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<h1>Source code for MMTK.PDB</h1><div class="highlight"><pre>
<span class="c"># This module deals with input and output of configurations in PDB format.</span>
<span class="c">#</span>
<span class="c"># Written by Konrad Hinsen</span>
<span class="c">#</span>
<span class="sd">"""</span>
<span class="sd">PDB files</span>
<span class="sd">This module provides classes that represent molecules in a PDB file.</span>
<span class="sd">They permit various manipulations and the creation of MMTK objects.</span>
<span class="sd">Note that the classes defined in this module are specializations</span>
<span class="sd">of classed defined in Scientific.IO.PDB; the methods defined in</span>
<span class="sd">that module are also available.</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">ChemicalObjects</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">Universe</span><span class="p">,</span> <span class="n">Utility</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">import</span> <span class="nn">Scientific.IO.PDB</span>
<span class="kn">import</span> <span class="nn">copy</span><span class="o">,</span> <span class="nn">string</span>
<span class="c">#</span>
<span class="c"># The chain classes from Scientific.IO.PDB are extended by methods</span>
<span class="c"># that construct MMTK objects and set configurations.</span>
<span class="c">#</span>
<span class="k">class</span> <span class="nc">PDBChain</span><span class="p">(</span><span class="nb">object</span><span class="p">):</span>
<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="n">chain</span><span class="p">,</span> <span class="nb">map</span> <span class="o">=</span> <span class="s">'pdbmap'</span><span class="p">,</span> <span class="n">alt</span> <span class="o">=</span> <span class="s">'pdb_alternative'</span><span class="p">,</span>
<span class="n">atom_map</span> <span class="o">=</span> <span class="bp">None</span><span class="p">):</span>
<span class="k">if</span> <span class="nb">len</span><span class="p">(</span><span class="n">chain</span><span class="p">)</span> <span class="o">!=</span> <span class="nb">len</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span>
<span class="k">raise</span> <span class="ne">ValueError</span><span class="p">(</span><span class="s">"chain lengths do not match"</span><span class="p">)</span>
<span class="k">for</span> <span class="n">i</span> <span class="ow">in</span> <span class="nb">range</span><span class="p">(</span><span class="nb">len</span><span class="p">(</span><span class="n">chain</span><span class="p">)):</span>
<span class="n">residue</span> <span class="o">=</span> <span class="n">chain</span><span class="p">[</span><span class="n">i</span><span class="p">]</span>
<span class="n">pdbmap</span> <span class="o">=</span> <span class="nb">getattr</span><span class="p">(</span><span class="n">residue</span><span class="p">,</span> <span class="nb">map</span><span class="p">)</span>
<span class="k">try</span><span class="p">:</span> <span class="n">altmap</span> <span class="o">=</span> <span class="nb">getattr</span><span class="p">(</span><span class="n">residue</span><span class="p">,</span> <span class="n">alt</span><span class="p">)</span>
<span class="k">except</span> <span class="ne">AttributeError</span><span class="p">:</span> <span class="n">altmap</span> <span class="o">=</span> <span class="p">{}</span>
<span class="n">setResidueConfiguration</span><span class="p">(</span><span class="n">residue</span><span class="p">,</span> <span class="bp">self</span><span class="p">[</span><span class="n">i</span><span class="p">],</span> <span class="n">pdbmap</span><span class="p">[</span><span class="mi">0</span><span class="p">],</span> <span class="n">altmap</span><span class="p">,</span>
<span class="n">atom_map</span><span class="p">)</span>
<div class="viewcode-block" id="PDBPeptideChain"><a class="viewcode-back" href="../../modules.html#MMTK.PDB.PDBPeptideChain">[docs]</a><span class="k">class</span> <span class="nc">PDBPeptideChain</span><span class="p">(</span><span class="n">Scientific</span><span class="o">.</span><span class="n">IO</span><span class="o">.</span><span class="n">PDB</span><span class="o">.</span><span class="n">PeptideChain</span><span class="p">,</span> <span class="n">PDBChain</span><span class="p">):</span>
<span class="sd">"""</span>
<span class="sd"> Peptide chain in a PDB file</span>
<span class="sd"> See the description of Scientific.IO.PDB.PeptideChain for the</span>
<span class="sd"> constructor and additional methods. In MMTK, PDBPeptideChain</span>
<span class="sd"> objects are usually obtained from a PDBConfiguration object via</span>
<span class="sd"> its attribute peptide_chains (see the documentation of</span>
<span class="sd"> Scientific.IO.PDB.Structure).</span>
<span class="sd"> """</span>
<div class="viewcode-block" id="PDBPeptideChain.createPeptideChain"><a class="viewcode-back" href="../../modules.html#MMTK.PDB.PDBPeptideChain.createPeptideChain">[docs]</a> <span class="k">def</span> <span class="nf">createPeptideChain</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">model</span> <span class="o">=</span> <span class="s">'all'</span><span class="p">,</span>
<span class="n">n_terminus</span><span class="o">=</span><span class="bp">None</span><span class="p">,</span> <span class="n">c_terminus</span><span class="o">=</span><span class="bp">None</span><span class="p">):</span>
<span class="sd">"""</span>
<span class="sd"> :returns: a :class:`~MMTK.Proteins.PeptideChain` object corresponding to the</span>
<span class="sd"> peptide chain in the PDB file. The parameter model</span>
<span class="sd"> has the same meaning as for the PeptideChain constructor.</span>
<span class="sd"> :rtype: :class:`~MMTK.Proteins.PeptideChain`</span>
<span class="sd"> """</span>
<span class="bp">self</span><span class="o">.</span><span class="n">identifyProtonation</span><span class="p">()</span>
<span class="kn">from</span> <span class="nn">MMTK</span> <span class="kn">import</span> <span class="n">Proteins</span>
<span class="n">properties</span> <span class="o">=</span> <span class="p">{</span><span class="s">'model'</span><span class="p">:</span> <span class="n">model</span><span class="p">}</span>
<span class="k">if</span> <span class="bp">self</span><span class="o">.</span><span class="n">segment_id</span> <span class="o">!=</span> <span class="s">''</span><span class="p">:</span>
<span class="n">properties</span><span class="p">[</span><span class="s">'name'</span><span class="p">]</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">segment_id</span>
<span class="k">elif</span> <span class="bp">self</span><span class="o">.</span><span class="n">chain_id</span> <span class="o">!=</span> <span class="s">''</span><span class="p">:</span>
<span class="n">properties</span><span class="p">[</span><span class="s">'name'</span><span class="p">]</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">chain_id</span>
<span class="k">if</span> <span class="n">c_terminus</span> <span class="ow">is</span> <span class="bp">None</span><span class="p">:</span>
<span class="n">properties</span><span class="p">[</span><span class="s">'c_terminus'</span><span class="p">]</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">isTerminated</span><span class="p">()</span>
<span class="k">else</span><span class="p">:</span>
<span class="n">properties</span><span class="p">[</span><span class="s">'c_terminus'</span><span class="p">]</span> <span class="o">=</span> <span class="n">c_terminus</span>
<span class="k">if</span> <span class="n">n_terminus</span> <span class="ow">is</span> <span class="ow">not</span> <span class="bp">None</span><span class="p">:</span>
<span class="n">properties</span><span class="p">[</span><span class="s">'n_terminus'</span><span class="p">]</span> <span class="o">=</span> <span class="n">n_terminus</span>
<span class="n">chain</span> <span class="o">=</span> <span class="nb">apply</span><span class="p">(</span><span class="n">Proteins</span><span class="o">.</span><span class="n">PeptideChain</span><span class="p">,</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">model</span> <span class="o">!=</span> <span class="s">'no_hydrogens'</span><span class="p">:</span>
<span class="n">chain</span><span class="o">.</span><span class="n">findHydrogenPositions</span><span class="p">()</span>
<span class="k">return</span> <span class="n">chain</span>
</div>
<span class="k">def</span> <span class="nf">identifyProtonation</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span>
<span class="k">for</span> <span class="n">residue</span> <span class="ow">in</span> <span class="bp">self</span><span class="o">.</span><span class="n">residues</span><span class="p">:</span>
<span class="k">if</span> <span class="n">residue</span><span class="o">.</span><span class="n">name</span> <span class="o">==</span> <span class="s">'HIS'</span><span class="p">:</span>
<span class="n">count_hd</span> <span class="o">=</span> <span class="mi">0</span>
<span class="n">count_he</span> <span class="o">=</span> <span class="mi">0</span>
<span class="k">for</span> <span class="n">atom</span> <span class="ow">in</span> <span class="n">residue</span><span class="p">:</span>
<span class="k">if</span> <span class="s">'HD'</span> <span class="ow">in</span> <span class="n">atom</span><span class="o">.</span><span class="n">name</span><span class="p">:</span>
<span class="n">count_hd</span> <span class="o">+=</span> <span class="mi">1</span>
<span class="k">if</span> <span class="s">'HE'</span> <span class="ow">in</span> <span class="n">atom</span><span class="o">.</span><span class="n">name</span><span class="p">:</span>
<span class="n">count_he</span> <span class="o">+=</span> <span class="mi">1</span>
<span class="k">if</span> <span class="n">count_hd</span> <span class="o">+</span> <span class="n">count_he</span> <span class="o">==</span> <span class="mi">0</span><span class="p">:</span>
<span class="c"># default for crystallographic structures without hydrogens</span>
<span class="n">residue</span><span class="o">.</span><span class="n">name</span> <span class="o">=</span> <span class="s">'HIE'</span>
<span class="k">elif</span> <span class="n">count_he</span> <span class="o">==</span> <span class="mi">2</span><span class="p">:</span>
<span class="k">if</span> <span class="n">count_hd</span> <span class="o">==</span> <span class="mi">2</span><span class="p">:</span>
<span class="n">residue</span><span class="o">.</span><span class="n">name</span> <span class="o">=</span> <span class="s">'HIP'</span>
<span class="k">else</span><span class="p">:</span>
<span class="n">residue</span><span class="o">.</span><span class="n">name</span> <span class="o">=</span> <span class="s">'HIE'</span>
<span class="k">else</span><span class="p">:</span>
<span class="n">residue</span><span class="o">.</span><span class="n">name</span> <span class="o">=</span> <span class="s">'HID'</span>
<span class="k">elif</span> <span class="n">residue</span><span class="o">.</span><span class="n">name</span> <span class="o">==</span> <span class="s">'GLU'</span><span class="p">:</span>
<span class="k">for</span> <span class="n">atom</span> <span class="ow">in</span> <span class="n">residue</span><span class="p">:</span>
<span class="k">if</span> <span class="s">'HE'</span> <span class="ow">in</span> <span class="n">atom</span><span class="o">.</span><span class="n">name</span><span class="p">:</span>
<span class="n">residue</span><span class="o">.</span><span class="n">name</span> <span class="o">=</span> <span class="s">'GLP'</span>
<span class="k">break</span>
<span class="k">elif</span> <span class="n">residue</span><span class="o">.</span><span class="n">name</span> <span class="o">==</span> <span class="s">'ASP'</span><span class="p">:</span>
<span class="k">for</span> <span class="n">atom</span> <span class="ow">in</span> <span class="n">residue</span><span class="p">:</span>
<span class="k">if</span> <span class="s">'HD'</span> <span class="ow">in</span> <span class="n">atom</span><span class="o">.</span><span class="n">name</span><span class="p">:</span>
<span class="n">residue</span><span class="o">.</span><span class="n">name</span> <span class="o">=</span> <span class="s">'APP'</span>
<span class="k">break</span>
<span class="k">elif</span> <span class="n">residue</span><span class="o">.</span><span class="n">name</span> <span class="o">==</span> <span class="s">'LYS'</span><span class="p">:</span>
<span class="n">count_hz</span> <span class="o">=</span> <span class="mi">0</span>
<span class="k">for</span> <span class="n">atom</span> <span class="ow">in</span> <span class="n">residue</span><span class="p">:</span>
<span class="k">if</span> <span class="s">'HZ'</span> <span class="ow">in</span> <span class="n">atom</span><span class="o">.</span><span class="n">name</span><span class="p">:</span>
<span class="n">count_hz</span> <span class="o">+=</span> <span class="mi">1</span>
<span class="k">if</span> <span class="n">count_hz</span> <span class="o">></span> <span class="mi">0</span> <span class="ow">and</span> <span class="n">count_hz</span> <span class="o"><</span> <span class="mi">3</span><span class="p">:</span>
<span class="c"># for count_hz == 0 (most probably a crystallographic</span>
<span class="c"># structure), keep LYS which is the most frequent one.</span>
<span class="n">residue</span><span class="o">.</span><span class="n">name</span> <span class="o">=</span> <span class="s">'LYP'</span>
</div>
<div class="viewcode-block" id="PDBNucleotideChain"><a class="viewcode-back" href="../../modules.html#MMTK.PDB.PDBNucleotideChain">[docs]</a><span class="k">class</span> <span class="nc">PDBNucleotideChain</span><span class="p">(</span><span class="n">Scientific</span><span class="o">.</span><span class="n">IO</span><span class="o">.</span><span class="n">PDB</span><span class="o">.</span><span class="n">NucleotideChain</span><span class="p">,</span> <span class="n">PDBChain</span><span class="p">):</span>
<span class="sd">"""</span>
<span class="sd"> Nucleotide chain in a PDB file</span>
<span class="sd"> See the description of Scientific.IO.PDB.NucleotideChain for the</span>
<span class="sd"> constructor and additional methods. In MMTK, PDBNucleotideChain</span>
<span class="sd"> objects are usually obtained from a PDBConfiguration object via</span>
<span class="sd"> its attribute nucleotide_chains (see the documentation of</span>
<span class="sd"> Scientific.IO.PDB.Structure).</span>
<span class="sd"> """</span>
<div class="viewcode-block" id="PDBNucleotideChain.createNucleotideChain"><a class="viewcode-back" href="../../modules.html#MMTK.PDB.PDBNucleotideChain.createNucleotideChain">[docs]</a> <span class="k">def</span> <span class="nf">createNucleotideChain</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">model</span><span class="o">=</span><span class="s">'all'</span><span class="p">):</span>
<span class="sd">"""</span>
<span class="sd"> :returns: a :class:`~MMTK.NucleicAcids.NucleotideChain` object corresponding </span>
<span class="sd"> to the nucleotide chain in the PDB file. The parameter model</span>
<span class="sd"> has the same meaning as for the NucleotideChain constructor.</span>
<span class="sd"> :rtype: :class:`~MMTK.NucleicAcids.NucleotideChain`</span>
<span class="sd"> """</span>
<span class="kn">from</span> <span class="nn">MMTK</span> <span class="kn">import</span> <span class="n">NucleicAcids</span>
<span class="n">properties</span> <span class="o">=</span> <span class="p">{</span><span class="s">'model'</span><span class="p">:</span> <span class="n">model</span><span class="p">}</span>
<span class="k">if</span> <span class="bp">self</span><span class="o">.</span><span class="n">segment_id</span> <span class="o">!=</span> <span class="s">''</span><span class="p">:</span>
<span class="n">properties</span><span class="p">[</span><span class="s">'name'</span><span class="p">]</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">segment_id</span>
<span class="k">elif</span> <span class="bp">self</span><span class="o">.</span><span class="n">chain_id</span> <span class="o">!=</span> <span class="s">''</span><span class="p">:</span>
<span class="n">properties</span><span class="p">[</span><span class="s">'name'</span><span class="p">]</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">chain_id</span>
<span class="k">if</span> <span class="bp">self</span><span class="p">[</span><span class="mi">0</span><span class="p">]</span><span class="o">.</span><span class="n">hasPhosphate</span><span class="p">():</span>
<span class="n">properties</span><span class="p">[</span><span class="s">'terminus_5'</span><span class="p">]</span> <span class="o">=</span> <span class="mi">0</span>
<span class="n">chain</span> <span class="o">=</span> <span class="nb">apply</span><span class="p">(</span><span class="n">NucleicAcids</span><span class="o">.</span><span class="n">NucleotideChain</span><span class="p">,</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">model</span> <span class="o">!=</span> <span class="s">'no_hydrogens'</span><span class="p">:</span>
<span class="n">chain</span><span class="o">.</span><span class="n">findHydrogenPositions</span><span class="p">()</span>
<span class="k">return</span> <span class="n">chain</span>
</div></div>
<div class="viewcode-block" id="PDBMolecule"><a class="viewcode-back" href="../../modules.html#MMTK.PDB.PDBMolecule">[docs]</a><span class="k">class</span> <span class="nc">PDBMolecule</span><span class="p">(</span><span class="n">Scientific</span><span class="o">.</span><span class="n">IO</span><span class="o">.</span><span class="n">PDB</span><span class="o">.</span><span class="n">Molecule</span><span class="p">):</span>
<span class="sd">"""</span>
<span class="sd"> Molecule in a PDB file</span>
<span class="sd"> See the description of Scientific.IO.PDB.Molecule for the</span>
<span class="sd"> constructor and additional methods. In MMTK, PDBMolecule objects</span>
<span class="sd"> are usually obtained from a PDBConfiguration object via its</span>
<span class="sd"> attribute molecules (see the documentation of</span>
<span class="sd"> Scientific.IO.PDB.Structure). A molecule is by definition any</span>
<span class="sd"> residue in a PDB file that is not an amino acid or nucleotide</span>
<span class="sd"> residue.</span>
<span class="sd"> """</span>
<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="n">molecule</span><span class="p">,</span> <span class="nb">map</span> <span class="o">=</span> <span class="s">'pdbmap'</span><span class="p">,</span> <span class="n">alt</span> <span class="o">=</span> <span class="s">'pdb_alternative'</span><span class="p">,</span>
<span class="n">atom_map</span> <span class="o">=</span> <span class="bp">None</span><span class="p">):</span>
<span class="n">pdbmap</span> <span class="o">=</span> <span class="nb">getattr</span><span class="p">(</span><span class="n">molecule</span><span class="p">,</span> <span class="nb">map</span><span class="p">)</span>
<span class="k">try</span><span class="p">:</span> <span class="n">altmap</span> <span class="o">=</span> <span class="nb">getattr</span><span class="p">(</span><span class="n">molecule</span><span class="p">,</span> <span class="n">alt</span><span class="p">)</span>
<span class="k">except</span> <span class="ne">AttributeError</span><span class="p">:</span> <span class="n">altmap</span> <span class="o">=</span> <span class="p">{}</span>
<span class="n">setResidueConfiguration</span><span class="p">(</span><span class="n">molecule</span><span class="p">,</span> <span class="bp">self</span><span class="p">,</span> <span class="n">pdbmap</span><span class="p">[</span><span class="mi">0</span><span class="p">],</span> <span class="n">altmap</span><span class="p">,</span> <span class="n">atom_map</span><span class="p">)</span>
<div class="viewcode-block" id="PDBMolecule.createMolecule"><a class="viewcode-back" href="../../modules.html#MMTK.PDB.PDBMolecule.createMolecule">[docs]</a> <span class="k">def</span> <span class="nf">createMolecule</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">name</span><span class="o">=</span><span class="bp">None</span><span class="p">):</span>
<span class="sd">"""</span>
<span class="sd"> :returns: a :class:`~MMTK.ChemicalObjects.Molecule` object corresponding </span>
<span class="sd"> to the molecule in the PDB file. The parameter name </span>
<span class="sd"> specifies the molecule name as defined in the chemical database.</span>
<span class="sd"> It can be left out for known molecules (currently</span>
<span class="sd"> only water).</span>
<span class="sd"> :rtype: :class:`~MMTK.ChemicalObjects.Molecule`</span>
<span class="sd"> """</span>
<span class="k">if</span> <span class="n">name</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="n">molecule_names</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="n">m</span> <span class="o">=</span> <span class="n">ChemicalObjects</span><span class="o">.</span><span class="n">Molecule</span><span class="p">(</span><span class="n">name</span><span class="p">)</span>
<span class="n">setConfiguration</span><span class="p">(</span><span class="n">m</span><span class="p">,</span> <span class="p">[</span><span class="bp">self</span><span class="p">])</span>
<span class="k">return</span> <span class="n">m</span>
<span class="c">#</span>
<span class="c"># The structure class from Scientific.IO.PDB is extended by methods</span>
<span class="c"># that construct MMTK objects and set configurations.</span>
<span class="c">#</span></div></div>
<div class="viewcode-block" id="PDBConfiguration"><a class="viewcode-back" href="../../modules.html#MMTK.PDB.PDBConfiguration">[docs]</a><span class="k">class</span> <span class="nc">PDBConfiguration</span><span class="p">(</span><span class="n">Scientific</span><span class="o">.</span><span class="n">IO</span><span class="o">.</span><span class="n">PDB</span><span class="o">.</span><span class="n">Structure</span><span class="p">):</span>
<span class="sd">"""</span>
<span class="sd"> Everything in a PDB file</span>
<span class="sd"> A PDBConfiguration object represents the full contents of a PDB</span>
<span class="sd"> file. It can be used to create MMTK objects for all or part</span>
<span class="sd"> of the molecules, or to change the configuration of an existing</span>
<span class="sd"> system.</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">file_or_filename</span><span class="p">,</span> <span class="n">model</span> <span class="o">=</span> <span class="mi">0</span><span class="p">,</span> <span class="n">alternate_code</span> <span class="o">=</span> <span class="s">'A'</span><span class="p">):</span>
<span class="sd">"""</span>
<span class="sd"> :param file_or_filename: the name of a PDB file, or a file object</span>
<span class="sd"> :param model: the number of the model to be used from a</span>
<span class="sd"> multiple model file</span>
<span class="sd"> :type model: int</span>
<span class="sd"> :param alternate_code: the alternate code to be used for atoms that</span>
<span class="sd"> have multiple positions</span>
<span class="sd"> :type alternate_code: str</span>
<span class="sd"> """</span>
<span class="k">if</span> <span class="nb">isinstance</span><span class="p">(</span><span class="n">file_or_filename</span><span class="p">,</span> <span class="nb">basestring</span><span class="p">):</span>
<span class="n">file_or_filename</span> <span class="o">=</span> <span class="n">Database</span><span class="o">.</span><span class="n">PDBPath</span><span class="p">(</span><span class="n">file_or_filename</span><span class="p">)</span>
<span class="n">Scientific</span><span class="o">.</span><span class="n">IO</span><span class="o">.</span><span class="n">PDB</span><span class="o">.</span><span class="n">Structure</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">file_or_filename</span><span class="p">,</span>
<span class="n">model</span><span class="p">,</span> <span class="n">alternate_code</span><span class="p">)</span>
<span class="bp">self</span><span class="o">.</span><span class="n">_numberAtoms</span><span class="p">()</span>
<span class="bp">self</span><span class="o">.</span><span class="n">_convertUnits</span><span class="p">()</span>
<span class="n">peptide_chain_constructor</span> <span class="o">=</span> <span class="n">PDBPeptideChain</span>
<span class="n">nucleotide_chain_constructor</span> <span class="o">=</span> <span class="n">PDBNucleotideChain</span>
<span class="n">molecule_constructor</span> <span class="o">=</span> <span class="n">PDBMolecule</span>
<span class="k">def</span> <span class="nf">_numberAtoms</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="mi">1</span>
<span class="k">for</span> <span class="n">residue</span> <span class="ow">in</span> <span class="bp">self</span><span class="o">.</span><span class="n">residues</span><span class="p">:</span>
<span class="k">for</span> <span class="n">atom</span> <span class="ow">in</span> <span class="n">residue</span><span class="p">:</span>
<span class="n">atom</span><span class="o">.</span><span class="n">number</span> <span class="o">=</span> <span class="n">n</span>
<span class="n">n</span> <span class="o">+=</span> <span class="mi">1</span>
<span class="k">def</span> <span class="nf">_convertUnits</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span>
<span class="k">for</span> <span class="n">residue</span> <span class="ow">in</span> <span class="bp">self</span><span class="o">.</span><span class="n">residues</span><span class="p">:</span>
<span class="k">for</span> <span class="n">atom</span> <span class="ow">in</span> <span class="n">residue</span><span class="p">:</span>
<span class="n">atom</span><span class="o">.</span><span class="n">position</span> <span class="o">=</span> <span class="n">atom</span><span class="o">.</span><span class="n">position</span><span class="o">*</span><span class="n">Units</span><span class="o">.</span><span class="n">Ang</span>
<span class="k">try</span><span class="p">:</span>
<span class="n">b</span> <span class="o">=</span> <span class="n">atom</span><span class="o">.</span><span class="n">properties</span><span class="p">[</span><span class="s">'temperature_factor'</span><span class="p">]</span>
<span class="n">atom</span><span class="o">.</span><span class="n">properties</span><span class="p">[</span><span class="s">'temperature_factor'</span><span class="p">]</span> <span class="o">=</span> <span class="n">b</span><span class="o">*</span><span class="n">Units</span><span class="o">.</span><span class="n">Ang</span><span class="o">**</span><span class="mi">2</span>
<span class="k">except</span> <span class="ne">KeyError</span><span class="p">:</span>
<span class="k">pass</span>
<span class="k">try</span><span class="p">:</span>
<span class="n">u</span> <span class="o">=</span> <span class="n">atom</span><span class="o">.</span><span class="n">properties</span><span class="p">[</span><span class="s">'u'</span><span class="p">]</span>
<span class="n">atom</span><span class="o">.</span><span class="n">properties</span><span class="p">[</span><span class="s">'u'</span><span class="p">]</span> <span class="o">=</span> <span class="n">u</span><span class="o">*</span><span class="n">Units</span><span class="o">.</span><span class="n">Ang</span><span class="o">**</span><span class="mi">2</span>
<span class="k">except</span> <span class="ne">KeyError</span><span class="p">:</span>
<span class="k">pass</span>
<span class="c"># All these attributes exist only if ScientificPython >= 2.7.5 is used.</span>
<span class="c"># The Scaling transformation was introduced with the same version,</span>
<span class="c"># so if it exists, the rest should work as well.</span>
<span class="k">try</span><span class="p">:</span>
<span class="kn">from</span> <span class="nn">Scientific.Geometry.Transformation</span> <span class="kn">import</span> <span class="n">Scaling</span>
<span class="k">except</span> <span class="ne">ImportError</span><span class="p">:</span>
<span class="k">return</span>
<span class="k">for</span> <span class="n">attribute</span> <span class="ow">in</span> <span class="p">[</span><span class="s">'a'</span><span class="p">,</span> <span class="s">'b'</span><span class="p">,</span> <span class="s">'c'</span><span class="p">]:</span>
<span class="n">value</span> <span class="o">=</span> <span class="nb">getattr</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">attribute</span><span class="p">)</span>
<span class="k">if</span> <span class="n">value</span> <span class="ow">is</span> <span class="ow">not</span> <span class="bp">None</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">attribute</span><span class="p">,</span> <span class="n">value</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="k">for</span> <span class="n">attribute</span> <span class="ow">in</span> <span class="p">[</span><span class="s">'alpha'</span><span class="p">,</span> <span class="s">'beta'</span><span class="p">,</span> <span class="s">'gamma'</span><span class="p">]:</span>
<span class="n">value</span> <span class="o">=</span> <span class="nb">getattr</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">attribute</span><span class="p">)</span>
<span class="k">if</span> <span class="n">value</span> <span class="ow">is</span> <span class="ow">not</span> <span class="bp">None</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">attribute</span><span class="p">,</span> <span class="n">value</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">if</span> <span class="bp">self</span><span class="o">.</span><span class="n">to_fractional</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">to_fractional</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">to_fractional</span><span class="o">*</span><span class="n">Scaling</span><span class="p">(</span><span class="mf">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">v1</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">to_fractional</span><span class="p">(</span><span class="n">Vector</span><span class="p">(</span><span class="mf">1.</span><span class="p">,</span> <span class="mf">0.</span><span class="p">,</span> <span class="mf">0.</span><span class="p">))</span>
<span class="n">v2</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">to_fractional</span><span class="p">(</span><span class="n">Vector</span><span class="p">(</span><span class="mf">0.</span><span class="p">,</span> <span class="mf">1.</span><span class="p">,</span> <span class="mf">0.</span><span class="p">))</span>
<span class="n">v3</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">to_fractional</span><span class="p">(</span><span class="n">Vector</span><span class="p">(</span><span class="mf">0.</span><span class="p">,</span> <span class="mf">0.</span><span class="p">,</span> <span class="mf">1.</span><span class="p">))</span>
<span class="bp">self</span><span class="o">.</span><span class="n">reciprocal_basis</span> <span class="o">=</span> <span class="p">(</span><span class="n">Vector</span><span class="p">(</span><span class="n">v1</span><span class="p">[</span><span class="mi">0</span><span class="p">],</span> <span class="n">v2</span><span class="p">[</span><span class="mi">0</span><span class="p">],</span> <span class="n">v3</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="n">v1</span><span class="p">[</span><span class="mi">1</span><span class="p">],</span> <span class="n">v2</span><span class="p">[</span><span class="mi">1</span><span class="p">],</span> <span class="n">v3</span><span class="p">[</span><span class="mi">1</span><span class="p">]),</span>
<span class="n">Vector</span><span class="p">(</span><span class="n">v1</span><span class="p">[</span><span class="mi">2</span><span class="p">],</span> <span class="n">v2</span><span class="p">[</span><span class="mi">2</span><span class="p">],</span> <span class="n">v3</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="bp">self</span><span class="o">.</span><span class="n">reciprocal_basis</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">from_fractional</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">from_fractional</span> <span class="o">=</span> <span class="n">Scaling</span><span class="p">(</span><span class="n">Units</span><span class="o">.</span><span class="n">Ang</span><span class="p">)</span><span class="o">*</span><span class="bp">self</span><span class="o">.</span><span class="n">from_fractional</span>
<span class="bp">self</span><span class="o">.</span><span class="n">basis</span> <span class="o">=</span> <span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">from_fractional</span><span class="p">(</span><span class="n">Vector</span><span class="p">(</span><span class="mf">1.</span><span class="p">,</span> <span class="mf">0.</span><span class="p">,</span> <span class="mf">0.</span><span class="p">)),</span>
<span class="bp">self</span><span class="o">.</span><span class="n">from_fractional</span><span class="p">(</span><span class="n">Vector</span><span class="p">(</span><span class="mf">0.</span><span class="p">,</span> <span class="mf">1.</span><span class="p">,</span> <span class="mf">0.</span><span class="p">)),</span>
<span class="bp">self</span><span class="o">.</span><span class="n">from_fractional</span><span class="p">(</span><span class="n">Vector</span><span class="p">(</span><span class="mf">0.</span><span class="p">,</span> <span class="mf">0.</span><span class="p">,</span> <span class="mf">1.</span><span class="p">)))</span>
<span class="k">else</span><span class="p">:</span>
<span class="bp">self</span><span class="o">.</span><span class="n">basis</span> <span class="o">=</span> <span class="bp">None</span>
<span class="k">for</span> <span class="n">i</span> <span class="ow">in</span> <span class="nb">range</span><span class="p">(</span><span class="nb">len</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">ncs_transformations</span><span class="p">)):</span>
<span class="n">tr</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">ncs_transformations</span><span class="p">[</span><span class="n">i</span><span class="p">]</span>
<span class="n">tr_new</span> <span class="o">=</span> <span class="n">Scaling</span><span class="p">(</span><span class="n">Units</span><span class="o">.</span><span class="n">Ang</span><span class="p">)</span><span class="o">*</span><span class="n">tr</span><span class="o">*</span><span class="n">Scaling</span><span class="p">(</span><span class="mf">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">tr_new</span><span class="o">.</span><span class="n">given</span> <span class="o">=</span> <span class="n">tr</span><span class="o">.</span><span class="n">given</span>
<span class="n">tr_new</span><span class="o">.</span><span class="n">serial</span> <span class="o">=</span> <span class="n">tr</span><span class="o">.</span><span class="n">serial</span>
<span class="bp">self</span><span class="o">.</span><span class="n">ncs_transformations</span><span class="p">[</span><span class="n">i</span><span class="p">]</span> <span class="o">=</span> <span class="n">tr_new</span>
<span class="k">for</span> <span class="n">i</span> <span class="ow">in</span> <span class="nb">range</span><span class="p">(</span><span class="nb">len</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">cs_transformations</span><span class="p">)):</span>
<span class="n">tr</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">cs_transformations</span><span class="p">[</span><span class="n">i</span><span class="p">]</span>
<span class="n">tr_new</span> <span class="o">=</span> <span class="n">Scaling</span><span class="p">(</span><span class="n">Units</span><span class="o">.</span><span class="n">Ang</span><span class="p">)</span><span class="o">*</span><span class="n">tr</span><span class="o">*</span><span class="n">Scaling</span><span class="p">(</span><span class="mf">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="bp">self</span><span class="o">.</span><span class="n">cs_transformations</span><span class="p">[</span><span class="n">i</span><span class="p">]</span> <span class="o">=</span> <span class="n">tr_new</span>
<div class="viewcode-block" id="PDBConfiguration.createUnitCellUniverse"><a class="viewcode-back" href="../../modules.html#MMTK.PDB.PDBConfiguration.createUnitCellUniverse">[docs]</a> <span class="k">def</span> <span class="nf">createUnitCellUniverse</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span>
<span class="sd">"""</span>
<span class="sd"> Constructs an empty universe (OrthrhombicPeriodicUniverse or</span>
<span class="sd"> ParallelepipedicPeriodicUniverse) representing the</span>
<span class="sd"> unit cell of the crystal. If the PDB file does not define</span>
<span class="sd"> a unit cell at all, an InfiniteUniverse is returned.</span>
<span class="sd"> </span>
<span class="sd"> :returns: a 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">from_fractional</span> <span class="ow">is</span> <span class="bp">None</span><span class="p">:</span>
<span class="k">return</span> <span class="n">Universe</span><span class="o">.</span><span class="n">InfiniteUniverse</span><span class="p">()</span>
<span class="n">e1</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">from_fractional</span><span class="p">(</span><span class="n">Vector</span><span class="p">(</span><span class="mf">1.</span><span class="p">,</span> <span class="mf">0.</span><span class="p">,</span> <span class="mf">0.</span><span class="p">))</span>
<span class="n">e2</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">from_fractional</span><span class="p">(</span><span class="n">Vector</span><span class="p">(</span><span class="mf">0.</span><span class="p">,</span> <span class="mf">1.</span><span class="p">,</span> <span class="mf">0.</span><span class="p">))</span>
<span class="n">e3</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">from_fractional</span><span class="p">(</span><span class="n">Vector</span><span class="p">(</span><span class="mf">0.</span><span class="p">,</span> <span class="mf">0.</span><span class="p">,</span> <span class="mf">1.</span><span class="p">))</span>
<span class="k">if</span> <span class="nb">abs</span><span class="p">(</span><span class="n">e1</span><span class="o">.</span><span class="n">normal</span><span class="p">()</span><span class="o">*</span><span class="n">Vector</span><span class="p">(</span><span class="mf">1.</span><span class="p">,</span> <span class="mf">0.</span><span class="p">,</span> <span class="mf">0.</span><span class="p">)</span><span class="o">-</span><span class="mf">1.</span><span class="p">)</span> <span class="o"><</span> <span class="mf">1.e-15</span> \
<span class="ow">and</span> <span class="nb">abs</span><span class="p">(</span><span class="n">e2</span><span class="o">.</span><span class="n">normal</span><span class="p">()</span><span class="o">*</span><span class="n">Vector</span><span class="p">(</span><span class="mf">0.</span><span class="p">,</span> <span class="mf">1.</span><span class="p">,</span> <span class="mf">0.</span><span class="p">)</span><span class="o">-</span><span class="mf">1.</span><span class="p">)</span> <span class="o"><</span> <span class="mf">1.e-15</span> \
<span class="ow">and</span> <span class="nb">abs</span><span class="p">(</span><span class="n">e3</span><span class="o">.</span><span class="n">normal</span><span class="p">()</span><span class="o">*</span><span class="n">Vector</span><span class="p">(</span><span class="mf">0.</span><span class="p">,</span> <span class="mf">0.</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="o"><</span> <span class="mf">1.e-15</span><span class="p">:</span>
<span class="k">return</span> \
<span class="n">Universe</span><span class="o">.</span><span class="n">OrthorhombicPeriodicUniverse</span><span class="p">((</span><span class="n">e1</span><span class="o">.</span><span class="n">length</span><span class="p">(),</span>
<span class="n">e2</span><span class="o">.</span><span class="n">length</span><span class="p">(),</span>
<span class="n">e3</span><span class="o">.</span><span class="n">length</span><span class="p">()))</span>
<span class="k">return</span> <span class="n">Universe</span><span class="o">.</span><span class="n">ParallelepipedicPeriodicUniverse</span><span class="p">((</span><span class="n">e1</span><span class="p">,</span> <span class="n">e2</span><span class="p">,</span> <span class="n">e3</span><span class="p">))</span>
</div>
<div class="viewcode-block" id="PDBConfiguration.createPeptideChains"><a class="viewcode-back" href="../../modules.html#MMTK.PDB.PDBConfiguration.createPeptideChains">[docs]</a> <span class="k">def</span> <span class="nf">createPeptideChains</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">model</span><span class="o">=</span><span class="s">'all'</span><span class="p">):</span>
<span class="sd">"""</span>
<span class="sd"> :returns: a list of :class:`~MMTK.Proteins.PeptideChain` objects, one for each</span>
<span class="sd"> peptide chain in the PDB file. The parameter model</span>
<span class="sd"> has the same meaning as for the PeptideChain constructor.</span>
<span class="sd"> :rtype: list</span>
<span class="sd"> """</span>
<span class="k">return</span> <span class="p">[</span><span class="n">chain</span><span class="o">.</span><span class="n">createPeptideChain</span><span class="p">(</span><span class="n">model</span><span class="p">)</span>
<span class="k">for</span> <span class="n">chain</span> <span class="ow">in</span> <span class="bp">self</span><span class="o">.</span><span class="n">peptide_chains</span><span class="p">]</span>
</div>
<div class="viewcode-block" id="PDBConfiguration.createNucleotideChains"><a class="viewcode-back" href="../../modules.html#MMTK.PDB.PDBConfiguration.createNucleotideChains">[docs]</a> <span class="k">def</span> <span class="nf">createNucleotideChains</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">model</span><span class="o">=</span><span class="s">'all'</span><span class="p">):</span>
<span class="sd">"""</span>
<span class="sd"> :returns: a list of :class:`~MMTK.NucleicAcids.NucleotideChain` objects, one for each</span>
<span class="sd"> nucleotide chain in the PDB file. The parameter model</span>
<span class="sd"> has the same meaning as for the NucleotideChain constructor.</span>
<span class="sd"> :rtype: list</span>
<span class="sd"> """</span>
<span class="k">return</span> <span class="p">[</span><span class="n">chain</span><span class="o">.</span><span class="n">createNucleotideChain</span><span class="p">(</span><span class="n">model</span><span class="p">)</span>
<span class="k">for</span> <span class="n">chain</span> <span class="ow">in</span> <span class="bp">self</span><span class="o">.</span><span class="n">nucleotide_chains</span><span class="p">]</span>
</div>
<div class="viewcode-block" id="PDBConfiguration.createMolecules"><a class="viewcode-back" href="../../modules.html#MMTK.PDB.PDBConfiguration.createMolecules">[docs]</a> <span class="k">def</span> <span class="nf">createMolecules</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">names</span> <span class="o">=</span> <span class="bp">None</span><span class="p">,</span> <span class="n">permit_undefined</span><span class="o">=</span><span class="bp">True</span><span class="p">):</span>
<span class="sd">"""</span>
<span class="sd"> :param names: If a list of molecule names (as defined in the</span>
<span class="sd"> chemical database) and/or PDB residue names,</span>
<span class="sd"> only molecules mentioned in this list will be</span>
<span class="sd"> constructed. If a dictionary, it is used to map</span>
<span class="sd"> PDB residue names to molecule names. With the</span>
<span class="sd"> default (None), only water molecules are</span>
<span class="sd"> built.</span>
<span class="sd"> :type names: list</span>
<span class="sd"> :param permit_undefined: If False, an exception is raised</span>
<span class="sd"> when a PDB residue is encountered for</span>
<span class="sd"> which no molecule name is supplied</span>
<span class="sd"> in names. If True, an AtomCluster</span>
<span class="sd"> object is constructed for each unknown</span>
<span class="sd"> molecule.</span>
<span class="sd"> :returns: a collection of :class:`~MMTK.ChemicalObjects.Molecule` objects,</span>
<span class="sd"> one for each molecule in the PDB file. Each PDB residue not </span>
<span class="sd"> describing an amino acid or nucleotide residue is considered a</span>
<span class="sd"> molecule.</span>
<span class="sd"> :rtype: :class:`~MMTK.Collections.Collection`</span>
<span class="sd"> """</span>
<span class="n">collection</span> <span class="o">=</span> <span class="n">Collections</span><span class="o">.</span><span class="n">Collection</span><span class="p">()</span>
<span class="n">mol_dicts</span> <span class="o">=</span> <span class="p">[</span><span class="n">molecule_names</span><span class="p">]</span>
<span class="k">if</span> <span class="nb">type</span><span class="p">(</span><span class="n">names</span><span class="p">)</span> <span class="o">==</span> <span class="nb">type</span><span class="p">({}):</span>
<span class="n">mol_dicts</span><span class="o">.</span><span class="n">append</span><span class="p">(</span><span class="n">names</span><span class="p">)</span>
<span class="n">names</span> <span class="o">=</span> <span class="bp">None</span>
<span class="k">for</span> <span class="n">name</span> <span class="ow">in</span> <span class="bp">self</span><span class="o">.</span><span class="n">molecules</span><span class="o">.</span><span class="n">keys</span><span class="p">():</span>
<span class="n">full_name</span> <span class="o">=</span> <span class="bp">None</span>
<span class="k">for</span> <span class="nb">dict</span> <span class="ow">in</span> <span class="n">mol_dicts</span><span class="p">:</span>
<span class="n">full_name</span> <span class="o">=</span> <span class="nb">dict</span><span class="o">.</span><span class="n">get</span><span class="p">(</span><span class="n">name</span><span class="p">,</span> <span class="bp">None</span><span class="p">)</span>
<span class="k">if</span> <span class="n">names</span> <span class="ow">is</span> <span class="bp">None</span> <span class="ow">or</span> <span class="n">name</span> <span class="ow">in</span> <span class="n">names</span> <span class="ow">or</span> <span class="n">full_name</span> <span class="ow">in</span> <span class="n">names</span><span class="p">:</span>
<span class="k">if</span> <span class="n">full_name</span> <span class="ow">is</span> <span class="bp">None</span> <span class="ow">and</span> <span class="ow">not</span> <span class="n">permit_undefined</span><span class="p">:</span>
<span class="k">raise</span> <span class="ne">ValueError</span><span class="p">(</span><span class="s">"no definition for molecule "</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="n">name</span><span class="p">]:</span>
<span class="k">if</span> <span class="n">full_name</span><span class="p">:</span>
<span class="n">m</span> <span class="o">=</span> <span class="n">ChemicalObjects</span><span class="o">.</span><span class="n">Molecule</span><span class="p">(</span><span class="n">full_name</span><span class="p">)</span>
<span class="n">setConfiguration</span><span class="p">(</span><span class="n">m</span><span class="p">,</span> <span class="p">[</span><span class="n">molecule</span><span class="p">])</span>
<span class="k">else</span><span class="p">:</span>
<span class="n">pdbdict</span> <span class="o">=</span> <span class="p">{}</span>
<span class="n">atoms</span> <span class="o">=</span> <span class="p">[]</span>
<span class="n">i</span> <span class="o">=</span> <span class="mi">0</span>
<span class="k">for</span> <span class="n">atom</span> <span class="ow">in</span> <span class="n">molecule</span><span class="p">:</span>
<span class="n">aname</span> <span class="o">=</span> <span class="n">atom</span><span class="o">.</span><span class="n">name</span>
<span class="k">while</span> <span class="n">aname</span><span class="p">[</span><span class="mi">0</span><span class="p">]</span> <span class="ow">in</span> <span class="n">string</span><span class="o">.</span><span class="n">digits</span><span class="p">:</span>
<span class="n">aname</span> <span class="o">=</span> <span class="n">aname</span><span class="p">[</span><span class="mi">1</span><span class="p">:]</span> <span class="o">+</span> <span class="n">aname</span><span class="p">[</span><span class="mi">0</span><span class="p">]</span>
<span class="k">try</span><span class="p">:</span>
<span class="n">element</span> <span class="o">=</span> <span class="n">atom</span><span class="p">[</span><span class="s">'element'</span><span class="p">]</span><span class="o">.</span><span class="n">strip</span><span class="p">()</span>
<span class="n">a</span> <span class="o">=</span> <span class="n">ChemicalObjects</span><span class="o">.</span><span class="n">Atom</span><span class="p">(</span><span class="n">element</span><span class="p">,</span> <span class="n">name</span> <span class="o">=</span> <span class="n">aname</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="n">a</span> <span class="o">=</span> <span class="n">ChemicalObjects</span><span class="o">.</span><span class="n">Atom</span><span class="p">(</span><span class="n">aname</span><span class="p">[:</span><span class="mi">2</span><span class="p">]</span><span class="o">.</span><span class="n">strip</span><span class="p">(),</span>
<span class="n">name</span> <span class="o">=</span> <span class="n">aname</span><span class="p">)</span>
<span class="k">except</span> <span class="ne">IOError</span><span class="p">:</span>
<span class="n">a</span> <span class="o">=</span> <span class="n">ChemicalObjects</span><span class="o">.</span><span class="n">Atom</span><span class="p">(</span><span class="n">aname</span><span class="p">[:</span><span class="mi">1</span><span class="p">],</span>
<span class="n">name</span> <span class="o">=</span> <span class="n">aname</span><span class="p">)</span>
<span class="n">a</span><span class="o">.</span><span class="n">setPosition</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">atoms</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="n">pdbdict</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="o">=</span> <span class="n">Database</span><span class="o">.</span><span class="n">AtomReference</span><span class="p">(</span><span class="n">i</span><span class="p">)</span>
<span class="n">i</span> <span class="o">+=</span> <span class="mi">1</span>
<span class="n">m</span> <span class="o">=</span> <span class="n">ChemicalObjects</span><span class="o">.</span><span class="n">AtomCluster</span><span class="p">(</span><span class="n">atoms</span><span class="p">,</span> <span class="n">name</span> <span class="o">=</span> <span class="n">name</span><span class="p">)</span>
<span class="k">if</span> <span class="nb">len</span><span class="p">(</span><span class="n">pdbdict</span><span class="p">)</span> <span class="o">==</span> <span class="nb">len</span><span class="p">(</span><span class="n">molecule</span><span class="p">):</span>
<span class="c"># pdbmap is correct only if the AtomCluster has</span>
<span class="c"># unique atom names</span>
<span class="n">m</span><span class="o">.</span><span class="n">pdbmap</span> <span class="o">=</span> <span class="p">[(</span><span class="n">name</span><span class="p">,</span> <span class="n">pdbdict</span><span class="p">)]</span>
<span class="n">setConfiguration</span><span class="p">(</span><span class="n">m</span><span class="p">,</span> <span class="p">[</span><span class="n">molecule</span><span class="p">])</span>
<span class="n">collection</span><span class="o">.</span><span class="n">addObject</span><span class="p">(</span><span class="n">m</span><span class="p">)</span>
<span class="k">return</span> <span class="n">collection</span>
</div>
<span class="k">def</span> <span class="nf">createGroups</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">mapping</span><span class="p">):</span>
<span class="n">groups</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="bp">self</span><span class="o">.</span><span class="n">molecules</span><span class="o">.</span><span class="n">keys</span><span class="p">():</span>
<span class="n">full_name</span> <span class="o">=</span> <span class="n">mapping</span><span class="o">.</span><span class="n">get</span><span class="p">(</span><span class="n">name</span><span class="p">,</span> <span class="bp">None</span><span class="p">)</span>
<span class="k">if</span> <span class="n">full_name</span> <span class="ow">is</span> <span class="ow">not</span> <span class="bp">None</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">name</span><span class="p">]:</span>
<span class="n">g</span> <span class="o">=</span> <span class="n">ChemicalObjects</span><span class="o">.</span><span class="n">Group</span><span class="p">(</span><span class="n">full_name</span><span class="p">)</span>
<span class="n">setConfiguration</span><span class="p">(</span><span class="n">g</span><span class="p">,</span> <span class="p">[</span><span class="n">molecule</span><span class="p">],</span> <span class="n">toplevel</span><span class="o">=</span><span class="mi">0</span><span class="p">)</span>
<span class="n">groups</span><span class="o">.</span><span class="n">append</span><span class="p">(</span><span class="n">g</span><span class="p">)</span>
<span class="k">return</span> <span class="n">groups</span>
<div class="viewcode-block" id="PDBConfiguration.createAll"><a class="viewcode-back" href="../../modules.html#MMTK.PDB.PDBConfiguration.createAll">[docs]</a> <span class="k">def</span> <span class="nf">createAll</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">molecule_names</span> <span class="o">=</span> <span class="bp">None</span><span class="p">,</span> <span class="n">permit_undefined</span><span class="o">=</span><span class="bp">True</span><span class="p">):</span>
<span class="sd">"""</span>
<span class="sd"> :returns: a collection containing all objects contained in the</span>
<span class="sd"> PDB file, i.e. the combination of the objects</span>
<span class="sd"> returned by :func:`~MMTK.PDB.PDBConfiguration.createPeptideChains`,</span>
<span class="sd"> :func:`~MMTK.PDB.PDBConfiguration.createNucleotideChains`,</span>
<span class="sd"> and :func:`~MMTK.PDB.PDBConfiguration.createMolecules`.</span>
<span class="sd"> The parameters have the same meaning as for</span>
<span class="sd"> :func:`~MMTK.PDB.PDBConfiguration.createMolecules`.</span>
<span class="sd"> :rtype: :class:`~MMTK.Collectionc.Collection`</span>
<span class="sd"> """</span>
<span class="n">collection</span> <span class="o">=</span> <span class="n">Collections</span><span class="o">.</span><span class="n">Collection</span><span class="p">()</span>
<span class="n">peptide_chains</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">createPeptideChains</span><span class="p">()</span>
<span class="k">if</span> <span class="n">peptide_chains</span><span class="p">:</span>
<span class="kn">import</span> <span class="nn">Proteins</span>
<span class="n">collection</span><span class="o">.</span><span class="n">addObject</span><span class="p">(</span><span class="n">Proteins</span><span class="o">.</span><span class="n">Protein</span><span class="p">(</span><span class="n">peptide_chains</span><span class="p">))</span>
<span class="n">nucleotide_chains</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">createNucleotideChains</span><span class="p">()</span>
<span class="n">collection</span><span class="o">.</span><span class="n">addObject</span><span class="p">(</span><span class="n">nucleotide_chains</span><span class="p">)</span>
<span class="n">molecules</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">createMolecules</span><span class="p">(</span><span class="n">molecule_names</span><span class="p">,</span> <span class="n">permit_undefined</span><span class="p">)</span>
<span class="n">collection</span><span class="o">.</span><span class="n">addObject</span><span class="p">(</span><span class="n">molecules</span><span class="p">)</span>
<span class="k">return</span> <span class="n">collection</span>
</div>
<div class="viewcode-block" id="PDBConfiguration.asuToUnitCell"><a class="viewcode-back" href="../../modules.html#MMTK.PDB.PDBConfiguration.asuToUnitCell">[docs]</a> <span class="k">def</span> <span class="nf">asuToUnitCell</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">asu_contents</span><span class="p">,</span> <span class="n">compact</span><span class="o">=</span><span class="bp">True</span><span class="p">):</span>
<span class="sd">"""</span>
<span class="sd"> :param asu_contents: the molecules in the asymmetric unit, usually</span>
<span class="sd"> obtained from :func:`~MMTK.PDB.PDBConfiguration.createAll()`.</span>
<span class="sd"> :param compact: if True, all molecules images are shifted such that</span>
<span class="sd"> their centers of mass lie inside the unit cell.</span>
<span class="sd"> :type compact: bool</span>
<span class="sd"> :returns: a collection containing all molecules in the unit cell,</span>
<span class="sd"> obtained by copying and moving the molecules from the</span>
<span class="sd"> asymmetric unit according to the crystallographic</span>
<span class="sd"> symmetry operations.</span>
<span class="sd"> :rtype: :class:`~MMTK.Collections.Collection`</span>
<span class="sd"> """</span>
<span class="n">unit_cell_contents</span> <span class="o">=</span> <span class="n">Collections</span><span class="o">.</span><span class="n">Collection</span><span class="p">()</span>
<span class="k">for</span> <span class="n">symop</span> <span class="ow">in</span> <span class="bp">self</span><span class="o">.</span><span class="n">cs_transformations</span><span class="p">:</span>
<span class="n">transformation</span> <span class="o">=</span> <span class="n">symop</span><span class="o">.</span><span class="n">asLinearTransformation</span><span class="p">()</span>
<span class="n">rotation</span> <span class="o">=</span> <span class="n">transformation</span><span class="o">.</span><span class="n">tensor</span>
<span class="n">translation</span> <span class="o">=</span> <span class="n">transformation</span><span class="o">.</span><span class="n">vector</span>
<span class="n">image</span> <span class="o">=</span> <span class="n">copy</span><span class="o">.</span><span class="n">deepcopy</span><span class="p">(</span><span class="n">asu_contents</span><span class="p">)</span>
<span class="k">for</span> <span class="n">atom</span> <span class="ow">in</span> <span class="n">image</span><span class="o">.</span><span class="n">atomList</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">symop</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="k">if</span> <span class="n">compact</span><span class="p">:</span>
<span class="n">cm</span> <span class="o">=</span> <span class="n">image</span><span class="o">.</span><span class="n">centerOfMass</span><span class="p">()</span>
<span class="n">cm_fr</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">to_fractional</span><span class="p">(</span><span class="n">cm</span><span class="p">)</span>
<span class="n">cm_fr</span> <span class="o">=</span> <span class="n">Vector</span><span class="p">(</span><span class="n">cm_fr</span><span class="p">[</span><span class="mi">0</span><span class="p">]</span> <span class="o">%</span> <span class="mf">1.</span><span class="p">,</span> <span class="n">cm_fr</span><span class="p">[</span><span class="mi">1</span><span class="p">]</span> <span class="o">%</span> <span class="mf">1.</span><span class="p">,</span> <span class="n">cm_fr</span><span class="p">[</span><span class="mi">2</span><span class="p">]</span> <span class="o">%</span> <span class="mf">1.</span><span class="p">)</span> \
<span class="o">-</span> <span class="n">Vector</span><span class="p">(</span><span class="mf">0.5</span><span class="p">,</span> <span class="mf">0.5</span><span class="p">,</span> <span class="mf">0.5</span><span class="p">)</span>
<span class="n">cm</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">from_fractional</span><span class="p">(</span><span class="n">cm_fr</span><span class="p">)</span>
<span class="n">image</span><span class="o">.</span><span class="n">translateTo</span><span class="p">(</span><span class="n">cm</span><span class="p">)</span>
<span class="n">unit_cell_contents</span><span class="o">.</span><span class="n">addObject</span><span class="p">(</span><span class="n">image</span><span class="p">)</span>
<span class="k">return</span> <span class="n">unit_cell_contents</span>
</div>
<div class="viewcode-block" id="PDBConfiguration.applyTo"><a class="viewcode-back" href="../../modules.html#MMTK.PDB.PDBConfiguration.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="n">atom_map</span><span class="o">=</span><span class="bp">None</span><span class="p">):</span>
<span class="sd">"""</span>
<span class="sd"> Sets the configuration of object from the coordinates in the</span>
<span class="sd"> PDB file. The object must be compatible with the PDB file, i.e.</span>
<span class="sd"> contain the same subobjects and in the same order. This is usually</span>
<span class="sd"> only guaranteed if the object was created by the method</span>
<span class="sd"> :func:`~MMTK.PDB.PDBConfiguration.createAll` from a PDB file with the same layout.</span>
<span class="sd"> :param object: a chemical object or collection of chemical objects</span>
<span class="sd"> """</span>
<span class="n">setConfiguration</span><span class="p">(</span><span class="nb">object</span><span class="p">,</span> <span class="bp">self</span><span class="o">.</span><span class="n">residues</span><span class="p">,</span> <span class="n">atom_map</span><span class="o">=</span><span class="n">atom_map</span><span class="p">)</span>
<span class="c">#</span>
<span class="c"># An alternative name for compatibility in Database files.</span>
<span class="c">#</span></div></div>
<span class="n">PDBFile</span> <span class="o">=</span> <span class="n">PDBConfiguration</span>
<span class="c">#</span>
<span class="c"># Set atom coordinates from PDB configuration.</span>
<span class="c">#</span>
<span class="k">def</span> <span class="nf">setResidueConfiguration</span><span class="p">(</span><span class="nb">object</span><span class="p">,</span> <span class="n">pdb_residue</span><span class="p">,</span> <span class="n">pdbmap</span><span class="p">,</span> <span class="n">altmap</span><span class="p">,</span>
<span class="n">atom_map</span> <span class="o">=</span> <span class="bp">None</span><span class="p">):</span>
<span class="n">defined</span> <span class="o">=</span> <span class="mi">0</span>
<span class="k">for</span> <span class="n">atom</span> <span class="ow">in</span> <span class="n">pdb_residue</span><span class="p">:</span>
<span class="n">name</span> <span class="o">=</span> <span class="n">atom</span><span class="o">.</span><span class="n">name</span>
<span class="k">try</span><span class="p">:</span> <span class="n">name</span> <span class="o">=</span> <span class="n">altmap</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">try</span><span class="p">:</span>
<span class="n">pdbname</span> <span class="o">=</span> <span class="n">pdbmap</span><span class="p">[</span><span class="mi">1</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="n">pdbname</span> <span class="o">=</span> <span class="bp">None</span>
<span class="k">if</span> <span class="ow">not</span> <span class="nb">object</span><span class="o">.</span><span class="n">isSubsetModel</span><span class="p">():</span>
<span class="k">raise</span> <span class="ne">IOError</span><span class="p">(</span><span class="s">'Atom '</span><span class="o">+</span><span class="n">atom</span><span class="o">.</span><span class="n">name</span><span class="o">+</span><span class="s">' of PDB residue '</span> <span class="o">+</span>
<span class="n">pdb_residue</span><span class="o">.</span><span class="n">name</span><span class="o">+</span><span class="s">' not found in residue '</span> <span class="o">+</span>
<span class="n">pdbmap</span><span class="p">[</span><span class="mi">0</span><span class="p">]</span> <span class="o">+</span> <span class="s">' of object '</span> <span class="o">+</span> <span class="nb">object</span><span class="o">.</span><span class="n">fullName</span><span class="p">())</span>
<span class="k">if</span> <span class="n">pdbname</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">pdbname</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="k">try</span><span class="p">:</span>
<span class="nb">object</span><span class="o">.</span><span class="n">setIndex</span><span class="p">(</span><span class="n">pdbname</span><span class="p">,</span> <span class="n">atom</span><span class="o">.</span><span class="n">number</span><span class="o">-</span><span class="mi">1</span><span class="p">)</span>
<span class="k">except</span> <span class="ne">ValueError</span><span class="p">:</span>
<span class="k">pass</span>
<span class="k">if</span> <span class="n">atom_map</span> <span class="ow">is</span> <span class="ow">not</span> <span class="bp">None</span><span class="p">:</span>
<span class="n">atom_map</span><span class="p">[</span><span class="nb">object</span><span class="o">.</span><span class="n">getAtom</span><span class="p">(</span><span class="n">pdbname</span><span class="p">)]</span> <span class="o">=</span> <span class="n">atom</span>
<span class="n">defined</span> <span class="o">+=</span> <span class="mi">1</span>
<span class="k">return</span> <span class="n">defined</span>
<span class="k">def</span> <span class="nf">setConfiguration</span><span class="p">(</span><span class="nb">object</span><span class="p">,</span> <span class="n">pdb_residues</span><span class="p">,</span>
<span class="nb">map</span> <span class="o">=</span> <span class="s">'pdbmap'</span><span class="p">,</span> <span class="n">alt</span> <span class="o">=</span> <span class="s">'pdb_alternative'</span><span class="p">,</span>
<span class="n">atom_map</span> <span class="o">=</span> <span class="bp">None</span><span class="p">,</span> <span class="n">toplevel</span> <span class="o">=</span> <span class="bp">True</span><span class="p">):</span>
<span class="n">defined</span> <span class="o">=</span> <span class="mi">0</span>
<span class="k">if</span> <span class="nb">hasattr</span><span class="p">(</span><span class="nb">object</span><span class="p">,</span> <span class="s">'is_protein'</span><span class="p">):</span>
<span class="n">i</span> <span class="o">=</span> <span class="mi">0</span>
<span class="k">for</span> <span class="n">chain</span> <span class="ow">in</span> <span class="nb">object</span><span class="p">:</span>
<span class="n">l</span> <span class="o">=</span> <span class="nb">len</span><span class="p">(</span><span class="n">chain</span><span class="p">)</span>
<span class="n">defined</span> <span class="o">+=</span> <span class="n">setConfiguration</span><span class="p">(</span><span class="n">chain</span><span class="p">,</span> <span class="n">pdb_residues</span><span class="p">[</span><span class="n">i</span><span class="p">:</span><span class="n">i</span><span class="o">+</span><span class="n">l</span><span class="p">],</span>
<span class="nb">map</span><span class="p">,</span> <span class="n">alt</span><span class="p">,</span> <span class="n">atom_map</span><span class="p">,</span> <span class="bp">False</span><span class="p">)</span>
<span class="n">i</span> <span class="o">=</span> <span class="n">i</span> <span class="o">+</span> <span class="n">l</span>
<span class="k">elif</span> <span class="nb">hasattr</span><span class="p">(</span><span class="nb">object</span><span class="p">,</span> <span class="s">'is_chain'</span><span class="p">):</span>
<span class="k">for</span> <span class="n">i</span> <span class="ow">in</span> <span class="nb">range</span><span class="p">(</span><span class="nb">len</span><span class="p">(</span><span class="nb">object</span><span class="p">)):</span>
<span class="n">defined</span> <span class="o">+=</span> <span class="n">setConfiguration</span><span class="p">(</span><span class="nb">object</span><span class="p">[</span><span class="n">i</span><span class="p">],</span> <span class="n">pdb_residues</span><span class="p">[</span><span class="n">i</span><span class="p">:</span><span class="n">i</span><span class="o">+</span><span class="mi">1</span><span class="p">],</span>
<span class="nb">map</span><span class="p">,</span> <span class="n">alt</span><span class="p">,</span> <span class="n">atom_map</span><span class="p">,</span> <span class="bp">False</span><span class="p">)</span>
<span class="k">elif</span> <span class="nb">hasattr</span><span class="p">(</span><span class="nb">object</span><span class="p">,</span> <span class="nb">map</span><span class="p">):</span>
<span class="n">pdbmap</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="nb">map</span><span class="p">)</span>
<span class="k">try</span><span class="p">:</span> <span class="n">altmap</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">alt</span><span class="p">)</span>
<span class="k">except</span> <span class="ne">AttributeError</span><span class="p">:</span> <span class="n">altmap</span> <span class="o">=</span> <span class="p">{}</span>
<span class="n">nres</span> <span class="o">=</span> <span class="nb">len</span><span class="p">(</span><span class="n">pdb_residues</span><span class="p">)</span>
<span class="k">if</span> <span class="nb">len</span><span class="p">(</span><span class="n">pdbmap</span><span class="p">)</span> <span class="o">!=</span> <span class="n">nres</span><span class="p">:</span>
<span class="k">raise</span> <span class="ne">IOError</span><span class="p">(</span><span class="s">'PDB configuration does not match object '</span> <span class="o">+</span>
<span class="nb">object</span><span class="o">.</span><span class="n">fullName</span><span class="p">())</span>
<span class="k">for</span> <span class="n">i</span> <span class="ow">in</span> <span class="nb">range</span><span class="p">(</span><span class="n">nres</span><span class="p">):</span>
<span class="n">defined</span> <span class="o">+=</span> <span class="n">setResidueConfiguration</span><span class="p">(</span><span class="nb">object</span><span class="p">,</span> <span class="n">pdb_residues</span><span class="p">[</span><span class="n">i</span><span class="p">],</span>
<span class="n">pdbmap</span><span class="p">[</span><span class="n">i</span><span class="p">],</span> <span class="n">altmap</span><span class="p">,</span> <span class="n">atom_map</span><span class="p">)</span>
<span class="k">elif</span> <span class="n">Collections</span><span class="o">.</span><span class="n">isCollection</span><span class="p">(</span><span class="nb">object</span><span class="p">):</span>
<span class="n">nres</span> <span class="o">=</span> <span class="nb">len</span><span class="p">(</span><span class="n">pdb_residues</span><span class="p">)</span>
<span class="k">if</span> <span class="nb">len</span><span class="p">(</span><span class="nb">object</span><span class="p">)</span> <span class="o">!=</span> <span class="n">nres</span><span class="p">:</span>
<span class="k">raise</span> <span class="ne">IOError</span><span class="p">(</span><span class="s">'PDB configuration does not match object '</span> <span class="o">+</span>
<span class="nb">object</span><span class="o">.</span><span class="n">fullName</span><span class="p">())</span>
<span class="k">for</span> <span class="n">i</span> <span class="ow">in</span> <span class="nb">range</span><span class="p">(</span><span class="n">nres</span><span class="p">):</span>
<span class="n">defined</span> <span class="o">+=</span> <span class="n">setConfiguration</span><span class="p">(</span><span class="nb">object</span><span class="p">[</span><span class="n">i</span><span class="p">],</span> <span class="p">[</span><span class="n">pdb_residues</span><span class="p">[</span><span class="n">i</span><span class="p">]],</span>
<span class="nb">map</span><span class="p">,</span> <span class="n">alt</span><span class="p">,</span> <span class="n">atom_map</span><span class="p">,</span> <span class="bp">False</span><span class="p">)</span>
<span class="k">else</span><span class="p">:</span>
<span class="k">try</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">fullName</span><span class="p">()</span>
<span class="k">except</span> <span class="ne">AttributeError</span><span class="p">:</span>
<span class="k">try</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="k">except</span> <span class="ne">AttributeError</span><span class="p">:</span>
<span class="n">name</span> <span class="o">=</span> <span class="s">'???'</span>
<span class="k">raise</span> <span class="ne">IOError</span><span class="p">(</span><span class="s">'PDB configuration does not match object '</span> <span class="o">+</span> <span class="n">name</span><span class="p">)</span>
<span class="k">if</span> <span class="n">toplevel</span> <span class="ow">and</span> <span class="n">defined</span> <span class="o"><</span> <span class="nb">object</span><span class="o">.</span><span class="n">numberOfAtoms</span><span class="p">():</span>
<span class="n">name</span> <span class="o">=</span> <span class="s">'[unnamed object]'</span>
<span class="k">try</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">fullName</span><span class="p">()</span>
<span class="k">except</span><span class="p">:</span> <span class="k">pass</span>
<span class="k">if</span> <span class="n">name</span><span class="p">:</span> <span class="n">name</span> <span class="o">=</span> <span class="s">' in '</span> <span class="o">+</span> <span class="n">name</span>
<span class="n">Utility</span><span class="o">.</span><span class="n">warning</span><span class="p">(</span><span class="sb">`object.numberOfAtoms()-defined`</span> <span class="o">+</span> <span class="s">' atom(s)'</span> <span class="o">+</span> <span class="n">name</span> <span class="o">+</span>
<span class="s">' were not assigned (new) positions.'</span><span class="p">)</span>
<span class="k">return</span> <span class="n">defined</span>
<span class="c">#</span>
<span class="c"># Create objects from a PDB configuration.</span>
<span class="c">#</span>
<span class="n">molecule_names</span> <span class="o">=</span> <span class="p">{</span><span class="s">'HOH'</span><span class="p">:</span> <span class="s">'water'</span><span class="p">,</span> <span class="s">'TIP'</span><span class="p">:</span> <span class="s">'water'</span><span class="p">,</span> <span class="s">'TIP3'</span><span class="p">:</span> <span class="s">'water'</span><span class="p">,</span>
<span class="s">'WAT'</span><span class="p">:</span> <span class="s">'water'</span><span class="p">,</span> <span class="s">'HEM'</span><span class="p">:</span> <span class="s">'heme'</span><span class="p">}</span>
<span class="k">def</span> <span class="nf">defineMolecule</span><span class="p">(</span><span class="n">code</span><span class="p">,</span> <span class="n">name</span><span class="p">):</span>
<span class="k">if</span> <span class="n">molecule_names</span><span class="o">.</span><span class="n">has_key</span><span class="p">(</span><span class="n">code</span><span class="p">):</span>
<span class="k">raise</span> <span class="ne">ValueError</span><span class="p">(</span><span class="s">"PDB code "</span> <span class="o">+</span> <span class="n">code</span> <span class="o">+</span> <span class="s">" already used"</span><span class="p">)</span>
<span class="n">molecule_names</span><span class="p">[</span><span class="n">code</span><span class="p">]</span> <span class="o">=</span> <span class="n">name</span>
<span class="c">#</span>
<span class="c"># This object represents a PDB file for output.</span>
<span class="c">#</span>
<div class="viewcode-block" id="PDBOutputFile"><a class="viewcode-back" href="../../modules.html#MMTK.PDB.PDBOutputFile">[docs]</a><span class="k">class</span> <span class="nc">PDBOutputFile</span><span class="p">(</span><span class="nb">object</span><span class="p">):</span>
<span class="sd">"""</span>
<span class="sd"> PDB file for output</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">filename</span><span class="p">,</span> <span class="n">subformat</span><span class="o">=</span> <span class="bp">None</span><span class="p">):</span>
<span class="sd">"""</span>
<span class="sd"> :param filename: the name of the PDB file that is created</span>
<span class="sd"> :type filename: str</span>
<span class="sd"> :param subformat: a variant of the PDB format; these subformats</span>
<span class="sd"> are defined in module Scientific.IO.PDB. The</span>
<span class="sd"> default is the standard PDB format.</span>
<span class="sd"> :type subformat: str</span>
<span class="sd"> """</span>
<span class="bp">self</span><span class="o">.</span><span class="n">file</span> <span class="o">=</span> <span class="n">Scientific</span><span class="o">.</span><span class="n">IO</span><span class="o">.</span><span class="n">PDB</span><span class="o">.</span><span class="n">PDBFile</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="n">subformat</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="bp">False</span>
<span class="bp">self</span><span class="o">.</span><span class="n">atom_sequence</span> <span class="o">=</span> <span class="p">[]</span>
<span class="bp">self</span><span class="o">.</span><span class="n">model_number</span> <span class="o">=</span> <span class="bp">None</span>
<div class="viewcode-block" id="PDBOutputFile.nextModel"><a class="viewcode-back" href="../../modules.html#MMTK.PDB.PDBOutputFile.nextModel">[docs]</a> <span class="k">def</span> <span class="nf">nextModel</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span>
<span class="sd">"""</span>
<span class="sd"> Start a new model</span>
<span class="sd"> """</span>
<span class="k">if</span> <span class="bp">self</span><span class="o">.</span><span class="n">model_number</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">model_number</span> <span class="o">=</span> <span class="mi">1</span>
<span class="k">else</span><span class="p">:</span>
<span class="bp">self</span><span class="o">.</span><span class="n">file</span><span class="o">.</span><span class="n">writeLine</span><span class="p">(</span><span class="s">'ENDMDL'</span><span class="p">,</span> <span class="s">''</span><span class="p">)</span>
<span class="bp">self</span><span class="o">.</span><span class="n">model_number</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">model_number</span> <span class="o">+</span> <span class="mi">1</span>
<span class="bp">self</span><span class="o">.</span><span class="n">file</span><span class="o">.</span><span class="n">writeLine</span><span class="p">(</span><span class="s">'MODEL'</span><span class="p">,</span> <span class="p">{</span><span class="s">'serial_number'</span><span class="p">:</span> <span class="bp">self</span><span class="o">.</span><span class="n">model_number</span><span class="p">})</span>
</div>
<div class="viewcode-block" id="PDBOutputFile.write"><a class="viewcode-back" href="../../modules.html#MMTK.PDB.PDBOutputFile.write">[docs]</a> <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">tag</span> <span class="o">=</span> <span class="bp">None</span><span class="p">):</span>
<span class="sd">"""</span>
<span class="sd"> Write an object to the file</span>
<span class="sd"> :param object: the object to be written</span>
<span class="sd"> :type object: :class:`~MMTK.Collections.GroupOfAtoms`</span>
<span class="sd"> :param configuration: the configuration from which the coordinates </span>
<span class="sd"> are taken (default: current configuration)</span>
<span class="sd"> :type configuration: :class:`~MMTK.ParticleProperties.Configuration`</span>
<span class="sd"> """</span>
<span class="k">if</span> <span class="ow">not</span> <span class="n">ChemicalObjects</span><span class="o">.</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="k">else</span><span class="p">:</span>
<span class="n">toplevel</span> <span class="o">=</span> <span class="n">tag</span> <span class="ow">is</span> <span class="bp">None</span>
<span class="k">if</span> <span class="n">toplevel</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="k">if</span> <span class="nb">hasattr</span><span class="p">(</span><span class="nb">object</span><span class="p">,</span> <span class="s">'pdbmap'</span><span class="p">):</span>
<span class="k">for</span> <span class="n">residue</span> <span class="ow">in</span> <span class="nb">object</span><span class="o">.</span><span class="n">pdbmap</span><span class="p">:</span>
<span class="bp">self</span><span class="o">.</span><span class="n">file</span><span class="o">.</span><span class="n">nextResidue</span><span class="p">(</span><span class="n">residue</span><span class="p">[</span><span class="mi">0</span><span class="p">],</span> <span class="p">)</span>
<span class="n">sorted_atoms</span> <span class="o">=</span> <span class="n">residue</span><span class="p">[</span><span class="mi">1</span><span class="p">]</span><span class="o">.</span><span class="n">items</span><span class="p">()</span>
<span class="n">sorted_atoms</span><span class="o">.</span><span class="n">sort</span><span class="p">(</span><span class="k">lambda</span> <span class="n">x</span><span class="p">,</span> <span class="n">y</span><span class="p">:</span>
<span class="nb">cmp</span><span class="p">(</span><span class="n">x</span><span class="p">[</span><span class="mi">1</span><span class="p">]</span><span class="o">.</span><span class="n">number</span><span class="p">,</span> <span class="n">y</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">for</span> <span class="n">atom_name</span><span class="p">,</span> <span class="n">atom</span> <span class="ow">in</span> <span class="n">sorted_atoms</span><span class="p">:</span>
<span class="n">atom</span> <span class="o">=</span> <span class="nb">object</span><span class="o">.</span><span class="n">getAtom</span><span class="p">(</span><span class="n">atom</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">Utility</span><span class="o">.</span><span class="n">isDefinedPosition</span><span class="p">(</span><span class="n">p</span><span class="p">):</span>
<span class="k">try</span><span class="p">:</span> <span class="n">occ</span> <span class="o">=</span> <span class="n">atom</span><span class="o">.</span><span class="n">occupancy</span>
<span class="k">except</span> <span class="ne">AttributeError</span><span class="p">:</span> <span class="n">occ</span> <span class="o">=</span> <span class="mf">0.</span>
<span class="k">try</span><span class="p">:</span> <span class="n">temp</span> <span class="o">=</span> <span class="n">atom</span><span class="o">.</span><span class="n">temperature_factor</span>
<span class="k">except</span> <span class="ne">AttributeError</span><span class="p">:</span> <span class="n">temp</span> <span class="o">=</span> <span class="mf">0.</span>
<span class="bp">self</span><span class="o">.</span><span class="n">file</span><span class="o">.</span><span class="n">writeAtom</span><span class="p">(</span><span class="n">atom_name</span><span class="p">,</span> <span class="n">p</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">occ</span><span class="p">,</span> <span class="n">temp</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="bp">self</span><span class="o">.</span><span class="n">atom_sequence</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="bp">self</span><span class="o">.</span><span class="n">warning</span> <span class="o">=</span> <span class="bp">True</span>
<span class="nb">setattr</span><span class="p">(</span><span class="n">atom</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">else</span><span class="p">:</span>
<span class="k">if</span> <span class="nb">hasattr</span><span class="p">(</span><span class="nb">object</span><span class="p">,</span> <span class="s">'is_protein'</span><span class="p">):</span>
<span class="k">for</span> <span class="n">chain</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">chain</span><span class="p">,</span> <span class="n">configuration</span><span class="p">,</span> <span class="n">tag</span><span class="p">)</span>
<span class="k">elif</span> <span class="nb">hasattr</span><span class="p">(</span><span class="nb">object</span><span class="p">,</span> <span class="s">'is_chain'</span><span class="p">):</span>
<span class="bp">self</span><span class="o">.</span><span class="n">file</span><span class="o">.</span><span class="n">nextChain</span><span class="p">(</span><span class="bp">None</span><span class="p">,</span> <span class="nb">object</span><span class="o">.</span><span class="n">name</span><span class="p">)</span>
<span class="k">for</span> <span class="n">residue</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">residue</span><span class="p">,</span> <span class="n">configuration</span><span class="p">,</span> <span class="n">tag</span><span class="p">)</span>
<span class="bp">self</span><span class="o">.</span><span class="n">file</span><span class="o">.</span><span class="n">terminateChain</span><span class="p">()</span>
<span class="k">elif</span> <span class="nb">hasattr</span><span class="p">(</span><span class="nb">object</span><span class="p">,</span> <span class="s">'molecules'</span><span class="p">):</span>
<span class="k">for</span> <span class="n">m</span> <span class="ow">in</span> <span class="nb">object</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">write</span><span class="p">(</span><span class="n">m</span><span class="p">,</span> <span class="n">configuration</span><span class="p">,</span> <span class="n">tag</span><span class="p">)</span>
<span class="k">elif</span> <span class="nb">hasattr</span><span class="p">(</span><span class="nb">object</span><span class="p">,</span> <span class="s">'groups'</span><span class="p">):</span>
<span class="k">for</span> <span class="n">g</span> <span class="ow">in</span> <span class="nb">object</span><span class="o">.</span><span class="n">groups</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">g</span><span class="p">,</span> <span class="n">configuration</span><span class="p">,</span> <span class="n">tag</span><span class="p">)</span>
<span class="k">if</span> <span class="n">toplevel</span><span class="p">:</span>
<span class="k">for</span> <span class="n">a</span> <span class="ow">in</span> <span class="nb">object</span><span class="o">.</span><span class="n">atomList</span><span class="p">():</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="bp">self</span><span class="o">.</span><span class="n">write</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="n">tag</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>
</div>
<div class="viewcode-block" id="PDBOutputFile.close"><a class="viewcode-back" href="../../modules.html#MMTK.PDB.PDBOutputFile.close">[docs]</a> <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="sd">"""</span>
<span class="sd"> Closes the file. Must be called in order to prevent data loss.</span>
<span class="sd"> """</span>
<span class="k">if</span> <span class="bp">self</span><span class="o">.</span><span class="n">model_number</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">file</span><span class="o">.</span><span class="n">writeLine</span><span class="p">(</span><span class="s">'ENDMDL'</span><span class="p">,</span> <span class="s">''</span><span class="p">)</span>
<span class="bp">self</span><span class="o">.</span><span class="n">file</span><span class="o">.</span><span class="n">close</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="bp">False</span></div></div>
</pre></div>
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