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diff --git a/_build/.doctrees/api/utilities/version.doctree b/_build/.doctrees/api/utilities/version.doctree
index 436e3d32e1416a029161508468ecc68d87c8d7e2..e154cab7dc98fa12c4d9ca5a505621c9e3cd7820 100644
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diff --git a/_build/.doctrees/environment.pickle b/_build/.doctrees/environment.pickle
index 1b6bbb0d5c3f845f641e5370492e10dc28b35e12..b35f2235acfee7c667d8a087cf3d83bc00c0f0f5 100644
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diff --git a/_build/html/_modules/arbdmodel/binary_manager.html b/_build/html/_modules/arbdmodel/binary_manager.html
index 461da706468a1b5e2075b457f0df376ba9b7f08d..d6a80cdf95f5c565d5a5e10629f1156953112e3c 100644
--- a/_build/html/_modules/arbdmodel/binary_manager.html
+++ b/_build/html/_modules/arbdmodel/binary_manager.html
@@ -301,10 +301,6 @@ document.write(`
<h1>Source code for arbdmodel.binary_manager</h1><div class="highlight"><pre>
<span></span><span class="c1"># -*- coding: utf-8 -*-</span>
-<span class="sd">"""</span>
-<span class="sd">Binary path management module for simulation engines and processors.</span>
-<span class="sd">This module provides a singleton object to manage paths to external binaries.</span>
-<span class="sd">"""</span>
<span class="kn">import</span><span class="w"> </span><span class="nn">os</span>
<span class="kn">import</span><span class="w"> </span><span class="nn">platform</span>
@@ -507,10 +503,9 @@ document.write(`
<span class="sd"> If users don't wish to call this function, they can set the paths manually.</span>
<span class="sd"> Example: </span>
-<span class="sd"> >>arbd_path = BinaryManager.get_binary_path("arbd")</span>
-<span class="sd"> >>print(f"ARBD binary path: {arbd_path}")</span>
-
-<span class="sd"> >>BinaryManager.set_binary_path("hydropro", "/path/to/hydropro")</span>
+<span class="sd"> >>> arbd_path = BinaryManager.get_binary_path("arbd")</span>
+<span class="sd"> >>> print(f"ARBD binary path: {arbd_path}")</span>
+<span class="sd"> >>> BinaryManager.set_binary_path("hydropro", "/path/to/hydropro")</span>
<span class="sd"> """</span>
<span class="c1"># Check environment variables for binary paths</span>
<span class="k">for</span> <span class="n">binary</span> <span class="ow">in</span> <span class="n">DEFAULT_BINARIES</span><span class="p">:</span>
diff --git a/_build/html/_modules/arbdmodel/core_objects.html b/_build/html/_modules/arbdmodel/core_objects.html
index 69922c8f8be5ab5bf61636a4cb036e54f11e83c6..97ab25a5a594b6aa39d7e70661dbbd6ac4b9e74b 100644
--- a/_build/html/_modules/arbdmodel/core_objects.html
+++ b/_build/html/_modules/arbdmodel/core_objects.html
@@ -317,20 +317,11 @@ document.write(`
<span class="sd"> objects in 3D space, as well as methods for applying transformations such as</span>
<span class="sd"> translations and rotations.</span>
-<span class="sd"> Attributes:</span>
+<span class="sd"> Parameters:</span>
<span class="sd"> position (numpy.ndarray): The position of the object in 3D space.</span>
<span class="sd"> orientation (numpy.ndarray or None): The orientation matrix of the object.</span>
<span class="sd"> If None, the object has no orientation.</span>
-<span class="sd"> Methods:</span>
-<span class="sd"> translate(offset): Translate the object by the given offset.</span>
-<span class="sd"> rotate(R, about): Rotate the object by the rotation matrix R about a center point.</span>
-<span class="sd"> transform(R, center, offset): Apply a general transformation to the object.</span>
-<span class="sd"> get_collapsed_position(): Get the absolute position of the object, taking into</span>
-<span class="sd"> account parent transformations if the object is a Child.</span>
-<span class="sd"> applyOrientation(obj): Apply the orientation chain to an object, considering</span>
-<span class="sd"> parent orientations if the object is a Child.</span>
-
<span class="sd"> Note:</span>
<span class="sd"> - The class is designed to work with the Child class for hierarchical transformations.</span>
<span class="sd"> - Orientation is represented as a rotation matrix.</span>
@@ -407,7 +398,7 @@ document.write(`
<span class="sd"> The Parent class implements a hierarchical tree structure for organizing objects in a simulation.</span>
<span class="sd"> This class serves as a container for child objects and provides methods for managing relationships, properties, and interactions between these objects within a molecular simulation context.</span>
-<span class="sd"> Attributes:</span>
+<span class="sd"> Parameters:</span>
<span class="sd"> children (list): A list of child objects belonging to this parent.</span>
<span class="sd"> remove_duplicate_bonded_terms (bool): Whether to remove duplicate bonded terms when collecting them.</span>
<span class="sd"> bonds (list): List of bond interactions between particles.</span>
@@ -819,7 +810,7 @@ document.write(`
<span class="sd"> can be looked up from the parent. This implementation allows for a form of delegation where </span>
<span class="sd"> attribute access is forwarded to the parent object.</span>
-<span class="sd"> Attributes:</span>
+<span class="sd"> Parameters:</span>
<span class="sd"> parent (Parent, optional): The parent object that this child is associated with.</span>
<span class="sd"> When set, the child registers itself with the parent.</span>
<span class="sd"> Defaults to None.</span>
@@ -927,8 +918,8 @@ document.write(`
<span class="sd"> It supports inheritance through parent types, attribute lookup, and provides mechanisms</span>
<span class="sd"> for comparing particle types.</span>
-<span class="sd"> Attributes:</span>
-<span class="sd"> excludedAttributes (tuple): Attributes that are not inherited from parent types.</span>
+<span class="sd"> Parameters:</span>
+<span class="sd"> excludedParameters (tuple): Parameters that are not inherited from parent types.</span>
<span class="sd"> name (str): Unique identifier for this particle type.</span>
<span class="sd"> charge (float): Electric charge of the particle. Defaults to 0.</span>
<span class="sd"> mass (float, optional): Mass of the particle.</span>
@@ -942,12 +933,12 @@ document.write(`
<span class="sd"> - The class implements custom copy behavior to prevent unnecessary duplication.</span>
<span class="sd"> Class that hold common attributes that particles can point to"""</span>
- <span class="n">excludedAttributes</span> <span class="o">=</span> <span class="p">(</span><span class="s2">"idx"</span><span class="p">,</span><span class="s2">"type_"</span><span class="p">,</span>
+ <span class="n">excludedParameters</span> <span class="o">=</span> <span class="p">(</span><span class="s2">"idx"</span><span class="p">,</span><span class="s2">"type_"</span><span class="p">,</span>
<span class="s2">"position"</span><span class="p">,</span>
<span class="s2">"orientation"</span><span class="p">,</span>
<span class="s2">"children"</span><span class="p">,</span>
<span class="s2">"name"</span><span class="p">,</span>
- <span class="s2">"parent"</span><span class="p">,</span> <span class="s2">"excludedAttributes"</span><span class="p">,</span>
+ <span class="s2">"parent"</span><span class="p">,</span> <span class="s2">"excludedParameters"</span><span class="p">,</span>
<span class="p">)</span>
<span class="k">def</span><span class="w"> </span><span class="fm">__init__</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">name</span><span class="p">,</span> <span class="n">charge</span><span class="o">=</span><span class="mi">0</span><span class="p">,</span> <span class="n">mass</span><span class="o">=</span><span class="kc">None</span><span class="p">,</span> <span class="n">diffusivity</span><span class="o">=</span><span class="kc">None</span><span class="p">,</span>
@@ -959,7 +950,7 @@ document.write(`
<span class="k">if</span> <span class="n">parent</span> <span class="ow">is</span> <span class="ow">not</span> <span class="kc">None</span><span class="p">:</span>
<span class="k">for</span> <span class="n">k</span><span class="p">,</span><span class="n">v</span> <span class="ow">in</span> <span class="n">parent</span><span class="o">.</span><span class="vm">__dict__</span><span class="o">.</span><span class="n">items</span><span class="p">():</span>
- <span class="k">if</span> <span class="n">k</span> <span class="ow">not</span> <span class="ow">in</span> <span class="n">ParticleType</span><span class="o">.</span><span class="n">excludedAttributes</span><span class="p">:</span>
+ <span class="k">if</span> <span class="n">k</span> <span class="ow">not</span> <span class="ow">in</span> <span class="n">ParticleType</span><span class="o">.</span><span class="n">excludedParameters</span><span class="p">:</span>
<span class="bp">self</span><span class="o">.</span><span class="vm">__dict__</span><span class="p">[</span><span class="n">k</span><span class="p">]</span> <span class="o">=</span> <span class="n">v</span>
<span class="k">assert</span><span class="p">(</span> <span class="nb">type</span><span class="p">(</span><span class="n">parent</span><span class="p">)</span> <span class="o">==</span> <span class="nb">type</span><span class="p">(</span><span class="bp">self</span><span class="p">)</span> <span class="p">)</span>
@@ -976,7 +967,7 @@ document.write(`
<span class="bp">self</span><span class="o">.</span><span class="n">rigid_body_potentials</span> <span class="o">=</span> <span class="n">rigid_body_potentials</span>
<span class="n">devlogger</span><span class="o">.</span><span class="n">debug</span><span class="p">(</span><span class="sa">f</span><span class="s1">'Created </span><span class="si">{</span><span class="nb">type</span><span class="p">(</span><span class="bp">self</span><span class="p">)</span><span class="si">}</span><span class="s1"> </span><span class="si">{</span><span class="n">name</span><span class="si">}</span><span class="s1"> @ </span><span class="si">{</span><span class="nb">hex</span><span class="p">(</span><span class="nb">id</span><span class="p">(</span><span class="bp">self</span><span class="p">))</span><span class="si">}</span><span class="s1">'</span><span class="p">)</span>
- <span class="k">for</span> <span class="n">key</span> <span class="ow">in</span> <span class="n">ParticleType</span><span class="o">.</span><span class="n">excludedAttributes</span><span class="p">:</span>
+ <span class="k">for</span> <span class="n">key</span> <span class="ow">in</span> <span class="n">ParticleType</span><span class="o">.</span><span class="n">excludedParameters</span><span class="p">:</span>
<span class="k">assert</span><span class="p">(</span> <span class="n">key</span> <span class="ow">not</span> <span class="ow">in</span> <span class="n">kwargs</span> <span class="p">)</span>
<span class="k">for</span> <span class="n">key</span><span class="p">,</span><span class="n">val</span> <span class="ow">in</span> <span class="n">kwargs</span><span class="o">.</span><span class="n">items</span><span class="p">():</span>
@@ -1063,7 +1054,7 @@ document.write(`
<span class="k">if</span> <span class="s2">"parent"</span> <span class="ow">not</span> <span class="ow">in</span> <span class="bp">self</span><span class="o">.</span><span class="vm">__dict__</span> <span class="ow">or</span> <span class="bp">self</span><span class="o">.</span><span class="vm">__dict__</span><span class="p">[</span><span class="s2">"parent"</span><span class="p">]</span> <span class="ow">is</span> <span class="kc">None</span> <span class="ow">or</span> <span class="n">name</span> <span class="o">==</span> <span class="s2">"children"</span><span class="p">:</span>
<span class="k">raise</span> <span class="ne">AttributeError</span><span class="p">(</span><span class="s2">"'</span><span class="si">{}</span><span class="s2">' object has no attribute '</span><span class="si">{}</span><span class="s2">'"</span><span class="o">.</span><span class="n">format</span><span class="p">(</span><span class="nb">type</span><span class="p">(</span><span class="bp">self</span><span class="p">)</span><span class="o">.</span><span class="vm">__name__</span><span class="p">,</span> <span class="n">name</span><span class="p">))</span>
- <span class="n">excluded_attributes</span> <span class="o">=</span> <span class="n">ParticleType</span><span class="o">.</span><span class="n">excludedAttributes</span>
+ <span class="n">excluded_attributes</span> <span class="o">=</span> <span class="n">ParticleType</span><span class="o">.</span><span class="n">excludedParameters</span>
<span class="k">if</span> <span class="n">name</span> <span class="ow">in</span> <span class="n">excluded_attributes</span><span class="p">:</span>
<span class="k">raise</span> <span class="ne">AttributeError</span><span class="p">(</span><span class="s2">"'</span><span class="si">{}</span><span class="s2">' object has no attribute '</span><span class="si">{}</span><span class="s2">' and cannot look it up from the parent"</span><span class="o">.</span><span class="n">format</span><span class="p">(</span><span class="nb">type</span><span class="p">(</span><span class="bp">self</span><span class="p">)</span><span class="o">.</span><span class="vm">__name__</span><span class="p">,</span> <span class="n">name</span><span class="p">))</span>
@@ -1125,7 +1116,7 @@ document.write(`
<span class="sd"> This class extends ParticleType to represent rigid bodies that can have</span>
<span class="sd"> attached particles, orientation, and rotational dynamics.</span>
-<span class="sd"> Attributes:</span>
+<span class="sd"> Parameters:</span>
<span class="sd"> name (str): Name identifier for the rigid body type.</span>
<span class="sd"> parent (ParticleType, optional): Parent type to fall back on for nonbonded interactions.</span>
<span class="sd"> moment_of_inertia (float or array-like, optional): Moment of inertia tensor for the rigid body.</span>
@@ -1196,7 +1187,7 @@ document.write(`
<span class="sd"> This class inherits from both Transformable and Child base classes, allowing</span>
<span class="sd"> it to be positioned in space and exist in a parent-child hierarchy.</span>
-<span class="sd"> Attributes:</span>
+<span class="sd"> Parameters:</span>
<span class="sd"> type_ (ParticleType): Type definition of the particle.</span>
<span class="sd"> idx (int): Index of the particle in the system, default is None.</span>
<span class="sd"> name (str): Name identifier for the particle, default is "A".</span>
@@ -1397,21 +1388,6 @@ document.write(`
<span class="sd"> ----------</span>
<span class="sd"> type_ : RigidBodyType</span>
<span class="sd"> The type definition for this rigid body.</span>
-<span class="sd"> position : array-like</span>
-<span class="sd"> The initial position of the rigid body in 3D space.</span>
-<span class="sd"> orientation : array-like or quaternion</span>
-<span class="sd"> The initial orientation of the rigid body.</span>
-<span class="sd"> name : str, optional</span>
-<span class="sd"> A name identifier for this rigid body. Defaults to "A".</span>
-<span class="sd"> attached_particles : tuple, optional</span>
-<span class="sd"> Particles to attach to the rigid body, which will move with it. Defaults to empty tuple.</span>
-<span class="sd"> **kwargs : </span>
-<span class="sd"> Additional keyword arguments to set as attributes.</span>
-
-<span class="sd"> Attributes</span>
-<span class="sd"> ----------</span>
-<span class="sd"> type_ : RigidBodyType</span>
-<span class="sd"> The type definition for this rigid body.</span>
<span class="sd"> idx : int or None</span>
<span class="sd"> Index identifier, assigned when added to a simulation.</span>
<span class="sd"> name : str</span>
@@ -1424,6 +1400,8 @@ document.write(`
<span class="sd"> Boolean flag indicating if the object is rigid, always True for this class.</span>
<span class="sd"> attached_particles : list</span>
<span class="sd"> Copied particles attached to the rigid body. </span>
+<span class="sd"> **kwargs : </span>
+<span class="sd"> Additional keyword arguments to set as attributes.</span>
<span class="sd"> Note</span>
<span class="sd"> ----------</span>
@@ -1501,7 +1479,7 @@ document.write(`
<span class="sd"> of all three classes. It allows for hierarchical grouping of objects, where each group can</span>
<span class="sd"> have a position, orientation, parent, and children.</span>
-<span class="sd"> Attributes:</span>
+<span class="sd"> Parameters:</span>
<span class="sd"> name (str, optional): The name of the group.</span>
<span class="sd"> children (list, optional): A list of child objects belonging to this group.</span>
<span class="sd"> parent (Parent, optional): The parent object of this group.</span>
@@ -1575,7 +1553,7 @@ document.write(`
<span class="sd"> This class groups multiple particles together and provides methods to calculate their center</span>
<span class="sd"> and manage restraints applied to the group.</span>
-<span class="sd"> Attributes</span>
+<span class="sd"> Parameters</span>
<span class="sd"> ----------</span>
<span class="sd"> particles : list</span>
<span class="sd"> List of particle objects to be included in the group.</span>
diff --git a/_build/html/_modules/arbdmodel/grid.html b/_build/html/_modules/arbdmodel/grid.html
index 2a498b6793d6c7cb438e8d1d727144d3712a53b3..e6810e82507747e2f79c02cb4a9a561433586377 100644
--- a/_build/html/_modules/arbdmodel/grid.html
+++ b/_build/html/_modules/arbdmodel/grid.html
@@ -399,15 +399,18 @@ document.write(`
<span class="w"> </span><span class="sd">"""</span>
<span class="sd"> Compute the average of multiple grids.</span>
-<span class="sd"> :param grids: The input grids to average.</span>
-<span class="sd"> :type grids: list of ndarrays</span>
-<span class="sd"> :param mask: The mask type to use for averaging. If 'nan', only non-NaN values are considered. Default is 'nan'.</span>
-<span class="sd"> :type mask: str</span>
-<span class="sd"> :return: The average grid.</span>
-<span class="sd"> :rtype: ndarray</span>
-<span class="sd"> :raises NotImplementedError: If the mask option is not implemented.</span>
+<span class="sd"> Parameters</span>
+<span class="sd"> ----------</span>
+<span class="sd"> param grids: The input grids to average.</span>
+<span class="sd"> type grids: list of ndarrays</span>
+<span class="sd"> param mask: The mask type to use for averaging. If 'nan', only non-NaN values are considered. Default is 'nan'.</span>
+<span class="sd"> type mask: str</span>
+<span class="sd"> return: The average grid.</span>
+<span class="sd"> rtype: ndarray</span>
+<span class="sd"> raises NotImplementedError: If the mask option is not implemented.</span>
<span class="sd"> Example:</span>
+<span class="sd"> ----------</span>
<span class="sd"> >>> grid1 = np.array([[1, 2, 3], [4, 5, 6], [7, 8, 9]])</span>
<span class="sd"> >>> grid2 = np.array([[2, 4, 6], [8, 10, 12], [14, 16, 18]])</span>
<span class="sd"> >>> averaged_grid = average_grids([grid1, grid2], mask='nan')</span>
diff --git a/_build/html/_modules/arbdmodel/interactions.html b/_build/html/_modules/arbdmodel/interactions.html
index 11fefccfbb966ebb9f10f09a151d6e4520854517..e1840bd031690170a84b99133882ca888e1c46fc 100644
--- a/_build/html/_modules/arbdmodel/interactions.html
+++ b/_build/html/_modules/arbdmodel/interactions.html
@@ -317,6 +317,7 @@ document.write(`
<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>
@@ -334,31 +335,10 @@ document.write(`
<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"> Note</span>
<span class="sd"> -----</span>
<span class="sd"> Subclasses must implement at minimum the `potential` and `filename` methods.</span>
<span class="sd"> """</span>
@@ -455,6 +435,31 @@ document.write(`
<div class="viewcode-block" id="AbstractPotential.write_file">
<a class="viewcode-back" href="../../api/interaction_potentials/interactions.html#arbdmodel.interactions.AbstractPotential.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">"""</span>
+<span class="sd"> Write potential energy values as a function of distance to a file.</span>
+
+<span class="sd"> This method evaluates the potential function over a range of distances and writes</span>
+<span class="sd"> the distance-potential pairs to a text file.</span>
+
+<span class="sd"> Parameters</span>
+<span class="sd"> ----------</span>
+<span class="sd"> filename : str, optional</span>
+<span class="sd"> The path to the output file. If None, a default filename will be generated using</span>
+<span class="sd"> the `filename` method with the given types.</span>
+<span class="sd"> types : tuple or list, optional</span>
+<span class="sd"> The particle types for which to calculate the potential. Used for both filename </span>
+<span class="sd"> generation (if filename is None) and potential evaluation. If None, defaults to </span>
+<span class="sd"> the types defined in the interaction model.</span>
+
+<span class="sd"> Note</span>
+<span class="sd"> -----</span>
+<span class="sd"> The potential values are capped using the `_cap_potential` method to handle</span>
+<span class="sd"> potential singularities or extreme values. The output file contains two columns:</span>
+<span class="sd"> distance (r) and potential energy (u).</span>
+
+<span class="sd"> Any 'divide by zero' or 'invalid value' numpy warnings are ignored during</span>
+<span class="sd"> the potential calculation.</span>
+<span class="sd"> """</span>
<span class="k">if</span> <span class="n">filename</span> <span class="ow">is</span> <span class="kc">None</span><span class="p">:</span>
<span class="n">filename</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">filename</span><span class="p">(</span><span class="n">types</span><span class="p">)</span>
<span class="n">rmin</span><span class="p">,</span><span class="n">rmax</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">range_</span>
diff --git a/_build/html/_modules/arbdmodel/onck_polymer_model.html b/_build/html/_modules/arbdmodel/onck_polymer_model.html
index 7c3cc0b6280b38120d3cdd8808f0e181a97f4dc4..9a7133c4f41c872ca55d976be277d5651b6b7563 100644
--- a/_build/html/_modules/arbdmodel/onck_polymer_model.html
+++ b/_build/html/_modules/arbdmodel/onck_polymer_model.html
@@ -529,20 +529,10 @@ document.write(`
<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"> Maximum allowed force in the system, used as a cap for stability. Default is 50</span>
-<span class="sd"> Notes</span>
+<span class="sd"> Note</span>
<span class="sd"> -----</span>
<span class="sd"> The potential includes:</span>
<span class="sd"> 1. Electrostatic interactions with distance-dependent dielectric constant</span>
@@ -633,21 +623,10 @@ document.write(`
<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>
@@ -656,7 +635,7 @@ document.write(`
<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"> Note</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>
@@ -744,6 +723,48 @@ document.write(`
<div class="viewcode-block" id="OnckModel">
<a class="viewcode-back" href="../../api/polymer_modeling/onck_polymer_model.html#arbdmodel.onck_polymer_model.OnckModel">[docs]</a>
<span class="k">class</span><span class="w"> </span><span class="nc">OnckModel</span><span class="p">(</span><span class="n">PolymerModel</span><span class="p">):</span>
+<span class="w"> </span><span class="sd">"""</span>
+<span class="sd"> A polymer model based on Onck's coarse-grained model for disordered FG-Nup peptides.</span>
+
+<span class="sd"> The OnckModel class implements a coarse-grained model of polymers based on the work by Onck et al.</span>
+<span class="sd"> This model is specifically designed for disordered FG-Nup peptides and incorporates</span>
+<span class="sd"> electrostatic interactions through a Debye-Hückel potential.</span>
+
+<span class="sd"> Parameters</span>
+<span class="sd"> ----------</span>
+<span class="sd"> polymers : list</span>
+<span class="sd"> List of polymers to be modeled.</span>
+<span class="sd"> sequences : list, optional</span>
+<span class="sd"> List of amino acid sequences corresponding to each polymer.</span>
+<span class="sd"> Must be provided. Default is None.</span>
+<span class="sd"> debye_length : float, optional</span>
+<span class="sd"> Debye screening length in angstroms. Default is 10.</span>
+<span class="sd"> damping_coefficient : float, optional</span>
+<span class="sd"> Damping coefficient in ns. Default is 100.</span>
+<span class="sd"> version : float, optional</span>
+<span class="sd"> Version of the Onck model to use. Default is 1.1 (corresponding to 1BPA-1.1 from 2023).</span>
+<span class="sd"> DEBUG : bool, optional</span>
+<span class="sd"> Whether to enable debug mode. Default is False.</span>
+<span class="sd"> **kwargs : dict</span>
+<span class="sd"> Additional keyword arguments to pass to the parent PolymerModel class.</span>
+<span class="sd"> Common options include:</span>
+<span class="sd"> - timestep: Simulation timestep (default: 20e-6)</span>
+<span class="sd"> - cutoff: Cutoff distance for non-bonded interactions (default: max(5*debye_length, 25))</span>
+<span class="sd"> - decomp_period: Decomposition period (default: 1000)</span>
+<span class="sd"> types_dict : dict</span>
+<span class="sd"> Dictionary mapping from type keys to type objects for the given version.</span>
+<span class="sd"> types : list</span>
+<span class="sd"> List of all types used in the model.</span>
+
+<span class="sd"> Note</span>
+<span class="sd"> -----</span>
+<span class="sd"> The model differs from the published Onck model if a Debye length other than 12.7 Ã… is chosen.</span>
+<span class="sd"> In such cases, the non-bonded cutoff is set to 5 * debye_length.</span>
+
+<span class="sd"> References</span>
+<span class="sd"> ----------</span>
+<span class="sd"> Please refer to the citations displayed during initialization.</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">polymers</span><span class="p">,</span>
<span class="n">sequences</span> <span class="o">=</span> <span class="kc">None</span><span class="p">,</span>
<span class="n">debye_length</span> <span class="o">=</span> <span class="mi">10</span><span class="p">,</span>
@@ -753,11 +774,6 @@ document.write(`
<span class="n">DEBUG</span><span class="o">=</span><span class="kc">False</span><span class="p">,</span>
<span class="o">**</span><span class="n">kwargs</span><span class="p">):</span>
-<span class="w"> </span><span class="sd">"""</span>
-<span class="sd"> [debye_length]: angstroms</span>
-<span class="sd"> [damping_coefficient]: ns</span>
-
-<span class="sd"> """</span>
<span class="k">if</span> <span class="n">version</span> <span class="ow">is</span> <span class="kc">None</span><span class="p">:</span>
<span class="n">logger</span><span class="o">.</span><span class="n">warning</span><span class="p">(</span><span class="sa">f</span><span class="s1">'No Onck model version specified; using version 1BPA-1.1 from 2023'</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..c95b7e634f8d27df3be6e4c572e9f00c82fa659c 100644
--- a/_build/html/_modules/arbdmodel/parmed_bd.html
+++ b/_build/html/_modules/arbdmodel/parmed_bd.html
@@ -319,7 +319,7 @@ document.write(`
<span class="sd"> into ARBD simulation models, preserving bonded and non-bonded interactions.</span>
<span class="sd"> It also supports creating dual topology models for free energy calculations.</span>
<span class="sd"> </span>
-<span class="sd"> Attributes:</span>
+<span class="sd"> Parameters:</span>
<span class="sd"> parmed_structure: The original ParmEd structure</span>
<span class="sd"> atom_types: Dictionary mapping atom type names to ParticleType objects</span>
<span class="sd"> atoms_map: Mapping from ParmEd atoms to ARBD atoms</span>
diff --git a/_build/html/_modules/arbdmodel/sim_config.html b/_build/html/_modules/arbdmodel/sim_config.html
index acbe3baf5ab564e907b995a9d2c88b832cc4d098..6b5ff6966d7cf994489dd5ac6946853541d0d486 100644
--- a/_build/html/_modules/arbdmodel/sim_config.html
+++ b/_build/html/_modules/arbdmodel/sim_config.html
@@ -330,7 +330,7 @@ document.write(`
<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"> Parameters:</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>
@@ -595,7 +595,7 @@ document.write(`
<span class="sd"> **kwargs</span>
<span class="sd"> Additional keyword arguments to pass to SimConf.</span>
-<span class="sd"> Attributes</span>
+<span class="sd"> Parameters</span>
<span class="sd"> ----------</span>
<span class="sd"> num_steps : float</span>
<span class="sd"> Number of simulation steps.</span>
diff --git a/_build/html/_sources/api/utilities/binary_manager.md b/_build/html/_sources/api/utilities/binary_manager.md
index 01a72af8593605b5b57fb3e09b0223d03ef98d21..695eae845fbeed48722584b6229b82d1a4eac0dd 100644
--- a/_build/html/_sources/api/utilities/binary_manager.md
+++ b/_build/html/_sources/api/utilities/binary_manager.md
@@ -1,7 +1,6 @@
# binary_manager
-Binary path management module for simulation engines and processors.
-This module provides a singleton object to manage paths to external binaries.
+Module documentation for `arbdmodel.binary_manager`.
```{eval-rst}
.. automodule:: arbdmodel.binary_manager
diff --git a/_build/html/_sources/api/utilities/index.md b/_build/html/_sources/api/utilities/index.md
index 905bdc17c401b5edf992d9ed964eddc9c1f4f796..a754152251c84d788b0d0841c6b4f5a6fea82562 100644
--- a/_build/html/_sources/api/utilities/index.md
+++ b/_build/html/_sources/api/utilities/index.md
@@ -4,7 +4,7 @@ This section documents the utilities components of the arbdmodel package.
## Modules
-- [binary_manager](binary_manager.md): Binary path management module for simulation engines and processors.
+- [binary_manager](binary_manager.md): Module documentation for `arbdmodel.binary_manager`.
- [coords](coords.md): Module documentation for `arbdmodel.coords`.
- [grid](grid.md): Module documentation for `arbdmodel.grid`.
- [logger](logger.md): Module documentation for `arbdmodel.logger`.
diff --git a/_build/html/api/core/core_objects.html b/_build/html/api/core/core_objects.html
index 466bb39b45c5ea0f10d7dbd16a2d126faf8f9074..92dbd3b84f4df35d0fe25c164c49b70630e137c0 100644
--- a/_build/html/api/core/core_objects.html
+++ b/_build/html/api/core/core_objects.html
@@ -346,22 +346,12 @@ 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.core_objects.Child"><code class="docutils literal notranslate"><span class="pre">Child</span></code></a><ul class="nav section-nav flex-column">
-<li class="toc-h3 nav-item toc-entry"><a class="reference internal nav-link" href="#arbdmodel.core_objects.Child.parent"><code class="docutils literal notranslate"><span class="pre">Child.parent</span></code></a></li>
-</ul>
-</li>
+<li class="toc-h2 nav-item toc-entry"><a class="reference internal nav-link" href="#arbdmodel.core_objects.Child"><code class="docutils literal notranslate"><span class="pre">Child</span></code></a></li>
<li class="toc-h2 nav-item toc-entry"><a class="reference internal nav-link" href="#arbdmodel.core_objects.Clone"><code class="docutils literal notranslate"><span class="pre">Clone</span></code></a><ul class="nav section-nav flex-column">
<li class="toc-h3 nav-item toc-entry"><a class="reference internal nav-link" href="#arbdmodel.core_objects.Clone.get_original_recursively"><code class="docutils literal notranslate"><span class="pre">Clone.get_original_recursively()</span></code></a></li>
</ul>
</li>
<li class="toc-h2 nav-item toc-entry"><a class="reference internal nav-link" href="#arbdmodel.core_objects.Group"><code class="docutils literal notranslate"><span class="pre">Group</span></code></a><ul class="nav section-nav flex-column">
-<li class="toc-h3 nav-item toc-entry"><a class="reference internal nav-link" href="#arbdmodel.core_objects.Group.name"><code class="docutils literal notranslate"><span class="pre">Group.name</span></code></a></li>
-<li class="toc-h3 nav-item toc-entry"><a class="reference internal nav-link" href="#arbdmodel.core_objects.Group.children"><code class="docutils literal notranslate"><span class="pre">Group.children</span></code></a></li>
-<li class="toc-h3 nav-item toc-entry"><a class="reference internal nav-link" href="#arbdmodel.core_objects.Group.parent"><code class="docutils literal notranslate"><span class="pre">Group.parent</span></code></a></li>
-<li class="toc-h3 nav-item toc-entry"><a class="reference internal nav-link" href="#arbdmodel.core_objects.Group.position"><code class="docutils literal notranslate"><span class="pre">Group.position</span></code></a></li>
-<li class="toc-h3 nav-item toc-entry"><a class="reference internal nav-link" href="#arbdmodel.core_objects.Group.orientation"><code class="docutils literal notranslate"><span class="pre">Group.orientation</span></code></a></li>
-<li class="toc-h3 nav-item toc-entry"><a class="reference internal nav-link" href="#arbdmodel.core_objects.Group.isClone"><code class="docutils literal notranslate"><span class="pre">Group.isClone</span></code></a></li>
-<li class="toc-h3 nav-item toc-entry"><a class="reference internal nav-link" href="#arbdmodel.core_objects.Group.remove_duplicate_bonded_terms"><code class="docutils literal notranslate"><span class="pre">Group.remove_duplicate_bonded_terms</span></code></a></li>
<li class="toc-h3 nav-item toc-entry"><a class="reference internal nav-link" href="#arbdmodel.core_objects.Group.clone"><code class="docutils literal notranslate"><span class="pre">Group.clone()</span></code></a></li>
<li class="toc-h3 nav-item toc-entry"><a class="reference internal nav-link" href="#arbdmodel.core_objects.Group.duplicate"><code class="docutils literal notranslate"><span class="pre">Group.duplicate()</span></code></a></li>
<li class="toc-h3 nav-item toc-entry"><a class="reference internal nav-link" href="#id0"><code class="docutils literal notranslate"><span class="pre">Group.clone()</span></code></a></li>
@@ -369,9 +359,6 @@ document.write(`
</ul>
</li>
<li class="toc-h2 nav-item toc-entry"><a class="reference internal nav-link" href="#arbdmodel.core_objects.GroupSite"><code class="docutils literal notranslate"><span class="pre">GroupSite</span></code></a><ul class="nav section-nav flex-column">
-<li class="toc-h3 nav-item toc-entry"><a class="reference internal nav-link" href="#arbdmodel.core_objects.GroupSite.particles"><code class="docutils literal notranslate"><span class="pre">GroupSite.particles</span></code></a></li>
-<li class="toc-h3 nav-item toc-entry"><a class="reference internal nav-link" href="#arbdmodel.core_objects.GroupSite.idx"><code class="docutils literal notranslate"><span class="pre">GroupSite.idx</span></code></a></li>
-<li class="toc-h3 nav-item toc-entry"><a class="reference internal nav-link" href="#arbdmodel.core_objects.GroupSite.restraints"><code class="docutils literal notranslate"><span class="pre">GroupSite.restraints</span></code></a></li>
<li class="toc-h3 nav-item toc-entry"><a class="reference internal nav-link" href="#arbdmodel.core_objects.GroupSite.get_center"><code class="docutils literal notranslate"><span class="pre">GroupSite.get_center()</span></code></a></li>
<li class="toc-h3 nav-item toc-entry"><a class="reference internal nav-link" href="#arbdmodel.core_objects.GroupSite.add_restraint"><code class="docutils literal notranslate"><span class="pre">GroupSite.add_restraint()</span></code></a></li>
<li class="toc-h3 nav-item toc-entry"><a class="reference internal nav-link" href="#arbdmodel.core_objects.GroupSite.get_restraints"><code class="docutils literal notranslate"><span class="pre">GroupSite.get_restraints()</span></code></a></li>
@@ -381,17 +368,6 @@ document.write(`
</ul>
</li>
<li class="toc-h2 nav-item toc-entry"><a class="reference internal nav-link" href="#arbdmodel.core_objects.Parent"><code class="docutils literal notranslate"><span class="pre">Parent</span></code></a><ul class="nav section-nav flex-column">
-<li class="toc-h3 nav-item toc-entry"><a class="reference internal nav-link" href="#arbdmodel.core_objects.Parent.children"><code class="docutils literal notranslate"><span class="pre">Parent.children</span></code></a></li>
-<li class="toc-h3 nav-item toc-entry"><a class="reference internal nav-link" href="#arbdmodel.core_objects.Parent.remove_duplicate_bonded_terms"><code class="docutils literal notranslate"><span class="pre">Parent.remove_duplicate_bonded_terms</span></code></a></li>
-<li class="toc-h3 nav-item toc-entry"><a class="reference internal nav-link" href="#arbdmodel.core_objects.Parent.bonds"><code class="docutils literal notranslate"><span class="pre">Parent.bonds</span></code></a></li>
-<li class="toc-h3 nav-item toc-entry"><a class="reference internal nav-link" href="#arbdmodel.core_objects.Parent.angles"><code class="docutils literal notranslate"><span class="pre">Parent.angles</span></code></a></li>
-<li class="toc-h3 nav-item toc-entry"><a class="reference internal nav-link" href="#arbdmodel.core_objects.Parent.dihedrals"><code class="docutils literal notranslate"><span class="pre">Parent.dihedrals</span></code></a></li>
-<li class="toc-h3 nav-item toc-entry"><a class="reference internal nav-link" href="#arbdmodel.core_objects.Parent.vector_angles"><code class="docutils literal notranslate"><span class="pre">Parent.vector_angles</span></code></a></li>
-<li class="toc-h3 nav-item toc-entry"><a class="reference internal nav-link" href="#arbdmodel.core_objects.Parent.impropers"><code class="docutils literal notranslate"><span class="pre">Parent.impropers</span></code></a></li>
-<li class="toc-h3 nav-item toc-entry"><a class="reference internal nav-link" href="#arbdmodel.core_objects.Parent.exclusions"><code class="docutils literal notranslate"><span class="pre">Parent.exclusions</span></code></a></li>
-<li class="toc-h3 nav-item toc-entry"><a class="reference internal nav-link" href="#arbdmodel.core_objects.Parent.bond_angles"><code class="docutils literal notranslate"><span class="pre">Parent.bond_angles</span></code></a></li>
-<li class="toc-h3 nav-item toc-entry"><a class="reference internal nav-link" href="#arbdmodel.core_objects.Parent.product_potentials"><code class="docutils literal notranslate"><span class="pre">Parent.product_potentials</span></code></a></li>
-<li class="toc-h3 nav-item toc-entry"><a class="reference internal nav-link" href="#arbdmodel.core_objects.Parent.group_sites"><code class="docutils literal notranslate"><span class="pre">Parent.group_sites</span></code></a></li>
<li class="toc-h3 nav-item toc-entry"><a class="reference internal nav-link" href="#arbdmodel.core_objects.Parent.add"><code class="docutils literal notranslate"><span class="pre">Parent.add()</span></code></a></li>
<li class="toc-h3 nav-item toc-entry"><a class="reference internal nav-link" href="#arbdmodel.core_objects.Parent.add_angle"><code class="docutils literal notranslate"><span class="pre">Parent.add_angle()</span></code></a></li>
<li class="toc-h3 nav-item toc-entry"><a class="reference internal nav-link" href="#arbdmodel.core_objects.Parent.add_bond"><code class="docutils literal notranslate"><span class="pre">Parent.add_bond()</span></code></a></li>
@@ -418,25 +394,12 @@ document.write(`
</ul>
</li>
<li class="toc-h2 nav-item toc-entry"><a class="reference internal nav-link" href="#arbdmodel.core_objects.ParticleType"><code class="docutils literal notranslate"><span class="pre">ParticleType</span></code></a><ul class="nav section-nav flex-column">
-<li class="toc-h3 nav-item toc-entry"><a class="reference internal nav-link" href="#arbdmodel.core_objects.ParticleType.excludedAttributes"><code class="docutils literal notranslate"><span class="pre">ParticleType.excludedAttributes</span></code></a></li>
-<li class="toc-h3 nav-item toc-entry"><a class="reference internal nav-link" href="#arbdmodel.core_objects.ParticleType.name"><code class="docutils literal notranslate"><span class="pre">ParticleType.name</span></code></a></li>
-<li class="toc-h3 nav-item toc-entry"><a class="reference internal nav-link" href="#arbdmodel.core_objects.ParticleType.charge"><code class="docutils literal notranslate"><span class="pre">ParticleType.charge</span></code></a></li>
-<li class="toc-h3 nav-item toc-entry"><a class="reference internal nav-link" href="#arbdmodel.core_objects.ParticleType.mass"><code class="docutils literal notranslate"><span class="pre">ParticleType.mass</span></code></a></li>
-<li class="toc-h3 nav-item toc-entry"><a class="reference internal nav-link" href="#arbdmodel.core_objects.ParticleType.diffusivity"><code class="docutils literal notranslate"><span class="pre">ParticleType.diffusivity</span></code></a></li>
-<li class="toc-h3 nav-item toc-entry"><a class="reference internal nav-link" href="#arbdmodel.core_objects.ParticleType.damping_coefficient"><code class="docutils literal notranslate"><span class="pre">ParticleType.damping_coefficient</span></code></a></li>
-<li class="toc-h3 nav-item toc-entry"><a class="reference internal nav-link" href="#arbdmodel.core_objects.ParticleType.parent"><code class="docutils literal notranslate"><span class="pre">ParticleType.parent</span></code></a></li>
<li class="toc-h3 nav-item toc-entry"><a class="reference internal nav-link" href="#arbdmodel.core_objects.ParticleType.add_grid_potential"><code class="docutils literal notranslate"><span class="pre">ParticleType.add_grid_potential()</span></code></a></li>
-<li class="toc-h3 nav-item toc-entry"><a class="reference internal nav-link" href="#id5"><code class="docutils literal notranslate"><span class="pre">ParticleType.excludedAttributes</span></code></a></li>
+<li class="toc-h3 nav-item toc-entry"><a class="reference internal nav-link" href="#arbdmodel.core_objects.ParticleType.excludedParameters"><code class="docutils literal notranslate"><span class="pre">ParticleType.excludedParameters</span></code></a></li>
<li class="toc-h3 nav-item toc-entry"><a class="reference internal nav-link" href="#arbdmodel.core_objects.ParticleType.is_same_type"><code class="docutils literal notranslate"><span class="pre">ParticleType.is_same_type()</span></code></a></li>
</ul>
</li>
<li class="toc-h2 nav-item toc-entry"><a class="reference internal nav-link" href="#arbdmodel.core_objects.PointParticle"><code class="docutils literal notranslate"><span class="pre">PointParticle</span></code></a><ul class="nav section-nav flex-column">
-<li class="toc-h3 nav-item toc-entry"><a class="reference internal nav-link" href="#arbdmodel.core_objects.PointParticle.type_"><code class="docutils literal notranslate"><span class="pre">PointParticle.type_</span></code></a></li>
-<li class="toc-h3 nav-item toc-entry"><a class="reference internal nav-link" href="#arbdmodel.core_objects.PointParticle.idx"><code class="docutils literal notranslate"><span class="pre">PointParticle.idx</span></code></a></li>
-<li class="toc-h3 nav-item toc-entry"><a class="reference internal nav-link" href="#arbdmodel.core_objects.PointParticle.name"><code class="docutils literal notranslate"><span class="pre">PointParticle.name</span></code></a></li>
-<li class="toc-h3 nav-item toc-entry"><a class="reference internal nav-link" href="#arbdmodel.core_objects.PointParticle.counter"><code class="docutils literal notranslate"><span class="pre">PointParticle.counter</span></code></a></li>
-<li class="toc-h3 nav-item toc-entry"><a class="reference internal nav-link" href="#arbdmodel.core_objects.PointParticle.restraints"><code class="docutils literal notranslate"><span class="pre">PointParticle.restraints</span></code></a></li>
-<li class="toc-h3 nav-item toc-entry"><a class="reference internal nav-link" href="#arbdmodel.core_objects.PointParticle.rigid"><code class="docutils literal notranslate"><span class="pre">PointParticle.rigid</span></code></a></li>
<li class="toc-h3 nav-item toc-entry"><a class="reference internal nav-link" href="#arbdmodel.core_objects.PointParticle.add_grid_potential"><code class="docutils literal notranslate"><span class="pre">PointParticle.add_grid_potential()</span></code></a></li>
<li class="toc-h3 nav-item toc-entry"><a class="reference internal nav-link" href="#arbdmodel.core_objects.PointParticle.add_restraint"><code class="docutils literal notranslate"><span class="pre">PointParticle.add_restraint()</span></code></a></li>
<li class="toc-h3 nav-item toc-entry"><a class="reference internal nav-link" href="#arbdmodel.core_objects.PointParticle.duplicate"><code class="docutils literal notranslate"><span class="pre">PointParticle.duplicate()</span></code></a></li>
@@ -444,44 +407,21 @@ document.write(`
</ul>
</li>
<li class="toc-h2 nav-item toc-entry"><a class="reference internal nav-link" href="#arbdmodel.core_objects.RigidBody"><code class="docutils literal notranslate"><span class="pre">RigidBody</span></code></a><ul class="nav section-nav flex-column">
-<li class="toc-h3 nav-item toc-entry"><a class="reference internal nav-link" href="#arbdmodel.core_objects.RigidBody.type_"><code class="docutils literal notranslate"><span class="pre">RigidBody.type_</span></code></a></li>
-<li class="toc-h3 nav-item toc-entry"><a class="reference internal nav-link" href="#arbdmodel.core_objects.RigidBody.idx"><code class="docutils literal notranslate"><span class="pre">RigidBody.idx</span></code></a></li>
-<li class="toc-h3 nav-item toc-entry"><a class="reference internal nav-link" href="#arbdmodel.core_objects.RigidBody.name"><code class="docutils literal notranslate"><span class="pre">RigidBody.name</span></code></a></li>
-<li class="toc-h3 nav-item toc-entry"><a class="reference internal nav-link" href="#arbdmodel.core_objects.RigidBody.counter"><code class="docutils literal notranslate"><span class="pre">RigidBody.counter</span></code></a></li>
-<li class="toc-h3 nav-item toc-entry"><a class="reference internal nav-link" href="#arbdmodel.core_objects.RigidBody.restraints"><code class="docutils literal notranslate"><span class="pre">RigidBody.restraints</span></code></a></li>
-<li class="toc-h3 nav-item toc-entry"><a class="reference internal nav-link" href="#arbdmodel.core_objects.RigidBody.rigid"><code class="docutils literal notranslate"><span class="pre">RigidBody.rigid</span></code></a></li>
-<li class="toc-h3 nav-item toc-entry"><a class="reference internal nav-link" href="#arbdmodel.core_objects.RigidBody.attached_particles"><code class="docutils literal notranslate"><span class="pre">RigidBody.attached_particles</span></code></a></li>
<li class="toc-h3 nav-item toc-entry"><a class="reference internal nav-link" href="#arbdmodel.core_objects.RigidBody.add_restraint"><code class="docutils literal notranslate"><span class="pre">RigidBody.add_restraint()</span></code></a></li>
<li class="toc-h3 nav-item toc-entry"><a class="reference internal nav-link" href="#arbdmodel.core_objects.RigidBody.duplicate"><code class="docutils literal notranslate"><span class="pre">RigidBody.duplicate()</span></code></a></li>
<li class="toc-h3 nav-item toc-entry"><a class="reference internal nav-link" href="#arbdmodel.core_objects.RigidBody.get_restraints"><code class="docutils literal notranslate"><span class="pre">RigidBody.get_restraints()</span></code></a></li>
</ul>
</li>
<li class="toc-h2 nav-item toc-entry"><a class="reference internal nav-link" href="#arbdmodel.core_objects.RigidBodyType"><code class="docutils literal notranslate"><span class="pre">RigidBodyType</span></code></a><ul class="nav section-nav flex-column">
-<li class="toc-h3 nav-item toc-entry"><a class="reference internal nav-link" href="#arbdmodel.core_objects.RigidBodyType.name"><code class="docutils literal notranslate"><span class="pre">RigidBodyType.name</span></code></a></li>
-<li class="toc-h3 nav-item toc-entry"><a class="reference internal nav-link" href="#arbdmodel.core_objects.RigidBodyType.parent"><code class="docutils literal notranslate"><span class="pre">RigidBodyType.parent</span></code></a></li>
-<li class="toc-h3 nav-item toc-entry"><a class="reference internal nav-link" href="#arbdmodel.core_objects.RigidBodyType.moment_of_inertia"><code class="docutils literal notranslate"><span class="pre">RigidBodyType.moment_of_inertia</span></code></a></li>
-<li class="toc-h3 nav-item toc-entry"><a class="reference internal nav-link" href="#arbdmodel.core_objects.RigidBodyType.rotational_diffusivity"><code class="docutils literal notranslate"><span class="pre">RigidBodyType.rotational_diffusivity</span></code></a></li>
-<li class="toc-h3 nav-item toc-entry"><a class="reference internal nav-link" href="#arbdmodel.core_objects.RigidBodyType.rotational_damping_coefficient"><code class="docutils literal notranslate"><span class="pre">RigidBodyType.rotational_damping_coefficient</span></code></a></li>
-<li class="toc-h3 nav-item toc-entry"><a class="reference internal nav-link" href="#arbdmodel.core_objects.RigidBodyType.attached_particles"><code class="docutils literal notranslate"><span class="pre">RigidBodyType.attached_particles</span></code></a></li>
-<li class="toc-h3 nav-item toc-entry"><a class="reference internal nav-link" href="#arbdmodel.core_objects.RigidBodyType.potential_grids"><code class="docutils literal notranslate"><span class="pre">RigidBodyType.potential_grids</span></code></a></li>
-<li class="toc-h3 nav-item toc-entry"><a class="reference internal nav-link" href="#arbdmodel.core_objects.RigidBodyType.charge_grids"><code class="docutils literal notranslate"><span class="pre">RigidBodyType.charge_grids</span></code></a></li>
-<li class="toc-h3 nav-item toc-entry"><a class="reference internal nav-link" href="#arbdmodel.core_objects.RigidBodyType.pmf_grids"><code class="docutils literal notranslate"><span class="pre">RigidBodyType.pmf_grids</span></code></a></li>
<li class="toc-h3 nav-item toc-entry"><a class="reference internal nav-link" href="#arbdmodel.core_objects.RigidBodyType.attach_particle"><code class="docutils literal notranslate"><span class="pre">RigidBodyType.attach_particle()</span></code></a></li>
</ul>
</li>
<li class="toc-h2 nav-item toc-entry"><a class="reference internal nav-link" href="#arbdmodel.core_objects.Transformable"><code class="docutils literal notranslate"><span class="pre">Transformable</span></code></a><ul class="nav section-nav flex-column">
-<li class="toc-h3 nav-item toc-entry"><a class="reference internal nav-link" href="#arbdmodel.core_objects.Transformable.position"><code class="docutils literal notranslate"><span class="pre">Transformable.position</span></code></a></li>
-<li class="toc-h3 nav-item toc-entry"><a class="reference internal nav-link" href="#arbdmodel.core_objects.Transformable.orientation"><code class="docutils literal notranslate"><span class="pre">Transformable.orientation</span></code></a></li>
-<li class="toc-h3 nav-item toc-entry"><a class="reference internal nav-link" href="#arbdmodel.core_objects.Transformable.translate"><code class="docutils literal notranslate"><span class="pre">Transformable.translate()</span></code></a></li>
+<li class="toc-h3 nav-item toc-entry"><a class="reference internal nav-link" href="#arbdmodel.core_objects.Transformable.applyOrientation"><code class="docutils literal notranslate"><span class="pre">Transformable.applyOrientation()</span></code></a></li>
+<li class="toc-h3 nav-item toc-entry"><a class="reference internal nav-link" href="#arbdmodel.core_objects.Transformable.get_collapsed_position"><code class="docutils literal notranslate"><span class="pre">Transformable.get_collapsed_position()</span></code></a></li>
<li class="toc-h3 nav-item toc-entry"><a class="reference internal nav-link" href="#arbdmodel.core_objects.Transformable.rotate"><code class="docutils literal notranslate"><span class="pre">Transformable.rotate()</span></code></a></li>
<li class="toc-h3 nav-item toc-entry"><a class="reference internal nav-link" href="#arbdmodel.core_objects.Transformable.transform"><code class="docutils literal notranslate"><span class="pre">Transformable.transform()</span></code></a></li>
-<li class="toc-h3 nav-item toc-entry"><a class="reference internal nav-link" href="#arbdmodel.core_objects.Transformable.get_collapsed_position"><code class="docutils literal notranslate"><span class="pre">Transformable.get_collapsed_position()</span></code></a></li>
-<li class="toc-h3 nav-item toc-entry"><a class="reference internal nav-link" href="#arbdmodel.core_objects.Transformable.applyOrientation"><code class="docutils literal notranslate"><span class="pre">Transformable.applyOrientation()</span></code></a></li>
-<li class="toc-h3 nav-item toc-entry"><a class="reference internal nav-link" href="#id6"><code class="docutils literal notranslate"><span class="pre">Transformable.applyOrientation()</span></code></a></li>
-<li class="toc-h3 nav-item toc-entry"><a class="reference internal nav-link" href="#id7"><code class="docutils literal notranslate"><span class="pre">Transformable.get_collapsed_position()</span></code></a></li>
-<li class="toc-h3 nav-item toc-entry"><a class="reference internal nav-link" href="#id8"><code class="docutils literal notranslate"><span class="pre">Transformable.rotate()</span></code></a></li>
-<li class="toc-h3 nav-item toc-entry"><a class="reference internal nav-link" href="#id9"><code class="docutils literal notranslate"><span class="pre">Transformable.transform()</span></code></a></li>
-<li class="toc-h3 nav-item toc-entry"><a class="reference internal nav-link" href="#id10"><code class="docutils literal notranslate"><span class="pre">Transformable.translate()</span></code></a></li>
+<li class="toc-h3 nav-item toc-entry"><a class="reference internal nav-link" href="#arbdmodel.core_objects.Transformable.translate"><code class="docutils literal notranslate"><span class="pre">Transformable.translate()</span></code></a></li>
</ul>
</li>
</ul>
@@ -506,19 +446,13 @@ document.write(`
This class establishes a parent-child relationship where attributes not found in the child
can be looked up from the parent. This implementation allows for a form of delegation where
attribute access is forwarded to the parent object.</p>
-<dl class="py attribute">
-<dt class="sig sig-object py" id="arbdmodel.core_objects.Child.parent">
-<span class="sig-name descname"><span class="pre">parent</span></span><a class="headerlink" href="#arbdmodel.core_objects.Child.parent" title="Link to this definition">#</a></dt>
-<dd><p>The parent object that this child is associated with.
+<dl class="field-list simple">
+<dt class="field-odd">Parameters<span class="colon">:</span></dt>
+<dd class="field-odd"><p><strong>parent</strong> (<a class="reference internal" href="#arbdmodel.core_objects.Parent" title="arbdmodel.core_objects.Parent"><em>Parent</em></a><em>, </em><em>optional</em>) – The parent object that this child is associated with.
When set, the child registers itself with the parent.
Defaults to None.</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="#arbdmodel.core_objects.Parent" title="arbdmodel.core_objects.Parent">Parent</a>, optional</p>
</dd>
</dl>
-</dd></dl>
-
<div class="admonition note">
<p class="admonition-title">Note</p>
<ul class="simple">
@@ -548,85 +482,21 @@ Defaults to None.</p>
The Group class inherits from Transformable, Parent, and Child, combining the functionality
of all three classes. It allows for hierarchical grouping of objects, where each group can
have a position, orientation, parent, and children.</p>
-<dl class="py attribute">
-<dt class="sig sig-object py" id="arbdmodel.core_objects.Group.name">
-<span class="sig-name descname"><span class="pre">name</span></span><a class="headerlink" href="#arbdmodel.core_objects.Group.name" title="Link to this definition">#</a></dt>
-<dd><p>The name of the group.</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>, optional</p>
-</dd>
-</dl>
-</dd></dl>
-
-<dl class="py attribute">
-<dt class="sig sig-object py" id="arbdmodel.core_objects.Group.children">
-<span class="sig-name descname"><span class="pre">children</span></span><a class="headerlink" href="#arbdmodel.core_objects.Group.children" title="Link to this definition">#</a></dt>
-<dd><p>A list of child objects belonging to this group.</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>, optional</p>
-</dd>
-</dl>
-</dd></dl>
-
-<dl class="py attribute">
-<dt class="sig sig-object py" id="arbdmodel.core_objects.Group.parent">
-<span class="sig-name descname"><span class="pre">parent</span></span><a class="headerlink" href="#arbdmodel.core_objects.Group.parent" title="Link to this definition">#</a></dt>
-<dd><p>The parent object of this group.</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="#arbdmodel.core_objects.Parent" title="arbdmodel.core_objects.Parent">Parent</a>, optional</p>
-</dd>
-</dl>
-</dd></dl>
-
-<dl class="py attribute">
-<dt class="sig sig-object py" id="arbdmodel.core_objects.Group.position">
-<span class="sig-name descname"><span class="pre">position</span></span><a class="headerlink" href="#arbdmodel.core_objects.Group.position" title="Link to this definition">#</a></dt>
-<dd><p>The 3D position of the group, defaults to origin (0,0,0).</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.core_objects.Group.orientation">
-<span class="sig-name descname"><span class="pre">orientation</span></span><a class="headerlink" href="#arbdmodel.core_objects.Group.orientation" title="Link to this definition">#</a></dt>
-<dd><p>The 3x3 rotation matrix representing the orientation,
-defaults to identity matrix.</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.core_objects.Group.isClone">
-<span class="sig-name descname"><span class="pre">isClone</span></span><a class="headerlink" href="#arbdmodel.core_objects.Group.isClone" title="Link to this definition">#</a></dt>
-<dd><p>Flag indicating whether this group is a clone, defaults to False.</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.core_objects.Group.remove_duplicate_bonded_terms">
-<span class="sig-name descname"><span class="pre">remove_duplicate_bonded_terms</span></span><a class="headerlink" href="#arbdmodel.core_objects.Group.remove_duplicate_bonded_terms" title="Link to this definition">#</a></dt>
-<dd><p>Whether to remove duplicate bonded terms when
-combining children, defaults to False.</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>
+<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><em>, </em><em>optional</em>) – The name of the group.</p></li>
+<li><p><strong>children</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>) – A list of child objects belonging to this group.</p></li>
+<li><p><strong>parent</strong> (<a class="reference internal" href="#arbdmodel.core_objects.Parent" title="arbdmodel.core_objects.Parent"><em>Parent</em></a><em>, </em><em>optional</em>) – The parent object of this group.</p></li>
+<li><p><strong>position</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>) – The 3D position of the group, defaults to origin (0,0,0).</p></li>
+<li><p><strong>orientation</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>) – The 3x3 rotation matrix representing the orientation,
+defaults to identity matrix.</p></li>
+<li><p><strong>isClone</strong> (<a class="hxr-hoverxref hxr-tooltip reference external" href="https://docs.python.org/3/library/functions.html#bool" title="(in Python v3.13)"><em>bool</em></a>) – Flag indicating whether this group is a clone, defaults to False.</p></li>
+<li><p><strong>remove_duplicate_bonded_terms</strong> (<a class="hxr-hoverxref hxr-tooltip reference external" href="https://docs.python.org/3/library/functions.html#bool" title="(in Python v3.13)"><em>bool</em></a>) – Whether to remove duplicate bonded terms when
+combining children, defaults to False.</p></li>
+</ul>
</dd>
</dl>
-</dd></dl>
-
<dl class="py method">
<dt class="sig sig-object py" id="arbdmodel.core_objects.Group.clone">
<span class="sig-name descname"><span class="pre">clone</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="reference internal" href="../../_modules/arbdmodel/core_objects.html#Group.clone"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#arbdmodel.core_objects.Group.clone" title="Link to this definition">#</a></dt>
@@ -658,39 +528,15 @@ combining children, defaults to False.</p>
<p>Class to represent a collection of particles that can be used by bond potentials in arbdmodel.
This class groups multiple particles together and provides methods to calculate their center
and manage restraints applied to the group.</p>
-<dl class="py attribute">
-<dt class="sig sig-object py" id="arbdmodel.core_objects.GroupSite.particles">
-<span class="sig-name descname"><span class="pre">particles</span></span><a class="headerlink" href="#arbdmodel.core_objects.GroupSite.particles" title="Link to this definition">#</a></dt>
-<dd><p>List of particle objects to be included in the group.</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.core_objects.GroupSite.idx">
-<span class="sig-name descname"><span class="pre">idx</span></span><a class="headerlink" href="#arbdmodel.core_objects.GroupSite.idx" title="Link to this definition">#</a></dt>
-<dd><p>Identifier for the group site, default is None.</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> or None</p>
-</dd>
-</dl>
-</dd></dl>
-
-<dl class="py attribute">
-<dt class="sig sig-object py" id="arbdmodel.core_objects.GroupSite.restraints">
-<span class="sig-name descname"><span class="pre">restraints</span></span><a class="headerlink" href="#arbdmodel.core_objects.GroupSite.restraints" title="Link to this definition">#</a></dt>
-<dd><p>List of restraints applied to the group site.</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>
+<dt class="field-odd">Parameters<span class="colon">:</span></dt>
+<dd class="field-odd"><ul class="simple">
+<li><p><strong>particles</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 particle objects to be included in the group.</p></li>
+<li><p><strong>idx</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>) – Identifier for the group site, default is None.</p></li>
+<li><p><strong>restraints</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 restraints applied to the group site.</p></li>
+</ul>
</dd>
</dl>
-</dd></dl>
-
<dl class="py method">
<dt class="sig sig-object py" id="arbdmodel.core_objects.GroupSite.get_center">
<span class="sig-name descname"><span class="pre">get_center</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="reference internal" href="../../_modules/arbdmodel/core_objects.html#GroupSite.get_center"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#arbdmodel.core_objects.GroupSite.get_center" title="Link to this definition">#</a></dt>
@@ -736,127 +582,23 @@ and manage restraints applied to the group.</p>
<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>The Parent class implements a hierarchical tree structure for organizing objects in a simulation.
This class serves as a container for child objects and provides methods for managing relationships, properties, and interactions between these objects within a molecular simulation context.</p>
-<dl class="py attribute">
-<dt class="sig sig-object py" id="arbdmodel.core_objects.Parent.children">
-<span class="sig-name descname"><span class="pre">children</span></span><a class="headerlink" href="#arbdmodel.core_objects.Parent.children" title="Link to this definition">#</a></dt>
-<dd><p>A list of child objects belonging to this parent.</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.core_objects.Parent.remove_duplicate_bonded_terms">
-<span class="sig-name descname"><span class="pre">remove_duplicate_bonded_terms</span></span><a class="headerlink" href="#arbdmodel.core_objects.Parent.remove_duplicate_bonded_terms" title="Link to this definition">#</a></dt>
-<dd><p>Whether to remove duplicate bonded terms when collecting them.</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.core_objects.Parent.bonds">
-<span class="sig-name descname"><span class="pre">bonds</span></span><a class="headerlink" href="#arbdmodel.core_objects.Parent.bonds" title="Link to this definition">#</a></dt>
-<dd><p>List of bond interactions between particles.</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.core_objects.Parent.angles">
-<span class="sig-name descname"><span class="pre">angles</span></span><a class="headerlink" href="#arbdmodel.core_objects.Parent.angles" title="Link to this definition">#</a></dt>
-<dd><p>List of angle interactions between triplets of particles.</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.core_objects.Parent.dihedrals">
-<span class="sig-name descname"><span class="pre">dihedrals</span></span><a class="headerlink" href="#arbdmodel.core_objects.Parent.dihedrals" title="Link to this definition">#</a></dt>
-<dd><p>List of dihedral interactions between quartets of particles.</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.core_objects.Parent.vector_angles">
-<span class="sig-name descname"><span class="pre">vector_angles</span></span><a class="headerlink" href="#arbdmodel.core_objects.Parent.vector_angles" title="Link to this definition">#</a></dt>
-<dd><p>List of vector angle 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/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.core_objects.Parent.impropers">
-<span class="sig-name descname"><span class="pre">impropers</span></span><a class="headerlink" href="#arbdmodel.core_objects.Parent.impropers" title="Link to this definition">#</a></dt>
-<dd><p>List of improper dihedral 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/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.core_objects.Parent.exclusions">
-<span class="sig-name descname"><span class="pre">exclusions</span></span><a class="headerlink" href="#arbdmodel.core_objects.Parent.exclusions" title="Link to this definition">#</a></dt>
-<dd><p>List of pairwise exclusions from non-bonded 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/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.core_objects.Parent.bond_angles">
-<span class="sig-name descname"><span class="pre">bond_angles</span></span><a class="headerlink" href="#arbdmodel.core_objects.Parent.bond_angles" title="Link to this definition">#</a></dt>
-<dd><p>List of combined bond-angle 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/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.core_objects.Parent.product_potentials">
-<span class="sig-name descname"><span class="pre">product_potentials</span></span><a class="headerlink" href="#arbdmodel.core_objects.Parent.product_potentials" title="Link to this definition">#</a></dt>
-<dd><p>List of product potentials.</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.core_objects.Parent.group_sites">
-<span class="sig-name descname"><span class="pre">group_sites</span></span><a class="headerlink" href="#arbdmodel.core_objects.Parent.group_sites" title="Link to this definition">#</a></dt>
-<dd><p>List of group sites.</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>
+<dt class="field-odd">Parameters<span class="colon">:</span></dt>
+<dd class="field-odd"><ul class="simple">
+<li><p><strong>children</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>) – A list of child objects belonging to this parent.</p></li>
+<li><p><strong>remove_duplicate_bonded_terms</strong> (<a class="hxr-hoverxref hxr-tooltip reference external" href="https://docs.python.org/3/library/functions.html#bool" title="(in Python v3.13)"><em>bool</em></a>) – Whether to remove duplicate bonded terms when collecting them.</p></li>
+<li><p><strong>bonds</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 bond interactions between particles.</p></li>
+<li><p><strong>angles</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 angle interactions between triplets of particles.</p></li>
+<li><p><strong>dihedrals</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 dihedral interactions between quartets of particles.</p></li>
+<li><p><strong>vector_angles</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 vector angle interactions.</p></li>
+<li><p><strong>impropers</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 improper dihedral interactions.</p></li>
+<li><p><strong>exclusions</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 pairwise exclusions from non-bonded interactions.</p></li>
+<li><p><strong>bond_angles</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 combined bond-angle interactions.</p></li>
+<li><p><strong>product_potentials</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 product potentials.</p></li>
+<li><p><strong>group_sites</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 group sites.</p></li>
+</ul>
</dd>
</dl>
-</dd></dl>
-
<p>This class implements iteration methods to traverse the tree structure depth-first.</p>
<dl class="py method">
<dt class="sig sig-object py" id="arbdmodel.core_objects.Parent.add">
@@ -1014,83 +756,19 @@ of the parent-child hierarchy.</p>
ParticleType serves as a template for properties shared across multiple particles.
It supports inheritance through parent types, attribute lookup, and provides mechanisms
for comparing particle types.</p>
-<dl class="py attribute">
-<dt class="sig sig-object py" id="arbdmodel.core_objects.ParticleType.excludedAttributes">
-<span class="sig-name descname"><span class="pre">excludedAttributes</span></span><a class="headerlink" href="#arbdmodel.core_objects.ParticleType.excludedAttributes" title="Link to this definition">#</a></dt>
-<dd><p>Attributes that are not inherited from parent 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#tuple" title="(in Python v3.13)">tuple</a></p>
-</dd>
-</dl>
-</dd></dl>
-
-<dl class="py attribute">
-<dt class="sig sig-object py" id="arbdmodel.core_objects.ParticleType.name">
-<span class="sig-name descname"><span class="pre">name</span></span><a class="headerlink" href="#arbdmodel.core_objects.ParticleType.name" title="Link to this definition">#</a></dt>
-<dd><p>Unique identifier for this particle type.</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.core_objects.ParticleType.charge">
-<span class="sig-name descname"><span class="pre">charge</span></span><a class="headerlink" href="#arbdmodel.core_objects.ParticleType.charge" title="Link to this definition">#</a></dt>
-<dd><p>Electric charge of the particle. Defaults to 0.</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.core_objects.ParticleType.mass">
-<span class="sig-name descname"><span class="pre">mass</span></span><a class="headerlink" href="#arbdmodel.core_objects.ParticleType.mass" title="Link to this definition">#</a></dt>
-<dd><p>Mass of the particle.</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>, optional</p>
-</dd>
-</dl>
-</dd></dl>
-
-<dl class="py attribute">
-<dt class="sig sig-object py" id="arbdmodel.core_objects.ParticleType.diffusivity">
-<span class="sig-name descname"><span class="pre">diffusivity</span></span><a class="headerlink" href="#arbdmodel.core_objects.ParticleType.diffusivity" title="Link to this definition">#</a></dt>
-<dd><p>Diffusion coefficient of the particle.</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>, optional</p>
-</dd>
-</dl>
-</dd></dl>
-
-<dl class="py attribute">
-<dt class="sig sig-object py" id="arbdmodel.core_objects.ParticleType.damping_coefficient">
-<span class="sig-name descname"><span class="pre">damping_coefficient</span></span><a class="headerlink" href="#arbdmodel.core_objects.ParticleType.damping_coefficient" title="Link to this definition">#</a></dt>
-<dd><p>Damping coefficient for dynamics.</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>, optional</p>
-</dd>
-</dl>
-</dd></dl>
-
-<dl class="py attribute">
-<dt class="sig sig-object py" id="arbdmodel.core_objects.ParticleType.parent">
-<span class="sig-name descname"><span class="pre">parent</span></span><a class="headerlink" href="#arbdmodel.core_objects.ParticleType.parent" title="Link to this definition">#</a></dt>
-<dd><p>Parent type to inherit properties from.</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="#arbdmodel.core_objects.ParticleType" title="arbdmodel.core_objects.ParticleType">ParticleType</a>, optional</p>
+<dt class="field-odd">Parameters<span class="colon">:</span></dt>
+<dd class="field-odd"><ul class="simple">
+<li><p><strong>excludedParameters</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>) – Parameters that are not inherited from parent types.</p></li>
+<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>) – Unique identifier for this particle type.</p></li>
+<li><p><strong>charge</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>) – Electric charge of the particle. Defaults to 0.</p></li>
+<li><p><strong>mass</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>) – Mass of the particle.</p></li>
+<li><p><strong>diffusivity</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>) – Diffusion coefficient of the particle.</p></li>
+<li><p><strong>damping_coefficient</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>) – Damping coefficient for dynamics.</p></li>
+<li><p><strong>parent</strong> (<a class="reference internal" href="#arbdmodel.core_objects.ParticleType" title="arbdmodel.core_objects.ParticleType"><em>ParticleType</em></a><em>, </em><em>optional</em>) – Parent type to inherit properties from.</p></li>
+</ul>
</dd>
</dl>
-</dd></dl>
-
<div class="admonition note">
<p class="admonition-title">Note</p>
<ul class="simple">
@@ -1125,8 +803,8 @@ Must be one of ‘dirichlet’, ‘neumann’, or ‘periodic’.</p></li>
</dd></dl>
<dl class="py attribute">
-<dt class="sig sig-object py" id="id5">
-<span class="sig-name descname"><span class="pre">excludedAttributes</span></span><em class="property"><span class="w"> </span><span class="p"><span class="pre">=</span></span><span class="w"> </span><span class="pre">('idx',</span> <span class="pre">'type_',</span> <span class="pre">'position',</span> <span class="pre">'orientation',</span> <span class="pre">'children',</span> <span class="pre">'name',</span> <span class="pre">'parent',</span> <span class="pre">'excludedAttributes')</span></em><a class="headerlink" href="#id5" title="Link to this definition">#</a></dt>
+<dt class="sig sig-object py" id="arbdmodel.core_objects.ParticleType.excludedParameters">
+<span class="sig-name descname"><span class="pre">excludedParameters</span></span><em class="property"><span class="w"> </span><span class="p"><span class="pre">=</span></span><span class="w"> </span><span class="pre">('idx',</span> <span class="pre">'type_',</span> <span class="pre">'position',</span> <span class="pre">'orientation',</span> <span class="pre">'children',</span> <span class="pre">'name',</span> <span class="pre">'parent',</span> <span class="pre">'excludedParameters')</span></em><a class="headerlink" href="#arbdmodel.core_objects.ParticleType.excludedParameters" title="Link to this definition">#</a></dt>
<dd></dd></dl>
<dl class="py method">
@@ -1165,72 +843,18 @@ of the other (when consider_parents=True).</p>
<p>A class representing a point particle in a simulation system.
This class inherits from both Transformable and Child base classes, allowing
it to be positioned in space and exist in a parent-child hierarchy.</p>
-<dl class="py attribute">
-<dt class="sig sig-object py" id="arbdmodel.core_objects.PointParticle.type_">
-<span class="sig-name descname"><span class="pre">type_</span></span><a class="headerlink" href="#arbdmodel.core_objects.PointParticle.type_" title="Link to this definition">#</a></dt>
-<dd><p>Type definition of the particle.</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="#arbdmodel.core_objects.ParticleType" title="arbdmodel.core_objects.ParticleType">ParticleType</a></p>
-</dd>
-</dl>
-</dd></dl>
-
-<dl class="py attribute">
-<dt class="sig sig-object py" id="arbdmodel.core_objects.PointParticle.idx">
-<span class="sig-name descname"><span class="pre">idx</span></span><a class="headerlink" href="#arbdmodel.core_objects.PointParticle.idx" title="Link to this definition">#</a></dt>
-<dd><p>Index of the particle in the system, default is None.</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.core_objects.PointParticle.name">
-<span class="sig-name descname"><span class="pre">name</span></span><a class="headerlink" href="#arbdmodel.core_objects.PointParticle.name" title="Link to this definition">#</a></dt>
-<dd><p>Name identifier for the particle, default is “Aâ€.</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.core_objects.PointParticle.counter">
-<span class="sig-name descname"><span class="pre">counter</span></span><a class="headerlink" href="#arbdmodel.core_objects.PointParticle.counter" title="Link to this definition">#</a></dt>
-<dd><p>Counter for operations on this particle, initialized to 0.</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.core_objects.PointParticle.restraints">
-<span class="sig-name descname"><span class="pre">restraints</span></span><a class="headerlink" href="#arbdmodel.core_objects.PointParticle.restraints" title="Link to this definition">#</a></dt>
-<dd><p>List of restraints applied to this particle.</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.core_objects.PointParticle.rigid">
-<span class="sig-name descname"><span class="pre">rigid</span></span><a class="headerlink" href="#arbdmodel.core_objects.PointParticle.rigid" title="Link to this definition">#</a></dt>
-<dd><p>Flag indicating whether the particle is rigid, default is False.</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>
+<dt class="field-odd">Parameters<span class="colon">:</span></dt>
+<dd class="field-odd"><ul class="simple">
+<li><p><strong>type</strong> (<a class="reference internal" href="#arbdmodel.core_objects.ParticleType" title="arbdmodel.core_objects.ParticleType"><em>ParticleType</em></a>) – Type definition of the particle.</p></li>
+<li><p><strong>idx</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>) – Index of the particle in the system, default is None.</p></li>
+<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 identifier for the particle, default is “Aâ€.</p></li>
+<li><p><strong>counter</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>) – Counter for operations on this particle, initialized to 0.</p></li>
+<li><p><strong>restraints</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 restraints applied to this particle.</p></li>
+<li><p><strong>rigid</strong> (<a class="hxr-hoverxref hxr-tooltip reference external" href="https://docs.python.org/3/library/functions.html#bool" title="(in Python v3.13)"><em>bool</em></a>) – Flag indicating whether the particle is rigid, default is False.</p></li>
+</ul>
</dd>
</dl>
-</dd></dl>
-
<dl class="py method">
<dt class="sig sig-object py" id="arbdmodel.core_objects.PointParticle.add_grid_potential">
<span class="sig-name descname"><span class="pre">add_grid_potential</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">gridfile</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">scale</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">1</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">boundary_condition</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">'dirichlet'</span></span></em><span class="sig-paren">)</span><a class="reference internal" href="../../_modules/arbdmodel/core_objects.html#PointParticle.add_grid_potential"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#arbdmodel.core_objects.PointParticle.add_grid_potential" title="Link to this definition">#</a></dt>
@@ -1323,91 +947,16 @@ It inherits from PointParticle and implements transformation capabilities to mov
<dt class="field-odd">Parameters<span class="colon">:</span></dt>
<dd class="field-odd"><ul class="simple">
<li><p><strong>type</strong> (<a class="reference internal" href="#arbdmodel.core_objects.RigidBodyType" title="arbdmodel.core_objects.RigidBodyType"><em>RigidBodyType</em></a>) – The type definition for this rigid body.</p></li>
-<li><p><strong>position</strong> (<em>array-like</em>) – The initial position of the rigid body in 3D space.</p></li>
-<li><p><strong>orientation</strong> (<em>array-like</em><em> or </em><em>quaternion</em>) – The initial orientation of the rigid body.</p></li>
-<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><em>, </em><em>optional</em>) – A name identifier for this rigid body. Defaults to “Aâ€.</p></li>
-<li><p><strong>attached_particles</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>) – Particles to attach to the rigid body, which will move with it. Defaults to empty tuple.</p></li>
+<li><p><strong>idx</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>) – Index identifier, assigned when added to a simulation.</p></li>
+<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 identifier for this rigid body.</p></li>
+<li><p><strong>counter</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>) – Counter value, initialized at 0.</p></li>
+<li><p><strong>restraints</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 restraints applied to this rigid body.</p></li>
+<li><p><strong>rigid</strong> (<a class="hxr-hoverxref hxr-tooltip reference external" href="https://docs.python.org/3/library/functions.html#bool" title="(in Python v3.13)"><em>bool</em></a>) – Boolean flag indicating if the object is rigid, always True for this class.</p></li>
+<li><p><strong>attached_particles</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>) – Copied particles attached to the rigid body.</p></li>
<li><p><strong>**kwargs</strong> – Additional keyword arguments to set as attributes.</p></li>
</ul>
</dd>
</dl>
-<dl class="py attribute">
-<dt class="sig sig-object py" id="arbdmodel.core_objects.RigidBody.type_">
-<span class="sig-name descname"><span class="pre">type_</span></span><a class="headerlink" href="#arbdmodel.core_objects.RigidBody.type_" title="Link to this definition">#</a></dt>
-<dd><p>The type definition for this rigid body.</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="#arbdmodel.core_objects.RigidBodyType" title="arbdmodel.core_objects.RigidBodyType">RigidBodyType</a></p>
-</dd>
-</dl>
-</dd></dl>
-
-<dl class="py attribute">
-<dt class="sig sig-object py" id="arbdmodel.core_objects.RigidBody.idx">
-<span class="sig-name descname"><span class="pre">idx</span></span><a class="headerlink" href="#arbdmodel.core_objects.RigidBody.idx" title="Link to this definition">#</a></dt>
-<dd><p>Index identifier, assigned when added to a simulation.</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> or None</p>
-</dd>
-</dl>
-</dd></dl>
-
-<dl class="py attribute">
-<dt class="sig sig-object py" id="arbdmodel.core_objects.RigidBody.name">
-<span class="sig-name descname"><span class="pre">name</span></span><a class="headerlink" href="#arbdmodel.core_objects.RigidBody.name" title="Link to this definition">#</a></dt>
-<dd><p>Name identifier for this rigid body.</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.core_objects.RigidBody.counter">
-<span class="sig-name descname"><span class="pre">counter</span></span><a class="headerlink" href="#arbdmodel.core_objects.RigidBody.counter" title="Link to this definition">#</a></dt>
-<dd><p>Counter value, initialized at 0.</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.core_objects.RigidBody.restraints">
-<span class="sig-name descname"><span class="pre">restraints</span></span><a class="headerlink" href="#arbdmodel.core_objects.RigidBody.restraints" title="Link to this definition">#</a></dt>
-<dd><p>List of restraints applied to this rigid body.</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.core_objects.RigidBody.rigid">
-<span class="sig-name descname"><span class="pre">rigid</span></span><a class="headerlink" href="#arbdmodel.core_objects.RigidBody.rigid" title="Link to this definition">#</a></dt>
-<dd><p>Boolean flag indicating if the object is rigid, always True for this class.</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.core_objects.RigidBody.attached_particles">
-<span class="sig-name descname"><span class="pre">attached_particles</span></span><a class="headerlink" href="#arbdmodel.core_objects.RigidBody.attached_particles" title="Link to this definition">#</a></dt>
-<dd><p>Copied particles attached to the rigid body.</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>
-
<div class="admonition note">
<p class="admonition-title">Note</p>
<p>TODO: for attached_particles, it should be possible to uniquely apply bonds/angles etc to these particles, but their types should be fixed or otherwise unified among rbs;
@@ -1471,105 +1020,21 @@ Any modifications to the returned object will not affect the original object.</p
<p>Class that holds common attributes for RigidBody objects.
This class extends ParticleType to represent rigid bodies that can have
attached particles, orientation, and rotational dynamics.</p>
-<dl class="py attribute">
-<dt class="sig sig-object py" id="arbdmodel.core_objects.RigidBodyType.name">
-<span class="sig-name descname"><span class="pre">name</span></span><a class="headerlink" href="#arbdmodel.core_objects.RigidBodyType.name" title="Link to this definition">#</a></dt>
-<dd><p>Name identifier for the rigid body type.</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.core_objects.RigidBodyType.parent">
-<span class="sig-name descname"><span class="pre">parent</span></span><a class="headerlink" href="#arbdmodel.core_objects.RigidBodyType.parent" title="Link to this definition">#</a></dt>
-<dd><p>Parent type to fall back on for nonbonded interactions.</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="#arbdmodel.core_objects.ParticleType" title="arbdmodel.core_objects.ParticleType">ParticleType</a>, optional</p>
-</dd>
-</dl>
-</dd></dl>
-
-<dl class="py attribute">
-<dt class="sig sig-object py" id="arbdmodel.core_objects.RigidBodyType.moment_of_inertia">
-<span class="sig-name descname"><span class="pre">moment_of_inertia</span></span><a class="headerlink" href="#arbdmodel.core_objects.RigidBodyType.moment_of_inertia" title="Link to this definition">#</a></dt>
-<dd><p>Moment of inertia tensor for the rigid body.</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 array-like, optional</p>
-</dd>
-</dl>
-</dd></dl>
-
-<dl class="py attribute">
-<dt class="sig sig-object py" id="arbdmodel.core_objects.RigidBodyType.rotational_diffusivity">
-<span class="sig-name descname"><span class="pre">rotational_diffusivity</span></span><a class="headerlink" href="#arbdmodel.core_objects.RigidBodyType.rotational_diffusivity" title="Link to this definition">#</a></dt>
-<dd><p>Rotational diffusivity coefficient.</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 array-like, optional</p>
-</dd>
-</dl>
-</dd></dl>
-
-<dl class="py attribute">
-<dt class="sig sig-object py" id="arbdmodel.core_objects.RigidBodyType.rotational_damping_coefficient">
-<span class="sig-name descname"><span class="pre">rotational_damping_coefficient</span></span><a class="headerlink" href="#arbdmodel.core_objects.RigidBodyType.rotational_damping_coefficient" title="Link to this definition">#</a></dt>
-<dd><p>Rotational damping coefficient.</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 array-like, optional</p>
-</dd>
-</dl>
-</dd></dl>
-
-<dl class="py attribute">
-<dt class="sig sig-object py" id="arbdmodel.core_objects.RigidBodyType.attached_particles">
-<span class="sig-name descname"><span class="pre">attached_particles</span></span><a class="headerlink" href="#arbdmodel.core_objects.RigidBodyType.attached_particles" title="Link to this definition">#</a></dt>
-<dd><p>Particles attached to this rigid body.</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> or <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.core_objects.RigidBodyType.potential_grids">
-<span class="sig-name descname"><span class="pre">potential_grids</span></span><a class="headerlink" href="#arbdmodel.core_objects.RigidBodyType.potential_grids" title="Link to this definition">#</a></dt>
-<dd><p>Collection of potential grid definitions, each with length 2 or 3.</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></p>
-</dd>
-</dl>
-</dd></dl>
-
-<dl class="py attribute">
-<dt class="sig sig-object py" id="arbdmodel.core_objects.RigidBodyType.charge_grids">
-<span class="sig-name descname"><span class="pre">charge_grids</span></span><a class="headerlink" href="#arbdmodel.core_objects.RigidBodyType.charge_grids" title="Link to this definition">#</a></dt>
-<dd><p>Collection of charge grid definitions, each with length 2 or 3.</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></p>
-</dd>
-</dl>
-</dd></dl>
-
-<dl class="py attribute">
-<dt class="sig sig-object py" id="arbdmodel.core_objects.RigidBodyType.pmf_grids">
-<span class="sig-name descname"><span class="pre">pmf_grids</span></span><a class="headerlink" href="#arbdmodel.core_objects.RigidBodyType.pmf_grids" title="Link to this definition">#</a></dt>
-<dd><p>Collection of pmf grid definitions, each with length 2 or 3.</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></p>
+<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 identifier for the rigid body type.</p></li>
+<li><p><strong>parent</strong> (<a class="reference internal" href="#arbdmodel.core_objects.ParticleType" title="arbdmodel.core_objects.ParticleType"><em>ParticleType</em></a><em>, </em><em>optional</em>) – Parent type to fall back on for nonbonded interactions.</p></li>
+<li><p><strong>moment_of_inertia</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>array-like</em><em>, </em><em>optional</em>) – Moment of inertia tensor for the rigid body.</p></li>
+<li><p><strong>rotational_diffusivity</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>array-like</em><em>, </em><em>optional</em>) – Rotational diffusivity coefficient.</p></li>
+<li><p><strong>rotational_damping_coefficient</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>array-like</em><em>, </em><em>optional</em>) – Rotational damping coefficient.</p></li>
+<li><p><strong>attached_particles</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> or </em><a class="hxr-hoverxref hxr-tooltip reference external" href="https://docs.python.org/3/library/stdtypes.html#list" title="(in Python v3.13)"><em>list</em></a>) – Particles attached to this rigid body.</p></li>
+<li><p><strong>potential_grids</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>) – Collection of potential grid definitions, each with length 2 or 3.</p></li>
+<li><p><strong>charge_grids</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>) – Collection of charge grid definitions, each with length 2 or 3.</p></li>
+<li><p><strong>pmf_grids</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>) – Collection of pmf grid definitions, each with length 2 or 3.</p></li>
+</ul>
</dd>
</dl>
-</dd></dl>
-
<div class="admonition note">
<p class="admonition-title">Note</p>
<p>If rotational_diffusivity is not provided, both moment_of_inertia and
@@ -1591,61 +1056,15 @@ rotational_damping_coefficient must be specified.</p>
The Transformable class provides basic functionality for positioning and orienting
objects in 3D space, as well as methods for applying transformations such as
translations and rotations.</p>
-<dl class="py attribute">
-<dt class="sig sig-object py" id="arbdmodel.core_objects.Transformable.position">
-<span class="sig-name descname"><span class="pre">position</span></span><a class="headerlink" href="#arbdmodel.core_objects.Transformable.position" title="Link to this definition">#</a></dt>
-<dd><p>The position of the object in 3D space.</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.core_objects.Transformable.orientation">
-<span class="sig-name descname"><span class="pre">orientation</span></span><a class="headerlink" href="#arbdmodel.core_objects.Transformable.orientation" title="Link to this definition">#</a></dt>
-<dd><p>The orientation matrix of the object.
-If None, the object has no orientation.</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> or None</p>
+<dt class="field-odd">Parameters<span class="colon">:</span></dt>
+<dd class="field-odd"><ul class="simple">
+<li><p><strong>position</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>) – The position of the object in 3D space.</p></li>
+<li><p><strong>orientation</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><em> or </em><em>None</em>) – The orientation matrix of the object.
+If None, the object has no orientation.</p></li>
+</ul>
</dd>
</dl>
-</dd></dl>
-
-<dl class="py method">
-<dt class="sig sig-object py" id="arbdmodel.core_objects.Transformable.translate">
-<span class="sig-name descname"><span class="pre">translate</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">offset</span></span></em><span class="sig-paren">)</span><a class="reference internal" href="../../_modules/arbdmodel/core_objects.html#Transformable.translate"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#arbdmodel.core_objects.Transformable.translate" title="Link to this definition">#</a></dt>
-<dd><p>Translate the object by the given offset.</p>
-</dd></dl>
-
-<dl class="py method">
-<dt class="sig sig-object py" id="arbdmodel.core_objects.Transformable.rotate">
-<span class="sig-name descname"><span class="pre">rotate</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">R</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">about</span></span></em><span class="sig-paren">)</span><a class="reference internal" href="../../_modules/arbdmodel/core_objects.html#Transformable.rotate"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#arbdmodel.core_objects.Transformable.rotate" title="Link to this definition">#</a></dt>
-<dd><p>Rotate the object by the rotation matrix R about a center point.</p>
-</dd></dl>
-
-<dl class="py method">
-<dt class="sig sig-object py" id="arbdmodel.core_objects.Transformable.transform">
-<span class="sig-name descname"><span class="pre">transform</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">R</span></span></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">offset</span></span></em><span class="sig-paren">)</span><a class="reference internal" href="../../_modules/arbdmodel/core_objects.html#Transformable.transform"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#arbdmodel.core_objects.Transformable.transform" title="Link to this definition">#</a></dt>
-<dd><p>Apply a general transformation to the object.</p>
-</dd></dl>
-
-<dl class="py method">
-<dt class="sig sig-object py" id="arbdmodel.core_objects.Transformable.get_collapsed_position">
-<span class="sig-name descname"><span class="pre">get_collapsed_position</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="reference internal" href="../../_modules/arbdmodel/core_objects.html#Transformable.get_collapsed_position"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#arbdmodel.core_objects.Transformable.get_collapsed_position" title="Link to this definition">#</a></dt>
-<dd><p>Get the absolute position of the object, taking into
-account parent transformations if the object is a Child.</p>
-</dd></dl>
-
-<dl class="py method">
-<dt class="sig sig-object py" id="arbdmodel.core_objects.Transformable.applyOrientation">
-<span class="sig-name descname"><span class="pre">applyOrientation</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">obj</span></span></em><span class="sig-paren">)</span><a class="reference internal" href="../../_modules/arbdmodel/core_objects.html#Transformable.applyOrientation"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#arbdmodel.core_objects.Transformable.applyOrientation" title="Link to this definition">#</a></dt>
-<dd><p>Apply the orientation chain to an object, considering
-parent orientations if the object is a Child.</p>
-</dd></dl>
-
<div class="admonition note">
<p class="admonition-title">Note</p>
<ul class="simple">
@@ -1655,28 +1074,28 @@ parent orientations if the object is a Child.</p>
</ul>
</div>
<dl class="py method">
-<dt class="sig sig-object py" id="id6">
-<span class="sig-name descname"><span class="pre">applyOrientation</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">obj</span></span></em><span class="sig-paren">)</span><a class="reference internal" href="../../_modules/arbdmodel/core_objects.html#Transformable.applyOrientation"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#id6" title="Link to this definition">#</a></dt>
+<dt class="sig sig-object py" id="arbdmodel.core_objects.Transformable.applyOrientation">
+<span class="sig-name descname"><span class="pre">applyOrientation</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">obj</span></span></em><span class="sig-paren">)</span><a class="reference internal" href="../../_modules/arbdmodel/core_objects.html#Transformable.applyOrientation"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#arbdmodel.core_objects.Transformable.applyOrientation" title="Link to this definition">#</a></dt>
<dd></dd></dl>
<dl class="py method">
-<dt class="sig sig-object py" id="id7">
-<span class="sig-name descname"><span class="pre">get_collapsed_position</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="reference internal" href="../../_modules/arbdmodel/core_objects.html#Transformable.get_collapsed_position"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#id7" title="Link to this definition">#</a></dt>
+<dt class="sig sig-object py" id="arbdmodel.core_objects.Transformable.get_collapsed_position">
+<span class="sig-name descname"><span class="pre">get_collapsed_position</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="reference internal" href="../../_modules/arbdmodel/core_objects.html#Transformable.get_collapsed_position"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#arbdmodel.core_objects.Transformable.get_collapsed_position" title="Link to this definition">#</a></dt>
<dd></dd></dl>
<dl class="py method">
-<dt class="sig sig-object py" id="id8">
-<span class="sig-name descname"><span class="pre">rotate</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">R</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">about</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">(0,</span> <span class="pre">0,</span> <span class="pre">0)</span></span></em><span class="sig-paren">)</span><a class="reference internal" href="../../_modules/arbdmodel/core_objects.html#Transformable.rotate"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#id8" title="Link to this definition">#</a></dt>
+<dt class="sig sig-object py" id="arbdmodel.core_objects.Transformable.rotate">
+<span class="sig-name descname"><span class="pre">rotate</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">R</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">about</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">(0,</span> <span class="pre">0,</span> <span class="pre">0)</span></span></em><span class="sig-paren">)</span><a class="reference internal" href="../../_modules/arbdmodel/core_objects.html#Transformable.rotate"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#arbdmodel.core_objects.Transformable.rotate" title="Link to this definition">#</a></dt>
<dd></dd></dl>
<dl class="py method">
-<dt class="sig sig-object py" id="id9">
-<span class="sig-name descname"><span class="pre">transform</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">R</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">((1,</span> <span class="pre">0,</span> <span class="pre">0),</span> <span class="pre">(0,</span> <span class="pre">1,</span> <span class="pre">0),</span> <span class="pre">(0,</span> <span class="pre">0,</span> <span class="pre">1))</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">center</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">(0,</span> <span class="pre">0,</span> <span class="pre">0)</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">offset</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">(0,</span> <span class="pre">0,</span> <span class="pre">0)</span></span></em><span class="sig-paren">)</span><a class="reference internal" href="../../_modules/arbdmodel/core_objects.html#Transformable.transform"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#id9" title="Link to this definition">#</a></dt>
+<dt class="sig sig-object py" id="arbdmodel.core_objects.Transformable.transform">
+<span class="sig-name descname"><span class="pre">transform</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">R</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">((1,</span> <span class="pre">0,</span> <span class="pre">0),</span> <span class="pre">(0,</span> <span class="pre">1,</span> <span class="pre">0),</span> <span class="pre">(0,</span> <span class="pre">0,</span> <span class="pre">1))</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">center</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">(0,</span> <span class="pre">0,</span> <span class="pre">0)</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">offset</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">(0,</span> <span class="pre">0,</span> <span class="pre">0)</span></span></em><span class="sig-paren">)</span><a class="reference internal" href="../../_modules/arbdmodel/core_objects.html#Transformable.transform"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#arbdmodel.core_objects.Transformable.transform" title="Link to this definition">#</a></dt>
<dd></dd></dl>
<dl class="py method">
-<dt class="sig sig-object py" id="id10">
-<span class="sig-name descname"><span class="pre">translate</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">offset</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">(0,</span> <span class="pre">0,</span> <span class="pre">0)</span></span></em><span class="sig-paren">)</span><a class="reference internal" href="../../_modules/arbdmodel/core_objects.html#Transformable.translate"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#id10" title="Link to this definition">#</a></dt>
+<dt class="sig sig-object py" id="arbdmodel.core_objects.Transformable.translate">
+<span class="sig-name descname"><span class="pre">translate</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">offset</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">(0,</span> <span class="pre">0,</span> <span class="pre">0)</span></span></em><span class="sig-paren">)</span><a class="reference internal" href="../../_modules/arbdmodel/core_objects.html#Transformable.translate"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#arbdmodel.core_objects.Transformable.translate" title="Link to this definition">#</a></dt>
<dd></dd></dl>
</dd></dl>
@@ -1729,22 +1148,12 @@ parent orientations if the object is a Child.</p>
</div>
<nav class="bd-toc-nav page-toc">
<ul class="visible nav section-nav flex-column">
-<li class="toc-h2 nav-item toc-entry"><a class="reference internal nav-link" href="#arbdmodel.core_objects.Child"><code class="docutils literal notranslate"><span class="pre">Child</span></code></a><ul class="nav section-nav flex-column">
-<li class="toc-h3 nav-item toc-entry"><a class="reference internal nav-link" href="#arbdmodel.core_objects.Child.parent"><code class="docutils literal notranslate"><span class="pre">Child.parent</span></code></a></li>
-</ul>
-</li>
+<li class="toc-h2 nav-item toc-entry"><a class="reference internal nav-link" href="#arbdmodel.core_objects.Child"><code class="docutils literal notranslate"><span class="pre">Child</span></code></a></li>
<li class="toc-h2 nav-item toc-entry"><a class="reference internal nav-link" href="#arbdmodel.core_objects.Clone"><code class="docutils literal notranslate"><span class="pre">Clone</span></code></a><ul class="nav section-nav flex-column">
<li class="toc-h3 nav-item toc-entry"><a class="reference internal nav-link" href="#arbdmodel.core_objects.Clone.get_original_recursively"><code class="docutils literal notranslate"><span class="pre">Clone.get_original_recursively()</span></code></a></li>
</ul>
</li>
<li class="toc-h2 nav-item toc-entry"><a class="reference internal nav-link" href="#arbdmodel.core_objects.Group"><code class="docutils literal notranslate"><span class="pre">Group</span></code></a><ul class="nav section-nav flex-column">
-<li class="toc-h3 nav-item toc-entry"><a class="reference internal nav-link" href="#arbdmodel.core_objects.Group.name"><code class="docutils literal notranslate"><span class="pre">Group.name</span></code></a></li>
-<li class="toc-h3 nav-item toc-entry"><a class="reference internal nav-link" href="#arbdmodel.core_objects.Group.children"><code class="docutils literal notranslate"><span class="pre">Group.children</span></code></a></li>
-<li class="toc-h3 nav-item toc-entry"><a class="reference internal nav-link" href="#arbdmodel.core_objects.Group.parent"><code class="docutils literal notranslate"><span class="pre">Group.parent</span></code></a></li>
-<li class="toc-h3 nav-item toc-entry"><a class="reference internal nav-link" href="#arbdmodel.core_objects.Group.position"><code class="docutils literal notranslate"><span class="pre">Group.position</span></code></a></li>
-<li class="toc-h3 nav-item toc-entry"><a class="reference internal nav-link" href="#arbdmodel.core_objects.Group.orientation"><code class="docutils literal notranslate"><span class="pre">Group.orientation</span></code></a></li>
-<li class="toc-h3 nav-item toc-entry"><a class="reference internal nav-link" href="#arbdmodel.core_objects.Group.isClone"><code class="docutils literal notranslate"><span class="pre">Group.isClone</span></code></a></li>
-<li class="toc-h3 nav-item toc-entry"><a class="reference internal nav-link" href="#arbdmodel.core_objects.Group.remove_duplicate_bonded_terms"><code class="docutils literal notranslate"><span class="pre">Group.remove_duplicate_bonded_terms</span></code></a></li>
<li class="toc-h3 nav-item toc-entry"><a class="reference internal nav-link" href="#arbdmodel.core_objects.Group.clone"><code class="docutils literal notranslate"><span class="pre">Group.clone()</span></code></a></li>
<li class="toc-h3 nav-item toc-entry"><a class="reference internal nav-link" href="#arbdmodel.core_objects.Group.duplicate"><code class="docutils literal notranslate"><span class="pre">Group.duplicate()</span></code></a></li>
<li class="toc-h3 nav-item toc-entry"><a class="reference internal nav-link" href="#id0"><code class="docutils literal notranslate"><span class="pre">Group.clone()</span></code></a></li>
@@ -1752,9 +1161,6 @@ parent orientations if the object is a Child.</p>
</ul>
</li>
<li class="toc-h2 nav-item toc-entry"><a class="reference internal nav-link" href="#arbdmodel.core_objects.GroupSite"><code class="docutils literal notranslate"><span class="pre">GroupSite</span></code></a><ul class="nav section-nav flex-column">
-<li class="toc-h3 nav-item toc-entry"><a class="reference internal nav-link" href="#arbdmodel.core_objects.GroupSite.particles"><code class="docutils literal notranslate"><span class="pre">GroupSite.particles</span></code></a></li>
-<li class="toc-h3 nav-item toc-entry"><a class="reference internal nav-link" href="#arbdmodel.core_objects.GroupSite.idx"><code class="docutils literal notranslate"><span class="pre">GroupSite.idx</span></code></a></li>
-<li class="toc-h3 nav-item toc-entry"><a class="reference internal nav-link" href="#arbdmodel.core_objects.GroupSite.restraints"><code class="docutils literal notranslate"><span class="pre">GroupSite.restraints</span></code></a></li>
<li class="toc-h3 nav-item toc-entry"><a class="reference internal nav-link" href="#arbdmodel.core_objects.GroupSite.get_center"><code class="docutils literal notranslate"><span class="pre">GroupSite.get_center()</span></code></a></li>
<li class="toc-h3 nav-item toc-entry"><a class="reference internal nav-link" href="#arbdmodel.core_objects.GroupSite.add_restraint"><code class="docutils literal notranslate"><span class="pre">GroupSite.add_restraint()</span></code></a></li>
<li class="toc-h3 nav-item toc-entry"><a class="reference internal nav-link" href="#arbdmodel.core_objects.GroupSite.get_restraints"><code class="docutils literal notranslate"><span class="pre">GroupSite.get_restraints()</span></code></a></li>
@@ -1764,17 +1170,6 @@ parent orientations if the object is a Child.</p>
</ul>
</li>
<li class="toc-h2 nav-item toc-entry"><a class="reference internal nav-link" href="#arbdmodel.core_objects.Parent"><code class="docutils literal notranslate"><span class="pre">Parent</span></code></a><ul class="nav section-nav flex-column">
-<li class="toc-h3 nav-item toc-entry"><a class="reference internal nav-link" href="#arbdmodel.core_objects.Parent.children"><code class="docutils literal notranslate"><span class="pre">Parent.children</span></code></a></li>
-<li class="toc-h3 nav-item toc-entry"><a class="reference internal nav-link" href="#arbdmodel.core_objects.Parent.remove_duplicate_bonded_terms"><code class="docutils literal notranslate"><span class="pre">Parent.remove_duplicate_bonded_terms</span></code></a></li>
-<li class="toc-h3 nav-item toc-entry"><a class="reference internal nav-link" href="#arbdmodel.core_objects.Parent.bonds"><code class="docutils literal notranslate"><span class="pre">Parent.bonds</span></code></a></li>
-<li class="toc-h3 nav-item toc-entry"><a class="reference internal nav-link" href="#arbdmodel.core_objects.Parent.angles"><code class="docutils literal notranslate"><span class="pre">Parent.angles</span></code></a></li>
-<li class="toc-h3 nav-item toc-entry"><a class="reference internal nav-link" href="#arbdmodel.core_objects.Parent.dihedrals"><code class="docutils literal notranslate"><span class="pre">Parent.dihedrals</span></code></a></li>
-<li class="toc-h3 nav-item toc-entry"><a class="reference internal nav-link" href="#arbdmodel.core_objects.Parent.vector_angles"><code class="docutils literal notranslate"><span class="pre">Parent.vector_angles</span></code></a></li>
-<li class="toc-h3 nav-item toc-entry"><a class="reference internal nav-link" href="#arbdmodel.core_objects.Parent.impropers"><code class="docutils literal notranslate"><span class="pre">Parent.impropers</span></code></a></li>
-<li class="toc-h3 nav-item toc-entry"><a class="reference internal nav-link" href="#arbdmodel.core_objects.Parent.exclusions"><code class="docutils literal notranslate"><span class="pre">Parent.exclusions</span></code></a></li>
-<li class="toc-h3 nav-item toc-entry"><a class="reference internal nav-link" href="#arbdmodel.core_objects.Parent.bond_angles"><code class="docutils literal notranslate"><span class="pre">Parent.bond_angles</span></code></a></li>
-<li class="toc-h3 nav-item toc-entry"><a class="reference internal nav-link" href="#arbdmodel.core_objects.Parent.product_potentials"><code class="docutils literal notranslate"><span class="pre">Parent.product_potentials</span></code></a></li>
-<li class="toc-h3 nav-item toc-entry"><a class="reference internal nav-link" href="#arbdmodel.core_objects.Parent.group_sites"><code class="docutils literal notranslate"><span class="pre">Parent.group_sites</span></code></a></li>
<li class="toc-h3 nav-item toc-entry"><a class="reference internal nav-link" href="#arbdmodel.core_objects.Parent.add"><code class="docutils literal notranslate"><span class="pre">Parent.add()</span></code></a></li>
<li class="toc-h3 nav-item toc-entry"><a class="reference internal nav-link" href="#arbdmodel.core_objects.Parent.add_angle"><code class="docutils literal notranslate"><span class="pre">Parent.add_angle()</span></code></a></li>
<li class="toc-h3 nav-item toc-entry"><a class="reference internal nav-link" href="#arbdmodel.core_objects.Parent.add_bond"><code class="docutils literal notranslate"><span class="pre">Parent.add_bond()</span></code></a></li>
@@ -1801,25 +1196,12 @@ parent orientations if the object is a Child.</p>
</ul>
</li>
<li class="toc-h2 nav-item toc-entry"><a class="reference internal nav-link" href="#arbdmodel.core_objects.ParticleType"><code class="docutils literal notranslate"><span class="pre">ParticleType</span></code></a><ul class="nav section-nav flex-column">
-<li class="toc-h3 nav-item toc-entry"><a class="reference internal nav-link" href="#arbdmodel.core_objects.ParticleType.excludedAttributes"><code class="docutils literal notranslate"><span class="pre">ParticleType.excludedAttributes</span></code></a></li>
-<li class="toc-h3 nav-item toc-entry"><a class="reference internal nav-link" href="#arbdmodel.core_objects.ParticleType.name"><code class="docutils literal notranslate"><span class="pre">ParticleType.name</span></code></a></li>
-<li class="toc-h3 nav-item toc-entry"><a class="reference internal nav-link" href="#arbdmodel.core_objects.ParticleType.charge"><code class="docutils literal notranslate"><span class="pre">ParticleType.charge</span></code></a></li>
-<li class="toc-h3 nav-item toc-entry"><a class="reference internal nav-link" href="#arbdmodel.core_objects.ParticleType.mass"><code class="docutils literal notranslate"><span class="pre">ParticleType.mass</span></code></a></li>
-<li class="toc-h3 nav-item toc-entry"><a class="reference internal nav-link" href="#arbdmodel.core_objects.ParticleType.diffusivity"><code class="docutils literal notranslate"><span class="pre">ParticleType.diffusivity</span></code></a></li>
-<li class="toc-h3 nav-item toc-entry"><a class="reference internal nav-link" href="#arbdmodel.core_objects.ParticleType.damping_coefficient"><code class="docutils literal notranslate"><span class="pre">ParticleType.damping_coefficient</span></code></a></li>
-<li class="toc-h3 nav-item toc-entry"><a class="reference internal nav-link" href="#arbdmodel.core_objects.ParticleType.parent"><code class="docutils literal notranslate"><span class="pre">ParticleType.parent</span></code></a></li>
<li class="toc-h3 nav-item toc-entry"><a class="reference internal nav-link" href="#arbdmodel.core_objects.ParticleType.add_grid_potential"><code class="docutils literal notranslate"><span class="pre">ParticleType.add_grid_potential()</span></code></a></li>
-<li class="toc-h3 nav-item toc-entry"><a class="reference internal nav-link" href="#id5"><code class="docutils literal notranslate"><span class="pre">ParticleType.excludedAttributes</span></code></a></li>
+<li class="toc-h3 nav-item toc-entry"><a class="reference internal nav-link" href="#arbdmodel.core_objects.ParticleType.excludedParameters"><code class="docutils literal notranslate"><span class="pre">ParticleType.excludedParameters</span></code></a></li>
<li class="toc-h3 nav-item toc-entry"><a class="reference internal nav-link" href="#arbdmodel.core_objects.ParticleType.is_same_type"><code class="docutils literal notranslate"><span class="pre">ParticleType.is_same_type()</span></code></a></li>
</ul>
</li>
<li class="toc-h2 nav-item toc-entry"><a class="reference internal nav-link" href="#arbdmodel.core_objects.PointParticle"><code class="docutils literal notranslate"><span class="pre">PointParticle</span></code></a><ul class="nav section-nav flex-column">
-<li class="toc-h3 nav-item toc-entry"><a class="reference internal nav-link" href="#arbdmodel.core_objects.PointParticle.type_"><code class="docutils literal notranslate"><span class="pre">PointParticle.type_</span></code></a></li>
-<li class="toc-h3 nav-item toc-entry"><a class="reference internal nav-link" href="#arbdmodel.core_objects.PointParticle.idx"><code class="docutils literal notranslate"><span class="pre">PointParticle.idx</span></code></a></li>
-<li class="toc-h3 nav-item toc-entry"><a class="reference internal nav-link" href="#arbdmodel.core_objects.PointParticle.name"><code class="docutils literal notranslate"><span class="pre">PointParticle.name</span></code></a></li>
-<li class="toc-h3 nav-item toc-entry"><a class="reference internal nav-link" href="#arbdmodel.core_objects.PointParticle.counter"><code class="docutils literal notranslate"><span class="pre">PointParticle.counter</span></code></a></li>
-<li class="toc-h3 nav-item toc-entry"><a class="reference internal nav-link" href="#arbdmodel.core_objects.PointParticle.restraints"><code class="docutils literal notranslate"><span class="pre">PointParticle.restraints</span></code></a></li>
-<li class="toc-h3 nav-item toc-entry"><a class="reference internal nav-link" href="#arbdmodel.core_objects.PointParticle.rigid"><code class="docutils literal notranslate"><span class="pre">PointParticle.rigid</span></code></a></li>
<li class="toc-h3 nav-item toc-entry"><a class="reference internal nav-link" href="#arbdmodel.core_objects.PointParticle.add_grid_potential"><code class="docutils literal notranslate"><span class="pre">PointParticle.add_grid_potential()</span></code></a></li>
<li class="toc-h3 nav-item toc-entry"><a class="reference internal nav-link" href="#arbdmodel.core_objects.PointParticle.add_restraint"><code class="docutils literal notranslate"><span class="pre">PointParticle.add_restraint()</span></code></a></li>
<li class="toc-h3 nav-item toc-entry"><a class="reference internal nav-link" href="#arbdmodel.core_objects.PointParticle.duplicate"><code class="docutils literal notranslate"><span class="pre">PointParticle.duplicate()</span></code></a></li>
@@ -1827,44 +1209,21 @@ parent orientations if the object is a Child.</p>
</ul>
</li>
<li class="toc-h2 nav-item toc-entry"><a class="reference internal nav-link" href="#arbdmodel.core_objects.RigidBody"><code class="docutils literal notranslate"><span class="pre">RigidBody</span></code></a><ul class="nav section-nav flex-column">
-<li class="toc-h3 nav-item toc-entry"><a class="reference internal nav-link" href="#arbdmodel.core_objects.RigidBody.type_"><code class="docutils literal notranslate"><span class="pre">RigidBody.type_</span></code></a></li>
-<li class="toc-h3 nav-item toc-entry"><a class="reference internal nav-link" href="#arbdmodel.core_objects.RigidBody.idx"><code class="docutils literal notranslate"><span class="pre">RigidBody.idx</span></code></a></li>
-<li class="toc-h3 nav-item toc-entry"><a class="reference internal nav-link" href="#arbdmodel.core_objects.RigidBody.name"><code class="docutils literal notranslate"><span class="pre">RigidBody.name</span></code></a></li>
-<li class="toc-h3 nav-item toc-entry"><a class="reference internal nav-link" href="#arbdmodel.core_objects.RigidBody.counter"><code class="docutils literal notranslate"><span class="pre">RigidBody.counter</span></code></a></li>
-<li class="toc-h3 nav-item toc-entry"><a class="reference internal nav-link" href="#arbdmodel.core_objects.RigidBody.restraints"><code class="docutils literal notranslate"><span class="pre">RigidBody.restraints</span></code></a></li>
-<li class="toc-h3 nav-item toc-entry"><a class="reference internal nav-link" href="#arbdmodel.core_objects.RigidBody.rigid"><code class="docutils literal notranslate"><span class="pre">RigidBody.rigid</span></code></a></li>
-<li class="toc-h3 nav-item toc-entry"><a class="reference internal nav-link" href="#arbdmodel.core_objects.RigidBody.attached_particles"><code class="docutils literal notranslate"><span class="pre">RigidBody.attached_particles</span></code></a></li>
<li class="toc-h3 nav-item toc-entry"><a class="reference internal nav-link" href="#arbdmodel.core_objects.RigidBody.add_restraint"><code class="docutils literal notranslate"><span class="pre">RigidBody.add_restraint()</span></code></a></li>
<li class="toc-h3 nav-item toc-entry"><a class="reference internal nav-link" href="#arbdmodel.core_objects.RigidBody.duplicate"><code class="docutils literal notranslate"><span class="pre">RigidBody.duplicate()</span></code></a></li>
<li class="toc-h3 nav-item toc-entry"><a class="reference internal nav-link" href="#arbdmodel.core_objects.RigidBody.get_restraints"><code class="docutils literal notranslate"><span class="pre">RigidBody.get_restraints()</span></code></a></li>
</ul>
</li>
<li class="toc-h2 nav-item toc-entry"><a class="reference internal nav-link" href="#arbdmodel.core_objects.RigidBodyType"><code class="docutils literal notranslate"><span class="pre">RigidBodyType</span></code></a><ul class="nav section-nav flex-column">
-<li class="toc-h3 nav-item toc-entry"><a class="reference internal nav-link" href="#arbdmodel.core_objects.RigidBodyType.name"><code class="docutils literal notranslate"><span class="pre">RigidBodyType.name</span></code></a></li>
-<li class="toc-h3 nav-item toc-entry"><a class="reference internal nav-link" href="#arbdmodel.core_objects.RigidBodyType.parent"><code class="docutils literal notranslate"><span class="pre">RigidBodyType.parent</span></code></a></li>
-<li class="toc-h3 nav-item toc-entry"><a class="reference internal nav-link" href="#arbdmodel.core_objects.RigidBodyType.moment_of_inertia"><code class="docutils literal notranslate"><span class="pre">RigidBodyType.moment_of_inertia</span></code></a></li>
-<li class="toc-h3 nav-item toc-entry"><a class="reference internal nav-link" href="#arbdmodel.core_objects.RigidBodyType.rotational_diffusivity"><code class="docutils literal notranslate"><span class="pre">RigidBodyType.rotational_diffusivity</span></code></a></li>
-<li class="toc-h3 nav-item toc-entry"><a class="reference internal nav-link" href="#arbdmodel.core_objects.RigidBodyType.rotational_damping_coefficient"><code class="docutils literal notranslate"><span class="pre">RigidBodyType.rotational_damping_coefficient</span></code></a></li>
-<li class="toc-h3 nav-item toc-entry"><a class="reference internal nav-link" href="#arbdmodel.core_objects.RigidBodyType.attached_particles"><code class="docutils literal notranslate"><span class="pre">RigidBodyType.attached_particles</span></code></a></li>
-<li class="toc-h3 nav-item toc-entry"><a class="reference internal nav-link" href="#arbdmodel.core_objects.RigidBodyType.potential_grids"><code class="docutils literal notranslate"><span class="pre">RigidBodyType.potential_grids</span></code></a></li>
-<li class="toc-h3 nav-item toc-entry"><a class="reference internal nav-link" href="#arbdmodel.core_objects.RigidBodyType.charge_grids"><code class="docutils literal notranslate"><span class="pre">RigidBodyType.charge_grids</span></code></a></li>
-<li class="toc-h3 nav-item toc-entry"><a class="reference internal nav-link" href="#arbdmodel.core_objects.RigidBodyType.pmf_grids"><code class="docutils literal notranslate"><span class="pre">RigidBodyType.pmf_grids</span></code></a></li>
<li class="toc-h3 nav-item toc-entry"><a class="reference internal nav-link" href="#arbdmodel.core_objects.RigidBodyType.attach_particle"><code class="docutils literal notranslate"><span class="pre">RigidBodyType.attach_particle()</span></code></a></li>
</ul>
</li>
<li class="toc-h2 nav-item toc-entry"><a class="reference internal nav-link" href="#arbdmodel.core_objects.Transformable"><code class="docutils literal notranslate"><span class="pre">Transformable</span></code></a><ul class="nav section-nav flex-column">
-<li class="toc-h3 nav-item toc-entry"><a class="reference internal nav-link" href="#arbdmodel.core_objects.Transformable.position"><code class="docutils literal notranslate"><span class="pre">Transformable.position</span></code></a></li>
-<li class="toc-h3 nav-item toc-entry"><a class="reference internal nav-link" href="#arbdmodel.core_objects.Transformable.orientation"><code class="docutils literal notranslate"><span class="pre">Transformable.orientation</span></code></a></li>
-<li class="toc-h3 nav-item toc-entry"><a class="reference internal nav-link" href="#arbdmodel.core_objects.Transformable.translate"><code class="docutils literal notranslate"><span class="pre">Transformable.translate()</span></code></a></li>
+<li class="toc-h3 nav-item toc-entry"><a class="reference internal nav-link" href="#arbdmodel.core_objects.Transformable.applyOrientation"><code class="docutils literal notranslate"><span class="pre">Transformable.applyOrientation()</span></code></a></li>
+<li class="toc-h3 nav-item toc-entry"><a class="reference internal nav-link" href="#arbdmodel.core_objects.Transformable.get_collapsed_position"><code class="docutils literal notranslate"><span class="pre">Transformable.get_collapsed_position()</span></code></a></li>
<li class="toc-h3 nav-item toc-entry"><a class="reference internal nav-link" href="#arbdmodel.core_objects.Transformable.rotate"><code class="docutils literal notranslate"><span class="pre">Transformable.rotate()</span></code></a></li>
<li class="toc-h3 nav-item toc-entry"><a class="reference internal nav-link" href="#arbdmodel.core_objects.Transformable.transform"><code class="docutils literal notranslate"><span class="pre">Transformable.transform()</span></code></a></li>
-<li class="toc-h3 nav-item toc-entry"><a class="reference internal nav-link" href="#arbdmodel.core_objects.Transformable.get_collapsed_position"><code class="docutils literal notranslate"><span class="pre">Transformable.get_collapsed_position()</span></code></a></li>
-<li class="toc-h3 nav-item toc-entry"><a class="reference internal nav-link" href="#arbdmodel.core_objects.Transformable.applyOrientation"><code class="docutils literal notranslate"><span class="pre">Transformable.applyOrientation()</span></code></a></li>
-<li class="toc-h3 nav-item toc-entry"><a class="reference internal nav-link" href="#id6"><code class="docutils literal notranslate"><span class="pre">Transformable.applyOrientation()</span></code></a></li>
-<li class="toc-h3 nav-item toc-entry"><a class="reference internal nav-link" href="#id7"><code class="docutils literal notranslate"><span class="pre">Transformable.get_collapsed_position()</span></code></a></li>
-<li class="toc-h3 nav-item toc-entry"><a class="reference internal nav-link" href="#id8"><code class="docutils literal notranslate"><span class="pre">Transformable.rotate()</span></code></a></li>
-<li class="toc-h3 nav-item toc-entry"><a class="reference internal nav-link" href="#id9"><code class="docutils literal notranslate"><span class="pre">Transformable.transform()</span></code></a></li>
-<li class="toc-h3 nav-item toc-entry"><a class="reference internal nav-link" href="#id10"><code class="docutils literal notranslate"><span class="pre">Transformable.translate()</span></code></a></li>
+<li class="toc-h3 nav-item toc-entry"><a class="reference internal nav-link" href="#arbdmodel.core_objects.Transformable.translate"><code class="docutils literal notranslate"><span class="pre">Transformable.translate()</span></code></a></li>
</ul>
</li>
</ul>
diff --git a/_build/html/api/core/sim_config.html b/_build/html/api/core/sim_config.html
index 42da4aa34d302f58d0dadc5faa2cb246ca616252..e96076b75c2ea777540df5adfdb25e04485fc82e 100644
--- a/_build/html/api/core/sim_config.html
+++ b/_build/html/api/core/sim_config.html
@@ -347,42 +347,15 @@ 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.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.combine"><code class="docutils literal notranslate"><span class="pre">SimConf.combine()</span></code></a></li>
<li class="toc-h3 nav-item toc-entry"><a class="reference internal nav-link" href="#arbdmodel.sim_config.SimConf.get_binary"><code class="docutils literal notranslate"><span class="pre">SimConf.get_binary()</span></code></a></li>
<li class="toc-h3 nav-item toc-entry"><a class="reference internal nav-link" href="#arbdmodel.sim_config.SimConf.items"><code class="docutils literal notranslate"><span class="pre">SimConf.items()</span></code></a></li>
<li class="toc-h3 nav-item toc-entry"><a class="reference internal nav-link" href="#arbdmodel.sim_config.SimConf.set_binary"><code class="docutils literal notranslate"><span class="pre">SimConf.set_binary()</span></code></a></li>
-<li class="toc-h3 nav-item toc-entry"><a class="reference internal nav-link" href="#id1"><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.temperature"><code class="docutils literal notranslate"><span class="pre">SimConf.temperature</span></code></a></li>
</ul>
</li>
</ul>
@@ -412,121 +385,43 @@ 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>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>) – 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>) – 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 ns, 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>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>) – 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>) – 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>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>) – 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>) – 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>) – Number of heavy atoms per cluster, default 3.</p></li>
<li><p><strong>**kwargs</strong> – Additional keyword arguments to pass to SimConf.</p></li>
+<li><p><strong>num_steps</strong> – Number of simulation steps.</p></li>
+<li><p><strong>output_period</strong> – Period for output generation.</p></li>
+<li><p><strong>pressure</strong> – Pressure value for barostat if used.</p></li>
+<li><p><strong>viscosity</strong> – Solvent viscosity.</p></li>
+<li><p><strong>solvent_density</strong> – Density of the solvent.</p></li>
+<li><p><strong>num_heavy_cluster</strong> – Number of heavy atoms per cluster.</p></li>
+<li><p><strong>Properties</strong></p></li>
+<li><p><strong>----------</strong></p></li>
+<li><p><strong>temperature</strong> – Simulation temperature with validation (must be positive).</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">
-<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>
+<dt class="sig sig-object py" id="arbdmodel.sim_config.DefaultSimConf.temperature">
+<em class="property"><span class="pre">property</span><span class="w"> </span></em><span class="sig-name descname"><span class="pre">temperature</span></span><a class="headerlink" href="#arbdmodel.sim_config.DefaultSimConf.temperature" title="Link to this definition">#</a></dt>
<dd></dd></dl>
</dd></dl>
@@ -538,225 +433,33 @@ Essential binaries (currently only ‘arbd’) will generate warnings if not fou
<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. in g/cm^3</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>
+<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#int" title="(in Python v3.13)"><em>int</em></a>) – Total number of simulation steps.</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#int" title="(in Python v3.13)"><em>int</em></a>) – Frequency of output generation.</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>) – Type of integrator used (e.g., ‘MD’, ‘BD’).</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>) – Simulation time step.</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>) – Type of thermostat used.</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>) – Type of barostat used.</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>) – Simulation temperature (must be positive).</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>) – Simulation pressure.</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>) – Cutoff distance for interactions.</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>) – Distance for generating pair lists.</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>) – Period for decomposition.</p></li>
+<li><p><strong>gpu</strong> (<a class="hxr-hoverxref hxr-tooltip reference external" href="https://docs.python.org/3/library/functions.html#bool" title="(in Python v3.13)"><em>bool</em></a>) – Whether to use GPU acceleration.</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>) – Random seed for reproducibility.</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>) – Path to restart file.</p></li>
+<li><p><strong>parameters</strong> (<em># SimpleARBD</em>)</p></li>
+<li><p><strong>rigid_body_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>) – Type of rigid body integrator.</p></li>
+<li><p><strong>rigid_body_grid_grid_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>) – Period for rigid body grid updates.</p></li>
+<li><p><strong>parameters</strong></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>) – Solvent viscosity.</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>) – Solvent density. in g/cm^3</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>) – Number of heavy clusters.</p></li>
+</ul>
</dd>
</dl>
-</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>
@@ -843,8 +546,8 @@ with the specified file path.</p>
</dd></dl>
<dl class="py property">
-<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">temperature</span></span><a class="headerlink" href="#id1" title="Link to this definition">#</a></dt>
+<dt class="sig sig-object py" id="arbdmodel.sim_config.SimConf.temperature">
+<em class="property"><span class="pre">property</span><span class="w"> </span></em><span class="sig-name descname"><span class="pre">temperature</span></span><a class="headerlink" href="#arbdmodel.sim_config.SimConf.temperature" title="Link to this definition">#</a></dt>
<dd></dd></dl>
</dd></dl>
@@ -898,42 +601,15 @@ with the specified file path.</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.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.combine"><code class="docutils literal notranslate"><span class="pre">SimConf.combine()</span></code></a></li>
<li class="toc-h3 nav-item toc-entry"><a class="reference internal nav-link" href="#arbdmodel.sim_config.SimConf.get_binary"><code class="docutils literal notranslate"><span class="pre">SimConf.get_binary()</span></code></a></li>
<li class="toc-h3 nav-item toc-entry"><a class="reference internal nav-link" href="#arbdmodel.sim_config.SimConf.items"><code class="docutils literal notranslate"><span class="pre">SimConf.items()</span></code></a></li>
<li class="toc-h3 nav-item toc-entry"><a class="reference internal nav-link" href="#arbdmodel.sim_config.SimConf.set_binary"><code class="docutils literal notranslate"><span class="pre">SimConf.set_binary()</span></code></a></li>
-<li class="toc-h3 nav-item toc-entry"><a class="reference internal nav-link" href="#id1"><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.temperature"><code class="docutils literal notranslate"><span class="pre">SimConf.temperature</span></code></a></li>
</ul>
</li>
</ul>
diff --git a/_build/html/api/interaction_potentials/ibi.html b/_build/html/api/interaction_potentials/ibi.html
index 70e23713c94ec99787de9a908ebc728de8d38cb2..e19662427c767812a5e86fd79fcc26b87ddceda2 100644
--- a/_build/html/api/interaction_potentials/ibi.html
+++ b/_build/html/api/interaction_potentials/ibi.html
@@ -545,7 +545,29 @@ The process involves:
<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><p>Write potential energy values as a function of distance to a file.</p>
+<p>This method evaluates the potential function over a range of distances and writes
+the distance-potential pairs to a text file.</p>
+<dl class="field-list simple">
+<dt class="field-odd">Parameters<span class="colon">:</span></dt>
+<dd class="field-odd"><ul class="simple">
+<li><p><strong>filename</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>) – The path to the output file. If None, a default filename will be generated using
+the <cite>filename</cite> method with the given types.</p></li>
+<li><p><strong>types</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> or </em><a class="hxr-hoverxref hxr-tooltip reference external" href="https://docs.python.org/3/library/stdtypes.html#list" title="(in Python v3.13)"><em>list</em></a><em>, </em><em>optional</em>) – The particle types for which to calculate the potential. Used for both filename
+generation (if filename is None) and potential evaluation. If None, defaults to
+the types defined in the interaction model.</p></li>
+</ul>
+</dd>
+</dl>
+<div class="admonition note">
+<p class="admonition-title">Note</p>
+<p>The potential values are capped using the <cite>_cap_potential</cite> method to handle
+potential singularities or extreme values. The output file contains two columns:
+distance (r) and potential energy (u).</p>
+<p>Any ‘divide by zero’ or ‘invalid value’ numpy warnings are ignored during
+the potential calculation.</p>
+</div>
+</dd></dl>
</dd></dl>
@@ -646,7 +668,29 @@ pairs of particle types (with exclusions!).</p>
<dl class="py method">
<dt class="sig sig-object py" id="arbdmodel.ibi.IBINonbonded.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/ibi.html#IBINonbonded.write_file"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#arbdmodel.ibi.IBINonbonded.write_file" title="Link to this definition">#</a></dt>
-<dd></dd></dl>
+<dd><p>Write potential energy values as a function of distance to a file.</p>
+<p>This method evaluates the potential function over a range of distances and writes
+the distance-potential pairs to a text file.</p>
+<dl class="field-list simple">
+<dt class="field-odd">Parameters<span class="colon">:</span></dt>
+<dd class="field-odd"><ul class="simple">
+<li><p><strong>filename</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>) – The path to the output file. If None, a default filename will be generated using
+the <cite>filename</cite> method with the given types.</p></li>
+<li><p><strong>types</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> or </em><a class="hxr-hoverxref hxr-tooltip reference external" href="https://docs.python.org/3/library/stdtypes.html#list" title="(in Python v3.13)"><em>list</em></a><em>, </em><em>optional</em>) – The particle types for which to calculate the potential. Used for both filename
+generation (if filename is None) and potential evaluation. If None, defaults to
+the types defined in the interaction model.</p></li>
+</ul>
+</dd>
+</dl>
+<div class="admonition note">
+<p class="admonition-title">Note</p>
+<p>The potential values are capped using the <cite>_cap_potential</cite> method to handle
+potential singularities or extreme values. The output file contains two columns:
+distance (r) and potential energy (u).</p>
+<p>Any ‘divide by zero’ or ‘invalid value’ numpy warnings are ignored during
+the potential calculation.</p>
+</div>
+</dd></dl>
</dd></dl>
diff --git a/_build/html/api/interaction_potentials/interactions.html b/_build/html/api/interaction_potentials/interactions.html
index 6958a868e90b6e7e88b6d2c9fea8a7f3d5fa7890..a3db873462ea8e9f749b656a7306586263b083ae 100644
--- a/_build/html/api/interaction_potentials/interactions.html
+++ b/_build/html/api/interaction_potentials/interactions.html
@@ -347,20 +347,11 @@ 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.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.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.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">
@@ -449,14 +440,12 @@ document.write(`
<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 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>
+functions that can be written to files and used in simulations.</p>
<dl class="field-list simple">
<dt class="field-odd">Parameters<span class="colon">:</span></dt>
<dd class="field-odd"><ul class="simple">
+<li><p><strong>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> of </em><em>(</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><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>) – The range of distances for the potential (min, max).
+If max is None, potential extends to infinity.</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 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
@@ -465,121 +454,60 @@ to ensure it doesn’t exceed this value.</p></li>
- ‘min’: Zero is at the minimum value
- ‘first’: Zero is at the first point
- ‘last’: Zero is at the last point</p></li>
+<li><p><strong>periodic</strong> (<a class="hxr-hoverxref hxr-tooltip reference external" href="https://docs.python.org/3/library/functions.html#bool" title="(in Python v3.13)"><em>bool</em></a>) – Whether the potential is periodic (False by default).</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>
-
+<div class="admonition note">
+<p class="admonition-title">Note</p>
+<p>Subclasses must implement at minimum the <cite>potential</cite> and <cite>filename</cite> methods.</p>
+</div>
<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="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>
+<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>
<dd></dd></dl>
<dl class="py method">
-<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>
+<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>
<dd></dd></dl>
<dl class="py property">
-<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>
+<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>
<dd></dd></dl>
<dl class="py method">
-<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>
+<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>Write potential energy values as a function of distance to a file.</p>
+<p>This method evaluates the potential function over a range of distances and writes
+the distance-potential pairs to a text file.</p>
+<dl class="field-list simple">
+<dt class="field-odd">Parameters<span class="colon">:</span></dt>
+<dd class="field-odd"><ul class="simple">
+<li><p><strong>filename</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>) – The path to the output file. If None, a default filename will be generated using
+the <cite>filename</cite> method with the given types.</p></li>
+<li><p><strong>types</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> or </em><a class="hxr-hoverxref hxr-tooltip reference external" href="https://docs.python.org/3/library/stdtypes.html#list" title="(in Python v3.13)"><em>list</em></a><em>, </em><em>optional</em>) – The particle types for which to calculate the potential. Used for both filename
+generation (if filename is None) and potential evaluation. If None, defaults to
+the types defined in the interaction model.</p></li>
+</ul>
+</dd>
+</dl>
+<div class="admonition note">
+<p class="admonition-title">Note</p>
+<p>The potential values are capped using the <cite>_cap_potential</cite> method to handle
+potential singularities or extreme values. The output file contains two columns:
+distance (r) and potential energy (u).</p>
+<p>Any ‘divide by zero’ or ‘invalid value’ numpy warnings are ignored during
+the potential calculation.</p>
+</div>
+</dd></dl>
</dd></dl>
@@ -754,7 +682,29 @@ for consistency with the AbstractPotential interface.</p>
<dl class="py method">
<dt class="sig sig-object py" id="arbdmodel.interactions.TabulatedNonbonded.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></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/interactions.html#TabulatedNonbonded.write_file"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#arbdmodel.interactions.TabulatedNonbonded.write_file" title="Link to this definition">#</a></dt>
-<dd></dd></dl>
+<dd><p>Write potential energy values as a function of distance to a file.</p>
+<p>This method evaluates the potential function over a range of distances and writes
+the distance-potential pairs to a text file.</p>
+<dl class="field-list simple">
+<dt class="field-odd">Parameters<span class="colon">:</span></dt>
+<dd class="field-odd"><ul class="simple">
+<li><p><strong>filename</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>) – The path to the output file. If None, a default filename will be generated using
+the <cite>filename</cite> method with the given types.</p></li>
+<li><p><strong>types</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> or </em><a class="hxr-hoverxref hxr-tooltip reference external" href="https://docs.python.org/3/library/stdtypes.html#list" title="(in Python v3.13)"><em>list</em></a><em>, </em><em>optional</em>) – The particle types for which to calculate the potential. Used for both filename
+generation (if filename is None) and potential evaluation. If None, defaults to
+the types defined in the interaction model.</p></li>
+</ul>
+</dd>
+</dl>
+<div class="admonition note">
+<p class="admonition-title">Note</p>
+<p>The potential values are capped using the <cite>_cap_potential</cite> method to handle
+potential singularities or extreme values. The output file contains two columns:
+distance (r) and potential energy (u).</p>
+<p>Any ‘divide by zero’ or ‘invalid value’ numpy warnings are ignored during
+the potential calculation.</p>
+</div>
+</dd></dl>
</dd></dl>
@@ -853,20 +803,11 @@ 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.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.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.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/onck_polymer_model.html b/_build/html/api/polymer_modeling/onck_polymer_model.html
index c651531d7bd453cbdec2b018f6174643f67e415c..2fc5a85d927c46950ccf91536c7a4db4bc377c5d 100644
--- a/_build/html/api/polymer_modeling/onck_polymer_model.html
+++ b/_build/html/api/polymer_modeling/onck_polymer_model.html
@@ -346,24 +346,13 @@ 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><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.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.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>
@@ -397,93 +386,60 @@ based on the amino acid types in the sequence.</p>
<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>
+<li><p><strong>types_dict</strong> (<a class="hxr-hoverxref hxr-tooltip reference external" href="https://docs.python.org/3/library/stdtypes.html#dict" title="(in Python v3.13)"><em>dict</em></a>) – Mapping between amino acid codes and bead types.</p></li>
+<li><p><strong>peptide_bond</strong> (<a class="reference internal" href="../interaction_potentials/interactions.html#arbdmodel.interactions.HarmonicBond" title="arbdmodel.interactions.HarmonicBond"><em>HarmonicBond</em></a>) – Bond potential used for peptide bonds between adjacent beads.</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">
+<dt class="field-even">Raises<span class="colon">:</span></dt>
+<dd class="field-even"><ul class="simple">
<li><p><a class="hxr-hoverxref hxr-tooltip reference external" href="https://docs.python.org/3/library/exceptions.html#ValueError" title="(in Python v3.13)"><strong>ValueError</strong></a> – If the 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>
+<div class="admonition note">
+<p class="admonition-title">Note</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>
+</div>
</dd></dl>
<dl class="py class">
<dt class="sig sig-object py" id="arbdmodel.onck_polymer_model.OnckModel">
<em class="property"><span class="pre">class</span><span class="w"> </span></em><span class="sig-name descname"><span class="pre">OnckModel</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">polymers</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">sequences</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">debye_length</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">10</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">damping_coefficient</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">100</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="n"><span class="pre">DEBUG</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">False</span></span></em>, <em class="sig-param"><span class="o"><span class="pre">**</span></span><span class="n"><span class="pre">kwargs</span></span></em><span class="sig-paren">)</span><a class="reference internal" href="../../_modules/arbdmodel/onck_polymer_model.html#OnckModel"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#arbdmodel.onck_polymer_model.OnckModel" title="Link to this definition">#</a></dt>
<dd><p>Bases: <a class="reference internal" href="polymer.html#arbdmodel.polymer.PolymerModel" title="arbdmodel.polymer.PolymerModel"><code class="xref py py-class docutils literal notranslate"><span class="pre">PolymerModel</span></code></a></p>
+<p>A polymer model based on Onck’s coarse-grained model for disordered FG-Nup peptides.</p>
+<p>The OnckModel class implements a coarse-grained model of polymers based on the work by Onck et al.
+This model is specifically designed for disordered FG-Nup peptides and incorporates
+electrostatic interactions through a Debye-Hückel potential.</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>polymers</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 polymers to be modeled.</p></li>
+<li><p><strong>sequences</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>) – List of amino acid sequences corresponding to each polymer.
+Must be provided. Default is None.</p></li>
+<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>) – Debye screening length in angstroms. Default is 10.</p></li>
+<li><p><strong>damping_coefficient</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>) – Damping coefficient in ns. Default is 100.</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. Default is 1.1 (corresponding to 1BPA-1.1 from 2023).</p></li>
+<li><p><strong>DEBUG</strong> (<a class="hxr-hoverxref hxr-tooltip reference external" href="https://docs.python.org/3/library/functions.html#bool" title="(in Python v3.13)"><em>bool</em></a><em>, </em><em>optional</em>) – Whether to enable debug mode. Default is False.</p></li>
+<li><p><strong>**kwargs</strong> (<a class="hxr-hoverxref hxr-tooltip reference external" href="https://docs.python.org/3/library/stdtypes.html#dict" title="(in Python v3.13)"><em>dict</em></a>) – Additional keyword arguments to pass to the parent PolymerModel class.
+Common options include:
+- timestep: Simulation timestep (default: 20e-6)
+- cutoff: Cutoff distance for non-bonded interactions (default: max(5*debye_length, 25))
+- decomp_period: Decomposition period (default: 1000)</p></li>
+<li><p><strong>types_dict</strong> (<a class="hxr-hoverxref hxr-tooltip reference external" href="https://docs.python.org/3/library/stdtypes.html#dict" title="(in Python v3.13)"><em>dict</em></a>) – Dictionary mapping from type keys to type objects for the given version.</p></li>
+<li><p><strong>types</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 all types used in the model.</p></li>
+</ul>
+</dd>
+</dl>
+<div class="admonition note">
+<p class="admonition-title">Note</p>
+<p>The model differs from the published Onck model if a Debye length other than 12.7 Ã… is chosen.
+In such cases, the non-bonded cutoff is set to 5 * debye_length.</p>
+</div>
+<p class="rubric">References</p>
+<p>Please refer to the citations displayed during initialization.</p>
<dl class="py method">
<dt class="sig sig-object py" id="arbdmodel.onck_polymer_model.OnckModel.set_damping_coefficient">
<span class="sig-name descname"><span class="pre">set_damping_coefficient</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">damping_coefficient</span></span></em><span class="sig-paren">)</span><a class="reference internal" href="../../_modules/arbdmodel/onck_polymer_model.html#OnckModel.set_damping_coefficient"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#arbdmodel.onck_polymer_model.OnckModel.set_damping_coefficient" title="Link to this definition">#</a></dt>
@@ -504,38 +460,12 @@ distance-dependent dielectric and Lennard-Jones type potentials.</p>
<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 Å.</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 Å.</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>
+<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>) – Maximum allowed force in the system, used as a cap for stability. Default is 50</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>
+<div class="admonition note">
+<p class="admonition-title">Note</p>
<p>The potential includes:
1. Electrostatic interactions with distance-dependent dielectric constant
2. Modified Lennard-Jones interactions that depend on residue types:</p>
@@ -546,9 +476,10 @@ distance-dependent dielectric and Lennard-Jones type potentials.</p>
</ul>
</div></blockquote>
<p>The effective dielectric D decreases with distance according to a specific formula.</p>
+</div>
<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>
+<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>Electrostatics</p>
</dd></dl>
@@ -602,24 +533,13 @@ distance-dependent dielectric and Lennard-Jones type potentials.</p>
</div>
<nav class="bd-toc-nav page-toc">
<ul class="visible nav section-nav flex-column">
-<li class="toc-h2 nav-item toc-entry"><a class="reference internal nav-link" href="#arbdmodel.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.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.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/simulation_engines/parmed_bd.html b/_build/html/api/simulation_engines/parmed_bd.html
index c99edfd8f447345fac7e5e3226c42f3f934362ee..45e48f1f19e19066a7c9f9a8db13c4e3827c8108 100644
--- a/_build/html/api/simulation_engines/parmed_bd.html
+++ b/_build/html/api/simulation_engines/parmed_bd.html
@@ -347,9 +347,6 @@ 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.parmed_bd.ParmedArbd"><code class="docutils literal notranslate"><span class="pre">ParmedArbd</span></code></a><ul class="nav section-nav flex-column">
-<li class="toc-h3 nav-item toc-entry"><a class="reference internal nav-link" href="#arbdmodel.parmed_bd.ParmedArbd.parmed_structure"><code class="docutils literal notranslate"><span class="pre">ParmedArbd.parmed_structure</span></code></a></li>
-<li class="toc-h3 nav-item toc-entry"><a class="reference internal nav-link" href="#arbdmodel.parmed_bd.ParmedArbd.atom_types"><code class="docutils literal notranslate"><span class="pre">ParmedArbd.atom_types</span></code></a></li>
-<li class="toc-h3 nav-item toc-entry"><a class="reference internal nav-link" href="#arbdmodel.parmed_bd.ParmedArbd.atoms_map"><code class="docutils literal notranslate"><span class="pre">ParmedArbd.atoms_map</span></code></a></li>
<li class="toc-h3 nav-item toc-entry"><a class="reference internal nav-link" href="#arbdmodel.parmed_bd.ParmedArbd.convert_sod_to_mg"><code class="docutils literal notranslate"><span class="pre">ParmedArbd.convert_sod_to_mg()</span></code></a></li>
<li class="toc-h3 nav-item toc-entry"><a class="reference internal nav-link" href="#arbdmodel.parmed_bd.ParmedArbd.create_dual_topology"><code class="docutils literal notranslate"><span class="pre">ParmedArbd.create_dual_topology()</span></code></a></li>
<li class="toc-h3 nav-item toc-entry"><a class="reference internal nav-link" href="#arbdmodel.parmed_bd.ParmedArbd.create_dual_topology_model"><code class="docutils literal notranslate"><span class="pre">ParmedArbd.create_dual_topology_model()</span></code></a></li>
@@ -380,24 +377,15 @@ document.write(`
<p>This class facilitates the conversion of molecular structures loaded with ParmEd
into ARBD simulation models, preserving bonded and non-bonded interactions.
It also supports creating dual topology models for free energy calculations.</p>
-<dl class="py attribute">
-<dt class="sig sig-object py" id="arbdmodel.parmed_bd.ParmedArbd.parmed_structure">
-<span class="sig-name descname"><span class="pre">parmed_structure</span></span><a class="headerlink" href="#arbdmodel.parmed_bd.ParmedArbd.parmed_structure" title="Link to this definition">#</a></dt>
-<dd><p>The original ParmEd structure</p>
-</dd></dl>
-
-<dl class="py attribute">
-<dt class="sig sig-object py" id="arbdmodel.parmed_bd.ParmedArbd.atom_types">
-<span class="sig-name descname"><span class="pre">atom_types</span></span><a class="headerlink" href="#arbdmodel.parmed_bd.ParmedArbd.atom_types" title="Link to this definition">#</a></dt>
-<dd><p>Dictionary mapping atom type names to ParticleType objects</p>
-</dd></dl>
-
-<dl class="py attribute">
-<dt class="sig sig-object py" id="arbdmodel.parmed_bd.ParmedArbd.atoms_map">
-<span class="sig-name descname"><span class="pre">atoms_map</span></span><a class="headerlink" href="#arbdmodel.parmed_bd.ParmedArbd.atoms_map" title="Link to this definition">#</a></dt>
-<dd><p>Mapping from ParmEd atoms to ARBD atoms</p>
-</dd></dl>
-
+<dl class="field-list simple">
+<dt class="field-odd">Parameters<span class="colon">:</span></dt>
+<dd class="field-odd"><ul class="simple">
+<li><p><strong>parmed_structure</strong> – The original ParmEd structure</p></li>
+<li><p><strong>atom_types</strong> – Dictionary mapping atom type names to ParticleType objects</p></li>
+<li><p><strong>atoms_map</strong> – Mapping from ParmEd atoms to ARBD atoms</p></li>
+</ul>
+</dd>
+</dl>
<dl class="py method">
<dt class="sig sig-object py" id="arbdmodel.parmed_bd.ParmedArbd.convert_sod_to_mg">
<em class="property"><span class="pre">static</span><span class="w"> </span></em><span class="sig-name descname"><span class="pre">convert_sod_to_mg</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">structure</span></span></em><span class="sig-paren">)</span><a class="reference internal" href="../../_modules/arbdmodel/parmed_bd.html#ParmedArbd.convert_sod_to_mg"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#arbdmodel.parmed_bd.ParmedArbd.convert_sod_to_mg" title="Link to this definition">#</a></dt>
@@ -560,9 +548,6 @@ It also supports creating dual topology models for free energy calculations.</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.parmed_bd.ParmedArbd"><code class="docutils literal notranslate"><span class="pre">ParmedArbd</span></code></a><ul class="nav section-nav flex-column">
-<li class="toc-h3 nav-item toc-entry"><a class="reference internal nav-link" href="#arbdmodel.parmed_bd.ParmedArbd.parmed_structure"><code class="docutils literal notranslate"><span class="pre">ParmedArbd.parmed_structure</span></code></a></li>
-<li class="toc-h3 nav-item toc-entry"><a class="reference internal nav-link" href="#arbdmodel.parmed_bd.ParmedArbd.atom_types"><code class="docutils literal notranslate"><span class="pre">ParmedArbd.atom_types</span></code></a></li>
-<li class="toc-h3 nav-item toc-entry"><a class="reference internal nav-link" href="#arbdmodel.parmed_bd.ParmedArbd.atoms_map"><code class="docutils literal notranslate"><span class="pre">ParmedArbd.atoms_map</span></code></a></li>
<li class="toc-h3 nav-item toc-entry"><a class="reference internal nav-link" href="#arbdmodel.parmed_bd.ParmedArbd.convert_sod_to_mg"><code class="docutils literal notranslate"><span class="pre">ParmedArbd.convert_sod_to_mg()</span></code></a></li>
<li class="toc-h3 nav-item toc-entry"><a class="reference internal nav-link" href="#arbdmodel.parmed_bd.ParmedArbd.create_dual_topology"><code class="docutils literal notranslate"><span class="pre">ParmedArbd.create_dual_topology()</span></code></a></li>
<li class="toc-h3 nav-item toc-entry"><a class="reference internal nav-link" href="#arbdmodel.parmed_bd.ParmedArbd.create_dual_topology_model"><code class="docutils literal notranslate"><span class="pre">ParmedArbd.create_dual_topology_model()</span></code></a></li>
diff --git a/_build/html/api/utilities/binary_manager.html b/_build/html/api/utilities/binary_manager.html
index d58cef4febe39c4931d90e0bcd774081f445d1f9..3a819325c1b18a3deac10723136107dc7a8df31b 100644
--- a/_build/html/api/utilities/binary_manager.html
+++ b/_build/html/api/utilities/binary_manager.html
@@ -360,20 +360,19 @@ document.write(`
<section class="tex2jax_ignore mathjax_ignore" id="binary-manager">
<h1>binary_manager<a class="headerlink" href="#binary-manager" title="Link to this heading">#</a></h1>
-<p>Binary path management module for simulation engines and processors.
-This module provides a singleton object to manage paths to external binaries.</p>
-<p id="module-arbdmodel.binary_manager">Binary path management module for simulation engines and processors.
-This module provides a singleton object to manage paths to external binaries.</p>
-<dl class="py function">
+<p>Module documentation for <code class="docutils literal notranslate"><span class="pre">arbdmodel.binary_manager</span></code>.</p>
+<dl class="py function" id="module-arbdmodel.binary_manager">
<dt class="sig sig-object py" id="arbdmodel.binary_manager.initialize_binary_paths">
<span class="sig-name descname"><span class="pre">initialize_binary_paths</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="reference internal" href="../../_modules/arbdmodel/binary_manager.html#initialize_binary_paths"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#arbdmodel.binary_manager.initialize_binary_paths" title="Link to this definition">#</a></dt>
<dd><p>Initialize binary paths from environment variables.
This function should be called during package initialization.
If users don’t wish to call this function, they can set the paths manually.</p>
-<p>Example:
->>arbd_path = BinaryManager.get_binary_path(“arbdâ€)
->>print(fâ€ARBD binary path: {arbd_path}â€)</p>
-<p>>>BinaryManager.set_binary_path(“hydroproâ€, “/path/to/hydroproâ€)</p>
+<p class="rubric">Example</p>
+<div class="doctest highlight-default notranslate"><div class="highlight"><pre><span></span><span class="gp">>>> </span><span class="n">arbd_path</span> <span class="o">=</span> <span class="n">BinaryManager</span><span class="o">.</span><span class="n">get_binary_path</span><span class="p">(</span><span class="s2">"arbd"</span><span class="p">)</span>
+<span class="gp">>>> </span><span class="nb">print</span><span class="p">(</span><span class="sa">f</span><span class="s2">"ARBD binary path: </span><span class="si">{</span><span class="n">arbd_path</span><span class="si">}</span><span class="s2">"</span><span class="p">)</span>
+<span class="gp">>>> </span><span class="n">BinaryManager</span><span class="o">.</span><span class="n">set_binary_path</span><span class="p">(</span><span class="s2">"hydropro"</span><span class="p">,</span> <span class="s2">"/path/to/hydropro"</span><span class="p">)</span>
+</pre></div>
+</div>
</dd></dl>
</section>
diff --git a/_build/html/api/utilities/grid.html b/_build/html/api/utilities/grid.html
index 1ecb2a8ad6d224182447100caa4e404c7c75b3be..11e2d8f237f2bd50d7397773a616bbd604b61384 100644
--- a/_build/html/api/utilities/grid.html
+++ b/_build/html/api/utilities/grid.html
@@ -417,27 +417,25 @@ document.write(`
<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>grids</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> of </em><em>ndarrays</em>) – The input grids to average.</p></li>
-<li><p><strong>mask</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>) – The mask type to use for averaging. If ‘nan’, only non-NaN values are considered. Default is ‘nan’.</p></li>
+<li><p><strong>grids</strong> (<a class="hxr-hoverxref hxr-tooltip reference external" href="https://docs.python.org/3/library/functions.html#type" title="(in Python v3.13)"><em>type</em></a>)</p></li>
+<li><p><strong>grids</strong></p></li>
+<li><p><strong>mask</strong> (<a class="hxr-hoverxref hxr-tooltip reference external" href="https://docs.python.org/3/library/functions.html#type" title="(in Python v3.13)"><em>type</em></a>)</p></li>
+<li><p><strong>mask</strong></p></li>
+<li><p><strong>return</strong> (<em>The average grid.</em>)</p></li>
+<li><p><strong>rtype</strong> (<em>ndarray</em>)</p></li>
+<li><p><strong>NotImplementedError</strong> (<em>raises</em>)</p></li>
</ul>
</dd>
-<dt class="field-even">Returns<span class="colon">:</span></dt>
-<dd class="field-even"><p>The average grid.</p>
-</dd>
-<dt class="field-odd">Return type<span class="colon">:</span></dt>
-<dd class="field-odd"><p>ndarray</p>
-</dd>
-<dt class="field-even">Raises<span class="colon">:</span></dt>
-<dd class="field-even"><p><a class="hxr-hoverxref hxr-tooltip reference external" href="https://docs.python.org/3/library/exceptions.html#NotImplementedError" title="(in Python v3.13)"><strong>NotImplementedError</strong></a> – If the mask option is not implemented.</p>
-</dd>
</dl>
-<p class="rubric">Example</p>
+<section id="example">
+<h2>Example:<a class="headerlink" href="#example" title="Link to this heading">#</a></h2>
<div class="doctest highlight-default notranslate"><div class="highlight"><pre><span></span><span class="gp">>>> </span><span class="n">grid1</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">2</span><span class="p">,</span> <span class="mi">3</span><span class="p">],</span> <span class="p">[</span><span class="mi">4</span><span class="p">,</span> <span class="mi">5</span><span class="p">,</span> <span class="mi">6</span><span class="p">],</span> <span class="p">[</span><span class="mi">7</span><span class="p">,</span> <span class="mi">8</span><span class="p">,</span> <span class="mi">9</span><span class="p">]])</span>
<span class="gp">>>> </span><span class="n">grid2</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">2</span><span class="p">,</span> <span class="mi">4</span><span class="p">,</span> <span class="mi">6</span><span class="p">],</span> <span class="p">[</span><span class="mi">8</span><span class="p">,</span> <span class="mi">10</span><span class="p">,</span> <span class="mi">12</span><span class="p">],</span> <span class="p">[</span><span class="mi">14</span><span class="p">,</span> <span class="mi">16</span><span class="p">,</span> <span class="mi">18</span><span class="p">]])</span>
<span class="gp">>>> </span><span class="n">averaged_grid</span> <span class="o">=</span> <span class="n">average_grids</span><span class="p">([</span><span class="n">grid1</span><span class="p">,</span> <span class="n">grid2</span><span class="p">],</span> <span class="n">mask</span><span class="o">=</span><span class="s1">'nan'</span><span class="p">)</span>
<span class="gp">>>> </span><span class="nb">print</span><span class="p">(</span><span class="n">averaged_grid</span><span class="p">)</span>
</pre></div>
</div>
+</section>
</dd></dl>
<dl class="py function">
diff --git a/_build/html/api/utilities/index.html b/_build/html/api/utilities/index.html
index 4ce4aa5d8948d249a1cfeb912f46af5b89c85dd4..dbe3c69cccbed4ca788dae975c5ffd250f2fa24c 100644
--- a/_build/html/api/utilities/index.html
+++ b/_build/html/api/utilities/index.html
@@ -363,7 +363,7 @@ document.write(`
<section id="modules">
<h2>Modules<a class="headerlink" href="#modules" title="Link to this heading">#</a></h2>
<ul class="simple">
-<li><p><a class="reference internal" href="binary_manager.html"><span class="std std-doc">binary_manager</span></a>: Binary path management module for simulation engines and processors.</p></li>
+<li><p><a class="reference internal" href="binary_manager.html"><span class="std std-doc">binary_manager</span></a>: Module documentation for <code class="docutils literal notranslate"><span class="pre">arbdmodel.binary_manager</span></code>.</p></li>
<li><p><a class="reference internal" href="coords.html"><span class="std std-doc">coords</span></a>: Module documentation for <code class="docutils literal notranslate"><span class="pre">arbdmodel.coords</span></code>.</p></li>
<li><p><a class="reference internal" href="grid.html"><span class="std std-doc">grid</span></a>: Module documentation for <code class="docutils literal notranslate"><span class="pre">arbdmodel.grid</span></code>.</p></li>
<li><p><a class="reference internal" href="logger.html"><span class="std std-doc">logger</span></a>: Module documentation for <code class="docutils literal notranslate"><span class="pre">arbdmodel.logger</span></code>.</p></li>
diff --git a/_build/html/genindex.html b/_build/html/genindex.html
index c735476f255624a05fea601c6533820c719e9eb3..dccd252fd8cbf29077282b4961e95882fda0a9cc 100644
--- a/_build/html/genindex.html
+++ b/_build/html/genindex.html
@@ -326,7 +326,6 @@ 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="_">_</h2>
@@ -403,14 +402,12 @@ document.write(`
<li><a href="api/rigidbody_models/structure_from_pdb.html#arbdmodel.structure_from_pdb.StructureProcessor.align_structure">align_structure() (StructureProcessor method)</a>
</li>
<li><a href="api/interaction_potentials/ibi.html#arbdmodel.ibi.AngleDof">AngleDof (class in arbdmodel.ibi)</a>
-</li>
- <li><a href="api/core/core_objects.html#arbdmodel.core_objects.Parent.angles">angles (Parent attribute)</a>
</li>
<li><a href="api/simulation_engines/engine.html#arbdmodel.engine.APBSRunner">APBSRunner (class in arbdmodel.engine)</a>
</li>
<li><a href="api/rigidbody_models/structure_from_pdb.html#arbdmodel.structure_from_pdb.StructureProcessor.apply_gaussian_smoothing">apply_gaussian_smoothing() (StructureProcessor method)</a>
</li>
- <li><a href="api/core/core_objects.html#arbdmodel.core_objects.Transformable.applyOrientation">applyOrientation() (Transformable method)</a>, <a href="api/core/core_objects.html#id6">[1]</a>
+ <li><a href="api/core/core_objects.html#arbdmodel.core_objects.Transformable.applyOrientation">applyOrientation() (Transformable method)</a>
</li>
<li><a href="api/simulation_engines/engine.html#arbdmodel.engine.ArbdEngine">ArbdEngine (class in arbdmodel.engine)</a>
</li>
@@ -458,6 +455,8 @@ document.write(`
<li><a href="api/utilities/grid.html#module-arbdmodel.grid">module</a>
</li>
</ul></li>
+ </ul></td>
+ <td style="width: 33%; vertical-align: top;"><ul>
<li>
arbdmodel.hps_polymer_model
@@ -465,8 +464,6 @@ document.write(`
<li><a href="api/polymer_modeling/hps_polymer_model.html#module-arbdmodel.hps_polymer_model">module</a>
</li>
</ul></li>
- </ul></td>
- <td style="width: 33%; vertical-align: top;"><ul>
<li>
arbdmodel.ibi
@@ -608,19 +605,9 @@ document.write(`
</li>
</ul></li>
<li><a href="api/core/model.html#arbdmodel.model.ArbdModel.assign_IBI_degrees_of_freedom">assign_IBI_degrees_of_freedom() (ArbdModel method)</a>
-</li>
- <li><a href="api/simulation_engines/parmed_bd.html#arbdmodel.parmed_bd.ParmedArbd.atom_types">atom_types (ParmedArbd attribute)</a>
-</li>
- <li><a href="api/simulation_engines/parmed_bd.html#arbdmodel.parmed_bd.ParmedArbd.atoms_map">atoms_map (ParmedArbd attribute)</a>
</li>
<li><a href="api/core/core_objects.html#arbdmodel.core_objects.RigidBodyType.attach_particle">attach_particle() (RigidBodyType method)</a>
</li>
- <li><a href="api/core/core_objects.html#arbdmodel.core_objects.RigidBody.attached_particles">attached_particles (RigidBody attribute)</a>
-
- <ul>
- <li><a href="api/core/core_objects.html#arbdmodel.core_objects.RigidBodyType.attached_particles">(RigidBodyType attribute)</a>
-</li>
- </ul></li>
<li><a href="api/utilities/grid.html#arbdmodel.grid.average_grids">average_grids() (in module arbdmodel.grid)</a>
</li>
</ul></td>
@@ -630,20 +617,14 @@ document.write(`
<table style="width: 100%" class="indextable genindextable"><tr>
<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/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>
- <li><a href="api/core/core_objects.html#arbdmodel.core_objects.Parent.bond_angles">bond_angles (Parent attribute)</a>
+ <li><a href="api/interaction_potentials/ibi.html#arbdmodel.ibi.BondAngleDof">BondAngleDof (class in arbdmodel.ibi)</a>
</li>
</ul></td>
<td style="width: 33%; vertical-align: top;"><ul>
- <li><a href="api/interaction_potentials/ibi.html#arbdmodel.ibi.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/core/core_objects.html#arbdmodel.core_objects.Parent.bonds">bonds (Parent attribute)</a>
</li>
<li><a href="api/utilities/grid.html#arbdmodel.grid.Bound_grid">Bound_grid() (in module arbdmodel.grid)</a>
</li>
@@ -672,21 +653,11 @@ document.write(`
<li><a href="api/shape-based_models/shape_cg.html#arbdmodel.shape_cg.ShapeCGModel.calculate_total_mass">calculate_total_mass() (ShapeCGModel method)</a>
</li>
<li><a href="api/utilities/version.html#arbdmodel.version.call_git_describe">call_git_describe() (in module arbdmodel.version)</a>
-</li>
- <li><a href="api/core/core_objects.html#arbdmodel.core_objects.ParticleType.charge">charge (ParticleType attribute)</a>
-</li>
- <li><a href="api/core/core_objects.html#arbdmodel.core_objects.RigidBodyType.charge_grids">charge_grids (RigidBodyType attribute)</a>
</li>
<li><a href="api/utilities/version.html#arbdmodel.version.check_git_repository">check_git_repository() (in module arbdmodel.version)</a>
</li>
<li><a href="api/core/core_objects.html#arbdmodel.core_objects.Child">Child (class in arbdmodel.core_objects)</a>
</li>
- <li><a href="api/core/core_objects.html#arbdmodel.core_objects.Group.children">children (Group attribute)</a>
-
- <ul>
- <li><a href="api/core/core_objects.html#arbdmodel.core_objects.Parent.children">(Parent attribute)</a>
-</li>
- </ul></li>
<li><a href="api/utilities/version.html#arbdmodel.version.Citation">Citation (class in arbdmodel.version)</a>
</li>
<li><a href="api/core/model.html#arbdmodel.model.ArbdModel.clear_all">clear_all() (ArbdModel method)</a>
@@ -741,12 +712,6 @@ document.write(`
</li>
<li><a href="api/utilities/grid.html#arbdmodel.grid.convolve_kernel_truncate">convolve_kernel_truncate() (in module arbdmodel.grid)</a>
</li>
- <li><a href="api/core/core_objects.html#arbdmodel.core_objects.PointParticle.counter">counter (PointParticle attribute)</a>
-
- <ul>
- <li><a href="api/core/core_objects.html#arbdmodel.core_objects.RigidBody.counter">(RigidBody attribute)</a>
-</li>
- </ul></li>
<li><a href="api/utilities/grid.html#arbdmodel.grid.create_bounding_grid">create_bounding_grid() (in module arbdmodel.grid)</a>
</li>
<li><a href="api/simulation_engines/parmed_bd.html#arbdmodel.parmed_bd.ParmedArbd.create_dual_topology">create_dual_topology() (ParmedArbd static method)</a>
@@ -758,8 +723,6 @@ 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>
@@ -767,15 +730,7 @@ 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/core/core_objects.html#arbdmodel.core_objects.ParticleType.damping_coefficient">damping_coefficient (ParticleType attribute)</a>
-</li>
<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>
@@ -795,11 +750,7 @@ document.write(`
</li>
</ul></td>
<td style="width: 33%; vertical-align: top;"><ul>
- <li><a href="api/core/core_objects.html#arbdmodel.core_objects.ParticleType.diffusivity">diffusivity (ParticleType attribute)</a>
-</li>
<li><a href="api/interaction_potentials/ibi.html#arbdmodel.ibi.DihedralDof">DihedralDof (class in arbdmodel.ibi)</a>
-</li>
- <li><a href="api/core/core_objects.html#arbdmodel.core_objects.Parent.dihedrals">dihedrals (Parent attribute)</a>
</li>
<li><a href="api/core/model.html#arbdmodel.model.ArbdModel.dimensions_from_structure">dimensions_from_structure() (ArbdModel method)</a>
@@ -829,9 +780,7 @@ document.write(`
<td style="width: 33%; vertical-align: top;"><ul>
<li><a href="api/polymer_modeling/polymer.html#arbdmodel.polymer.PolymerSection.end_position">end_position (PolymerSection attribute)</a>
</li>
- <li><a href="api/core/core_objects.html#arbdmodel.core_objects.ParticleType.excludedAttributes">excludedAttributes (ParticleType attribute)</a>, <a href="api/core/core_objects.html#id5">[1]</a>
-</li>
- <li><a href="api/core/core_objects.html#arbdmodel.core_objects.Parent.exclusions">exclusions (Parent attribute)</a>
+ <li><a href="api/core/core_objects.html#arbdmodel.core_objects.ParticleType.excludedParameters">excludedParameters (ParticleType attribute)</a>
</li>
</ul></td>
<td style="width: 33%; vertical-align: top;"><ul>
@@ -852,7 +801,7 @@ document.write(`
<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>, <a href="api/interaction_potentials/interactions.html#id0">[1]</a>
+ <li><a href="api/interaction_potentials/interactions.html#arbdmodel.interactions.AbstractPotential.filename">(AbstractPotential method)</a>
</li>
<li><a href="api/interaction_potentials/interactions.html#arbdmodel.interactions.HarmonicBondedPotential.filename">(HarmonicBondedPotential method)</a>
</li>
@@ -939,18 +888,18 @@ document.write(`
</li>
<li><a href="api/shape-based_models/shape_cg.html#arbdmodel.shape_cg.ShapeCGFactory.get_coarse_types">get_coarse_types() (ShapeCGFactory method)</a>
</li>
- <li><a href="api/core/core_objects.html#arbdmodel.core_objects.Transformable.get_collapsed_position">get_collapsed_position() (Transformable method)</a>, <a href="api/core/core_objects.html#id7">[1]</a>
+ <li><a href="api/core/core_objects.html#arbdmodel.core_objects.Transformable.get_collapsed_position">get_collapsed_position() (Transformable method)</a>
</li>
<li><a href="api/polymer_modeling/polymer.html#arbdmodel.polymer.Location.get_connected_location">get_connected_location() (Location method)</a>
</li>
<li><a href="api/polymer_modeling/polymer.html#arbdmodel.polymer.PolymerGroup.get_connections">get_connections() (PolymerGroup method)</a>
</li>
<li><a href="api/polymer_modeling/polymer.html#arbdmodel.polymer.ConnectableElement.get_connections_and_locations">get_connections_and_locations() (ConnectableElement method)</a>, <a href="api/polymer_modeling/polymer.html#id0">[1]</a>
-</li>
- <li><a href="api/polymer_modeling/polymer.html#arbdmodel.polymer.PolymerSection.get_contour_sorted_connections_and_locations">get_contour_sorted_connections_and_locations() (PolymerSection method)</a>
</li>
</ul></td>
<td style="width: 33%; vertical-align: top;"><ul>
+ <li><a href="api/polymer_modeling/polymer.html#arbdmodel.polymer.PolymerSection.get_contour_sorted_connections_and_locations">get_contour_sorted_connections_and_locations() (PolymerSection method)</a>
+</li>
<li><a href="api/simulation_engines/engine.html#arbdmodel.engine.ArbdEngine.get_default_conf">get_default_conf() (ArbdEngine method)</a>
<ul>
@@ -1008,12 +957,8 @@ 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>
- <li><a href="api/core/core_objects.html#arbdmodel.core_objects.Parent.group_sites">group_sites (Parent attribute)</a>
</li>
<li><a href="api/core/core_objects.html#arbdmodel.core_objects.GroupSite">GroupSite (class in arbdmodel.core_objects)</a>
</li>
@@ -1058,34 +1003,20 @@ document.write(`
<li><a href="api/interaction_potentials/ibi.html#arbdmodel.ibi.IBIDihedral">IBIDihedral (class in arbdmodel.ibi)</a>
</li>
<li><a href="api/interaction_potentials/ibi.html#arbdmodel.ibi.IBINonbonded">IBINonbonded (class in arbdmodel.ibi)</a>
-</li>
- <li><a href="api/core/core_objects.html#arbdmodel.core_objects.GroupSite.idx">idx (GroupSite attribute)</a>
-
- <ul>
- <li><a href="api/core/core_objects.html#arbdmodel.core_objects.PointParticle.idx">(PointParticle attribute)</a>
-</li>
- <li><a href="api/core/core_objects.html#arbdmodel.core_objects.RigidBody.idx">(RigidBody attribute)</a>
-</li>
- </ul></li>
- <li><a href="api/core/core_objects.html#arbdmodel.core_objects.Parent.impropers">impropers (Parent attribute)</a>
</li>
<li><a href="api/core/core_objects.html#arbdmodel.core_objects.Parent.index">index() (Parent method)</a>
</li>
- </ul></td>
- <td style="width: 33%; vertical-align: top;"><ul>
<li><a href="api/utilities/binary_manager.html#arbdmodel.binary_manager.initialize_binary_paths">initialize_binary_paths() (in module arbdmodel.binary_manager)</a>
</li>
+ </ul></td>
+ <td style="width: 33%; vertical-align: top;"><ul>
<li><a href="api/core/core_objects.html#arbdmodel.core_objects.Parent.insert">insert() (Parent method)</a>
</li>
<li><a href="api/polymer_modeling/polymer.html#arbdmodel.polymer.PolymerSection.insert_monomers">insert_monomers() (PolymerSection method)</a>
-</li>
- <li><a href="api/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>
<li><a href="api/core/core_objects.html#arbdmodel.core_objects.ParticleType.is_same_type">is_same_type() (ParticleType method)</a>
-</li>
- <li><a href="api/core/core_objects.html#arbdmodel.core_objects.Group.isClone">isClone (Group attribute)</a>
</li>
<li><a href="api/utilities/grid.html#arbdmodel.grid.isotropic_kernel">isotropic_kernel() (in module arbdmodel.grid)</a>
</li>
@@ -1147,17 +1078,7 @@ document.write(`
<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/core/core_objects.html#arbdmodel.core_objects.ParticleType.mass">mass (ParticleType attribute)</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><a href="api/polymer_modeling/kh_polymer_model.html#arbdmodel.kh_polymer_model.KhNonbonded.max_force">max_force (KhNonbonded 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>
@@ -1232,8 +1153,6 @@ document.write(`
</ul></li>
</ul></td>
<td style="width: 33%; vertical-align: top;"><ul>
- <li><a href="api/core/core_objects.html#arbdmodel.core_objects.RigidBodyType.moment_of_inertia">moment_of_inertia (RigidBodyType attribute)</a>
-</li>
<li><a href="api/polymer_modeling/polymer.html#arbdmodel.polymer.PolymerSection.monomer_index_to_contour">monomer_index_to_contour() (PolymerSection method)</a>
</li>
<li><a href="api/polymer_modeling/polymer.html#arbdmodel.polymer.PolymerSection.monomer_length">monomer_length (PolymerSection attribute)</a>
@@ -1254,18 +1173,6 @@ document.write(`
<td style="width: 33%; vertical-align: top;"><ul>
<li><a href="api/simulation_engines/engine.html#arbdmodel.engine.NamdEngine">NamdEngine (class in arbdmodel.engine)</a>
</li>
- <li><a href="api/core/core_objects.html#arbdmodel.core_objects.Group.name">name (Group attribute)</a>
-
- <ul>
- <li><a href="api/core/core_objects.html#arbdmodel.core_objects.ParticleType.name">(ParticleType attribute)</a>
-</li>
- <li><a href="api/core/core_objects.html#arbdmodel.core_objects.PointParticle.name">(PointParticle attribute)</a>
-</li>
- <li><a href="api/core/core_objects.html#arbdmodel.core_objects.RigidBody.name">(RigidBody attribute)</a>
-</li>
- <li><a href="api/core/core_objects.html#arbdmodel.core_objects.RigidBodyType.name">(RigidBodyType attribute)</a>
-</li>
- </ul></li>
<li><a href="api/utilities/grid.html#arbdmodel.grid.neighborhood_average">neighborhood_average() (in module arbdmodel.grid)</a>
</li>
<li><a href="api/polymer_modeling/ssdna_two_bead.html#arbdmodel.ssdna_two_bead.DnaStrandBeads.nt">nt (DnaStrandBeads attribute)</a>
@@ -1276,22 +1183,10 @@ document.write(`
</li>
<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/polymer_modeling/polymer.html#arbdmodel.polymer.PolymerSection.num_monomers">num_monomers (PolymerSection attribute)</a>
</li>
<li><a href="api/simulation_engines/engine.html#arbdmodel.engine.ArbdEngine.num_particles">num_particles (ArbdEngine attribute)</a>
</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>
@@ -1302,24 +1197,12 @@ 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>
- <li><a href="api/polymer_modeling/onck_polymer_model.html#arbdmodel.onck_polymer_model.OnckNonbonded">OnckNonbonded (class in arbdmodel.onck_polymer_model)</a>
-</li>
- <li><a href="api/core/core_objects.html#arbdmodel.core_objects.Group.orientation">orientation (Group attribute)</a>
-
- <ul>
- <li><a href="api/core/core_objects.html#arbdmodel.core_objects.Transformable.orientation">(Transformable 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.Connection.other">other() (Connection method)</a>
+ <li><a href="api/polymer_modeling/onck_polymer_model.html#arbdmodel.onck_polymer_model.OnckNonbonded">OnckNonbonded (class in arbdmodel.onck_polymer_model)</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><a href="api/polymer_modeling/polymer.html#arbdmodel.polymer.Connection.other">other() (Connection method)</a>
</li>
- </ul></li>
</ul></td>
</tr></table>
@@ -1329,54 +1212,28 @@ 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.Child.parent">parent (Child attribute)</a>
</li>
<li><a href="api/core/core_objects.html#arbdmodel.core_objects.Parent">Parent (class in arbdmodel.core_objects)</a>
-</li>
- <li><a href="api/core/core_objects.html#arbdmodel.core_objects.Group.parent">parent (Group attribute)</a>
-
- <ul>
- <li><a href="api/core/core_objects.html#arbdmodel.core_objects.ParticleType.parent">(ParticleType attribute)</a>
-</li>
- <li><a href="api/core/core_objects.html#arbdmodel.core_objects.RigidBodyType.parent">(RigidBodyType attribute)</a>
-</li>
- </ul></li>
- <li><a href="api/simulation_engines/parmed_bd.html#arbdmodel.parmed_bd.ParmedArbd.parmed_structure">parmed_structure (ParmedArbd attribute)</a>
</li>
<li><a href="api/simulation_engines/parmed_bd.html#arbdmodel.parmed_bd.ParmedArbd">ParmedArbd (class in arbdmodel.parmed_bd)</a>
</li>
<li><a href="api/simulation_engines/engine.html#arbdmodel.engine.HydroProRunner.parse_output">parse_output() (HydroProRunner method)</a>
</li>
<li><a href="api/simulation_engines/engine.html#arbdmodel.engine.ArbdEngine.particles">particles (ArbdEngine attribute)</a>
-
- <ul>
- <li><a href="api/core/core_objects.html#arbdmodel.core_objects.GroupSite.particles">(GroupSite attribute)</a>
</li>
- </ul></li>
<li><a href="api/core/core_objects.html#arbdmodel.core_objects.ParticleType">ParticleType (class in arbdmodel.core_objects)</a>
</li>
<li><a href="api/core/model.html#arbdmodel.model.PdbModel">PdbModel (class in arbdmodel.model)</a>
</li>
- <li><a href="api/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>
+ <li><a href="api/interaction_potentials/interactions.html#arbdmodel.interactions.AbstractPotential.periodic">periodic (AbstractPotential property)</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.RigidBodyType.pmf_grids">pmf_grids (RigidBodyType attribute)</a>
-</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>
@@ -1386,22 +1243,14 @@ 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/core/core_objects.html#arbdmodel.core_objects.Group.position">position (Group attribute)</a>
-
- <ul>
- <li><a href="api/core/core_objects.html#arbdmodel.core_objects.Transformable.position">(Transformable attribute)</a>
-</li>
- </ul></li>
<li><a href="api/polymer_modeling/polymer.html#arbdmodel.polymer.PolymerSection.position_spline_params">position_spline_params (PolymerSection attribute)</a>
</li>
- </ul></td>
- <td style="width: 33%; vertical-align: top;"><ul>
<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>, <a href="api/interaction_potentials/interactions.html#id2">[1]</a>
+ <li><a href="api/interaction_potentials/interactions.html#arbdmodel.interactions.AbstractPotential.potential">(AbstractPotential method)</a>
</li>
<li><a href="api/interaction_potentials/interactions.html#arbdmodel.interactions.BoundaryPotential.potential">(BoundaryPotential method)</a>
</li>
@@ -1423,7 +1272,7 @@ 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>, <a href="api/polymer_modeling/onck_polymer_model.html#id0">[1]</a>
+ <li><a href="api/polymer_modeling/onck_polymer_model.html#arbdmodel.onck_polymer_model.OnckNonbonded.potential">(OnckNonbonded method)</a>
</li>
<li><a href="api/polymer_modeling/sali_polymer_model.html#arbdmodel.sali_polymer_model.SaliNonbonded.potential">(SaliNonbonded method)</a>
</li>
@@ -1436,18 +1285,12 @@ document.write(`
<li><a href="api/interaction_potentials/interactions.html#arbdmodel.interactions.WLCSKBond.potential">(WLCSKBond method)</a>
</li>
</ul></li>
+ </ul></td>
+ <td style="width: 33%; vertical-align: top;"><ul>
<li><a href="api/simulation_engines/engine.html#arbdmodel.engine.ArbdEngine.potential_directory">potential_directory (ArbdEngine attribute)</a>
-</li>
- <li><a href="api/core/core_objects.html#arbdmodel.core_objects.RigidBodyType.potential_grids">potential_grids (RigidBodyType attribute)</a>
</li>
<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>
@@ -1455,10 +1298,6 @@ 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/core_objects.html#arbdmodel.core_objects.Parent.product_potentials">product_potentials (Parent attribute)</a>
-</li>
- <li><a href="api/core/sim_config.html#arbdmodel.sim_config.DefaultSimConf.Properties">Properties (DefaultSimConf attribute)</a>
</li>
</ul></td>
</tr></table>
@@ -1490,12 +1329,8 @@ 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 attribute)</a>
-
- <ul>
- <li><a href="api/interaction_potentials/interactions.html#id3">(AbstractPotential property)</a>
+ <li><a href="api/interaction_potentials/interactions.html#arbdmodel.interactions.AbstractPotential.range_">range_ (AbstractPotential property)</a>
</li>
- </ul></li>
<li><a href="api/simulation_engines/engine.html#arbdmodel.engine.ArbdEngine.rb_type_dirs">rb_type_dirs (ArbdEngine attribute)</a>
</li>
<li><a href="api/utilities/coords.html#arbdmodel.coords.read_arbd_coordinates">read_arbd_coordinates() (in module arbdmodel.coords)</a>
@@ -1516,39 +1351,11 @@ document.write(`
</li>
<li><a href="api/core/core_objects.html#arbdmodel.core_objects.Parent.remove">remove() (Parent method)</a>
</li>
- <li><a href="api/core/core_objects.html#arbdmodel.core_objects.Group.remove_duplicate_bonded_terms">remove_duplicate_bonded_terms (Group attribute)</a>
-
- <ul>
- <li><a href="api/core/core_objects.html#arbdmodel.core_objects.Parent.remove_duplicate_bonded_terms">(Parent attribute)</a>
-</li>
- </ul></li>
<li><a href="api/polymer_modeling/polymer.html#arbdmodel.polymer.PolymerSection.remove_monomers">remove_monomers() (PolymerSection method)</a>
</li>
- <li><a href="api/utilities/grid.html#arbdmodel.grid.replace_false_with_distance">replace_false_with_distance() (in module arbdmodel.grid)</a>
-</li>
- <li><a href="api/interaction_potentials/interactions.html#arbdmodel.interactions.AbstractPotential.resolution">resolution (AbstractPotential attribute)</a>
-</li>
- <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/core_objects.html#arbdmodel.core_objects.GroupSite.restraints">restraints (GroupSite attribute)</a>
-
- <ul>
- <li><a href="api/core/core_objects.html#arbdmodel.core_objects.PointParticle.restraints">(PointParticle attribute)</a>
-</li>
- <li><a href="api/core/core_objects.html#arbdmodel.core_objects.RigidBody.restraints">(RigidBody attribute)</a>
-</li>
- </ul></li>
</ul></td>
<td style="width: 33%; vertical-align: top;"><ul>
- <li><a href="api/core/core_objects.html#arbdmodel.core_objects.PointParticle.rigid">rigid (PointParticle attribute)</a>
-
- <ul>
- <li><a href="api/core/core_objects.html#arbdmodel.core_objects.RigidBody.rigid">(RigidBody attribute)</a>
-</li>
- </ul></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><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/core/core_objects.html#arbdmodel.core_objects.RigidBody">RigidBody (class in arbdmodel.core_objects)</a>
</li>
@@ -1559,14 +1366,10 @@ document.write(`
<ul>
<li><a href="api/polymer_modeling/polymer.html#arbdmodel.polymer.PolymerSection.rotate">(PolymerSection method)</a>
</li>
- <li><a href="api/core/core_objects.html#arbdmodel.core_objects.Transformable.rotate">(Transformable method)</a>, <a href="api/core/core_objects.html#id8">[1]</a>
+ <li><a href="api/core/core_objects.html#arbdmodel.core_objects.Transformable.rotate">(Transformable method)</a>
</li>
</ul></li>
<li><a href="api/utilities/coords.html#arbdmodel.coords.rotationAboutAxis">rotationAboutAxis() (in module arbdmodel.coords)</a>
-</li>
- <li><a href="api/core/core_objects.html#arbdmodel.core_objects.RigidBodyType.rotational_damping_coefficient">rotational_damping_coefficient (RigidBodyType attribute)</a>
-</li>
- <li><a href="api/core/core_objects.html#arbdmodel.core_objects.RigidBodyType.rotational_diffusivity">rotational_diffusivity (RigidBodyType attribute)</a>
</li>
<li><a href="api/simulation_engines/engine.html#arbdmodel.engine.APBSRunner.run_calculation">run_calculation() (APBSRunner method)</a>
@@ -1612,16 +1415,10 @@ 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.seed">seed (SimConf attribute)</a>
-</li>
<li><a href="api/polymer_modeling/polymer.html#arbdmodel.polymer.PolymerSection.segname">segname (PolymerSection attribute)</a>
</li>
- <li><a href="api/polymer_modeling/onck_polymer_model.html#arbdmodel.onck_polymer_model.OnckBeads.sequence">sequence (OnckBeads attribute)</a>
-
- <ul>
- <li><a href="api/polymer_modeling/polymer.html#arbdmodel.polymer.PolymerSection.sequence">(PolymerSection attribute)</a>
+ <li><a href="api/polymer_modeling/polymer.html#arbdmodel.polymer.PolymerSection.sequence">sequence (PolymerSection attribute)</a>
</li>
- </ul></li>
<li><a href="api/core/sim_config.html#arbdmodel.sim_config.SimConf.set_binary">set_binary() (SimConf method)</a>
</li>
<li><a href="api/polymer_modeling/polymer.html#arbdmodel.polymer.Location.set_connection">set_connection() (Location method)</a>
@@ -1645,11 +1442,11 @@ document.write(`
<li><a href="api/shape-based_models/shape_cg.html#arbdmodel.shape_cg.ShapeCGModel.setup_and_run">setup_and_run() (ShapeCGModel method)</a>
</li>
<li><a href="api/rigidbody_models/simplearbd.html#arbdmodel.simplearbd.SimpleArbdConfig.setup_diffusible_objects">setup_diffusible_objects() (SimpleArbdConfig method)</a>
-</li>
- <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/rigidbody_models/simplearbd.html#arbdmodel.simplearbd.SimpleArbdConfig.setup_static_objects">setup_static_objects() (SimpleArbdConfig method)</a>
+</li>
<li><a href="api/shape-based_models/shape_cg.html#arbdmodel.shape_cg.ShapeCGFactory">ShapeCGFactory (class in arbdmodel.shape_cg)</a>
</li>
<li><a href="api/shape-based_models/shape_cg.html#arbdmodel.shape_cg.ShapeCGModel">ShapeCGModel (class in arbdmodel.shape_cg)</a>
@@ -1674,12 +1471,6 @@ 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>
@@ -1688,8 +1479,6 @@ 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/polymer_modeling/polymer.html#arbdmodel.polymer.PolymerSection.start_orientation">start_orientation (PolymerSection attribute)</a>
@@ -1712,25 +1501,17 @@ 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 attribute)</a>
+ <li><a href="api/core/sim_config.html#arbdmodel.sim_config.DefaultSimConf.temperature">temperature (DefaultSimConf property)</a>
<ul>
- <li><a href="api/core/sim_config.html#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#id1">(SimConf property)</a>
+ <li><a href="api/core/sim_config.html#arbdmodel.sim_config.SimConf.temperature">(SimConf property)</a>
</li>
</ul></li>
<li><a href="api/utilities/grid.html#arbdmodel.grid.TestAverageGrids.test_average_grids">test_average_grids() (TestAverageGrids method)</a>
</li>
<li><a href="api/utilities/grid.html#arbdmodel.grid.TestAverageGrids">TestAverageGrids (class in arbdmodel.grid)</a>
</li>
- <li><a href="api/core/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>, <a href="api/core/core_objects.html#id9">[1]</a>
+ <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>
@@ -1739,7 +1520,7 @@ document.write(`
<ul>
<li><a href="api/polymer_modeling/polymer.html#arbdmodel.polymer.PolymerSection.translate">(PolymerSection method)</a>
</li>
- <li><a href="api/core/core_objects.html#arbdmodel.core_objects.Transformable.translate">(Transformable method)</a>, <a href="api/core/core_objects.html#id10">[1]</a>
+ <li><a href="api/core/core_objects.html#arbdmodel.core_objects.Transformable.translate">(Transformable method)</a>
</li>
</ul></li>
</ul></td>
@@ -1754,10 +1535,6 @@ document.write(`
<li><a href="api/interaction_potentials/interactions.html#arbdmodel.interactions.HarmonicDihedral.type_">(HarmonicDihedral property)</a>
</li>
<li><a href="api/interaction_potentials/interactions.html#arbdmodel.interactions.HarmonicVectorAngle.type_">(HarmonicVectorAngle property)</a>
-</li>
- <li><a href="api/core/core_objects.html#arbdmodel.core_objects.PointParticle.type_">(PointParticle attribute)</a>
-</li>
- <li><a href="api/core/core_objects.html#arbdmodel.core_objects.RigidBody.type_">(RigidBody attribute)</a>
</li>
<li><a href="api/interaction_potentials/interactions.html#arbdmodel.interactions.WLCSKAngle.type_">(WLCSKAngle property)</a>
</li>
@@ -1765,8 +1542,6 @@ document.write(`
</li>
</ul></li>
<li><a href="api/simulation_engines/engine.html#arbdmodel.engine.ArbdEngine.type_counts">type_counts (ArbdEngine attribute)</a>
-</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>
@@ -1798,20 +1573,10 @@ 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/core/core_objects.html#arbdmodel.core_objects.Parent.vector_angles">vector_angles (Parent attribute)</a>
-</li>
- <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><a href="api/polymer_modeling/polymer.html#arbdmodel.polymer.PolymerGroup.vmd_cylinder_tcl">vmd_cylinder_tcl() (PolymerGroup method)</a>
</li>
- </ul></li>
</ul></td>
<td style="width: 33%; vertical-align: top;"><ul>
- <li><a href="api/polymer_modeling/polymer.html#arbdmodel.polymer.PolymerGroup.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>
@@ -1843,7 +1608,7 @@ document.write(`
<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>, <a href="api/interaction_potentials/interactions.html#id4">[1]</a>
+ <li><a href="api/interaction_potentials/interactions.html#arbdmodel.interactions.AbstractPotential.write_file">(AbstractPotential method)</a>
</li>
<li><a href="api/interaction_potentials/interactions.html#arbdmodel.interactions.BoundaryPotential.write_file">(BoundaryPotential method)</a>
</li>
@@ -1883,14 +1648,6 @@ 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/objects.inv b/_build/html/objects.inv
index f77aaca57db6af9241c94aa90a81d73848de7efe..d88bc801b868a9506ba6074edcf4436b2cde0a35 100644
Binary files a/_build/html/objects.inv and b/_build/html/objects.inv differ
diff --git a/_build/html/searchindex.js b/_build/html/searchindex.js
index c4a75e71a1d6377cfbf2706763dbabc9c1fe3f3d..487c229fbd68b846b8bfdfbde572dc517ae01635 100644
--- a/_build/html/searchindex.js
+++ b/_build/html/searchindex.js
@@ -1 +1 @@
-Search.setIndex({"alltitles": {"1-basics": [[41, "basics"]], "2-polymer-objects": [[41, "polymer-objects"]], "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, "collaborate-with-your-team"]], "Contributing": [[0, "contributing"]], "Core": [[2, null]], "Description": [[0, "description"]], "Editing this README": [[0, "editing-this-readme"]], "Features": [[36, "features"]], "Getting Started": [[36, "getting-started"]], "Getting started": [[0, "getting-started"]], "Implementing customized coarse-grained polymer models": [[39, null]], "Installation": [[0, "installation"]], "Integrate with your tools": [[0, "integrate-with-your-tools"]], "Interaction Potentials": [[7, null]], "License": [[0, "license"]], "Modeling rigid-body objects": [[40, null]], "Module Categories": [[5, "module-categories"]], "Modules": [[2, "modules"], [7, "modules"], [11, "modules"], [18, "modules"], [25, "modules"], [28, "modules"], [33, "modules"]], "Name": [[0, "name"]], "Overview": [[36, "overview"]], "Polymer Modeling": [[11, null]], "Project status": [[0, "project-status"]], "Python API Reference": [[36, "python-api-reference"]], "RigidBody Models": [[18, null]], "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, "step-5-visualize-the-results"]], "Step 6: Customize the interactions": [[37, "step-6-customize-the-interactions"]], "Step 7: Add bonds": [[37, "step-7-add-bonds"]], "Suggestions for a good README": [[0, "suggestions-for-a-good-readme"]], "Support": [[0, "support"]], "Test and Deploy": [[0, "test-and-deploy"]], "Tutorials": [[41, null]], "Usage": [[0, "usage"]], "Utilities": [[33, null]], "Visuals": [[0, "visuals"]], "arbdmodel-docs": [[0, null]], "binary_manager": [[30, null]], "coords": [[31, null]], "core_objects": [[1, null]], "engine": [[27, null]], "fjc_polymer_model": [[9, null]], "grid": [[32, null]], "hps_polymer_model": [[10, null]], "ibi": [[6, null]], "interactions": [[8, null]], "kh_polymer_model": [[12, null]], "logger": [[34, null]], "mesh_process_surface": [[19, null]], "mesh_process_volume": [[20, null]], "mesh_rigidbody": [[21, null]], "model": [[3, null]], "mpipi_polymer": [[13, null]], "onck_polymer_model": [[14, null]], "parmed_bd": [[29, null]], "polymer": [[15, null]], "sali_polymer_model": [[16, null]], "shape_cg": [[26, null]], "sim_config": [[4, null]], "simplearbd": [[22, null]], "ssdna_two_bead": [[17, null]], "structure_from_pdb": [[23, null]], "structure_rigidbody": [[24, null]], "version": [[35, null]]}, "docnames": ["README", "api/core/core_objects", "api/core/index", "api/core/model", "api/core/sim_config", "api/index", "api/interaction_potentials/ibi", "api/interaction_potentials/index", "api/interaction_potentials/interactions", "api/polymer_modeling/fjc_polymer_model", "api/polymer_modeling/hps_polymer_model", "api/polymer_modeling/index", "api/polymer_modeling/kh_polymer_model", "api/polymer_modeling/mpipi_polymer", "api/polymer_modeling/onck_polymer_model", "api/polymer_modeling/polymer", "api/polymer_modeling/sali_polymer_model", "api/polymer_modeling/ssdna_two_bead", "api/rigidbody_models/index", "api/rigidbody_models/mesh_process_surface", "api/rigidbody_models/mesh_process_volume", "api/rigidbody_models/mesh_rigidbody", "api/rigidbody_models/simplearbd", "api/rigidbody_models/structure_from_pdb", "api/rigidbody_models/structure_rigidbody", "api/shape-based_models/index", "api/shape-based_models/shape_cg", "api/simulation_engines/engine", "api/simulation_engines/index", "api/simulation_engines/parmed_bd", "api/utilities/binary_manager", "api/utilities/coords", "api/utilities/grid", "api/utilities/index", "api/utilities/logger", "api/utilities/version", "intro", "tutorials/1-basics/1-basics", "tutorials/2-polymer-objects/2-polymer-objects", "tutorials/3-iterative-boltzmann-inversion/3-ibi", "tutorials/4-rigid-bodies/4-rigid-bodies", "tutorials/index"], "envversion": {"sphinx": 62, "sphinx.domains.c": 3, "sphinx.domains.changeset": 1, "sphinx.domains.citation": 1, "sphinx.domains.cpp": 9, "sphinx.domains.index": 1, "sphinx.domains.javascript": 3, "sphinx.domains.math": 2, "sphinx.domains.python": 4, "sphinx.domains.rst": 2, "sphinx.domains.std": 2, "sphinx.ext.intersphinx": 1, "sphinx.ext.viewcode": 1}, "filenames": ["README.md", "api/core/core_objects.md", "api/core/index.md", "api/core/model.md", "api/core/sim_config.md", "api/index.md", "api/interaction_potentials/ibi.md", "api/interaction_potentials/index.md", "api/interaction_potentials/interactions.md", "api/polymer_modeling/fjc_polymer_model.md", "api/polymer_modeling/hps_polymer_model.md", "api/polymer_modeling/index.md", "api/polymer_modeling/kh_polymer_model.md", "api/polymer_modeling/mpipi_polymer.md", "api/polymer_modeling/onck_polymer_model.md", "api/polymer_modeling/polymer.md", "api/polymer_modeling/sali_polymer_model.md", "api/polymer_modeling/ssdna_two_bead.md", "api/rigidbody_models/index.md", "api/rigidbody_models/mesh_process_surface.md", "api/rigidbody_models/mesh_process_volume.md", "api/rigidbody_models/mesh_rigidbody.md", "api/rigidbody_models/simplearbd.md", "api/rigidbody_models/structure_from_pdb.md", "api/rigidbody_models/structure_rigidbody.md", "api/shape-based_models/index.md", "api/shape-based_models/shape_cg.md", "api/simulation_engines/engine.md", "api/simulation_engines/index.md", "api/simulation_engines/parmed_bd.md", "api/utilities/binary_manager.md", "api/utilities/coords.md", "api/utilities/grid.md", "api/utilities/index.md", "api/utilities/logger.md", "api/utilities/version.md", "intro.md", "tutorials/1-basics/1-basics.ipynb", "tutorials/2-polymer-objects/2-polymer-objects.ipynb", "tutorials/3-iterative-boltzmann-inversion/3-ibi.ipynb", "tutorials/4-rigid-bodies/4-rigid-bodies.ipynb", "tutorials/index.md"], "indexentries": {"_written_bond_files (arbdengine attribute)": [[27, "arbdmodel.engine.ArbdEngine._written_bond_files", false]], "abstractibipotential (class in arbdmodel.ibi)": [[6, "arbdmodel.ibi.AbstractIBIpotential", false]], "abstractpotential (class in arbdmodel.interactions)": [[8, "arbdmodel.interactions.AbstractPotential", false]], "add() (arbdmodel method)": [[3, "arbdmodel.model.ArbdModel.add", false]], "add() (parent method)": [[1, "arbdmodel.core_objects.Parent.add", false]], "add_angle() (parent method)": [[1, "arbdmodel.core_objects.Parent.add_angle", false]], "add_bond() (parent method)": [[1, "arbdmodel.core_objects.Parent.add_bond", false]], "add_bond_angle() (parent method)": [[1, "arbdmodel.core_objects.Parent.add_bond_angle", false]], "add_confinement() (shapecgmodel method)": [[26, "arbdmodel.shape_cg.ShapeCGModel.add_confinement", false]], "add_diffusible_object() (structurerigidbodymodel method)": [[24, "arbdmodel.structure_rigidbody.StructureRigidBodyModel.add_diffusible_object", false]], "add_dihedral() (parent method)": [[1, "arbdmodel.core_objects.Parent.add_dihedral", false]], "add_exclusion() (parent method)": [[1, "arbdmodel.core_objects.Parent.add_exclusion", false]], "add_grid_potential() (particletype method)": [[1, "arbdmodel.core_objects.ParticleType.add_grid_potential", false]], "add_grid_potential() (pointparticle method)": [[1, "arbdmodel.core_objects.PointParticle.add_grid_potential", false]], "add_grid_potential() (polymergroup method)": [[15, "arbdmodel.polymer.PolymerGroup.add_grid_potential", false]], "add_group_site() (arbdmodel method)": [[3, "arbdmodel.model.ArbdModel.add_group_site", false]], "add_improper() (parent method)": [[1, "arbdmodel.core_objects.Parent.add_improper", false]], "add_location() (polymersection method)": [[15, "arbdmodel.polymer.PolymerSection.add_location", false]], "add_nonbonded_interaction() (arbdmodel method)": [[3, "arbdmodel.model.ArbdModel.add_nonbonded_interaction", false]], "add_product_potential() (parent method)": [[1, "arbdmodel.core_objects.Parent.add_product_potential", false]], "add_protein_nb_interactions() (shapecgmodel method)": [[26, "arbdmodel.shape_cg.ShapeCGModel.add_protein_nb_interactions", false]], "add_proteins() (shapecgmodel method)": [[26, "arbdmodel.shape_cg.ShapeCGModel.add_proteins", false]], "add_restraint() (groupsite method)": [[1, "arbdmodel.core_objects.GroupSite.add_restraint", false], [1, "id2", false]], "add_restraint() (pointparticle method)": [[1, "arbdmodel.core_objects.PointParticle.add_restraint", false]], "add_restraint() (rigidbody method)": [[1, "arbdmodel.core_objects.RigidBody.add_restraint", false]], "add_smaller_grid() (in module arbdmodel.grid)": [[32, "arbdmodel.grid.add_smaller_grid", false]], "add_static_object() (structurerigidbodymodel method)": [[24, "arbdmodel.structure_rigidbody.StructureRigidBodyModel.add_static_object", false]], "add_vector_angle() (parent method)": [[1, "arbdmodel.core_objects.Parent.add_vector_angle", false]], "align_structure() (structureprocessor method)": [[23, "arbdmodel.structure_from_pdb.StructureProcessor.align_structure", false]], "angledof (class in arbdmodel.ibi)": [[6, "arbdmodel.ibi.AngleDof", false]], "angles (parent attribute)": [[1, "arbdmodel.core_objects.Parent.angles", false]], "apbsrunner (class in arbdmodel.engine)": [[27, "arbdmodel.engine.APBSRunner", false]], "apply_gaussian_smoothing() (structureprocessor method)": [[23, "arbdmodel.structure_from_pdb.StructureProcessor.apply_gaussian_smoothing", false]], "applyorientation() (transformable method)": [[1, "arbdmodel.core_objects.Transformable.applyOrientation", false], [1, "id6", false]], "arbdengine (class in arbdmodel.engine)": [[27, "arbdmodel.engine.ArbdEngine", false]], "arbdmodel (class in arbdmodel.model)": [[3, "arbdmodel.model.ArbdModel", false]], "arbdmodel.binary_manager": [[30, "module-arbdmodel.binary_manager", false]], "arbdmodel.coords": [[31, "module-arbdmodel.coords", false]], "arbdmodel.core_objects": [[1, "module-arbdmodel.core_objects", false]], "arbdmodel.engine": [[27, "module-arbdmodel.engine", false]], "arbdmodel.fjc_polymer_model": [[9, "module-arbdmodel.fjc_polymer_model", false]], "arbdmodel.grid": [[32, "module-arbdmodel.grid", false]], "arbdmodel.hps_polymer_model": [[10, "module-arbdmodel.hps_polymer_model", false]], "arbdmodel.ibi": [[6, "module-arbdmodel.ibi", false]], "arbdmodel.interactions": [[8, "module-arbdmodel.interactions", false]], "arbdmodel.kh_polymer_model": [[12, "module-arbdmodel.kh_polymer_model", false]], "arbdmodel.logger": [[34, "module-arbdmodel.logger", false]], "arbdmodel.mesh_process_surface": [[19, "module-arbdmodel.mesh_process_surface", false]], "arbdmodel.mesh_process_volume": [[20, "module-arbdmodel.mesh_process_volume", false]], "arbdmodel.mesh_rigidbody": [[21, "module-arbdmodel.mesh_rigidbody", false]], "arbdmodel.model": [[3, "module-arbdmodel.model", false]], "arbdmodel.mpipi_polymer": [[13, "module-arbdmodel.mpipi_polymer", false]], "arbdmodel.onck_polymer_model": [[14, "module-arbdmodel.onck_polymer_model", false]], "arbdmodel.parmed_bd": [[29, "module-arbdmodel.parmed_bd", false]], "arbdmodel.polymer": [[15, "module-arbdmodel.polymer", false]], "arbdmodel.sali_polymer_model": [[16, "module-arbdmodel.sali_polymer_model", false]], "arbdmodel.shape_cg": [[26, "module-arbdmodel.shape_cg", false]], "arbdmodel.sim_config": [[4, "module-arbdmodel.sim_config", false]], "arbdmodel.simplearbd": [[22, "module-arbdmodel.simplearbd", false]], "arbdmodel.ssdna_two_bead": [[17, "module-arbdmodel.ssdna_two_bead", false]], "arbdmodel.structure_from_pdb": [[23, "module-arbdmodel.structure_from_pdb", false]], "arbdmodel.structure_rigidbody": [[24, "module-arbdmodel.structure_rigidbody", false]], "arbdmodel.version": [[35, "module-arbdmodel.version", false]], "assign_ibi_degrees_of_freedom() (arbdmodel method)": [[3, "arbdmodel.model.ArbdModel.assign_IBI_degrees_of_freedom", false]], "atom_types (parmedarbd attribute)": [[29, "arbdmodel.parmed_bd.ParmedArbd.atom_types", false]], "atoms_map (parmedarbd attribute)": [[29, "arbdmodel.parmed_bd.ParmedArbd.atoms_map", false]], "attach_particle() (rigidbodytype method)": [[1, "arbdmodel.core_objects.RigidBodyType.attach_particle", false]], "attached_particles (rigidbody attribute)": [[1, "arbdmodel.core_objects.RigidBody.attached_particles", false]], "attached_particles (rigidbodytype attribute)": [[1, "arbdmodel.core_objects.RigidBodyType.attached_particles", false]], "average_grids() (in module arbdmodel.grid)": [[32, "arbdmodel.grid.average_grids", false]], "b (dnastrandbeads attribute)": [[17, "arbdmodel.ssdna_two_bead.DnaStrandBeads.b", false]], "barostat (simconf attribute)": [[4, "arbdmodel.sim_config.SimConf.barostat", false]], "bins (abstractibipotential attribute)": [[6, "arbdmodel.ibi.AbstractIBIpotential.bins", false]], "bond_angles (parent attribute)": [[1, "arbdmodel.core_objects.Parent.bond_angles", false]], "bondangledof (class in arbdmodel.ibi)": [[6, "arbdmodel.ibi.BondAngleDof", false]], "bonddof (class in arbdmodel.ibi)": [[6, "arbdmodel.ibi.BondDof", false]], "bonds (parent attribute)": [[1, "arbdmodel.core_objects.Parent.bonds", false]], "bound_grid() (in module arbdmodel.grid)": [[32, "arbdmodel.grid.Bound_grid", false]], "boundarypotential (class in arbdmodel.interactions)": [[8, "arbdmodel.interactions.BoundaryPotential", false]], "cacheuptodate (arbdengine attribute)": [[27, "arbdmodel.engine.ArbdEngine.cacheUpToDate", false]], "calc_atom_sasa() (shapecgfactory method)": [[26, "arbdmodel.shape_cg.ShapeCGFactory.calc_atom_sasa", false]], "calculate_damping() (meshprocessor method)": [[20, "arbdmodel.mesh_process_volume.MeshProcessor.calculate_damping", false]], "calculate_damping() (surfacemeshprocessor method)": [[19, "arbdmodel.mesh_process_surface.SurfaceMeshProcessor.calculate_damping", false]], "calculate_dimensions_from_cell_vectors() (in module arbdmodel.coords)": [[31, "arbdmodel.coords.calculate_dimensions_from_cell_vectors", false]], "calculate_hydrodynamic_properties() (structureprocessor method)": [[23, "arbdmodel.structure_from_pdb.StructureProcessor.calculate_hydrodynamic_properties", false]], "calculate_total_mass() (shapecgmodel method)": [[26, "arbdmodel.shape_cg.ShapeCGModel.calculate_total_mass", false]], "call_git_describe() (in module arbdmodel.version)": [[35, "arbdmodel.version.call_git_describe", false]], "charge (particletype attribute)": [[1, "arbdmodel.core_objects.ParticleType.charge", false]], "charge_grids (rigidbodytype attribute)": [[1, "arbdmodel.core_objects.RigidBodyType.charge_grids", false]], "check_git_repository() (in module arbdmodel.version)": [[35, "arbdmodel.version.check_git_repository", false]], "child (class in arbdmodel.core_objects)": [[1, "arbdmodel.core_objects.Child", false]], "children (group attribute)": [[1, "arbdmodel.core_objects.Group.children", false]], "children (parent attribute)": [[1, "arbdmodel.core_objects.Parent.children", false]], "citation (class in arbdmodel.version)": [[35, "arbdmodel.version.Citation", false]], "clear_all() (arbdmodel method)": [[3, "arbdmodel.model.ArbdModel.clear_all", false]], "clear_all() (parent method)": [[1, "arbdmodel.core_objects.Parent.clear_all", false]], "clone (class in arbdmodel.core_objects)": [[1, "arbdmodel.core_objects.Clone", false]], "clone() (group method)": [[1, "arbdmodel.core_objects.Group.clone", false], [1, "id0", false]], "combine() (simconf method)": [[4, "arbdmodel.sim_config.SimConf.combine", false]], "compute_volume() (angledof method)": [[6, "arbdmodel.ibi.AngleDof.compute_volume", false]], "compute_volume() (bonddof method)": [[6, "arbdmodel.ibi.BondDof.compute_volume", false]], "compute_volume() (degreeoffreedom method)": [[6, "arbdmodel.ibi.DegreeOfFreedom.compute_volume", false]], "compute_volume() (pairdistributiondof method)": [[6, "arbdmodel.ibi.PairDistributionDof.compute_volume", false]], "compute_volume() (radiusdof method)": [[6, "arbdmodel.ibi.RadiusDof.compute_volume", false]], "concentration_to_debye_length() (shapecgmodel method)": [[26, "arbdmodel.shape_cg.ShapeCGModel.concentration_to_debye_length", false]], "configuration (arbdengine attribute)": [[27, "arbdmodel.engine.ArbdEngine.configuration", false]], "connectableelement (class in arbdmodel.polymer)": [[15, "arbdmodel.polymer.ConnectableElement", false]], "connection (class in arbdmodel.polymer)": [[15, "arbdmodel.polymer.Connection", false]], "connection_locations (connectableelement attribute)": [[15, "arbdmodel.polymer.ConnectableElement.connection_locations", false]], "connections (connectableelement attribute)": [[15, "arbdmodel.polymer.ConnectableElement.connections", false]], "constant_force() (in module arbdmodel.grid)": [[32, "arbdmodel.grid.constant_force", false]], "contour_to_monomer_index() (polymersection method)": [[15, "arbdmodel.polymer.PolymerSection.contour_to_monomer_index", false]], "contour_to_orientation() (polymersection method)": [[15, "arbdmodel.polymer.PolymerSection.contour_to_orientation", false]], "contour_to_position() (polymersection method)": [[15, "arbdmodel.polymer.PolymerSection.contour_to_position", false]], "contour_to_tangent() (polymersection method)": [[15, "arbdmodel.polymer.PolymerSection.contour_to_tangent", false]], "convert_sod_to_mg() (parmedarbd static method)": [[29, "arbdmodel.parmed_bd.ParmedArbd.convert_sod_to_mg", false]], "convolve_kernel_truncate() (in module arbdmodel.grid)": [[32, "arbdmodel.grid.convolve_kernel_truncate", false]], "counter (pointparticle attribute)": [[1, "arbdmodel.core_objects.PointParticle.counter", false]], "counter (rigidbody attribute)": [[1, "arbdmodel.core_objects.RigidBody.counter", false]], "create_bounding_grid() (in module arbdmodel.grid)": [[32, "arbdmodel.grid.create_bounding_grid", false]], "create_dual_topology() (parmedarbd static method)": [[29, "arbdmodel.parmed_bd.ParmedArbd.create_dual_topology", false]], "create_dual_topology_model() (parmedarbd class method)": [[29, "arbdmodel.parmed_bd.ParmedArbd.create_dual_topology_model", false]], "create_engine() (simplearbdconfig method)": [[22, "arbdmodel.simplearbd.SimpleArbdConfig.create_engine", false]], "create_model() (simplearbdconfig method)": [[22, "arbdmodel.simplearbd.SimpleArbdConfig.create_model", false]], "create_null() (in module arbdmodel.grid)": [[32, "arbdmodel.grid.Create_null", false]], "cutoff (simconf attribute)": [[4, "arbdmodel.sim_config.SimConf.cutoff", false]], "damping_coefficient (particletype attribute)": [[1, "arbdmodel.core_objects.ParticleType.damping_coefficient", false]], "debye_length (khnonbonded attribute)": [[12, "arbdmodel.kh_polymer_model.KhNonbonded.debye_length", false]], "debye_length (oncknonbonded attribute)": [[14, "arbdmodel.onck_polymer_model.OnckNonbonded.debye_length", false]], "decomp_period (simconf attribute)": [[4, "arbdmodel.sim_config.SimConf.decomp_period", false]], "default_binary (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]], "diffusivity (particletype attribute)": [[1, "arbdmodel.core_objects.ParticleType.diffusivity", false]], "dihedraldof (class in arbdmodel.ibi)": [[6, "arbdmodel.ibi.DihedralDof", false]], "dihedrals (parent attribute)": [[1, "arbdmodel.core_objects.Parent.dihedrals", 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], [1, "id1", false]], "duplicate() (pointparticle method)": [[1, "arbdmodel.core_objects.PointParticle.duplicate", false]], "duplicate() (rigidbody method)": [[1, "arbdmodel.core_objects.RigidBody.duplicate", false]], "end_position (polymersection attribute)": [[15, "arbdmodel.polymer.PolymerSection.end_position", false]], "excludedattributes (particletype attribute)": [[1, "arbdmodel.core_objects.ParticleType.excludedAttributes", false], [1, "id5", false]], "exclusions (parent attribute)": [[1, "arbdmodel.core_objects.Parent.exclusions", false]], "extend() (arbdmodel method)": [[3, "arbdmodel.model.ArbdModel.extend", false]], "extend() (polymergroup method)": [[15, "arbdmodel.polymer.PolymerGroup.extend", false]], "extra_bd_file_lines (arbdengine attribute)": [[27, "arbdmodel.engine.ArbdEngine.extra_bd_file_lines", 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]], "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], [1, "id3", 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], [1, "id7", 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], [15, "id0", 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], [15, "id1", false]], "get_locations() (connectableelement method)": [[15, "arbdmodel.polymer.ConnectableElement.get_locations", false], [15, "id2", 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], [1, "id4", 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]], "group_sites (parent attribute)": [[1, "arbdmodel.core_objects.Parent.group_sites", 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]], "idx (groupsite attribute)": [[1, "arbdmodel.core_objects.GroupSite.idx", false]], "idx (pointparticle attribute)": [[1, "arbdmodel.core_objects.PointParticle.idx", false]], "idx (rigidbody attribute)": [[1, "arbdmodel.core_objects.RigidBody.idx", false]], "impropers (parent attribute)": [[1, "arbdmodel.core_objects.Parent.impropers", 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]], "isclone (group attribute)": [[1, "arbdmodel.core_objects.Group.isClone", 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]], "locations (connectableelement attribute)": [[15, "arbdmodel.polymer.ConnectableElement.locations", false]], "main() (in module arbdmodel.simplearbd)": [[22, "arbdmodel.simplearbd.main", false]], "mass (particletype attribute)": [[1, "arbdmodel.core_objects.ParticleType.mass", 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]], "moment_of_inertia (rigidbodytype attribute)": [[1, "arbdmodel.core_objects.RigidBodyType.moment_of_inertia", false]], "monomer_index_to_contour() (polymersection method)": [[15, "arbdmodel.polymer.PolymerSection.monomer_index_to_contour", false]], "monomer_length (polymersection attribute)": [[15, "arbdmodel.polymer.PolymerSection.monomer_length", 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]], "name (group attribute)": [[1, "arbdmodel.core_objects.Group.name", false]], "name (particletype attribute)": [[1, "arbdmodel.core_objects.ParticleType.name", false]], "name (pointparticle attribute)": [[1, "arbdmodel.core_objects.PointParticle.name", false]], "name (rigidbody attribute)": [[1, "arbdmodel.core_objects.RigidBody.name", false]], "name (rigidbodytype attribute)": [[1, "arbdmodel.core_objects.RigidBodyType.name", 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_monomers (polymersection attribute)": [[15, "arbdmodel.polymer.PolymerSection.num_monomers", false]], "num_particles (arbdengine attribute)": [[27, "arbdmodel.engine.ArbdEngine.num_particles", 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]], "orientation (group attribute)": [[1, "arbdmodel.core_objects.Group.orientation", false]], "orientation (transformable attribute)": [[1, "arbdmodel.core_objects.Transformable.orientation", 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 (child attribute)": [[1, "arbdmodel.core_objects.Child.parent", false]], "parent (class in arbdmodel.core_objects)": [[1, "arbdmodel.core_objects.Parent", false]], "parent (group attribute)": [[1, "arbdmodel.core_objects.Group.parent", false]], "parent (particletype attribute)": [[1, "arbdmodel.core_objects.ParticleType.parent", false]], "parent (rigidbodytype attribute)": [[1, "arbdmodel.core_objects.RigidBodyType.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]], "particles (arbdengine attribute)": [[27, "arbdmodel.engine.ArbdEngine.particles", false]], "particles (groupsite attribute)": [[1, "arbdmodel.core_objects.GroupSite.particles", 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]], "pmf_grids (rigidbodytype attribute)": [[1, "arbdmodel.core_objects.RigidBodyType.pmf_grids", 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]], "position (group attribute)": [[1, "arbdmodel.core_objects.Group.position", false]], "position (transformable attribute)": [[1, "arbdmodel.core_objects.Transformable.position", false]], "position_spline_params (polymersection attribute)": [[15, "arbdmodel.polymer.PolymerSection.position_spline_params", 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, "arbdmodel.onck_polymer_model.OnckNonbonded.potential", false], [14, "id0", 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]], "potential_directory (arbdengine attribute)": [[27, "arbdmodel.engine.ArbdEngine.potential_directory", false]], "potential_grids (rigidbodytype attribute)": [[1, "arbdmodel.core_objects.RigidBodyType.potential_grids", false]], "prepare_for_simulation() (arbdmodel method)": [[3, "arbdmodel.model.ArbdModel.prepare_for_simulation", false]], "pressure (defaultsimconf attribute)": [[4, "arbdmodel.sim_config.DefaultSimConf.pressure", false]], "pressure (simconf attribute)": [[4, "arbdmodel.sim_config.SimConf.pressure", 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]], "product_potentials (parent attribute)": [[1, "arbdmodel.core_objects.Parent.product_potentials", false]], "properties (defaultsimconf attribute)": [[4, "arbdmodel.sim_config.DefaultSimConf.Properties", 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_spline_params (polymersection attribute)": [[15, "arbdmodel.polymer.PolymerSection.quaternion_spline_params", 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 attribute)": [[8, "arbdmodel.interactions.AbstractPotential.range_", false]], "range_ (abstractpotential property)": [[8, "id3", false]], "rb_type_dirs (arbdengine attribute)": [[27, "arbdmodel.engine.ArbdEngine.rb_type_dirs", 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], [6, "id5", 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_duplicate_bonded_terms (group attribute)": [[1, "arbdmodel.core_objects.Group.remove_duplicate_bonded_terms", false]], "remove_duplicate_bonded_terms (parent attribute)": [[1, "arbdmodel.core_objects.Parent.remove_duplicate_bonded_terms", 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]], "resolution (abstractpotential attribute)": [[8, "arbdmodel.interactions.AbstractPotential.resolution", false]], "restart_file (simconf attribute)": [[4, "arbdmodel.sim_config.SimConf.restart_file", false]], "restraints (groupsite attribute)": [[1, "arbdmodel.core_objects.GroupSite.restraints", false]], "restraints (pointparticle attribute)": [[1, "arbdmodel.core_objects.PointParticle.restraints", false]], "restraints (rigidbody attribute)": [[1, "arbdmodel.core_objects.RigidBody.restraints", false]], "rigid (pointparticle attribute)": [[1, "arbdmodel.core_objects.PointParticle.rigid", false]], "rigid (rigidbody attribute)": [[1, "arbdmodel.core_objects.RigidBody.rigid", false]], "rigid_body_grid_grid_period (simconf attribute)": [[4, "arbdmodel.sim_config.SimConf.rigid_body_grid_grid_period", false]], "rigid_body_integrator (simconf attribute)": [[4, "arbdmodel.sim_config.SimConf.rigid_body_integrator", 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], [1, "id8", false]], "rotationaboutaxis() (in module arbdmodel.coords)": [[31, "arbdmodel.coords.rotationAboutAxis", false]], "rotational_damping_coefficient (rigidbodytype attribute)": [[1, "arbdmodel.core_objects.RigidBodyType.rotational_damping_coefficient", false]], "rotational_diffusivity (rigidbodytype attribute)": [[1, "arbdmodel.core_objects.RigidBodyType.rotational_diffusivity", 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]], "seed (simconf attribute)": [[4, "arbdmodel.sim_config.SimConf.seed", false]], "segname (polymersection attribute)": [[15, "arbdmodel.polymer.PolymerSection.segname", false]], "sequence (onckbeads attribute)": [[14, "arbdmodel.onck_polymer_model.OnckBeads.sequence", false]], "sequence (polymersection attribute)": [[15, "arbdmodel.polymer.PolymerSection.sequence", 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]], "solvent_density (defaultsimconf attribute)": [[4, "arbdmodel.sim_config.DefaultSimConf.solvent_density", false]], "solvent_density (simconf attribute)": [[4, "arbdmodel.sim_config.SimConf.solvent_density", 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]], "spring_constant (onckbeads attribute)": [[14, "arbdmodel.onck_polymer_model.OnckBeads.spring_constant", false]], "start_orientation (polymersection attribute)": [[15, "arbdmodel.polymer.PolymerSection.start_orientation", false]], "start_position (polymersection attribute)": [[15, "arbdmodel.polymer.PolymerSection.start_position", 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 attribute)": [[4, "arbdmodel.sim_config.DefaultSimConf.temperature", false]], "temperature (defaultsimconf property)": [[4, "id0", false]], "temperature 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"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]], "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], [1, "id3", 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], [15, "id0", 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], [15, "id1", false]], "get_locations() (connectableelement method)": [[15, "arbdmodel.polymer.ConnectableElement.get_locations", false], [15, "id2", 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], [1, "id4", 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]], "group (class in arbdmodel.core_objects)": [[1, "arbdmodel.core_objects.Group", false]], "groupsite (class in arbdmodel.core_objects)": [[1, "arbdmodel.core_objects.GroupSite", false]], "halfharmonic (class in arbdmodel.interactions)": [[8, "arbdmodel.interactions.HalfHarmonic", false]], "harmonicangle (class in arbdmodel.interactions)": [[8, "arbdmodel.interactions.HarmonicAngle", false]], "harmonicbond (class in arbdmodel.interactions)": [[8, "arbdmodel.interactions.HarmonicBond", false]], "harmonicbondedpotential (class in arbdmodel.interactions)": [[8, "arbdmodel.interactions.HarmonicBondedPotential", false]], "harmonicdihedral (class in arbdmodel.interactions)": [[8, "arbdmodel.interactions.HarmonicDihedral", false]], "harmonicvectorangle (class in arbdmodel.interactions)": [[8, "arbdmodel.interactions.HarmonicVectorAngle", false]], "hpsbeads (class in arbdmodel.hps_polymer_model)": [[10, "arbdmodel.hps_polymer_model.HpsBeads", false]], "hpsmodel (class in arbdmodel.hps_polymer_model)": [[10, "arbdmodel.hps_polymer_model.HpsModel", false]], "hpsnonbonded (class in arbdmodel.hps_polymer_model)": [[10, "arbdmodel.hps_polymer_model.HpsNonbonded", false]], "hydroprorunner (class in arbdmodel.engine)": [[27, "arbdmodel.engine.HydroProRunner", false]], "ibiangle (class in arbdmodel.ibi)": [[6, "arbdmodel.ibi.IBIAngle", false]], "ibibond (class in arbdmodel.ibi)": [[6, "arbdmodel.ibi.IBIBond", false]], "ibidihedral (class in arbdmodel.ibi)": [[6, "arbdmodel.ibi.IBIDihedral", false]], "ibinonbonded (class in arbdmodel.ibi)": [[6, "arbdmodel.ibi.IBINonbonded", false]], "index() (parent method)": [[1, "arbdmodel.core_objects.Parent.index", false]], "initialize_binary_paths() (in module arbdmodel.binary_manager)": [[30, "arbdmodel.binary_manager.initialize_binary_paths", false]], "insert() (parent method)": [[1, "arbdmodel.core_objects.Parent.insert", false]], "insert_monomers() (polymersection method)": [[15, "arbdmodel.polymer.PolymerSection.insert_monomers", false]], "is_dirty() (in module arbdmodel.version)": [[35, "arbdmodel.version.is_dirty", false]], "is_same_type() (particletype method)": [[1, "arbdmodel.core_objects.ParticleType.is_same_type", false]], "isotropic_kernel() (in module arbdmodel.grid)": [[32, "arbdmodel.grid.isotropic_kernel", false]], "items() (simconf method)": [[4, "arbdmodel.sim_config.SimConf.items", false]], "iterate_connections_and_locations() (polymersection method)": [[15, "arbdmodel.polymer.PolymerSection.iterate_connections_and_locations", false]], "khbeads (class in arbdmodel.kh_polymer_model)": [[12, "arbdmodel.kh_polymer_model.KhBeads", false]], "khmodel (class in arbdmodel.kh_polymer_model)": [[12, "arbdmodel.kh_polymer_model.KhModel", false]], "khnonbonded (class in arbdmodel.kh_polymer_model)": [[12, "arbdmodel.kh_polymer_model.KhNonbonded", false]], "kscale (harmonicangle property)": [[8, "arbdmodel.interactions.HarmonicAngle.kscale", false]], "kscale (harmonicbond property)": [[8, "arbdmodel.interactions.HarmonicBond.kscale", false]], "kscale (harmonicbondedpotential property)": [[8, "arbdmodel.interactions.HarmonicBondedPotential.kscale", false]], "kscale (harmonicdihedral property)": [[8, "arbdmodel.interactions.HarmonicDihedral.kscale", false]], "kscale (harmonicvectorangle property)": [[8, "arbdmodel.interactions.HarmonicVectorAngle.kscale", false]], "lennardjones (class in arbdmodel.interactions)": [[8, "arbdmodel.interactions.LennardJones", false]], "linearbond (class in arbdmodel.sali_polymer_model)": [[16, "arbdmodel.sali_polymer_model.LinearBond", false]], "load_structure() (parmedarbd method)": [[29, "arbdmodel.parmed_bd.ParmedArbd.load_structure", false]], "load_target_ibi_distributions() (arbdmodel method)": [[3, "arbdmodel.model.ArbdModel.load_target_IBI_distributions", false]], "loadgrid() (in module arbdmodel.grid)": [[32, "arbdmodel.grid.loadGrid", false]], "location (class in arbdmodel.polymer)": [[15, "arbdmodel.polymer.Location", false]], "locations (connectableelement attribute)": [[15, "arbdmodel.polymer.ConnectableElement.locations", false]], "main() (in module arbdmodel.simplearbd)": [[22, "arbdmodel.simplearbd.main", false]], "max_force (khnonbonded attribute)": [[12, "arbdmodel.kh_polymer_model.KhNonbonded.max_force", 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]], "monomer_length (polymersection attribute)": [[15, "arbdmodel.polymer.PolymerSection.monomer_length", 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_monomers (polymersection attribute)": [[15, "arbdmodel.polymer.PolymerSection.num_monomers", false]], "num_particles (arbdengine attribute)": [[27, "arbdmodel.engine.ArbdEngine.num_particles", 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]], "parmedarbd (class in arbdmodel.parmed_bd)": [[29, "arbdmodel.parmed_bd.ParmedArbd", false]], "parse_output() (hydroprorunner method)": [[27, "arbdmodel.engine.HydroProRunner.parse_output", false]], "particles (arbdengine attribute)": [[27, "arbdmodel.engine.ArbdEngine.particles", 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]], "position_spline_params (polymersection attribute)": [[15, "arbdmodel.polymer.PolymerSection.position_spline_params", 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]], "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, "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]], "potential_directory (arbdengine attribute)": [[27, "arbdmodel.engine.ArbdEngine.potential_directory", 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_spline_params (polymersection attribute)": [[15, "arbdmodel.polymer.PolymerSection.quaternion_spline_params", 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]], "rb_type_dirs (arbdengine attribute)": [[27, "arbdmodel.engine.ArbdEngine.rb_type_dirs", 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], [6, "id5", 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 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\ No newline at end of file
diff --git a/api/utilities/binary_manager.md b/api/utilities/binary_manager.md
index 01a72af8593605b5b57fb3e09b0223d03ef98d21..695eae845fbeed48722584b6229b82d1a4eac0dd 100644
--- a/api/utilities/binary_manager.md
+++ b/api/utilities/binary_manager.md
@@ -1,7 +1,6 @@
# binary_manager
-Binary path management module for simulation engines and processors.
-This module provides a singleton object to manage paths to external binaries.
+Module documentation for `arbdmodel.binary_manager`.
```{eval-rst}
.. automodule:: arbdmodel.binary_manager
diff --git a/api/utilities/index.md b/api/utilities/index.md
index 905bdc17c401b5edf992d9ed964eddc9c1f4f796..a754152251c84d788b0d0841c6b4f5a6fea82562 100644
--- a/api/utilities/index.md
+++ b/api/utilities/index.md
@@ -4,7 +4,7 @@ This section documents the utilities components of the arbdmodel package.
## Modules
-- [binary_manager](binary_manager.md): Binary path management module for simulation engines and processors.
+- [binary_manager](binary_manager.md): Module documentation for `arbdmodel.binary_manager`.
- [coords](coords.md): Module documentation for `arbdmodel.coords`.
- [grid](grid.md): Module documentation for `arbdmodel.grid`.
- [logger](logger.md): Module documentation for `arbdmodel.logger`.