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<h1>Source code for MMTK.ConfigIO</h1><div class="highlight"><pre>
<span class="c"># This module deals with input and output of configurations.</span>
<span class="c">#</span>
<span class="c"># Written by Konrad Hinsen</span>
<span class="c">#</span>
<span class="sd">"""</span>
<span class="sd">I/O of molecular configurations</span>
<span class="sd">Input: Z-Matrix and Cartesian</span>
<span class="sd">Output: VRML</span>
<span class="sd">PDB files are handled in :class:`~MMTK.PDB`.</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">PDB</span><span class="p">,</span> <span class="n">Units</span><span class="p">,</span> <span class="n">Utility</span>
<span class="kn">from</span> <span class="nn">Scientific.Geometry.Objects3D</span> <span class="kn">import</span> <span class="n">Sphere</span><span class="p">,</span> <span class="n">Cone</span><span class="p">,</span> <span class="n">Plane</span><span class="p">,</span> <span class="n">Line</span><span class="p">,</span> \
<span class="n">rotatePoint</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.Visualization</span> <span class="kn">import</span> <span class="n">VRML</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">os</span>
<span class="c">#</span>
<span class="c"># This class represents a Z-Matrix. Z-Matrix data consists of a list</span>
<span class="c"># with one element for each atom being defined. Each entry is a</span>
<span class="c"># list containing the data defining the atom.</span>
<span class="c">#</span>
<div class="viewcode-block" id="ZMatrix"><a class="viewcode-back" href="../../modules.html#MMTK.ConfigIO.ZMatrix">[docs]</a><span class="k">class</span> <span class="nc">ZMatrix</span><span class="p">(</span><span class="nb">object</span><span class="p">):</span>
<span class="sd">"""</span>
<span class="sd"> Z-Matrix specification of a molecule conformation</span>
<span class="sd"> ZMatrix objects can be used in chemical database entries</span>
<span class="sd"> to specify molecule conformations by internal coordinates.</span>
<span class="sd"> With the exception of the three first atoms, each atom is</span>
<span class="sd"> defined relative to three previously atoms by a distance,</span>
<span class="sd"> an angle, and a dihedral angle.</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">data</span><span class="p">):</span>
<span class="sd">"""</span>
<span class="sd"> :param data: a list of atom definitions. Each atom definition (except</span>
<span class="sd"> for the first three ones) is a list containing seven</span>
<span class="sd"> elements:</span>
<span class="sd"> - the atom to be defined</span>
<span class="sd"> - a previously defined atom and the distance to it</span>
<span class="sd"> - another previously defined atom and the angle to it</span>
<span class="sd"> - a third previously defined atom and the dihedral</span>
<span class="sd"> angle to it</span>
<span class="sd"> The definition of the first atom contains only the first</span>
<span class="sd"> element, the second atom needs the first three elements,</span>
<span class="sd"> and the third atom is defined by the first five elements.</span>
<span class="sd"> """</span>
<span class="bp">self</span><span class="o">.</span><span class="n">data</span> <span class="o">=</span> <span class="n">data</span>
<span class="bp">self</span><span class="o">.</span><span class="n">coordinates</span> <span class="o">=</span> <span class="p">{}</span>
<span class="n">_substitute</span> <span class="o">=</span> <span class="bp">True</span>
<span class="k">def</span> <span class="nf">findPositions</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span>
<span class="c"># First atom at origin</span>
<span class="bp">self</span><span class="o">.</span><span class="n">coordinates</span><span class="p">[</span><span class="bp">self</span><span class="o">.</span><span class="n">data</span><span class="p">[</span><span class="mi">0</span><span class="p">][</span><span class="mi">0</span><span class="p">]]</span> <span class="o">=</span> <span class="n">Vector</span><span class="p">(</span><span class="mi">0</span><span class="p">,</span><span class="mi">0</span><span class="p">,</span><span class="mi">0</span><span class="p">)</span>
<span class="c"># Second atom along x-axis</span>
<span class="bp">self</span><span class="o">.</span><span class="n">coordinates</span><span class="p">[</span><span class="bp">self</span><span class="o">.</span><span class="n">data</span><span class="p">[</span><span class="mi">1</span><span class="p">][</span><span class="mi">0</span><span class="p">]]</span> <span class="o">=</span> <span class="n">Vector</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">data</span><span class="p">[</span><span class="mi">1</span><span class="p">][</span><span class="mi">2</span><span class="p">],</span><span class="mi">0</span><span class="p">,</span><span class="mi">0</span><span class="p">)</span>
<span class="c"># Third atom in xy-plane</span>
<span class="k">try</span><span class="p">:</span>
<span class="n">pos1</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">coordinates</span><span class="p">[</span><span class="bp">self</span><span class="o">.</span><span class="n">data</span><span class="p">[</span><span class="mi">2</span><span class="p">][</span><span class="mi">1</span><span class="p">]]</span>
<span class="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">"atom </span><span class="si">%d</span><span class="s"> has no defined position"</span>
<span class="o">%</span> <span class="bp">self</span><span class="o">.</span><span class="n">data</span><span class="p">[</span><span class="mi">2</span><span class="p">][</span><span class="mi">1</span><span class="p">]</span><span class="o">.</span><span class="n">number</span><span class="p">)</span>
<span class="k">try</span><span class="p">:</span>
<span class="n">pos2</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">coordinates</span><span class="p">[</span><span class="bp">self</span><span class="o">.</span><span class="n">data</span><span class="p">[</span><span class="mi">2</span><span class="p">][</span><span class="mi">3</span><span class="p">]]</span>
<span class="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">"atom </span><span class="si">%d</span><span class="s"> has no defined position"</span>
<span class="o">%</span> <span class="bp">self</span><span class="o">.</span><span class="n">data</span><span class="p">[</span><span class="mi">2</span><span class="p">][</span><span class="mi">3</span><span class="p">]</span><span class="o">.</span><span class="n">number</span><span class="p">)</span>
<span class="n">sphere</span> <span class="o">=</span> <span class="n">Sphere</span><span class="p">(</span><span class="n">pos1</span><span class="p">,</span> <span class="bp">self</span><span class="o">.</span><span class="n">data</span><span class="p">[</span><span class="mi">2</span><span class="p">][</span><span class="mi">2</span><span class="p">])</span>
<span class="n">cone</span> <span class="o">=</span> <span class="n">Cone</span><span class="p">(</span><span class="n">pos1</span><span class="p">,</span> <span class="n">pos2</span><span class="o">-</span><span class="n">pos1</span><span class="p">,</span> <span class="bp">self</span><span class="o">.</span><span class="n">data</span><span class="p">[</span><span class="mi">2</span><span class="p">][</span><span class="mi">4</span><span class="p">])</span>
<span class="n">plane</span> <span class="o">=</span> <span class="n">Plane</span><span class="p">(</span><span class="n">Vector</span><span class="p">(</span><span class="mi">0</span><span class="p">,</span><span class="mi">0</span><span class="p">,</span><span class="mi">0</span><span class="p">),</span> <span class="n">Vector</span><span class="p">(</span><span class="mi">0</span><span class="p">,</span><span class="mi">0</span><span class="p">,</span><span class="mi">1</span><span class="p">))</span>
<span class="n">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="bp">self</span><span class="o">.</span><span class="n">coordinates</span><span class="p">[</span><span class="bp">self</span><span class="o">.</span><span class="n">data</span><span class="p">[</span><span class="mi">2</span><span class="p">][</span><span class="mi">0</span><span class="p">]]</span> <span class="o">=</span> <span class="n">points</span><span class="p">[</span><span class="mi">0</span><span class="p">]</span>
<span class="c"># All following atoms defined by distance + angle + dihedral</span>
<span class="k">for</span> <span class="n">entry</span> <span class="ow">in</span> <span class="bp">self</span><span class="o">.</span><span class="n">data</span><span class="p">[</span><span class="mi">3</span><span class="p">:]:</span>
<span class="k">try</span><span class="p">:</span>
<span class="n">pos1</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">coordinates</span><span class="p">[</span><span class="n">entry</span><span class="p">[</span><span class="mi">1</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">"atom </span><span class="si">%d</span><span class="s"> has no defined position"</span>
<span class="o">%</span> <span class="n">entry</span><span class="p">[</span><span class="mi">1</span><span class="p">]</span><span class="o">.</span><span class="n">number</span><span class="p">)</span>
<span class="k">try</span><span class="p">:</span>
<span class="n">pos2</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">coordinates</span><span class="p">[</span><span class="n">entry</span><span class="p">[</span><span class="mi">3</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">"atom </span><span class="si">%d</span><span class="s"> has no defined position"</span>
<span class="o">%</span> <span class="n">entry</span><span class="p">[</span><span class="mi">3</span><span class="p">]</span><span class="o">.</span><span class="n">number</span><span class="p">)</span>
<span class="k">try</span><span class="p">:</span>
<span class="n">pos3</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">coordinates</span><span class="p">[</span><span class="n">entry</span><span class="p">[</span><span class="mi">5</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">"atom </span><span class="si">%d</span><span class="s"> has no defined position"</span>
<span class="o">%</span> <span class="n">entry</span><span class="p">[</span><span class="mi">5</span><span class="p">]</span><span class="o">.</span><span class="n">number</span><span class="p">)</span>
<span class="n">distance</span> <span class="o">=</span> <span class="n">entry</span><span class="p">[</span><span class="mi">2</span><span class="p">]</span>
<span class="n">angle</span> <span class="o">=</span> <span class="n">entry</span><span class="p">[</span><span class="mi">4</span><span class="p">]</span>
<span class="n">dihedral</span> <span class="o">=</span> <span class="n">entry</span><span class="p">[</span><span class="mi">6</span><span class="p">]</span>
<span class="n">sphere</span> <span class="o">=</span> <span class="n">Sphere</span><span class="p">(</span><span class="n">pos1</span><span class="p">,</span> <span class="n">distance</span><span class="p">)</span>
<span class="n">cone</span> <span class="o">=</span> <span class="n">Cone</span><span class="p">(</span><span class="n">pos1</span><span class="p">,</span> <span class="n">pos2</span><span class="o">-</span><span class="n">pos1</span><span class="p">,</span> <span class="n">angle</span><span class="p">)</span>
<span class="n">plane123</span> <span class="o">=</span> <span class="n">Plane</span><span class="p">(</span><span class="n">pos3</span><span class="p">,</span> <span class="n">pos2</span><span class="p">,</span> <span class="n">pos1</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">plane123</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="n">Plane</span><span class="p">(</span><span class="n">pos2</span><span class="p">,</span> <span class="n">pos1</span><span class="p">,</span> <span class="n">p</span><span class="p">)</span><span class="o">.</span><span class="n">normal</span> <span class="o">*</span> <span class="n">plane123</span><span class="o">.</span><span class="n">normal</span> <span class="o">></span> <span class="mi">0</span><span class="p">:</span>
<span class="k">break</span>
<span class="n">p</span> <span class="o">=</span> <span class="n">rotatePoint</span><span class="p">(</span><span class="n">p</span><span class="p">,</span> <span class="n">Line</span><span class="p">(</span><span class="n">pos1</span><span class="p">,</span> <span class="n">pos2</span><span class="o">-</span><span class="n">pos1</span><span class="p">),</span> <span class="n">dihedral</span><span class="p">)</span>
<span class="bp">self</span><span class="o">.</span><span class="n">coordinates</span><span class="p">[</span><span class="n">entry</span><span class="p">[</span><span class="mi">0</span><span class="p">]]</span> <span class="o">=</span> <span class="n">p</span>
<div class="viewcode-block" id="ZMatrix.applyTo"><a class="viewcode-back" href="../../modules.html#MMTK.ConfigIO.ZMatrix.applyTo">[docs]</a> <span class="k">def</span> <span class="nf">applyTo</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="sd">"""</span>
<span class="sd"> Define the positions of the atoms in a chemical object by the</span>
<span class="sd"> internal coordinates of the Z-Matrix.</span>
<span class="sd"> :param object: the object to which the Z-Matrix is applied</span>
<span class="sd"> """</span>
<span class="k">if</span> <span class="ow">not</span> <span class="nb">len</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">coordinates</span><span class="p">):</span>
<span class="bp">self</span><span class="o">.</span><span class="n">findPositions</span><span class="p">()</span>
<span class="k">for</span> <span class="n">entry</span> <span class="ow">in</span> <span class="bp">self</span><span class="o">.</span><span class="n">coordinates</span><span class="o">.</span><span class="n">items</span><span class="p">():</span>
<span class="nb">object</span><span class="o">.</span><span class="n">setPosition</span><span class="p">(</span><span class="n">entry</span><span class="p">[</span><span class="mi">0</span><span class="p">],</span> <span class="n">entry</span><span class="p">[</span><span class="mi">1</span><span class="p">])</span>
<span class="nb">object</span><span class="o">.</span><span class="n">normalizePosition</span><span class="p">()</span>
<span class="c">#</span>
<span class="c"># This class represents a dictionary of Cartesian positions</span>
<span class="c">#</span></div></div>
<div class="viewcode-block" id="Cartesian"><a class="viewcode-back" href="../../modules.html#MMTK.ConfigIO.Cartesian">[docs]</a><span class="k">class</span> <span class="nc">Cartesian</span><span class="p">(</span><span class="nb">object</span><span class="p">):</span>
<span class="sd">"""</span>
<span class="sd"> Cartesian specification of a molecule conformation</span>
<span class="sd"> Cartesian objects can be used in chemical database entries</span>
<span class="sd"> to specify molecule conformations by Cartesian coordinates.</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">data</span><span class="p">):</span>
<span class="sd">"""</span>
<span class="sd"> :param data: a dictionary mapping atoms to tuples of length three</span>
<span class="sd"> that define its Cartesian coordinates</span>
<span class="sd"> """</span>
<span class="bp">self</span><span class="o">.</span><span class="n">dict</span> <span class="o">=</span> <span class="n">data</span>
<span class="n">_substitute</span> <span class="o">=</span> <span class="bp">True</span>
<div class="viewcode-block" id="Cartesian.applyTo"><a class="viewcode-back" href="../../modules.html#MMTK.ConfigIO.Cartesian.applyTo">[docs]</a> <span class="k">def</span> <span class="nf">applyTo</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="sd">"""</span>
<span class="sd"> Define the positions of the atoms in a chemical object by the</span>
<span class="sd"> stored coordinates.</span>
<span class="sd"> :param object: the object to which the coordinates are applied</span>
<span class="sd"> """</span>
<span class="k">for</span> <span class="n">a</span><span class="p">,</span> <span class="n">r</span> <span class="ow">in</span> <span class="bp">self</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="nb">object</span><span class="o">.</span><span class="n">setPosition</span><span class="p">(</span><span class="n">a</span><span class="p">,</span> <span class="n">Vector</span><span class="p">(</span><span class="n">r</span><span class="p">[</span><span class="mi">0</span><span class="p">],</span> <span class="n">r</span><span class="p">[</span><span class="mi">1</span><span class="p">],</span> <span class="n">r</span><span class="p">[</span><span class="mi">2</span><span class="p">]))</span>
<span class="c">#</span>
<span class="c"># VRML output</span>
<span class="c">#</span></div></div>
<span class="k">class</span> <span class="nc">VRMLWireframeFile</span><span class="p">(</span><span class="n">VRML</span><span class="o">.</span><span class="n">VRMLFile</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">filename</span><span class="p">,</span> <span class="n">color_values</span> <span class="o">=</span> <span class="bp">None</span><span class="p">):</span>
<span class="n">VRML</span><span class="o">.</span><span class="n">VRMLFile</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">filename</span><span class="p">,</span> <span class="s">'w'</span><span class="p">)</span>
<span class="bp">self</span><span class="o">.</span><span class="n">warning</span> <span class="o">=</span> <span class="mi">0</span>
<span class="bp">self</span><span class="o">.</span><span class="n">color_values</span> <span class="o">=</span> <span class="n">color_values</span>
<span class="k">if</span> <span class="bp">self</span><span class="o">.</span><span class="n">color_values</span> <span class="ow">is</span> <span class="ow">not</span> <span class="bp">None</span><span class="p">:</span>
<span class="n">lower</span> <span class="o">=</span> <span class="n">N</span><span class="o">.</span><span class="n">minimum</span><span class="o">.</span><span class="n">reduce</span><span class="p">(</span><span class="n">color_values</span><span class="o">.</span><span class="n">array</span><span class="p">)</span>
<span class="n">upper</span> <span class="o">=</span> <span class="n">N</span><span class="o">.</span><span class="n">maximum</span><span class="o">.</span><span class="n">reduce</span><span class="p">(</span><span class="n">color_values</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">color_scale</span> <span class="o">=</span> <span class="n">VRML</span><span class="o">.</span><span class="n">ColorScale</span><span class="p">((</span><span class="n">lower</span><span class="p">,</span> <span class="n">upper</span><span class="p">))</span>
<span class="k">def</span> <span class="nf">write</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">configuration</span> <span class="o">=</span> <span class="bp">None</span><span class="p">,</span> <span class="n">distance</span> <span class="o">=</span> <span class="bp">None</span><span class="p">):</span>
<span class="kn">from</span> <span class="nn">MMTK.ChemicalObjects</span> <span class="kn">import</span> <span class="n">isChemicalObject</span>
<span class="kn">from</span> <span class="nn">MMTK.Universe</span> <span class="kn">import</span> <span class="n">InfiniteUniverse</span>
<span class="k">if</span> <span class="n">distance</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="n">distance</span> <span class="o">=</span> <span class="nb">object</span><span class="o">.</span><span class="n">universe</span><span class="p">()</span><span class="o">.</span><span class="n">distanceVector</span>
<span class="k">except</span> <span class="ne">AttributeError</span><span class="p">:</span>
<span class="n">distance</span> <span class="o">=</span> <span class="n">InfiniteUniverse</span><span class="p">()</span><span class="o">.</span><span class="n">distanceVector</span>
<span class="k">if</span> <span class="ow">not</span> <span class="n">isChemicalObject</span><span class="p">(</span><span class="nb">object</span><span class="p">):</span>
<span class="k">for</span> <span class="n">o</span> <span class="ow">in</span> <span class="nb">object</span><span class="p">:</span>
<span class="bp">self</span><span class="o">.</span><span class="n">write</span><span class="p">(</span><span class="n">o</span><span class="p">,</span> <span class="n">configuration</span><span class="p">,</span> <span class="n">distance</span><span class="p">)</span>
<span class="k">else</span><span class="p">:</span>
<span class="k">for</span> <span class="n">bu</span> <span class="ow">in</span> <span class="nb">object</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="bp">self</span><span class="o">.</span><span class="n">writeAtom</span><span class="p">(</span><span class="n">a</span><span class="p">,</span> <span class="n">configuration</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="bp">self</span><span class="o">.</span><span class="n">writeBond</span><span class="p">(</span><span class="n">b</span><span class="p">,</span> <span class="n">configuration</span><span class="p">,</span> <span class="n">distance</span><span class="p">)</span>
<span class="k">def</span> <span class="nf">close</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span>
<span class="n">VRML</span><span class="o">.</span><span class="n">VRMLFile</span><span class="o">.</span><span class="n">close</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">warning</span><span class="p">:</span>
<span class="n">Utility</span><span class="o">.</span><span class="n">warning</span><span class="p">(</span><span class="s">'Some atoms are missing in the output file '</span> <span class="o">+</span> \
<span class="s">'because their positions are undefined.'</span><span class="p">)</span>
<span class="bp">self</span><span class="o">.</span><span class="n">warning</span> <span class="o">=</span> <span class="mi">0</span>
<span class="k">def</span> <span class="nf">atomColor</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">color_values</span> <span class="ow">is</span> <span class="bp">None</span><span class="p">:</span>
<span class="k">return</span> <span class="n">atom</span><span class="o">.</span><span class="n">color</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">color_scale</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">color_values</span><span class="p">[</span><span class="n">atom</span><span class="p">])</span>
<span class="k">def</span> <span class="nf">writeAtom</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">configuration</span><span class="p">):</span>
<span class="k">pass</span>
<span class="k">def</span> <span class="nf">writeBond</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">bond</span><span class="p">,</span> <span class="n">configuration</span><span class="p">,</span> <span class="n">distance</span><span class="p">):</span>
<span class="n">p1</span> <span class="o">=</span> <span class="n">bond</span><span class="o">.</span><span class="n">a1</span><span class="o">.</span><span class="n">position</span><span class="p">(</span><span class="n">configuration</span><span class="p">)</span>
<span class="n">p2</span> <span class="o">=</span> <span class="n">bond</span><span class="o">.</span><span class="n">a2</span><span class="o">.</span><span class="n">position</span><span class="p">(</span><span class="n">configuration</span><span class="p">)</span>
<span class="k">if</span> <span class="n">p1</span> <span class="ow">is</span> <span class="ow">not</span> <span class="bp">None</span> <span class="ow">and</span> <span class="n">p2</span> <span class="ow">is</span> <span class="ow">not</span> <span class="bp">None</span><span class="p">:</span>
<span class="n">bond_vector</span> <span class="o">=</span> <span class="mf">0.5</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="n">configuration</span><span class="p">)</span>
<span class="n">cut</span> <span class="o">=</span> <span class="n">bond_vector</span> <span class="o">!=</span> <span class="mf">0.5</span><span class="o">*</span><span class="p">(</span><span class="n">p2</span><span class="o">-</span><span class="n">p1</span><span class="p">)</span>
<span class="n">color1</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="n">bond</span><span class="o">.</span><span class="n">a1</span><span class="p">)</span>
<span class="n">color2</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="n">bond</span><span class="o">.</span><span class="n">a2</span><span class="p">)</span>
<span class="n">material1</span> <span class="o">=</span> <span class="n">VRML</span><span class="o">.</span><span class="n">EmissiveMaterial</span><span class="p">(</span><span class="n">color1</span><span class="p">)</span>
<span class="n">material2</span> <span class="o">=</span> <span class="n">VRML</span><span class="o">.</span><span class="n">EmissiveMaterial</span><span class="p">(</span><span class="n">color2</span><span class="p">)</span>
<span class="k">if</span> <span class="n">color1</span> <span class="o">==</span> <span class="n">color2</span> <span class="ow">and</span> <span class="ow">not</span> <span class="n">cut</span><span class="p">:</span>
<span class="n">c</span> <span class="o">=</span> <span class="n">VRML</span><span class="o">.</span><span class="n">Line</span><span class="p">(</span><span class="n">p1</span><span class="p">,</span> <span class="n">p2</span><span class="p">,</span> <span class="n">material</span> <span class="o">=</span> <span class="n">material1</span><span class="p">)</span>
<span class="n">c</span><span class="o">.</span><span class="n">writeToFile</span><span class="p">(</span><span class="bp">self</span><span class="p">)</span>
<span class="k">else</span><span class="p">:</span>
<span class="n">c</span> <span class="o">=</span> <span class="n">VRML</span><span class="o">.</span><span class="n">Line</span><span class="p">(</span><span class="n">p1</span><span class="p">,</span> <span class="n">p1</span><span class="o">+</span><span class="n">bond_vector</span><span class="p">,</span> <span class="n">material</span> <span class="o">=</span> <span class="n">material1</span><span class="p">)</span>
<span class="n">c</span><span class="o">.</span><span class="n">writeToFile</span><span class="p">(</span><span class="bp">self</span><span class="p">)</span>
<span class="n">c</span> <span class="o">=</span> <span class="n">VRML</span><span class="o">.</span><span class="n">Line</span><span class="p">(</span><span class="n">p2</span><span class="p">,</span> <span class="n">p2</span><span class="o">-</span><span class="n">bond_vector</span><span class="p">,</span> <span class="n">material</span> <span class="o">=</span> <span class="n">material2</span><span class="p">)</span>
<span class="n">c</span><span class="o">.</span><span class="n">writeToFile</span><span class="p">(</span><span class="bp">self</span><span class="p">)</span>
<span class="k">class</span> <span class="nc">VRMLHighlight</span><span class="p">(</span><span class="n">VRMLWireframeFile</span><span class="p">):</span>
<span class="k">def</span> <span class="nf">writeAtom</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">configuration</span><span class="p">):</span>
<span class="k">try</span><span class="p">:</span>
<span class="n">highlight</span> <span class="o">=</span> <span class="n">atom</span><span class="o">.</span><span class="n">highlight</span>
<span class="k">except</span> <span class="ne">AttributeError</span><span class="p">:</span>
<span class="n">highlight</span> <span class="o">=</span> <span class="mi">0</span>
<span class="k">if</span> <span class="n">highlight</span><span class="p">:</span>
<span class="n">p</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">configuration</span><span class="p">)</span>
<span class="k">if</span> <span class="n">p</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">warning</span> <span class="o">=</span> <span class="mi">1</span>
<span class="k">else</span><span class="p">:</span>
<span class="n">s</span> <span class="o">=</span> <span class="n">VRML</span><span class="o">.</span><span class="n">Sphere</span><span class="p">(</span><span class="n">p</span><span class="p">,</span> <span class="mf">0.1</span><span class="o">*</span><span class="n">Units</span><span class="o">.</span><span class="n">Ang</span><span class="p">,</span>
<span class="n">material</span> <span class="o">=</span> <span class="n">VRML</span><span class="o">.</span><span class="n">DiffuseMaterial</span><span class="p">(</span><span class="n">atom</span><span class="o">.</span><span class="n">color</span><span class="p">),</span>
<span class="n">reuse</span> <span class="o">=</span> <span class="mi">1</span><span class="p">)</span>
<span class="n">s</span><span class="o">.</span><span class="n">writeToFile</span><span class="p">(</span><span class="bp">self</span><span class="p">)</span>
<span class="k">class</span> <span class="nc">VRMLBallAndStickFile</span><span class="p">(</span><span class="n">VRMLWireframeFile</span><span class="p">):</span>
<span class="k">def</span> <span class="nf">writeAtom</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">configuration</span><span class="p">):</span>
<span class="n">p</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">configuration</span><span class="p">)</span>
<span class="k">if</span> <span class="n">p</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">warning</span> <span class="o">=</span> <span class="mi">1</span>
<span class="k">else</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="n">atom</span><span class="p">)</span>
<span class="n">s</span> <span class="o">=</span> <span class="n">VRML</span><span class="o">.</span><span class="n">Sphere</span><span class="p">(</span><span class="n">p</span><span class="p">,</span> <span class="mf">0.1</span><span class="o">*</span><span class="n">Units</span><span class="o">.</span><span class="n">Ang</span><span class="p">,</span>
<span class="n">material</span> <span class="o">=</span> <span class="n">VRML</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">reuse</span> <span class="o">=</span> <span class="mi">1</span><span class="p">)</span>
<span class="n">s</span><span class="o">.</span><span class="n">writeToFile</span><span class="p">(</span><span class="bp">self</span><span class="p">)</span>
<span class="k">def</span> <span class="nf">writeBond</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">bond</span><span class="p">,</span> <span class="n">configuration</span><span class="p">,</span> <span class="n">distance</span><span class="p">):</span>
<span class="n">p1</span> <span class="o">=</span> <span class="n">bond</span><span class="o">.</span><span class="n">a1</span><span class="o">.</span><span class="n">position</span><span class="p">(</span><span class="n">configuration</span><span class="p">)</span>
<span class="n">p2</span> <span class="o">=</span> <span class="n">bond</span><span class="o">.</span><span class="n">a2</span><span class="o">.</span><span class="n">position</span><span class="p">(</span><span class="n">configuration</span><span class="p">)</span>
<span class="k">if</span> <span class="n">p1</span> <span class="ow">is</span> <span class="ow">not</span> <span class="bp">None</span> <span class="ow">and</span> <span class="n">p2</span> <span class="ow">is</span> <span class="ow">not</span> <span class="bp">None</span><span class="p">:</span>
<span class="n">bond_vector</span> <span class="o">=</span> <span class="mf">0.5</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="n">configuration</span><span class="p">)</span>
<span class="n">cut</span> <span class="o">=</span> <span class="n">bond_vector</span> <span class="o">!=</span> <span class="mf">0.5</span><span class="o">*</span><span class="p">(</span><span class="n">p2</span><span class="o">-</span><span class="n">p1</span><span class="p">)</span>
<span class="n">color1</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="n">bond</span><span class="o">.</span><span class="n">a1</span><span class="p">)</span>
<span class="n">color2</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="n">bond</span><span class="o">.</span><span class="n">a2</span><span class="p">)</span>
<span class="n">material1</span> <span class="o">=</span> <span class="n">VRML</span><span class="o">.</span><span class="n">EmissiveMaterial</span><span class="p">(</span><span class="n">color1</span><span class="p">)</span>
<span class="n">material2</span> <span class="o">=</span> <span class="n">VRML</span><span class="o">.</span><span class="n">EmissiveMaterial</span><span class="p">(</span><span class="n">color2</span><span class="p">)</span>
<span class="k">if</span> <span class="n">color1</span> <span class="o">==</span> <span class="n">color2</span> <span class="ow">and</span> <span class="ow">not</span> <span class="n">cut</span><span class="p">:</span>
<span class="n">c</span> <span class="o">=</span> <span class="n">VRML</span><span class="o">.</span><span class="n">Cylinder</span><span class="p">(</span><span class="n">p1</span><span class="p">,</span> <span class="n">p2</span><span class="p">,</span> <span class="mf">0.03</span><span class="o">*</span><span class="n">Units</span><span class="o">.</span><span class="n">Ang</span><span class="p">,</span>
<span class="n">material</span> <span class="o">=</span> <span class="n">material1</span><span class="p">)</span>
<span class="n">c</span><span class="o">.</span><span class="n">writeToFile</span><span class="p">(</span><span class="bp">self</span><span class="p">)</span>
<span class="k">else</span><span class="p">:</span>
<span class="n">c</span> <span class="o">=</span> <span class="n">VRML</span><span class="o">.</span><span class="n">Cylinder</span><span class="p">(</span><span class="n">p1</span><span class="p">,</span> <span class="n">p1</span><span class="o">+</span><span class="n">bond_vector</span><span class="p">,</span> <span class="mf">0.03</span><span class="o">*</span><span class="n">Units</span><span class="o">.</span><span class="n">Ang</span><span class="p">,</span>
<span class="n">material</span> <span class="o">=</span> <span class="n">material1</span><span class="p">)</span>
<span class="n">c</span><span class="o">.</span><span class="n">writeToFile</span><span class="p">(</span><span class="bp">self</span><span class="p">)</span>
<span class="n">c</span> <span class="o">=</span> <span class="n">VRML</span><span class="o">.</span><span class="n">Cylinder</span><span class="p">(</span><span class="n">p2</span><span class="p">,</span> <span class="n">p2</span><span class="o">-</span><span class="n">bond_vector</span><span class="p">,</span> <span class="mf">0.03</span><span class="o">*</span><span class="n">Units</span><span class="o">.</span><span class="n">Ang</span><span class="p">,</span>
<span class="n">material</span> <span class="o">=</span> <span class="n">material2</span><span class="p">)</span>
<span class="n">c</span><span class="o">.</span><span class="n">writeToFile</span><span class="p">(</span><span class="bp">self</span><span class="p">)</span>
<span class="k">class</span> <span class="nc">VRMLChargeFile</span><span class="p">(</span><span class="n">VRMLWireframeFile</span><span class="p">):</span>
<span class="n">color_scale</span> <span class="o">=</span> <span class="n">VRML</span><span class="o">.</span><span class="n">SymmetricColorScale</span><span class="p">(</span><span class="mf">1.</span><span class="p">)</span>
<span class="k">def</span> <span class="nf">writeAtom</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">configuration</span><span class="p">):</span>
<span class="n">p</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">configuration</span><span class="p">)</span>
<span class="n">c</span> <span class="o">=</span> <span class="n">atom</span><span class="o">.</span><span class="n">charge</span><span class="p">()</span>
<span class="n">c</span> <span class="o">=</span> <span class="nb">max</span><span class="p">(</span><span class="nb">min</span><span class="p">(</span><span class="n">c</span><span class="p">,</span> <span class="mf">1.</span><span class="p">),</span> <span class="o">-</span><span class="mf">1.</span><span class="p">)</span>
<span class="k">if</span> <span class="n">p</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">warning</span> <span class="o">=</span> <span class="mi">1</span>
<span class="k">else</span><span class="p">:</span>
<span class="n">s</span> <span class="o">=</span> <span class="n">VRML</span><span class="o">.</span><span class="n">Sphere</span><span class="p">(</span><span class="n">p</span><span class="p">,</span> <span class="mf">0.1</span><span class="o">*</span><span class="n">Units</span><span class="o">.</span><span class="n">Ang</span><span class="p">,</span>
<span class="n">material</span> <span class="o">=</span> <span class="n">VRML</span><span class="o">.</span><span class="n">Material</span><span class="p">(</span><span class="n">diffuse_color</span> <span class="o">=</span>
<span class="bp">self</span><span class="o">.</span><span class="n">color_scale</span><span class="p">(</span><span class="n">c</span><span class="p">)))</span>
<span class="n">s</span><span class="o">.</span><span class="n">writeToFile</span><span class="p">(</span><span class="bp">self</span><span class="p">)</span>
<span class="n">bond_material</span> <span class="o">=</span> <span class="n">VRML</span><span class="o">.</span><span class="n">DiffuseMaterial</span><span class="p">(</span><span class="s">'black'</span><span class="p">)</span>
<span class="k">def</span> <span class="nf">writeBond</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">bond</span><span class="p">,</span> <span class="n">configuration</span><span class="p">,</span> <span class="n">distance</span><span class="p">):</span>
<span class="n">p1</span> <span class="o">=</span> <span class="n">bond</span><span class="o">.</span><span class="n">a1</span><span class="o">.</span><span class="n">position</span><span class="p">(</span><span class="n">configuration</span><span class="p">)</span>
<span class="n">p2</span> <span class="o">=</span> <span class="n">bond</span><span class="o">.</span><span class="n">a2</span><span class="o">.</span><span class="n">position</span><span class="p">(</span><span class="n">configuration</span><span class="p">)</span>
<span class="k">if</span> <span class="n">p1</span> <span class="ow">is</span> <span class="ow">not</span> <span class="bp">None</span> <span class="ow">and</span> <span class="n">p2</span> <span class="ow">is</span> <span class="ow">not</span> <span class="bp">None</span><span class="p">:</span>
<span class="n">bond_vector</span> <span class="o">=</span> <span class="mf">0.5</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="n">configuration</span><span class="p">)</span>
<span class="n">cut</span> <span class="o">=</span> <span class="n">bond_vector</span> <span class="o">!=</span> <span class="mf">0.5</span><span class="o">*</span><span class="p">(</span><span class="n">p2</span><span class="o">-</span><span class="n">p1</span><span class="p">)</span>
<span class="k">if</span> <span class="ow">not</span> <span class="n">cut</span><span class="p">:</span>
<span class="n">c</span> <span class="o">=</span> <span class="n">VRML</span><span class="o">.</span><span class="n">Line</span><span class="p">(</span><span class="n">p1</span><span class="p">,</span> <span class="n">p2</span><span class="p">,</span> <span class="n">material</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">bond_material</span><span class="p">)</span>
<span class="n">c</span><span class="o">.</span><span class="n">writeToFile</span><span class="p">(</span><span class="bp">self</span><span class="p">)</span>
<span class="k">else</span><span class="p">:</span>
<span class="n">c</span> <span class="o">=</span> <span class="n">VRML</span><span class="o">.</span><span class="n">Line</span><span class="p">(</span><span class="n">p1</span><span class="p">,</span> <span class="n">p1</span><span class="o">+</span><span class="n">bond_vector</span><span class="p">,</span> <span class="n">material</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">bond_material</span><span class="p">)</span>
<span class="n">c</span><span class="o">.</span><span class="n">writeToFile</span><span class="p">(</span><span class="bp">self</span><span class="p">)</span>
<span class="n">c</span> <span class="o">=</span> <span class="n">VRML</span><span class="o">.</span><span class="n">Line</span><span class="p">(</span><span class="n">p2</span><span class="p">,</span> <span class="n">p2</span><span class="o">-</span><span class="n">bond_vector</span><span class="p">,</span> <span class="n">material</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">bond_material</span><span class="p">)</span>
<span class="n">c</span><span class="o">.</span><span class="n">writeToFile</span><span class="p">(</span><span class="bp">self</span><span class="p">)</span>
<span class="n">VRMLFile</span> <span class="o">=</span> <span class="n">VRMLWireframeFile</span>
<span class="c">#</span>
<span class="c"># Recognize some standard file types by their extensions</span>
<span class="c">#</span>
<span class="k">def</span> <span class="nf">fileFormatFromExtension</span><span class="p">(</span><span class="n">filename</span><span class="p">):</span>
<span class="n">filename</span><span class="p">,</span> <span class="n">ext</span> <span class="o">=</span> <span class="n">os</span><span class="o">.</span><span class="n">path</span><span class="o">.</span><span class="n">splitext</span><span class="p">(</span><span class="n">filename</span><span class="p">)</span>
<span class="k">if</span> <span class="n">ext</span> <span class="ow">in</span> <span class="n">_file_compressions</span><span class="p">:</span>
<span class="n">filename</span><span class="p">,</span> <span class="n">ext</span> <span class="o">=</span> <span class="n">os</span><span class="o">.</span><span class="n">path</span><span class="o">.</span><span class="n">splitext</span><span class="p">(</span><span class="n">filename</span><span class="p">)</span>
<span class="k">try</span><span class="p">:</span>
<span class="k">return</span> <span class="n">_file_formats</span><span class="p">[</span><span class="n">ext</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">IOError</span><span class="p">(</span><span class="s">'Unknown file format'</span><span class="p">)</span>
<span class="n">_file_formats</span> <span class="o">=</span> <span class="p">{</span><span class="s">'.pdb'</span><span class="p">:</span> <span class="s">'pdb'</span><span class="p">,</span> <span class="s">'.wrl'</span><span class="p">:</span> <span class="s">'vrml'</span><span class="p">}</span>
<span class="n">_file_compressions</span> <span class="o">=</span> <span class="p">[</span><span class="s">'.gz'</span><span class="p">,</span> <span class="s">'.Z'</span><span class="p">]</span>
<span class="c">#</span>
<span class="c"># Output file for a specified format</span>
<span class="c">#</span>
<span class="k">def</span> <span class="nf">OutputFile</span><span class="p">(</span><span class="n">filename</span><span class="p">,</span> <span class="n">format</span> <span class="o">=</span> <span class="bp">None</span><span class="p">):</span>
<span class="k">if</span> <span class="n">format</span> <span class="ow">is</span> <span class="bp">None</span><span class="p">:</span>
<span class="n">format</span> <span class="o">=</span> <span class="n">fileFormatFromExtension</span><span class="p">(</span><span class="n">filename</span><span class="p">)</span>
<span class="n">format</span> <span class="o">=</span> <span class="nb">tuple</span><span class="p">(</span><span class="n">format</span><span class="o">.</span><span class="n">split</span><span class="p">(</span><span class="s">'.'</span><span class="p">))</span>
<span class="k">try</span><span class="p">:</span>
<span class="k">return</span> <span class="n">_file_types</span><span class="p">[</span><span class="n">format</span><span class="p">](</span><span class="n">filename</span><span class="p">)</span>
<span class="k">except</span> <span class="ne">KeyError</span><span class="p">:</span>
<span class="k">if</span> <span class="nb">len</span><span class="p">(</span><span class="n">format</span><span class="p">)</span> <span class="o">==</span> <span class="mi">1</span><span class="p">:</span>
<span class="k">return</span> <span class="n">_file_types</span><span class="p">[</span><span class="n">format</span><span class="p">[</span><span class="mi">0</span><span class="p">]](</span><span class="n">filename</span><span class="p">)</span>
<span class="k">else</span><span class="p">:</span>
<span class="n">_file_types</span><span class="p">[</span><span class="n">format</span><span class="p">[</span><span class="mi">0</span><span class="p">]](</span><span class="n">filename</span><span class="p">,</span> <span class="n">format</span><span class="p">[</span><span class="mi">1</span><span class="p">])</span>
<span class="n">_file_types</span> <span class="o">=</span> <span class="p">{</span><span class="s">'pdb'</span><span class="p">:</span> <span class="n">PDB</span><span class="o">.</span><span class="n">PDBOutputFile</span><span class="p">,</span>
<span class="p">(</span><span class="s">'vrml'</span><span class="p">,):</span> <span class="n">VRMLFile</span><span class="p">,</span>
<span class="p">(</span><span class="s">'vrml'</span><span class="p">,</span> <span class="s">'wireframe'</span><span class="p">):</span> <span class="n">VRMLWireframeFile</span><span class="p">,</span>
<span class="p">(</span><span class="s">'vrml'</span><span class="p">,</span> <span class="s">'highlight'</span><span class="p">):</span> <span class="n">VRMLHighlight</span><span class="p">,</span>
<span class="p">(</span><span class="s">'vrml'</span><span class="p">,</span> <span class="s">'ball_and_stick'</span><span class="p">):</span> <span class="n">VRMLBallAndStickFile</span><span class="p">,</span>
<span class="p">(</span><span class="s">'vrml'</span><span class="p">,</span> <span class="s">'charge'</span><span class="p">):</span> <span class="n">VRMLChargeFile</span><span class="p">}</span>
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