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<h1>Source code for MMTK.ChemicalObjects</h1><div class="highlight"><pre>
<span class="c"># This module implements classes that represent atoms, molecules, and</span>
<span class="c"># complexes. They are made as copies from blueprints in the database.</span>
<span class="c">#</span>
<span class="c"># Written by Konrad Hinsen</span>
<span class="c">#</span>
<span class="sd">"""</span>
<span class="sd">Atoms, groups, molecules and similar objects</span>
<span class="sd">"""</span>
<span class="n">__docformat__</span> <span class="o">=</span> <span class="s">'restructuredtext'</span>
<span class="kn">from</span> <span class="nn">MMTK</span> <span class="kn">import</span> <span class="n">Bonds</span><span class="p">,</span> <span class="n">Collections</span><span class="p">,</span> <span class="n">Database</span><span class="p">,</span> \
<span class="n">Units</span><span class="p">,</span> <span class="n">Utility</span><span class="p">,</span> <span class="n">Visualization</span>
<span class="kn">from</span> <span class="nn">Scientific.Geometry</span> <span class="kn">import</span> <span class="n">Vector</span>
<span class="kn">from</span> <span class="nn">Scientific.Geometry</span> <span class="kn">import</span> <span class="n">Objects3D</span>
<span class="kn">from</span> <span class="nn">Scientific</span> <span class="kn">import</span> <span class="n">N</span>
<span class="kn">import</span> <span class="nn">copy</span>
<span class="c">#</span>
<span class="c"># The base class for all chemical objects.</span>
<span class="c">#</span>
<div class="viewcode-block" id="ChemicalObject"><a class="viewcode-back" href="../../modules.html#MMTK.ChemicalObjects.ChemicalObject">[docs]</a><span class="k">class</span> <span class="nc">ChemicalObject</span><span class="p">(</span><span class="n">Collections</span><span class="o">.</span><span class="n">GroupOfAtoms</span><span class="p">,</span> <span class="n">Visualization</span><span class="o">.</span><span class="n">Viewable</span><span class="p">):</span>
<span class="sd">"""</span>
<span class="sd"> General chemical object</span>
<span class="sd"> This is an abstract base class that implements methods which</span>
<span class="sd"> are applicable to any chemical object (atom, molecule, etc.).</span>
<span class="sd"> """</span>
<span class="k">def</span> <span class="nf">__init__</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">blueprint</span><span class="p">,</span> <span class="n">memo</span><span class="p">):</span>
<span class="k">if</span> <span class="nb">isinstance</span><span class="p">(</span><span class="n">blueprint</span><span class="p">,</span> <span class="nb">basestring</span><span class="p">):</span>
<span class="n">blueprint</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">blueprintclass</span><span class="p">(</span><span class="n">blueprint</span><span class="p">)</span>
<span class="bp">self</span><span class="o">.</span><span class="n">type</span> <span class="o">=</span> <span class="n">blueprint</span><span class="o">.</span><span class="n">type</span>
<span class="k">if</span> <span class="nb">hasattr</span><span class="p">(</span><span class="n">blueprint</span><span class="p">,</span> <span class="s">'name'</span><span class="p">):</span>
<span class="bp">self</span><span class="o">.</span><span class="n">name</span> <span class="o">=</span> <span class="n">blueprint</span><span class="o">.</span><span class="n">name</span>
<span class="k">if</span> <span class="n">memo</span> <span class="ow">is</span> <span class="bp">None</span><span class="p">:</span> <span class="n">memo</span> <span class="o">=</span> <span class="p">{}</span>
<span class="n">memo</span><span class="p">[</span><span class="nb">id</span><span class="p">(</span><span class="n">blueprint</span><span class="p">)]</span> <span class="o">=</span> <span class="bp">self</span>
<span class="k">for</span> <span class="n">attr</span> <span class="ow">in</span> <span class="n">blueprint</span><span class="o">.</span><span class="n">instance</span><span class="p">:</span>
<span class="nb">setattr</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">attr</span><span class="p">,</span>
<span class="n">Database</span><span class="o">.</span><span class="n">instantiate</span><span class="p">(</span><span class="nb">getattr</span><span class="p">(</span><span class="n">blueprint</span><span class="p">,</span> <span class="n">attr</span><span class="p">),</span> <span class="n">memo</span><span class="p">))</span>
<span class="n">is_chemical_object</span> <span class="o">=</span> <span class="bp">True</span>
<span class="n">is_incomplete</span> <span class="o">=</span> <span class="bp">False</span>
<span class="n">is_modified</span> <span class="o">=</span> <span class="bp">False</span>
<span class="n">__safe_for_unpickling__</span> <span class="o">=</span> <span class="bp">True</span>
<span class="n">__had_initargs__</span> <span class="o">=</span> <span class="bp">True</span>
<span class="k">def</span> <span class="nf">__hash__</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span>
<span class="k">return</span> <span class="nb">id</span><span class="p">(</span><span class="bp">self</span><span class="p">)</span>
<span class="k">def</span> <span class="nf">__getattr__</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">attr</span><span class="p">):</span>
<span class="k">if</span> <span class="n">attr</span><span class="p">[:</span><span class="mi">1</span><span class="p">]</span> <span class="o">==</span> <span class="s">'_'</span> <span class="ow">or</span> <span class="n">attr</span><span class="p">[:</span><span class="mi">3</span><span class="p">]</span> <span class="o">==</span> <span class="s">'is_'</span><span class="p">:</span>
<span class="k">raise</span> <span class="ne">AttributeError</span>
<span class="k">else</span><span class="p">:</span>
<span class="k">return</span> <span class="nb">getattr</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">type</span><span class="p">,</span> <span class="n">attr</span><span class="p">)</span>
<span class="k">def</span> <span class="nf">isSubsetModel</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span>
<span class="k">return</span> <span class="bp">False</span>
<span class="k">def</span> <span class="nf">addProperties</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">properties</span><span class="p">):</span>
<span class="k">if</span> <span class="n">properties</span><span class="p">:</span>
<span class="k">for</span> <span class="n">item</span> <span class="ow">in</span> <span class="n">properties</span><span class="o">.</span><span class="n">items</span><span class="p">():</span>
<span class="k">if</span> <span class="nb">hasattr</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">item</span><span class="p">[</span><span class="mi">0</span><span class="p">])</span> <span class="ow">and</span> <span class="n">item</span><span class="p">[</span><span class="mi">0</span><span class="p">]</span> <span class="o">!=</span> <span class="s">'name'</span><span class="p">:</span>
<span class="k">raise</span> <span class="ne">TypeError</span><span class="p">(</span><span class="s">'attribute '</span><span class="o">+</span><span class="n">item</span><span class="p">[</span><span class="mi">0</span><span class="p">]</span><span class="o">+</span><span class="s">' already defined'</span><span class="p">)</span>
<span class="nb">setattr</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">item</span><span class="p">[</span><span class="mi">0</span><span class="p">],</span> <span class="n">item</span><span class="p">[</span><span class="mi">1</span><span class="p">])</span>
<span class="k">def</span> <span class="nf">binaryProperty</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">properties</span><span class="p">,</span> <span class="n">name</span><span class="p">,</span> <span class="n">default</span><span class="p">):</span>
<span class="n">value</span> <span class="o">=</span> <span class="n">default</span>
<span class="k">try</span><span class="p">:</span>
<span class="n">value</span> <span class="o">=</span> <span class="n">properties</span><span class="p">[</span><span class="n">name</span><span class="p">]</span>
<span class="k">del</span> <span class="n">properties</span><span class="p">[</span><span class="n">name</span><span class="p">]</span>
<span class="k">except</span> <span class="ne">KeyError</span><span class="p">:</span>
<span class="k">pass</span>
<span class="k">return</span> <span class="n">value</span>
<div class="viewcode-block" id="ChemicalObject.topLevelChemicalObject"><a class="viewcode-back" href="../../modules.html#MMTK.ChemicalObjects.ChemicalObject.topLevelChemicalObject">[docs]</a> <span class="k">def</span> <span class="nf">topLevelChemicalObject</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span>
<span class="sd">"""Returns the highest-level chemical object of which</span>
<span class="sd"> the current object is a part."""</span>
<span class="k">if</span> <span class="bp">self</span><span class="o">.</span><span class="n">parent</span> <span class="ow">is</span> <span class="bp">None</span> <span class="ow">or</span> <span class="ow">not</span> <span class="n">isChemicalObject</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">parent</span><span class="p">):</span>
<span class="k">return</span> <span class="bp">self</span>
<span class="k">else</span><span class="p">:</span>
<span class="k">return</span> <span class="bp">self</span><span class="o">.</span><span class="n">parent</span><span class="o">.</span><span class="n">topLevelChemicalObject</span><span class="p">()</span>
</div>
<div class="viewcode-block" id="ChemicalObject.universe"><a class="viewcode-back" href="../../modules.html#MMTK.ChemicalObjects.ChemicalObject.universe">[docs]</a> <span class="k">def</span> <span class="nf">universe</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span>
<span class="sd">"""</span>
<span class="sd"> :returns: the universe to which the object belongs,</span>
<span class="sd"> or None if the object does not belong to any universe</span>
<span class="sd"> :rtype: :class:`~MMTK.Universe.Universe`</span>
<span class="sd"> """</span>
<span class="k">if</span> <span class="bp">self</span><span class="o">.</span><span class="n">parent</span> <span class="ow">is</span> <span class="bp">None</span><span class="p">:</span>
<span class="k">return</span> <span class="bp">None</span>
<span class="k">else</span><span class="p">:</span>
<span class="k">return</span> <span class="bp">self</span><span class="o">.</span><span class="n">parent</span><span class="o">.</span><span class="n">universe</span><span class="p">()</span>
</div>
<div class="viewcode-block" id="ChemicalObject.bondedUnits"><a class="viewcode-back" href="../../modules.html#MMTK.ChemicalObjects.ChemicalObject.bondedUnits">[docs]</a> <span class="k">def</span> <span class="nf">bondedUnits</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span>
<span class="sd">"""</span>
<span class="sd"> :returns: the largest subobjects which can contain bonds.</span>
<span class="sd"> There are no bonds between any of the subobjects</span>
<span class="sd"> in the list.</span>
<span class="sd"> :rtype: list</span>
<span class="sd"> """</span>
<span class="k">return</span> <span class="p">[</span><span class="bp">self</span><span class="p">]</span>
</div>
<div class="viewcode-block" id="ChemicalObject.atomList"><a class="viewcode-back" href="../../modules.html#MMTK.ChemicalObjects.ChemicalObject.atomList">[docs]</a> <span class="k">def</span> <span class="nf">atomList</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span>
<span class="sd">"""</span>
<span class="sd"> :returns: a list containing all atoms in the object</span>
<span class="sd"> :rtype: list</span>
<span class="sd"> """</span>
<span class="k">pass</span>
</div>
<div class="viewcode-block" id="ChemicalObject.atomIterator"><a class="viewcode-back" href="../../modules.html#MMTK.ChemicalObjects.ChemicalObject.atomIterator">[docs]</a> <span class="k">def</span> <span class="nf">atomIterator</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span>
<span class="sd">"""</span>
<span class="sd"> :returns: an iterator over all atoms in the object</span>
<span class="sd"> :rtype: iterator</span>
<span class="sd"> """</span>
<span class="k">pass</span>
</div>
<div class="viewcode-block" id="ChemicalObject.fullName"><a class="viewcode-back" href="../../modules.html#MMTK.ChemicalObjects.ChemicalObject.fullName">[docs]</a> <span class="k">def</span> <span class="nf">fullName</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span>
<span class="sd">"""</span>
<span class="sd"> :returns: the full name of the object. The full name consists</span>
<span class="sd"> of the proper name of the object preceded by</span>
<span class="sd"> the full name of its parent separated by a dot.</span>
<span class="sd"> :rtype: str</span>
<span class="sd"> """</span>
<span class="k">if</span> <span class="bp">self</span><span class="o">.</span><span class="n">parent</span> <span class="ow">is</span> <span class="bp">None</span> <span class="ow">or</span> <span class="ow">not</span> <span class="n">isChemicalObject</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">parent</span><span class="p">):</span>
<span class="k">return</span> <span class="bp">self</span><span class="o">.</span><span class="n">name</span>
<span class="k">else</span><span class="p">:</span>
<span class="k">return</span> <span class="bp">self</span><span class="o">.</span><span class="n">parent</span><span class="o">.</span><span class="n">fullName</span><span class="p">()</span> <span class="o">+</span> <span class="s">'.'</span> <span class="o">+</span> <span class="bp">self</span><span class="o">.</span><span class="n">name</span>
</div>
<div class="viewcode-block" id="ChemicalObject.degreesOfFreedom"><a class="viewcode-back" href="../../modules.html#MMTK.ChemicalObjects.ChemicalObject.degreesOfFreedom">[docs]</a> <span class="k">def</span> <span class="nf">degreesOfFreedom</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span>
<span class="sd">"""</span>
<span class="sd"> :returns: the number of degrees of freedom of the object</span>
<span class="sd"> :rtype: int</span>
<span class="sd"> """</span>
<span class="k">return</span> <span class="n">Collections</span><span class="o">.</span><span class="n">GroupOfAtoms</span><span class="o">.</span><span class="n">degreesOfFreedom</span><span class="p">(</span><span class="bp">self</span><span class="p">)</span> \
<span class="o">-</span> <span class="bp">self</span><span class="o">.</span><span class="n">numberOfDistanceConstraints</span><span class="p">()</span>
</div>
<div class="viewcode-block" id="ChemicalObject.distanceConstraintList"><a class="viewcode-back" href="../../modules.html#MMTK.ChemicalObjects.ChemicalObject.distanceConstraintList">[docs]</a> <span class="k">def</span> <span class="nf">distanceConstraintList</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span>
<span class="sd">"""</span>
<span class="sd"> :returns: the distance constraints of the object</span>
<span class="sd"> :rtype: list</span>
<span class="sd"> """</span>
<span class="k">return</span> <span class="p">[]</span>
</div>
<span class="k">def</span> <span class="nf">_distanceConstraintList</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span>
<span class="k">return</span> <span class="p">[]</span>
<span class="k">def</span> <span class="nf">traverseBondTree</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">function</span> <span class="o">=</span> <span class="bp">None</span><span class="p">):</span>
<span class="k">return</span> <span class="p">[]</span>
<div class="viewcode-block" id="ChemicalObject.numberOfDistanceConstraints"><a class="viewcode-back" href="../../modules.html#MMTK.ChemicalObjects.ChemicalObject.numberOfDistanceConstraints">[docs]</a> <span class="k">def</span> <span class="nf">numberOfDistanceConstraints</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span>
<span class="sd">"""</span>
<span class="sd"> :returns: the number of distance constraints of the object</span>
<span class="sd"> :rtype: int</span>
<span class="sd"> """</span>
<span class="k">return</span> <span class="mi">0</span>
</div>
<div class="viewcode-block" id="ChemicalObject.setBondConstraints"><a class="viewcode-back" href="../../modules.html#MMTK.ChemicalObjects.ChemicalObject.setBondConstraints">[docs]</a> <span class="k">def</span> <span class="nf">setBondConstraints</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">universe</span><span class="o">=</span><span class="bp">None</span><span class="p">):</span>
<span class="sd">"""</span>
<span class="sd"> Sets distance constraints for all bonds.</span>
<span class="sd"> """</span>
<span class="k">pass</span>
</div>
<div class="viewcode-block" id="ChemicalObject.removeDistanceConstraints"><a class="viewcode-back" href="../../modules.html#MMTK.ChemicalObjects.ChemicalObject.removeDistanceConstraints">[docs]</a> <span class="k">def</span> <span class="nf">removeDistanceConstraints</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">universe</span><span class="o">=</span><span class="bp">None</span><span class="p">):</span>
<span class="sd">"""</span>
<span class="sd"> Removes all distance constraints.</span>
<span class="sd"> """</span>
<span class="k">pass</span>
</div>
<div class="viewcode-block" id="ChemicalObject.setRigidBodyConstraints"><a class="viewcode-back" href="../../modules.html#MMTK.ChemicalObjects.ChemicalObject.setRigidBodyConstraints">[docs]</a> <span class="k">def</span> <span class="nf">setRigidBodyConstraints</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">universe</span> <span class="o">=</span> <span class="bp">None</span><span class="p">):</span>
<span class="sd">"""</span>
<span class="sd"> Sets distance constraints that make the object fully rigid.</span>
<span class="sd"> """</span>
<span class="k">if</span> <span class="n">universe</span> <span class="ow">is</span> <span class="bp">None</span><span class="p">:</span>
<span class="n">universe</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">universe</span><span class="p">()</span>
<span class="k">if</span> <span class="n">universe</span> <span class="ow">is</span> <span class="bp">None</span><span class="p">:</span>
<span class="kn">import</span> <span class="nn">Universe</span>
<span class="n">universe</span> <span class="o">=</span> <span class="n">Universe</span><span class="o">.</span><span class="n">InfiniteUniverse</span><span class="p">()</span>
<span class="n">atoms</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">atomList</span><span class="p">()</span>
<span class="k">if</span> <span class="nb">len</span><span class="p">(</span><span class="n">atoms</span><span class="p">)</span> <span class="o">></span> <span class="mi">1</span><span class="p">:</span>
<span class="bp">self</span><span class="o">.</span><span class="n">addDistanceConstraint</span><span class="p">(</span><span class="n">atoms</span><span class="p">[</span><span class="mi">0</span><span class="p">],</span> <span class="n">atoms</span><span class="p">[</span><span class="mi">1</span><span class="p">],</span>
<span class="n">universe</span><span class="o">.</span><span class="n">distance</span><span class="p">(</span><span class="n">atoms</span><span class="p">[</span><span class="mi">0</span><span class="p">],</span> <span class="n">atoms</span><span class="p">[</span><span class="mi">1</span><span class="p">]))</span>
<span class="k">if</span> <span class="nb">len</span><span class="p">(</span><span class="n">atoms</span><span class="p">)</span> <span class="o">></span> <span class="mi">2</span><span class="p">:</span>
<span class="bp">self</span><span class="o">.</span><span class="n">addDistanceConstraint</span><span class="p">(</span><span class="n">atoms</span><span class="p">[</span><span class="mi">0</span><span class="p">],</span> <span class="n">atoms</span><span class="p">[</span><span class="mi">2</span><span class="p">],</span>
<span class="n">universe</span><span class="o">.</span><span class="n">distance</span><span class="p">(</span><span class="n">atoms</span><span class="p">[</span><span class="mi">0</span><span class="p">],</span> <span class="n">atoms</span><span class="p">[</span><span class="mi">2</span><span class="p">]))</span>
<span class="bp">self</span><span class="o">.</span><span class="n">addDistanceConstraint</span><span class="p">(</span><span class="n">atoms</span><span class="p">[</span><span class="mi">1</span><span class="p">],</span> <span class="n">atoms</span><span class="p">[</span><span class="mi">2</span><span class="p">],</span>
<span class="n">universe</span><span class="o">.</span><span class="n">distance</span><span class="p">(</span><span class="n">atoms</span><span class="p">[</span><span class="mi">1</span><span class="p">],</span> <span class="n">atoms</span><span class="p">[</span><span class="mi">2</span><span class="p">]))</span>
<span class="k">if</span> <span class="nb">len</span><span class="p">(</span><span class="n">atoms</span><span class="p">)</span> <span class="o">></span> <span class="mi">3</span><span class="p">:</span>
<span class="k">for</span> <span class="n">a</span> <span class="ow">in</span> <span class="n">atoms</span><span class="p">[</span><span class="mi">3</span><span class="p">:]:</span>
<span class="bp">self</span><span class="o">.</span><span class="n">addDistanceConstraint</span><span class="p">(</span><span class="n">atoms</span><span class="p">[</span><span class="mi">0</span><span class="p">],</span> <span class="n">a</span><span class="p">,</span>
<span class="n">universe</span><span class="o">.</span><span class="n">distance</span><span class="p">(</span><span class="n">atoms</span><span class="p">[</span><span class="mi">0</span><span class="p">],</span> <span class="n">a</span><span class="p">))</span>
<span class="bp">self</span><span class="o">.</span><span class="n">addDistanceConstraint</span><span class="p">(</span><span class="n">atoms</span><span class="p">[</span><span class="mi">1</span><span class="p">],</span> <span class="n">a</span><span class="p">,</span>
<span class="n">universe</span><span class="o">.</span><span class="n">distance</span><span class="p">(</span><span class="n">atoms</span><span class="p">[</span><span class="mi">1</span><span class="p">],</span> <span class="n">a</span><span class="p">))</span>
<span class="bp">self</span><span class="o">.</span><span class="n">addDistanceConstraint</span><span class="p">(</span><span class="n">atoms</span><span class="p">[</span><span class="mi">2</span><span class="p">],</span> <span class="n">a</span><span class="p">,</span>
<span class="n">universe</span><span class="o">.</span><span class="n">distance</span><span class="p">(</span><span class="n">atoms</span><span class="p">[</span><span class="mi">2</span><span class="p">],</span> <span class="n">a</span><span class="p">))</span>
</div>
<div class="viewcode-block" id="ChemicalObject.getAtomProperty"><a class="viewcode-back" href="../../modules.html#MMTK.ChemicalObjects.ChemicalObject.getAtomProperty">[docs]</a> <span class="k">def</span> <span class="nf">getAtomProperty</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">atom</span><span class="p">,</span> <span class="nb">property</span><span class="p">):</span>
<span class="sd">"""</span>
<span class="sd"> Retrieve atom properties from the chemical database.</span>
<span class="sd"> Note: the property is first looked up in the database entry</span>
<span class="sd"> for the object on which the method is called. If the lookup</span>
<span class="sd"> fails, the complete hierarchy from the atom to the top-level</span>
<span class="sd"> object is constructed and traversed starting from the top-level</span>
<span class="sd"> object until the property is found. This permits database entries</span>
<span class="sd"> for higher-level objects to override property definitions in</span>
<span class="sd"> its constituents.</span>
<span class="sd"> At the atom level, the property is retrieved from an attribute</span>
<span class="sd"> with the same name. This means that properties at the atom</span>
<span class="sd"> level can be defined both in the chemical database and for</span>
<span class="sd"> each atom individually by assignment to the attribute.</span>
<span class="sd"> </span>
<span class="sd"> :returns: the value of the specified property for the given</span>
<span class="sd"> atom from the chemical database.</span>
<span class="sd"> """</span>
</div>
<span class="k">def</span> <span class="nf">writeXML</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="nb">file</span><span class="p">,</span> <span class="n">memo</span><span class="p">,</span> <span class="n">toplevel</span><span class="o">=</span><span class="mi">1</span><span class="p">):</span>
<span class="k">if</span> <span class="bp">self</span><span class="o">.</span><span class="n">type</span> <span class="ow">is</span> <span class="bp">None</span><span class="p">:</span>
<span class="n">name</span> <span class="o">=</span> <span class="s">'m'</span> <span class="o">+</span> <span class="sb">`memo['counter']`</span>
<span class="n">memo</span><span class="p">[</span><span class="s">'counter'</span><span class="p">]</span> <span class="o">=</span> <span class="n">memo</span><span class="p">[</span><span class="s">'counter'</span><span class="p">]</span> <span class="o">+</span> <span class="mi">1</span>
<span class="n">memo</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="o">=</span> <span class="n">name</span>
<span class="n">atoms</span> <span class="o">=</span> <span class="n">copy</span><span class="o">.</span><span class="n">copy</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">atoms</span><span class="p">)</span>
<span class="n">bonds</span> <span class="o">=</span> <span class="n">copy</span><span class="o">.</span><span class="n">copy</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">bonds</span><span class="p">)</span>
<span class="k">for</span> <span class="n">group</span> <span class="ow">in</span> <span class="bp">self</span><span class="o">.</span><span class="n">groups</span><span class="p">:</span>
<span class="n">group</span><span class="o">.</span><span class="n">writeXML</span><span class="p">(</span><span class="nb">file</span><span class="p">,</span> <span class="n">memo</span><span class="p">,</span> <span class="mi">0</span><span class="p">)</span>
<span class="k">for</span> <span class="n">atom</span> <span class="ow">in</span> <span class="n">group</span><span class="o">.</span><span class="n">atoms</span><span class="p">:</span>
<span class="n">atoms</span><span class="o">.</span><span class="n">remove</span><span class="p">(</span><span class="n">atom</span><span class="p">)</span>
<span class="k">for</span> <span class="n">bond</span> <span class="ow">in</span> <span class="n">group</span><span class="o">.</span><span class="n">bonds</span><span class="p">:</span>
<span class="n">bonds</span><span class="o">.</span><span class="n">remove</span><span class="p">(</span><span class="n">bond</span><span class="p">)</span>
<span class="nb">file</span><span class="o">.</span><span class="n">write</span><span class="p">(</span><span class="s">'<molecule id="</span><span class="si">%s</span><span class="s">"></span><span class="se">\n</span><span class="s">'</span> <span class="o">%</span> <span class="n">name</span><span class="p">)</span>
<span class="k">for</span> <span class="n">group</span> <span class="ow">in</span> <span class="bp">self</span><span class="o">.</span><span class="n">groups</span><span class="p">:</span>
<span class="nb">file</span><span class="o">.</span><span class="n">write</span><span class="p">(</span><span class="s">' <molecule ref="</span><span class="si">%s</span><span class="s">" title="</span><span class="si">%s</span><span class="s">"/></span><span class="se">\n</span><span class="s">'</span>
<span class="o">%</span> <span class="p">(</span><span class="n">memo</span><span class="p">[</span><span class="nb">id</span><span class="p">(</span><span class="n">group</span><span class="o">.</span><span class="n">type</span><span class="p">)],</span> <span class="n">group</span><span class="o">.</span><span class="n">name</span><span class="p">))</span>
<span class="k">if</span> <span class="n">atoms</span><span class="p">:</span>
<span class="nb">file</span><span class="o">.</span><span class="n">write</span><span class="p">(</span><span class="s">' <atomArray></span><span class="se">\n</span><span class="s">'</span><span class="p">)</span>
<span class="k">for</span> <span class="n">atom</span> <span class="ow">in</span> <span class="n">atoms</span><span class="p">:</span>
<span class="nb">file</span><span class="o">.</span><span class="n">write</span><span class="p">(</span><span class="s">' <atom title="</span><span class="si">%s</span><span class="s">" elementType="</span><span class="si">%s</span><span class="s">"/></span><span class="se">\n</span><span class="s">'</span>
<span class="o">%</span> <span class="p">(</span><span class="n">atom</span><span class="o">.</span><span class="n">name</span><span class="p">,</span> <span class="n">atom</span><span class="o">.</span><span class="n">type</span><span class="o">.</span><span class="n">symbol</span><span class="p">))</span>
<span class="nb">file</span><span class="o">.</span><span class="n">write</span><span class="p">(</span><span class="s">' </atomArray></span><span class="se">\n</span><span class="s">'</span><span class="p">)</span>
<span class="k">if</span> <span class="n">bonds</span><span class="p">:</span>
<span class="nb">file</span><span class="o">.</span><span class="n">write</span><span class="p">(</span><span class="s">' <bondArray></span><span class="se">\n</span><span class="s">'</span><span class="p">)</span>
<span class="k">for</span> <span class="n">bond</span> <span class="ow">in</span> <span class="n">bonds</span><span class="p">:</span>
<span class="n">a1n</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">relativeName</span><span class="p">(</span><span class="n">bond</span><span class="o">.</span><span class="n">a1</span><span class="p">)</span>
<span class="n">a2n</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">relativeName</span><span class="p">(</span><span class="n">bond</span><span class="o">.</span><span class="n">a2</span><span class="p">)</span>
<span class="nb">file</span><span class="o">.</span><span class="n">write</span><span class="p">(</span><span class="s">' <bond atomRefs2="</span><span class="si">%s</span><span class="s"> </span><span class="si">%s</span><span class="s">"/></span><span class="se">\n</span><span class="s">'</span> <span class="o">%</span> <span class="p">(</span><span class="n">a1n</span><span class="p">,</span> <span class="n">a2n</span><span class="p">))</span>
<span class="nb">file</span><span class="o">.</span><span class="n">write</span><span class="p">(</span><span class="s">' </bondArray></span><span class="se">\n</span><span class="s">'</span><span class="p">)</span>
<span class="nb">file</span><span class="o">.</span><span class="n">write</span><span class="p">(</span><span class="s">'</molecule></span><span class="se">\n</span><span class="s">'</span><span class="p">)</span>
<span class="k">else</span><span class="p">:</span>
<span class="n">name</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">name</span>
<span class="bp">self</span><span class="o">.</span><span class="n">type</span><span class="o">.</span><span class="n">writeXML</span><span class="p">(</span><span class="nb">file</span><span class="p">,</span> <span class="n">memo</span><span class="p">)</span>
<span class="n">atom_names</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">type</span><span class="o">.</span><span class="n">getXMLAtomOrder</span><span class="p">()</span>
<span class="k">if</span> <span class="n">toplevel</span><span class="p">:</span>
<span class="k">return</span> <span class="p">[</span><span class="s">'<molecule ref="</span><span class="si">%s</span><span class="s">"/>'</span> <span class="o">%</span> <span class="n">name</span><span class="p">]</span>
<span class="k">else</span><span class="p">:</span>
<span class="k">return</span> <span class="bp">None</span>
<span class="k">def</span> <span class="nf">getXMLAtomOrder</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span>
<span class="k">if</span> <span class="bp">self</span><span class="o">.</span><span class="n">type</span> <span class="ow">is</span> <span class="bp">None</span><span class="p">:</span>
<span class="n">atoms</span> <span class="o">=</span> <span class="p">[]</span>
<span class="k">for</span> <span class="n">group</span> <span class="ow">in</span> <span class="bp">self</span><span class="o">.</span><span class="n">groups</span><span class="p">:</span>
<span class="n">atoms</span><span class="o">.</span><span class="n">extend</span><span class="p">(</span><span class="n">group</span><span class="o">.</span><span class="n">getXMLAtomOrder</span><span class="p">())</span>
<span class="k">for</span> <span class="n">atom</span> <span class="ow">in</span> <span class="bp">self</span><span class="o">.</span><span class="n">atoms</span><span class="p">:</span>
<span class="k">if</span> <span class="n">atom</span> <span class="ow">not</span> <span class="ow">in</span> <span class="n">atoms</span><span class="p">:</span>
<span class="n">atoms</span><span class="o">.</span><span class="n">append</span><span class="p">(</span><span class="n">atom</span><span class="p">)</span>
<span class="k">else</span><span class="p">:</span>
<span class="n">atom_names</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">type</span><span class="o">.</span><span class="n">getXMLAtomOrder</span><span class="p">()</span>
<span class="n">atoms</span> <span class="o">=</span> <span class="p">[]</span>
<span class="k">for</span> <span class="n">name</span> <span class="ow">in</span> <span class="n">atom_names</span><span class="p">:</span>
<span class="n">parts</span> <span class="o">=</span> <span class="n">name</span><span class="o">.</span><span class="n">split</span><span class="p">(</span><span class="s">':'</span><span class="p">)</span>
<span class="nb">object</span> <span class="o">=</span> <span class="bp">self</span>
<span class="k">for</span> <span class="n">attr</span> <span class="ow">in</span> <span class="n">parts</span><span class="p">:</span>
<span class="nb">object</span> <span class="o">=</span> <span class="nb">getattr</span><span class="p">(</span><span class="nb">object</span><span class="p">,</span> <span class="n">attr</span><span class="p">)</span>
<span class="n">atoms</span><span class="o">.</span><span class="n">append</span><span class="p">(</span><span class="nb">object</span><span class="p">)</span>
<span class="k">return</span> <span class="n">atoms</span>
<span class="k">def</span> <span class="nf">relativeName</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="nb">object</span><span class="p">):</span>
<span class="n">name</span> <span class="o">=</span> <span class="s">''</span>
<span class="k">while</span> <span class="nb">object</span> <span class="ow">is</span> <span class="ow">not</span> <span class="bp">None</span> <span class="ow">and</span> <span class="nb">object</span> <span class="o">!=</span> <span class="bp">self</span><span class="p">:</span>
<span class="n">name</span> <span class="o">=</span> <span class="nb">object</span><span class="o">.</span><span class="n">name</span> <span class="o">+</span> <span class="s">':'</span> <span class="o">+</span> <span class="n">name</span>
<span class="nb">object</span> <span class="o">=</span> <span class="nb">object</span><span class="o">.</span><span class="n">parent</span>
<span class="k">return</span> <span class="n">name</span><span class="p">[:</span><span class="o">-</span><span class="mi">1</span><span class="p">]</span>
<span class="k">def</span> <span class="nf">relativeName_unused</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="nb">object</span><span class="p">):</span>
<span class="n">name</span> <span class="o">=</span> <span class="s">''</span>
<span class="k">while</span> <span class="nb">object</span> <span class="ow">is</span> <span class="ow">not</span> <span class="bp">None</span> <span class="ow">and</span> <span class="nb">object</span> <span class="o">!=</span> <span class="bp">self</span><span class="p">:</span>
<span class="k">for</span> <span class="n">attr</span><span class="p">,</span> <span class="n">value</span> <span class="ow">in</span> <span class="nb">object</span><span class="o">.</span><span class="n">parent</span><span class="o">.</span><span class="n">__dict__</span><span class="o">.</span><span class="n">items</span><span class="p">():</span>
<span class="k">if</span> <span class="n">value</span> <span class="ow">is</span> <span class="nb">object</span><span class="p">:</span>
<span class="n">name</span> <span class="o">=</span> <span class="n">attr</span> <span class="o">+</span> <span class="s">':'</span> <span class="o">+</span> <span class="n">name</span>
<span class="k">break</span>
<span class="nb">object</span> <span class="o">=</span> <span class="nb">object</span><span class="o">.</span><span class="n">parent</span>
<span class="k">return</span> <span class="n">name</span><span class="p">[:</span><span class="o">-</span><span class="mi">1</span><span class="p">]</span>
<span class="k">def</span> <span class="nf">description</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">index_map</span> <span class="o">=</span> <span class="bp">None</span><span class="p">):</span>
<span class="n">tag</span> <span class="o">=</span> <span class="n">Utility</span><span class="o">.</span><span class="n">uniqueAttribute</span><span class="p">()</span>
<span class="n">s</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">_description</span><span class="p">(</span><span class="n">tag</span><span class="p">,</span> <span class="n">index_map</span><span class="p">,</span> <span class="mi">1</span><span class="p">)</span>
<span class="k">for</span> <span class="n">a</span> <span class="ow">in</span> <span class="bp">self</span><span class="o">.</span><span class="n">atomList</span><span class="p">():</span>
<span class="nb">delattr</span><span class="p">(</span><span class="n">a</span><span class="p">,</span> <span class="n">tag</span><span class="p">)</span>
<span class="k">return</span> <span class="n">s</span>
<span class="k">def</span> <span class="nf">__repr__</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span>
<span class="k">return</span> <span class="bp">self</span><span class="o">.</span><span class="n">__class__</span><span class="o">.</span><span class="n">__name__</span> <span class="o">+</span> <span class="s">' '</span> <span class="o">+</span> <span class="bp">self</span><span class="o">.</span><span class="n">fullName</span><span class="p">()</span>
<span class="n">__str__</span> <span class="o">=</span> <span class="n">__repr__</span>
<span class="k">def</span> <span class="nf">__copy__</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span>
<span class="k">return</span> <span class="n">copy</span><span class="o">.</span><span class="n">deepcopy</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="p">{</span><span class="nb">id</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">parent</span><span class="p">):</span> <span class="bp">None</span><span class="p">})</span>
<span class="c"># Type check</span>
</div>
<div class="viewcode-block" id="isChemicalObject"><a class="viewcode-back" href="../../modules.html#MMTK.ChemicalObjects.isChemicalObject">[docs]</a><span class="k">def</span> <span class="nf">isChemicalObject</span><span class="p">(</span><span class="nb">object</span><span class="p">):</span>
<span class="sd">"""</span>
<span class="sd"> :returns: True if object is a chemical object</span>
<span class="sd"> """</span>
<span class="k">return</span> <span class="nb">hasattr</span><span class="p">(</span><span class="nb">object</span><span class="p">,</span> <span class="s">'is_chemical_object'</span><span class="p">)</span>
<span class="c">#</span>
<span class="c"># The second base class for all composite chemical objects.</span>
<span class="c">#</span></div>
<div class="viewcode-block" id="CompositeChemicalObject"><a class="viewcode-back" href="../../modules.html#MMTK.ChemicalObjects.CompositeChemicalObject">[docs]</a><span class="k">class</span> <span class="nc">CompositeChemicalObject</span><span class="p">(</span><span class="nb">object</span><span class="p">):</span>
<span class="sd">"""</span>
<span class="sd"> Chemical object containing subobjects</span>
<span class="sd"> This is an abstract base class that implements methods</span>
<span class="sd"> which can be used with any composite chemical object,</span>
<span class="sd"> i.e. any chemical object that is not an atom.</span>
<span class="sd"> """</span>
<span class="k">def</span> <span class="nf">__init__</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">properties</span><span class="p">):</span>
<span class="k">if</span> <span class="n">properties</span><span class="o">.</span><span class="n">has_key</span><span class="p">(</span><span class="s">'configuration'</span><span class="p">):</span>
<span class="n">conf</span> <span class="o">=</span> <span class="n">properties</span><span class="p">[</span><span class="s">'configuration'</span><span class="p">]</span>
<span class="bp">self</span><span class="o">.</span><span class="n">configurations</span><span class="p">[</span><span class="n">conf</span><span class="p">]</span><span class="o">.</span><span class="n">applyTo</span><span class="p">(</span><span class="bp">self</span><span class="p">)</span>
<span class="k">del</span> <span class="n">properties</span><span class="p">[</span><span class="s">'configuration'</span><span class="p">]</span>
<span class="k">elif</span> <span class="nb">hasattr</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="s">'configurations'</span><span class="p">)</span> <span class="ow">and</span> \
<span class="bp">self</span><span class="o">.</span><span class="n">configurations</span><span class="o">.</span><span class="n">has_key</span><span class="p">(</span><span class="s">'default'</span><span class="p">):</span>
<span class="bp">self</span><span class="o">.</span><span class="n">configurations</span><span class="p">[</span><span class="s">'default'</span><span class="p">]</span><span class="o">.</span><span class="n">applyTo</span><span class="p">(</span><span class="bp">self</span><span class="p">)</span>
<span class="k">if</span> <span class="n">properties</span><span class="o">.</span><span class="n">has_key</span><span class="p">(</span><span class="s">'position'</span><span class="p">):</span>
<span class="bp">self</span><span class="o">.</span><span class="n">translateTo</span><span class="p">(</span><span class="n">properties</span><span class="p">[</span><span class="s">'position'</span><span class="p">])</span>
<span class="k">del</span> <span class="n">properties</span><span class="p">[</span><span class="s">'position'</span><span class="p">]</span>
<span class="bp">self</span><span class="o">.</span><span class="n">addProperties</span><span class="p">(</span><span class="n">properties</span><span class="p">)</span>
<span class="k">def</span> <span class="nf">atomList</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span>
<span class="k">return</span> <span class="bp">self</span><span class="o">.</span><span class="n">atoms</span>
<span class="k">def</span> <span class="nf">atomIterator</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span>
<span class="k">return</span> <span class="nb">iter</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">atoms</span><span class="p">)</span>
<span class="k">def</span> <span class="nf">setPosition</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">atom</span><span class="p">,</span> <span class="n">position</span><span class="p">):</span>
<span class="k">if</span> <span class="n">atom</span><span class="o">.</span><span class="n">__class__</span> <span class="ow">is</span> <span class="n">Database</span><span class="o">.</span><span class="n">AtomReference</span><span class="p">:</span>
<span class="n">atom</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">atoms</span><span class="p">[</span><span class="n">atom</span><span class="o">.</span><span class="n">number</span><span class="p">]</span>
<span class="n">atom</span><span class="o">.</span><span class="n">setPosition</span><span class="p">(</span><span class="n">position</span><span class="p">)</span>
<span class="k">def</span> <span class="nf">setIndex</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">atom</span><span class="p">,</span> <span class="n">index</span><span class="p">):</span>
<span class="k">if</span> <span class="n">atom</span><span class="o">.</span><span class="n">__class__</span> <span class="ow">is</span> <span class="n">Database</span><span class="o">.</span><span class="n">AtomReference</span><span class="p">:</span>
<span class="n">atom</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">atoms</span><span class="p">[</span><span class="n">atom</span><span class="o">.</span><span class="n">number</span><span class="p">]</span>
<span class="n">atom</span><span class="o">.</span><span class="n">setIndex</span><span class="p">(</span><span class="n">index</span><span class="p">)</span>
<span class="k">def</span> <span class="nf">getAtom</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">atom</span><span class="p">):</span>
<span class="k">if</span> <span class="n">atom</span><span class="o">.</span><span class="n">__class__</span> <span class="ow">is</span> <span class="n">Database</span><span class="o">.</span><span class="n">AtomReference</span><span class="p">:</span>
<span class="n">atom</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">atoms</span><span class="p">[</span><span class="n">atom</span><span class="o">.</span><span class="n">number</span><span class="p">]</span>
<span class="k">return</span> <span class="n">atom</span>
<span class="k">def</span> <span class="nf">getReference</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">atom</span><span class="p">):</span>
<span class="k">if</span> <span class="n">atom</span><span class="o">.</span><span class="n">__class__</span> <span class="ow">is</span> <span class="n">Database</span><span class="o">.</span><span class="n">AtomReference</span><span class="p">:</span>
<span class="k">return</span> <span class="n">atom</span>
<span class="k">return</span> <span class="n">Database</span><span class="o">.</span><span class="n">AtomReference</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">atoms</span><span class="o">.</span><span class="n">index</span><span class="p">(</span><span class="n">atom</span><span class="p">))</span>
<span class="k">def</span> <span class="nf">getAtomProperty</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">atom</span><span class="p">,</span> <span class="nb">property</span><span class="p">,</span> <span class="n">levels</span> <span class="o">=</span> <span class="bp">None</span><span class="p">):</span>
<span class="k">try</span><span class="p">:</span>
<span class="k">return</span> <span class="n">atom</span><span class="o">.</span><span class="n">__dict__</span><span class="p">[</span><span class="nb">property</span><span class="p">]</span>
<span class="k">except</span> <span class="ne">KeyError</span><span class="p">:</span>
<span class="k">try</span><span class="p">:</span>
<span class="k">return</span> <span class="nb">getattr</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="nb">property</span><span class="p">)[</span><span class="bp">self</span><span class="o">.</span><span class="n">getReference</span><span class="p">(</span><span class="n">atom</span><span class="p">)]</span>
<span class="k">except</span> <span class="p">(</span><span class="ne">AttributeError</span><span class="p">,</span> <span class="ne">KeyError</span><span class="p">):</span>
<span class="k">if</span> <span class="n">levels</span> <span class="ow">is</span> <span class="bp">None</span><span class="p">:</span>
<span class="nb">object</span> <span class="o">=</span> <span class="n">atom</span>
<span class="n">levels</span> <span class="o">=</span> <span class="p">[]</span>
<span class="k">while</span> <span class="nb">object</span> <span class="o">!=</span> <span class="bp">self</span><span class="p">:</span>
<span class="n">levels</span><span class="o">.</span><span class="n">append</span><span class="p">(</span><span class="nb">object</span><span class="p">)</span>
<span class="nb">object</span> <span class="o">=</span> <span class="nb">object</span><span class="o">.</span><span class="n">parent</span>
<span class="k">if</span> <span class="ow">not</span> <span class="n">levels</span><span class="p">:</span>
<span class="k">raise</span> <span class="ne">KeyError</span><span class="p">(</span><span class="s">'Property '</span> <span class="o">+</span> <span class="nb">property</span> <span class="o">+</span>
<span class="s">' not defined for '</span><span class="p">,</span> <span class="sb">`atom`</span><span class="p">)</span>
<span class="k">return</span> <span class="n">levels</span><span class="p">[</span><span class="o">-</span><span class="mi">1</span><span class="p">]</span><span class="o">.</span><span class="n">getAtomProperty</span><span class="p">(</span><span class="n">atom</span><span class="p">,</span> <span class="nb">property</span><span class="p">,</span> <span class="n">levels</span><span class="p">[:</span><span class="o">-</span><span class="mi">1</span><span class="p">])</span>
<span class="k">def</span> <span class="nf">deleteUndefinedAtoms</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span>
<span class="n">delete</span> <span class="o">=</span> <span class="p">[</span><span class="n">a</span> <span class="k">for</span> <span class="n">a</span> <span class="ow">in</span> <span class="bp">self</span><span class="o">.</span><span class="n">atoms</span> <span class="k">if</span> <span class="n">a</span><span class="o">.</span><span class="n">position</span><span class="p">()</span> <span class="ow">is</span> <span class="bp">None</span><span class="p">]</span>
<span class="k">for</span> <span class="n">a</span> <span class="ow">in</span> <span class="n">delete</span><span class="p">:</span>
<span class="n">a</span><span class="o">.</span><span class="n">delete</span><span class="p">()</span>
<span class="k">def</span> <span class="nf">_deleteAtom</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">atom</span><span class="p">):</span>
<span class="bp">self</span><span class="o">.</span><span class="n">atoms</span><span class="o">.</span><span class="n">remove</span><span class="p">(</span><span class="n">atom</span><span class="p">)</span>
<span class="bp">self</span><span class="o">.</span><span class="n">is_modified</span> <span class="o">=</span> <span class="bp">True</span>
<span class="bp">self</span><span class="o">.</span><span class="n">type</span> <span class="o">=</span> <span class="bp">None</span>
<span class="k">if</span> <span class="bp">self</span><span class="o">.</span><span class="n">parent</span> <span class="ow">is</span> <span class="ow">not</span> <span class="bp">None</span><span class="p">:</span>
<span class="bp">self</span><span class="o">.</span><span class="n">parent</span><span class="o">.</span><span class="n">_deleteAtom</span><span class="p">(</span><span class="n">atom</span><span class="p">)</span>
<span class="k">def</span> <span class="nf">distanceConstraintList</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span>
<span class="n">dc</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">_distanceConstraintList</span><span class="p">()</span>
<span class="k">for</span> <span class="n">o</span> <span class="ow">in</span> <span class="bp">self</span><span class="o">.</span><span class="n">_subunits</span><span class="p">():</span>
<span class="n">dc</span> <span class="o">=</span> <span class="n">dc</span> <span class="o">+</span> <span class="n">o</span><span class="o">.</span><span class="n">_distanceConstraintList</span><span class="p">()</span>
<span class="k">return</span> <span class="n">dc</span>
<span class="k">def</span> <span class="nf">_distanceConstraintList</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span>
<span class="k">try</span><span class="p">:</span>
<span class="k">return</span> <span class="bp">self</span><span class="o">.</span><span class="n">distance_constraints</span>
<span class="k">except</span> <span class="ne">AttributeError</span><span class="p">:</span>
<span class="k">return</span> <span class="p">[]</span>
<span class="k">def</span> <span class="nf">numberOfDistanceConstraints</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span>
<span class="n">n</span> <span class="o">=</span> <span class="nb">len</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">_distanceConstraintList</span><span class="p">())</span> <span class="o">+</span> \
<span class="nb">sum</span><span class="p">(</span><span class="nb">len</span><span class="p">(</span><span class="n">o</span><span class="o">.</span><span class="n">_distanceConstraintList</span><span class="p">())</span> <span class="k">for</span> <span class="n">o</span> <span class="ow">in</span> <span class="bp">self</span><span class="o">.</span><span class="n">_subunits</span><span class="p">())</span>
<span class="k">return</span> <span class="n">n</span>
<span class="k">def</span> <span class="nf">setBondConstraints</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">universe</span><span class="o">=</span><span class="bp">None</span><span class="p">):</span>
<span class="k">if</span> <span class="n">universe</span> <span class="ow">is</span> <span class="bp">None</span><span class="p">:</span>
<span class="n">universe</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">universe</span><span class="p">()</span>
<span class="n">bond_database</span> <span class="o">=</span> <span class="n">universe</span><span class="o">.</span><span class="n">bondLengthDatabase</span><span class="p">()</span>
<span class="k">for</span> <span class="n">o</span> <span class="ow">in</span> <span class="bp">self</span><span class="o">.</span><span class="n">bondedUnits</span><span class="p">():</span>
<span class="n">o</span><span class="o">.</span><span class="n">_setBondConstraints</span><span class="p">(</span><span class="n">universe</span><span class="p">,</span> <span class="n">bond_database</span><span class="p">)</span>
<span class="k">def</span> <span class="nf">_setBondConstraints</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">universe</span><span class="p">,</span> <span class="n">bond_database</span><span class="p">):</span>
<span class="bp">self</span><span class="o">.</span><span class="n">distance_constraints</span> <span class="o">=</span> <span class="p">[]</span>
<span class="k">for</span> <span class="n">bond</span> <span class="ow">in</span> <span class="bp">self</span><span class="o">.</span><span class="n">bonds</span><span class="p">:</span>
<span class="n">d</span> <span class="o">=</span> <span class="n">bond_database</span><span class="o">.</span><span class="n">bondLength</span><span class="p">(</span><span class="n">bond</span><span class="p">)</span>
<span class="k">if</span> <span class="n">d</span> <span class="ow">is</span> <span class="bp">None</span><span class="p">:</span>
<span class="n">d</span> <span class="o">=</span> <span class="n">universe</span><span class="o">.</span><span class="n">distance</span><span class="p">(</span><span class="n">bond</span><span class="o">.</span><span class="n">a1</span><span class="p">,</span> <span class="n">bond</span><span class="o">.</span><span class="n">a2</span><span class="p">)</span>
<span class="bp">self</span><span class="o">.</span><span class="n">addDistanceConstraint</span><span class="p">(</span><span class="n">bond</span><span class="o">.</span><span class="n">a1</span><span class="p">,</span> <span class="n">bond</span><span class="o">.</span><span class="n">a2</span><span class="p">,</span> <span class="n">d</span><span class="p">)</span>
<span class="k">def</span> <span class="nf">addDistanceConstraint</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">atom1</span><span class="p">,</span> <span class="n">atom2</span><span class="p">,</span> <span class="n">distance</span><span class="p">):</span>
<span class="k">try</span><span class="p">:</span>
<span class="bp">self</span><span class="o">.</span><span class="n">distance_constraints</span><span class="o">.</span><span class="n">append</span><span class="p">((</span><span class="n">atom1</span><span class="p">,</span> <span class="n">atom2</span><span class="p">,</span> <span class="n">distance</span><span class="p">))</span>
<span class="k">except</span> <span class="ne">AttributeError</span><span class="p">:</span>
<span class="bp">self</span><span class="o">.</span><span class="n">distance_constraints</span> <span class="o">=</span> <span class="p">[(</span><span class="n">atom1</span><span class="p">,</span> <span class="n">atom2</span><span class="p">,</span> <span class="n">distance</span><span class="p">)]</span>
<span class="k">def</span> <span class="nf">removeDistanceConstraints</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">universe</span><span class="o">=</span><span class="bp">None</span><span class="p">):</span>
<span class="k">try</span><span class="p">:</span>
<span class="k">del</span> <span class="bp">self</span><span class="o">.</span><span class="n">distance_constraints</span>
<span class="k">except</span> <span class="ne">AttributeError</span><span class="p">:</span>
<span class="k">pass</span>
<span class="k">for</span> <span class="n">o</span> <span class="ow">in</span> <span class="bp">self</span><span class="o">.</span><span class="n">_subunits</span><span class="p">():</span>
<span class="n">o</span><span class="o">.</span><span class="n">removeDistanceConstraints</span><span class="p">()</span>
<span class="k">def</span> <span class="nf">traverseBondTree</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">function</span> <span class="o">=</span> <span class="bp">None</span><span class="p">):</span>
<span class="bp">self</span><span class="o">.</span><span class="n">setBondAttributes</span><span class="p">()</span>
<span class="n">todo</span> <span class="o">=</span> <span class="p">[</span><span class="bp">self</span><span class="o">.</span><span class="n">atoms</span><span class="p">[</span><span class="mi">0</span><span class="p">]]</span>
<span class="n">done</span> <span class="o">=</span> <span class="p">{</span><span class="n">todo</span><span class="p">[</span><span class="mi">0</span><span class="p">]:</span> <span class="bp">True</span><span class="p">}</span>
<span class="n">bonds</span> <span class="o">=</span> <span class="p">[]</span>
<span class="k">while</span> <span class="n">todo</span><span class="p">:</span>
<span class="n">next_todo</span> <span class="o">=</span> <span class="p">[]</span>
<span class="k">for</span> <span class="n">atom</span> <span class="ow">in</span> <span class="n">todo</span><span class="p">:</span>
<span class="n">bonded</span> <span class="o">=</span> <span class="n">atom</span><span class="o">.</span><span class="n">bondedTo</span><span class="p">()</span>
<span class="k">for</span> <span class="n">other</span> <span class="ow">in</span> <span class="n">bonded</span><span class="p">:</span>
<span class="k">if</span> <span class="ow">not</span> <span class="n">done</span><span class="o">.</span><span class="n">get</span><span class="p">(</span><span class="n">other</span><span class="p">,</span> <span class="bp">False</span><span class="p">):</span>
<span class="k">if</span> <span class="n">function</span> <span class="ow">is</span> <span class="bp">None</span><span class="p">:</span>
<span class="n">bonds</span><span class="o">.</span><span class="n">append</span><span class="p">((</span><span class="n">atom</span><span class="p">,</span> <span class="n">other</span><span class="p">))</span>
<span class="k">else</span><span class="p">:</span>
<span class="n">bonds</span><span class="o">.</span><span class="n">append</span><span class="p">((</span><span class="n">function</span><span class="p">(</span><span class="n">atom</span><span class="p">),</span> <span class="n">function</span><span class="p">(</span><span class="n">other</span><span class="p">)))</span>
<span class="n">next_todo</span><span class="o">.</span><span class="n">append</span><span class="p">(</span><span class="n">other</span><span class="p">)</span>
<span class="n">done</span><span class="p">[</span><span class="n">other</span><span class="p">]</span> <span class="o">=</span> <span class="bp">True</span>
<span class="n">todo</span> <span class="o">=</span> <span class="n">next_todo</span>
<span class="bp">self</span><span class="o">.</span><span class="n">clearBondAttributes</span><span class="p">()</span>
<span class="k">return</span> <span class="n">bonds</span>
<span class="k">def</span> <span class="nf">_description</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">tag</span><span class="p">,</span> <span class="n">index_map</span><span class="p">,</span> <span class="n">toplevel</span><span class="p">):</span>
<span class="n">letter</span><span class="p">,</span> <span class="n">kwargs</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">_descriptionSpec</span><span class="p">()</span>
<span class="n">s</span> <span class="o">=</span> <span class="p">[</span><span class="n">letter</span><span class="p">,</span> <span class="s">'('</span><span class="p">,</span> <span class="sb">`self.name`</span><span class="p">,</span> <span class="s">',['</span><span class="p">]</span>
<span class="n">s</span><span class="o">.</span><span class="n">extend</span><span class="p">([</span><span class="n">o</span><span class="o">.</span><span class="n">_description</span><span class="p">(</span><span class="n">tag</span><span class="p">,</span> <span class="n">index_map</span><span class="p">,</span> <span class="mi">0</span><span class="p">)</span> <span class="o">+</span> <span class="s">','</span>
<span class="k">for</span> <span class="n">o</span> <span class="ow">in</span> <span class="bp">self</span><span class="o">.</span><span class="n">_subunits</span><span class="p">()])</span>
<span class="n">s</span><span class="o">.</span><span class="n">extend</span><span class="p">([</span><span class="n">a</span><span class="o">.</span><span class="n">_description</span><span class="p">(</span><span class="n">tag</span><span class="p">,</span> <span class="n">index_map</span><span class="p">,</span> <span class="mi">0</span><span class="p">)</span> <span class="o">+</span> <span class="s">','</span>
<span class="k">for</span> <span class="n">a</span> <span class="ow">in</span> <span class="bp">self</span><span class="o">.</span><span class="n">atoms</span> <span class="k">if</span> <span class="ow">not</span> <span class="nb">hasattr</span><span class="p">(</span><span class="n">a</span><span class="p">,</span> <span class="n">tag</span><span class="p">)])</span>
<span class="n">s</span><span class="o">.</span><span class="n">append</span><span class="p">(</span><span class="s">']'</span><span class="p">)</span>
<span class="k">if</span> <span class="n">toplevel</span><span class="p">:</span>
<span class="n">s</span><span class="o">.</span><span class="n">extend</span><span class="p">([</span><span class="s">','</span><span class="p">,</span> <span class="sb">`self._typeName()`</span><span class="p">])</span>
<span class="k">if</span> <span class="n">kwargs</span> <span class="ow">is</span> <span class="ow">not</span> <span class="bp">None</span><span class="p">:</span>
<span class="n">s</span><span class="o">.</span><span class="n">extend</span><span class="p">([</span><span class="s">','</span><span class="p">,</span> <span class="n">kwargs</span><span class="p">])</span>
<span class="n">constraints</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">_distanceConstraintList</span><span class="p">()</span>
<span class="k">if</span> <span class="n">constraints</span><span class="p">:</span>
<span class="n">s</span><span class="o">.</span><span class="n">append</span><span class="p">(</span><span class="s">',dc=['</span><span class="p">)</span>
<span class="k">if</span> <span class="n">index_map</span> <span class="ow">is</span> <span class="bp">None</span><span class="p">:</span>
<span class="n">s</span><span class="o">.</span><span class="n">extend</span><span class="p">([</span><span class="s">'(</span><span class="si">%d</span><span class="s">,</span><span class="si">%d</span><span class="s">,</span><span class="si">%f</span><span class="s">),'</span> <span class="o">%</span> <span class="p">(</span><span class="n">c</span><span class="p">[</span><span class="mi">0</span><span class="p">]</span><span class="o">.</span><span class="n">index</span><span class="p">,</span> <span class="n">c</span><span class="p">[</span><span class="mi">1</span><span class="p">]</span><span class="o">.</span><span class="n">index</span><span class="p">,</span> <span class="n">c</span><span class="p">[</span><span class="mi">2</span><span class="p">])</span>
<span class="k">for</span> <span class="n">c</span> <span class="ow">in</span> <span class="n">constraints</span><span class="p">])</span>
<span class="k">else</span><span class="p">:</span>
<span class="n">s</span><span class="o">.</span><span class="n">extend</span><span class="p">([</span><span class="s">'(</span><span class="si">%d</span><span class="s">,</span><span class="si">%d</span><span class="s">,</span><span class="si">%f</span><span class="s">),'</span> <span class="o">%</span> <span class="p">(</span><span class="n">index_map</span><span class="p">[</span><span class="n">c</span><span class="p">[</span><span class="mi">0</span><span class="p">]</span><span class="o">.</span><span class="n">index</span><span class="p">],</span>
<span class="n">index_map</span><span class="p">[</span><span class="n">c</span><span class="p">[</span><span class="mi">1</span><span class="p">]</span><span class="o">.</span><span class="n">index</span><span class="p">],</span> <span class="n">c</span><span class="p">[</span><span class="mi">2</span><span class="p">])</span>
<span class="k">for</span> <span class="n">c</span> <span class="ow">in</span> <span class="n">constraints</span><span class="p">])</span>
<span class="n">s</span><span class="o">.</span><span class="n">append</span><span class="p">(</span><span class="s">']'</span><span class="p">)</span>
<span class="n">s</span><span class="o">.</span><span class="n">append</span><span class="p">(</span><span class="s">')'</span><span class="p">)</span>
<span class="k">return</span> <span class="s">''</span><span class="o">.</span><span class="n">join</span><span class="p">(</span><span class="n">s</span><span class="p">)</span>
<span class="k">def</span> <span class="nf">_typeName</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span>
<span class="k">return</span> <span class="bp">self</span><span class="o">.</span><span class="n">type</span><span class="o">.</span><span class="n">name</span>
<span class="k">def</span> <span class="nf">_graphics</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">conf</span><span class="p">,</span> <span class="n">distance_fn</span><span class="p">,</span> <span class="n">model</span><span class="p">,</span> <span class="n">module</span><span class="p">,</span> <span class="n">options</span><span class="p">):</span>
<span class="n">glist</span> <span class="o">=</span> <span class="p">[]</span>
<span class="k">for</span> <span class="n">bu</span> <span class="ow">in</span> <span class="bp">self</span><span class="o">.</span><span class="n">bondedUnits</span><span class="p">():</span>
<span class="k">for</span> <span class="n">a</span> <span class="ow">in</span> <span class="n">bu</span><span class="o">.</span><span class="n">atomList</span><span class="p">():</span>
<span class="n">glist</span><span class="o">.</span><span class="n">extend</span><span class="p">(</span><span class="n">a</span><span class="o">.</span><span class="n">_graphics</span><span class="p">(</span><span class="n">conf</span><span class="p">,</span> <span class="n">distance_fn</span><span class="p">,</span> <span class="n">model</span><span class="p">,</span>
<span class="n">module</span><span class="p">,</span> <span class="n">options</span><span class="p">))</span>
<span class="k">if</span> <span class="nb">hasattr</span><span class="p">(</span><span class="n">bu</span><span class="p">,</span> <span class="s">'bonds'</span><span class="p">):</span>
<span class="k">for</span> <span class="n">b</span> <span class="ow">in</span> <span class="n">bu</span><span class="o">.</span><span class="n">bonds</span><span class="p">:</span>
<span class="n">glist</span><span class="o">.</span><span class="n">extend</span><span class="p">(</span><span class="n">b</span><span class="o">.</span><span class="n">_graphics</span><span class="p">(</span><span class="n">conf</span><span class="p">,</span> <span class="n">distance_fn</span><span class="p">,</span> <span class="n">model</span><span class="p">,</span>
<span class="n">module</span><span class="p">,</span> <span class="n">options</span><span class="p">))</span>
<span class="k">return</span> <span class="n">glist</span>
<span class="c">#</span>
<span class="c"># The classes for atoms, groups, molecules, and complexes.</span>
<span class="c">#</span></div>
<div class="viewcode-block" id="Atom"><a class="viewcode-back" href="../../modules.html#MMTK.ChemicalObjects.Atom">[docs]</a><span class="k">class</span> <span class="nc">Atom</span><span class="p">(</span><span class="n">ChemicalObject</span><span class="p">):</span>
<span class="sd">"""</span>
<span class="sd"> Atom</span>
<span class="sd"> """</span>
<span class="k">def</span> <span class="nf">__init__</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">atom_spec</span><span class="p">,</span> <span class="n">_memo</span> <span class="o">=</span> <span class="bp">None</span><span class="p">,</span> <span class="o">**</span><span class="n">properties</span><span class="p">):</span>
<span class="sd">"""</span>
<span class="sd"> :param atom_spec: a string (not case sensitive) specifying</span>
<span class="sd"> the chemical element</span>
<span class="sd"> :type atom_spec: str</span>
<span class="sd"> :keyword position: the position of the atom</span>
<span class="sd"> :type position: Scientific.Geometry.Vector</span>
<span class="sd"> :keyword name: a name given to the atom</span>
<span class="sd"> :type name: str</span>
<span class="sd"> """</span>
<span class="n">Utility</span><span class="o">.</span><span class="n">uniqueID</span><span class="o">.</span><span class="n">registerObject</span><span class="p">(</span><span class="bp">self</span><span class="p">)</span>
<span class="n">ChemicalObject</span><span class="o">.</span><span class="n">__init__</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">atom_spec</span><span class="p">,</span> <span class="n">_memo</span><span class="p">)</span>
<span class="bp">self</span><span class="o">.</span><span class="n">_mass</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">type</span><span class="o">.</span><span class="n">average_mass</span>
<span class="bp">self</span><span class="o">.</span><span class="n">array</span> <span class="o">=</span> <span class="bp">None</span>
<span class="bp">self</span><span class="o">.</span><span class="n">index</span> <span class="o">=</span> <span class="bp">None</span>
<span class="k">if</span> <span class="n">properties</span><span class="o">.</span><span class="n">has_key</span><span class="p">(</span><span class="s">'position'</span><span class="p">):</span>
<span class="bp">self</span><span class="o">.</span><span class="n">setPosition</span><span class="p">(</span><span class="n">properties</span><span class="p">[</span><span class="s">'position'</span><span class="p">])</span>
<span class="k">del</span> <span class="n">properties</span><span class="p">[</span><span class="s">'position'</span><span class="p">]</span>
<span class="bp">self</span><span class="o">.</span><span class="n">addProperties</span><span class="p">(</span><span class="n">properties</span><span class="p">)</span>
<span class="n">blueprintclass</span> <span class="o">=</span> <span class="n">Database</span><span class="o">.</span><span class="n">BlueprintAtom</span>
<span class="k">def</span> <span class="nf">__getstate__</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span>
<span class="n">state</span> <span class="o">=</span> <span class="n">copy</span><span class="o">.</span><span class="n">copy</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">__dict__</span><span class="p">)</span>
<span class="k">if</span> <span class="bp">self</span><span class="o">.</span><span class="n">array</span> <span class="ow">is</span> <span class="ow">not</span> <span class="bp">None</span><span class="p">:</span>
<span class="n">state</span><span class="p">[</span><span class="s">'array'</span><span class="p">]</span> <span class="o">=</span> <span class="bp">None</span>
<span class="n">state</span><span class="p">[</span><span class="s">'pos'</span><span class="p">]</span> <span class="o">=</span> <span class="n">Vector</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">array</span><span class="p">[</span><span class="bp">self</span><span class="o">.</span><span class="n">index</span><span class="p">,:])</span>
<span class="k">return</span> <span class="n">state</span>
<span class="k">def</span> <span class="nf">atomList</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span>
<span class="k">return</span> <span class="p">[</span><span class="bp">self</span><span class="p">]</span>
<span class="k">def</span> <span class="nf">atomIterator</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span>
<span class="k">yield</span> <span class="bp">self</span>
<div class="viewcode-block" id="Atom.setPosition"><a class="viewcode-back" href="../../modules.html#MMTK.ChemicalObjects.Atom.setPosition">[docs]</a> <span class="k">def</span> <span class="nf">setPosition</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">position</span><span class="p">):</span>
<span class="sd">"""</span>
<span class="sd"> Changes the position of the atom.</span>
<span class="sd"> :param position: the new position</span>
<span class="sd"> :type position: Scientific.Geometry.Vector</span>
<span class="sd"> """</span>
<span class="k">if</span> <span class="n">position</span> <span class="ow">is</span> <span class="bp">None</span><span class="p">:</span>
<span class="k">if</span> <span class="bp">self</span><span class="o">.</span><span class="n">array</span> <span class="ow">is</span> <span class="bp">None</span><span class="p">:</span>
<span class="k">try</span><span class="p">:</span> <span class="k">del</span> <span class="bp">self</span><span class="o">.</span><span class="n">pos</span>
<span class="k">except</span> <span class="ne">AttributeError</span><span class="p">:</span> <span class="k">pass</span>
<span class="k">else</span><span class="p">:</span>
<span class="bp">self</span><span class="o">.</span><span class="n">array</span><span class="p">[</span><span class="bp">self</span><span class="o">.</span><span class="n">index</span><span class="p">,</span><span class="mi">0</span><span class="p">]</span> <span class="o">=</span> <span class="n">Utility</span><span class="o">.</span><span class="n">undefined</span>
<span class="bp">self</span><span class="o">.</span><span class="n">array</span><span class="p">[</span><span class="bp">self</span><span class="o">.</span><span class="n">index</span><span class="p">,</span><span class="mi">1</span><span class="p">]</span> <span class="o">=</span> <span class="n">Utility</span><span class="o">.</span><span class="n">undefined</span>
<span class="bp">self</span><span class="o">.</span><span class="n">array</span><span class="p">[</span><span class="bp">self</span><span class="o">.</span><span class="n">index</span><span class="p">,</span><span class="mi">2</span><span class="p">]</span> <span class="o">=</span> <span class="n">Utility</span><span class="o">.</span><span class="n">undefined</span>
<span class="k">else</span><span class="p">:</span>
<span class="k">if</span> <span class="bp">self</span><span class="o">.</span><span class="n">array</span> <span class="ow">is</span> <span class="bp">None</span><span class="p">:</span>
<span class="bp">self</span><span class="o">.</span><span class="n">pos</span> <span class="o">=</span> <span class="n">position</span>
<span class="k">else</span><span class="p">:</span>
<span class="bp">self</span><span class="o">.</span><span class="n">array</span><span class="p">[</span><span class="bp">self</span><span class="o">.</span><span class="n">index</span><span class="p">,</span><span class="mi">0</span><span class="p">]</span> <span class="o">=</span> <span class="n">position</span><span class="p">[</span><span class="mi">0</span><span class="p">]</span>
<span class="bp">self</span><span class="o">.</span><span class="n">array</span><span class="p">[</span><span class="bp">self</span><span class="o">.</span><span class="n">index</span><span class="p">,</span><span class="mi">1</span><span class="p">]</span> <span class="o">=</span> <span class="n">position</span><span class="p">[</span><span class="mi">1</span><span class="p">]</span>
<span class="bp">self</span><span class="o">.</span><span class="n">array</span><span class="p">[</span><span class="bp">self</span><span class="o">.</span><span class="n">index</span><span class="p">,</span><span class="mi">2</span><span class="p">]</span> <span class="o">=</span> <span class="n">position</span><span class="p">[</span><span class="mi">2</span><span class="p">]</span>
</div>
<span class="n">translateTo</span> <span class="o">=</span> <span class="n">setPosition</span>
<div class="viewcode-block" id="Atom.position"><a class="viewcode-back" href="../../modules.html#MMTK.ChemicalObjects.Atom.position">[docs]</a> <span class="k">def</span> <span class="nf">position</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">conf</span> <span class="o">=</span> <span class="bp">None</span><span class="p">):</span>
<span class="sd">"""</span>
<span class="sd"> :returns: the position in configuration conf. If conf is </span>
<span class="sd"> 'None', use the current configuration. If the atom has</span>
<span class="sd"> not been assigned a position, the return value is None.</span>
<span class="sd"> :rtype: Scientific.Geometry.Vector</span>
<span class="sd"> """</span>
<span class="k">if</span> <span class="n">conf</span> <span class="ow">is</span> <span class="bp">None</span><span class="p">:</span>
<span class="k">if</span> <span class="bp">self</span><span class="o">.</span><span class="n">array</span> <span class="ow">is</span> <span class="bp">None</span><span class="p">:</span>
<span class="k">try</span><span class="p">:</span>
<span class="k">return</span> <span class="bp">self</span><span class="o">.</span><span class="n">pos</span>
<span class="k">except</span> <span class="ne">AttributeError</span><span class="p">:</span>
<span class="k">return</span> <span class="bp">None</span>
<span class="k">else</span><span class="p">:</span>
<span class="k">if</span> <span class="n">N</span><span class="o">.</span><span class="n">logical_or</span><span class="o">.</span><span class="n">reduce</span><span class="p">(</span>
<span class="n">N</span><span class="o">.</span><span class="n">greater</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">array</span><span class="p">[</span><span class="bp">self</span><span class="o">.</span><span class="n">index</span><span class="p">,</span> <span class="p">:],</span>
<span class="n">Utility</span><span class="o">.</span><span class="n">undefined_limit</span><span class="p">)):</span>
<span class="k">return</span> <span class="bp">None</span>
<span class="k">else</span><span class="p">:</span>
<span class="k">return</span> <span class="n">Vector</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">array</span><span class="p">[</span><span class="bp">self</span><span class="o">.</span><span class="n">index</span><span class="p">,:])</span>
<span class="k">else</span><span class="p">:</span>
<span class="k">return</span> <span class="n">conf</span><span class="p">[</span><span class="bp">self</span><span class="p">]</span>
</div>
<span class="n">centerOfMass</span> <span class="o">=</span> <span class="n">position</span>
<div class="viewcode-block" id="Atom.setMass"><a class="viewcode-back" href="../../modules.html#MMTK.ChemicalObjects.Atom.setMass">[docs]</a> <span class="k">def</span> <span class="nf">setMass</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">mass</span><span class="p">):</span>
<span class="sd">"""</span>
<span class="sd"> Changes the mass of the atom.</span>
<span class="sd"> :param mass: the mass</span>
<span class="sd"> :type mass: float</span>
<span class="sd"> """</span>
<span class="bp">self</span><span class="o">.</span><span class="n">_mass</span> <span class="o">=</span> <span class="n">mass</span>
<span class="n">universe</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">universe</span><span class="p">()</span>
<span class="k">if</span> <span class="n">universe</span> <span class="ow">is</span> <span class="ow">not</span> <span class="bp">None</span><span class="p">:</span>
<span class="n">universe</span><span class="o">.</span><span class="n">_changed</span><span class="p">(</span><span class="bp">True</span><span class="p">)</span>
</div>
<span class="k">def</span> <span class="nf">getAtom</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">atom</span><span class="p">):</span>
<span class="k">return</span> <span class="bp">self</span>
<span class="k">def</span> <span class="nf">translateBy</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">vector</span><span class="p">):</span>
<span class="k">if</span> <span class="bp">self</span><span class="o">.</span><span class="n">array</span> <span class="ow">is</span> <span class="bp">None</span><span class="p">:</span>
<span class="bp">self</span><span class="o">.</span><span class="n">pos</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">pos</span> <span class="o">+</span> <span class="n">vector</span>
<span class="k">else</span><span class="p">:</span>
<span class="bp">self</span><span class="o">.</span><span class="n">array</span><span class="p">[</span><span class="bp">self</span><span class="o">.</span><span class="n">index</span><span class="p">,</span><span class="mi">0</span><span class="p">]</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">array</span><span class="p">[</span><span class="bp">self</span><span class="o">.</span><span class="n">index</span><span class="p">,</span><span class="mi">0</span><span class="p">]</span> <span class="o">+</span> <span class="n">vector</span><span class="p">[</span><span class="mi">0</span><span class="p">]</span>
<span class="bp">self</span><span class="o">.</span><span class="n">array</span><span class="p">[</span><span class="bp">self</span><span class="o">.</span><span class="n">index</span><span class="p">,</span><span class="mi">1</span><span class="p">]</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">array</span><span class="p">[</span><span class="bp">self</span><span class="o">.</span><span class="n">index</span><span class="p">,</span><span class="mi">1</span><span class="p">]</span> <span class="o">+</span> <span class="n">vector</span><span class="p">[</span><span class="mi">1</span><span class="p">]</span>
<span class="bp">self</span><span class="o">.</span><span class="n">array</span><span class="p">[</span><span class="bp">self</span><span class="o">.</span><span class="n">index</span><span class="p">,</span><span class="mi">2</span><span class="p">]</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">array</span><span class="p">[</span><span class="bp">self</span><span class="o">.</span><span class="n">index</span><span class="p">,</span><span class="mi">2</span><span class="p">]</span> <span class="o">+</span> <span class="n">vector</span><span class="p">[</span><span class="mi">2</span><span class="p">]</span>
<span class="k">def</span> <span class="nf">numberOfPoints</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span>
<span class="k">return</span> <span class="mi">1</span>
<span class="n">numberOfCartesianCoordinates</span> <span class="o">=</span> <span class="n">numberOfPoints</span>
<span class="k">def</span> <span class="nf">setIndex</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">index</span><span class="p">):</span>
<span class="k">if</span> <span class="bp">self</span><span class="o">.</span><span class="n">index</span> <span class="ow">is</span> <span class="ow">not</span> <span class="bp">None</span> <span class="ow">and</span> <span class="bp">self</span><span class="o">.</span><span class="n">index</span> <span class="o">!=</span> <span class="n">index</span><span class="p">:</span>
<span class="k">raise</span> <span class="ne">ValueError</span><span class="p">(</span><span class="s">'Wrong atom index'</span><span class="p">)</span>
<span class="bp">self</span><span class="o">.</span><span class="n">index</span> <span class="o">=</span> <span class="n">index</span>
<span class="k">def</span> <span class="nf">setArray</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">index</span><span class="p">):</span>
<span class="bp">self</span><span class="o">.</span><span class="n">index</span> <span class="o">=</span> <span class="n">index</span>
<span class="bp">self</span><span class="o">.</span><span class="n">array</span> <span class="o">=</span> <span class="bp">None</span>
<span class="k">def</span> <span class="nf">getArray</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span>
<span class="k">return</span> <span class="bp">self</span><span class="o">.</span><span class="n">array</span>
<span class="k">def</span> <span class="nf">unsetArray</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span>
<span class="bp">self</span><span class="o">.</span><span class="n">pos</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">position</span><span class="p">()</span>
<span class="bp">self</span><span class="o">.</span><span class="n">array</span> <span class="o">=</span> <span class="bp">None</span>
<span class="k">def</span> <span class="nf">setBondAttribute</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">atom</span><span class="p">):</span>
<span class="k">try</span><span class="p">:</span>
<span class="bp">self</span><span class="o">.</span><span class="n">bonded_to__</span><span class="o">.</span><span class="n">append</span><span class="p">(</span><span class="n">atom</span><span class="p">)</span>
<span class="k">except</span> <span class="ne">AttributeError</span><span class="p">:</span>
<span class="bp">self</span><span class="o">.</span><span class="n">bonded_to__</span> <span class="o">=</span> <span class="p">[</span><span class="n">atom</span><span class="p">]</span>
<span class="k">def</span> <span class="nf">clearBondAttribute</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span>
<span class="k">try</span><span class="p">:</span>
<span class="k">del</span> <span class="bp">self</span><span class="o">.</span><span class="n">bonded_to__</span>
<span class="k">except</span> <span class="ne">AttributeError</span><span class="p">:</span>
<span class="k">pass</span>
<div class="viewcode-block" id="Atom.bondedTo"><a class="viewcode-back" href="../../modules.html#MMTK.ChemicalObjects.Atom.bondedTo">[docs]</a> <span class="k">def</span> <span class="nf">bondedTo</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span>
<span class="sd">"""</span>
<span class="sd"> :returns: a list of all atoms to which a chemical bond exists.</span>
<span class="sd"> :rtype: list</span>
<span class="sd"> """</span>
<span class="k">try</span><span class="p">:</span>
<span class="k">return</span> <span class="bp">self</span><span class="o">.</span><span class="n">bonded_to__</span>
<span class="k">except</span> <span class="ne">AttributeError</span><span class="p">:</span>
<span class="k">if</span> <span class="bp">self</span><span class="o">.</span><span class="n">parent</span> <span class="ow">is</span> <span class="bp">None</span> <span class="ow">or</span> <span class="ow">not</span> <span class="n">isChemicalObject</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">parent</span><span class="p">):</span>
<span class="k">return</span> <span class="p">[]</span>
<span class="k">else</span><span class="p">:</span>
<span class="k">return</span> <span class="bp">self</span><span class="o">.</span><span class="n">parent</span><span class="o">.</span><span class="n">bondedTo</span><span class="p">(</span><span class="bp">self</span><span class="p">)</span>
</div>
<span class="k">def</span> <span class="nf">delete</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span>
<span class="k">if</span> <span class="bp">self</span><span class="o">.</span><span class="n">parent</span> <span class="ow">is</span> <span class="ow">not</span> <span class="bp">None</span><span class="p">:</span>
<span class="bp">self</span><span class="o">.</span><span class="n">parent</span><span class="o">.</span><span class="n">_deleteAtom</span><span class="p">(</span><span class="bp">self</span><span class="p">)</span>
<span class="k">def</span> <span class="nf">getAtomProperty</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">atom</span><span class="p">,</span> <span class="nb">property</span><span class="p">,</span> <span class="n">levels</span> <span class="o">=</span> <span class="bp">None</span><span class="p">):</span>
<span class="k">if</span> <span class="bp">self</span> <span class="o">!=</span> <span class="n">atom</span><span class="p">:</span>
<span class="k">raise</span> <span class="ne">ValueError</span><span class="p">(</span><span class="s">"Wrong atom"</span><span class="p">)</span>
<span class="k">return</span> <span class="nb">getattr</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="nb">property</span><span class="p">)</span>
<span class="k">def</span> <span class="nf">_description</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">tag</span><span class="p">,</span> <span class="n">index_map</span><span class="p">,</span> <span class="n">toplevel</span><span class="p">):</span>
<span class="nb">setattr</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">tag</span><span class="p">,</span> <span class="bp">None</span><span class="p">)</span>
<span class="k">if</span> <span class="n">index_map</span> <span class="ow">is</span> <span class="bp">None</span><span class="p">:</span>
<span class="n">index</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">index</span>
<span class="k">else</span><span class="p">:</span>
<span class="n">index</span> <span class="o">=</span> <span class="n">index_map</span><span class="p">[</span><span class="bp">self</span><span class="o">.</span><span class="n">index</span><span class="p">]</span>
<span class="k">if</span> <span class="n">toplevel</span><span class="p">:</span>
<span class="k">return</span> <span class="s">'A('</span> <span class="o">+</span> <span class="sb">`self.name`</span> <span class="o">+</span> <span class="s">','</span> <span class="o">+</span> <span class="sb">`index`</span> <span class="o">+</span> <span class="s">','</span> <span class="o">+</span> \
<span class="sb">`self.symbol`</span> <span class="o">+</span> <span class="s">')'</span>
<span class="k">else</span><span class="p">:</span>
<span class="k">return</span> <span class="s">'A('</span> <span class="o">+</span> <span class="sb">`self.name`</span> <span class="o">+</span> <span class="s">','</span> <span class="o">+</span> <span class="sb">`index`</span> <span class="o">+</span> <span class="s">')'</span>
<span class="k">def</span> <span class="nf">_graphics</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">conf</span><span class="p">,</span> <span class="n">distance_fn</span><span class="p">,</span> <span class="n">model</span><span class="p">,</span> <span class="n">module</span><span class="p">,</span> <span class="n">options</span><span class="p">):</span>
<span class="c">#PJC change:</span>
<span class="k">if</span> <span class="n">model</span> <span class="o">==</span> <span class="s">'ball_and_stick'</span><span class="p">:</span>
<span class="n">color</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">_atomColor</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">options</span><span class="p">)</span>
<span class="n">material</span> <span class="o">=</span> <span class="n">module</span><span class="o">.</span><span class="n">DiffuseMaterial</span><span class="p">(</span><span class="n">color</span><span class="p">)</span>
<span class="n">radius</span> <span class="o">=</span> <span class="n">options</span><span class="o">.</span><span class="n">get</span><span class="p">(</span><span class="s">'ball_radius'</span><span class="p">,</span> <span class="mf">0.03</span><span class="p">)</span>
<span class="k">return</span> <span class="p">[</span><span class="n">module</span><span class="o">.</span><span class="n">Sphere</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">position</span><span class="p">(),</span> <span class="n">radius</span><span class="p">,</span> <span class="n">material</span><span class="o">=</span><span class="n">material</span><span class="p">)]</span>
<span class="k">elif</span> <span class="n">model</span> <span class="o">==</span> <span class="s">'vdw'</span> <span class="ow">or</span> <span class="n">model</span> <span class="o">==</span> <span class="s">'vdw_and_stick'</span><span class="p">:</span>
<span class="n">color</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">_atomColor</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">options</span><span class="p">)</span>
<span class="n">material</span> <span class="o">=</span> <span class="n">module</span><span class="o">.</span><span class="n">DiffuseMaterial</span><span class="p">(</span><span class="n">color</span><span class="p">)</span>
<span class="k">try</span><span class="p">:</span>
<span class="n">radius</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">vdW_radius</span>
<span class="k">except</span><span class="p">:</span>
<span class="n">radius</span> <span class="o">=</span> <span class="n">options</span><span class="o">.</span><span class="n">get</span><span class="p">(</span><span class="s">'ball_radius'</span><span class="p">,</span> <span class="mf">0.03</span><span class="p">)</span>
<span class="k">return</span> <span class="p">[</span><span class="n">module</span><span class="o">.</span><span class="n">Sphere</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">position</span><span class="p">(),</span> <span class="n">radius</span><span class="p">,</span> <span class="n">material</span><span class="o">=</span><span class="n">material</span><span class="p">)]</span>
<span class="k">else</span><span class="p">:</span>
<span class="k">return</span> <span class="p">[]</span>
<span class="k">if</span> <span class="n">model</span> <span class="o">!=</span> <span class="s">'ball_and_stick'</span><span class="p">:</span>
<span class="k">return</span> <span class="p">[]</span>
<span class="n">color</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">_atomColor</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">options</span><span class="p">)</span>
<span class="n">material</span> <span class="o">=</span> <span class="n">module</span><span class="o">.</span><span class="n">DiffuseMaterial</span><span class="p">(</span><span class="n">color</span><span class="p">)</span>
<span class="n">radius</span> <span class="o">=</span> <span class="n">options</span><span class="o">.</span><span class="n">get</span><span class="p">(</span><span class="s">'ball_radius'</span><span class="p">,</span> <span class="mf">0.03</span><span class="p">)</span>
<span class="k">return</span> <span class="p">[</span><span class="n">module</span><span class="o">.</span><span class="n">Sphere</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">position</span><span class="p">(),</span> <span class="n">radius</span><span class="p">,</span> <span class="n">material</span><span class="o">=</span><span class="n">material</span><span class="p">)]</span>
<span class="k">def</span> <span class="nf">writeXML</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="nb">file</span><span class="p">,</span> <span class="n">memo</span><span class="p">,</span> <span class="n">toplevel</span><span class="o">=</span><span class="mi">1</span><span class="p">):</span>
<span class="k">return</span> <span class="p">[</span><span class="s">'<atom title="</span><span class="si">%s</span><span class="s">" elementType="</span><span class="si">%s</span><span class="s">"/>'</span>
<span class="o">%</span> <span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">name</span><span class="p">,</span> <span class="bp">self</span><span class="o">.</span><span class="n">type</span><span class="o">.</span><span class="n">symbol</span><span class="p">)]</span>
<span class="k">def</span> <span class="nf">getXMLAtomOrder</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span>
<span class="k">return</span> <span class="p">[</span><span class="bp">self</span><span class="p">]</span>
</div>
<div class="viewcode-block" id="Group"><a class="viewcode-back" href="../../modules.html#MMTK.ChemicalObjects.Group">[docs]</a><span class="k">class</span> <span class="nc">Group</span><span class="p">(</span><span class="n">CompositeChemicalObject</span><span class="p">,</span> <span class="n">ChemicalObject</span><span class="p">):</span>
<span class="sd">"""</span>
<span class="sd"> Group of bonded atoms</span>
<span class="sd"> Groups can contain atoms and other groups, and link them by chemical</span>
<span class="sd"> bonds. They are used to represent functional groups or any other</span>
<span class="sd"> part of a molecule that has a well-defined identity.</span>
<span class="sd"> Groups cannot be created in application programs, but only in</span>
<span class="sd"> database definitions for molecules or through a MoleculeFactory.</span>
<span class="sd"> """</span>
<span class="k">def</span> <span class="nf">__init__</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">group_spec</span><span class="p">,</span> <span class="n">_memo</span> <span class="o">=</span> <span class="bp">None</span><span class="p">,</span> <span class="o">**</span><span class="n">properties</span><span class="p">):</span>
<span class="sd">"""</span>
<span class="sd"> :param group_spec: a string (not case sensitive) that specifies</span>
<span class="sd"> the group name in the chemical database</span>
<span class="sd"> :type group_spec: str</span>
<span class="sd"> :keyword position: the position of the center of mass of the group</span>
<span class="sd"> :type position: Scientific.Geometry.Vector</span>
<span class="sd"> :keyword name: a name given to the group</span>
<span class="sd"> :type name: str</span>
<span class="sd"> """</span>
<span class="k">if</span> <span class="n">group_spec</span> <span class="ow">is</span> <span class="ow">not</span> <span class="bp">None</span><span class="p">:</span>
<span class="c"># group_spec is None when called from MoleculeFactory</span>
<span class="n">ChemicalObject</span><span class="o">.</span><span class="n">__init__</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">group_spec</span><span class="p">,</span> <span class="n">_memo</span><span class="p">)</span>
<span class="bp">self</span><span class="o">.</span><span class="n">addProperties</span><span class="p">(</span><span class="n">properties</span><span class="p">)</span>
<span class="n">blueprintclass</span> <span class="o">=</span> <span class="n">Database</span><span class="o">.</span><span class="n">BlueprintGroup</span>
<span class="n">is_incomplete</span> <span class="o">=</span> <span class="bp">True</span>
<span class="k">def</span> <span class="nf">bondedTo</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">atom</span><span class="p">):</span>
<span class="k">if</span> <span class="bp">self</span><span class="o">.</span><span class="n">parent</span> <span class="ow">is</span> <span class="bp">None</span> <span class="ow">or</span> <span class="ow">not</span> <span class="n">isChemicalObject</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">parent</span><span class="p">):</span>
<span class="k">return</span> <span class="p">[]</span>
<span class="k">else</span><span class="p">:</span>
<span class="k">return</span> <span class="bp">self</span><span class="o">.</span><span class="n">parent</span><span class="o">.</span><span class="n">bondedTo</span><span class="p">(</span><span class="n">atom</span><span class="p">)</span>
<span class="k">def</span> <span class="nf">setBondAttributes</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span>
<span class="k">pass</span>
<span class="k">def</span> <span class="nf">clearBondAttributes</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span>
<span class="k">pass</span>
<span class="k">def</span> <span class="nf">_subunits</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span>
<span class="k">return</span> <span class="bp">self</span><span class="o">.</span><span class="n">groups</span>
<span class="k">def</span> <span class="nf">_descriptionSpec</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span>
<span class="k">return</span> <span class="s">"G"</span><span class="p">,</span> <span class="bp">None</span>
</div>
<div class="viewcode-block" id="Molecule"><a class="viewcode-back" href="../../modules.html#MMTK.ChemicalObjects.Molecule">[docs]</a><span class="k">class</span> <span class="nc">Molecule</span><span class="p">(</span><span class="n">CompositeChemicalObject</span><span class="p">,</span> <span class="n">ChemicalObject</span><span class="p">):</span>
<span class="sd">"""Molecule</span>
<span class="sd"> Molecules consist of atoms and groups linked by bonds.</span>
<span class="sd"> """</span>
<span class="k">def</span> <span class="nf">__init__</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">molecule_spec</span><span class="p">,</span> <span class="n">_memo</span> <span class="o">=</span> <span class="bp">None</span><span class="p">,</span> <span class="o">**</span><span class="n">properties</span><span class="p">):</span>
<span class="sd">"""</span>
<span class="sd"> :param molecule_spec: a string (not case sensitive) that specifies</span>
<span class="sd"> the molecule name in the chemical database</span>
<span class="sd"> :type molecule_spec: str</span>
<span class="sd"> :keyword position: the position of the center of mass of the molecule</span>
<span class="sd"> :type position: Scientific.Geometry.Vector</span>
<span class="sd"> :keyword name: a name given to the molecule</span>
<span class="sd"> :type name: str</span>
<span class="sd"> :keyword configuration: the name of a configuration listed in the</span>
<span class="sd"> database definition of the molecule, which</span>
<span class="sd"> is used to initialize the atom positions.</span>
<span class="sd"> If no configuration is specified, the</span>
<span class="sd"> configuration named "default" will be used,</span>
<span class="sd"> if it exists. Otherwise the atom positions</span>
<span class="sd"> are undefined.</span>
<span class="sd"> :type configuration: str</span>
<span class="sd"> """</span>
<span class="k">if</span> <span class="n">molecule_spec</span> <span class="ow">is</span> <span class="ow">not</span> <span class="bp">None</span><span class="p">:</span>
<span class="c"># molecule_spec is None when called from MoleculeFactory</span>
<span class="n">ChemicalObject</span><span class="o">.</span><span class="n">__init__</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">molecule_spec</span><span class="p">,</span> <span class="n">_memo</span><span class="p">)</span>
<span class="n">properties</span> <span class="o">=</span> <span class="n">copy</span><span class="o">.</span><span class="n">copy</span><span class="p">(</span><span class="n">properties</span><span class="p">)</span>
<span class="n">CompositeChemicalObject</span><span class="o">.</span><span class="n">__init__</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">properties</span><span class="p">)</span>
<span class="bp">self</span><span class="o">.</span><span class="n">bonds</span> <span class="o">=</span> <span class="n">Bonds</span><span class="o">.</span><span class="n">BondList</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">bonds</span><span class="p">)</span>
<span class="n">blueprintclass</span> <span class="o">=</span> <span class="n">Database</span><span class="o">.</span><span class="n">BlueprintMolecule</span>
<span class="k">def</span> <span class="nf">bondedTo</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">atom</span><span class="p">):</span>
<span class="k">return</span> <span class="bp">self</span><span class="o">.</span><span class="n">bonds</span><span class="o">.</span><span class="n">bondedTo</span><span class="p">(</span><span class="n">atom</span><span class="p">)</span>
<span class="k">def</span> <span class="nf">setBondAttributes</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span>
<span class="bp">self</span><span class="o">.</span><span class="n">bonds</span><span class="o">.</span><span class="n">setBondAttributes</span><span class="p">()</span>
<span class="k">def</span> <span class="nf">clearBondAttributes</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span>
<span class="k">for</span> <span class="n">a</span> <span class="ow">in</span> <span class="bp">self</span><span class="o">.</span><span class="n">atoms</span><span class="p">:</span>
<span class="n">a</span><span class="o">.</span><span class="n">clearBondAttribute</span><span class="p">()</span>
<span class="k">def</span> <span class="nf">_subunits</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span>
<span class="k">return</span> <span class="bp">self</span><span class="o">.</span><span class="n">groups</span>
<span class="k">def</span> <span class="nf">_descriptionSpec</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span>
<span class="k">return</span> <span class="s">"M"</span><span class="p">,</span> <span class="bp">None</span>
<span class="k">def</span> <span class="nf">addGroup</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">group</span><span class="p">,</span> <span class="n">bond_atom_pairs</span><span class="p">):</span>
<span class="k">for</span> <span class="n">a1</span><span class="p">,</span> <span class="n">a2</span> <span class="ow">in</span> <span class="n">bond_atom_pairs</span><span class="p">:</span>
<span class="n">o1</span> <span class="o">=</span> <span class="n">a1</span><span class="o">.</span><span class="n">topLevelChemicalObject</span><span class="p">()</span>
<span class="n">o2</span> <span class="o">=</span> <span class="n">a2</span><span class="o">.</span><span class="n">topLevelChemicalObject</span><span class="p">()</span>
<span class="k">if</span> <span class="nb">set</span><span class="p">([</span><span class="n">o1</span><span class="p">,</span> <span class="n">o2</span><span class="p">])</span> <span class="o">!=</span> <span class="nb">set</span><span class="p">([</span><span class="bp">self</span><span class="p">,</span> <span class="n">group</span><span class="p">]):</span>
<span class="k">raise</span> <span class="ne">ValueError</span><span class="p">(</span><span class="s">"bond </span><span class="si">%s</span><span class="s">-</span><span class="si">%s</span><span class="s"> outside object"</span> <span class="o">%</span>
<span class="p">(</span><span class="nb">str</span><span class="p">(</span><span class="n">a1</span><span class="p">),</span> <span class="nb">str</span><span class="p">(</span><span class="n">a2</span><span class="p">)))</span>
<span class="bp">self</span><span class="o">.</span><span class="n">groups</span><span class="o">.</span><span class="n">append</span><span class="p">(</span><span class="n">group</span><span class="p">)</span>
<span class="bp">self</span><span class="o">.</span><span class="n">atoms</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">atoms</span> <span class="o">+</span> <span class="n">group</span><span class="o">.</span><span class="n">atoms</span>
<span class="n">group</span><span class="o">.</span><span class="n">parent</span> <span class="o">=</span> <span class="bp">self</span>
<span class="bp">self</span><span class="o">.</span><span class="n">clearBondAttributes</span><span class="p">()</span>
<span class="k">for</span> <span class="n">a1</span><span class="p">,</span> <span class="n">a2</span> <span class="ow">in</span> <span class="n">bond_atom_pairs</span><span class="p">:</span>
<span class="bp">self</span><span class="o">.</span><span class="n">bonds</span><span class="o">.</span><span class="n">append</span><span class="p">(</span><span class="n">Bonds</span><span class="o">.</span><span class="n">Bond</span><span class="p">((</span><span class="n">a1</span><span class="p">,</span> <span class="n">a2</span><span class="p">)))</span>
<span class="k">for</span> <span class="n">b</span> <span class="ow">in</span> <span class="n">group</span><span class="o">.</span><span class="n">bonds</span><span class="p">:</span>
<span class="bp">self</span><span class="o">.</span><span class="n">bonds</span><span class="o">.</span><span class="n">append</span><span class="p">(</span><span class="n">b</span><span class="p">)</span>
<span class="c"># construct positions of missing hydrogens</span>
<div class="viewcode-block" id="Molecule.findHydrogenPositions"><a class="viewcode-back" href="../../modules.html#MMTK.ChemicalObjects.Molecule.findHydrogenPositions">[docs]</a> <span class="k">def</span> <span class="nf">findHydrogenPositions</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span>
<span class="sd">"""</span>
<span class="sd"> Find reasonable positions for hydrogen atoms that have no</span>
<span class="sd"> position assigned.</span>
<span class="sd"> This method uses a heuristic approach based on standard geometry</span>
<span class="sd"> data. It was developed for proteins and DNA and may not give</span>
<span class="sd"> good results for other molecules. It raises an exception</span>
<span class="sd"> if presented with a topology it cannot handle.</span>
<span class="sd"> """</span>
<span class="bp">self</span><span class="o">.</span><span class="n">setBondAttributes</span><span class="p">()</span>
<span class="k">try</span><span class="p">:</span>
<span class="n">unknown</span> <span class="o">=</span> <span class="p">{}</span>
<span class="k">for</span> <span class="n">a</span> <span class="ow">in</span> <span class="bp">self</span><span class="o">.</span><span class="n">atoms</span><span class="p">:</span>
<span class="k">if</span> <span class="n">a</span><span class="o">.</span><span class="n">position</span><span class="p">()</span> <span class="ow">is</span> <span class="bp">None</span><span class="p">:</span>
<span class="k">if</span> <span class="n">a</span><span class="o">.</span><span class="n">symbol</span> <span class="o">!=</span> <span class="s">'H'</span><span class="p">:</span>
<span class="k">raise</span> <span class="ne">ValueError</span><span class="p">(</span><span class="s">'position of '</span> <span class="o">+</span> <span class="n">a</span><span class="o">.</span><span class="n">fullName</span><span class="p">()</span> <span class="o">+</span> \
<span class="s">' is undefined'</span><span class="p">)</span>
<span class="n">bonded</span> <span class="o">=</span> <span class="n">a</span><span class="o">.</span><span class="n">bondedTo</span><span class="p">()[</span><span class="mi">0</span><span class="p">]</span>
<span class="n">unknown</span><span class="o">.</span><span class="n">setdefault</span><span class="p">(</span><span class="n">bonded</span><span class="p">,</span> <span class="p">[])</span><span class="o">.</span><span class="n">append</span><span class="p">(</span><span class="n">a</span><span class="p">)</span>
<span class="k">for</span> <span class="n">a</span><span class="p">,</span> <span class="nb">list</span> <span class="ow">in</span> <span class="n">unknown</span><span class="o">.</span><span class="n">items</span><span class="p">():</span>
<span class="n">bonded</span> <span class="o">=</span> <span class="n">a</span><span class="o">.</span><span class="n">bondedTo</span><span class="p">()</span>
<span class="n">n</span> <span class="o">=</span> <span class="nb">len</span><span class="p">(</span><span class="n">bonded</span><span class="p">)</span>
<span class="n">known</span> <span class="o">=</span> <span class="p">[</span><span class="n">b</span> <span class="k">for</span> <span class="n">b</span> <span class="ow">in</span> <span class="n">bonded</span> <span class="k">if</span> <span class="n">b</span><span class="o">.</span><span class="n">position</span><span class="p">()</span> <span class="ow">is</span> <span class="ow">not</span> <span class="bp">None</span><span class="p">]</span>
<span class="n">nb</span> <span class="o">=</span> <span class="nb">len</span><span class="p">(</span><span class="nb">list</span><span class="p">)</span>
<span class="k">try</span><span class="p">:</span>
<span class="n">method</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">_h_methods</span><span class="p">[</span><span class="n">a</span><span class="o">.</span><span class="n">symbol</span><span class="p">][</span><span class="n">n</span><span class="p">][</span><span class="n">nb</span><span class="p">]</span>
<span class="k">except</span> <span class="ne">KeyError</span><span class="p">:</span>
<span class="k">raise</span> <span class="ne">ValueError</span><span class="p">(</span><span class="s">"Can't handle this yet: "</span> <span class="o">+</span>
<span class="n">a</span><span class="o">.</span><span class="n">symbol</span> <span class="o">+</span> <span class="s">' with '</span> <span class="o">+</span> <span class="sb">`n`</span> <span class="o">+</span> <span class="s">' bonds ('</span> <span class="o">+</span>
<span class="n">a</span><span class="o">.</span><span class="n">fullName</span><span class="p">()</span> <span class="o">+</span> <span class="s">').'</span><span class="p">)</span>
<span class="n">method</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">a</span><span class="p">,</span> <span class="n">known</span><span class="p">,</span> <span class="nb">list</span><span class="p">)</span>
<span class="k">finally</span><span class="p">:</span>
<span class="bp">self</span><span class="o">.</span><span class="n">clearBondAttributes</span><span class="p">()</span>
<span class="c"># default C-H bond length and X-C-H angle</span></div>
<span class="n">_ch_bond</span> <span class="o">=</span> <span class="mf">1.09</span><span class="o">*</span><span class="n">Units</span><span class="o">.</span><span class="n">Ang</span>
<span class="n">_hch_angle</span> <span class="o">=</span> <span class="n">N</span><span class="o">.</span><span class="n">arccos</span><span class="p">(</span><span class="o">-</span><span class="mf">1.</span><span class="o">/</span><span class="mf">3.</span><span class="p">)</span><span class="o">*</span><span class="n">Units</span><span class="o">.</span><span class="n">rad</span>
<span class="n">_nh_bond</span> <span class="o">=</span> <span class="mf">1.03</span><span class="o">*</span><span class="n">Units</span><span class="o">.</span><span class="n">Ang</span>
<span class="n">_hnh_angle</span> <span class="o">=</span> <span class="mf">120.</span><span class="o">*</span><span class="n">Units</span><span class="o">.</span><span class="n">deg</span>
<span class="n">_oh_bond</span> <span class="o">=</span> <span class="mf">0.95</span><span class="o">*</span><span class="n">Units</span><span class="o">.</span><span class="n">Ang</span>
<span class="n">_coh_angle</span> <span class="o">=</span> <span class="mf">114.9</span><span class="o">*</span><span class="n">Units</span><span class="o">.</span><span class="n">deg</span>
<span class="n">_sh_bond</span> <span class="o">=</span> <span class="mf">1.007</span><span class="o">*</span><span class="n">Units</span><span class="o">.</span><span class="n">Ang</span>
<span class="n">_csh_angle</span> <span class="o">=</span> <span class="mf">96.5</span><span class="o">*</span><span class="n">Units</span><span class="o">.</span><span class="n">deg</span>
<span class="k">def</span> <span class="nf">_C4oneH</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">atom</span><span class="p">,</span> <span class="n">known</span><span class="p">,</span> <span class="n">unknown</span><span class="p">):</span>
<span class="n">r</span> <span class="o">=</span> <span class="n">atom</span><span class="o">.</span><span class="n">position</span><span class="p">()</span>
<span class="n">n0</span> <span class="o">=</span> <span class="p">(</span><span class="n">known</span><span class="p">[</span><span class="mi">0</span><span class="p">]</span><span class="o">.</span><span class="n">position</span><span class="p">()</span><span class="o">-</span><span class="n">r</span><span class="p">)</span><span class="o">.</span><span class="n">normal</span><span class="p">()</span>
<span class="n">n1</span> <span class="o">=</span> <span class="p">(</span><span class="n">known</span><span class="p">[</span><span class="mi">1</span><span class="p">]</span><span class="o">.</span><span class="n">position</span><span class="p">()</span><span class="o">-</span><span class="n">r</span><span class="p">)</span><span class="o">.</span><span class="n">normal</span><span class="p">()</span>
<span class="n">n2</span> <span class="o">=</span> <span class="p">(</span><span class="n">known</span><span class="p">[</span><span class="mi">2</span><span class="p">]</span><span class="o">.</span><span class="n">position</span><span class="p">()</span><span class="o">-</span><span class="n">r</span><span class="p">)</span><span class="o">.</span><span class="n">normal</span><span class="p">()</span>
<span class="n">n3</span> <span class="o">=</span> <span class="p">(</span><span class="n">n0</span> <span class="o">+</span> <span class="n">n1</span> <span class="o">+</span> <span class="n">n2</span><span class="p">)</span><span class="o">.</span><span class="n">normal</span><span class="p">()</span>
<span class="n">unknown</span><span class="p">[</span><span class="mi">0</span><span class="p">]</span><span class="o">.</span><span class="n">setPosition</span><span class="p">(</span><span class="n">r</span><span class="o">-</span><span class="bp">self</span><span class="o">.</span><span class="n">_ch_bond</span><span class="o">*</span><span class="n">n3</span><span class="p">)</span>
<span class="k">def</span> <span class="nf">_C4twoH</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">atom</span><span class="p">,</span> <span class="n">known</span><span class="p">,</span> <span class="n">unknown</span><span class="p">):</span>
<span class="n">r</span> <span class="o">=</span> <span class="n">atom</span><span class="o">.</span><span class="n">position</span><span class="p">()</span>
<span class="n">r1</span> <span class="o">=</span> <span class="n">known</span><span class="p">[</span><span class="mi">0</span><span class="p">]</span><span class="o">.</span><span class="n">position</span><span class="p">()</span>
<span class="n">r2</span> <span class="o">=</span> <span class="n">known</span><span class="p">[</span><span class="mi">1</span><span class="p">]</span><span class="o">.</span><span class="n">position</span><span class="p">()</span>
<span class="n">plane</span> <span class="o">=</span> <span class="n">Objects3D</span><span class="o">.</span><span class="n">Plane</span><span class="p">(</span><span class="n">r</span><span class="p">,</span> <span class="n">r1</span><span class="p">,</span> <span class="n">r2</span><span class="p">)</span>
<span class="n">axis</span> <span class="o">=</span> <span class="o">-</span><span class="p">((</span><span class="n">r1</span><span class="o">-</span><span class="n">r</span><span class="p">)</span><span class="o">+</span><span class="p">(</span><span class="n">r2</span><span class="o">-</span><span class="n">r</span><span class="p">))</span><span class="o">.</span><span class="n">normal</span><span class="p">()</span>
<span class="n">plane</span> <span class="o">=</span> <span class="n">plane</span><span class="o">.</span><span class="n">rotate</span><span class="p">(</span><span class="n">Objects3D</span><span class="o">.</span><span class="n">Line</span><span class="p">(</span><span class="n">r</span><span class="p">,</span> <span class="n">axis</span><span class="p">),</span> <span class="mf">90.</span><span class="o">*</span><span class="n">Units</span><span class="o">.</span><span class="n">deg</span><span class="p">)</span>
<span class="n">cone</span> <span class="o">=</span> <span class="n">Objects3D</span><span class="o">.</span><span class="n">Cone</span><span class="p">(</span><span class="n">r</span><span class="p">,</span> <span class="n">axis</span><span class="p">,</span> <span class="mf">0.5</span><span class="o">*</span><span class="bp">self</span><span class="o">.</span><span class="n">_hch_angle</span><span class="p">)</span>
<span class="n">sphere</span> <span class="o">=</span> <span class="n">Objects3D</span><span class="o">.</span><span class="n">Sphere</span><span class="p">(</span><span class="n">r</span><span class="p">,</span> <span class="bp">self</span><span class="o">.</span><span class="n">_ch_bond</span><span class="p">)</span>
<span class="n">circle</span> <span class="o">=</span> <span class="n">sphere</span><span class="o">.</span><span class="n">intersectWith</span><span class="p">(</span><span class="n">cone</span><span class="p">)</span>
<span class="n">points</span> <span class="o">=</span> <span class="n">circle</span><span class="o">.</span><span class="n">intersectWith</span><span class="p">(</span><span class="n">plane</span><span class="p">)</span>
<span class="n">unknown</span><span class="p">[</span><span class="mi">0</span><span class="p">]</span><span class="o">.</span><span class="n">setPosition</span><span class="p">(</span><span class="n">points</span><span class="p">[</span><span class="mi">0</span><span class="p">])</span>
<span class="n">unknown</span><span class="p">[</span><span class="mi">1</span><span class="p">]</span><span class="o">.</span><span class="n">setPosition</span><span class="p">(</span><span class="n">points</span><span class="p">[</span><span class="mi">1</span><span class="p">])</span>
<span class="k">def</span> <span class="nf">_C4threeH</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">atom</span><span class="p">,</span> <span class="n">known</span><span class="p">,</span> <span class="n">unknown</span><span class="p">):</span>
<span class="bp">self</span><span class="o">.</span><span class="n">_tetrahedralH</span><span class="p">(</span><span class="n">atom</span><span class="p">,</span> <span class="n">known</span><span class="p">,</span> <span class="n">unknown</span><span class="p">,</span> <span class="bp">self</span><span class="o">.</span><span class="n">_ch_bond</span><span class="p">)</span>
<span class="k">def</span> <span class="nf">_C3oneH</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">atom</span><span class="p">,</span> <span class="n">known</span><span class="p">,</span> <span class="n">unknown</span><span class="p">):</span>
<span class="n">r</span> <span class="o">=</span> <span class="n">atom</span><span class="o">.</span><span class="n">position</span><span class="p">()</span>
<span class="n">n1</span> <span class="o">=</span> <span class="p">(</span><span class="n">known</span><span class="p">[</span><span class="mi">0</span><span class="p">]</span><span class="o">.</span><span class="n">position</span><span class="p">()</span><span class="o">-</span><span class="n">r</span><span class="p">)</span><span class="o">.</span><span class="n">normal</span><span class="p">()</span>
<span class="n">n2</span> <span class="o">=</span> <span class="p">(</span><span class="n">known</span><span class="p">[</span><span class="mi">1</span><span class="p">]</span><span class="o">.</span><span class="n">position</span><span class="p">()</span><span class="o">-</span><span class="n">r</span><span class="p">)</span><span class="o">.</span><span class="n">normal</span><span class="p">()</span>
<span class="n">n3</span> <span class="o">=</span> <span class="o">-</span><span class="p">(</span><span class="n">n1</span> <span class="o">+</span> <span class="n">n2</span><span class="p">)</span><span class="o">.</span><span class="n">normal</span><span class="p">()</span>
<span class="n">unknown</span><span class="p">[</span><span class="mi">0</span><span class="p">]</span><span class="o">.</span><span class="n">setPosition</span><span class="p">(</span><span class="n">r</span><span class="o">+</span><span class="bp">self</span><span class="o">.</span><span class="n">_ch_bond</span><span class="o">*</span><span class="n">n3</span><span class="p">)</span>
<span class="k">def</span> <span class="nf">_C3twoH</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">atom</span><span class="p">,</span> <span class="n">known</span><span class="p">,</span> <span class="n">unknown</span><span class="p">):</span>
<span class="n">r</span> <span class="o">=</span> <span class="n">atom</span><span class="o">.</span><span class="n">position</span><span class="p">()</span>
<span class="n">r1</span> <span class="o">=</span> <span class="n">known</span><span class="p">[</span><span class="mi">0</span><span class="p">]</span><span class="o">.</span><span class="n">position</span><span class="p">()</span>
<span class="n">others</span> <span class="o">=</span> <span class="nb">filter</span><span class="p">(</span><span class="k">lambda</span> <span class="n">a</span><span class="p">:</span> <span class="n">a</span><span class="o">.</span><span class="n">symbol</span> <span class="o">!=</span> <span class="s">'H'</span><span class="p">,</span> <span class="n">known</span><span class="p">[</span><span class="mi">0</span><span class="p">]</span><span class="o">.</span><span class="n">bondedTo</span><span class="p">())</span>
<span class="n">r2</span> <span class="o">=</span> <span class="n">others</span><span class="p">[</span><span class="mi">0</span><span class="p">]</span><span class="o">.</span><span class="n">position</span><span class="p">()</span>
<span class="k">try</span><span class="p">:</span>
<span class="n">plane</span> <span class="o">=</span> <span class="n">Objects3D</span><span class="o">.</span><span class="n">Plane</span><span class="p">(</span><span class="n">r</span><span class="p">,</span> <span class="n">r1</span><span class="p">,</span> <span class="n">r2</span><span class="p">)</span>
<span class="k">except</span> <span class="ne">ZeroDivisionError</span><span class="p">:</span>
<span class="c"># We get here if all three points are colinear.</span>
<span class="c"># Add a small random displacement as a fix.</span>
<span class="kn">from</span> <span class="nn">MMTK.Random</span> <span class="kn">import</span> <span class="n">randomPointInSphere</span>
<span class="n">plane</span> <span class="o">=</span> <span class="n">Objects3D</span><span class="o">.</span><span class="n">Plane</span><span class="p">(</span><span class="n">r</span><span class="p">,</span> <span class="n">r1</span><span class="p">,</span> <span class="n">r2</span> <span class="o">+</span> <span class="n">randomPointInSphere</span><span class="p">(</span><span class="mf">0.001</span><span class="p">))</span>
<span class="n">axis</span> <span class="o">=</span> <span class="p">(</span><span class="n">r</span><span class="o">-</span><span class="n">r1</span><span class="p">)</span><span class="o">.</span><span class="n">normal</span><span class="p">()</span>
<span class="n">cone</span> <span class="o">=</span> <span class="n">Objects3D</span><span class="o">.</span><span class="n">Cone</span><span class="p">(</span><span class="n">r</span><span class="p">,</span> <span class="n">axis</span><span class="p">,</span> <span class="mf">0.5</span><span class="o">*</span><span class="bp">self</span><span class="o">.</span><span class="n">_hch_angle</span><span class="p">)</span>
<span class="n">sphere</span> <span class="o">=</span> <span class="n">Objects3D</span><span class="o">.</span><span class="n">Sphere</span><span class="p">(</span><span class="n">r</span><span class="p">,</span> <span class="bp">self</span><span class="o">.</span><span class="n">_ch_bond</span><span class="p">)</span>
<span class="n">circle</span> <span class="o">=</span> <span class="n">sphere</span><span class="o">.</span><span class="n">intersectWith</span><span class="p">(</span><span class="n">cone</span><span class="p">)</span>
<span class="n">points</span> <span class="o">=</span> <span class="n">circle</span><span class="o">.</span><span class="n">intersectWith</span><span class="p">(</span><span class="n">plane</span><span class="p">)</span>
<span class="n">unknown</span><span class="p">[</span><span class="mi">0</span><span class="p">]</span><span class="o">.</span><span class="n">setPosition</span><span class="p">(</span><span class="n">points</span><span class="p">[</span><span class="mi">0</span><span class="p">])</span>
<span class="n">unknown</span><span class="p">[</span><span class="mi">1</span><span class="p">]</span><span class="o">.</span><span class="n">setPosition</span><span class="p">(</span><span class="n">points</span><span class="p">[</span><span class="mi">1</span><span class="p">])</span>
<span class="k">def</span> <span class="nf">_C2oneH</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">atom</span><span class="p">,</span> <span class="n">known</span><span class="p">,</span> <span class="n">unknown</span><span class="p">):</span>
<span class="n">r</span> <span class="o">=</span> <span class="n">atom</span><span class="o">.</span><span class="n">position</span><span class="p">()</span>
<span class="n">r1</span> <span class="o">=</span> <span class="n">known</span><span class="p">[</span><span class="mi">0</span><span class="p">]</span><span class="o">.</span><span class="n">position</span><span class="p">()</span>
<span class="n">x</span> <span class="o">=</span> <span class="n">r</span> <span class="o">+</span> <span class="bp">self</span><span class="o">.</span><span class="n">_ch_bond</span> <span class="o">*</span> <span class="p">(</span><span class="n">r</span> <span class="o">-</span> <span class="n">r1</span><span class="p">)</span><span class="o">.</span><span class="n">normal</span><span class="p">()</span>
<span class="n">unknown</span><span class="p">[</span><span class="mi">0</span><span class="p">]</span><span class="o">.</span><span class="n">setPosition</span><span class="p">(</span><span class="n">x</span><span class="p">)</span>
<span class="k">def</span> <span class="nf">_N2oneH</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">atom</span><span class="p">,</span> <span class="n">known</span><span class="p">,</span> <span class="n">unknown</span><span class="p">):</span>
<span class="n">r</span> <span class="o">=</span> <span class="n">atom</span><span class="o">.</span><span class="n">position</span><span class="p">()</span>
<span class="n">r1</span> <span class="o">=</span> <span class="n">known</span><span class="p">[</span><span class="mi">0</span><span class="p">]</span><span class="o">.</span><span class="n">position</span><span class="p">()</span>
<span class="n">others</span> <span class="o">=</span> <span class="nb">filter</span><span class="p">(</span><span class="k">lambda</span> <span class="n">a</span><span class="p">:</span> <span class="n">a</span><span class="o">.</span><span class="n">symbol</span> <span class="o">!=</span> <span class="s">'H'</span><span class="p">,</span> <span class="n">known</span><span class="p">[</span><span class="mi">0</span><span class="p">]</span><span class="o">.</span><span class="n">bondedTo</span><span class="p">())</span>
<span class="n">r2</span> <span class="o">=</span> <span class="n">others</span><span class="p">[</span><span class="mi">0</span><span class="p">]</span><span class="o">.</span><span class="n">position</span><span class="p">()</span>
<span class="k">try</span><span class="p">:</span>
<span class="n">plane</span> <span class="o">=</span> <span class="n">Objects3D</span><span class="o">.</span><span class="n">Plane</span><span class="p">(</span><span class="n">r</span><span class="p">,</span> <span class="n">r1</span><span class="p">,</span> <span class="n">r2</span><span class="p">)</span>
<span class="k">except</span> <span class="ne">ZeroDivisionError</span><span class="p">:</span>
<span class="c"># We get here when all three points are colinear.</span>
<span class="c"># Add a small random displacement as a fix.</span>
<span class="kn">from</span> <span class="nn">MMTK.Random</span> <span class="kn">import</span> <span class="n">randomPointInSphere</span>
<span class="n">plane</span> <span class="o">=</span> <span class="n">Objects3D</span><span class="o">.</span><span class="n">Plane</span><span class="p">(</span><span class="n">r</span><span class="p">,</span> <span class="n">r1</span><span class="p">,</span> <span class="n">r2</span> <span class="o">+</span> <span class="n">randomPointInSphere</span><span class="p">(</span><span class="mf">0.001</span><span class="p">))</span>
<span class="n">axis</span> <span class="o">=</span> <span class="p">(</span><span class="n">r</span><span class="o">-</span><span class="n">r1</span><span class="p">)</span><span class="o">.</span><span class="n">normal</span><span class="p">()</span>
<span class="n">cone</span> <span class="o">=</span> <span class="n">Objects3D</span><span class="o">.</span><span class="n">Cone</span><span class="p">(</span><span class="n">r</span><span class="p">,</span> <span class="n">axis</span><span class="p">,</span> <span class="mf">0.5</span><span class="o">*</span><span class="bp">self</span><span class="o">.</span><span class="n">_hch_angle</span><span class="p">)</span>
<span class="n">sphere</span> <span class="o">=</span> <span class="n">Objects3D</span><span class="o">.</span><span class="n">Sphere</span><span class="p">(</span><span class="n">r</span><span class="p">,</span> <span class="bp">self</span><span class="o">.</span><span class="n">_nh_bond</span><span class="p">)</span>
<span class="n">circle</span> <span class="o">=</span> <span class="n">sphere</span><span class="o">.</span><span class="n">intersectWith</span><span class="p">(</span><span class="n">cone</span><span class="p">)</span>
<span class="n">points</span> <span class="o">=</span> <span class="n">circle</span><span class="o">.</span><span class="n">intersectWith</span><span class="p">(</span><span class="n">plane</span><span class="p">)</span>
<span class="n">unknown</span><span class="p">[</span><span class="mi">0</span><span class="p">]</span><span class="o">.</span><span class="n">setPosition</span><span class="p">(</span><span class="n">points</span><span class="p">[</span><span class="mi">0</span><span class="p">])</span>
<span class="k">def</span> <span class="nf">_N3oneH</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">atom</span><span class="p">,</span> <span class="n">known</span><span class="p">,</span> <span class="n">unknown</span><span class="p">):</span>
<span class="n">r</span> <span class="o">=</span> <span class="n">atom</span><span class="o">.</span><span class="n">position</span><span class="p">()</span>
<span class="n">n1</span> <span class="o">=</span> <span class="p">(</span><span class="n">known</span><span class="p">[</span><span class="mi">0</span><span class="p">]</span><span class="o">.</span><span class="n">position</span><span class="p">()</span><span class="o">-</span><span class="n">r</span><span class="p">)</span><span class="o">.</span><span class="n">normal</span><span class="p">()</span>
<span class="n">n2</span> <span class="o">=</span> <span class="p">(</span><span class="n">known</span><span class="p">[</span><span class="mi">1</span><span class="p">]</span><span class="o">.</span><span class="n">position</span><span class="p">()</span><span class="o">-</span><span class="n">r</span><span class="p">)</span><span class="o">.</span><span class="n">normal</span><span class="p">()</span>
<span class="n">n3</span> <span class="o">=</span> <span class="o">-</span><span class="p">(</span><span class="n">n1</span> <span class="o">+</span> <span class="n">n2</span><span class="p">)</span><span class="o">.</span><span class="n">normal</span><span class="p">()</span>
<span class="n">unknown</span><span class="p">[</span><span class="mi">0</span><span class="p">]</span><span class="o">.</span><span class="n">setPosition</span><span class="p">(</span><span class="n">r</span><span class="o">+</span><span class="bp">self</span><span class="o">.</span><span class="n">_nh_bond</span><span class="o">*</span><span class="n">n3</span><span class="p">)</span>
<span class="k">def</span> <span class="nf">_N3twoH</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">atom</span><span class="p">,</span> <span class="n">known</span><span class="p">,</span> <span class="n">unknown</span><span class="p">):</span>
<span class="n">r</span> <span class="o">=</span> <span class="n">atom</span><span class="o">.</span><span class="n">position</span><span class="p">()</span>
<span class="n">r1</span> <span class="o">=</span> <span class="n">known</span><span class="p">[</span><span class="mi">0</span><span class="p">]</span><span class="o">.</span><span class="n">position</span><span class="p">()</span>
<span class="n">others</span> <span class="o">=</span> <span class="nb">filter</span><span class="p">(</span><span class="k">lambda</span> <span class="n">a</span><span class="p">:</span> <span class="n">a</span><span class="o">.</span><span class="n">symbol</span> <span class="o">!=</span> <span class="s">'H'</span><span class="p">,</span> <span class="n">known</span><span class="p">[</span><span class="mi">0</span><span class="p">]</span><span class="o">.</span><span class="n">bondedTo</span><span class="p">())</span>
<span class="n">r2</span> <span class="o">=</span> <span class="n">others</span><span class="p">[</span><span class="mi">0</span><span class="p">]</span><span class="o">.</span><span class="n">position</span><span class="p">()</span>
<span class="n">plane</span> <span class="o">=</span> <span class="n">Objects3D</span><span class="o">.</span><span class="n">Plane</span><span class="p">(</span><span class="n">r</span><span class="p">,</span> <span class="n">r1</span><span class="p">,</span> <span class="n">r2</span><span class="p">)</span>
<span class="n">axis</span> <span class="o">=</span> <span class="p">(</span><span class="n">r</span><span class="o">-</span><span class="n">r1</span><span class="p">)</span><span class="o">.</span><span class="n">normal</span><span class="p">()</span>
<span class="n">cone</span> <span class="o">=</span> <span class="n">Objects3D</span><span class="o">.</span><span class="n">Cone</span><span class="p">(</span><span class="n">r</span><span class="p">,</span> <span class="n">axis</span><span class="p">,</span> <span class="mf">0.5</span><span class="o">*</span><span class="bp">self</span><span class="o">.</span><span class="n">_hnh_angle</span><span class="p">)</span>
<span class="n">sphere</span> <span class="o">=</span> <span class="n">Objects3D</span><span class="o">.</span><span class="n">Sphere</span><span class="p">(</span><span class="n">r</span><span class="p">,</span> <span class="bp">self</span><span class="o">.</span><span class="n">_nh_bond</span><span class="p">)</span>
<span class="n">circle</span> <span class="o">=</span> <span class="n">sphere</span><span class="o">.</span><span class="n">intersectWith</span><span class="p">(</span><span class="n">cone</span><span class="p">)</span>
<span class="n">points</span> <span class="o">=</span> <span class="n">circle</span><span class="o">.</span><span class="n">intersectWith</span><span class="p">(</span><span class="n">plane</span><span class="p">)</span>
<span class="n">unknown</span><span class="p">[</span><span class="mi">0</span><span class="p">]</span><span class="o">.</span><span class="n">setPosition</span><span class="p">(</span><span class="n">points</span><span class="p">[</span><span class="mi">0</span><span class="p">])</span>
<span class="n">unknown</span><span class="p">[</span><span class="mi">1</span><span class="p">]</span><span class="o">.</span><span class="n">setPosition</span><span class="p">(</span><span class="n">points</span><span class="p">[</span><span class="mi">1</span><span class="p">])</span>
<span class="k">def</span> <span class="nf">_N4threeH</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">atom</span><span class="p">,</span> <span class="n">known</span><span class="p">,</span> <span class="n">unknown</span><span class="p">):</span>
<span class="bp">self</span><span class="o">.</span><span class="n">_tetrahedralH</span><span class="p">(</span><span class="n">atom</span><span class="p">,</span> <span class="n">known</span><span class="p">,</span> <span class="n">unknown</span><span class="p">,</span> <span class="bp">self</span><span class="o">.</span><span class="n">_nh_bond</span><span class="p">)</span>
<span class="k">def</span> <span class="nf">_N4twoH</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">atom</span><span class="p">,</span> <span class="n">known</span><span class="p">,</span> <span class="n">unknown</span><span class="p">):</span>
<span class="n">r</span> <span class="o">=</span> <span class="n">atom</span><span class="o">.</span><span class="n">position</span><span class="p">()</span>
<span class="n">r1</span> <span class="o">=</span> <span class="n">known</span><span class="p">[</span><span class="mi">0</span><span class="p">]</span><span class="o">.</span><span class="n">position</span><span class="p">()</span>
<span class="n">r2</span> <span class="o">=</span> <span class="n">known</span><span class="p">[</span><span class="mi">1</span><span class="p">]</span><span class="o">.</span><span class="n">position</span><span class="p">()</span>
<span class="n">plane</span> <span class="o">=</span> <span class="n">Objects3D</span><span class="o">.</span><span class="n">Plane</span><span class="p">(</span><span class="n">r</span><span class="p">,</span> <span class="n">r1</span><span class="p">,</span> <span class="n">r2</span><span class="p">)</span>
<span class="n">axis</span> <span class="o">=</span> <span class="o">-</span><span class="p">((</span><span class="n">r1</span><span class="o">-</span><span class="n">r</span><span class="p">)</span><span class="o">+</span><span class="p">(</span><span class="n">r2</span><span class="o">-</span><span class="n">r</span><span class="p">))</span><span class="o">.</span><span class="n">normal</span><span class="p">()</span>
<span class="n">plane</span> <span class="o">=</span> <span class="n">plane</span><span class="o">.</span><span class="n">rotate</span><span class="p">(</span><span class="n">Objects3D</span><span class="o">.</span><span class="n">Line</span><span class="p">(</span><span class="n">r</span><span class="p">,</span> <span class="n">axis</span><span class="p">),</span> <span class="mf">90.</span><span class="o">*</span><span class="n">Units</span><span class="o">.</span><span class="n">deg</span><span class="p">)</span>
<span class="n">cone</span> <span class="o">=</span> <span class="n">Objects3D</span><span class="o">.</span><span class="n">Cone</span><span class="p">(</span><span class="n">r</span><span class="p">,</span> <span class="n">axis</span><span class="p">,</span> <span class="mf">0.5</span><span class="o">*</span><span class="bp">self</span><span class="o">.</span><span class="n">_hnh_angle</span><span class="p">)</span>
<span class="n">sphere</span> <span class="o">=</span> <span class="n">Objects3D</span><span class="o">.</span><span class="n">Sphere</span><span class="p">(</span><span class="n">r</span><span class="p">,</span> <span class="bp">self</span><span class="o">.</span><span class="n">_nh_bond</span><span class="p">)</span>
<span class="n">circle</span> <span class="o">=</span> <span class="n">sphere</span><span class="o">.</span><span class="n">intersectWith</span><span class="p">(</span><span class="n">cone</span><span class="p">)</span>
<span class="n">points</span> <span class="o">=</span> <span class="n">circle</span><span class="o">.</span><span class="n">intersectWith</span><span class="p">(</span><span class="n">plane</span><span class="p">)</span>
<span class="n">unknown</span><span class="p">[</span><span class="mi">0</span><span class="p">]</span><span class="o">.</span><span class="n">setPosition</span><span class="p">(</span><span class="n">points</span><span class="p">[</span><span class="mi">0</span><span class="p">])</span>
<span class="n">unknown</span><span class="p">[</span><span class="mi">1</span><span class="p">]</span><span class="o">.</span><span class="n">setPosition</span><span class="p">(</span><span class="n">points</span><span class="p">[</span><span class="mi">1</span><span class="p">])</span>
<span class="k">def</span> <span class="nf">_N4oneH</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">atom</span><span class="p">,</span> <span class="n">known</span><span class="p">,</span> <span class="n">unknown</span><span class="p">):</span>
<span class="n">r</span> <span class="o">=</span> <span class="n">atom</span><span class="o">.</span><span class="n">position</span><span class="p">()</span>
<span class="n">n0</span> <span class="o">=</span> <span class="p">(</span><span class="n">known</span><span class="p">[</span><span class="mi">0</span><span class="p">]</span><span class="o">.</span><span class="n">position</span><span class="p">()</span><span class="o">-</span><span class="n">r</span><span class="p">)</span><span class="o">.</span><span class="n">normal</span><span class="p">()</span>
<span class="n">n1</span> <span class="o">=</span> <span class="p">(</span><span class="n">known</span><span class="p">[</span><span class="mi">1</span><span class="p">]</span><span class="o">.</span><span class="n">position</span><span class="p">()</span><span class="o">-</span><span class="n">r</span><span class="p">)</span><span class="o">.</span><span class="n">normal</span><span class="p">()</span>
<span class="n">n2</span> <span class="o">=</span> <span class="p">(</span><span class="n">known</span><span class="p">[</span><span class="mi">2</span><span class="p">]</span><span class="o">.</span><span class="n">position</span><span class="p">()</span><span class="o">-</span><span class="n">r</span><span class="p">)</span><span class="o">.</span><span class="n">normal</span><span class="p">()</span>
<span class="n">n3</span> <span class="o">=</span> <span class="p">(</span><span class="n">n0</span> <span class="o">+</span> <span class="n">n1</span> <span class="o">+</span> <span class="n">n2</span><span class="p">)</span><span class="o">.</span><span class="n">normal</span><span class="p">()</span>
<span class="n">unknown</span><span class="p">[</span><span class="mi">0</span><span class="p">]</span><span class="o">.</span><span class="n">setPosition</span><span class="p">(</span><span class="n">r</span><span class="o">-</span><span class="bp">self</span><span class="o">.</span><span class="n">_nh_bond</span><span class="o">*</span><span class="n">n3</span><span class="p">)</span>
<span class="k">def</span> <span class="nf">_O2</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">atom</span><span class="p">,</span> <span class="n">known</span><span class="p">,</span> <span class="n">unknown</span><span class="p">):</span>
<span class="n">others</span> <span class="o">=</span> <span class="n">known</span><span class="p">[</span><span class="mi">0</span><span class="p">]</span><span class="o">.</span><span class="n">bondedTo</span><span class="p">()</span>
<span class="k">for</span> <span class="n">a</span> <span class="ow">in</span> <span class="n">others</span><span class="p">:</span>
<span class="n">r</span> <span class="o">=</span> <span class="n">a</span><span class="o">.</span><span class="n">position</span><span class="p">()</span>
<span class="k">if</span> <span class="n">a</span> <span class="o">!=</span> <span class="n">atom</span> <span class="ow">and</span> <span class="n">r</span> <span class="ow">is</span> <span class="ow">not</span> <span class="bp">None</span><span class="p">:</span> <span class="k">break</span>
<span class="n">dihedral</span> <span class="o">=</span> <span class="mf">180.</span><span class="o">*</span><span class="n">Units</span><span class="o">.</span><span class="n">deg</span>
<span class="bp">self</span><span class="o">.</span><span class="n">_findPosition</span><span class="p">(</span><span class="n">unknown</span><span class="p">[</span><span class="mi">0</span><span class="p">],</span> <span class="n">atom</span><span class="o">.</span><span class="n">position</span><span class="p">(),</span> <span class="n">known</span><span class="p">[</span><span class="mi">0</span><span class="p">]</span><span class="o">.</span><span class="n">position</span><span class="p">(),</span> <span class="n">r</span><span class="p">,</span>
<span class="bp">self</span><span class="o">.</span><span class="n">_oh_bond</span><span class="p">,</span> <span class="bp">self</span><span class="o">.</span><span class="n">_coh_angle</span><span class="p">,</span> <span class="n">dihedral</span><span class="p">)</span>
<span class="k">def</span> <span class="nf">_S2</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">atom</span><span class="p">,</span> <span class="n">known</span><span class="p">,</span> <span class="n">unknown</span><span class="p">):</span>
<span class="n">c2</span> <span class="o">=</span> <span class="nb">filter</span><span class="p">(</span><span class="k">lambda</span> <span class="n">a</span><span class="p">:</span> <span class="n">a</span><span class="o">.</span><span class="n">symbol</span> <span class="o">==</span> <span class="s">'C'</span><span class="p">,</span> <span class="n">known</span><span class="p">[</span><span class="mi">0</span><span class="p">]</span><span class="o">.</span><span class="n">bondedTo</span><span class="p">())[</span><span class="mi">0</span><span class="p">]</span>
<span class="bp">self</span><span class="o">.</span><span class="n">_findPosition</span><span class="p">(</span><span class="n">unknown</span><span class="p">[</span><span class="mi">0</span><span class="p">],</span> <span class="n">atom</span><span class="o">.</span><span class="n">position</span><span class="p">(),</span> <span class="n">known</span><span class="p">[</span><span class="mi">0</span><span class="p">]</span><span class="o">.</span><span class="n">position</span><span class="p">(),</span>
<span class="n">c2</span><span class="o">.</span><span class="n">position</span><span class="p">(),</span>
<span class="bp">self</span><span class="o">.</span><span class="n">_sh_bond</span><span class="p">,</span> <span class="bp">self</span><span class="o">.</span><span class="n">_csh_angle</span><span class="p">,</span>
<span class="mf">180.</span><span class="o">*</span><span class="n">Units</span><span class="o">.</span><span class="n">deg</span><span class="p">)</span>
<span class="k">def</span> <span class="nf">_tetrahedralH</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">atom</span><span class="p">,</span> <span class="n">known</span><span class="p">,</span> <span class="n">unknown</span><span class="p">,</span> <span class="n">bond</span><span class="p">):</span>
<span class="n">r</span> <span class="o">=</span> <span class="n">atom</span><span class="o">.</span><span class="n">position</span><span class="p">()</span>
<span class="n">n</span> <span class="o">=</span> <span class="p">(</span><span class="n">known</span><span class="p">[</span><span class="mi">0</span><span class="p">]</span><span class="o">.</span><span class="n">position</span><span class="p">()</span><span class="o">-</span><span class="n">r</span><span class="p">)</span><span class="o">.</span><span class="n">normal</span><span class="p">()</span>
<span class="n">cone</span> <span class="o">=</span> <span class="n">Objects3D</span><span class="o">.</span><span class="n">Cone</span><span class="p">(</span><span class="n">r</span><span class="p">,</span> <span class="n">n</span><span class="p">,</span> <span class="n">N</span><span class="o">.</span><span class="n">arccos</span><span class="p">(</span><span class="o">-</span><span class="mf">1.</span><span class="o">/</span><span class="mf">3.</span><span class="p">))</span>
<span class="n">sphere</span> <span class="o">=</span> <span class="n">Objects3D</span><span class="o">.</span><span class="n">Sphere</span><span class="p">(</span><span class="n">r</span><span class="p">,</span> <span class="n">bond</span><span class="p">)</span>
<span class="n">circle</span> <span class="o">=</span> <span class="n">sphere</span><span class="o">.</span><span class="n">intersectWith</span><span class="p">(</span><span class="n">cone</span><span class="p">)</span>
<span class="n">others</span> <span class="o">=</span> <span class="nb">filter</span><span class="p">(</span><span class="k">lambda</span> <span class="n">a</span><span class="p">:</span> <span class="n">a</span><span class="o">.</span><span class="n">symbol</span> <span class="o">!=</span> <span class="s">'H'</span><span class="p">,</span> <span class="n">known</span><span class="p">[</span><span class="mi">0</span><span class="p">]</span><span class="o">.</span><span class="n">bondedTo</span><span class="p">())</span>
<span class="n">others</span><span class="o">.</span><span class="n">remove</span><span class="p">(</span><span class="n">atom</span><span class="p">)</span>
<span class="n">other</span> <span class="o">=</span> <span class="n">others</span><span class="p">[</span><span class="mi">0</span><span class="p">]</span>
<span class="n">ref</span> <span class="o">=</span> <span class="p">(</span><span class="n">Objects3D</span><span class="o">.</span><span class="n">Plane</span><span class="p">(</span><span class="n">circle</span><span class="o">.</span><span class="n">center</span><span class="p">,</span> <span class="n">circle</span><span class="o">.</span><span class="n">normal</span><span class="p">)</span> \
<span class="o">.</span><span class="n">projectionOf</span><span class="p">(</span><span class="n">other</span><span class="o">.</span><span class="n">position</span><span class="p">())</span><span class="o">-</span><span class="n">circle</span><span class="o">.</span><span class="n">center</span><span class="p">)</span><span class="o">.</span><span class="n">normal</span><span class="p">()</span>
<span class="n">p0</span> <span class="o">=</span> <span class="n">circle</span><span class="o">.</span><span class="n">center</span> <span class="o">+</span> <span class="n">ref</span><span class="o">*</span><span class="n">circle</span><span class="o">.</span><span class="n">radius</span>
<span class="n">p0</span> <span class="o">=</span> <span class="n">Objects3D</span><span class="o">.</span><span class="n">rotatePoint</span><span class="p">(</span><span class="n">p0</span><span class="p">,</span>
<span class="n">Objects3D</span><span class="o">.</span><span class="n">Line</span><span class="p">(</span><span class="n">circle</span><span class="o">.</span><span class="n">center</span><span class="p">,</span> <span class="n">circle</span><span class="o">.</span><span class="n">normal</span><span class="p">),</span>
<span class="mf">60.</span><span class="o">*</span><span class="n">Units</span><span class="o">.</span><span class="n">deg</span><span class="p">)</span>
<span class="n">p1</span> <span class="o">=</span> <span class="n">Objects3D</span><span class="o">.</span><span class="n">rotatePoint</span><span class="p">(</span><span class="n">p0</span><span class="p">,</span>
<span class="n">Objects3D</span><span class="o">.</span><span class="n">Line</span><span class="p">(</span><span class="n">circle</span><span class="o">.</span><span class="n">center</span><span class="p">,</span> <span class="n">circle</span><span class="o">.</span><span class="n">normal</span><span class="p">),</span>
<span class="mf">120.</span><span class="o">*</span><span class="n">Units</span><span class="o">.</span><span class="n">deg</span><span class="p">)</span>
<span class="n">p2</span> <span class="o">=</span> <span class="n">Objects3D</span><span class="o">.</span><span class="n">rotatePoint</span><span class="p">(</span><span class="n">p1</span><span class="p">,</span>
<span class="n">Objects3D</span><span class="o">.</span><span class="n">Line</span><span class="p">(</span><span class="n">circle</span><span class="o">.</span><span class="n">center</span><span class="p">,</span> <span class="n">circle</span><span class="o">.</span><span class="n">normal</span><span class="p">),</span>
<span class="mf">120.</span><span class="o">*</span><span class="n">Units</span><span class="o">.</span><span class="n">deg</span><span class="p">)</span>
<span class="n">unknown</span><span class="p">[</span><span class="mi">0</span><span class="p">]</span><span class="o">.</span><span class="n">setPosition</span><span class="p">(</span><span class="n">p0</span><span class="p">)</span>
<span class="n">unknown</span><span class="p">[</span><span class="mi">1</span><span class="p">]</span><span class="o">.</span><span class="n">setPosition</span><span class="p">(</span><span class="n">p1</span><span class="p">)</span>
<span class="n">unknown</span><span class="p">[</span><span class="mi">2</span><span class="p">]</span><span class="o">.</span><span class="n">setPosition</span><span class="p">(</span><span class="n">p2</span><span class="p">)</span>
<span class="k">def</span> <span class="nf">_findPosition</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">unknown</span><span class="p">,</span> <span class="n">a1</span><span class="p">,</span> <span class="n">a2</span><span class="p">,</span> <span class="n">a3</span><span class="p">,</span> <span class="n">bond</span><span class="p">,</span> <span class="n">angle</span><span class="p">,</span> <span class="n">dihedral</span><span class="p">):</span>
<span class="n">sphere</span> <span class="o">=</span> <span class="n">Objects3D</span><span class="o">.</span><span class="n">Sphere</span><span class="p">(</span><span class="n">a1</span><span class="p">,</span> <span class="n">bond</span><span class="p">)</span>
<span class="n">cone</span> <span class="o">=</span> <span class="n">Objects3D</span><span class="o">.</span><span class="n">Cone</span><span class="p">(</span><span class="n">a1</span><span class="p">,</span> <span class="n">a2</span><span class="o">-</span><span class="n">a1</span><span class="p">,</span> <span class="n">angle</span><span class="p">)</span>
<span class="n">plane</span> <span class="o">=</span> <span class="n">Objects3D</span><span class="o">.</span><span class="n">Plane</span><span class="p">(</span><span class="n">a3</span><span class="p">,</span> <span class="n">a2</span><span class="p">,</span> <span class="n">a1</span><span class="p">)</span>
<span class="n">plane</span> <span class="o">=</span> <span class="n">plane</span><span class="o">.</span><span class="n">rotate</span><span class="p">(</span><span class="n">Objects3D</span><span class="o">.</span><span class="n">Line</span><span class="p">(</span><span class="n">a1</span><span class="p">,</span> <span class="n">a2</span><span class="o">-</span><span class="n">a1</span><span class="p">),</span> <span class="n">dihedral</span><span class="p">)</span>
<span class="n">points</span> <span class="o">=</span> <span class="n">sphere</span><span class="o">.</span><span class="n">intersectWith</span><span class="p">(</span><span class="n">cone</span><span class="p">)</span><span class="o">.</span><span class="n">intersectWith</span><span class="p">(</span><span class="n">plane</span><span class="p">)</span>
<span class="k">for</span> <span class="n">p</span> <span class="ow">in</span> <span class="n">points</span><span class="p">:</span>
<span class="k">if</span> <span class="p">(</span><span class="n">a1</span><span class="o">-</span><span class="n">a2</span><span class="p">)</span><span class="o">.</span><span class="n">cross</span><span class="p">(</span><span class="n">p</span><span class="o">-</span><span class="n">a1</span><span class="p">)</span><span class="o">*</span><span class="p">(</span><span class="n">plane</span><span class="o">.</span><span class="n">normal</span><span class="p">)</span> <span class="o">></span> <span class="mi">0</span><span class="p">:</span>
<span class="n">unknown</span><span class="o">.</span><span class="n">setPosition</span><span class="p">(</span><span class="n">p</span><span class="p">)</span>
<span class="k">break</span>
<span class="n">_h_methods</span> <span class="o">=</span> <span class="p">{</span><span class="s">'C'</span><span class="p">:</span> <span class="p">{</span><span class="mi">4</span><span class="p">:</span> <span class="p">{</span><span class="mi">3</span><span class="p">:</span> <span class="n">_C4threeH</span><span class="p">,</span>
<span class="mi">2</span><span class="p">:</span> <span class="n">_C4twoH</span><span class="p">,</span>
<span class="mi">1</span><span class="p">:</span> <span class="n">_C4oneH</span><span class="p">},</span>
<span class="mi">3</span><span class="p">:</span> <span class="p">{</span><span class="mi">2</span><span class="p">:</span> <span class="n">_C3twoH</span><span class="p">,</span>
<span class="mi">1</span><span class="p">:</span> <span class="n">_C3oneH</span><span class="p">},</span>
<span class="mi">2</span><span class="p">:</span> <span class="p">{</span><span class="mi">1</span><span class="p">:</span> <span class="n">_C2oneH</span><span class="p">}},</span>
<span class="s">'N'</span><span class="p">:</span> <span class="p">{</span><span class="mi">4</span><span class="p">:</span> <span class="p">{</span><span class="mi">3</span><span class="p">:</span> <span class="n">_N4threeH</span><span class="p">,</span>
<span class="mi">2</span><span class="p">:</span> <span class="n">_N4twoH</span><span class="p">,</span>
<span class="mi">1</span><span class="p">:</span> <span class="n">_N4oneH</span><span class="p">},</span>
<span class="mi">3</span><span class="p">:</span> <span class="p">{</span><span class="mi">2</span><span class="p">:</span> <span class="n">_N3twoH</span><span class="p">,</span>
<span class="mi">1</span><span class="p">:</span> <span class="n">_N3oneH</span><span class="p">},</span>
<span class="mi">2</span><span class="p">:</span> <span class="p">{</span><span class="mi">1</span><span class="p">:</span> <span class="n">_N2oneH</span><span class="p">}},</span>
<span class="s">'O'</span><span class="p">:</span> <span class="p">{</span><span class="mi">2</span><span class="p">:</span> <span class="p">{</span><span class="mi">1</span><span class="p">:</span> <span class="n">_O2</span><span class="p">}},</span>
<span class="s">'S'</span><span class="p">:</span> <span class="p">{</span><span class="mi">2</span><span class="p">:</span> <span class="p">{</span><span class="mi">1</span><span class="p">:</span> <span class="n">_S2</span><span class="p">}},</span>
<span class="p">}</span>
</div>
<div class="viewcode-block" id="ChainMolecule"><a class="viewcode-back" href="../../modules.html#MMTK.ChemicalObjects.ChainMolecule">[docs]</a><span class="k">class</span> <span class="nc">ChainMolecule</span><span class="p">(</span><span class="n">Molecule</span><span class="p">):</span>
<span class="sd">"""</span>
<span class="sd"> ChainMolecule</span>
<span class="sd"> ChainMolecules are generated by a MoleculeFactory from</span>
<span class="sd"> templates that have a sequence attribute.</span>
<span class="sd"> """</span>
<span class="k">def</span> <span class="nf">__len__</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span>
<span class="k">return</span> <span class="nb">len</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">sequence</span><span class="p">)</span>
<span class="k">def</span> <span class="nf">__getitem__</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">item</span><span class="p">):</span>
<span class="k">return</span> <span class="nb">getattr</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="bp">self</span><span class="o">.</span><span class="n">sequence</span><span class="p">[</span><span class="n">item</span><span class="p">])</span>
</div>
<span class="k">class</span> <span class="nc">Crystal</span><span class="p">(</span><span class="n">CompositeChemicalObject</span><span class="p">,</span> <span class="n">ChemicalObject</span><span class="p">):</span>
<span class="k">def</span> <span class="nf">__init__</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">blueprint</span><span class="p">,</span> <span class="n">_memo</span> <span class="o">=</span> <span class="bp">None</span><span class="p">,</span> <span class="o">**</span><span class="n">properties</span><span class="p">):</span>
<span class="n">ChemicalObject</span><span class="o">.</span><span class="n">__init__</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">blueprint</span><span class="p">,</span> <span class="n">_memo</span><span class="p">)</span>
<span class="n">properties</span> <span class="o">=</span> <span class="n">copy</span><span class="o">.</span><span class="n">copy</span><span class="p">(</span><span class="n">properties</span><span class="p">)</span>
<span class="n">CompositeChemicalObject</span><span class="o">.</span><span class="n">__init__</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">properties</span><span class="p">)</span>
<span class="bp">self</span><span class="o">.</span><span class="n">bonds</span> <span class="o">=</span> <span class="n">Bonds</span><span class="o">.</span><span class="n">BondList</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">bonds</span><span class="p">)</span>
<span class="n">blueprintclass</span> <span class="o">=</span> <span class="n">Database</span><span class="o">.</span><span class="n">BlueprintCrystal</span>
<span class="k">def</span> <span class="nf">_subunits</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span>
<span class="k">return</span> <span class="bp">self</span><span class="o">.</span><span class="n">groups</span>
<span class="k">def</span> <span class="nf">_descriptionSpec</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span>
<span class="k">return</span> <span class="s">"X"</span><span class="p">,</span> <span class="bp">None</span>
<div class="viewcode-block" id="Complex"><a class="viewcode-back" href="../../modules.html#MMTK.ChemicalObjects.Complex">[docs]</a><span class="k">class</span> <span class="nc">Complex</span><span class="p">(</span><span class="n">CompositeChemicalObject</span><span class="p">,</span> <span class="n">ChemicalObject</span><span class="p">):</span>
<span class="sd">"""</span>
<span class="sd"> Complex</span>
<span class="sd"> A complex is an assembly of molecules that are not connected by</span>
<span class="sd"> chemical bonds.</span>
<span class="sd"> """</span>
<span class="k">def</span> <span class="nf">__init__</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">complex_spec</span><span class="p">,</span> <span class="n">_memo</span> <span class="o">=</span> <span class="bp">None</span><span class="p">,</span> <span class="o">**</span><span class="n">properties</span><span class="p">):</span>
<span class="sd">"""</span>
<span class="sd"> :param complex_spec: a string (not case sensitive) that specifies</span>
<span class="sd"> the complex name in the chemical database</span>
<span class="sd"> :type complex_spec: str</span>
<span class="sd"> :keyword position: the position of the center of mass of the complex</span>
<span class="sd"> :type position: Scientific.Geometry.Vector</span>
<span class="sd"> :keyword name: a name given to the complex</span>
<span class="sd"> :type name: str</span>
<span class="sd"> :keyword configuration: the name of a configuration listed in the</span>
<span class="sd"> database definition of the complex, which</span>
<span class="sd"> is used to initialize the atom positions.</span>
<span class="sd"> If no configuration is specified, the</span>
<span class="sd"> configuration named "default" will be used,</span>
<span class="sd"> if it exists. Otherwise the atom positions</span>
<span class="sd"> are undefined.</span>
<span class="sd"> :type configuration: str</span>
<span class="sd"> """</span>
<span class="n">ChemicalObject</span><span class="o">.</span><span class="n">__init__</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">complex_spec</span><span class="p">,</span> <span class="n">_memo</span><span class="p">)</span>
<span class="n">properties</span> <span class="o">=</span> <span class="n">copy</span><span class="o">.</span><span class="n">copy</span><span class="p">(</span><span class="n">properties</span><span class="p">)</span>
<span class="n">CompositeChemicalObject</span><span class="o">.</span><span class="n">__init__</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">properties</span><span class="p">)</span>
<span class="n">blueprintclass</span> <span class="o">=</span> <span class="n">Database</span><span class="o">.</span><span class="n">BlueprintComplex</span>
<span class="k">def</span> <span class="nf">recreateAtomList</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span>
<span class="bp">self</span><span class="o">.</span><span class="n">atoms</span> <span class="o">=</span> <span class="p">[]</span>
<span class="k">for</span> <span class="n">m</span> <span class="ow">in</span> <span class="bp">self</span><span class="o">.</span><span class="n">molecules</span><span class="p">:</span>
<span class="bp">self</span><span class="o">.</span><span class="n">atoms</span><span class="o">.</span><span class="n">extend</span><span class="p">(</span><span class="n">m</span><span class="o">.</span><span class="n">atoms</span><span class="p">)</span>
<span class="k">def</span> <span class="nf">bondedUnits</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span>
<span class="k">return</span> <span class="bp">self</span><span class="o">.</span><span class="n">molecules</span>
<span class="k">def</span> <span class="nf">setBondAttributes</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span>
<span class="k">for</span> <span class="n">m</span> <span class="ow">in</span> <span class="bp">self</span><span class="o">.</span><span class="n">molecules</span><span class="p">:</span>
<span class="n">m</span><span class="o">.</span><span class="n">setBondAttributes</span><span class="p">()</span>
<span class="k">def</span> <span class="nf">clearBondAttributes</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span>
<span class="k">for</span> <span class="n">m</span> <span class="ow">in</span> <span class="bp">self</span><span class="o">.</span><span class="n">molecules</span><span class="p">:</span>
<span class="n">m</span><span class="o">.</span><span class="n">clearBondAttributes</span><span class="p">()</span>
<span class="k">def</span> <span class="nf">_subunits</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span>
<span class="k">return</span> <span class="bp">self</span><span class="o">.</span><span class="n">molecules</span>
<span class="k">def</span> <span class="nf">_descriptionSpec</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span>
<span class="k">return</span> <span class="s">"C"</span><span class="p">,</span> <span class="bp">None</span>
<span class="k">def</span> <span class="nf">writeXML</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="nb">file</span><span class="p">,</span> <span class="n">memo</span><span class="p">,</span> <span class="n">toplevel</span><span class="o">=</span><span class="mi">1</span><span class="p">):</span>
<span class="k">if</span> <span class="bp">self</span><span class="o">.</span><span class="n">type</span> <span class="ow">is</span> <span class="bp">None</span><span class="p">:</span>
<span class="n">name</span> <span class="o">=</span> <span class="s">'m'</span> <span class="o">+</span> <span class="sb">`memo['counter']`</span>
<span class="n">memo</span><span class="p">[</span><span class="s">'counter'</span><span class="p">]</span> <span class="o">=</span> <span class="n">memo</span><span class="p">[</span><span class="s">'counter'</span><span class="p">]</span> <span class="o">+</span> <span class="mi">1</span>
<span class="n">memo</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="o">=</span> <span class="n">name</span>
<span class="k">for</span> <span class="n">molecule</span> <span class="ow">in</span> <span class="bp">self</span><span class="o">.</span><span class="n">molecules</span><span class="p">:</span>
<span class="n">molecule</span><span class="o">.</span><span class="n">writeXML</span><span class="p">(</span><span class="nb">file</span><span class="p">,</span> <span class="n">memo</span><span class="p">,</span> <span class="mi">0</span><span class="p">)</span>
<span class="nb">file</span><span class="o">.</span><span class="n">write</span><span class="p">(</span><span class="s">'<molecule id="</span><span class="si">%s</span><span class="s">"></span><span class="se">\n</span><span class="s">'</span> <span class="o">%</span> <span class="n">name</span><span class="p">)</span>
<span class="k">for</span> <span class="n">molecule</span> <span class="ow">in</span> <span class="bp">self</span><span class="o">.</span><span class="n">molecules</span><span class="p">:</span>
<span class="nb">file</span><span class="o">.</span><span class="n">write</span><span class="p">(</span><span class="s">' <molecule ref="</span><span class="si">%s</span><span class="s">"/></span><span class="se">\n</span><span class="s">'</span> <span class="o">%</span> <span class="n">memo</span><span class="p">[</span><span class="nb">id</span><span class="p">(</span><span class="n">molecule</span><span class="p">)])</span>
<span class="nb">file</span><span class="o">.</span><span class="n">write</span><span class="p">(</span><span class="s">'</molecule></span><span class="se">\n</span><span class="s">'</span><span class="p">)</span>
<span class="k">else</span><span class="p">:</span>
<span class="n">ChemicalObject</span><span class="o">.</span><span class="n">writeXML</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="nb">file</span><span class="p">,</span> <span class="n">memo</span><span class="p">,</span> <span class="n">toplevel</span><span class="p">)</span>
<span class="k">if</span> <span class="n">toplevel</span><span class="p">:</span>
<span class="k">return</span> <span class="p">[</span><span class="s">'<molecule ref="</span><span class="si">%s</span><span class="s">"/>'</span> <span class="o">%</span> <span class="n">name</span><span class="p">]</span>
<span class="k">else</span><span class="p">:</span>
<span class="k">return</span> <span class="bp">None</span>
<span class="k">def</span> <span class="nf">getXMLAtomOrder</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span>
<span class="k">if</span> <span class="bp">self</span><span class="o">.</span><span class="n">type</span> <span class="ow">is</span> <span class="bp">None</span><span class="p">:</span>
<span class="n">atoms</span> <span class="o">=</span> <span class="p">[]</span>
<span class="k">for</span> <span class="n">molecule</span> <span class="ow">in</span> <span class="bp">self</span><span class="o">.</span><span class="n">molecules</span><span class="p">:</span>
<span class="n">atoms</span><span class="o">.</span><span class="n">extend</span><span class="p">(</span><span class="n">molecule</span><span class="o">.</span><span class="n">getXMLAtomOrder</span><span class="p">())</span>
<span class="k">return</span> <span class="n">atoms</span>
<span class="k">else</span><span class="p">:</span>
<span class="k">return</span> <span class="n">ChemicalObject</span><span class="o">.</span><span class="n">getXMLAtomOrder</span><span class="p">(</span><span class="bp">self</span><span class="p">)</span>
</div>
<span class="n">Database</span><span class="o">.</span><span class="n">registerInstanceClass</span><span class="p">(</span><span class="n">Atom</span><span class="o">.</span><span class="n">blueprintclass</span><span class="p">,</span> <span class="n">Atom</span><span class="p">)</span>
<span class="n">Database</span><span class="o">.</span><span class="n">registerInstanceClass</span><span class="p">(</span><span class="n">Group</span><span class="o">.</span><span class="n">blueprintclass</span><span class="p">,</span> <span class="n">Group</span><span class="p">)</span>
<span class="n">Database</span><span class="o">.</span><span class="n">registerInstanceClass</span><span class="p">(</span><span class="n">Molecule</span><span class="o">.</span><span class="n">blueprintclass</span><span class="p">,</span> <span class="n">Molecule</span><span class="p">)</span>
<span class="n">Database</span><span class="o">.</span><span class="n">registerInstanceClass</span><span class="p">(</span><span class="n">Crystal</span><span class="o">.</span><span class="n">blueprintclass</span><span class="p">,</span> <span class="n">Crystal</span><span class="p">)</span>
<span class="n">Database</span><span class="o">.</span><span class="n">registerInstanceClass</span><span class="p">(</span><span class="n">Complex</span><span class="o">.</span><span class="n">blueprintclass</span><span class="p">,</span> <span class="n">Complex</span><span class="p">)</span>
<div class="viewcode-block" id="AtomCluster"><a class="viewcode-back" href="../../modules.html#MMTK.ChemicalObjects.AtomCluster">[docs]</a><span class="k">class</span> <span class="nc">AtomCluster</span><span class="p">(</span><span class="n">CompositeChemicalObject</span><span class="p">,</span> <span class="n">ChemicalObject</span><span class="p">):</span>
<span class="sd">"""</span>
<span class="sd"> An agglomeration of atoms</span>
<span class="sd"> An atom cluster acts like a molecule without any bonds or atom</span>
<span class="sd"> properties. It can be used to represent a group of atoms that</span>
<span class="sd"> are known to form a chemical unit but whose chemical properties</span>
<span class="sd"> are not sufficiently known to define a molecule.</span>
<span class="sd"> """</span>
<span class="k">def</span> <span class="nf">__init__</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">atoms</span><span class="p">,</span> <span class="o">**</span><span class="n">properties</span><span class="p">):</span>
<span class="sd">"""</span>
<span class="sd"> :param atoms: a list of atoms in the cluster</span>
<span class="sd"> :type atoms: list</span>
<span class="sd"> :keyword position: the position of the center of mass of the cluster</span>
<span class="sd"> :type position: Scientific.Geometry.Vector</span>
<span class="sd"> :keyword name: a name given to the cluster</span>
<span class="sd"> :type name: str</span>
<span class="sd"> """</span>
<span class="bp">self</span><span class="o">.</span><span class="n">atoms</span> <span class="o">=</span> <span class="nb">list</span><span class="p">(</span><span class="n">atoms</span><span class="p">)</span>
<span class="bp">self</span><span class="o">.</span><span class="n">parent</span> <span class="o">=</span> <span class="bp">None</span>
<span class="bp">self</span><span class="o">.</span><span class="n">name</span> <span class="o">=</span> <span class="s">''</span>
<span class="bp">self</span><span class="o">.</span><span class="n">type</span> <span class="o">=</span> <span class="bp">None</span>
<span class="k">for</span> <span class="n">a</span> <span class="ow">in</span> <span class="bp">self</span><span class="o">.</span><span class="n">atoms</span><span class="p">:</span>
<span class="k">if</span> <span class="n">a</span><span class="o">.</span><span class="n">parent</span> <span class="ow">is</span> <span class="ow">not</span> <span class="bp">None</span><span class="p">:</span>
<span class="k">raise</span> <span class="ne">ValueError</span><span class="p">(</span><span class="nb">repr</span><span class="p">(</span><span class="n">a</span><span class="p">)</span><span class="o">+</span><span class="s">' is part of '</span> <span class="o">+</span> <span class="nb">repr</span><span class="p">(</span><span class="n">a</span><span class="o">.</span><span class="n">parent</span><span class="p">))</span>
<span class="n">a</span><span class="o">.</span><span class="n">parent</span> <span class="o">=</span> <span class="bp">self</span>
<span class="k">if</span> <span class="n">a</span><span class="o">.</span><span class="n">name</span> <span class="o">!=</span> <span class="s">''</span><span class="p">:</span>
<span class="nb">setattr</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">a</span><span class="o">.</span><span class="n">name</span><span class="p">,</span> <span class="n">a</span><span class="p">)</span>
<span class="n">properties</span> <span class="o">=</span> <span class="n">copy</span><span class="o">.</span><span class="n">copy</span><span class="p">(</span><span class="n">properties</span><span class="p">)</span>
<span class="n">CompositeChemicalObject</span><span class="o">.</span><span class="n">__init__</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">properties</span><span class="p">)</span>
<span class="bp">self</span><span class="o">.</span><span class="n">bonds</span> <span class="o">=</span> <span class="n">Bonds</span><span class="o">.</span><span class="n">BondList</span><span class="p">([])</span>
<span class="k">def</span> <span class="nf">bondedTo</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">atom</span><span class="p">):</span>
<span class="k">return</span> <span class="p">[]</span>
<span class="k">def</span> <span class="nf">setBondAttributes</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span>
<span class="k">pass</span>
<span class="k">def</span> <span class="nf">clearBondAttributes</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span>
<span class="k">pass</span>
<span class="k">def</span> <span class="nf">_subunits</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span>
<span class="k">return</span> <span class="p">[]</span>
<span class="k">def</span> <span class="nf">_description</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">tag</span><span class="p">,</span> <span class="n">index_map</span><span class="p">,</span> <span class="n">toplevel</span><span class="p">):</span>
<span class="n">s</span> <span class="o">=</span> <span class="s">'AC('</span> <span class="o">+</span> <span class="sb">`self.name`</span> <span class="o">+</span> <span class="s">',['</span>
<span class="k">for</span> <span class="n">a</span> <span class="ow">in</span> <span class="bp">self</span><span class="o">.</span><span class="n">atoms</span><span class="p">:</span>
<span class="n">s</span> <span class="o">=</span> <span class="n">s</span> <span class="o">+</span> <span class="n">a</span><span class="o">.</span><span class="n">_description</span><span class="p">(</span><span class="n">tag</span><span class="p">,</span> <span class="n">index_map</span><span class="p">,</span> <span class="mi">1</span><span class="p">)</span> <span class="o">+</span> <span class="s">','</span>
<span class="n">s</span> <span class="o">=</span> <span class="n">s</span> <span class="o">+</span> <span class="s">']'</span>
<span class="n">constraints</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">_distanceConstraintList</span><span class="p">()</span>
<span class="k">if</span> <span class="n">constraints</span><span class="p">:</span>
<span class="n">s</span> <span class="o">=</span> <span class="n">s</span> <span class="o">+</span> <span class="s">',dc=['</span>
<span class="k">if</span> <span class="n">index_map</span> <span class="ow">is</span> <span class="bp">None</span><span class="p">:</span>
<span class="k">for</span> <span class="n">c</span> <span class="ow">in</span> <span class="n">constraints</span><span class="p">:</span>
<span class="n">s</span> <span class="o">=</span> <span class="n">s</span> <span class="o">+</span> <span class="s">'(</span><span class="si">%d</span><span class="s">,</span><span class="si">%d</span><span class="s">,</span><span class="si">%f</span><span class="s">),'</span> <span class="o">%</span> <span class="p">(</span><span class="n">c</span><span class="p">[</span><span class="mi">0</span><span class="p">]</span><span class="o">.</span><span class="n">index</span><span class="p">,</span> <span class="n">c</span><span class="p">[</span><span class="mi">1</span><span class="p">]</span><span class="o">.</span><span class="n">index</span><span class="p">,</span> <span class="n">c</span><span class="p">[</span><span class="mi">2</span><span class="p">])</span>
<span class="k">else</span><span class="p">:</span>
<span class="k">for</span> <span class="n">c</span> <span class="ow">in</span> <span class="n">constraints</span><span class="p">:</span>
<span class="n">s</span> <span class="o">=</span> <span class="n">s</span> <span class="o">+</span> <span class="s">'(</span><span class="si">%d</span><span class="s">,</span><span class="si">%d</span><span class="s">,</span><span class="si">%f</span><span class="s">),'</span> <span class="o">%</span> <span class="p">(</span><span class="n">index_map</span><span class="p">[</span><span class="n">c</span><span class="p">[</span><span class="mi">0</span><span class="p">]</span><span class="o">.</span><span class="n">index</span><span class="p">],</span>
<span class="n">index_map</span><span class="p">[</span><span class="n">c</span><span class="p">[</span><span class="mi">1</span><span class="p">]</span><span class="o">.</span><span class="n">index</span><span class="p">],</span> <span class="n">c</span><span class="p">[</span><span class="mi">2</span><span class="p">])</span>
<span class="n">s</span> <span class="o">=</span> <span class="n">s</span> <span class="o">+</span> <span class="s">']'</span>
<span class="k">return</span> <span class="n">s</span> <span class="o">+</span> <span class="s">')'</span></div>
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