">:</span></dt> +<dd class="field-odd"><p><a class="hxr-hoverxref hxr-tooltip reference external" href="https://docs.python.org/3/library/functions.html#float" title="(in Python v3.13)">float</a></p> +</dd> +</dl> +</dd></dl> + +<dl class="py attribute"> +<dt class="sig sig-object py" id="arbdmodel.sim_config.SimConf.solvent_density"> +<span class="sig-name descname"><span class="pre">solvent_density</span></span><a class="headerlink" href="#arbdmodel.sim_config.SimConf.solvent_density" title="Link to this definition">#</a></dt> +<dd><p>Solvent density.</p> +<dl class="field-list simple"> +<dt class="field-odd">Type<span class="colon">:</span></dt> +<dd class="field-odd"><p><a class="hxr-hoverxref hxr-tooltip reference external" href="https://docs.python.org/3/library/functions.html#float" title="(in Python v3.13)">float</a></p> +</dd> +</dl> +</dd></dl> + +<dl class="py attribute"> +<dt class="sig sig-object py" id="arbdmodel.sim_config.SimConf.num_heavy_cluster"> +<span class="sig-name descname"><span class="pre">num_heavy_cluster</span></span><a class="headerlink" href="#arbdmodel.sim_config.SimConf.num_heavy_cluster" title="Link to this definition">#</a></dt> +<dd><p>Number of heavy clusters.</p> +<dl class="field-list simple"> +<dt class="field-odd">Type<span class="colon">:</span></dt> +<dd class="field-odd"><p><a class="hxr-hoverxref hxr-tooltip reference external" href="https://docs.python.org/3/library/functions.html#int" title="(in Python v3.13)">int</a></p> +</dd> +</dl> +</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.</p> +</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 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>Combine two SimConf objects.</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><p>Iterate over attribute name-value pairs.</p> +</dd></dl> + +<dl class="py method"> +<dt class="sig sig-object py" id="id1"> +<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="#id1" 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> +<dt class="sig sig-object py" id="id2"> +<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="#id2" 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> @@ -417,19 +810,19 @@ 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> +<dt class="sig sig-object py" id="id3"> +<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="#id3" 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> +<dt class="sig sig-object py" id="id4"> +<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="#id4" 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> +<dt class="sig sig-object py" id="id5"> +<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="#id5" title="Link to this definition">#</a></dt> <dd></dd></dl> </dd></dl> @@ -483,15 +876,46 @@ for graceful handling of missing optional dependencies.</p> <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.num_steps"><code class="docutils literal notranslate"><span class="pre">DefaultSimConf.num_steps</span></code></a></li> +<li class="toc-h3 nav-item toc-entry"><a class="reference internal nav-link" href="#arbdmodel.sim_config.DefaultSimConf.output_period"><code class="docutils literal notranslate"><span class="pre">DefaultSimConf.output_period</span></code></a></li> +<li class="toc-h3 nav-item toc-entry"><a class="reference internal nav-link" href="#arbdmodel.sim_config.DefaultSimConf.pressure"><code class="docutils literal notranslate"><span class="pre">DefaultSimConf.pressure</span></code></a></li> +<li class="toc-h3 nav-item toc-entry"><a class="reference internal nav-link" href="#arbdmodel.sim_config.DefaultSimConf.viscosity"><code class="docutils literal notranslate"><span class="pre">DefaultSimConf.viscosity</span></code></a></li> +<li class="toc-h3 nav-item toc-entry"><a class="reference internal nav-link" href="#arbdmodel.sim_config.DefaultSimConf.solvent_density"><code class="docutils literal notranslate"><span class="pre">DefaultSimConf.solvent_density</span></code></a></li> +<li class="toc-h3 nav-item toc-entry"><a class="reference internal nav-link" href="#arbdmodel.sim_config.DefaultSimConf.num_heavy_cluster"><code class="docutils literal notranslate"><span class="pre">DefaultSimConf.num_heavy_cluster</span></code></a></li> +<li class="toc-h3 nav-item toc-entry"><a class="reference internal nav-link" href="#arbdmodel.sim_config.DefaultSimConf.Properties"><code class="docutils literal notranslate"><span class="pre">DefaultSimConf.Properties</span></code></a></li> <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> +<li class="toc-h3 nav-item toc-entry"><a class="reference internal nav-link" href="#id0"><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.num_steps"><code class="docutils literal notranslate"><span class="pre">SimConf.num_steps</span></code></a></li> +<li class="toc-h3 nav-item toc-entry"><a class="reference internal nav-link" href="#arbdmodel.sim_config.SimConf.output_period"><code class="docutils literal notranslate"><span class="pre">SimConf.output_period</span></code></a></li> +<li class="toc-h3 nav-item toc-entry"><a class="reference internal nav-link" href="#arbdmodel.sim_config.SimConf.integrator"><code class="docutils literal notranslate"><span class="pre">SimConf.integrator</span></code></a></li> +<li class="toc-h3 nav-item toc-entry"><a class="reference internal nav-link" href="#arbdmodel.sim_config.SimConf.timestep"><code class="docutils literal notranslate"><span class="pre">SimConf.timestep</span></code></a></li> +<li class="toc-h3 nav-item toc-entry"><a class="reference internal nav-link" href="#arbdmodel.sim_config.SimConf.thermostat"><code class="docutils literal notranslate"><span class="pre">SimConf.thermostat</span></code></a></li> +<li class="toc-h3 nav-item toc-entry"><a class="reference internal nav-link" href="#arbdmodel.sim_config.SimConf.barostat"><code class="docutils literal notranslate"><span class="pre">SimConf.barostat</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> +<li class="toc-h3 nav-item toc-entry"><a class="reference internal nav-link" href="#arbdmodel.sim_config.SimConf.pressure"><code class="docutils literal notranslate"><span class="pre">SimConf.pressure</span></code></a></li> +<li class="toc-h3 nav-item toc-entry"><a class="reference internal nav-link" href="#arbdmodel.sim_config.SimConf.cutoff"><code class="docutils literal notranslate"><span class="pre">SimConf.cutoff</span></code></a></li> +<li class="toc-h3 nav-item toc-entry"><a class="reference internal nav-link" href="#arbdmodel.sim_config.SimConf.pairlist_distance"><code class="docutils literal notranslate"><span class="pre">SimConf.pairlist_distance</span></code></a></li> +<li class="toc-h3 nav-item toc-entry"><a class="reference internal nav-link" href="#arbdmodel.sim_config.SimConf.decomp_period"><code class="docutils literal notranslate"><span class="pre">SimConf.decomp_period</span></code></a></li> +<li class="toc-h3 nav-item toc-entry"><a class="reference internal nav-link" href="#arbdmodel.sim_config.SimConf.gpu"><code class="docutils literal notranslate"><span class="pre">SimConf.gpu</span></code></a></li> +<li class="toc-h3 nav-item toc-entry"><a class="reference internal nav-link" href="#arbdmodel.sim_config.SimConf.seed"><code class="docutils literal notranslate"><span class="pre">SimConf.seed</span></code></a></li> +<li class="toc-h3 nav-item toc-entry"><a class="reference internal nav-link" href="#arbdmodel.sim_config.SimConf.restart_file"><code class="docutils literal notranslate"><span class="pre">SimConf.restart_file</span></code></a></li> +<li class="toc-h3 nav-item toc-entry"><a class="reference internal nav-link" href="#arbdmodel.sim_config.SimConf.rigid_body_integrator"><code class="docutils literal notranslate"><span class="pre">SimConf.rigid_body_integrator</span></code></a></li> +<li class="toc-h3 nav-item toc-entry"><a class="reference internal nav-link" href="#arbdmodel.sim_config.SimConf.rigid_body_grid_grid_period"><code class="docutils literal notranslate"><span class="pre">SimConf.rigid_body_grid_grid_period</span></code></a></li> +<li class="toc-h3 nav-item toc-entry"><a class="reference internal nav-link" href="#arbdmodel.sim_config.SimConf.viscosity"><code class="docutils literal notranslate"><span class="pre">SimConf.viscosity</span></code></a></li> +<li class="toc-h3 nav-item toc-entry"><a class="reference internal nav-link" href="#arbdmodel.sim_config.SimConf.solvent_density"><code class="docutils literal notranslate"><span class="pre">SimConf.solvent_density</span></code></a></li> +<li class="toc-h3 nav-item toc-entry"><a class="reference internal nav-link" href="#arbdmodel.sim_config.SimConf.num_heavy_cluster"><code class="docutils literal notranslate"><span class="pre">SimConf.num_heavy_cluster</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> +<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.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="#id1"><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="#id2"><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="#id3"><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="#id4"><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="#id5"><code class="docutils literal notranslate"><span class="pre">SimConf.temperature</span></code></a></li> </ul> </li> </ul> diff --git a/_build/html/api/index.html b/_build/html/api/index.html index 1fa2ea59524b1f75a2c4cc623ba731e2d4d45073..362e8a4d7ab380fa6e05152d80b48054c0615ba0 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?v=be8a1c11" /> + <link rel="stylesheet" type="text/css" href="../_static/mystnb.4510f1fc1dee50b3e5859aac5469c37c29e427902b24a333a5f9fcb2f0b3ac41.css" /> 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a/_build/html/api/interaction_potentials/ibi.html b/_build/html/api/interaction_potentials/ibi.html index 2b68869596205923953f5ca90b6cb5f9e69fd35d..adf2bcf6492c23c1d2b59ea8504b02f9788b6c0f 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?v=be8a1c11" /> + <link rel="stylesheet" type="text/css" href="../../_static/mystnb.4510f1fc1dee50b3e5859aac5469c37c29e427902b24a333a5f9fcb2f0b3ac41.css" /> <link rel="stylesheet" type="text/css" href="../../_static/sphinx-thebe.css?v=4fa983c6" /> <link 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href="../../_static/css/micromodal.css" /> <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?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 src="../../_static/js/hoverxref.js"></script> + <script src="../../_static/js/tooltipster.bundle.min.js"></script> + <script src="../../_static/js/micromodal.min.js"></script> <script>let toggleHintShow = 'Click to show';</script> <script>let toggleHintHide = 'Click to hide';</script> <script>let toggleOpenOnPrint = 'true';</script> @@ -347,13 +347,22 @@ document.write(` <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.ibi.AbstractIBIpotential"><code class="docutils literal notranslate"><span class="pre">AbstractIBIpotential</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.ibi.AbstractIBIpotential.bins"><code class="docutils literal notranslate"><span class="pre">AbstractIBIpotential.bins</span></code></a></li> +<li class="toc-h3 nav-item toc-entry"><a class="reference internal nav-link" href="#arbdmodel.ibi.AbstractIBIpotential.potential"><code class="docutils literal notranslate"><span class="pre">AbstractIBIpotential.potential</span></code></a></li> +<li class="toc-h3 nav-item toc-entry"><a class="reference internal nav-link" href="#id0"><code class="docutils literal notranslate"><span class="pre">AbstractIBIpotential.potential()</span></code></a></li> <li class="toc-h3 nav-item toc-entry"><a class="reference internal nav-link" href="#arbdmodel.ibi.AbstractIBIpotential.filename"><code class="docutils literal notranslate"><span class="pre">AbstractIBIpotential.filename()</span></code></a></li> -<li class="toc-h3 nav-item toc-entry"><a class="reference internal nav-link" href="#arbdmodel.ibi.AbstractIBIpotential.get_cg_distribution"><code class="docutils literal notranslate"><span class="pre">AbstractIBIpotential.get_cg_distribution()</span></code></a></li> +<li class="toc-h3 nav-item toc-entry"><a class="reference internal nav-link" href="#arbdmodel.ibi.AbstractIBIpotential.write_file"><code class="docutils literal notranslate"><span class="pre">AbstractIBIpotential.write_file()</span></code></a></li> <li class="toc-h3 nav-item toc-entry"><a class="reference internal nav-link" href="#arbdmodel.ibi.AbstractIBIpotential.get_target_distribution"><code class="docutils literal notranslate"><span class="pre">AbstractIBIpotential.get_target_distribution()</span></code></a></li> -<li class="toc-h3 nav-item toc-entry"><a class="reference internal nav-link" href="#arbdmodel.ibi.AbstractIBIpotential.potential"><code class="docutils literal notranslate"><span class="pre">AbstractIBIpotential.potential()</span></code></a></li> +<li class="toc-h3 nav-item toc-entry"><a class="reference internal nav-link" href="#arbdmodel.ibi.AbstractIBIpotential.get_cg_distribution"><code class="docutils literal notranslate"><span class="pre">AbstractIBIpotential.get_cg_distribution()</span></code></a></li> <li class="toc-h3 nav-item toc-entry"><a class="reference internal nav-link" href="#arbdmodel.ibi.AbstractIBIpotential.read_cg_potential"><code class="docutils literal notranslate"><span class="pre">AbstractIBIpotential.read_cg_potential()</span></code></a></li> <li class="toc-h3 nav-item toc-entry"><a class="reference internal nav-link" href="#arbdmodel.ibi.AbstractIBIpotential.write_cg_potential"><code class="docutils literal notranslate"><span class="pre">AbstractIBIpotential.write_cg_potential()</span></code></a></li> -<li class="toc-h3 nav-item toc-entry"><a class="reference internal nav-link" href="#arbdmodel.ibi.AbstractIBIpotential.write_file"><code class="docutils literal notranslate"><span class="pre">AbstractIBIpotential.write_file()</span></code></a></li> +<li class="toc-h3 nav-item toc-entry"><a class="reference internal nav-link" href="#id1"><code class="docutils literal notranslate"><span class="pre">AbstractIBIpotential.filename()</span></code></a></li> +<li class="toc-h3 nav-item toc-entry"><a class="reference internal nav-link" href="#id2"><code class="docutils literal notranslate"><span class="pre">AbstractIBIpotential.get_cg_distribution()</span></code></a></li> +<li class="toc-h3 nav-item toc-entry"><a class="reference internal nav-link" href="#id3"><code class="docutils literal notranslate"><span class="pre">AbstractIBIpotential.get_target_distribution()</span></code></a></li> +<li class="toc-h3 nav-item toc-entry"><a class="reference internal nav-link" href="#id4"><code class="docutils literal notranslate"><span class="pre">AbstractIBIpotential.potential()</span></code></a></li> +<li class="toc-h3 nav-item toc-entry"><a class="reference internal nav-link" href="#id5"><code class="docutils literal notranslate"><span class="pre">AbstractIBIpotential.read_cg_potential()</span></code></a></li> +<li class="toc-h3 nav-item toc-entry"><a class="reference internal nav-link" href="#id6"><code class="docutils literal notranslate"><span class="pre">AbstractIBIpotential.write_cg_potential()</span></code></a></li> +<li class="toc-h3 nav-item toc-entry"><a class="reference internal nav-link" href="#id7"><code class="docutils literal notranslate"><span class="pre">AbstractIBIpotential.write_file()</span></code></a></li> </ul> </li> <li class="toc-h2 nav-item toc-entry"><a class="reference internal nav-link" href="#arbdmodel.ibi.AngleDof"><code class="docutils literal notranslate"><span class="pre">AngleDof</span></code></a><ul class="nav section-nav flex-column"> @@ -409,39 +418,133 @@ document.write(` <dt class="sig sig-object py" id="arbdmodel.ibi.AbstractIBIpotential"> <em class="property"><span class="pre">class</span><span class="w"> </span></em><span class="sig-name descname"><span class="pre">AbstractIBIpotential</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">degrees_of_freedom</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">range_</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">(0,</span> <span class="pre">30)</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">out_of_bounds_force</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">'max_force'</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>, <em class="sig-param"><span class="n"><span class="pre">smooth</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_rate</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">0.9</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">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">filename_prefix</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">'IBIPotentials/'</span></span></em><span class="sig-paren">)</span><a class="reference internal" href="../../_modules/arbdmodel/ibi.html#AbstractIBIpotential"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#arbdmodel.ibi.AbstractIBIpotential" title="Link to this definition">#</a></dt> <dd><p>Bases: <a class="reference internal" href="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>A class that implements the Iterative Boltzmann Inversion method for generating potentials.</p> +<p>This abstract class provides the foundation for creating IBI potentials that are derived +from target distributions. IBI is a method to derive effective pair potentials from radial +distribution functions in molecular systems.</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>name</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>) – Name of the potential, used for file naming.</p></li> +<li><p><strong>degrees_of_freedom</strong> (<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>) – List of degrees of freedom to consider in the potential.</p></li> +<li><p><strong>range</strong> (<a class="hxr-hoverxref hxr-tooltip reference external" href="https://docs.python.org/3/library/stdtypes.html#tuple" title="(in Python v3.13)"><em>tuple</em></a><em>, </em><em>optional</em>) – Range of distances to consider (min, max), default is (0, 30).</p></li> +<li><p><strong>resolution</strong> (<a class="hxr-hoverxref hxr-tooltip reference external" href="https://docs.python.org/3/library/functions.html#float" title="(in Python v3.13)"><em>float</em></a><em>, </em><em>optional</em>) – Resolution of the binning for the distribution, default is 0.1.</p></li> +<li><p><strong>max_force</strong> (<a class="hxr-hoverxref hxr-tooltip reference external" href="https://docs.python.org/3/library/functions.html#float" title="(in Python v3.13)"><em>float</em></a><em>, </em><em>optional</em>) – Maximum force allowed in the potential.</p></li> +<li><p><strong>max_potential</strong> (<a class="hxr-hoverxref hxr-tooltip reference external" href="https://docs.python.org/3/library/functions.html#float" title="(in Python v3.13)"><em>float</em></a><em>, </em><em>optional</em>) – Maximum potential value allowed.</p></li> +<li><p><strong>out_of_bounds_force</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/functions.html#float" title="(in Python v3.13)"><em>float</em></a><em>, </em><em>optional</em>) – Force to apply outside the well-defined density region, default is ‘max_force’.</p></li> +<li><p><strong>zero</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>) – Method to set the zero point of the potential, default is ‘last’.</p></li> +<li><p><strong>smooth</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> or </em><em>None</em><em>, </em><em>optional</em>) – Window size for Savitzky-Golay filter, if None will be calculated automatically.</p></li> +<li><p><strong>learning_rate</strong> (<a class="hxr-hoverxref hxr-tooltip reference external" href="https://docs.python.org/3/library/functions.html#float" title="(in Python v3.13)"><em>float</em></a><em> or </em><em>callable</em><em>, </em><em>optional</em>) – Learning rate for potential updates, default is 0.9.</p></li> +<li><p><strong>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>) – Current iteration number, default is 1.</p></li> +<li><p><strong>filename_prefix</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>) – Path prefix for saving potentials, default is ‘IBIPotentials/’.</p></li> +</ul> +</dd> +</dl> +<dl class="py attribute"> +<dt class="sig sig-object py" id="arbdmodel.ibi.AbstractIBIpotential.bins"> +<span class="sig-name descname"><span class="pre">bins</span></span><a class="headerlink" href="#arbdmodel.ibi.AbstractIBIpotential.bins" title="Link to this definition">#</a></dt> +<dd><p>Bin edges for the distribution.</p> +<dl class="field-list simple"> +<dt class="field-odd">Type<span class="colon">:</span></dt> +<dd class="field-odd"><p><a class="hxr-hoverxref hxr-tooltip reference external" href="https://numpy.org/doc/stable/reference/generated/numpy.ndarray.html#numpy.ndarray" title="(in NumPy v2.2)">numpy.ndarray</a></p> +</dd> +</dl> +</dd></dl> + +<dl class="py attribute"> +<dt class="sig sig-object py" id="arbdmodel.ibi.AbstractIBIpotential.potential"> +<span class="sig-name descname"><span class="pre">potential</span></span><a class="reference internal" href="../../_modules/arbdmodel/ibi.html#AbstractIBIpotential.potential"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#arbdmodel.ibi.AbstractIBIpotential.potential" title="Link to this definition">#</a></dt> +<dd><p>Current potential values.</p> +<dl class="field-list simple"> +<dt class="field-odd">Type<span class="colon">:</span></dt> +<dd class="field-odd"><p><a class="hxr-hoverxref hxr-tooltip reference external" href="https://numpy.org/doc/stable/reference/generated/numpy.ndarray.html#numpy.ndarray" title="(in NumPy v2.2)">numpy.ndarray</a></p> +</dd> +</dl> +</dd></dl> + +<dl class="py method"> +<dt class="sig sig-object py" id="id0"> +<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/ibi.html#AbstractIBIpotential.potential"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#id0" title="Link to this definition">#</a></dt> +<dd><p>Abstract method to calculate potential at distance r.</p> +</dd></dl> + <dl class="py method"> <dt class="sig sig-object py" id="arbdmodel.ibi.AbstractIBIpotential.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>, <em class="sig-param"><span class="n"><span class="pre">iteration</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">smoothed</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/ibi.html#AbstractIBIpotential.filename"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#arbdmodel.ibi.AbstractIBIpotential.filename" title="Link to this definition">#</a></dt> -<dd></dd></dl> +<dd><p>Generate filename for the potential.</p> +</dd></dl> <dl class="py method"> -<dt class="sig sig-object py" id="arbdmodel.ibi.AbstractIBIpotential.get_cg_distribution"> -<span class="sig-name descname"><span class="pre">get_cg_distribution</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">universe</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">trajectory</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</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">recalculate</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/ibi.html#AbstractIBIpotential.get_cg_distribution"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#arbdmodel.ibi.AbstractIBIpotential.get_cg_distribution" title="Link to this definition">#</a></dt> -<dd></dd></dl> +<dt class="sig sig-object py" id="arbdmodel.ibi.AbstractIBIpotential.write_file"> +<span class="sig-name descname"><span class="pre">write_file</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="reference internal" href="../../_modules/arbdmodel/ibi.html#AbstractIBIpotential.write_file"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#arbdmodel.ibi.AbstractIBIpotential.write_file" title="Link to this definition">#</a></dt> +<dd><p>Write the potential to a file.</p> +</dd></dl> <dl class="py method"> <dt class="sig sig-object py" id="arbdmodel.ibi.AbstractIBIpotential.get_target_distribution"> <span class="sig-name descname"><span class="pre">get_target_distribution</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">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">trajectory</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">recalculate</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/ibi.html#AbstractIBIpotential.get_target_distribution"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#arbdmodel.ibi.AbstractIBIpotential.get_target_distribution" title="Link to this definition">#</a></dt> -<dd></dd></dl> +<dd><p>Get or calculate the target distribution.</p> +</dd></dl> <dl class="py method"> -<dt class="sig sig-object py" id="arbdmodel.ibi.AbstractIBIpotential.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/ibi.html#AbstractIBIpotential.potential"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#arbdmodel.ibi.AbstractIBIpotential.potential" title="Link to this definition">#</a></dt> -<dd></dd></dl> +<dt class="sig sig-object py" id="arbdmodel.ibi.AbstractIBIpotential.get_cg_distribution"> +<span class="sig-name descname"><span class="pre">get_cg_distribution</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">universe</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">trajectory</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</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">recalculate</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/ibi.html#AbstractIBIpotential.get_cg_distribution"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#arbdmodel.ibi.AbstractIBIpotential.get_cg_distribution" title="Link to this definition">#</a></dt> +<dd><p>Get or calculate the coarse-grained distribution.</p> +</dd></dl> <dl class="py method"> <dt class="sig sig-object py" id="arbdmodel.ibi.AbstractIBIpotential.read_cg_potential"> <span class="sig-name descname"><span class="pre">read_cg_potential</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">iteration</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/ibi.html#AbstractIBIpotential.read_cg_potential"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#arbdmodel.ibi.AbstractIBIpotential.read_cg_potential" title="Link to this definition">#</a></dt> -<dd></dd></dl> +<dd><p>Read a potential from a file.</p> +</dd></dl> <dl class="py method"> <dt class="sig sig-object py" id="arbdmodel.ibi.AbstractIBIpotential.write_cg_potential"> <span class="sig-name descname"><span class="pre">write_cg_potential</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">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">scaling_factor</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">tol</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">clean_edges</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">box</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/ibi.html#AbstractIBIpotential.write_cg_potential"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#arbdmodel.ibi.AbstractIBIpotential.write_cg_potential" title="Link to this definition">#</a></dt> +<dd><p>Calculate and save the potential based on distributions.</p> +</dd></dl> + +<p class="rubric">Notes</p> +<p>IBI is an iterative method that refines potentials to match target distributions. +The process involves: +1. Starting with an initial guess (usually Boltzmann inversion of the target) +2. Running simulations with the current potential +3. Comparing resulting distributions with the target +4. Updating the potential based on the difference +5. Repeating until convergence</p> +<dl class="py method"> +<dt class="sig sig-object py" id="id1"> +<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>, <em class="sig-param"><span class="n"><span class="pre">iteration</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">smoothed</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/ibi.html#AbstractIBIpotential.filename"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#id1" title="Link to this definition">#</a></dt> <dd></dd></dl> <dl class="py method"> -<dt class="sig sig-object py" id="arbdmodel.ibi.AbstractIBIpotential.write_file"> -<span class="sig-name descname"><span class="pre">write_file</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="reference internal" href="../../_modules/arbdmodel/ibi.html#AbstractIBIpotential.write_file"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#arbdmodel.ibi.AbstractIBIpotential.write_file" title="Link to this definition">#</a></dt> +<dt class="sig sig-object py" id="id2"> +<span class="sig-name descname"><span class="pre">get_cg_distribution</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">universe</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">trajectory</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</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">recalculate</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/ibi.html#AbstractIBIpotential.get_cg_distribution"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#id2" title="Link to this definition">#</a></dt> +<dd></dd></dl> + +<dl class="py method"> +<dt class="sig sig-object py" id="id3"> +<span class="sig-name descname"><span class="pre">get_target_distribution</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">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">trajectory</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">recalculate</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/ibi.html#AbstractIBIpotential.get_target_distribution"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#id3" title="Link to this definition">#</a></dt> +<dd></dd></dl> + +<dl class="py method"> +<dt class="sig sig-object py" id="id4"> +<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/ibi.html#AbstractIBIpotential.potential"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#id4" title="Link to this definition">#</a></dt> +<dd></dd></dl> + +<dl class="py method"> +<dt class="sig sig-object py" id="id5"> +<span class="sig-name descname"><span class="pre">read_cg_potential</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">iteration</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/ibi.html#AbstractIBIpotential.read_cg_potential"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#id5" title="Link to this definition">#</a></dt> +<dd></dd></dl> + +<dl class="py method"> +<dt class="sig sig-object py" id="id6"> +<span class="sig-name descname"><span class="pre">write_cg_potential</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">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">scaling_factor</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">tol</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">clean_edges</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">box</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/ibi.html#AbstractIBIpotential.write_cg_potential"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#id6" title="Link to this definition">#</a></dt> +<dd></dd></dl> + +<dl class="py method"> +<dt class="sig sig-object py" id="id7"> +<span class="sig-name descname"><span class="pre">write_file</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="reference internal" href="../../_modules/arbdmodel/ibi.html#AbstractIBIpotential.write_file"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#id7" title="Link to this definition">#</a></dt> <dd></dd></dl> </dd></dl> @@ -623,13 +726,22 @@ pairs of particle types (with exclusions!).</p> <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.ibi.AbstractIBIpotential"><code class="docutils literal notranslate"><span class="pre">AbstractIBIpotential</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.ibi.AbstractIBIpotential.bins"><code class="docutils literal notranslate"><span class="pre">AbstractIBIpotential.bins</span></code></a></li> +<li class="toc-h3 nav-item toc-entry"><a class="reference internal nav-link" href="#arbdmodel.ibi.AbstractIBIpotential.potential"><code class="docutils literal notranslate"><span class="pre">AbstractIBIpotential.potential</span></code></a></li> +<li class="toc-h3 nav-item toc-entry"><a class="reference internal nav-link" href="#id0"><code class="docutils literal notranslate"><span class="pre">AbstractIBIpotential.potential()</span></code></a></li> <li class="toc-h3 nav-item toc-entry"><a class="reference internal nav-link" href="#arbdmodel.ibi.AbstractIBIpotential.filename"><code class="docutils literal notranslate"><span class="pre">AbstractIBIpotential.filename()</span></code></a></li> -<li class="toc-h3 nav-item toc-entry"><a class="reference internal nav-link" href="#arbdmodel.ibi.AbstractIBIpotential.get_cg_distribution"><code class="docutils literal notranslate"><span class="pre">AbstractIBIpotential.get_cg_distribution()</span></code></a></li> +<li class="toc-h3 nav-item toc-entry"><a class="reference internal nav-link" href="#arbdmodel.ibi.AbstractIBIpotential.write_file"><code class="docutils literal notranslate"><span class="pre">AbstractIBIpotential.write_file()</span></code></a></li> <li class="toc-h3 nav-item toc-entry"><a class="reference internal nav-link" href="#arbdmodel.ibi.AbstractIBIpotential.get_target_distribution"><code class="docutils literal notranslate"><span class="pre">AbstractIBIpotential.get_target_distribution()</span></code></a></li> -<li class="toc-h3 nav-item toc-entry"><a class="reference internal nav-link" href="#arbdmodel.ibi.AbstractIBIpotential.potential"><code class="docutils literal notranslate"><span class="pre">AbstractIBIpotential.potential()</span></code></a></li> +<li class="toc-h3 nav-item toc-entry"><a class="reference internal nav-link" href="#arbdmodel.ibi.AbstractIBIpotential.get_cg_distribution"><code class="docutils literal notranslate"><span class="pre">AbstractIBIpotential.get_cg_distribution()</span></code></a></li> <li class="toc-h3 nav-item toc-entry"><a class="reference internal nav-link" href="#arbdmodel.ibi.AbstractIBIpotential.read_cg_potential"><code class="docutils literal notranslate"><span class="pre">AbstractIBIpotential.read_cg_potential()</span></code></a></li> <li class="toc-h3 nav-item toc-entry"><a class="reference internal nav-link" href="#arbdmodel.ibi.AbstractIBIpotential.write_cg_potential"><code class="docutils literal notranslate"><span class="pre">AbstractIBIpotential.write_cg_potential()</span></code></a></li> -<li class="toc-h3 nav-item toc-entry"><a class="reference internal nav-link" href="#arbdmodel.ibi.AbstractIBIpotential.write_file"><code class="docutils literal notranslate"><span class="pre">AbstractIBIpotential.write_file()</span></code></a></li> +<li class="toc-h3 nav-item toc-entry"><a class="reference internal nav-link" href="#id1"><code class="docutils literal notranslate"><span class="pre">AbstractIBIpotential.filename()</span></code></a></li> +<li class="toc-h3 nav-item toc-entry"><a class="reference internal nav-link" href="#id2"><code class="docutils literal notranslate"><span class="pre">AbstractIBIpotential.get_cg_distribution()</span></code></a></li> +<li class="toc-h3 nav-item toc-entry"><a class="reference internal nav-link" href="#id3"><code class="docutils literal notranslate"><span class="pre">AbstractIBIpotential.get_target_distribution()</span></code></a></li> +<li class="toc-h3 nav-item toc-entry"><a class="reference internal nav-link" href="#id4"><code class="docutils literal notranslate"><span class="pre">AbstractIBIpotential.potential()</span></code></a></li> +<li class="toc-h3 nav-item toc-entry"><a class="reference internal nav-link" href="#id5"><code class="docutils literal notranslate"><span class="pre">AbstractIBIpotential.read_cg_potential()</span></code></a></li> +<li class="toc-h3 nav-item toc-entry"><a class="reference internal nav-link" href="#id6"><code class="docutils literal notranslate"><span class="pre">AbstractIBIpotential.write_cg_potential()</span></code></a></li> +<li class="toc-h3 nav-item toc-entry"><a class="reference internal nav-link" href="#id7"><code class="docutils literal notranslate"><span class="pre">AbstractIBIpotential.write_file()</span></code></a></li> </ul> </li> <li class="toc-h2 nav-item toc-entry"><a class="reference internal nav-link" href="#arbdmodel.ibi.AngleDof"><code class="docutils literal notranslate"><span class="pre">AngleDof</span></code></a><ul class="nav section-nav flex-column"> diff --git a/_build/html/api/interaction_potentials/index.html b/_build/html/api/interaction_potentials/index.html index 48ad74db3b1a3307b629d5285d928c56dd79acb9..a113e418c96adac24300a50ad0867e68dd1f8d22 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?v=be8a1c11" /> + <link rel="stylesheet" type="text/css" href="../../_static/mystnb.4510f1fc1dee50b3e5859aac5469c37c29e427902b24a333a5f9fcb2f0b3ac41.css" /> <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?v=b4b7a797" /> + <link rel="stylesheet" type="text/css" href="../../_static/proof.css" /> <link rel="stylesheet" type="text/css" href="../../_static/styles/sphinx-examples.css?v=e236af4b" /> - <link rel="stylesheet" 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src="../../_static/tabs.js?v=3ee01567"></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 src="../../_static/js/hoverxref.js"></script> + <script src="../../_static/js/tooltipster.bundle.min.js"></script> + <script src="../../_static/js/micromodal.min.js"></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 537d965a5c68341edcd4ae0e4ad0fd55f2e1974e..5fa3af25f29e4d9c9b47362d331ee96ded65bbb0 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?v=be8a1c11" /> + <link rel="stylesheet" type="text/css" href="../../_static/mystnb.4510f1fc1dee50b3e5859aac5469c37c29e427902b24a333a5f9fcb2f0b3ac41.css" /> <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?v=b4b7a797" /> + <link rel="stylesheet" type="text/css" href="../../_static/proof.css" /> <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?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/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/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?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 src="../../_static/js/hoverxref.js"></script> + <script src="../../_static/js/tooltipster.bundle.min.js"></script> + <script src="../../_static/js/micromodal.min.js"></script> <script>let toggleHintShow = 'Click to show';</script> <script>let toggleHintHide = 'Click to hide';</script> <script>let toggleOpenOnPrint = 'true';</script> @@ -347,11 +347,20 @@ document.write(` <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.interactions.AbstractPotential"><code class="docutils literal notranslate"><span class="pre">AbstractPotential</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.AbstractPotential.filename"><code class="docutils literal notranslate"><span class="pre">AbstractPotential.filename()</span></code></a></li> +<li class="toc-h3 nav-item toc-entry"><a class="reference internal nav-link" href="#arbdmodel.interactions.AbstractPotential.range_"><code class="docutils literal notranslate"><span class="pre">AbstractPotential.range_</span></code></a></li> +<li class="toc-h3 nav-item toc-entry"><a class="reference internal nav-link" href="#arbdmodel.interactions.AbstractPotential.resolution"><code class="docutils literal notranslate"><span class="pre">AbstractPotential.resolution</span></code></a></li> +<li class="toc-h3 nav-item toc-entry"><a class="reference internal nav-link" href="#arbdmodel.interactions.AbstractPotential.max_force"><code class="docutils literal notranslate"><span class="pre">AbstractPotential.max_force</span></code></a></li> +<li class="toc-h3 nav-item toc-entry"><a class="reference internal nav-link" href="#arbdmodel.interactions.AbstractPotential.max_potential"><code class="docutils literal notranslate"><span class="pre">AbstractPotential.max_potential</span></code></a></li> +<li class="toc-h3 nav-item toc-entry"><a class="reference internal nav-link" href="#arbdmodel.interactions.AbstractPotential.zero"><code class="docutils literal notranslate"><span class="pre">AbstractPotential.zero</span></code></a></li> <li class="toc-h3 nav-item toc-entry"><a class="reference internal nav-link" href="#arbdmodel.interactions.AbstractPotential.periodic"><code class="docutils literal notranslate"><span class="pre">AbstractPotential.periodic</span></code></a></li> <li class="toc-h3 nav-item toc-entry"><a class="reference internal nav-link" href="#arbdmodel.interactions.AbstractPotential.potential"><code class="docutils literal notranslate"><span class="pre">AbstractPotential.potential()</span></code></a></li> -<li class="toc-h3 nav-item toc-entry"><a class="reference internal nav-link" href="#arbdmodel.interactions.AbstractPotential.range_"><code class="docutils literal notranslate"><span class="pre">AbstractPotential.range_</span></code></a></li> <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> +<li class="toc-h3 nav-item toc-entry"><a class="reference internal nav-link" href="#arbdmodel.interactions.AbstractPotential.filename"><code class="docutils literal notranslate"><span class="pre">AbstractPotential.filename()</span></code></a></li> +<li class="toc-h3 nav-item toc-entry"><a class="reference internal nav-link" href="#id0"><code class="docutils literal notranslate"><span class="pre">AbstractPotential.filename()</span></code></a></li> +<li class="toc-h3 nav-item toc-entry"><a class="reference internal nav-link" href="#id1"><code class="docutils literal notranslate"><span class="pre">AbstractPotential.periodic</span></code></a></li> +<li class="toc-h3 nav-item toc-entry"><a class="reference internal nav-link" href="#id2"><code class="docutils literal notranslate"><span class="pre">AbstractPotential.potential()</span></code></a></li> +<li class="toc-h3 nav-item toc-entry"><a class="reference internal nav-link" href="#id3"><code class="docutils literal notranslate"><span class="pre">AbstractPotential.range_</span></code></a></li> +<li class="toc-h3 nav-item toc-entry"><a class="reference internal nav-link" href="#id4"><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"> @@ -438,30 +447,138 @@ document.write(` <dt class="sig sig-object py" id="arbdmodel.interactions.AbstractPotential"> <em class="property"><span class="pre">class</span><span class="w"> </span></em><span class="sig-name descname"><span class="pre">AbstractPotential</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#AbstractPotential"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#arbdmodel.interactions.AbstractPotential" 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 writing potentials</p> +<p>Abstract base class for implementing interaction potentials. +This class defines the basic structure for creating and managing interaction potential +functions that can be written to files and used in simulations. +:param <a href="#id1"><span class="problematic" id="id2">range_</span></a>: The range of distances for the potential (min, max).</p> +<blockquote> +<div><p>If max is None, potential extends to infinity.</p> +</div></blockquote> +<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>resolution</strong> (<a class="hxr-hoverxref hxr-tooltip reference external" href="https://docs.python.org/3/library/functions.html#float" title="(in Python v3.13)"><em>float</em></a><em>, </em><em>optional</em>) – The spacing between points in the discretized potential. Default is 0.1.</p></li> +<li><p><strong>max_force</strong> (<a class="hxr-hoverxref hxr-tooltip reference external" href="https://docs.python.org/3/library/functions.html#float" title="(in Python v3.13)"><em>float</em></a><em> or </em><em>None</em><em>, </em><em>optional</em>) – Maximum allowed force magnitude. If provided, forces exceeding this value will be capped.</p></li> +<li><p><strong>max_potential</strong> (<a class="hxr-hoverxref hxr-tooltip reference external" href="https://docs.python.org/3/library/functions.html#float" title="(in Python v3.13)"><em>float</em></a><em> or </em><em>None</em><em>, </em><em>optional</em>) – Maximum allowed potential energy. If provided, the potential will be modified +to ensure it doesn’t exceed this value.</p></li> +<li><p><strong>zero</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>) – Method to set the zero of the potential. Options are: +- ‘min’: Zero is at the minimum value +- ‘first’: Zero is at the first point +- ‘last’: Zero is at the last point</p></li> +</ul> +</dd> +</dl> +<dl class="py attribute"> +<dt class="sig sig-object py" id="arbdmodel.interactions.AbstractPotential.range_"> +<span class="sig-name descname"><span class="pre">range_</span></span><a class="headerlink" href="#arbdmodel.interactions.AbstractPotential.range_" title="Link to this definition">#</a></dt> +<dd><p>The range of distances for the potential.</p> +<dl class="field-list simple"> +<dt class="field-odd">Type<span class="colon">:</span></dt> +<dd class="field-odd"><p><a class="hxr-hoverxref hxr-tooltip reference external" href="https://docs.python.org/3/library/stdtypes.html#tuple" title="(in Python v3.13)">tuple</a> of (<a class="hxr-hoverxref hxr-tooltip reference external" href="https://docs.python.org/3/library/functions.html#float" title="(in Python v3.13)">float</a>, <a class="hxr-hoverxref hxr-tooltip reference external" href="https://docs.python.org/3/library/functions.html#float" title="(in Python v3.13)">float</a> or None)</p> +</dd> +</dl> +</dd></dl> + +<dl class="py attribute"> +<dt class="sig sig-object py" id="arbdmodel.interactions.AbstractPotential.resolution"> +<span class="sig-name descname"><span class="pre">resolution</span></span><a class="headerlink" href="#arbdmodel.interactions.AbstractPotential.resolution" title="Link to this definition">#</a></dt> +<dd><p>The spacing between points in the discretized potential.</p> +<dl class="field-list simple"> +<dt class="field-odd">Type<span class="colon">:</span></dt> +<dd class="field-odd"><p><a class="hxr-hoverxref hxr-tooltip reference external" href="https://docs.python.org/3/library/functions.html#float" title="(in Python v3.13)">float</a></p> +</dd> +</dl> +</dd></dl> + +<dl class="py attribute"> +<dt class="sig sig-object py" id="arbdmodel.interactions.AbstractPotential.max_force"> +<span class="sig-name descname"><span class="pre">max_force</span></span><a class="headerlink" href="#arbdmodel.interactions.AbstractPotential.max_force" title="Link to this definition">#</a></dt> +<dd><p>Maximum allowed force magnitude.</p> +<dl class="field-list simple"> +<dt class="field-odd">Type<span class="colon">:</span></dt> +<dd class="field-odd"><p><a class="hxr-hoverxref hxr-tooltip reference external" href="https://docs.python.org/3/library/functions.html#float" title="(in Python v3.13)">float</a> or None</p> +</dd> +</dl> +</dd></dl> + +<dl class="py attribute"> +<dt class="sig sig-object py" id="arbdmodel.interactions.AbstractPotential.max_potential"> +<span class="sig-name descname"><span class="pre">max_potential</span></span><a class="headerlink" href="#arbdmodel.interactions.AbstractPotential.max_potential" title="Link to this definition">#</a></dt> +<dd><p>Maximum allowed potential energy.</p> +<dl class="field-list simple"> +<dt class="field-odd">Type<span class="colon">:</span></dt> +<dd class="field-odd"><p><a class="hxr-hoverxref hxr-tooltip reference external" href="https://docs.python.org/3/library/functions.html#float" title="(in Python v3.13)">float</a> or None</p> +</dd> +</dl> +</dd></dl> + +<dl class="py attribute"> +<dt class="sig sig-object py" id="arbdmodel.interactions.AbstractPotential.zero"> +<span class="sig-name descname"><span class="pre">zero</span></span><a class="headerlink" href="#arbdmodel.interactions.AbstractPotential.zero" title="Link to this definition">#</a></dt> +<dd><p>Method to set the zero of the potential.</p> +<dl class="field-list simple"> +<dt class="field-odd">Type<span class="colon">:</span></dt> +<dd class="field-odd"><p><a class="hxr-hoverxref hxr-tooltip reference external" href="https://docs.python.org/3/library/stdtypes.html#str" title="(in Python v3.13)">str</a></p> +</dd> +</dl> +</dd></dl> + +<dl class="py attribute"> +<dt class="sig sig-object py" id="arbdmodel.interactions.AbstractPotential.periodic"> +<span class="sig-name descname"><span class="pre">periodic</span></span><a class="headerlink" href="#arbdmodel.interactions.AbstractPotential.periodic" title="Link to this definition">#</a></dt> +<dd><p>Whether the potential is periodic (False by default).</p> +<dl class="field-list simple"> +<dt class="field-odd">Type<span class="colon">:</span></dt> +<dd class="field-odd"><p><a class="hxr-hoverxref hxr-tooltip reference external" href="https://docs.python.org/3/library/functions.html#bool" title="(in Python v3.13)">bool</a></p> +</dd> +</dl> +</dd></dl> + +<dl class="py method"> +<dt class="sig sig-object py" id="arbdmodel.interactions.AbstractPotential.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#AbstractPotential.potential"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#arbdmodel.interactions.AbstractPotential.potential" title="Link to this definition">#</a></dt> +<dd><p>Abstract method that must be implemented by subclasses. +Calculates the potential value at distance r.</p> +</dd></dl> + +<dl class="py method"> +<dt class="sig sig-object py" id="arbdmodel.interactions.AbstractPotential.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#AbstractPotential.write_file"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#arbdmodel.interactions.AbstractPotential.write_file" title="Link to this definition">#</a></dt> +<dd><p>Writes the potential to a file.</p> +</dd></dl> + <dl class="py method"> <dt class="sig sig-object py" id="arbdmodel.interactions.AbstractPotential.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/interactions.html#AbstractPotential.filename"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#arbdmodel.interactions.AbstractPotential.filename" title="Link to this definition">#</a></dt> +<dd><p>Abstract method that should be implemented by subclasses. +Returns a filename for the potential.</p> +</dd></dl> + +<p class="rubric">Notes</p> +<p>Subclasses must implement at minimum the <cite>potential</cite> and <cite>filename</cite> methods.</p> +<dl class="py method"> +<dt class="sig sig-object py" id="id0"> +<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/interactions.html#AbstractPotential.filename"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#id0" title="Link to this definition">#</a></dt> <dd></dd></dl> <dl class="py property"> -<dt class="sig sig-object py" id="arbdmodel.interactions.AbstractPotential.periodic"> -<em class="property"><span class="pre">property</span><span class="w"> </span></em><span class="sig-name descname"><span class="pre">periodic</span></span><a class="headerlink" href="#arbdmodel.interactions.AbstractPotential.periodic" title="Link to this definition">#</a></dt> +<dt class="sig sig-object py" id="id1"> +<em class="property"><span class="pre">property</span><span class="w"> </span></em><span class="sig-name descname"><span class="pre">periodic</span></span><a class="headerlink" href="#id1" title="Link to this definition">#</a></dt> <dd></dd></dl> <dl class="py method"> -<dt class="sig sig-object py" id="arbdmodel.interactions.AbstractPotential.potential"> -<em class="property"><span class="pre">abstract</span><span class="w"> </span></em><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#AbstractPotential.potential"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#arbdmodel.interactions.AbstractPotential.potential" title="Link to this definition">#</a></dt> +<dt class="sig sig-object py" id="id2"> +<em class="property"><span class="pre">abstract</span><span class="w"> </span></em><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#AbstractPotential.potential"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#id2" title="Link to this definition">#</a></dt> <dd></dd></dl> <dl class="py property"> -<dt class="sig sig-object py" id="arbdmodel.interactions.AbstractPotential.range_"> -<em class="property"><span class="pre">property</span><span class="w"> </span></em><span class="sig-name descname"><span class="pre">range_</span></span><a class="headerlink" href="#arbdmodel.interactions.AbstractPotential.range_" title="Link to this definition">#</a></dt> +<dt class="sig sig-object py" id="id3"> +<em class="property"><span class="pre">property</span><span class="w"> </span></em><span class="sig-name descname"><span class="pre">range_</span></span><a class="headerlink" href="#id3" title="Link to this definition">#</a></dt> <dd></dd></dl> <dl class="py method"> -<dt class="sig sig-object py" id="arbdmodel.interactions.AbstractPotential.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#AbstractPotential.write_file"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#arbdmodel.interactions.AbstractPotential.write_file" title="Link to this definition">#</a></dt> +<dt class="sig sig-object py" id="id4"> +<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#AbstractPotential.write_file"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#id4" title="Link to this definition">#</a></dt> <dd></dd></dl> </dd></dl> @@ -736,11 +853,20 @@ for consistency with the AbstractPotential interface.</p> <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.interactions.AbstractPotential"><code class="docutils literal notranslate"><span class="pre">AbstractPotential</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.AbstractPotential.filename"><code class="docutils literal notranslate"><span class="pre">AbstractPotential.filename()</span></code></a></li> +<li class="toc-h3 nav-item toc-entry"><a class="reference internal nav-link" href="#arbdmodel.interactions.AbstractPotential.range_"><code class="docutils literal notranslate"><span class="pre">AbstractPotential.range_</span></code></a></li> +<li class="toc-h3 nav-item toc-entry"><a class="reference internal nav-link" href="#arbdmodel.interactions.AbstractPotential.resolution"><code class="docutils literal notranslate"><span class="pre">AbstractPotential.resolution</span></code></a></li> +<li class="toc-h3 nav-item toc-entry"><a class="reference internal nav-link" href="#arbdmodel.interactions.AbstractPotential.max_force"><code class="docutils literal notranslate"><span class="pre">AbstractPotential.max_force</span></code></a></li> +<li class="toc-h3 nav-item toc-entry"><a class="reference internal nav-link" href="#arbdmodel.interactions.AbstractPotential.max_potential"><code class="docutils literal notranslate"><span class="pre">AbstractPotential.max_potential</span></code></a></li> +<li class="toc-h3 nav-item toc-entry"><a class="reference internal nav-link" href="#arbdmodel.interactions.AbstractPotential.zero"><code class="docutils literal notranslate"><span class="pre">AbstractPotential.zero</span></code></a></li> <li class="toc-h3 nav-item toc-entry"><a class="reference internal nav-link" href="#arbdmodel.interactions.AbstractPotential.periodic"><code class="docutils literal notranslate"><span class="pre">AbstractPotential.periodic</span></code></a></li> <li class="toc-h3 nav-item toc-entry"><a class="reference internal nav-link" href="#arbdmodel.interactions.AbstractPotential.potential"><code class="docutils literal notranslate"><span class="pre">AbstractPotential.potential()</span></code></a></li> -<li class="toc-h3 nav-item toc-entry"><a class="reference internal nav-link" href="#arbdmodel.interactions.AbstractPotential.range_"><code class="docutils literal notranslate"><span class="pre">AbstractPotential.range_</span></code></a></li> <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> +<li class="toc-h3 nav-item toc-entry"><a class="reference internal nav-link" href="#arbdmodel.interactions.AbstractPotential.filename"><code class="docutils literal notranslate"><span class="pre">AbstractPotential.filename()</span></code></a></li> +<li class="toc-h3 nav-item toc-entry"><a class="reference internal nav-link" href="#id0"><code class="docutils literal notranslate"><span class="pre">AbstractPotential.filename()</span></code></a></li> +<li class="toc-h3 nav-item toc-entry"><a class="reference internal nav-link" href="#id1"><code class="docutils literal notranslate"><span class="pre">AbstractPotential.periodic</span></code></a></li> +<li class="toc-h3 nav-item toc-entry"><a class="reference internal nav-link" href="#id2"><code class="docutils literal notranslate"><span class="pre">AbstractPotential.potential()</span></code></a></li> +<li class="toc-h3 nav-item toc-entry"><a class="reference internal nav-link" href="#id3"><code class="docutils literal notranslate"><span class="pre">AbstractPotential.range_</span></code></a></li> +<li class="toc-h3 nav-item toc-entry"><a class="reference internal nav-link" href="#id4"><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"> diff --git a/_build/html/api/polymer_modeling/fjc_polymer_model.html b/_build/html/api/polymer_modeling/fjc_polymer_model.html index 64a5b45512e8fc57f5690e8a14876faf2e8a8c0f..8babd4b9dd5d1df29c6510559c0ea606bb7b501b 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?v=be8a1c11" /> + <link rel="stylesheet" type="text/css" href="../../_static/mystnb.4510f1fc1dee50b3e5859aac5469c37c29e427902b24a333a5f9fcb2f0b3ac41.css" /> <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?v=b4b7a797" /> + <link rel="stylesheet" type="text/css" href="../../_static/proof.css" /> <link rel="stylesheet" type="text/css" href="../../_static/styles/sphinx-examples.css?v=e236af4b" /> - <link 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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/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?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 src="../../_static/js/hoverxref.js"></script> + <script src="../../_static/js/tooltipster.bundle.min.js"></script> + <script src="../../_static/js/micromodal.min.js"></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 8b1e2842379dc66b94d65b2501673ffb0bf94366..5f13b6fd7d98625a9b64da9c39476bb81e4a0999 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?v=be8a1c11" /> + <link rel="stylesheet" type="text/css" href="../../_static/mystnb.4510f1fc1dee50b3e5859aac5469c37c29e427902b24a333a5f9fcb2f0b3ac41.css" /> <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?v=b4b7a797" /> + <link rel="stylesheet" type="text/css" href="../../_static/proof.css" /> <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?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/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/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?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 src="../../_static/js/hoverxref.js"></script> + <script src="../../_static/js/tooltipster.bundle.min.js"></script> + <script src="../../_static/js/micromodal.min.js"></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 aff54d1930cca49815ea5fec3f84749d5f135a99..d64c0d2c13d32e4ebf0b48f7eaf388ebad1cf96c 100644 --- a/_build/html/api/polymer_modeling/index.html +++ b/_build/html/api/polymer_modeling/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?v=be8a1c11" /> + <link rel="stylesheet" type="text/css" href="../../_static/mystnb.4510f1fc1dee50b3e5859aac5469c37c29e427902b24a333a5f9fcb2f0b3ac41.css" /> <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?v=b4b7a797" /> + <link rel="stylesheet" type="text/css" href="../../_static/proof.css" /> <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?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/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/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?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 src="../../_static/js/hoverxref.js"></script> + <script src="../../_static/js/tooltipster.bundle.min.js"></script> + <script src="../../_static/js/micromodal.min.js"></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 7da886fc925c29b37aeaa7e7efcf1a05c3d33604..f2dd7dc7c36a714f2a729d9cd9096fa5632627b0 100644 --- a/_build/html/api/polymer_modeling/kh_polymer_model.html +++ b/_build/html/api/polymer_modeling/kh_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?v=be8a1c11" /> + <link rel="stylesheet" type="text/css" href="../../_static/mystnb.4510f1fc1dee50b3e5859aac5469c37c29e427902b24a333a5f9fcb2f0b3ac41.css" /> <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?v=b4b7a797" /> + <link rel="stylesheet" type="text/css" href="../../_static/proof.css" /> <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?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/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/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?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 src="../../_static/js/hoverxref.js"></script> + <script src="../../_static/js/tooltipster.bundle.min.js"></script> + <script src="../../_static/js/micromodal.min.js"></script> <script>let toggleHintShow = 'Click to show';</script> <script>let toggleHintHide = 'Click to hide';</script> <script>let toggleOpenOnPrint = 'true';</script> @@ -353,7 +353,10 @@ document.write(` </ul> </li> <li class="toc-h2 nav-item toc-entry"><a class="reference internal nav-link" href="#arbdmodel.kh_polymer_model.KhNonbonded"><code class="docutils literal notranslate"><span class="pre">KhNonbonded</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.kh_polymer_model.KhNonbonded.debye_length"><code class="docutils literal notranslate"><span class="pre">KhNonbonded.debye_length</span></code></a></li> +<li class="toc-h3 nav-item toc-entry"><a class="reference internal nav-link" href="#arbdmodel.kh_polymer_model.KhNonbonded.max_force"><code class="docutils literal notranslate"><span class="pre">KhNonbonded.max_force</span></code></a></li> <li class="toc-h3 nav-item toc-entry"><a class="reference internal nav-link" href="#arbdmodel.kh_polymer_model.KhNonbonded.potential"><code class="docutils literal notranslate"><span class="pre">KhNonbonded.potential()</span></code></a></li> +<li class="toc-h3 nav-item toc-entry"><a class="reference internal nav-link" href="#id0"><code class="docutils literal notranslate"><span class="pre">KhNonbonded.potential()</span></code></a></li> </ul> </li> </ul> @@ -397,9 +400,57 @@ document.write(` <dt class="sig sig-object py" id="arbdmodel.kh_polymer_model.KhNonbonded"> <em class="property"><span class="pre">class</span><span class="w"> </span></em><span class="sig-name descname"><span class="pre">KhNonbonded</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">0.1</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">None)</span></span></em><span class="sig-paren">)</span><a class="reference internal" href="../../_modules/arbdmodel/kh_polymer_model.html#KhNonbonded"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#arbdmodel.kh_polymer_model.KhNonbonded" 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>A class implementing the Kim-Hummer nonbonded potential energy model for protein interactions. +This model combines electrostatic interactions with a modified Lennard-Jones potential +that accounts for hydrophobic effects using the KH (Kim-Hummer) scaling approach. +The potential is particularly useful for modeling interactions between intrinsically +disordered proteins (IDPs) and folded proteins.</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>debye_length</strong> (<a class="hxr-hoverxref hxr-tooltip reference external" href="https://docs.python.org/3/library/functions.html#float" title="(in Python v3.13)"><em>float</em></a><em>, </em><em>optional</em>) – The Debye screening length in Angstroms, default is 10Ã…</p></li> +<li><p><strong>resolution</strong> (<a class="hxr-hoverxref hxr-tooltip reference external" href="https://docs.python.org/3/library/functions.html#float" title="(in Python v3.13)"><em>float</em></a><em>, </em><em>optional</em>) – The spatial resolution for potential calculations, default is 0.1Ã…</p></li> +<li><p><strong>range</strong> (<a class="hxr-hoverxref hxr-tooltip reference external" href="https://docs.python.org/3/library/stdtypes.html#tuple" title="(in Python v3.13)"><em>tuple</em></a><em>, </em><em>optional</em>) – The range of distances (min, max) over which to compute the potential, +default is (0, None) where None means no upper limit</p></li> +</ul> +</dd> +</dl> +<dl class="py attribute"> +<dt class="sig sig-object py" id="arbdmodel.kh_polymer_model.KhNonbonded.debye_length"> +<span class="sig-name descname"><span class="pre">debye_length</span></span><a class="headerlink" href="#arbdmodel.kh_polymer_model.KhNonbonded.debye_length" title="Link to this definition">#</a></dt> +<dd><p>The Debye screening length in Angstroms</p> +<dl class="field-list simple"> +<dt class="field-odd">Type<span class="colon">:</span></dt> +<dd class="field-odd"><p><a class="hxr-hoverxref hxr-tooltip reference external" href="https://docs.python.org/3/library/functions.html#float" title="(in Python v3.13)">float</a></p> +</dd> +</dl> +</dd></dl> + +<dl class="py attribute"> +<dt class="sig sig-object py" id="arbdmodel.kh_polymer_model.KhNonbonded.max_force"> +<span class="sig-name descname"><span class="pre">max_force</span></span><a class="headerlink" href="#arbdmodel.kh_polymer_model.KhNonbonded.max_force" title="Link to this definition">#</a></dt> +<dd><p>Maximum allowed force from this potential, set to 50</p> +<dl class="field-list simple"> +<dt class="field-odd">Type<span class="colon">:</span></dt> +<dd class="field-odd"><p><a class="hxr-hoverxref hxr-tooltip reference external" href="https://docs.python.org/3/library/functions.html#float" title="(in Python v3.13)">float</a></p> +</dd> +</dl> +</dd></dl> + <dl class="py method"> <dt class="sig sig-object py" id="arbdmodel.kh_polymer_model.KhNonbonded.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/kh_polymer_model.html#KhNonbonded.potential"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#arbdmodel.kh_polymer_model.KhNonbonded.potential" title="Link to this definition">#</a></dt> +<dd><p>Calculates the nonbonded potential energy between two atom types at distance r. +Combines electrostatic interactions with a modified Lennard-Jones potential.</p> +</dd></dl> + +<p class="rubric">References</p> +<p>Kim, Y. C., & Hummer, G. (2008). Coarse-grained models for simulations of +multiprotein complexes: application to ubiquitin binding. Journal of molecular +biology, 375(5), 1416-1433.</p> +<dl class="py method"> +<dt class="sig sig-object py" id="id0"> +<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/kh_polymer_model.html#KhNonbonded.potential"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#id0" title="Link to this definition">#</a></dt> <dd><p>Electrostatics</p> </dd></dl> @@ -460,7 +511,10 @@ document.write(` </ul> </li> <li class="toc-h2 nav-item toc-entry"><a class="reference internal nav-link" href="#arbdmodel.kh_polymer_model.KhNonbonded"><code class="docutils literal notranslate"><span class="pre">KhNonbonded</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.kh_polymer_model.KhNonbonded.debye_length"><code class="docutils literal notranslate"><span class="pre">KhNonbonded.debye_length</span></code></a></li> +<li class="toc-h3 nav-item toc-entry"><a class="reference internal nav-link" href="#arbdmodel.kh_polymer_model.KhNonbonded.max_force"><code class="docutils literal notranslate"><span class="pre">KhNonbonded.max_force</span></code></a></li> <li class="toc-h3 nav-item toc-entry"><a class="reference internal nav-link" href="#arbdmodel.kh_polymer_model.KhNonbonded.potential"><code class="docutils literal notranslate"><span class="pre">KhNonbonded.potential()</span></code></a></li> +<li class="toc-h3 nav-item toc-entry"><a class="reference internal nav-link" href="#id0"><code class="docutils literal notranslate"><span class="pre">KhNonbonded.potential()</span></code></a></li> </ul> </li> </ul> diff --git a/_build/html/api/polymer_modeling/mpipi_polymer.html b/_build/html/api/polymer_modeling/mpipi_polymer.html index 5dad403b28fad6c0c0a234d3e5b3d42480ec5dca..7e755840719e5a7a621949ccd0dfb64ca25e903d 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?v=be8a1c11" /> + <link rel="stylesheet" type="text/css" href="../../_static/mystnb.4510f1fc1dee50b3e5859aac5469c37c29e427902b24a333a5f9fcb2f0b3ac41.css" /> <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?v=b4b7a797" /> + <link rel="stylesheet" type="text/css" href="../../_static/proof.css" /> <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?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/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/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?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 src="../../_static/js/hoverxref.js"></script> + <script src="../../_static/js/tooltipster.bundle.min.js"></script> + <script src="../../_static/js/micromodal.min.js"></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 4cbc83c3ccba60db0cb36e1f3f9e851b3cd0e28e..b95148bcda67979906b92126675252a4fe39568e 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?v=be8a1c11" /> + <link rel="stylesheet" type="text/css" href="../../_static/mystnb.4510f1fc1dee50b3e5859aac5469c37c29e427902b24a333a5f9fcb2f0b3ac41.css" /> <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?v=b4b7a797" /> + <link rel="stylesheet" type="text/css" href="../../_static/proof.css" /> <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?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/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/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?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 src="../../_static/js/hoverxref.js"></script> + <script src="../../_static/js/tooltipster.bundle.min.js"></script> + <script src="../../_static/js/micromodal.min.js"></script> <script>let toggleHintShow = 'Click to show';</script> <script>let toggleHintHide = 'Click to hide';</script> <script>let toggleOpenOnPrint = 'true';</script> @@ -346,13 +346,24 @@ 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.onck_polymer_model.OnckBeads"><code class="docutils literal notranslate"><span class="pre">OnckBeads</span></code></a></li> +<li class="toc-h2 nav-item toc-entry"><a class="reference internal nav-link" href="#arbdmodel.onck_polymer_model.OnckBeads"><code class="docutils literal notranslate"><span class="pre">OnckBeads</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.onck_polymer_model.OnckBeads.version"><code class="docutils literal notranslate"><span class="pre">OnckBeads.version</span></code></a></li> +<li class="toc-h3 nav-item toc-entry"><a class="reference internal nav-link" href="#arbdmodel.onck_polymer_model.OnckBeads.types_dict"><code class="docutils literal notranslate"><span class="pre">OnckBeads.types_dict</span></code></a></li> +<li class="toc-h3 nav-item toc-entry"><a class="reference internal nav-link" href="#arbdmodel.onck_polymer_model.OnckBeads.peptide_bond"><code class="docutils literal notranslate"><span class="pre">OnckBeads.peptide_bond</span></code></a></li> +<li class="toc-h3 nav-item toc-entry"><a class="reference internal nav-link" href="#arbdmodel.onck_polymer_model.OnckBeads.polymer"><code class="docutils literal notranslate"><span class="pre">OnckBeads.polymer</span></code></a></li> +<li class="toc-h3 nav-item toc-entry"><a class="reference internal nav-link" href="#arbdmodel.onck_polymer_model.OnckBeads.sequence"><code class="docutils literal notranslate"><span class="pre">OnckBeads.sequence</span></code></a></li> +<li class="toc-h3 nav-item toc-entry"><a class="reference internal nav-link" href="#arbdmodel.onck_polymer_model.OnckBeads.spring_constant"><code class="docutils literal notranslate"><span class="pre">OnckBeads.spring_constant</span></code></a></li> +</ul> +</li> <li class="toc-h2 nav-item toc-entry"><a class="reference internal nav-link" href="#arbdmodel.onck_polymer_model.OnckModel"><code class="docutils literal notranslate"><span class="pre">OnckModel</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.onck_polymer_model.OnckModel.set_damping_coefficient"><code class="docutils literal notranslate"><span class="pre">OnckModel.set_damping_coefficient()</span></code></a></li> </ul> </li> <li class="toc-h2 nav-item toc-entry"><a class="reference internal nav-link" href="#arbdmodel.onck_polymer_model.OnckNonbonded"><code class="docutils literal notranslate"><span class="pre">OnckNonbonded</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.onck_polymer_model.OnckNonbonded.debye_length"><code class="docutils literal notranslate"><span class="pre">OnckNonbonded.debye_length</span></code></a></li> +<li class="toc-h3 nav-item toc-entry"><a class="reference internal nav-link" href="#arbdmodel.onck_polymer_model.OnckNonbonded.max_force"><code class="docutils literal notranslate"><span class="pre">OnckNonbonded.max_force</span></code></a></li> <li class="toc-h3 nav-item toc-entry"><a class="reference internal nav-link" href="#arbdmodel.onck_polymer_model.OnckNonbonded.potential"><code class="docutils literal notranslate"><span class="pre">OnckNonbonded.potential()</span></code></a></li> +<li class="toc-h3 nav-item toc-entry"><a class="reference internal nav-link" href="#id0"><code class="docutils literal notranslate"><span class="pre">OnckNonbonded.potential()</span></code></a></li> </ul> </li> </ul> @@ -373,6 +384,100 @@ document.write(` <dt class="sig sig-object py" id="arbdmodel.onck_polymer_model.OnckBeads"> <em class="property"><span class="pre">class</span><span class="w"> </span></em><span class="sig-name descname"><span class="pre">OnckBeads</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">spring_constant</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">38.422562</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">3.8</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">version</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/onck_polymer_model.html#OnckBeads"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#arbdmodel.onck_polymer_model.OnckBeads" title="Link to this definition">#</a></dt> <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> +<p>A class that represents polymer beads in the Onck model.</p> +<p>The Onck model is a coarse-grained model for proteins where each amino acid is represented +by a single bead. The model includes specific bonded interactions (bonds, angles, dihedrals) +based on the amino acid types in the sequence.</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>polymer</strong> (<em>Polymer</em>) – The parent polymer object to which these beads belong.</p></li> +<li><p><strong>sequence</strong> (<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>) – The sequence of amino acid types for each bead, must match polymer length.</p></li> +<li><p><strong>spring_constant</strong> (<a class="hxr-hoverxref hxr-tooltip reference external" href="https://docs.python.org/3/library/functions.html#float" title="(in Python v3.13)"><em>float</em></a><em>, </em><em>default=38.422562</em>) – Spring constant for peptide bonds in units of 8038 kJ/(N_A nm^2) or 0.5 kcal_mol/AA^2.</p></li> +<li><p><strong>rest_length</strong> (<a class="hxr-hoverxref hxr-tooltip reference external" href="https://docs.python.org/3/library/functions.html#float" title="(in Python v3.13)"><em>float</em></a><em>, </em><em>default=3.8</em>) – Equilibrium length of peptide bonds.</p></li> +<li><p><strong>version</strong> (<a class="hxr-hoverxref hxr-tooltip reference external" href="https://docs.python.org/3/library/functions.html#float" title="(in Python v3.13)"><em>float</em></a><em>, </em><em>optional</em>) – Version of the Onck model to use. Defaults to 1.1 if not specified.</p></li> +<li><p><strong>**kwargs</strong> – Additional keyword arguments passed to the parent PolymerBeads constructor.</p></li> +</ul> +</dd> +</dl> +<dl class="py attribute"> +<dt class="sig sig-object py" id="arbdmodel.onck_polymer_model.OnckBeads.version"> +<span class="sig-name descname"><span class="pre">version</span></span><a class="headerlink" href="#arbdmodel.onck_polymer_model.OnckBeads.version" title="Link to this definition">#</a></dt> +<dd><p>The version of the Onck model being used.</p> +<dl class="field-list simple"> +<dt class="field-odd">Type<span class="colon">:</span></dt> +<dd class="field-odd"><p><a class="hxr-hoverxref hxr-tooltip reference external" href="https://docs.python.org/3/library/functions.html#float" title="(in Python v3.13)">float</a></p> +</dd> +</dl> +</dd></dl> + +<dl class="py attribute"> +<dt class="sig sig-object py" id="arbdmodel.onck_polymer_model.OnckBeads.types_dict"> +<span class="sig-name descname"><span class="pre">types_dict</span></span><a class="headerlink" href="#arbdmodel.onck_polymer_model.OnckBeads.types_dict" title="Link to this definition">#</a></dt> +<dd><p>Mapping between amino acid codes and bead types.</p> +<dl class="field-list simple"> +<dt class="field-odd">Type<span class="colon">:</span></dt> +<dd class="field-odd"><p><a class="hxr-hoverxref hxr-tooltip reference external" href="https://docs.python.org/3/library/stdtypes.html#dict" title="(in Python v3.13)">dict</a></p> +</dd> +</dl> +</dd></dl> + +<dl class="py attribute"> +<dt class="sig sig-object py" id="arbdmodel.onck_polymer_model.OnckBeads.peptide_bond"> +<span class="sig-name descname"><span class="pre">peptide_bond</span></span><a class="headerlink" href="#arbdmodel.onck_polymer_model.OnckBeads.peptide_bond" title="Link to this definition">#</a></dt> +<dd><p>Bond potential used for peptide bonds between adjacent beads.</p> +<dl class="field-list simple"> +<dt class="field-odd">Type<span class="colon">:</span></dt> +<dd class="field-odd"><p><a class="reference internal" href="../interaction_potentials/interactions.html#arbdmodel.interactions.HarmonicBond" title="arbdmodel.interactions.HarmonicBond">HarmonicBond</a></p> +</dd> +</dl> +</dd></dl> + +<dl class="py attribute"> +<dt class="sig sig-object py" id="arbdmodel.onck_polymer_model.OnckBeads.polymer"> +<span class="sig-name descname"><span class="pre">polymer</span></span><a class="headerlink" href="#arbdmodel.onck_polymer_model.OnckBeads.polymer" title="Link to this definition">#</a></dt> +<dd><p>Reference to the parent polymer object.</p> +<dl class="field-list simple"> +<dt class="field-odd">Type<span class="colon">:</span></dt> +<dd class="field-odd"><p>Polymer</p> +</dd> +</dl> +</dd></dl> + +<dl class="py attribute"> +<dt class="sig sig-object py" id="arbdmodel.onck_polymer_model.OnckBeads.sequence"> +<span class="sig-name descname"><span class="pre">sequence</span></span><a class="headerlink" href="#arbdmodel.onck_polymer_model.OnckBeads.sequence" title="Link to this definition">#</a></dt> +<dd><p>The amino acid sequence.</p> +<dl class="field-list simple"> +<dt class="field-odd">Type<span class="colon">:</span></dt> +<dd class="field-odd"><p><a class="hxr-hoverxref hxr-tooltip reference external" href="https://docs.python.org/3/library/stdtypes.html#list" title="(in Python v3.13)">list</a></p> +</dd> +</dl> +</dd></dl> + +<dl class="py attribute"> +<dt class="sig sig-object py" id="arbdmodel.onck_polymer_model.OnckBeads.spring_constant"> +<span class="sig-name descname"><span class="pre">spring_constant</span></span><a class="headerlink" href="#arbdmodel.onck_polymer_model.OnckBeads.spring_constant" title="Link to this definition">#</a></dt> +<dd><p>The spring constant used for peptide bonds.</p> +<dl class="field-list simple"> +<dt class="field-odd">Type<span class="colon">:</span></dt> +<dd class="field-odd"><p><a class="hxr-hoverxref hxr-tooltip reference external" href="https://docs.python.org/3/library/functions.html#float" title="(in Python v3.13)">float</a></p> +</dd> +</dl> +</dd></dl> + +<dl class="field-list simple"> +<dt class="field-odd">Raises<span class="colon">:</span></dt> +<dd class="field-odd"><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 version is not supported or if the sequence length doesn’t match the polymer length.</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 sequence is None (random sequence generation not implemented).</p></li> +</ul> +</dd> +</dl> +<p class="rubric">Notes</p> +<p>The Onck model distinguishes between proline (P), glycine (G), and all other amino acids (X) +for certain bonded interactions. Special potentials are loaded from files for angle and +dihedral interactions based on this classification.</p> </dd></dl> <dl class="py class"> @@ -390,10 +495,60 @@ document.write(` <dt class="sig sig-object py" id="arbdmodel.onck_polymer_model.OnckNonbonded"> <em class="property"><span class="pre">class</span><span class="w"> </span></em><span class="sig-name descname"><span class="pre">OnckNonbonded</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">12.7</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">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><span class="sig-paren">)</span><a class="reference internal" href="../../_modules/arbdmodel/onck_polymer_model.html#OnckNonbonded"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#arbdmodel.onck_polymer_model.OnckNonbonded" 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 interaction for 1BPA and 1BPA-1.1</p> +<p>Nonbonded interaction potential for 1BPA and 1BPA-1.1.</p> +<p>This class implements nonbonded interactions including electrostatics with +distance-dependent dielectric and Lennard-Jones type potentials.</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>debye_length</strong> (<a class="hxr-hoverxref hxr-tooltip reference external" href="https://docs.python.org/3/library/functions.html#float" title="(in Python v3.13)"><em>float</em></a><em>, </em><em>optional</em>) – The Debye-Hückel screening length in angstroms. Default is 12.7 Ã….</p></li> +<li><p><strong>resolution</strong> (<a class="hxr-hoverxref hxr-tooltip reference external" href="https://docs.python.org/3/library/functions.html#float" title="(in Python v3.13)"><em>float</em></a><em>, </em><em>optional</em>) – The spatial resolution for potential calculation. Default is 0.1 Ã….</p></li> +<li><p><strong>range</strong> (<a class="hxr-hoverxref hxr-tooltip reference external" href="https://docs.python.org/3/library/stdtypes.html#tuple" title="(in Python v3.13)"><em>tuple</em></a><em>, </em><em>optional</em>) – The range of distances for which to calculate the potential. Default is (0, None).</p></li> +</ul> +</dd> +</dl> +<dl class="py attribute"> +<dt class="sig sig-object py" id="arbdmodel.onck_polymer_model.OnckNonbonded.debye_length"> +<span class="sig-name descname"><span class="pre">debye_length</span></span><a class="headerlink" href="#arbdmodel.onck_polymer_model.OnckNonbonded.debye_length" title="Link to this definition">#</a></dt> +<dd><p>The Debye-Hückel screening length in angstroms.</p> +<dl class="field-list simple"> +<dt class="field-odd">Type<span class="colon">:</span></dt> +<dd class="field-odd"><p><a class="hxr-hoverxref hxr-tooltip reference external" href="https://docs.python.org/3/library/functions.html#float" title="(in Python v3.13)">float</a></p> +</dd> +</dl> +</dd></dl> + +<dl class="py attribute"> +<dt class="sig sig-object py" id="arbdmodel.onck_polymer_model.OnckNonbonded.max_force"> +<span class="sig-name descname"><span class="pre">max_force</span></span><a class="headerlink" href="#arbdmodel.onck_polymer_model.OnckNonbonded.max_force" title="Link to this definition">#</a></dt> +<dd><p>Maximum allowed force in the system, used as a cap for stability.</p> +<dl class="field-list simple"> +<dt class="field-odd">Type<span class="colon">:</span></dt> +<dd class="field-odd"><p><a class="hxr-hoverxref hxr-tooltip reference external" href="https://docs.python.org/3/library/functions.html#float" title="(in Python v3.13)">float</a></p> +</dd> +</dl> +</dd></dl> + <dl class="py method"> <dt class="sig sig-object py" id="arbdmodel.onck_polymer_model.OnckNonbonded.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/onck_polymer_model.html#OnckNonbonded.potential"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#arbdmodel.onck_polymer_model.OnckNonbonded.potential" title="Link to this definition">#</a></dt> +<dd><p>Calculate the nonbonded potential energy between two residue types at distance r.</p> +</dd></dl> + +<p class="rubric">Notes</p> +<p>The potential includes: +1. Electrostatic interactions with distance-dependent dielectric constant +2. Modified Lennard-Jones interactions that depend on residue types:</p> +<blockquote> +<div><ul class="simple"> +<li><p>Special 8-6 LJ potential for cationic-aromatic interactions in 1.0cp/1.1 versions</p></li> +<li><p>General LJ-type potential for other interactions</p></li> +</ul> +</div></blockquote> +<p>The effective dielectric D decreases with distance according to a specific formula.</p> +<dl class="py method"> +<dt class="sig sig-object py" id="id0"> +<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/onck_polymer_model.html#OnckNonbonded.potential"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#id0" title="Link to this definition">#</a></dt> <dd><p>Electrostatics</p> </dd></dl> @@ -447,13 +602,24 @@ 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.onck_polymer_model.OnckBeads"><code class="docutils literal notranslate"><span class="pre">OnckBeads</span></code></a></li> +<li class="toc-h2 nav-item toc-entry"><a class="reference internal nav-link" href="#arbdmodel.onck_polymer_model.OnckBeads"><code class="docutils literal notranslate"><span class="pre">OnckBeads</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.onck_polymer_model.OnckBeads.version"><code class="docutils literal notranslate"><span class="pre">OnckBeads.version</span></code></a></li> +<li class="toc-h3 nav-item toc-entry"><a class="reference internal nav-link" href="#arbdmodel.onck_polymer_model.OnckBeads.types_dict"><code class="docutils literal notranslate"><span class="pre">OnckBeads.types_dict</span></code></a></li> +<li class="toc-h3 nav-item toc-entry"><a class="reference internal nav-link" href="#arbdmodel.onck_polymer_model.OnckBeads.peptide_bond"><code class="docutils literal notranslate"><span class="pre">OnckBeads.peptide_bond</span></code></a></li> +<li class="toc-h3 nav-item toc-entry"><a class="reference internal nav-link" href="#arbdmodel.onck_polymer_model.OnckBeads.polymer"><code class="docutils literal notranslate"><span class="pre">OnckBeads.polymer</span></code></a></li> +<li class="toc-h3 nav-item toc-entry"><a class="reference internal nav-link" href="#arbdmodel.onck_polymer_model.OnckBeads.sequence"><code class="docutils literal notranslate"><span class="pre">OnckBeads.sequence</span></code></a></li> +<li class="toc-h3 nav-item toc-entry"><a class="reference internal nav-link" href="#arbdmodel.onck_polymer_model.OnckBeads.spring_constant"><code class="docutils literal notranslate"><span class="pre">OnckBeads.spring_constant</span></code></a></li> +</ul> +</li> <li class="toc-h2 nav-item toc-entry"><a class="reference internal nav-link" href="#arbdmodel.onck_polymer_model.OnckModel"><code class="docutils literal notranslate"><span class="pre">OnckModel</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.onck_polymer_model.OnckModel.set_damping_coefficient"><code class="docutils literal notranslate"><span class="pre">OnckModel.set_damping_coefficient()</span></code></a></li> </ul> </li> <li class="toc-h2 nav-item toc-entry"><a class="reference internal nav-link" href="#arbdmodel.onck_polymer_model.OnckNonbonded"><code class="docutils literal notranslate"><span class="pre">OnckNonbonded</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.onck_polymer_model.OnckNonbonded.debye_length"><code class="docutils literal notranslate"><span class="pre">OnckNonbonded.debye_length</span></code></a></li> +<li class="toc-h3 nav-item toc-entry"><a class="reference internal nav-link" href="#arbdmodel.onck_polymer_model.OnckNonbonded.max_force"><code class="docutils literal notranslate"><span class="pre">OnckNonbonded.max_force</span></code></a></li> <li class="toc-h3 nav-item toc-entry"><a class="reference internal nav-link" href="#arbdmodel.onck_polymer_model.OnckNonbonded.potential"><code class="docutils literal notranslate"><span class="pre">OnckNonbonded.potential()</span></code></a></li> +<li class="toc-h3 nav-item toc-entry"><a class="reference internal nav-link" href="#id0"><code class="docutils literal notranslate"><span class="pre">OnckNonbonded.potential()</span></code></a></li> </ul> </li> </ul> diff --git a/_build/html/api/polymer_modeling/polymer.html b/_build/html/api/polymer_modeling/polymer.html index 3c00dc073280c440ff894ff1fa43a90b20414af3..9f2e00fd24b2056146b8c1046ac71719749ba221 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?v=be8a1c11" /> + <link rel="stylesheet" type="text/css" href="../../_static/mystnb.4510f1fc1dee50b3e5859aac5469c37c29e427902b24a333a5f9fcb2f0b3ac41.css" /> <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?v=b4b7a797" /> + <link rel="stylesheet" type="text/css" href="../../_static/proof.css" /> <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?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/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/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?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 src="../../_static/js/hoverxref.js"></script> + <script src="../../_static/js/tooltipster.bundle.min.js"></script> + <script src="../../_static/js/micromodal.min.js"></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/sali_polymer_model.html b/_build/html/api/polymer_modeling/sali_polymer_model.html index 1feeb534e607b5fcf5ee9fb59232955ecbc29cb2..2742a95159799b42a3e6453d8e00a13e1d0d96f2 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?v=be8a1c11" /> + <link rel="stylesheet" type="text/css" href="../../_static/mystnb.4510f1fc1dee50b3e5859aac5469c37c29e427902b24a333a5f9fcb2f0b3ac41.css" /> <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?v=b4b7a797" /> + <link rel="stylesheet" type="text/css" href="../../_static/proof.css" /> <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?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/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" /> + 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'true';</script> diff --git a/_build/html/api/polymer_modeling/ssdna_two_bead.html b/_build/html/api/polymer_modeling/ssdna_two_bead.html index 9cddcd48dc13841fd0d52475835e442c07c62e30..2d017b03ab09b5bd8c786a58d431a8aefe097900 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?v=be8a1c11" /> + <link rel="stylesheet" type="text/css" href="../../_static/mystnb.4510f1fc1dee50b3e5859aac5469c37c29e427902b24a333a5f9fcb2f0b3ac41.css" /> <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?v=b4b7a797" /> + <link rel="stylesheet" type="text/css" href="../../_static/proof.css" /> <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?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/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/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?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 src="../../_static/js/hoverxref.js"></script> + <script src="../../_static/js/tooltipster.bundle.min.js"></script> + <script src="../../_static/js/micromodal.min.js"></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/rigidbody_models/index.html b/_build/html/api/rigidbody_models/index.html index 05bb82ed4904227335e1ef61f7b875738b2f6496..1bb772d34fe8dbbe9e45090a8fc2ac5baaf874fc 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?v=be8a1c11" /> + <link rel="stylesheet" type="text/css" href="../../_static/mystnb.4510f1fc1dee50b3e5859aac5469c37c29e427902b24a333a5f9fcb2f0b3ac41.css" /> <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?v=b4b7a797" /> + <link rel="stylesheet" type="text/css" href="../../_static/proof.css" /> <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?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/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" /> + 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'true';</script> diff --git a/_build/html/api/rigidbody_models/mesh_process_surface.html b/_build/html/api/rigidbody_models/mesh_process_surface.html index 7a72f906f33d6121c29559b523c71109ef3ad646..952b3c4bc624c5e39ab3fb0136e3e4d4e819d0d5 100644 --- a/_build/html/api/rigidbody_models/mesh_process_surface.html +++ b/_build/html/api/rigidbody_models/mesh_process_surface.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?v=be8a1c11" /> + <link rel="stylesheet" type="text/css" href="../../_static/mystnb.4510f1fc1dee50b3e5859aac5469c37c29e427902b24a333a5f9fcb2f0b3ac41.css" /> <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?v=b4b7a797" /> + <link rel="stylesheet" type="text/css" href="../../_static/proof.css" /> <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?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/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/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?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 src="../../_static/js/hoverxref.js"></script> + <script src="../../_static/js/tooltipster.bundle.min.js"></script> + <script src="../../_static/js/micromodal.min.js"></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/rigidbody_models/mesh_process_volume.html b/_build/html/api/rigidbody_models/mesh_process_volume.html index 1487ed12a0ab8f7f869c60d3bb39083c534dbe21..4c5f804f52a3331d1e4c65ac28338cd20a3df75a 100644 --- a/_build/html/api/rigidbody_models/mesh_process_volume.html +++ b/_build/html/api/rigidbody_models/mesh_process_volume.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?v=be8a1c11" /> + <link rel="stylesheet" type="text/css" href="../../_static/mystnb.4510f1fc1dee50b3e5859aac5469c37c29e427902b24a333a5f9fcb2f0b3ac41.css" /> <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?v=b4b7a797" /> + <link rel="stylesheet" type="text/css" href="../../_static/proof.css" /> <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?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/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/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?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 src="../../_static/js/hoverxref.js"></script> + <script src="../../_static/js/tooltipster.bundle.min.js"></script> + <script src="../../_static/js/micromodal.min.js"></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/rigidbody_models/mesh_rigidbody.html b/_build/html/api/rigidbody_models/mesh_rigidbody.html index e7fabf249dc9adf83ad1d677dbdb9048176d46c9..299cd6c60e6a098b1d27a628de6bcafa7310ff23 100644 --- a/_build/html/api/rigidbody_models/mesh_rigidbody.html +++ b/_build/html/api/rigidbody_models/mesh_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?v=be8a1c11" /> + <link rel="stylesheet" type="text/css" href="../../_static/mystnb.4510f1fc1dee50b3e5859aac5469c37c29e427902b24a333a5f9fcb2f0b3ac41.css" /> <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?v=b4b7a797" /> + <link rel="stylesheet" type="text/css" href="../../_static/proof.css" /> <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?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/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/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?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 src="../../_static/js/hoverxref.js"></script> + 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href="../../_static/mystnb.4510f1fc1dee50b3e5859aac5469c37c29e427902b24a333a5f9fcb2f0b3ac41.css?v=be8a1c11" /> + <link rel="stylesheet" type="text/css" href="../../_static/mystnb.4510f1fc1dee50b3e5859aac5469c37c29e427902b24a333a5f9fcb2f0b3ac41.css" /> <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?v=b4b7a797" /> + <link rel="stylesheet" type="text/css" href="../../_static/proof.css" /> <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?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/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/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?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 src="../../_static/js/hoverxref.js"></script> + <script src="../../_static/js/tooltipster.bundle.min.js"></script> + <script src="../../_static/js/micromodal.min.js"></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/rigidbody_models/structure_from_pdb.html b/_build/html/api/rigidbody_models/structure_from_pdb.html index 0c5538e4dc25170b20c63bef858b9086e006bc00..2228ccb9553f199f27a5113fd5d11835e192ad3b 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" /> <link rel="stylesheet" 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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/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/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?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 src="../../_static/js/hoverxref.js"></script> + <script src="../../_static/js/tooltipster.bundle.min.js"></script> + <script src="../../_static/js/micromodal.min.js"></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/rigidbody_models/structure_rigidbody.html b/_build/html/api/rigidbody_models/structure_rigidbody.html index 67ab6610aa9ffa085fe79e6be64ae3e1c1ccaf20..aa1b2fd24eeaead389e76bff56a10bd05fce285e 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?v=be8a1c11" /> + <link rel="stylesheet" type="text/css" href="../../_static/mystnb.4510f1fc1dee50b3e5859aac5469c37c29e427902b24a333a5f9fcb2f0b3ac41.css" /> <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?v=b4b7a797" /> + <link rel="stylesheet" type="text/css" href="../../_static/proof.css" /> <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?v=7bc2f056" /> - <link 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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/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?v=c95ade4f"></script> - 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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?v=be8a1c11" /> + <link rel="stylesheet" type="text/css" href="../../_static/mystnb.4510f1fc1dee50b3e5859aac5469c37c29e427902b24a333a5f9fcb2f0b3ac41.css" /> <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?v=b4b7a797" /> + <link rel="stylesheet" type="text/css" href="../../_static/proof.css" /> <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?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/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/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?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 src="../../_static/js/hoverxref.js"></script> + <script src="../../_static/js/tooltipster.bundle.min.js"></script> + <script src="../../_static/js/micromodal.min.js"></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/shape-based_models/shape_cg.html b/_build/html/api/shape-based_models/shape_cg.html index 45673d830a4a8a6ef3f67045769590d59e9bdfb9..2d8486b44e6512e86dedc337a54de31b576758b8 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 @@ <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?v=be8a1c11" /> + <link rel="stylesheet" type="text/css" href="../../_static/mystnb.4510f1fc1dee50b3e5859aac5469c37c29e427902b24a333a5f9fcb2f0b3ac41.css" /> <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?v=b4b7a797" /> + <link rel="stylesheet" type="text/css" href="../../_static/proof.css" /> <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?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/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/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?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 src="../../_static/js/hoverxref.js"></script> + <script src="../../_static/js/tooltipster.bundle.min.js"></script> + <script src="../../_static/js/micromodal.min.js"></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/engine.html b/_build/html/api/simulation_engines/engine.html index b963931b11a8ba59cffe1329d112f0f273c932cb..c20d9fcde8fdc96a6bbdb40fa44d2585cc4e304d 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?v=be8a1c11" /> + <link rel="stylesheet" type="text/css" href="../../_static/mystnb.4510f1fc1dee50b3e5859aac5469c37c29e427902b24a333a5f9fcb2f0b3ac41.css" /> <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?v=b4b7a797" /> + <link rel="stylesheet" type="text/css" href="../../_static/proof.css" /> <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?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/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/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?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 src="../../_static/js/hoverxref.js"></script> + <script src="../../_static/js/tooltipster.bundle.min.js"></script> + <script src="../../_static/js/micromodal.min.js"></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/index.html b/_build/html/api/simulation_engines/index.html index 2dec772f8a93eed9e1686cd7f157d8db0dcdff31..550c28923e8b14d77c07b9c1f5decccc78cdd46b 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?v=be8a1c11" /> + <link rel="stylesheet" type="text/css" href="../../_static/mystnb.4510f1fc1dee50b3e5859aac5469c37c29e427902b24a333a5f9fcb2f0b3ac41.css" /> <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?v=b4b7a797" /> + <link rel="stylesheet" type="text/css" href="../../_static/proof.css" /> <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?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/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/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?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 src="../../_static/js/hoverxref.js"></script> + <script src="../../_static/js/tooltipster.bundle.min.js"></script> + <script src="../../_static/js/micromodal.min.js"></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 c99edfd8f447345fac7e5e3226c42f3f934362ee..b0e495c1d213c8675fe3e5c6ac1a4038f54d57ed 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?v=be8a1c11" /> + <link rel="stylesheet" type="text/css" href="../../_static/mystnb.4510f1fc1dee50b3e5859aac5469c37c29e427902b24a333a5f9fcb2f0b3ac41.css" /> <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?v=b4b7a797" /> + <link rel="stylesheet" type="text/css" href="../../_static/proof.css" /> <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?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/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/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?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 src="../../_static/js/hoverxref.js"></script> + <script src="../../_static/js/tooltipster.bundle.min.js"></script> + <script src="../../_static/js/micromodal.min.js"></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/binary_manager.html b/_build/html/api/utilities/binary_manager.html index cdf5ceaef2b137d1fba3e181ec878f861559b782..8a861bedf804c0a0d45f3d829ab729f328e1d969 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" /> <link rel="stylesheet" type="text/css" href="../../_static/copybutton.css?v=76b2166b" /> - <link rel="stylesheet" type="text/css" href="../../_static/mystnb.4510f1fc1dee50b3e5859aac5469c37c29e427902b24a333a5f9fcb2f0b3ac41.css?v=be8a1c11" /> + <link rel="stylesheet" type="text/css" href="../../_static/mystnb.4510f1fc1dee50b3e5859aac5469c37c29e427902b24a333a5f9fcb2f0b3ac41.css" /> <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?v=b4b7a797" /> + <link rel="stylesheet" type="text/css" href="../../_static/proof.css" /> <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?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/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/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?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 src="../../_static/js/hoverxref.js"></script> + <script src="../../_static/js/tooltipster.bundle.min.js"></script> + <script src="../../_static/js/micromodal.min.js"></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/coords.html b/_build/html/api/utilities/coords.html index 1e2da889a84bd5f1f6a30235ba76c176297186e4..185f75e3ca14a19bbdad70c9ee492e8d64d34aee 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 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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/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?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 src="../../_static/js/hoverxref.js"></script> + <script src="../../_static/js/tooltipster.bundle.min.js"></script> + <script src="../../_static/js/micromodal.min.js"></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/grid.html b/_build/html/api/utilities/grid.html index 6916b5a51aaf50cbef038be38d22438a0f5bada1..f4626ec8eb99b31cecc1fc0532e03006d05b7596 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" 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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/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/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?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 src="../../_static/js/hoverxref.js"></script> + <script src="../../_static/js/tooltipster.bundle.min.js"></script> + <script src="../../_static/js/micromodal.min.js"></script> <script>let toggleHintShow = 'Click to show';</script> <script>let toggleHintHide = 'Click to hide';</script> <script>let toggleOpenOnPrint = 'true';</script> @@ -614,7 +614,30 @@ It should accept a scalar or an array-like object and return a scalar or an arra <dl class="py function"> <dt class="sig sig-object py" id="arbdmodel.grid.slab_potential_z"> <span class="sig-name descname"><span class="pre">slab_potential_z</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">force_constant</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">center</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">resolution</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">exponent</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/grid.html#slab_potential_z"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#arbdmodel.grid.slab_potential_z" title="Link to this definition">#</a></dt> -<dd></dd></dl> +<dd><p>Generate a potential energy field that depends only on the z-coordinate, creating a slab-like potential. +:param force_constant: The strength of the potential (energy per unit distance^exponent). +:type force_constant: float +:param center: The (x, y, z) coordinates of the center of the potential. +:type center: list or tuple +:param dimensions: The (x, y, z) dimensions of the grid in length units. +:type dimensions: list or tuple +:param resolution: The grid spacing in length units. If a single value is provided, it’s used for all dimensions. +:type resolution: float or list or tuple +:param exponent: The exponent determining the shape of the potential. Default is 2 (harmonic potential). +:type exponent: int, optional</p> +<dl class="field-list simple"> +<dt class="field-odd">Returns<span class="colon">:</span></dt> +<dd class="field-odd"><p>A 3D array representing the potential energy field, where the energy depends only +on the distance from the z-center raised to the specified exponent.</p> +</dd> +<dt class="field-even">Return type<span class="colon">:</span></dt> +<dd class="field-even"><p><a class="hxr-hoverxref hxr-tooltip reference external" href="https://numpy.org/doc/stable/reference/generated/numpy.ndarray.html#numpy.ndarray" title="(in NumPy v2.2)">numpy.ndarray</a></p> +</dd> +</dl> +<p class="rubric">Notes</p> +<p>The potential U at each point is calculated as: +U = (force_constant/exponent) * <a href="#id1"><span class="problematic" id="id2">|</span></a>z - center_z|^exponent</p> +</dd></dl> <dl class="py function"> <dt class="sig sig-object py" id="arbdmodel.grid.spherical_confinement"> @@ -624,7 +647,32 @@ It should accept a scalar or an array-like object and return a scalar or an arra <dl class="py function"> <dt class="sig sig-object py" id="arbdmodel.grid.writeDx"> <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> +<dd><p>Write 3D grid data to an OpenDX format file. +Write 3D grid data to an OpenDX format file.</p> +<p>OpenDX is a visualization software format that can be used to visualize +volumetric data.</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>outfile</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><em>file-like object</em>) – The path to the output file or a file-like object.</p></li> +<li><p><strong>data</strong> (<a class="hxr-hoverxref hxr-tooltip reference external" href="https://numpy.org/doc/stable/reference/generated/numpy.ndarray.html#numpy.ndarray" title="(in NumPy v2.2)"><em>numpy.ndarray</em></a>) – 3D array containing the grid data to be written.</p></li> +<li><p><strong>origin</strong> (<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> or </em><a class="hxr-hoverxref hxr-tooltip reference external" href="https://docs.python.org/3/library/stdtypes.html#tuple" title="(in Python v3.13)"><em>tuple</em></a>) – The (x, y, z) coordinates of the origin of the grid.</p></li> +<li><p><strong>delta</strong> (<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> or </em><a class="hxr-hoverxref hxr-tooltip reference external" href="https://docs.python.org/3/library/stdtypes.html#tuple" title="(in Python v3.13)"><em>tuple</em></a>) – The grid spacing in the (x, y, z) directions.</p></li> +<li><p><strong>fmt</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>) – Format string for the data values. Default is “%.12fâ€.</p></li> +</ul> +</dd> +</dl> +<p class="rubric">Notes</p> +<p>The output file follows the OpenDX format specification: +<a class="reference external" href="http://opendx.sdsc.edu/docs/html/pages/usrgu068.htm#HDREDF">http://opendx.sdsc.edu/docs/html/pages/usrgu068.htm#HDREDF</a></p> +<p>The data is written in a way that is compatible with visualization software +that accepts OpenDX format.</p> +<dl class="field-list simple"> +<dt class="field-odd">Raises<span class="colon">:</span></dt> +<dd class="field-odd"><p><a class="hxr-hoverxref hxr-tooltip reference external" href="https://docs.python.org/3/library/exceptions.html#AssertionError" title="(in Python v3.13)"><strong>AssertionError</strong></a> – If data is not a 3D array or if origin or delta do not have length 3.</p> +</dd> +</dl> +</dd></dl> <dl class="py function"> <dt class="sig sig-object py" id="arbdmodel.grid.write_confine_dx"> diff --git a/_build/html/api/utilities/index.html 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index b2019818b85ebaa370635bf6ed2d0b831a843568..521b3ed392a0df800d8fa476389efc6e859185b7 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?v=be8a1c11" /> + <link rel="stylesheet" type="text/css" href="../../_static/mystnb.4510f1fc1dee50b3e5859aac5469c37c29e427902b24a333a5f9fcb2f0b3ac41.css" /> <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?v=b4b7a797" /> + <link rel="stylesheet" type="text/css" href="../../_static/proof.css" /> <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?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/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/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?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 src="../../_static/js/hoverxref.js"></script> + <script src="../../_static/js/tooltipster.bundle.min.js"></script> + <script src="../../_static/js/micromodal.min.js"></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/version.html b/_build/html/api/utilities/version.html index 4ffe2535c2cd64764a3bda79974f171e5bea75d5..63b2cdfefc749166d64c1dfc04f91aa4ffd9e879 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?v=be8a1c11" /> + <link rel="stylesheet" type="text/css" href="../../_static/mystnb.4510f1fc1dee50b3e5859aac5469c37c29e427902b24a333a5f9fcb2f0b3ac41.css" /> <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?v=b4b7a797" /> + <link rel="stylesheet" type="text/css" href="../../_static/proof.css" /> <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?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/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/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?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 src="../../_static/js/hoverxref.js"></script> + <script src="../../_static/js/tooltipster.bundle.min.js"></script> + <script src="../../_static/js/micromodal.min.js"></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 de0f0c4473dd11545e1e9c02370e3894d8dd9632..a3fff7f010832c515fd1863a17794a886fff000b 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?v=be8a1c11" /> + <link rel="stylesheet" type="text/css" href="_static/mystnb.4510f1fc1dee50b3e5859aac5469c37c29e427902b24a333a5f9fcb2f0b3ac41.css" /> <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?v=b4b7a797" /> + <link rel="stylesheet" type="text/css" href="_static/proof.css" /> <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?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/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/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?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 src="_static/js/hoverxref.js"></script> + <script src="_static/js/tooltipster.bundle.min.js"></script> + <script src="_static/js/micromodal.min.js"></script> <script>let toggleHintShow = 'Click to show';</script> <script>let toggleHintHide = 'Click to hide';</script> <script>let toggleOpenOnPrint = 'true';</script> @@ -325,6 +325,7 @@ document.write(` | <a href="#U"><strong>U</strong></a> | <a href="#V"><strong>V</strong></a> | <a href="#W"><strong>W</strong></a> + | <a href="#Z"><strong>Z</strong></a> </div> <h2 id="A">A</h2> @@ -613,10 +614,14 @@ 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> - <li><a href="api/interaction_potentials/ibi.html#arbdmodel.ibi.BondAngleDof">BondAngleDof (class in arbdmodel.ibi)</a> + <li><a href="api/core/sim_config.html#arbdmodel.sim_config.SimConf.barostat">barostat (SimConf attribute)</a> +</li> + <li><a href="api/interaction_potentials/ibi.html#arbdmodel.ibi.AbstractIBIpotential.bins">bins (AbstractIBIpotential 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> <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> @@ -661,7 +666,7 @@ document.write(` </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><a href="api/core/sim_config.html#arbdmodel.sim_config.SimConf.combine">combine() (SimConf method)</a>, <a href="api/core/sim_config.html#id1">[1]</a> </li> <li><a href="api/interaction_potentials/ibi.html#arbdmodel.ibi.AngleDof.compute_volume">compute_volume() (AngleDof method)</a> @@ -708,6 +713,8 @@ document.write(` <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> + <li><a href="api/core/sim_config.html#arbdmodel.sim_config.SimConf.cutoff">cutoff (SimConf attribute)</a> </li> </ul></td> </tr></table> @@ -715,6 +722,14 @@ 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/polymer_modeling/kh_polymer_model.html#arbdmodel.kh_polymer_model.KhNonbonded.debye_length">debye_length (KhNonbonded attribute)</a> + + <ul> + <li><a href="api/polymer_modeling/onck_polymer_model.html#arbdmodel.onck_polymer_model.OnckNonbonded.debye_length">(OnckNonbonded attribute)</a> +</li> + </ul></li> + <li><a href="api/core/sim_config.html#arbdmodel.sim_config.SimConf.decomp_period">decomp_period (SimConf attribute)</a> +</li> <li><a href="api/simulation_engines/engine.html#arbdmodel.engine.ArbdEngine.default_binary">default_binary (ArbdEngine property)</a> <ul> @@ -729,12 +744,12 @@ document.write(` </li> <li><a href="api/polymer_modeling/polymer.html#arbdmodel.polymer.Connection.delete">delete() (Connection method)</a> </li> + </ul></td> + <td style="width: 33%; vertical-align: top;"><ul> <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/core/model.html#arbdmodel.model.ArbdModel.dimensions_from_structure">dimensions_from_structure() (ArbdModel method)</a> <ul> @@ -777,10 +792,10 @@ document.write(` <h2 id="F">F</h2> <table style="width: 100%" class="indextable genindextable"><tr> <td style="width: 33%; vertical-align: top;"><ul> - <li><a href="api/interaction_potentials/ibi.html#arbdmodel.ibi.AbstractIBIpotential.filename">filename() (AbstractIBIpotential method)</a> + <li><a href="api/interaction_potentials/ibi.html#arbdmodel.ibi.AbstractIBIpotential.filename">filename() (AbstractIBIpotential method)</a>, <a href="api/interaction_potentials/ibi.html#id1">[1]</a> <ul> - <li><a href="api/interaction_potentials/interactions.html#arbdmodel.interactions.AbstractPotential.filename">(AbstractPotential method)</a> + <li><a href="api/interaction_potentials/interactions.html#arbdmodel.interactions.AbstractPotential.filename">(AbstractPotential method)</a>, <a href="api/interaction_potentials/interactions.html#id0">[1]</a> </li> <li><a href="api/interaction_potentials/interactions.html#arbdmodel.interactions.HarmonicBondedPotential.filename">(HarmonicBondedPotential method)</a> </li> @@ -845,7 +860,7 @@ document.write(` <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><a href="api/core/sim_config.html#arbdmodel.sim_config.SimConf.get_binary">get_binary() (SimConf method)</a>, <a href="api/core/sim_config.html#id2">[1]</a> </li> <li><a href="api/core/core_objects.html#arbdmodel.core_objects.Parent.get_bond_angles">get_bond_angles() (Parent method)</a> </li> @@ -861,7 +876,7 @@ document.write(` <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><a href="api/interaction_potentials/ibi.html#arbdmodel.ibi.AbstractIBIpotential.get_cg_distribution">get_cg_distribution() (AbstractIBIpotential method)</a>, <a href="api/interaction_potentials/ibi.html#id2">[1]</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> @@ -923,7 +938,7 @@ document.write(` </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> + <li><a href="api/interaction_potentials/ibi.html#arbdmodel.ibi.AbstractIBIpotential.get_target_distribution">get_target_distribution() (AbstractIBIpotential method)</a>, <a href="api/interaction_potentials/ibi.html#id3">[1]</a> </li> <li><a href="api/interaction_potentials/ibi.html#arbdmodel.ibi.DegreeOfFreedom.get_values">get_values() (DegreeOfFreedom method)</a> @@ -936,6 +951,8 @@ document.write(` <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/sim_config.html#arbdmodel.sim_config.SimConf.gpu">gpu (SimConf attribute)</a> </li> <li><a href="api/core/core_objects.html#arbdmodel.core_objects.Group">Group (class in arbdmodel.core_objects)</a> </li> @@ -987,11 +1004,13 @@ document.write(` </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> + </ul></td> + <td style="width: 33%; vertical-align: top;"><ul> <li><a href="api/polymer_modeling/polymer.html#arbdmodel.polymer.PolymerSection.insert_monomers">insert_monomers() (PolymerSection method)</a> +</li> + <li><a href="api/core/sim_config.html#arbdmodel.sim_config.SimConf.integrator">integrator (SimConf attribute)</a> </li> <li><a href="api/utilities/version.html#arbdmodel.version.is_dirty">is_dirty() (in module arbdmodel.version)</a> </li> @@ -999,7 +1018,7 @@ document.write(` </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><a href="api/core/sim_config.html#arbdmodel.sim_config.SimConf.items">items() (SimConf method)</a>, <a href="api/core/sim_config.html#id3">[1]</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> @@ -1054,6 +1073,16 @@ document.write(` <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/interaction_potentials/interactions.html#arbdmodel.interactions.AbstractPotential.max_force">max_force (AbstractPotential attribute)</a> + + <ul> + <li><a href="api/polymer_modeling/kh_polymer_model.html#arbdmodel.kh_polymer_model.KhNonbonded.max_force">(KhNonbonded attribute)</a> +</li> + <li><a href="api/polymer_modeling/onck_polymer_model.html#arbdmodel.onck_polymer_model.OnckNonbonded.max_force">(OnckNonbonded attribute)</a> +</li> + </ul></li> + <li><a href="api/interaction_potentials/interactions.html#arbdmodel.interactions.AbstractPotential.max_potential">max_potential (AbstractPotential attribute)</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> @@ -1148,14 +1177,26 @@ document.write(` </li> <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> + </ul></td> + <td style="width: 33%; vertical-align: top;"><ul> <li><a href="api/polymer_modeling/polymer.html#arbdmodel.polymer.PolymerBeads.num_bead_groups">num_bead_groups (PolymerBeads property)</a> </li> + <li><a href="api/core/sim_config.html#arbdmodel.sim_config.DefaultSimConf.num_heavy_cluster">num_heavy_cluster (DefaultSimConf attribute)</a> + + <ul> + <li><a href="api/core/sim_config.html#arbdmodel.sim_config.SimConf.num_heavy_cluster">(SimConf attribute)</a> +</li> + </ul></li> + <li><a href="api/core/sim_config.html#arbdmodel.sim_config.DefaultSimConf.num_steps">num_steps (DefaultSimConf attribute)</a> + + <ul> + <li><a href="api/core/sim_config.html#arbdmodel.sim_config.SimConf.num_steps">(SimConf attribute)</a> +</li> + </ul></li> </ul></td> </tr></table> @@ -1166,12 +1207,18 @@ document.write(` </li> <li><a href="api/polymer_modeling/onck_polymer_model.html#arbdmodel.onck_polymer_model.OnckModel">OnckModel (class in arbdmodel.onck_polymer_model)</a> </li> - </ul></td> - <td style="width: 33%; vertical-align: top;"><ul> <li><a href="api/polymer_modeling/onck_polymer_model.html#arbdmodel.onck_polymer_model.OnckNonbonded">OnckNonbonded (class in arbdmodel.onck_polymer_model)</a> </li> + </ul></td> + <td style="width: 33%; vertical-align: top;"><ul> <li><a href="api/polymer_modeling/polymer.html#arbdmodel.polymer.Connection.other">other() (Connection method)</a> </li> + <li><a href="api/core/sim_config.html#arbdmodel.sim_config.DefaultSimConf.output_period">output_period (DefaultSimConf attribute)</a> + + <ul> + <li><a href="api/core/sim_config.html#arbdmodel.sim_config.SimConf.output_period">(SimConf attribute)</a> +</li> + </ul></li> </ul></td> </tr></table> @@ -1181,6 +1228,8 @@ 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/sim_config.html#arbdmodel.sim_config.SimConf.pairlist_distance">pairlist_distance (SimConf attribute)</a> </li> <li><a href="api/core/core_objects.html#arbdmodel.core_objects.Parent">Parent (class in arbdmodel.core_objects)</a> </li> @@ -1194,15 +1243,21 @@ document.write(` </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> + <li><a href="api/polymer_modeling/onck_polymer_model.html#arbdmodel.onck_polymer_model.OnckBeads.peptide_bond">peptide_bond (OnckBeads attribute)</a> +</li> + <li><a href="api/interaction_potentials/interactions.html#arbdmodel.interactions.AbstractPotential.periodic">periodic (AbstractPotential attribute)</a> <ul> + <li><a href="api/interaction_potentials/interactions.html#id1">(AbstractPotential property)</a> +</li> <li><a href="api/interaction_potentials/interactions.html#arbdmodel.interactions.HarmonicDihedral.periodic">(HarmonicDihedral property)</a> </li> <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/onck_polymer_model.html#arbdmodel.onck_polymer_model.OnckBeads.polymer">polymer (OnckBeads attribute)</a> </li> <li><a href="api/polymer_modeling/polymer.html#arbdmodel.polymer.PolymerBeads">PolymerBeads (class in arbdmodel.polymer)</a> </li> @@ -1212,10 +1267,12 @@ document.write(` </li> <li><a href="api/polymer_modeling/polymer.html#arbdmodel.polymer.PolymerSection">PolymerSection (class in arbdmodel.polymer)</a> </li> - <li><a href="api/interaction_potentials/ibi.html#arbdmodel.ibi.AbstractIBIpotential.potential">potential() (AbstractIBIpotential method)</a> + <li><a href="api/interaction_potentials/ibi.html#arbdmodel.ibi.AbstractIBIpotential.potential">potential (AbstractIBIpotential attribute)</a> +</li> + <li><a href="api/interaction_potentials/ibi.html#id0">potential() (AbstractIBIpotential method)</a>, <a href="api/interaction_potentials/ibi.html#id4">[1]</a> <ul> - <li><a href="api/interaction_potentials/interactions.html#arbdmodel.interactions.AbstractPotential.potential">(AbstractPotential method)</a> + <li><a href="api/interaction_potentials/interactions.html#arbdmodel.interactions.AbstractPotential.potential">(AbstractPotential method)</a>, <a href="api/interaction_potentials/interactions.html#id2">[1]</a> </li> <li><a href="api/interaction_potentials/interactions.html#arbdmodel.interactions.BoundaryPotential.potential">(BoundaryPotential method)</a> </li> @@ -1227,7 +1284,7 @@ document.write(` </li> <li><a href="api/polymer_modeling/hps_polymer_model.html#arbdmodel.hps_polymer_model.HpsNonbonded.potential">(HpsNonbonded method)</a> </li> - <li><a href="api/polymer_modeling/kh_polymer_model.html#arbdmodel.kh_polymer_model.KhNonbonded.potential">(KhNonbonded method)</a> + <li><a href="api/polymer_modeling/kh_polymer_model.html#arbdmodel.kh_polymer_model.KhNonbonded.potential">(KhNonbonded method)</a>, <a href="api/polymer_modeling/kh_polymer_model.html#id0">[1]</a> </li> <li><a href="api/interaction_potentials/interactions.html#arbdmodel.interactions.LennardJones.potential">(LennardJones method)</a> </li> @@ -1237,7 +1294,7 @@ document.write(` </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><a href="api/polymer_modeling/onck_polymer_model.html#arbdmodel.onck_polymer_model.OnckNonbonded.potential">(OnckNonbonded method)</a>, <a href="api/polymer_modeling/onck_polymer_model.html#id0">[1]</a> </li> <li><a href="api/polymer_modeling/sali_polymer_model.html#arbdmodel.sali_polymer_model.SaliNonbonded.potential">(SaliNonbonded method)</a> </li> @@ -1254,6 +1311,12 @@ document.write(` <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/core/sim_config.html#arbdmodel.sim_config.DefaultSimConf.pressure">pressure (DefaultSimConf attribute)</a> + + <ul> + <li><a href="api/core/sim_config.html#arbdmodel.sim_config.SimConf.pressure">(SimConf attribute)</a> +</li> + </ul></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> @@ -1261,6 +1324,8 @@ document.write(` <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> + <li><a href="api/core/sim_config.html#arbdmodel.sim_config.DefaultSimConf.Properties">Properties (DefaultSimConf attribute)</a> </li> </ul></td> </tr></table> @@ -1290,13 +1355,17 @@ document.write(` <td style="width: 33%; vertical-align: top;"><ul> <li><a href="api/interaction_potentials/ibi.html#arbdmodel.ibi.RadiusDof">RadiusDof (class in arbdmodel.ibi)</a> </li> - <li><a href="api/interaction_potentials/interactions.html#arbdmodel.interactions.AbstractPotential.range_">range_ (AbstractPotential property)</a> + <li><a href="api/interaction_potentials/interactions.html#arbdmodel.interactions.AbstractPotential.range_">range_ (AbstractPotential attribute)</a> + + <ul> + <li><a href="api/interaction_potentials/interactions.html#id3">(AbstractPotential property)</a> </li> + </ul></li> <li><a href="api/utilities/coords.html#arbdmodel.coords.read_arbd_coordinates">read_arbd_coordinates() (in module arbdmodel.coords)</a> </li> <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><a href="api/interaction_potentials/ibi.html#arbdmodel.ibi.AbstractIBIpotential.read_cg_potential">read_cg_potential() (AbstractIBIpotential method)</a>, <a href="api/interaction_potentials/ibi.html#id5">[1]</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> @@ -1313,9 +1382,17 @@ document.write(` <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> + <li><a href="api/interaction_potentials/interactions.html#arbdmodel.interactions.AbstractPotential.resolution">resolution (AbstractPotential attribute)</a> </li> </ul></td> <td style="width: 33%; vertical-align: top;"><ul> + <li><a href="api/core/sim_config.html#arbdmodel.sim_config.SimConf.restart_file">restart_file (SimConf attribute)</a> +</li> + <li><a href="api/core/sim_config.html#arbdmodel.sim_config.SimConf.rigid_body_grid_grid_period">rigid_body_grid_grid_period (SimConf attribute)</a> +</li> + <li><a href="api/core/sim_config.html#arbdmodel.sim_config.SimConf.rigid_body_integrator">rigid_body_integrator (SimConf attribute)</a> +</li> <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> @@ -1374,7 +1451,11 @@ document.write(` <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><a href="api/core/sim_config.html#arbdmodel.sim_config.SimConf.seed">seed (SimConf attribute)</a> +</li> + <li><a href="api/polymer_modeling/onck_polymer_model.html#arbdmodel.onck_polymer_model.OnckBeads.sequence">sequence (OnckBeads attribute)</a> +</li> + <li><a href="api/core/sim_config.html#arbdmodel.sim_config.SimConf.set_binary">set_binary() (SimConf method)</a>, <a href="api/core/sim_config.html#id4">[1]</a> </li> <li><a href="api/polymer_modeling/polymer.html#arbdmodel.polymer.Location.set_connection">set_connection() (Location method)</a> </li> @@ -1398,10 +1479,10 @@ document.write(` </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> + </ul></td> + <td style="width: 33%; vertical-align: top;"><ul> <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> @@ -1426,6 +1507,12 @@ document.write(` </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/core/sim_config.html#arbdmodel.sim_config.DefaultSimConf.solvent_density">solvent_density (DefaultSimConf attribute)</a> + + <ul> + <li><a href="api/core/sim_config.html#arbdmodel.sim_config.SimConf.solvent_density">(SimConf attribute)</a> +</li> + </ul></li> <li><a href="api/utilities/grid.html#arbdmodel.grid.spherical_confinement">spherical_confinement() (in module arbdmodel.grid)</a> </li> <li><a href="api/polymer_modeling/hps_polymer_model.html#arbdmodel.hps_polymer_model.HpsModel.spring_constant">spring_constant (HpsModel attribute)</a> @@ -1434,6 +1521,8 @@ document.write(` <li><a href="api/polymer_modeling/kh_polymer_model.html#arbdmodel.kh_polymer_model.KhModel.spring_constant">(KhModel attribute)</a> </li> <li><a href="api/polymer_modeling/mpipi_polymer.html#arbdmodel.mpipi_polymer.MpipiModel.spring_constant">(MpipiModel attribute)</a> +</li> + <li><a href="api/polymer_modeling/onck_polymer_model.html#arbdmodel.onck_polymer_model.OnckBeads.spring_constant">(OnckBeads 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> @@ -1452,20 +1541,30 @@ 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> + <li><a href="api/core/sim_config.html#arbdmodel.sim_config.DefaultSimConf.temperature">temperature (DefaultSimConf attribute)</a> <ul> - <li><a href="api/core/sim_config.html#arbdmodel.sim_config.SimConf.temperature">(SimConf property)</a> + <li><a href="api/core/sim_config.html#id0">(DefaultSimConf property)</a> +</li> + <li><a href="api/core/sim_config.html#arbdmodel.sim_config.SimConf.temperature">(SimConf attribute)</a> +</li> + <li><a href="api/core/sim_config.html#id5">(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/sim_config.html#arbdmodel.sim_config.SimConf.thermostat">thermostat (SimConf attribute)</a> +</li> + <li><a href="api/core/sim_config.html#arbdmodel.sim_config.SimConf.timestep">timestep (SimConf attribute)</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> + </ul></td> + <td style="width: 33%; vertical-align: top;"><ul> <li><a href="api/polymer_modeling/polymer.html#arbdmodel.polymer.PolymerGroup.translate">translate() (PolymerGroup method)</a> <ul> @@ -1474,8 +1573,6 @@ document.write(` <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> @@ -1492,6 +1589,8 @@ document.write(` <li><a href="api/interaction_potentials/interactions.html#arbdmodel.interactions.WLCSKBond.type_">(WLCSKBond property)</a> </li> </ul></li> + <li><a href="api/polymer_modeling/onck_polymer_model.html#arbdmodel.onck_polymer_model.OnckBeads.types_dict">types_dict (OnckBeads attribute)</a> +</li> </ul></td> </tr></table> @@ -1522,10 +1621,18 @@ document.write(` <h2 id="V">V</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.vmd_cylinder_tcl">vmd_cylinder_tcl() (PolymerGroup method)</a> + <li><a href="api/polymer_modeling/onck_polymer_model.html#arbdmodel.onck_polymer_model.OnckBeads.version">version (OnckBeads attribute)</a> </li> + <li><a href="api/core/sim_config.html#arbdmodel.sim_config.DefaultSimConf.viscosity">viscosity (DefaultSimConf attribute)</a> + + <ul> + <li><a href="api/core/sim_config.html#arbdmodel.sim_config.SimConf.viscosity">(SimConf attribute)</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.vmd_cylinder_tcl">vmd_cylinder_tcl() (PolymerGroup method)</a> +</li> <li><a href="api/polymer_modeling/polymer.html#arbdmodel.polymer.PolymerGroup.vmd_tube_tcl">vmd_tube_tcl() (PolymerGroup method)</a> </li> </ul></td> @@ -1542,7 +1649,7 @@ document.write(` </li> <li><a href="api/interaction_potentials/ibi.html#arbdmodel.ibi.DegreeOfFreedom.wrap_vector">wrap_vector() (DegreeOfFreedom method)</a> </li> - <li><a href="api/interaction_potentials/ibi.html#arbdmodel.ibi.AbstractIBIpotential.write_cg_potential">write_cg_potential() (AbstractIBIpotential method)</a> + <li><a href="api/interaction_potentials/ibi.html#arbdmodel.ibi.AbstractIBIpotential.write_cg_potential">write_cg_potential() (AbstractIBIpotential method)</a>, <a href="api/interaction_potentials/ibi.html#id6">[1]</a> </li> <li><a href="api/simulation_engines/engine.html#arbdmodel.engine.NamdEngine.write_conf">write_conf() (NamdEngine method)</a> </li> @@ -1554,10 +1661,10 @@ document.write(` </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> + <li><a href="api/interaction_potentials/ibi.html#arbdmodel.ibi.AbstractIBIpotential.write_file">write_file() (AbstractIBIpotential method)</a>, <a href="api/interaction_potentials/ibi.html#id7">[1]</a> <ul> - <li><a href="api/interaction_potentials/interactions.html#arbdmodel.interactions.AbstractPotential.write_file">(AbstractPotential method)</a> + <li><a href="api/interaction_potentials/interactions.html#arbdmodel.interactions.AbstractPotential.write_file">(AbstractPotential method)</a>, <a href="api/interaction_potentials/interactions.html#id4">[1]</a> </li> <li><a href="api/interaction_potentials/interactions.html#arbdmodel.interactions.BoundaryPotential.write_file">(BoundaryPotential method)</a> </li> @@ -1597,6 +1704,14 @@ document.write(` </ul></td> </tr></table> +<h2 id="Z">Z</h2> +<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.AbstractPotential.zero">zero (AbstractPotential attribute)</a> +</li> + </ul></td> +</tr></table> + </article> diff --git a/_build/html/intro.html b/_build/html/intro.html index 753237cd058dac596899227ba10636e2407315b6..204712db74a591400bb9cc0a1d4c937880774fc5 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?v=be8a1c11" /> + <link rel="stylesheet" type="text/css" 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'true';</script> diff --git a/_build/html/reports/tutorials/3-iterative-boltzmann-inversion/3-ibi.err.log b/_build/html/reports/tutorials/3-iterative-boltzmann-inversion/3-ibi.err.log index 7282d32ef8e1ac20c65776f0cd5e0b5d10df2f73..c32f9870e2d1ec9b920e789a4dd67152060d3683 100644 --- a/_build/html/reports/tutorials/3-iterative-boltzmann-inversion/3-ibi.err.log +++ b/_build/html/reports/tutorials/3-iterative-boltzmann-inversion/3-ibi.err.log @@ -68,27 +68,46 @@ if not Path(f'{directory}/output/{outname}.dcd').exists(): [0;31m---------------------------------------------------------------------------[0m -[0;31mException[0m Traceback (most recent call last) -Cell [0;32mIn[2], line 45[0m -[1;32m 43[0m [38;5;250m[39m[38;5;124;03m""" Production """[39;00m -[1;32m 44[0m model[38;5;241m.[39mset_damping_coefficient( [38;5;241m100[39m ) -[0;32m---> 45[0m [43mengine[49m[38;5;241;43m.[39;49m[43msimulate[49m[43m([49m[43mmodel[49m[43m,[49m[43m [49m[43moutput_name[49m[38;5;241;43m=[39;49m[43moutname[49m[43m,[49m -[1;32m 46[0m [43m [49m[43mdirectory[49m[43m [49m[38;5;241;43m=[39;49m[43m [49m[43mdirectory[49m -[1;32m 47[0m [43m [49m[43m)[49m - -File [0;32m/usr/local/Caskroom/miniconda/base/envs/pybd/lib/python3.9/site-packages/arbdmodel-0.0.0-py3.9.egg/arbdmodel/__init__.py:1629[0m, in [0;36mSimEngine.simulate[0;34m(self, model, output_name, output_directory, directory, log_file, binary, num_procs, dry_run, configuration, replicas, **conf_params)[0m -[1;32m 1627[0m [38;5;28;01mif[39;00m binary [38;5;129;01mis[39;00m [38;5;28;01mNone[39;00m: binary[38;5;241m=[39m[38;5;28mself[39m[38;5;241m.[39mdefault_binary -[1;32m 1628[0m [38;5;28;01melse[39;00m: -[0;32m-> 1629[0m binary [38;5;241m=[39m [38;5;28;43mself[39;49m[38;5;241;43m.[39;49m[43m_get_binary[49m[43m([49m[43mbinary[49m[43m)[49m -[1;32m 1631[0m [38;5;28;01mif[39;00m [38;5;129;01mnot[39;00m os[38;5;241m.[39mpath[38;5;241m.[39mexists(output_directory): -[1;32m 1632[0m os[38;5;241m.[39mmakedirs(output_directory) - -File [0;32m/usr/local/Caskroom/miniconda/base/envs/pybd/lib/python3.9/site-packages/arbdmodel-0.0.0-py3.9.egg/arbdmodel/__init__.py:1676[0m, in [0;36mSimEngine._get_binary[0;34m(self, binary)[0m -[1;32m 1673[0m binary [38;5;241m=[39m fname -[1;32m 1674[0m [38;5;28;01mbreak[39;00m -[0;32m-> 1676[0m [38;5;28;01mif[39;00m binary [38;5;129;01mis[39;00m [38;5;28;01mNone[39;00m: [38;5;28;01mraise[39;00m [38;5;167;01mException[39;00m([38;5;124m"[39m[38;5;132;01m{}[39;00m[38;5;124m was not found[39m[38;5;124m"[39m[38;5;241m.[39mformat([38;5;28mself[39m[38;5;241m.[39mdefault_binary)) -[1;32m 1678[0m [38;5;28;01mif[39;00m [38;5;129;01mnot[39;00m os[38;5;241m.[39mpath[38;5;241m.[39mexists(binary): -[1;32m 1679[0m [38;5;28;01mraise[39;00m [38;5;167;01mException[39;00m([38;5;124m"[39m[38;5;132;01m{}[39;00m[38;5;124m was not found[39m[38;5;124m"[39m[38;5;241m.[39mformat([38;5;28mself[39m[38;5;241m.[39mdefault_binary)) - -[0;31mException[0m: arbd was not found +[0;31mTypeError[0m Traceback (most recent call last) +Cell [0;32mIn[2], line 17[0m +[1;32m 13[0m debye_length [38;5;241m=[39m [38;5;241m10[39m +[1;32m 15[0m polymers, sequences [38;5;241m=[39m create_arbd_polymer_objects() +[0;32m---> 17[0m model [38;5;241m=[39m [43mNupModel[49m[43m([49m[43m [49m[43mpolymers[49m[43m,[49m[43m [49m[43msequences[49m[43m,[49m +[1;32m 18[0m [43m [49m[43mdebye_length[49m[43m [49m[38;5;241;43m=[39;49m[43m [49m[43mdebye_length[49m[43m,[49m +[1;32m 19[0m [43m [49m[43mtemperature[49m[38;5;241;43m=[39;49m[43mtemperature[49m[43m,[49m +[1;32m 20[0m [43m [49m[43mdamping_coefficient[49m[43m [49m[38;5;241;43m=[39;49m[43m [49m[38;5;241;43m50000[39;49m[43m,[49m[43m [49m[38;5;66;43;03m# units of 1/ns[39;49;00m +[1;32m 21[0m [43m [49m[43mdecomp_period[49m[43m [49m[38;5;241;43m=[39;49m[43m [49m[43mdecomp_period[49m[43m,[49m +[1;32m 22[0m [43m [49m[43mpairlist_distance[49m[43m [49m[38;5;241;43m=[39;49m[43m [49m[38;5;241;43m50[39;49m[38;5;241;43m+[39;49m[43mskin_depth[49m[43m,[49m +[1;32m 23[0m [43m [49m[43mdimensions[49m[43m [49m[38;5;241;43m=[39;49m[43m [49m[43mdimensions[49m +[1;32m 24[0m [43m [49m[43m)[49m +[1;32m 25[0m engine [38;5;241m=[39m ArbdEngine( integrator [38;5;241m=[39m [38;5;124m'[39m[38;5;124mLangevin[39m[38;5;124m'[39m, +[1;32m 26[0m num_steps[38;5;241m=[39m[38;5;241m1e7[39m, +[1;32m 27[0m output_period[38;5;241m=[39m[38;5;241m1e4[39m, +[1;32m 28[0m gpu [38;5;241m=[39m [38;5;241m0[39m +[1;32m 29[0m ) +[1;32m 30[0m directory [38;5;241m=[39m [38;5;124mf[39m[38;5;124m'[39m[38;5;124m1-one_bead_per_res-[39m[38;5;132;01m{[39;00mmodel_name[38;5;132;01m}[39;00m[38;5;124m'[39m + +File [0;32m~/Documents/research/arbdmodel-simple/arbdmodel/hps_polymer_model.py:239[0m, in [0;36mHpsModel.__init__[0;34m(self, polymers, sequences, rest_length, spring_constant, debye_length, damping_coefficient, DEBUG, **kwargs)[0m +[1;32m 236[0m [38;5;28;01mif[39;00m sequences [38;5;129;01mis[39;00m [38;5;28;01mNone[39;00m: +[1;32m 237[0m [38;5;28;01mraise[39;00m [38;5;167;01mNotImplementedError[39;00m([38;5;124m"[39m[38;5;124mHpsModel must be provided a sequences argument[39m[38;5;124m"[39m) +[0;32m--> 239[0m [43mPolymerModel[49m[38;5;241;43m.[39;49m[38;5;21;43m__init__[39;49m[43m([49m[38;5;28;43mself[39;49m[43m,[49m[43m [49m[43mpolymers[49m[43m,[49m[43m [49m[43msequences[49m[43m,[49m[43m [49m[43mmonomers_per_bead_group[49m[38;5;241;43m=[39;49m[38;5;241;43m1[39;49m[43m,[49m[43m [49m[38;5;241;43m*[39;49m[38;5;241;43m*[39;49m[43mkwargs[49m[43m)[49m +[1;32m 241[0m [38;5;250m[39m[38;5;124;03m""" Update type diffusion coefficients """[39;00m +[1;32m 242[0m [38;5;28mself[39m[38;5;241m.[39mtypes [38;5;241m=[39m all_types [38;5;241m=[39m [t [38;5;28;01mfor[39;00m key,t [38;5;129;01min[39;00m _types[38;5;241m.[39mitems()] + +File [0;32m~/Documents/research/arbdmodel-simple/arbdmodel/polymer.py:648[0m, in [0;36mPolymerModel.__init__[0;34m(self, polymers, sequences, monomers_per_bead_group, **kwargs)[0m +[1;32m 646[0m [38;5;28mself[39m[38;5;241m.[39msequences [38;5;241m=[39m sequences +[1;32m 647[0m [38;5;28mself[39m[38;5;241m.[39mmonomers_per_bead_group [38;5;241m=[39m monomers_per_bead_group +[0;32m--> 648[0m [43mArbdModel[49m[38;5;241;43m.[39;49m[38;5;21;43m__init__[39;49m[43m([49m[38;5;28;43mself[39;49m[43m,[49m[43m [49m[43m[[49m[43m][49m[43m,[49m[43m [49m[38;5;241;43m*[39;49m[38;5;241;43m*[39;49m[43mkwargs[49m[43m)[49m +[1;32m 650[0m [38;5;250m[39m[38;5;124;03m""" Generate beads """[39;00m +[1;32m 651[0m [38;5;28mself[39m[38;5;241m.[39mgenerate_beads() + +File [0;32m~/Documents/research/arbdmodel-simple/arbdmodel/model.py:231[0m, in [0;36mArbdModel.__init__[0;34m(self, children, cell_vectors, cell_origin, dimensions, remove_duplicate_bonded_terms, buffer_factor, configuration, dummy_types, **conf_params)[0m +[1;32m 228[0m cell_origin [38;5;241m=[39m [[38;5;241m0[39m, [38;5;241m0[39m, [38;5;241m0[39m] +[1;32m 230[0m [38;5;66;03m# Initialize parent class[39;00m +[0;32m--> 231[0m [43mPdbModel[49m[38;5;241;43m.[39;49m[38;5;21;43m__init__[39;49m[43m([49m[38;5;28;43mself[39;49m[43m,[49m[43m [49m[43mchildren[49m[43m,[49m[43m [49m[43mdimensions[49m[43m,[49m[43m [49m[43mremove_duplicate_bonded_terms[49m[43m,[49m +[1;32m 232[0m [43m [49m[43mcell_vectors[49m[43m,[49m[43m [49m[43mcell_origin[49m[43m)[49m +[1;32m 235[0m [38;5;66;03m# Store origin which might be different from cell_origin[39;00m +[1;32m 236[0m [38;5;28mself[39m[38;5;241m.[39morigin [38;5;241m=[39m cell_origin + +[0;31mTypeError[0m: __init__() takes from 1 to 4 positional arguments but 6 were given diff --git a/_build/html/reports/tutorials/4-rigid-bodies/4-rigid-bodies.err.log b/_build/html/reports/tutorials/4-rigid-bodies/4-rigid-bodies.err.log index 25fd7d7831bcb1dbc04f4f58e6071c9529cb779e..a9b25c307310a154502b789525056832b3f2ec6c 100644 --- a/_build/html/reports/tutorials/4-rigid-bodies/4-rigid-bodies.err.log +++ b/_build/html/reports/tutorials/4-rigid-bodies/4-rigid-bodies.err.log @@ -25,33 +25,45 @@ model.simulate(output_name='run', [0;31m---------------------------------------------------------------------------[0m -[0;31mException[0m Traceback (most recent call last) -Cell [0;32mIn[4], line 3[0m +[0;31mTypeError[0m Traceback (most recent call last) +Cell [0;32mIn[4], line 2[0m [1;32m 1[0m [38;5;66;03m## Optionally simulate the DNA-only model to see how it performs and behaves[39;00m -[1;32m 2[0m model [38;5;241m=[39m make_dna_model() -[0;32m----> 3[0m [43mmodel[49m[38;5;241;43m.[39;49m[43msimulate[49m[43m([49m[43moutput_name[49m[38;5;241;43m=[39;49m[38;5;124;43m'[39;49m[38;5;124;43mrun[39;49m[38;5;124;43m'[39;49m[43m,[49m -[1;32m 4[0m [43m [49m[43mdirectory[49m[38;5;241;43m=[39;49m[38;5;124;43m'[39;49m[38;5;124;43mtrombone-no_ssb[39;49m[38;5;124;43m'[39;49m[43m,[49m -[1;32m 5[0m [43m [49m[43mnum_steps[49m[38;5;241;43m=[39;49m[38;5;241;43m1e5[39;49m[43m,[49m[43m [49m[43moutput_period[49m[38;5;241;43m=[39;49m[38;5;241;43m1e3[39;49m[43m,[49m -[1;32m 6[0m [43m)[49m - -File [0;32m/usr/local/Caskroom/miniconda/base/envs/pybd/lib/python3.9/site-packages/arbdmodel-0.0.0-py3.9.egg/arbdmodel/__init__.py:1454[0m, in [0;36mArbdModel.simulate[0;34m(self, output_name, **kwargs)[0m -[1;32m 1452[0m engine_kwargs [38;5;241m=[39m {k:v [38;5;28;01mfor[39;00m k,v [38;5;129;01min[39;00m kwargs[38;5;241m.[39mitems() [38;5;28;01mif[39;00m k [38;5;129;01mnot[39;00m [38;5;129;01min[39;00m sim_kws} -[1;32m 1453[0m engine [38;5;241m=[39m ArbdEngine([38;5;241m*[39m[38;5;241m*[39mengine_kwargs) -[0;32m-> 1454[0m [38;5;28;01mreturn[39;00m [43mengine[49m[38;5;241;43m.[39;49m[43msimulate[49m[43m([49m[38;5;28;43mself[39;49m[43m,[49m[43m [49m[43moutput_name[49m[43m,[49m[43m [49m[38;5;241;43m*[39;49m[38;5;241;43m*[39;49m[43msim_kwargs[49m[43m)[49m - -File [0;32m/usr/local/Caskroom/miniconda/base/envs/pybd/lib/python3.9/site-packages/arbdmodel-0.0.0-py3.9.egg/arbdmodel/__init__.py:1629[0m, in [0;36mSimEngine.simulate[0;34m(self, model, output_name, output_directory, directory, log_file, binary, num_procs, dry_run, configuration, replicas, **conf_params)[0m -[1;32m 1627[0m [38;5;28;01mif[39;00m binary [38;5;129;01mis[39;00m [38;5;28;01mNone[39;00m: binary[38;5;241m=[39m[38;5;28mself[39m[38;5;241m.[39mdefault_binary -[1;32m 1628[0m [38;5;28;01melse[39;00m: -[0;32m-> 1629[0m binary [38;5;241m=[39m [38;5;28;43mself[39;49m[38;5;241;43m.[39;49m[43m_get_binary[49m[43m([49m[43mbinary[49m[43m)[49m -[1;32m 1631[0m [38;5;28;01mif[39;00m [38;5;129;01mnot[39;00m os[38;5;241m.[39mpath[38;5;241m.[39mexists(output_directory): -[1;32m 1632[0m os[38;5;241m.[39mmakedirs(output_directory) - -File [0;32m/usr/local/Caskroom/miniconda/base/envs/pybd/lib/python3.9/site-packages/arbdmodel-0.0.0-py3.9.egg/arbdmodel/__init__.py:1676[0m, in [0;36mSimEngine._get_binary[0;34m(self, binary)[0m -[1;32m 1673[0m binary [38;5;241m=[39m fname -[1;32m 1674[0m [38;5;28;01mbreak[39;00m -[0;32m-> 1676[0m [38;5;28;01mif[39;00m binary [38;5;129;01mis[39;00m [38;5;28;01mNone[39;00m: [38;5;28;01mraise[39;00m [38;5;167;01mException[39;00m([38;5;124m"[39m[38;5;132;01m{}[39;00m[38;5;124m was not found[39m[38;5;124m"[39m[38;5;241m.[39mformat([38;5;28mself[39m[38;5;241m.[39mdefault_binary)) -[1;32m 1678[0m [38;5;28;01mif[39;00m [38;5;129;01mnot[39;00m os[38;5;241m.[39mpath[38;5;241m.[39mexists(binary): -[1;32m 1679[0m [38;5;28;01mraise[39;00m [38;5;167;01mException[39;00m([38;5;124m"[39m[38;5;132;01m{}[39;00m[38;5;124m was not found[39m[38;5;124m"[39m[38;5;241m.[39mformat([38;5;28mself[39m[38;5;241m.[39mdefault_binary)) - -[0;31mException[0m: arbd was not found +[0;32m----> 2[0m model [38;5;241m=[39m [43mmake_dna_model[49m[43m([49m[43m)[49m +[1;32m 3[0m model[38;5;241m.[39msimulate(output_name[38;5;241m=[39m[38;5;124m'[39m[38;5;124mrun[39m[38;5;124m'[39m, +[1;32m 4[0m directory[38;5;241m=[39m[38;5;124m'[39m[38;5;124mtrombone-no_ssb[39m[38;5;124m'[39m, +[1;32m 5[0m num_steps[38;5;241m=[39m[38;5;241m1e5[39m, output_period[38;5;241m=[39m[38;5;241m1e3[39m, +[1;32m 6[0m ) + +Cell [0;32mIn[3], line 23[0m, in [0;36mmake_dna_model[0;34m()[0m +[1;32m 20[0m _P[38;5;241m.[39mgrid [38;5;241m=[39m (replisome_grid, [38;5;241m500[39m) [38;5;66;03m# scale it up by a big factor[39;00m +[1;32m 21[0m _B[38;5;241m.[39mgrid [38;5;241m=[39m (replisome_grid, [38;5;241m500[39m) +[0;32m---> 23[0m model [38;5;241m=[39m [43mDnaModel[49m[43m([49m[43m[[49m[43ma[49m[43m][49m[43m,[49m[43m [49m[43mdimensions[49m[38;5;241;43m=[39;49m[43m([49m[38;5;241;43m3000[39;49m[43m,[49m[38;5;241;43m3000[39;49m[43m,[49m[38;5;241;43m3000[39;49m[43m)[49m[43m,[49m +[1;32m 24[0m [43m [49m[43mtimestep[49m[43m [49m[38;5;241;43m=[39;49m[43m [49m[38;5;241;43m20e-6[39;49m +[1;32m 25[0m [43m [49m[43m)[49m +[1;32m 27[0m [38;5;66;03m## Restrain DNA ends[39;00m +[1;32m 28[0m end1 [38;5;241m=[39m model[38;5;241m.[39mstrands[[38;5;241m0[39m][38;5;241m.[39mchildren[[38;5;241m0[39m][38;5;241m.[39mchildren[[38;5;241m0[39m] + +File [0;32m~/Documents/research/arbdmodel-simple/arbdmodel/ssdna_two_bead.py:164[0m, in [0;36mDnaModel.__init__[0;34m(self, polymers, sequences, DEBUG, **kwargs)[0m +[1;32m 161[0m [38;5;28;01mif[39;00m [38;5;124m'[39m[38;5;124mtimestep[39m[38;5;124m'[39m [38;5;129;01mnot[39;00m [38;5;129;01min[39;00m kwargs: kwargs[[38;5;124m'[39m[38;5;124mtimestep[39m[38;5;124m'[39m] [38;5;241m=[39m [38;5;241m20e-6[39m +[1;32m 162[0m [38;5;28;01mif[39;00m [38;5;124m'[39m[38;5;124mcutoff[39m[38;5;124m'[39m [38;5;129;01mnot[39;00m [38;5;129;01min[39;00m kwargs: kwargs[[38;5;124m'[39m[38;5;124mcutoff[39m[38;5;124m'[39m] [38;5;241m=[39m [38;5;241m35[39m +[0;32m--> 164[0m [43mPolymerModel[49m[38;5;241;43m.[39;49m[38;5;21;43m__init__[39;49m[43m([49m[38;5;28;43mself[39;49m[43m,[49m[43m [49m[43mpolymers[49m[43m,[49m[43m [49m[43msequences[49m[43m,[49m[43m [49m[43mmonomers_per_bead_group[49m[38;5;241;43m=[39;49m[38;5;241;43m1[39;49m[43m,[49m[43m [49m[38;5;241;43m*[39;49m[38;5;241;43m*[39;49m[43mkwargs[49m[43m)[49m +[1;32m 165[0m [38;5;28mself[39m[38;5;241m.[39mstrands [38;5;241m=[39m [38;5;28mself[39m[38;5;241m.[39mchildren [38;5;66;03m# make a nice alias[39;00m +[1;32m 167[0m [38;5;28mself[39m[38;5;241m.[39madd_nonbonded_interaction( TabulatedNonbonded(get_resource_path([38;5;124m'[39m[38;5;124mtwo_bead_model/NBBB.dat[39m[38;5;124m'[39m)), typeA[38;5;241m=[39m_B, typeB[38;5;241m=[39m_B ) + +File [0;32m~/Documents/research/arbdmodel-simple/arbdmodel/polymer.py:648[0m, in [0;36mPolymerModel.__init__[0;34m(self, polymers, sequences, monomers_per_bead_group, **kwargs)[0m +[1;32m 646[0m [38;5;28mself[39m[38;5;241m.[39msequences [38;5;241m=[39m sequences +[1;32m 647[0m [38;5;28mself[39m[38;5;241m.[39mmonomers_per_bead_group [38;5;241m=[39m monomers_per_bead_group +[0;32m--> 648[0m [43mArbdModel[49m[38;5;241;43m.[39;49m[38;5;21;43m__init__[39;49m[43m([49m[38;5;28;43mself[39;49m[43m,[49m[43m [49m[43m[[49m[43m][49m[43m,[49m[43m [49m[38;5;241;43m*[39;49m[38;5;241;43m*[39;49m[43mkwargs[49m[43m)[49m +[1;32m 650[0m [38;5;250m[39m[38;5;124;03m""" Generate beads """[39;00m +[1;32m 651[0m [38;5;28mself[39m[38;5;241m.[39mgenerate_beads() + +File [0;32m~/Documents/research/arbdmodel-simple/arbdmodel/model.py:231[0m, in [0;36mArbdModel.__init__[0;34m(self, children, cell_vectors, cell_origin, dimensions, remove_duplicate_bonded_terms, buffer_factor, configuration, dummy_types, **conf_params)[0m +[1;32m 228[0m cell_origin [38;5;241m=[39m [[38;5;241m0[39m, [38;5;241m0[39m, [38;5;241m0[39m] +[1;32m 230[0m [38;5;66;03m# Initialize parent class[39;00m +[0;32m--> 231[0m [43mPdbModel[49m[38;5;241;43m.[39;49m[38;5;21;43m__init__[39;49m[43m([49m[38;5;28;43mself[39;49m[43m,[49m[43m [49m[43mchildren[49m[43m,[49m[43m [49m[43mdimensions[49m[43m,[49m[43m [49m[43mremove_duplicate_bonded_terms[49m[43m,[49m +[1;32m 232[0m [43m [49m[43mcell_vectors[49m[43m,[49m[43m [49m[43mcell_origin[49m[43m)[49m +[1;32m 235[0m [38;5;66;03m# Store origin which might be different from cell_origin[39;00m +[1;32m 236[0m [38;5;28mself[39m[38;5;241m.[39morigin [38;5;241m=[39m cell_origin + +[0;31mTypeError[0m: __init__() takes from 1 to 4 positional arguments but 6 were given diff --git a/_build/html/search.html b/_build/html/search.html index 1c37f7609c2ca9f5b9547c9c07ff90bb4d113eb5..8d6d51fadffaf9f424dc07dbab36f24022114cff 100644 --- a/_build/html/search.html +++ b/_build/html/search.html @@ -30,19 +30,19 @@ <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?v=be8a1c11" /> + <link rel="stylesheet" type="text/css" href="_static/mystnb.4510f1fc1dee50b3e5859aac5469c37c29e427902b24a333a5f9fcb2f0b3ac41.css" /> <link rel="stylesheet" type="text/css" href="_static/sphinx-thebe.css?v=4fa983c6" /> <link rel="stylesheet" type="text/css" 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b/_build/html/searchindex.js @@ -1 +1 @@ -Search.setIndex({"alltitles": {"3-iterative-boltzmann-inversion": [[41, "iterative-boltzmann-inversion"]], "4-rigid-bodies": [[41, "rigid-bodies"]], "API Reference": [[5, null]], "ARBD Model Documentation": [[36, null]], "ARBD is configured through plain text files": [[37, "arbd-is-configured-through-plain-text-files"]], "Add a constant-force to the ends of the polymers to determine their elastic properties": [[38, "add-a-constant-force-to-the-ends-of-the-polymers-to-determine-their-elastic-properties"]], "Add your files": [[0, "add-your-files"]], "Adding single-stranded DNA binding protein": [[40, "adding-single-stranded-dna-binding-protein"]], "Attaching point particles": [[40, "attaching-point-particles"]], "Authors and acknowledgment": [[0, "authors-and-acknowledgment"]], "Available Tutorials": [[41, "available-tutorials"]], "Badges": [[0, "badges"]], "Basic usage of the arbdmodel package": [[37, null]], "Collaborate with your team": [[0, 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"Roadmap": [[0, "roadmap"]], "Shape-Based Models": [[25, null]], "Simulation Engines": [[28, null]], "Some polymer models may have multiple beads per monomer": [[38, null]], "Step 1: Create particle types": [[37, "step-1-create-particle-types"]], "Step 1: Model Construction": [[39, "step-1-model-construction"]], "Step 2: Build a system": [[37, "step-2-build-a-system"]], "Step 2: Setting up a coarser model": [[39, "step-2-setting-up-a-coarser-model"]], "Step 3: Describe the interactions between the particles": [[37, "step-3-describe-the-interactions-between-the-particles"]], "Step 3: Mapping the fine grained trajectory to a coarser representation": [[39, "step-3-mapping-the-fine-grained-trajectory-to-a-coarser-representation"]], "Step 4: Run the coarser IBI simulations": [[39, "step-4-run-the-coarser-ibi-simulations"]], "Step 4: Run the simulation": [[37, "step-4-run-the-simulation"]], "Step 5: Visualization": [[39, "step-5-visualization"]], "Step 5: Visualize the results": [[37, 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"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 in arbdmodel.structure_rigidbody)": [[24, "arbdmodel.structure_rigidbody.StaticObject", false]], "structureprocessor (class in arbdmodel.structure_from_pdb)": [[23, "arbdmodel.structure_from_pdb.StructureProcessor", false]], "structurerigidbodymodel (class in arbdmodel.structure_rigidbody)": [[24, "arbdmodel.structure_rigidbody.StructureRigidBodyModel", false]], "surfacemeshprocessor (class in arbdmodel.mesh_process_surface)": [[19, "arbdmodel.mesh_process_surface.SurfaceMeshProcessor", false]], "tabulatednonbonded (class in arbdmodel.interactions)": [[8, "arbdmodel.interactions.TabulatedNonbonded", false]], "temperature (defaultsimconf property)": [[4, "arbdmodel.sim_config.DefaultSimConf.temperature", false]], "temperature (simconf property)": [[4, "arbdmodel.sim_config.SimConf.temperature", false]], "test_average_grids() (testaveragegrids method)": [[32, "arbdmodel.grid.TestAverageGrids.test_average_grids", false]], "testaveragegrids (class in arbdmodel.grid)": [[32, 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(arbdengine property)": [[27, "arbdmodel.engine.ArbdEngine.default_binary", false]], "default_binary (namdengine property)": [[27, "arbdmodel.engine.NamdEngine.default_binary", false]], "default_binary (simengine property)": [[27, "arbdmodel.engine.SimEngine.default_binary", false]], "defaultsimconf (class in arbdmodel.sim_config)": [[4, "arbdmodel.sim_config.DefaultSimConf", false]], "degreeoffreedom (class in arbdmodel.ibi)": [[6, "arbdmodel.ibi.DegreeOfFreedom", false]], "delete() (connection method)": [[15, "arbdmodel.polymer.Connection.delete", false]], "diffusiverigidbodytype (class in arbdmodel.structure_rigidbody)": [[24, "arbdmodel.structure_rigidbody.DiffusiveRigidBodyType", false]], "dihedraldof (class in arbdmodel.ibi)": [[6, "arbdmodel.ibi.DihedralDof", false]], "dimensions_from_structure() (arbdmodel method)": [[3, "arbdmodel.model.ArbdModel.dimensions_from_structure", false]], "dimensions_from_structure() (polymergroup method)": [[15, "arbdmodel.polymer.PolymerGroup.dimensions_from_structure", false]], "display() (citation method)": [[35, "arbdmodel.version.Citation.display", false]], "dnamodel (class in arbdmodel.ssdna_two_bead)": [[17, "arbdmodel.ssdna_two_bead.DnaModel", false]], "dnastrandbeads (class in arbdmodel.ssdna_two_bead)": [[17, "arbdmodel.ssdna_two_bead.DnaStrandBeads", false]], "duplicate() (group method)": [[1, "arbdmodel.core_objects.Group.duplicate", false]], "duplicate() (pointparticle method)": [[1, "arbdmodel.core_objects.PointParticle.duplicate", false]], "duplicate() (rigidbody method)": [[1, "arbdmodel.core_objects.RigidBody.duplicate", false]], "excludedattributes (particletype attribute)": [[1, "arbdmodel.core_objects.ParticleType.excludedAttributes", false]], "extend() (arbdmodel method)": [[3, "arbdmodel.model.ArbdModel.extend", false]], "extend() (polymergroup method)": [[15, "arbdmodel.polymer.PolymerGroup.extend", false]], "filename() (abstractibipotential method)": [[6, "arbdmodel.ibi.AbstractIBIpotential.filename", false], [6, "id1", false]], "filename() (abstractpotential method)": [[8, "arbdmodel.interactions.AbstractPotential.filename", false], [8, "id0", false]], "filename() (harmonicbondedpotential method)": [[8, "arbdmodel.interactions.HarmonicBondedPotential.filename", false]], "filename() (nullpotential method)": [[8, "arbdmodel.interactions.NullPotential.filename", false]], "filename() (shapecgnonbonded method)": [[26, "arbdmodel.shape_cg.ShapeCGNonbonded.filename", false]], "filename() (wlcskpotential method)": [[8, "arbdmodel.interactions.WLCSKPotential.filename", false]], "fill_nans() (in module arbdmodel.grid)": [[32, "arbdmodel.grid.fill_nans", false]], "find_shape_based_sites() (in module arbdmodel.shape_cg)": [[26, "arbdmodel.shape_cg.find_shape_based_sites", false]], "fjcbeadsfrompolymer (class in arbdmodel.fjc_polymer_model)": [[9, "arbdmodel.fjc_polymer_model.FjcBeadsFromPolymer", false]], "fjcmodel (class in arbdmodel.fjc_polymer_model)": [[9, "arbdmodel.fjc_polymer_model.FjcModel", false]], "from_protein_list() (shapecgmodel class method)": [[26, "arbdmodel.shape_cg.ShapeCGModel.from_protein_list", false]], "gaussian_kernel() (in module arbdmodel.grid)": [[32, "arbdmodel.grid.gaussian_kernel", false]], "generate_beads() (polymermodel method)": [[15, "arbdmodel.polymer.PolymerModel.generate_beads", false]], "generate_beads() (salimodel method)": [[16, "arbdmodel.sali_polymer_model.SaliModel.generate_beads", false]], "generate_charge_distribution() (structureprocessor method)": [[23, "arbdmodel.structure_from_pdb.StructureProcessor.generate_charge_distribution", false]], "generate_coordinates() (in module arbdmodel.coords)": [[31, "arbdmodel.coords.Generate_coordinates", false]], "generate_electrostatic_map() (structureprocessor method)": [[23, "arbdmodel.structure_from_pdb.StructureProcessor.generate_electrostatic_map", false]], "generate_potential_grid() (meshprocessor method)": [[20, "arbdmodel.mesh_process_volume.MeshProcessor.generate_potential_grid", false]], "generate_potential_grid() (surfacemeshprocessor method)": [[19, "arbdmodel.mesh_process_surface.SurfaceMeshProcessor.generate_potential_grid", false]], "generate_protein() (shapecgfactory method)": [[26, "arbdmodel.shape_cg.ShapeCGFactory.generate_protein", false]], "generate_random_protein_positions() (shapecgmodel method)": [[26, "arbdmodel.shape_cg.ShapeCGModel.generate_random_protein_positions", false]], "generate_spanning_vectors() (in module arbdmodel.coords)": [[31, "arbdmodel.coords.Generate_spanning_vectors", false]], "generate_vdw_maps() (structureprocessor method)": [[23, "arbdmodel.structure_from_pdb.StructureProcessor.generate_vdw_maps", false]], "get_angles() (parent method)": [[1, "arbdmodel.core_objects.Parent.get_angles", false]], "get_attached_particles() (meshprocessor method)": [[20, "arbdmodel.mesh_process_volume.MeshProcessor.get_attached_particles", false]], "get_attached_particles() (surfacemeshprocessor method)": [[19, "arbdmodel.mesh_process_surface.SurfaceMeshProcessor.get_attached_particles", false]], "get_binary() (simconf method)": [[4, "arbdmodel.sim_config.SimConf.get_binary", false], [4, "id2", false]], "get_bond_angles() (parent method)": [[1, "arbdmodel.core_objects.Parent.get_bond_angles", false]], "get_bonds() (parent method)": [[1, "arbdmodel.core_objects.Parent.get_bonds", false]], "get_center() (groupsite method)": [[1, "arbdmodel.core_objects.GroupSite.get_center", false]], "get_center() (parent method)": [[1, "arbdmodel.core_objects.Parent.get_center", false]], "get_center() (polymergroup method)": [[15, "arbdmodel.polymer.PolymerGroup.get_center", false]], "get_center() (polymersection method)": [[15, "arbdmodel.polymer.PolymerSection.get_center", false]], "get_cg_distribution() (abstractibipotential method)": [[6, "arbdmodel.ibi.AbstractIBIpotential.get_cg_distribution", false], [6, "id2", false]], "get_coarse_protein() (shapecgfactory method)": [[26, "arbdmodel.shape_cg.ShapeCGFactory.get_coarse_protein", false]], "get_coarse_types() (shapecgfactory method)": [[26, "arbdmodel.shape_cg.ShapeCGFactory.get_coarse_types", false]], "get_collapsed_position() (transformable method)": [[1, "arbdmodel.core_objects.Transformable.get_collapsed_position", false]], "get_connected_location() (location method)": [[15, "arbdmodel.polymer.Location.get_connected_location", false]], "get_connections() (polymergroup method)": [[15, "arbdmodel.polymer.PolymerGroup.get_connections", false]], "get_connections_and_locations() (connectableelement method)": [[15, "arbdmodel.polymer.ConnectableElement.get_connections_and_locations", false]], "get_contour_sorted_connections_and_locations() (polymersection method)": [[15, "arbdmodel.polymer.PolymerSection.get_contour_sorted_connections_and_locations", false]], "get_default_conf() (arbdengine method)": [[27, "arbdmodel.engine.ArbdEngine.get_default_conf", false]], "get_default_conf() (namdengine method)": [[27, "arbdmodel.engine.NamdEngine.get_default_conf", false]], "get_default_conf() (simengine method)": [[27, "arbdmodel.engine.SimEngine.get_default_conf", false]], "get_dihedrals() (parent method)": [[1, "arbdmodel.core_objects.Parent.get_dihedrals", false]], "get_exclusions() (parent method)": [[1, "arbdmodel.core_objects.Parent.get_exclusions", false]], "get_grid_files() (structureprocessor method)": [[23, "arbdmodel.structure_from_pdb.StructureProcessor.get_grid_files", false]], "get_impropers() (parent method)": [[1, "arbdmodel.core_objects.Parent.get_impropers", false]], "get_location_at() (connectableelement method)": [[15, "arbdmodel.polymer.ConnectableElement.get_location_at", false]], "get_locations() (connectableelement method)": [[15, "arbdmodel.polymer.ConnectableElement.get_locations", false]], "get_monomer_index() (location method)": [[15, "arbdmodel.polymer.Location.get_monomer_index", false]], "get_original_recursively() (clone method)": [[1, "arbdmodel.core_objects.Clone.get_original_recursively", false]], "get_particle_assignments() (in module arbdmodel.shape_cg)": [[26, "arbdmodel.shape_cg.get_particle_assignments", false]], "get_product_potentials() (parent method)": [[1, "arbdmodel.core_objects.Parent.get_product_potentials", false]], "get_protein_types() (shapecgmodel method)": [[26, "arbdmodel.shape_cg.ShapeCGModel.get_protein_types", false]], "get_resource_path() (in module arbdmodel.logger)": [[34, "arbdmodel.logger.get_resource_path", false]], "get_restraints() (groupsite method)": [[1, "arbdmodel.core_objects.GroupSite.get_restraints", false]], "get_restraints() (parent method)": [[1, "arbdmodel.core_objects.Parent.get_restraints", false]], "get_restraints() (pointparticle method)": [[1, "arbdmodel.core_objects.PointParticle.get_restraints", false]], "get_restraints() (rigidbody method)": [[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], [6, "id3", 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]], "gpu (simconf attribute)": [[4, "arbdmodel.sim_config.SimConf.gpu", 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]], "integrator (simconf attribute)": [[4, "arbdmodel.sim_config.SimConf.integrator", 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], [4, "id3", 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]], "max_force (abstractpotential attribute)": [[8, "arbdmodel.interactions.AbstractPotential.max_force", false]], "max_force (khnonbonded attribute)": [[12, "arbdmodel.kh_polymer_model.KhNonbonded.max_force", false]], "max_force (oncknonbonded attribute)": [[14, "arbdmodel.onck_polymer_model.OnckNonbonded.max_force", false]], "max_potential (abstractpotential attribute)": [[8, "arbdmodel.interactions.AbstractPotential.max_potential", 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]], "num_heavy_cluster (defaultsimconf attribute)": [[4, "arbdmodel.sim_config.DefaultSimConf.num_heavy_cluster", false]], "num_heavy_cluster (simconf attribute)": [[4, "arbdmodel.sim_config.SimConf.num_heavy_cluster", false]], "num_steps (defaultsimconf attribute)": [[4, "arbdmodel.sim_config.DefaultSimConf.num_steps", false]], "num_steps (simconf attribute)": [[4, "arbdmodel.sim_config.SimConf.num_steps", 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]], "output_period (defaultsimconf attribute)": [[4, "arbdmodel.sim_config.DefaultSimConf.output_period", false]], "output_period (simconf attribute)": [[4, "arbdmodel.sim_config.SimConf.output_period", false]], "p (dnastrandbeads attribute)": [[17, "arbdmodel.ssdna_two_bead.DnaStrandBeads.p", false]], "pairdistributiondof (class in arbdmodel.ibi)": [[6, "arbdmodel.ibi.PairDistributionDof", false]], "pairlist_distance (simconf attribute)": [[4, "arbdmodel.sim_config.SimConf.pairlist_distance", 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]], "peptide_bond (onckbeads attribute)": [[14, "arbdmodel.onck_polymer_model.OnckBeads.peptide_bond", false]], "periodic (abstractpotential attribute)": [[8, "arbdmodel.interactions.AbstractPotential.periodic", false]], "periodic (abstractpotential property)": [[8, "id1", 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]], "polymer (onckbeads attribute)": [[14, "arbdmodel.onck_polymer_model.OnckBeads.polymer", 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 attribute)": [[6, "arbdmodel.ibi.AbstractIBIpotential.potential", false]], "potential() (abstractibipotential method)": [[6, "id0", false], [6, "id4", false]], "potential() (abstractpotential method)": [[8, "arbdmodel.interactions.AbstractPotential.potential", false], [8, "id2", 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], [12, "id0", 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, 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38, "protein": 40, "python": 36, "readm": 0, "refer": [5, 36], "represent": 39, "result": 37, "rigid": [40, 41], "rigidbodi": 18, "roadmap": 0, "run": [37, 39], "sali_polymer_model": 16, "set": 39, "shape": 25, "shape_cg": 26, "sim_config": 4, "simplearbd": 22, "simul": [28, 37, 39], "singl": 40, "some": 38, "ssdna_two_bead": 17, "start": [0, 36], "statu": 0, "step": [37, 39], "strand": 40, "structure_from_pdb": 23, "structure_rigidbodi": 24, "suggest": 0, "support": 0, "system": 37, "team": 0, "test": 0, "text": 37, "thi": 0, "through": 37, "tool": 0, "trajectori": 39, "tutori": 41, "type": 37, "up": 39, "usag": [0, 37], "util": 33, "version": 35, "visual": [0, 37, 39], "your": 0}}) \ No newline at end of file diff --git a/_build/html/tutorials/3-iterative-boltzmann-inversion/3-ibi.html b/_build/html/tutorials/3-iterative-boltzmann-inversion/3-ibi.html index 19a244c510b8e30ce29d61130d3b41b6a96d93ab..275386a6ab0bfd2fcf34d4641ed09a65bac8fee8 100644 --- a/_build/html/tutorials/3-iterative-boltzmann-inversion/3-ibi.html +++ b/_build/html/tutorials/3-iterative-boltzmann-inversion/3-ibi.html @@ -500,29 +500,48 @@ document.write(` </div> <div class="cell_output docutils container"> <div class="output traceback highlight-ipythontb notranslate"><div class="highlight"><pre><span></span><span class="gt">---------------------------------------------------------------------------</span> -<span class="ne">Exception</span><span class="g g-Whitespace"> </span>Traceback (most recent call last) -<span class="n">Cell</span> <span class="n">In</span><span class="p">[</span><span class="mi">2</span><span class="p">],</span> <span class="n">line</span> <span class="mi">45</span> -<span class="g g-Whitespace"> </span><span class="mi">43</span><span class="w"> </span><span class="sd">""" Production """</span> -<span class="g g-Whitespace"> </span><span class="mi">44</span> <span class="n">model</span><span class="o">.</span><span class="n">set_damping_coefficient</span><span class="p">(</span> <span class="mi">100</span> <span class="p">)</span> -<span class="ne">---> </span><span class="mi">45</span> <span class="n">engine</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">output_name</span><span class="o">=</span><span class="n">outname</span><span class="p">,</span> -<span class="g g-Whitespace"> </span><span class="mi">46</span> <span class="n">directory</span> <span class="o">=</span> <span class="n">directory</span> -<span class="g g-Whitespace"> </span><span class="mi">47</span> <span class="p">)</span> - -<span class="nn">File /usr/local/Caskroom/miniconda/base/envs/pybd/lib/python3.9/site-packages/arbdmodel-0.0.0-py3.9.egg/arbdmodel/__init__.py:1629,</span> in <span class="ni">SimEngine.simulate</span><span class="nt">(self, model, output_name, output_directory, directory, log_file, binary, num_procs, dry_run, configuration, replicas, **conf_params)</span> -<span class="g g-Whitespace"> </span><span class="mi">1627</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="g g-Whitespace"> </span><span class="mi">1628</span> <span class="k">else</span><span class="p">:</span> -<span class="ne">-> </span><span class="mi">1629</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="g g-Whitespace"> </span><span class="mi">1631</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="g g-Whitespace"> </span><span class="mi">1632</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="nn">File /usr/local/Caskroom/miniconda/base/envs/pybd/lib/python3.9/site-packages/arbdmodel-0.0.0-py3.9.egg/arbdmodel/__init__.py:1676,</span> in <span class="ni">SimEngine._get_binary</span><span class="nt">(self, binary)</span> -<span class="g g-Whitespace"> </span><span class="mi">1673</span> <span class="n">binary</span> <span class="o">=</span> <span class="n">fname</span> -<span class="g g-Whitespace"> </span><span class="mi">1674</span> <span class="k">break</span> -<span class="ne">-> </span><span class="mi">1676</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="g g-Whitespace"> </span><span class="mi">1678</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="g g-Whitespace"> </span><span class="mi">1679</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="ne">Exception</span>: arbd was not found +<span class="ne">TypeError</span><span class="g g-Whitespace"> </span>Traceback (most recent call last) +<span class="n">Cell</span> <span class="n">In</span><span class="p">[</span><span class="mi">2</span><span class="p">],</span> <span class="n">line</span> <span class="mi">17</span> +<span class="g g-Whitespace"> </span><span class="mi">13</span> <span class="n">debye_length</span> <span class="o">=</span> <span class="mi">10</span> +<span class="g g-Whitespace"> </span><span class="mi">15</span> <span class="n">polymers</span><span class="p">,</span> <span class="n">sequences</span> <span class="o">=</span> <span class="n">create_arbd_polymer_objects</span><span class="p">()</span> +<span class="ne">---> </span><span class="mi">17</span> <span class="n">model</span> <span class="o">=</span> <span class="n">NupModel</span><span class="p">(</span> <span class="n">polymers</span><span class="p">,</span> <span class="n">sequences</span><span class="p">,</span> +<span class="g g-Whitespace"> </span><span class="mi">18</span> <span class="n">debye_length</span> <span class="o">=</span> <span class="n">debye_length</span><span class="p">,</span> +<span class="g g-Whitespace"> </span><span class="mi">19</span> <span class="n">temperature</span><span class="o">=</span><span class="n">temperature</span><span class="p">,</span> +<span class="g g-Whitespace"> </span><span class="mi">20</span> <span class="n">damping_coefficient</span> <span class="o">=</span> <span class="mi">50000</span><span class="p">,</span> <span class="c1"># units of 1/ns</span> +<span class="g g-Whitespace"> </span><span class="mi">21</span> <span class="n">decomp_period</span> <span class="o">=</span> <span class="n">decomp_period</span><span class="p">,</span> +<span class="g g-Whitespace"> </span><span class="mi">22</span> <span class="n">pairlist_distance</span> <span class="o">=</span> <span class="mi">50</span><span class="o">+</span><span class="n">skin_depth</span><span class="p">,</span> +<span class="g g-Whitespace"> </span><span class="mi">23</span> <span class="n">dimensions</span> <span class="o">=</span> <span class="n">dimensions</span> +<span class="g g-Whitespace"> </span><span class="mi">24</span> <span class="p">)</span> +<span class="g g-Whitespace"> </span><span class="mi">25</span> <span class="n">engine</span> <span class="o">=</span> <span class="n">ArbdEngine</span><span class="p">(</span> <span class="n">integrator</span> <span class="o">=</span> <span class="s1">'Langevin'</span><span class="p">,</span> +<span class="g g-Whitespace"> </span><span class="mi">26</span> <span class="n">num_steps</span><span class="o">=</span><span class="mf">1e7</span><span class="p">,</span> +<span class="g g-Whitespace"> </span><span class="mi">27</span> <span class="n">output_period</span><span class="o">=</span><span class="mf">1e4</span><span class="p">,</span> +<span class="g g-Whitespace"> </span><span class="mi">28</span> <span class="n">gpu</span> <span class="o">=</span> <span class="mi">0</span> +<span class="g g-Whitespace"> </span><span class="mi">29</span> <span class="p">)</span> +<span class="g g-Whitespace"> </span><span class="mi">30</span> <span class="n">directory</span> <span class="o">=</span> <span class="sa">f</span><span class="s1">'1-one_bead_per_res-</span><span class="si">{</span><span class="n">model_name</span><span class="si">}</span><span class="s1">'</span> + +<span class="nn">File ~/Documents/research/arbdmodel-simple/arbdmodel/hps_polymer_model.py:239,</span> in <span class="ni">HpsModel.__init__</span><span class="nt">(self, polymers, sequences, rest_length, spring_constant, debye_length, damping_coefficient, DEBUG, **kwargs)</span> +<span class="g g-Whitespace"> </span><span class="mi">236</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="g g-Whitespace"> </span><span class="mi">237</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="ne">--> </span><span class="mi">239</span> <span class="n">PolymerModel</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">polymers</span><span class="p">,</span> <span class="n">sequences</span><span class="p">,</span> <span class="n">monomers_per_bead_group</span><span class="o">=</span><span class="mi">1</span><span class="p">,</span> <span class="o">**</span><span class="n">kwargs</span><span class="p">)</span> +<span class="g g-Whitespace"> </span><span class="mi">241</span><span class="w"> </span><span class="sd">""" Update type diffusion coefficients """</span> +<span class="g g-Whitespace"> </span><span class="mi">242</span> <span class="bp">self</span><span class="o">.</span><span class="n">types</span> <span class="o">=</span> <span class="n">all_types</span> <span class="o">=</span> <span class="p">[</span><span class="n">t</span> <span class="k">for</span> <span class="n">key</span><span class="p">,</span><span class="n">t</span> <span class="ow">in</span> <span class="n">_types</span><span class="o">.</span><span class="n">items</span><span class="p">()]</span> + +<span class="nn">File ~/Documents/research/arbdmodel-simple/arbdmodel/polymer.py:648,</span> in <span class="ni">PolymerModel.__init__</span><span class="nt">(self, polymers, sequences, monomers_per_bead_group, **kwargs)</span> +<span class="g g-Whitespace"> </span><span class="mi">646</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="g g-Whitespace"> </span><span class="mi">647</span> <span class="bp">self</span><span class="o">.</span><span class="n">monomers_per_bead_group</span> <span class="o">=</span> <span class="n">monomers_per_bead_group</span> +<span class="ne">--> </span><span class="mi">648</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="g g-Whitespace"> </span><span class="mi">650</span><span class="w"> </span><span class="sd">""" Generate beads """</span> +<span class="g g-Whitespace"> </span><span class="mi">651</span> <span class="bp">self</span><span class="o">.</span><span class="n">generate_beads</span><span class="p">()</span> + +<span class="nn">File ~/Documents/research/arbdmodel-simple/arbdmodel/model.py:231,</span> in <span class="ni">ArbdModel.__init__</span><span class="nt">(self, children, cell_vectors, cell_origin, dimensions, remove_duplicate_bonded_terms, buffer_factor, configuration, dummy_types, **conf_params)</span> +<span class="g g-Whitespace"> </span><span class="mi">228</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="g g-Whitespace"> </span><span class="mi">230</span> <span class="c1"># Initialize parent class</span> +<span class="ne">--> </span><span class="mi">231</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="g g-Whitespace"> </span><span class="mi">232</span> <span class="n">cell_vectors</span><span class="p">,</span> <span class="n">cell_origin</span><span class="p">)</span> +<span class="g g-Whitespace"> </span><span class="mi">235</span> <span class="c1"># Store origin which might be different from cell_origin</span> +<span class="g g-Whitespace"> </span><span class="mi">236</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="ne">TypeError</span>: __init__() takes from 1 to 4 positional arguments but 6 were given </pre></div> </div> </div> diff --git a/_build/html/tutorials/4-rigid-bodies/4-rigid-bodies.html b/_build/html/tutorials/4-rigid-bodies/4-rigid-bodies.html index 3cec5a056d9a045511fb096f71a42bd963fff946..c2753c50ac4b1a73cf896d496712763c6374015b 100644 --- a/_build/html/tutorials/4-rigid-bodies/4-rigid-bodies.html +++ b/_build/html/tutorials/4-rigid-bodies/4-rigid-bodies.html @@ -442,35 +442,47 @@ document.write(` </div> <div class="cell_output docutils container"> <div class="output traceback highlight-ipythontb notranslate"><div class="highlight"><pre><span></span><span class="gt">---------------------------------------------------------------------------</span> -<span class="ne">Exception</span><span class="g g-Whitespace"> </span>Traceback (most recent call last) -<span class="n">Cell</span> <span class="n">In</span><span class="p">[</span><span class="mi">4</span><span class="p">],</span> <span class="n">line</span> <span class="mi">3</span> +<span class="ne">TypeError</span><span class="g g-Whitespace"> </span>Traceback (most recent call last) +<span class="n">Cell</span> <span class="n">In</span><span class="p">[</span><span class="mi">4</span><span class="p">],</span> <span class="n">line</span> <span class="mi">2</span> <span class="g g-Whitespace"> </span><span class="mi">1</span> <span class="c1">## Optionally simulate the DNA-only model to see how it performs and behaves</span> -<span class="g g-Whitespace"> </span><span class="mi">2</span> <span class="n">model</span> <span class="o">=</span> <span class="n">make_dna_model</span><span class="p">()</span> -<span class="ne">----> </span><span class="mi">3</span> <span class="n">model</span><span class="o">.</span><span class="n">simulate</span><span class="p">(</span><span class="n">output_name</span><span class="o">=</span><span class="s1">'run'</span><span class="p">,</span> +<span class="ne">----> </span><span class="mi">2</span> <span class="n">model</span> <span class="o">=</span> <span class="n">make_dna_model</span><span class="p">()</span> +<span class="g g-Whitespace"> </span><span class="mi">3</span> <span class="n">model</span><span class="o">.</span><span class="n">simulate</span><span class="p">(</span><span class="n">output_name</span><span class="o">=</span><span class="s1">'run'</span><span class="p">,</span> <span class="g g-Whitespace"> </span><span class="mi">4</span> <span class="n">directory</span><span class="o">=</span><span class="s1">'trombone-no_ssb'</span><span class="p">,</span> <span class="g g-Whitespace"> </span><span class="mi">5</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="g g-Whitespace"> </span><span class="mi">6</span> <span class="p">)</span> -<span class="nn">File /usr/local/Caskroom/miniconda/base/envs/pybd/lib/python3.9/site-packages/arbdmodel-0.0.0-py3.9.egg/arbdmodel/__init__.py:1454,</span> in <span class="ni">ArbdModel.simulate</span><span class="nt">(self, output_name, **kwargs)</span> -<span class="g g-Whitespace"> </span><span class="mi">1452</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="g g-Whitespace"> </span><span class="mi">1453</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="ne">-> </span><span class="mi">1454</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> - -<span class="nn">File /usr/local/Caskroom/miniconda/base/envs/pybd/lib/python3.9/site-packages/arbdmodel-0.0.0-py3.9.egg/arbdmodel/__init__.py:1629,</span> in <span class="ni">SimEngine.simulate</span><span class="nt">(self, model, output_name, output_directory, directory, log_file, binary, num_procs, dry_run, configuration, replicas, **conf_params)</span> -<span class="g g-Whitespace"> </span><span class="mi">1627</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="g g-Whitespace"> </span><span class="mi">1628</span> <span class="k">else</span><span class="p">:</span> -<span class="ne">-> </span><span class="mi">1629</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="g g-Whitespace"> </span><span class="mi">1631</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="g g-Whitespace"> </span><span class="mi">1632</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="nn">File /usr/local/Caskroom/miniconda/base/envs/pybd/lib/python3.9/site-packages/arbdmodel-0.0.0-py3.9.egg/arbdmodel/__init__.py:1676,</span> in <span class="ni">SimEngine._get_binary</span><span class="nt">(self, binary)</span> -<span class="g g-Whitespace"> </span><span class="mi">1673</span> <span class="n">binary</span> <span class="o">=</span> <span class="n">fname</span> -<span class="g g-Whitespace"> </span><span class="mi">1674</span> <span class="k">break</span> -<span class="ne">-> </span><span class="mi">1676</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="g g-Whitespace"> </span><span class="mi">1678</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="g g-Whitespace"> </span><span class="mi">1679</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="ne">Exception</span>: arbd was not found +<span class="nn">Cell In[3], line 23,</span> in <span class="ni">make_dna_model</span><span class="nt">()</span> +<span class="g g-Whitespace"> </span><span class="mi">20</span> <span class="n">_P</span><span class="o">.</span><span class="n">grid</span> <span class="o">=</span> <span class="p">(</span><span class="n">replisome_grid</span><span class="p">,</span> <span class="mi">500</span><span class="p">)</span> <span class="c1"># scale it up by a big factor</span> +<span class="g g-Whitespace"> </span><span class="mi">21</span> <span class="n">_B</span><span class="o">.</span><span class="n">grid</span> <span class="o">=</span> <span class="p">(</span><span class="n">replisome_grid</span><span class="p">,</span> <span class="mi">500</span><span class="p">)</span> +<span class="ne">---> </span><span class="mi">23</span> <span class="n">model</span> <span class="o">=</span> <span class="n">DnaModel</span><span class="p">([</span><span class="n">a</span><span class="p">],</span> <span class="n">dimensions</span><span class="o">=</span><span class="p">(</span><span class="mi">3000</span><span class="p">,</span><span class="mi">3000</span><span class="p">,</span><span class="mi">3000</span><span class="p">),</span> +<span class="g g-Whitespace"> </span><span class="mi">24</span> <span class="n">timestep</span> <span class="o">=</span> <span class="mf">20e-6</span> +<span class="g g-Whitespace"> </span><span class="mi">25</span> <span class="p">)</span> +<span class="g g-Whitespace"> </span><span class="mi">27</span> <span class="c1">## Restrain DNA ends</span> +<span class="g g-Whitespace"> </span><span class="mi">28</span> <span class="n">end1</span> <span class="o">=</span> <span class="n">model</span><span class="o">.</span><span class="n">strands</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="o">.</span><span class="n">children</span><span class="p">[</span><span class="mi">0</span><span class="p">]</span> + +<span class="nn">File ~/Documents/research/arbdmodel-simple/arbdmodel/ssdna_two_bead.py:164,</span> in <span class="ni">DnaModel.__init__</span><span class="nt">(self, polymers, sequences, DEBUG, **kwargs)</span> +<span class="g g-Whitespace"> </span><span class="mi">161</span> <span class="k">if</span> <span class="s1">'timestep'</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">'timestep'</span><span class="p">]</span> <span class="o">=</span> <span class="mf">20e-6</span> +<span class="g g-Whitespace"> </span><span class="mi">162</span> <span class="k">if</span> <span class="s1">'cutoff'</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">'cutoff'</span><span class="p">]</span> <span class="o">=</span> <span class="mi">35</span> +<span class="ne">--> </span><span class="mi">164</span> <span class="n">PolymerModel</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">polymers</span><span class="p">,</span> <span class="n">sequences</span><span class="p">,</span> <span class="n">monomers_per_bead_group</span><span class="o">=</span><span class="mi">1</span><span class="p">,</span> <span class="o">**</span><span class="n">kwargs</span><span class="p">)</span> +<span class="g g-Whitespace"> </span><span class="mi">165</span> <span class="bp">self</span><span class="o">.</span><span class="n">strands</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">children</span> <span class="c1"># make a nice alias</span> +<span class="g g-Whitespace"> </span><span class="mi">167</span> <span class="bp">self</span><span class="o">.</span><span class="n">add_nonbonded_interaction</span><span class="p">(</span> <span class="n">TabulatedNonbonded</span><span class="p">(</span><span class="n">get_resource_path</span><span class="p">(</span><span class="s1">'two_bead_model/NBBB.dat'</span><span class="p">)),</span> <span class="n">typeA</span><span class="o">=</span><span class="n">_B</span><span class="p">,</span> <span class="n">typeB</span><span class="o">=</span><span class="n">_B</span> <span class="p">)</span> + +<span class="nn">File ~/Documents/research/arbdmodel-simple/arbdmodel/polymer.py:648,</span> in <span class="ni">PolymerModel.__init__</span><span class="nt">(self, polymers, sequences, monomers_per_bead_group, **kwargs)</span> +<span class="g g-Whitespace"> </span><span class="mi">646</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="g g-Whitespace"> </span><span class="mi">647</span> <span class="bp">self</span><span class="o">.</span><span class="n">monomers_per_bead_group</span> <span class="o">=</span> <span class="n">monomers_per_bead_group</span> +<span class="ne">--> </span><span class="mi">648</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="g g-Whitespace"> </span><span class="mi">650</span><span class="w"> </span><span class="sd">""" Generate beads """</span> +<span class="g g-Whitespace"> </span><span class="mi">651</span> <span class="bp">self</span><span class="o">.</span><span class="n">generate_beads</span><span class="p">()</span> + +<span class="nn">File ~/Documents/research/arbdmodel-simple/arbdmodel/model.py:231,</span> in <span class="ni">ArbdModel.__init__</span><span class="nt">(self, children, cell_vectors, cell_origin, dimensions, remove_duplicate_bonded_terms, buffer_factor, configuration, dummy_types, **conf_params)</span> +<span class="g g-Whitespace"> </span><span class="mi">228</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="g g-Whitespace"> </span><span class="mi">230</span> <span class="c1"># Initialize parent class</span> +<span class="ne">--> </span><span class="mi">231</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="g g-Whitespace"> </span><span class="mi">232</span> <span class="n">cell_vectors</span><span class="p">,</span> <span class="n">cell_origin</span><span class="p">)</span> +<span class="g g-Whitespace"> </span><span class="mi">235</span> <span class="c1"># Store origin which might be different from cell_origin</span> +<span class="g g-Whitespace"> </span><span class="mi">236</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="ne">TypeError</span>: __init__() takes from 1 to 4 positional arguments but 6 were given </pre></div> </div> </div> diff --git a/_build/html/tutorials/index.html b/_build/html/tutorials/index.html index e5e6773fd178236b1fe6afd4811a0f83dc9404a1..992f6d07bf0fb62ed6cb3f79217bee6d2563e2ad 100644 --- a/_build/html/tutorials/index.html +++ b/_build/html/tutorials/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?v=be8a1c11" /> + <link rel="stylesheet" type="text/css" href="../_static/mystnb.4510f1fc1dee50b3e5859aac5469c37c29e427902b24a333a5f9fcb2f0b3ac41.css" /> <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?v=b4b7a797" /> + <link rel="stylesheet" type="text/css" href="../_static/proof.css" /> <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?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/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/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?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 src="../_static/js/hoverxref.js"></script> + <script src="../_static/js/tooltipster.bundle.min.js"></script> + <script src="../_static/js/micromodal.min.js"></script> <script>let toggleHintShow = 'Click to show';</script> <script>let toggleHintHide = 'Click to hide';</script> <script>let toggleOpenOnPrint = 'true';</script> diff --git a/_build/jupyter_execute/tutorials/3-iterative-boltzmann-inversion/3-ibi.ipynb b/_build/jupyter_execute/tutorials/3-iterative-boltzmann-inversion/3-ibi.ipynb index 9e08897f8b16c807ae29dbde57153682b0077fdd..059e02e382fc71a8995fd56c48653f70a85448e2 100644 --- a/_build/jupyter_execute/tutorials/3-iterative-boltzmann-inversion/3-ibi.ipynb +++ b/_build/jupyter_execute/tutorials/3-iterative-boltzmann-inversion/3-ibi.ipynb @@ -103,16 +103,17 @@ "metadata": {}, "outputs": [ { - "ename": "Exception", - "evalue": "arbd was not found", + "ename": "TypeError", + "evalue": "__init__() takes from 1 to 4 positional arguments but 6 were given", "output_type": "error", "traceback": [ "\u001b[0;31m---------------------------------------------------------------------------\u001b[0m", - "\u001b[0;31mException\u001b[0m Traceback (most recent call last)", - "Cell \u001b[0;32mIn[2], line 45\u001b[0m\n\u001b[1;32m 43\u001b[0m \u001b[38;5;250m\u001b[39m\u001b[38;5;124;03m\"\"\" Production \"\"\"\u001b[39;00m\n\u001b[1;32m 44\u001b[0m model\u001b[38;5;241m.\u001b[39mset_damping_coefficient( \u001b[38;5;241m100\u001b[39m )\n\u001b[0;32m---> 45\u001b[0m \u001b[43mengine\u001b[49m\u001b[38;5;241;43m.\u001b[39;49m\u001b[43msimulate\u001b[49m\u001b[43m(\u001b[49m\u001b[43mmodel\u001b[49m\u001b[43m,\u001b[49m\u001b[43m \u001b[49m\u001b[43moutput_name\u001b[49m\u001b[38;5;241;43m=\u001b[39;49m\u001b[43moutname\u001b[49m\u001b[43m,\u001b[49m\n\u001b[1;32m 46\u001b[0m \u001b[43m \u001b[49m\u001b[43mdirectory\u001b[49m\u001b[43m \u001b[49m\u001b[38;5;241;43m=\u001b[39;49m\u001b[43m \u001b[49m\u001b[43mdirectory\u001b[49m\n\u001b[1;32m 47\u001b[0m \u001b[43m \u001b[49m\u001b[43m)\u001b[49m\n", - "File \u001b[0;32m/usr/local/Caskroom/miniconda/base/envs/pybd/lib/python3.9/site-packages/arbdmodel-0.0.0-py3.9.egg/arbdmodel/__init__.py:1629\u001b[0m, in \u001b[0;36mSimEngine.simulate\u001b[0;34m(self, model, output_name, output_directory, directory, log_file, binary, num_procs, dry_run, configuration, replicas, **conf_params)\u001b[0m\n\u001b[1;32m 1627\u001b[0m \u001b[38;5;28;01mif\u001b[39;00m binary \u001b[38;5;129;01mis\u001b[39;00m \u001b[38;5;28;01mNone\u001b[39;00m: binary\u001b[38;5;241m=\u001b[39m\u001b[38;5;28mself\u001b[39m\u001b[38;5;241m.\u001b[39mdefault_binary\n\u001b[1;32m 1628\u001b[0m \u001b[38;5;28;01melse\u001b[39;00m:\n\u001b[0;32m-> 1629\u001b[0m binary \u001b[38;5;241m=\u001b[39m \u001b[38;5;28;43mself\u001b[39;49m\u001b[38;5;241;43m.\u001b[39;49m\u001b[43m_get_binary\u001b[49m\u001b[43m(\u001b[49m\u001b[43mbinary\u001b[49m\u001b[43m)\u001b[49m\n\u001b[1;32m 1631\u001b[0m \u001b[38;5;28;01mif\u001b[39;00m \u001b[38;5;129;01mnot\u001b[39;00m os\u001b[38;5;241m.\u001b[39mpath\u001b[38;5;241m.\u001b[39mexists(output_directory):\n\u001b[1;32m 1632\u001b[0m os\u001b[38;5;241m.\u001b[39mmakedirs(output_directory)\n", - "File \u001b[0;32m/usr/local/Caskroom/miniconda/base/envs/pybd/lib/python3.9/site-packages/arbdmodel-0.0.0-py3.9.egg/arbdmodel/__init__.py:1676\u001b[0m, in \u001b[0;36mSimEngine._get_binary\u001b[0;34m(self, binary)\u001b[0m\n\u001b[1;32m 1673\u001b[0m binary \u001b[38;5;241m=\u001b[39m fname\n\u001b[1;32m 1674\u001b[0m \u001b[38;5;28;01mbreak\u001b[39;00m\n\u001b[0;32m-> 1676\u001b[0m \u001b[38;5;28;01mif\u001b[39;00m binary \u001b[38;5;129;01mis\u001b[39;00m \u001b[38;5;28;01mNone\u001b[39;00m: \u001b[38;5;28;01mraise\u001b[39;00m \u001b[38;5;167;01mException\u001b[39;00m(\u001b[38;5;124m\"\u001b[39m\u001b[38;5;132;01m{}\u001b[39;00m\u001b[38;5;124m was not found\u001b[39m\u001b[38;5;124m\"\u001b[39m\u001b[38;5;241m.\u001b[39mformat(\u001b[38;5;28mself\u001b[39m\u001b[38;5;241m.\u001b[39mdefault_binary))\n\u001b[1;32m 1678\u001b[0m \u001b[38;5;28;01mif\u001b[39;00m \u001b[38;5;129;01mnot\u001b[39;00m os\u001b[38;5;241m.\u001b[39mpath\u001b[38;5;241m.\u001b[39mexists(binary):\n\u001b[1;32m 1679\u001b[0m \u001b[38;5;28;01mraise\u001b[39;00m \u001b[38;5;167;01mException\u001b[39;00m(\u001b[38;5;124m\"\u001b[39m\u001b[38;5;132;01m{}\u001b[39;00m\u001b[38;5;124m was not found\u001b[39m\u001b[38;5;124m\"\u001b[39m\u001b[38;5;241m.\u001b[39mformat(\u001b[38;5;28mself\u001b[39m\u001b[38;5;241m.\u001b[39mdefault_binary))\n", - "\u001b[0;31mException\u001b[0m: arbd was not found" + "\u001b[0;31mTypeError\u001b[0m Traceback (most recent call last)", + "Cell \u001b[0;32mIn[2], line 17\u001b[0m\n\u001b[1;32m 13\u001b[0m debye_length \u001b[38;5;241m=\u001b[39m \u001b[38;5;241m10\u001b[39m\n\u001b[1;32m 15\u001b[0m polymers, sequences \u001b[38;5;241m=\u001b[39m create_arbd_polymer_objects()\n\u001b[0;32m---> 17\u001b[0m model \u001b[38;5;241m=\u001b[39m \u001b[43mNupModel\u001b[49m\u001b[43m(\u001b[49m\u001b[43m \u001b[49m\u001b[43mpolymers\u001b[49m\u001b[43m,\u001b[49m\u001b[43m \u001b[49m\u001b[43msequences\u001b[49m\u001b[43m,\u001b[49m\n\u001b[1;32m 18\u001b[0m \u001b[43m \u001b[49m\u001b[43mdebye_length\u001b[49m\u001b[43m \u001b[49m\u001b[38;5;241;43m=\u001b[39;49m\u001b[43m \u001b[49m\u001b[43mdebye_length\u001b[49m\u001b[43m,\u001b[49m\n\u001b[1;32m 19\u001b[0m \u001b[43m \u001b[49m\u001b[43mtemperature\u001b[49m\u001b[38;5;241;43m=\u001b[39;49m\u001b[43mtemperature\u001b[49m\u001b[43m,\u001b[49m\n\u001b[1;32m 20\u001b[0m \u001b[43m \u001b[49m\u001b[43mdamping_coefficient\u001b[49m\u001b[43m \u001b[49m\u001b[38;5;241;43m=\u001b[39;49m\u001b[43m \u001b[49m\u001b[38;5;241;43m50000\u001b[39;49m\u001b[43m,\u001b[49m\u001b[43m \u001b[49m\u001b[38;5;66;43;03m# units of 1/ns\u001b[39;49;00m\n\u001b[1;32m 21\u001b[0m \u001b[43m \u001b[49m\u001b[43mdecomp_period\u001b[49m\u001b[43m \u001b[49m\u001b[38;5;241;43m=\u001b[39;49m\u001b[43m \u001b[49m\u001b[43mdecomp_period\u001b[49m\u001b[43m,\u001b[49m\n\u001b[1;32m 22\u001b[0m \u001b[43m \u001b[49m\u001b[43mpairlist_distance\u001b[49m\u001b[43m \u001b[49m\u001b[38;5;241;43m=\u001b[39;49m\u001b[43m \u001b[49m\u001b[38;5;241;43m50\u001b[39;49m\u001b[38;5;241;43m+\u001b[39;49m\u001b[43mskin_depth\u001b[49m\u001b[43m,\u001b[49m\n\u001b[1;32m 23\u001b[0m \u001b[43m \u001b[49m\u001b[43mdimensions\u001b[49m\u001b[43m \u001b[49m\u001b[38;5;241;43m=\u001b[39;49m\u001b[43m \u001b[49m\u001b[43mdimensions\u001b[49m\n\u001b[1;32m 24\u001b[0m \u001b[43m \u001b[49m\u001b[43m)\u001b[49m\n\u001b[1;32m 25\u001b[0m engine \u001b[38;5;241m=\u001b[39m ArbdEngine( integrator \u001b[38;5;241m=\u001b[39m \u001b[38;5;124m'\u001b[39m\u001b[38;5;124mLangevin\u001b[39m\u001b[38;5;124m'\u001b[39m,\n\u001b[1;32m 26\u001b[0m num_steps\u001b[38;5;241m=\u001b[39m\u001b[38;5;241m1e7\u001b[39m,\n\u001b[1;32m 27\u001b[0m output_period\u001b[38;5;241m=\u001b[39m\u001b[38;5;241m1e4\u001b[39m,\n\u001b[1;32m 28\u001b[0m gpu \u001b[38;5;241m=\u001b[39m \u001b[38;5;241m0\u001b[39m\n\u001b[1;32m 29\u001b[0m )\n\u001b[1;32m 30\u001b[0m directory \u001b[38;5;241m=\u001b[39m \u001b[38;5;124mf\u001b[39m\u001b[38;5;124m'\u001b[39m\u001b[38;5;124m1-one_bead_per_res-\u001b[39m\u001b[38;5;132;01m{\u001b[39;00mmodel_name\u001b[38;5;132;01m}\u001b[39;00m\u001b[38;5;124m'\u001b[39m\n", + "File \u001b[0;32m~/Documents/research/arbdmodel-simple/arbdmodel/hps_polymer_model.py:239\u001b[0m, in \u001b[0;36mHpsModel.__init__\u001b[0;34m(self, polymers, sequences, rest_length, spring_constant, debye_length, damping_coefficient, DEBUG, **kwargs)\u001b[0m\n\u001b[1;32m 236\u001b[0m \u001b[38;5;28;01mif\u001b[39;00m sequences \u001b[38;5;129;01mis\u001b[39;00m \u001b[38;5;28;01mNone\u001b[39;00m:\n\u001b[1;32m 237\u001b[0m \u001b[38;5;28;01mraise\u001b[39;00m \u001b[38;5;167;01mNotImplementedError\u001b[39;00m(\u001b[38;5;124m\"\u001b[39m\u001b[38;5;124mHpsModel must be provided a sequences argument\u001b[39m\u001b[38;5;124m\"\u001b[39m)\n\u001b[0;32m--> 239\u001b[0m \u001b[43mPolymerModel\u001b[49m\u001b[38;5;241;43m.\u001b[39;49m\u001b[38;5;21;43m__init__\u001b[39;49m\u001b[43m(\u001b[49m\u001b[38;5;28;43mself\u001b[39;49m\u001b[43m,\u001b[49m\u001b[43m \u001b[49m\u001b[43mpolymers\u001b[49m\u001b[43m,\u001b[49m\u001b[43m \u001b[49m\u001b[43msequences\u001b[49m\u001b[43m,\u001b[49m\u001b[43m \u001b[49m\u001b[43mmonomers_per_bead_group\u001b[49m\u001b[38;5;241;43m=\u001b[39;49m\u001b[38;5;241;43m1\u001b[39;49m\u001b[43m,\u001b[49m\u001b[43m \u001b[49m\u001b[38;5;241;43m*\u001b[39;49m\u001b[38;5;241;43m*\u001b[39;49m\u001b[43mkwargs\u001b[49m\u001b[43m)\u001b[49m\n\u001b[1;32m 241\u001b[0m \u001b[38;5;250m\u001b[39m\u001b[38;5;124;03m\"\"\" Update type diffusion coefficients \"\"\"\u001b[39;00m\n\u001b[1;32m 242\u001b[0m \u001b[38;5;28mself\u001b[39m\u001b[38;5;241m.\u001b[39mtypes \u001b[38;5;241m=\u001b[39m all_types \u001b[38;5;241m=\u001b[39m [t \u001b[38;5;28;01mfor\u001b[39;00m key,t \u001b[38;5;129;01min\u001b[39;00m _types\u001b[38;5;241m.\u001b[39mitems()]\n", + "File \u001b[0;32m~/Documents/research/arbdmodel-simple/arbdmodel/polymer.py:648\u001b[0m, in \u001b[0;36mPolymerModel.__init__\u001b[0;34m(self, polymers, sequences, monomers_per_bead_group, **kwargs)\u001b[0m\n\u001b[1;32m 646\u001b[0m \u001b[38;5;28mself\u001b[39m\u001b[38;5;241m.\u001b[39msequences \u001b[38;5;241m=\u001b[39m sequences\n\u001b[1;32m 647\u001b[0m \u001b[38;5;28mself\u001b[39m\u001b[38;5;241m.\u001b[39mmonomers_per_bead_group \u001b[38;5;241m=\u001b[39m monomers_per_bead_group\n\u001b[0;32m--> 648\u001b[0m \u001b[43mArbdModel\u001b[49m\u001b[38;5;241;43m.\u001b[39;49m\u001b[38;5;21;43m__init__\u001b[39;49m\u001b[43m(\u001b[49m\u001b[38;5;28;43mself\u001b[39;49m\u001b[43m,\u001b[49m\u001b[43m \u001b[49m\u001b[43m[\u001b[49m\u001b[43m]\u001b[49m\u001b[43m,\u001b[49m\u001b[43m \u001b[49m\u001b[38;5;241;43m*\u001b[39;49m\u001b[38;5;241;43m*\u001b[39;49m\u001b[43mkwargs\u001b[49m\u001b[43m)\u001b[49m\n\u001b[1;32m 650\u001b[0m \u001b[38;5;250m\u001b[39m\u001b[38;5;124;03m\"\"\" Generate beads \"\"\"\u001b[39;00m\n\u001b[1;32m 651\u001b[0m \u001b[38;5;28mself\u001b[39m\u001b[38;5;241m.\u001b[39mgenerate_beads()\n", + "File \u001b[0;32m~/Documents/research/arbdmodel-simple/arbdmodel/model.py:231\u001b[0m, in \u001b[0;36mArbdModel.__init__\u001b[0;34m(self, children, cell_vectors, cell_origin, dimensions, remove_duplicate_bonded_terms, buffer_factor, configuration, dummy_types, **conf_params)\u001b[0m\n\u001b[1;32m 228\u001b[0m cell_origin \u001b[38;5;241m=\u001b[39m [\u001b[38;5;241m0\u001b[39m, \u001b[38;5;241m0\u001b[39m, \u001b[38;5;241m0\u001b[39m]\n\u001b[1;32m 230\u001b[0m \u001b[38;5;66;03m# Initialize parent class\u001b[39;00m\n\u001b[0;32m--> 231\u001b[0m \u001b[43mPdbModel\u001b[49m\u001b[38;5;241;43m.\u001b[39;49m\u001b[38;5;21;43m__init__\u001b[39;49m\u001b[43m(\u001b[49m\u001b[38;5;28;43mself\u001b[39;49m\u001b[43m,\u001b[49m\u001b[43m \u001b[49m\u001b[43mchildren\u001b[49m\u001b[43m,\u001b[49m\u001b[43m \u001b[49m\u001b[43mdimensions\u001b[49m\u001b[43m,\u001b[49m\u001b[43m \u001b[49m\u001b[43mremove_duplicate_bonded_terms\u001b[49m\u001b[43m,\u001b[49m\n\u001b[1;32m 232\u001b[0m \u001b[43m \u001b[49m\u001b[43mcell_vectors\u001b[49m\u001b[43m,\u001b[49m\u001b[43m \u001b[49m\u001b[43mcell_origin\u001b[49m\u001b[43m)\u001b[49m\n\u001b[1;32m 235\u001b[0m \u001b[38;5;66;03m# Store origin which might be different from cell_origin\u001b[39;00m\n\u001b[1;32m 236\u001b[0m \u001b[38;5;28mself\u001b[39m\u001b[38;5;241m.\u001b[39morigin \u001b[38;5;241m=\u001b[39m cell_origin\n", + "\u001b[0;31mTypeError\u001b[0m: __init__() takes from 1 to 4 positional arguments but 6 were given" ] } ], diff --git a/_build/jupyter_execute/tutorials/4-rigid-bodies/4-rigid-bodies.ipynb b/_build/jupyter_execute/tutorials/4-rigid-bodies/4-rigid-bodies.ipynb index 1744053e4f2a9d4c9238d14e604762ef98c8f66a..69ef24f929355b9baee16e1046ce3793d12ba68c 100644 --- a/_build/jupyter_execute/tutorials/4-rigid-bodies/4-rigid-bodies.ipynb +++ b/_build/jupyter_execute/tutorials/4-rigid-bodies/4-rigid-bodies.ipynb @@ -95,17 +95,18 @@ "metadata": {}, "outputs": [ { - "ename": "Exception", - "evalue": "arbd was not found", + "ename": "TypeError", + "evalue": "__init__() takes from 1 to 4 positional arguments but 6 were given", "output_type": "error", "traceback": [ "\u001b[0;31m---------------------------------------------------------------------------\u001b[0m", - "\u001b[0;31mException\u001b[0m Traceback (most recent call last)", - "Cell \u001b[0;32mIn[4], line 3\u001b[0m\n\u001b[1;32m 1\u001b[0m \u001b[38;5;66;03m## Optionally simulate the DNA-only model to see how it performs and behaves\u001b[39;00m\n\u001b[1;32m 2\u001b[0m model \u001b[38;5;241m=\u001b[39m make_dna_model()\n\u001b[0;32m----> 3\u001b[0m \u001b[43mmodel\u001b[49m\u001b[38;5;241;43m.\u001b[39;49m\u001b[43msimulate\u001b[49m\u001b[43m(\u001b[49m\u001b[43moutput_name\u001b[49m\u001b[38;5;241;43m=\u001b[39;49m\u001b[38;5;124;43m'\u001b[39;49m\u001b[38;5;124;43mrun\u001b[39;49m\u001b[38;5;124;43m'\u001b[39;49m\u001b[43m,\u001b[49m\n\u001b[1;32m 4\u001b[0m \u001b[43m \u001b[49m\u001b[43mdirectory\u001b[49m\u001b[38;5;241;43m=\u001b[39;49m\u001b[38;5;124;43m'\u001b[39;49m\u001b[38;5;124;43mtrombone-no_ssb\u001b[39;49m\u001b[38;5;124;43m'\u001b[39;49m\u001b[43m,\u001b[49m\n\u001b[1;32m 5\u001b[0m \u001b[43m \u001b[49m\u001b[43mnum_steps\u001b[49m\u001b[38;5;241;43m=\u001b[39;49m\u001b[38;5;241;43m1e5\u001b[39;49m\u001b[43m,\u001b[49m\u001b[43m \u001b[49m\u001b[43moutput_period\u001b[49m\u001b[38;5;241;43m=\u001b[39;49m\u001b[38;5;241;43m1e3\u001b[39;49m\u001b[43m,\u001b[49m\n\u001b[1;32m 6\u001b[0m \u001b[43m)\u001b[49m\n", - "File \u001b[0;32m/usr/local/Caskroom/miniconda/base/envs/pybd/lib/python3.9/site-packages/arbdmodel-0.0.0-py3.9.egg/arbdmodel/__init__.py:1454\u001b[0m, in \u001b[0;36mArbdModel.simulate\u001b[0;34m(self, output_name, **kwargs)\u001b[0m\n\u001b[1;32m 1452\u001b[0m engine_kwargs \u001b[38;5;241m=\u001b[39m {k:v \u001b[38;5;28;01mfor\u001b[39;00m k,v \u001b[38;5;129;01min\u001b[39;00m kwargs\u001b[38;5;241m.\u001b[39mitems() \u001b[38;5;28;01mif\u001b[39;00m k \u001b[38;5;129;01mnot\u001b[39;00m \u001b[38;5;129;01min\u001b[39;00m sim_kws}\n\u001b[1;32m 1453\u001b[0m engine \u001b[38;5;241m=\u001b[39m ArbdEngine(\u001b[38;5;241m*\u001b[39m\u001b[38;5;241m*\u001b[39mengine_kwargs)\n\u001b[0;32m-> 1454\u001b[0m \u001b[38;5;28;01mreturn\u001b[39;00m \u001b[43mengine\u001b[49m\u001b[38;5;241;43m.\u001b[39;49m\u001b[43msimulate\u001b[49m\u001b[43m(\u001b[49m\u001b[38;5;28;43mself\u001b[39;49m\u001b[43m,\u001b[49m\u001b[43m \u001b[49m\u001b[43moutput_name\u001b[49m\u001b[43m,\u001b[49m\u001b[43m \u001b[49m\u001b[38;5;241;43m*\u001b[39;49m\u001b[38;5;241;43m*\u001b[39;49m\u001b[43msim_kwargs\u001b[49m\u001b[43m)\u001b[49m\n", - "File \u001b[0;32m/usr/local/Caskroom/miniconda/base/envs/pybd/lib/python3.9/site-packages/arbdmodel-0.0.0-py3.9.egg/arbdmodel/__init__.py:1629\u001b[0m, in \u001b[0;36mSimEngine.simulate\u001b[0;34m(self, model, output_name, output_directory, directory, log_file, binary, num_procs, dry_run, configuration, replicas, **conf_params)\u001b[0m\n\u001b[1;32m 1627\u001b[0m \u001b[38;5;28;01mif\u001b[39;00m binary \u001b[38;5;129;01mis\u001b[39;00m \u001b[38;5;28;01mNone\u001b[39;00m: binary\u001b[38;5;241m=\u001b[39m\u001b[38;5;28mself\u001b[39m\u001b[38;5;241m.\u001b[39mdefault_binary\n\u001b[1;32m 1628\u001b[0m \u001b[38;5;28;01melse\u001b[39;00m:\n\u001b[0;32m-> 1629\u001b[0m binary \u001b[38;5;241m=\u001b[39m \u001b[38;5;28;43mself\u001b[39;49m\u001b[38;5;241;43m.\u001b[39;49m\u001b[43m_get_binary\u001b[49m\u001b[43m(\u001b[49m\u001b[43mbinary\u001b[49m\u001b[43m)\u001b[49m\n\u001b[1;32m 1631\u001b[0m \u001b[38;5;28;01mif\u001b[39;00m \u001b[38;5;129;01mnot\u001b[39;00m os\u001b[38;5;241m.\u001b[39mpath\u001b[38;5;241m.\u001b[39mexists(output_directory):\n\u001b[1;32m 1632\u001b[0m os\u001b[38;5;241m.\u001b[39mmakedirs(output_directory)\n", - "File \u001b[0;32m/usr/local/Caskroom/miniconda/base/envs/pybd/lib/python3.9/site-packages/arbdmodel-0.0.0-py3.9.egg/arbdmodel/__init__.py:1676\u001b[0m, in \u001b[0;36mSimEngine._get_binary\u001b[0;34m(self, binary)\u001b[0m\n\u001b[1;32m 1673\u001b[0m binary \u001b[38;5;241m=\u001b[39m fname\n\u001b[1;32m 1674\u001b[0m \u001b[38;5;28;01mbreak\u001b[39;00m\n\u001b[0;32m-> 1676\u001b[0m \u001b[38;5;28;01mif\u001b[39;00m binary \u001b[38;5;129;01mis\u001b[39;00m \u001b[38;5;28;01mNone\u001b[39;00m: \u001b[38;5;28;01mraise\u001b[39;00m \u001b[38;5;167;01mException\u001b[39;00m(\u001b[38;5;124m\"\u001b[39m\u001b[38;5;132;01m{}\u001b[39;00m\u001b[38;5;124m was not found\u001b[39m\u001b[38;5;124m\"\u001b[39m\u001b[38;5;241m.\u001b[39mformat(\u001b[38;5;28mself\u001b[39m\u001b[38;5;241m.\u001b[39mdefault_binary))\n\u001b[1;32m 1678\u001b[0m \u001b[38;5;28;01mif\u001b[39;00m \u001b[38;5;129;01mnot\u001b[39;00m os\u001b[38;5;241m.\u001b[39mpath\u001b[38;5;241m.\u001b[39mexists(binary):\n\u001b[1;32m 1679\u001b[0m \u001b[38;5;28;01mraise\u001b[39;00m \u001b[38;5;167;01mException\u001b[39;00m(\u001b[38;5;124m\"\u001b[39m\u001b[38;5;132;01m{}\u001b[39;00m\u001b[38;5;124m was not found\u001b[39m\u001b[38;5;124m\"\u001b[39m\u001b[38;5;241m.\u001b[39mformat(\u001b[38;5;28mself\u001b[39m\u001b[38;5;241m.\u001b[39mdefault_binary))\n", - "\u001b[0;31mException\u001b[0m: arbd was not found" + "\u001b[0;31mTypeError\u001b[0m Traceback (most recent call last)", + "Cell \u001b[0;32mIn[4], line 2\u001b[0m\n\u001b[1;32m 1\u001b[0m \u001b[38;5;66;03m## Optionally simulate the DNA-only model to see how it performs and behaves\u001b[39;00m\n\u001b[0;32m----> 2\u001b[0m model \u001b[38;5;241m=\u001b[39m \u001b[43mmake_dna_model\u001b[49m\u001b[43m(\u001b[49m\u001b[43m)\u001b[49m\n\u001b[1;32m 3\u001b[0m model\u001b[38;5;241m.\u001b[39msimulate(output_name\u001b[38;5;241m=\u001b[39m\u001b[38;5;124m'\u001b[39m\u001b[38;5;124mrun\u001b[39m\u001b[38;5;124m'\u001b[39m,\n\u001b[1;32m 4\u001b[0m directory\u001b[38;5;241m=\u001b[39m\u001b[38;5;124m'\u001b[39m\u001b[38;5;124mtrombone-no_ssb\u001b[39m\u001b[38;5;124m'\u001b[39m,\n\u001b[1;32m 5\u001b[0m num_steps\u001b[38;5;241m=\u001b[39m\u001b[38;5;241m1e5\u001b[39m, output_period\u001b[38;5;241m=\u001b[39m\u001b[38;5;241m1e3\u001b[39m,\n\u001b[1;32m 6\u001b[0m )\n", + "Cell \u001b[0;32mIn[3], line 23\u001b[0m, in \u001b[0;36mmake_dna_model\u001b[0;34m()\u001b[0m\n\u001b[1;32m 20\u001b[0m _P\u001b[38;5;241m.\u001b[39mgrid \u001b[38;5;241m=\u001b[39m (replisome_grid, \u001b[38;5;241m500\u001b[39m) \u001b[38;5;66;03m# scale it up by a big factor\u001b[39;00m\n\u001b[1;32m 21\u001b[0m _B\u001b[38;5;241m.\u001b[39mgrid \u001b[38;5;241m=\u001b[39m (replisome_grid, \u001b[38;5;241m500\u001b[39m)\n\u001b[0;32m---> 23\u001b[0m model \u001b[38;5;241m=\u001b[39m \u001b[43mDnaModel\u001b[49m\u001b[43m(\u001b[49m\u001b[43m[\u001b[49m\u001b[43ma\u001b[49m\u001b[43m]\u001b[49m\u001b[43m,\u001b[49m\u001b[43m \u001b[49m\u001b[43mdimensions\u001b[49m\u001b[38;5;241;43m=\u001b[39;49m\u001b[43m(\u001b[49m\u001b[38;5;241;43m3000\u001b[39;49m\u001b[43m,\u001b[49m\u001b[38;5;241;43m3000\u001b[39;49m\u001b[43m,\u001b[49m\u001b[38;5;241;43m3000\u001b[39;49m\u001b[43m)\u001b[49m\u001b[43m,\u001b[49m\n\u001b[1;32m 24\u001b[0m \u001b[43m \u001b[49m\u001b[43mtimestep\u001b[49m\u001b[43m \u001b[49m\u001b[38;5;241;43m=\u001b[39;49m\u001b[43m \u001b[49m\u001b[38;5;241;43m20e-6\u001b[39;49m\n\u001b[1;32m 25\u001b[0m \u001b[43m \u001b[49m\u001b[43m)\u001b[49m\n\u001b[1;32m 27\u001b[0m \u001b[38;5;66;03m## Restrain DNA ends\u001b[39;00m\n\u001b[1;32m 28\u001b[0m end1 \u001b[38;5;241m=\u001b[39m model\u001b[38;5;241m.\u001b[39mstrands[\u001b[38;5;241m0\u001b[39m]\u001b[38;5;241m.\u001b[39mchildren[\u001b[38;5;241m0\u001b[39m]\u001b[38;5;241m.\u001b[39mchildren[\u001b[38;5;241m0\u001b[39m]\n", + "File \u001b[0;32m~/Documents/research/arbdmodel-simple/arbdmodel/ssdna_two_bead.py:164\u001b[0m, in \u001b[0;36mDnaModel.__init__\u001b[0;34m(self, polymers, sequences, DEBUG, **kwargs)\u001b[0m\n\u001b[1;32m 161\u001b[0m \u001b[38;5;28;01mif\u001b[39;00m \u001b[38;5;124m'\u001b[39m\u001b[38;5;124mtimestep\u001b[39m\u001b[38;5;124m'\u001b[39m \u001b[38;5;129;01mnot\u001b[39;00m \u001b[38;5;129;01min\u001b[39;00m kwargs: kwargs[\u001b[38;5;124m'\u001b[39m\u001b[38;5;124mtimestep\u001b[39m\u001b[38;5;124m'\u001b[39m] \u001b[38;5;241m=\u001b[39m \u001b[38;5;241m20e-6\u001b[39m\n\u001b[1;32m 162\u001b[0m \u001b[38;5;28;01mif\u001b[39;00m \u001b[38;5;124m'\u001b[39m\u001b[38;5;124mcutoff\u001b[39m\u001b[38;5;124m'\u001b[39m \u001b[38;5;129;01mnot\u001b[39;00m \u001b[38;5;129;01min\u001b[39;00m kwargs: kwargs[\u001b[38;5;124m'\u001b[39m\u001b[38;5;124mcutoff\u001b[39m\u001b[38;5;124m'\u001b[39m] \u001b[38;5;241m=\u001b[39m \u001b[38;5;241m35\u001b[39m\n\u001b[0;32m--> 164\u001b[0m \u001b[43mPolymerModel\u001b[49m\u001b[38;5;241;43m.\u001b[39;49m\u001b[38;5;21;43m__init__\u001b[39;49m\u001b[43m(\u001b[49m\u001b[38;5;28;43mself\u001b[39;49m\u001b[43m,\u001b[49m\u001b[43m \u001b[49m\u001b[43mpolymers\u001b[49m\u001b[43m,\u001b[49m\u001b[43m \u001b[49m\u001b[43msequences\u001b[49m\u001b[43m,\u001b[49m\u001b[43m \u001b[49m\u001b[43mmonomers_per_bead_group\u001b[49m\u001b[38;5;241;43m=\u001b[39;49m\u001b[38;5;241;43m1\u001b[39;49m\u001b[43m,\u001b[49m\u001b[43m \u001b[49m\u001b[38;5;241;43m*\u001b[39;49m\u001b[38;5;241;43m*\u001b[39;49m\u001b[43mkwargs\u001b[49m\u001b[43m)\u001b[49m\n\u001b[1;32m 165\u001b[0m \u001b[38;5;28mself\u001b[39m\u001b[38;5;241m.\u001b[39mstrands \u001b[38;5;241m=\u001b[39m \u001b[38;5;28mself\u001b[39m\u001b[38;5;241m.\u001b[39mchildren \u001b[38;5;66;03m# make a nice alias\u001b[39;00m\n\u001b[1;32m 167\u001b[0m \u001b[38;5;28mself\u001b[39m\u001b[38;5;241m.\u001b[39madd_nonbonded_interaction( TabulatedNonbonded(get_resource_path(\u001b[38;5;124m'\u001b[39m\u001b[38;5;124mtwo_bead_model/NBBB.dat\u001b[39m\u001b[38;5;124m'\u001b[39m)), typeA\u001b[38;5;241m=\u001b[39m_B, typeB\u001b[38;5;241m=\u001b[39m_B )\n", + "File \u001b[0;32m~/Documents/research/arbdmodel-simple/arbdmodel/polymer.py:648\u001b[0m, in \u001b[0;36mPolymerModel.__init__\u001b[0;34m(self, polymers, sequences, monomers_per_bead_group, **kwargs)\u001b[0m\n\u001b[1;32m 646\u001b[0m \u001b[38;5;28mself\u001b[39m\u001b[38;5;241m.\u001b[39msequences \u001b[38;5;241m=\u001b[39m sequences\n\u001b[1;32m 647\u001b[0m \u001b[38;5;28mself\u001b[39m\u001b[38;5;241m.\u001b[39mmonomers_per_bead_group \u001b[38;5;241m=\u001b[39m monomers_per_bead_group\n\u001b[0;32m--> 648\u001b[0m \u001b[43mArbdModel\u001b[49m\u001b[38;5;241;43m.\u001b[39;49m\u001b[38;5;21;43m__init__\u001b[39;49m\u001b[43m(\u001b[49m\u001b[38;5;28;43mself\u001b[39;49m\u001b[43m,\u001b[49m\u001b[43m \u001b[49m\u001b[43m[\u001b[49m\u001b[43m]\u001b[49m\u001b[43m,\u001b[49m\u001b[43m \u001b[49m\u001b[38;5;241;43m*\u001b[39;49m\u001b[38;5;241;43m*\u001b[39;49m\u001b[43mkwargs\u001b[49m\u001b[43m)\u001b[49m\n\u001b[1;32m 650\u001b[0m \u001b[38;5;250m\u001b[39m\u001b[38;5;124;03m\"\"\" Generate beads \"\"\"\u001b[39;00m\n\u001b[1;32m 651\u001b[0m \u001b[38;5;28mself\u001b[39m\u001b[38;5;241m.\u001b[39mgenerate_beads()\n", + "File \u001b[0;32m~/Documents/research/arbdmodel-simple/arbdmodel/model.py:231\u001b[0m, in \u001b[0;36mArbdModel.__init__\u001b[0;34m(self, children, cell_vectors, cell_origin, dimensions, remove_duplicate_bonded_terms, buffer_factor, configuration, dummy_types, **conf_params)\u001b[0m\n\u001b[1;32m 228\u001b[0m cell_origin \u001b[38;5;241m=\u001b[39m [\u001b[38;5;241m0\u001b[39m, \u001b[38;5;241m0\u001b[39m, \u001b[38;5;241m0\u001b[39m]\n\u001b[1;32m 230\u001b[0m \u001b[38;5;66;03m# Initialize parent class\u001b[39;00m\n\u001b[0;32m--> 231\u001b[0m \u001b[43mPdbModel\u001b[49m\u001b[38;5;241;43m.\u001b[39;49m\u001b[38;5;21;43m__init__\u001b[39;49m\u001b[43m(\u001b[49m\u001b[38;5;28;43mself\u001b[39;49m\u001b[43m,\u001b[49m\u001b[43m \u001b[49m\u001b[43mchildren\u001b[49m\u001b[43m,\u001b[49m\u001b[43m \u001b[49m\u001b[43mdimensions\u001b[49m\u001b[43m,\u001b[49m\u001b[43m \u001b[49m\u001b[43mremove_duplicate_bonded_terms\u001b[49m\u001b[43m,\u001b[49m\n\u001b[1;32m 232\u001b[0m \u001b[43m \u001b[49m\u001b[43mcell_vectors\u001b[49m\u001b[43m,\u001b[49m\u001b[43m \u001b[49m\u001b[43mcell_origin\u001b[49m\u001b[43m)\u001b[49m\n\u001b[1;32m 235\u001b[0m \u001b[38;5;66;03m# Store origin which might be different from cell_origin\u001b[39;00m\n\u001b[1;32m 236\u001b[0m \u001b[38;5;28mself\u001b[39m\u001b[38;5;241m.\u001b[39morigin \u001b[38;5;241m=\u001b[39m cell_origin\n", + "\u001b[0;31mTypeError\u001b[0m: __init__() takes from 1 to 4 positional arguments but 6 were given" ] } ],