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<h1>Source code for MMTK.PDBMoleculeFactory</h1><div class="highlight"><pre>
<span class="c"># This module constructs molecules and universes corresponding exactly</span>
<span class="c"># to the contents of a PDB file, using residue and atom names as</span>
<span class="c"># given in the file.</span>
<span class="c">#</span>
<span class="c"># Written by Konrad Hinsen</span>
<span class="c">#</span>
<span class="sd">"""</span>
<span class="sd">Molecule factory defined by a PDB file</span>
<span class="sd">This module permits the construction of molecular objects that correspond</span>
<span class="sd">exactly to the contents of a PDB file. It is used for working with</span>
<span class="sd">experimental data. Note that most force fields cannot be applied to the</span>
<span class="sd">systems generated in this way because the molecule factory does not know</span>
<span class="sd">any force field parameters.</span>
<span class="sd">"""</span>
<span class="n">__docformat__</span> <span class="o">=</span> <span class="s">'restructuredtext'</span>
<span class="kn">import</span> <span class="nn">MMTK</span>
<span class="kn">from</span> <span class="nn">MMTK.MoleculeFactory</span> <span class="kn">import</span> <span class="n">MoleculeFactory</span>
<span class="kn">from</span> <span class="nn">Scientific.Geometry</span> <span class="kn">import</span> <span class="n">Vector</span><span class="p">,</span> <span class="n">delta</span>
<span class="kn">from</span> <span class="nn">Scientific</span> <span class="kn">import</span> <span class="n">N</span>
<span class="kn">import</span> <span class="nn">copy</span>
<div class="viewcode-block" id="PDBMoleculeFactory"><a class="viewcode-back" href="../../modules.html#MMTK.PDBMoleculeFactory.PDBMoleculeFactory">[docs]</a><span class="k">class</span> <span class="nc">PDBMoleculeFactory</span><span class="p">(</span><span class="n">MoleculeFactory</span><span class="p">):</span>
<span class="sd">"""</span>
<span class="sd"> A PDBMoleculeFactory generates molecules and universes from the</span>
<span class="sd"> contents of a PDBConfiguration. Nothing is added or left out</span>
<span class="sd"> (except as defined by the optional residue and atom filters), and</span>
<span class="sd"> the atom and residue names are exactly those of the original PDB</span>
<span class="sd"> file.</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">pdb_conf</span><span class="p">,</span> <span class="n">residue_filter</span><span class="o">=</span><span class="bp">None</span><span class="p">,</span> <span class="n">atom_filter</span><span class="o">=</span><span class="bp">None</span><span class="p">):</span>
<span class="sd">"""</span>
<span class="sd"> :param pdb_conf: a PDBConfiguration</span>
<span class="sd"> :type pdb_conf: :class:`~MMTK.PDB.PDBConfiguration`</span>
<span class="sd"> :param residue_filter: a function taking a residue object</span>
<span class="sd"> (as defined in Scientific.IO.PDB)</span>
<span class="sd"> and returning True if that residue is</span>
<span class="sd"> to be kept in the molecule factory</span>
<span class="sd"> :type residue_filter: callable</span>
<span class="sd"> :param atom_filter: a function taking a residue object and an</span>
<span class="sd"> atom object (as defined in Scientific.IO.PDB) </span>
<span class="sd"> and returning True if that atom is </span>
<span class="sd"> to be kept in the molecule factory</span>
<span class="sd"> :type atom_filter: callable</span>
<span class="sd"> """</span>
<span class="n">MoleculeFactory</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="k">if</span> <span class="n">residue_filter</span> <span class="ow">is</span> <span class="bp">None</span> <span class="ow">and</span> <span class="n">atom_filter</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">pdb_conf</span> <span class="o">=</span> <span class="n">pdb_conf</span>
<span class="k">else</span><span class="p">:</span>
<span class="bp">self</span><span class="o">.</span><span class="n">pdb_conf</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">pdb_conf</span><span class="p">)</span>
<span class="k">if</span> <span class="n">atom_filter</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">residue</span> <span class="ow">in</span> <span class="bp">self</span><span class="o">.</span><span class="n">pdb_conf</span><span class="o">.</span><span class="n">residues</span><span class="p">:</span>
<span class="n">delete</span> <span class="o">=</span> <span class="p">[</span><span class="n">atom</span> <span class="k">for</span> <span class="n">atom</span> <span class="ow">in</span> <span class="n">residue</span>
<span class="k">if</span> <span class="ow">not</span> <span class="n">atom_filter</span><span class="p">(</span><span class="n">residue</span><span class="p">,</span> <span class="n">atom</span><span class="p">)]</span>
<span class="k">for</span> <span class="n">atom</span> <span class="ow">in</span> <span class="n">delete</span><span class="p">:</span>
<span class="n">residue</span><span class="o">.</span><span class="n">deleteAtom</span><span class="p">(</span><span class="n">atom</span><span class="p">)</span>
<span class="k">if</span> <span class="n">residue_filter</span> <span class="ow">is</span> <span class="ow">not</span> <span class="bp">None</span><span class="p">:</span>
<span class="n">delete</span> <span class="o">=</span> <span class="p">[</span><span class="n">residue</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">pdb_conf</span><span class="o">.</span><span class="n">residues</span>
<span class="k">if</span> <span class="nb">len</span><span class="p">(</span><span class="n">residue</span><span class="p">)</span> <span class="o">==</span> <span class="mi">0</span> <span class="ow">or</span> <span class="ow">not</span> <span class="n">residue_filter</span><span class="p">(</span><span class="n">residue</span><span class="p">)]</span>
<span class="k">for</span> <span class="n">residue</span> <span class="ow">in</span> <span class="n">delete</span><span class="p">:</span>
<span class="bp">self</span><span class="o">.</span><span class="n">pdb_conf</span><span class="o">.</span><span class="n">deleteResidue</span><span class="p">(</span><span class="n">residue</span><span class="p">)</span>
<span class="bp">self</span><span class="o">.</span><span class="n">peptide_chains</span> <span class="o">=</span> <span class="p">[]</span>
<span class="bp">self</span><span class="o">.</span><span class="n">nucleotide_chains</span> <span class="o">=</span> <span class="p">[]</span>
<span class="bp">self</span><span class="o">.</span><span class="n">molecules</span> <span class="o">=</span> <span class="p">{}</span>
<span class="bp">self</span><span class="o">.</span><span class="n">makeAll</span><span class="p">()</span>
<div class="viewcode-block" id="PDBMoleculeFactory.retrieveMolecules"><a class="viewcode-back" href="../../modules.html#MMTK.PDBMoleculeFactory.PDBMoleculeFactory.retrieveMolecules">[docs]</a> <span class="k">def</span> <span class="nf">retrieveMolecules</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span>
<span class="sd">"""</span>
<span class="sd"> Constructs Molecule objects corresponding to the contents of the</span>
<span class="sd"> PDBConfiguration. Each peptide or nucleotide chain becomes</span>
<span class="sd"> one molecule. For residues that are neither amino acids nor</span>
<span class="sd"> nucleic acids, each residue becomes one molecule.</span>
<span class="sd"> Chain molecules (peptide and nucleotide chains) can be iterated</span>
<span class="sd"> over to retrieve the individual residues. The residues can also</span>
<span class="sd"> be accessed as attributes whose names are the three-letter</span>
<span class="sd"> residue name (upper case) followed by an underscore and the</span>
<span class="sd"> residue number from the PDB file (e.g. 'GLY_34').</span>
<span class="sd"> Each object that corresponds to a PDB residue (i.e. each</span>
<span class="sd"> residue in a chain and each non-chain molecule) has the</span>
<span class="sd"> attributes 'residue_name' and 'residue_number'. Each atom has</span>
<span class="sd"> the attributes 'serial_number', 'occupancy' and</span>
<span class="sd"> 'temperature_factor'. Atoms for which a ANISOU record exists</span>
<span class="sd"> also have an attribute 'u' whose value is a tensor object.</span>
<span class="sd"> </span>
<span class="sd"> :returns: a list of Molecule objects</span>
<span class="sd"> :rtype: list</span>
<span class="sd"> """</span>
<span class="n">objects</span> <span class="o">=</span> <span class="p">[</span><span class="bp">self</span><span class="o">.</span><span class="n">retrieveMolecule</span><span class="p">(</span><span class="n">o</span><span class="p">)</span>
<span class="k">for</span> <span class="n">o</span> <span class="ow">in</span> <span class="bp">self</span><span class="o">.</span><span class="n">peptide_chains</span>
<span class="o">+</span> <span class="bp">self</span><span class="o">.</span><span class="n">nucleotide_chains</span><span class="p">]</span>
<span class="k">for</span> <span class="n">mollist</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">values</span><span class="p">():</span>
<span class="n">objects</span><span class="o">.</span><span class="n">extend</span><span class="p">([</span><span class="bp">self</span><span class="o">.</span><span class="n">retrieveMolecule</span><span class="p">(</span><span class="n">residue</span><span class="p">)</span>
<span class="k">for</span> <span class="n">residue</span> <span class="ow">in</span> <span class="n">mollist</span><span class="p">])</span>
<span class="k">return</span> <span class="n">objects</span>
</div>
<div class="viewcode-block" id="PDBMoleculeFactory.retrieveUniverse"><a class="viewcode-back" href="../../modules.html#MMTK.PDBMoleculeFactory.PDBMoleculeFactory.retrieveUniverse">[docs]</a> <span class="k">def</span> <span class="nf">retrieveUniverse</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">return</span> <span class="bp">self</span><span class="o">.</span><span class="n">pdb_conf</span><span class="o">.</span><span class="n">createUnitCellUniverse</span><span class="p">()</span>
</div>
<div class="viewcode-block" id="PDBMoleculeFactory.retrieveAsymmetricUnit"><a class="viewcode-back" href="../../modules.html#MMTK.PDBMoleculeFactory.PDBMoleculeFactory.retrieveAsymmetricUnit">[docs]</a> <span class="k">def</span> <span class="nf">retrieveAsymmetricUnit</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span>
<span class="sd">"""</span>
<span class="sd"> Constructs a universe (OrthrhombicPeriodicUniverse or</span>
<span class="sd"> ParallelepipedicPeriodicUniverse) representing the</span>
<span class="sd"> unit cell of the crystal and adds the molecules representing</span>
<span class="sd"> the asymmetric unit.</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="n">universe</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">retrieveUniverse</span><span class="p">()</span>
<span class="n">universe</span><span class="o">.</span><span class="n">addObject</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">retrieveMolecules</span><span class="p">())</span>
<span class="k">return</span> <span class="n">universe</span>
</div>
<div class="viewcode-block" id="PDBMoleculeFactory.retrieveUnitCell"><a class="viewcode-back" href="../../modules.html#MMTK.PDBMoleculeFactory.PDBMoleculeFactory.retrieveUnitCell">[docs]</a> <span class="k">def</span> <span class="nf">retrieveUnitCell</span><span class="p">(</span><span class="bp">self</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"> Constructs a universe (OrthrhombicPeriodicUniverse or</span>
<span class="sd"> ParallelepipedicPeriodicUniverse) representing the</span>
<span class="sd"> unit cell of the crystal and adds all the molecules it</span>
<span class="sd"> contains, i.e. the molecules of the asymmetric unit and</span>
<span class="sd"> its images obtained by applying the crystallographic</span>
<span class="sd"> symmetry operations.</span>
<span class="sd"> :param compact: if True, the 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 universe</span>
<span class="sd"> :rtype: :class:`~MMTK.Universe.Universe`</span>
<span class="sd"> """</span>
<span class="k">if</span> <span class="ow">not</span> <span class="bp">self</span><span class="o">.</span><span class="n">pdb_conf</span><span class="o">.</span><span class="n">cs_transformations</span><span class="p">:</span>
<span class="k">return</span> <span class="bp">self</span><span class="o">.</span><span class="n">retrieveAsymmetricUnit</span><span class="p">()</span>
<span class="n">universe</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">retrieveUniverse</span><span class="p">()</span>
<span class="n">asu_count</span> <span class="o">=</span> <span class="mi">0</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">pdb_conf</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">is_asu</span> <span class="o">=</span> <span class="n">translation</span><span class="o">.</span><span class="n">length</span><span class="p">()</span> <span class="o"><</span> <span class="mf">1.e-8</span> <span class="ow">and</span> \
<span class="n">N</span><span class="o">.</span><span class="n">maximum</span><span class="o">.</span><span class="n">reduce</span><span class="p">(</span><span class="n">N</span><span class="o">.</span><span class="n">ravel</span><span class="p">(</span><span class="n">N</span><span class="o">.</span><span class="n">fabs</span><span class="p">((</span><span class="n">rotation</span>
<span class="o">-</span><span class="n">delta</span><span class="p">)</span><span class="o">.</span><span class="n">array</span><span class="p">)))</span> <span class="o"><</span> <span class="mf">1.e-8</span>
<span class="k">if</span> <span class="n">is_asu</span><span class="p">:</span>
<span class="n">asu_count</span> <span class="o">+=</span> <span class="mi">1</span>
<span class="n">asu</span> <span class="o">=</span> <span class="n">MMTK</span><span class="o">.</span><span class="n">Collection</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">retrieveMolecules</span><span class="p">())</span>
<span class="k">for</span> <span class="n">atom</span> <span class="ow">in</span> <span class="n">asu</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="nb">hasattr</span><span class="p">(</span><span class="n">atom</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">u</span> <span class="o">=</span> <span class="n">rotation</span><span class="o">.</span><span class="n">dot</span><span class="p">(</span><span class="n">atom</span><span class="o">.</span><span class="n">u</span><span class="o">.</span><span class="n">dot</span><span class="p">(</span><span class="n">rotation</span><span class="o">.</span><span class="n">transpose</span><span class="p">()))</span>
<span class="n">atom</span><span class="o">.</span><span class="n">u</span> <span class="o">=</span> <span class="n">atom</span><span class="o">.</span><span class="n">u</span><span class="o">.</span><span class="n">symmetricalPart</span><span class="p">()</span>
<span class="n">atom</span><span class="o">.</span><span class="n">in_asu</span> <span class="o">=</span> <span class="n">is_asu</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">asu</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">pdb_conf</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">pdb_conf</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">asu</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">universe</span><span class="o">.</span><span class="n">addObject</span><span class="p">(</span><span class="n">asu</span><span class="p">)</span>
<span class="k">assert</span> <span class="n">asu_count</span> <span class="o">==</span> <span class="mi">1</span>
<span class="k">return</span> <span class="n">universe</span>
</div>
<span class="k">def</span> <span class="nf">makeAll</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span>
<span class="n">cystines</span> <span class="o">=</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">pdb_conf</span><span class="o">.</span><span class="n">peptide_chains</span><span class="p">:</span>
<span class="n">chain_id</span> <span class="o">=</span> <span class="n">chain</span><span class="o">.</span><span class="n">chain_id</span>
<span class="k">if</span> <span class="ow">not</span> <span class="n">chain_id</span><span class="p">:</span>
<span class="n">chain_id</span> <span class="o">=</span> <span class="s">'PeptideChain'</span><span class="o">+</span><span class="nb">str</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">peptide_chains</span><span class="p">)</span><span class="o">+</span><span class="mi">1</span><span class="p">)</span>
<span class="k">for</span> <span class="n">residue</span> <span class="ow">in</span> <span class="n">chain</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">'CYS'</span> <span class="ow">and</span> <span class="n">residue</span><span class="o">.</span><span class="n">atoms</span><span class="o">.</span><span class="n">has_key</span><span class="p">(</span><span class="s">'SG'</span><span class="p">):</span>
<span class="n">cystines</span><span class="o">.</span><span class="n">append</span><span class="p">((</span><span class="n">chain_id</span><span class="p">,</span> <span class="n">residue</span><span class="p">,</span> <span class="n">residue</span><span class="o">.</span><span class="n">atoms</span><span class="p">[</span><span class="s">'SG'</span><span class="p">]))</span>
<span class="bp">self</span><span class="o">.</span><span class="n">makeChain</span><span class="p">(</span><span class="n">chain</span><span class="p">,</span> <span class="n">chain_id</span><span class="p">)</span>
<span class="bp">self</span><span class="o">.</span><span class="n">peptide_chains</span><span class="o">.</span><span class="n">append</span><span class="p">(</span><span class="n">chain_id</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">cystines</span><span class="p">)):</span>
<span class="k">for</span> <span class="n">j</span> <span class="ow">in</span> <span class="nb">range</span><span class="p">(</span><span class="n">i</span><span class="o">+</span><span class="mi">1</span><span class="p">,</span> <span class="nb">len</span><span class="p">(</span><span class="n">cystines</span><span class="p">)):</span>
<span class="n">d</span> <span class="o">=</span> <span class="p">(</span><span class="n">cystines</span><span class="p">[</span><span class="n">i</span><span class="p">][</span><span class="mi">2</span><span class="p">]</span><span class="o">.</span><span class="n">position</span><span class="o">-</span><span class="n">cystines</span><span class="p">[</span><span class="n">j</span><span class="p">][</span><span class="mi">2</span><span class="p">]</span><span class="o">.</span><span class="n">position</span><span class="p">)</span><span class="o">.</span><span class="n">length</span><span class="p">()</span>
<span class="k">if</span> <span class="n">d</span> <span class="o"><</span> <span class="mf">0.25</span><span class="p">:</span>
<span class="k">if</span> <span class="n">cystines</span><span class="p">[</span><span class="n">i</span><span class="p">][</span><span class="mi">0</span><span class="p">]</span> <span class="ow">is</span> <span class="n">cystines</span><span class="p">[</span><span class="n">j</span><span class="p">][</span><span class="mi">0</span><span class="p">]:</span>
<span class="n">cys1</span> <span class="o">=</span> <span class="n">cystines</span><span class="p">[</span><span class="n">i</span><span class="p">][</span><span class="mi">1</span><span class="p">]</span>
<span class="n">cys2</span> <span class="o">=</span> <span class="n">cystines</span><span class="p">[</span><span class="n">j</span><span class="p">][</span><span class="mi">1</span><span class="p">]</span>
<span class="n">cys1</span> <span class="o">=</span> <span class="n">cys1</span><span class="o">.</span><span class="n">name</span> <span class="o">+</span> <span class="s">'_'</span> <span class="o">+</span> <span class="nb">str</span><span class="p">(</span><span class="n">cys1</span><span class="o">.</span><span class="n">number</span><span class="p">)</span>
<span class="n">cys2</span> <span class="o">=</span> <span class="n">cys2</span><span class="o">.</span><span class="n">name</span> <span class="o">+</span> <span class="s">'_'</span> <span class="o">+</span> <span class="nb">str</span><span class="p">(</span><span class="n">cys2</span><span class="o">.</span><span class="n">number</span><span class="p">)</span>
<span class="bp">self</span><span class="o">.</span><span class="n">addBond</span><span class="p">(</span><span class="n">cystines</span><span class="p">[</span><span class="n">i</span><span class="p">][</span><span class="mi">0</span><span class="p">],</span> <span class="n">cys1</span><span class="o">+</span><span class="s">'.SG'</span><span class="p">,</span> <span class="n">cys2</span><span class="o">+</span><span class="s">'.SG'</span><span class="p">)</span>
<span class="k">else</span><span class="p">:</span>
<span class="k">raise</span> <span class="bp">NotImplemented</span><span class="p">(</span><span class="s">'Inter-chain disulfide bridges'</span>
<span class="s">' not yet implemented'</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">pdb_conf</span><span class="o">.</span><span class="n">nucleotide_chains</span><span class="p">:</span>
<span class="n">chain_id</span> <span class="o">=</span> <span class="n">chain</span><span class="o">.</span><span class="n">chain_id</span>
<span class="k">if</span> <span class="ow">not</span> <span class="n">chain_id</span><span class="p">:</span>
<span class="n">chain_id</span> <span class="o">=</span> <span class="s">'NucleotideChain'</span><span class="o">+</span><span class="nb">str</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">nucleotide_chains</span><span class="p">)</span><span class="o">+</span><span class="mi">1</span><span class="p">)</span>
<span class="bp">self</span><span class="o">.</span><span class="n">makeChain</span><span class="p">(</span><span class="n">chain</span><span class="p">,</span> <span class="n">chain_id</span><span class="p">)</span>
<span class="bp">self</span><span class="o">.</span><span class="n">nucleotide_chains</span><span class="o">.</span><span class="n">append</span><span class="p">(</span><span class="n">chain_id</span><span class="p">)</span>
<span class="k">for</span> <span class="n">molname</span><span class="p">,</span> <span class="n">mollist</span> <span class="ow">in</span> <span class="bp">self</span><span class="o">.</span><span class="n">pdb_conf</span><span class="o">.</span><span class="n">molecules</span><span class="o">.</span><span class="n">items</span><span class="p">():</span>
<span class="bp">self</span><span class="o">.</span><span class="n">molecules</span><span class="p">[</span><span class="n">molname</span><span class="p">]</span> <span class="o">=</span> <span class="p">[]</span>
<span class="k">for</span> <span class="n">residue</span> <span class="ow">in</span> <span class="n">mollist</span><span class="p">:</span>
<span class="n">base_resname</span> <span class="o">=</span> <span class="n">residue</span><span class="o">.</span><span class="n">name</span> <span class="o">+</span> <span class="s">'_'</span> <span class="o">+</span> <span class="nb">str</span><span class="p">(</span><span class="n">residue</span><span class="o">.</span><span class="n">number</span><span class="p">)</span>
<span class="n">suffix</span> <span class="o">=</span> <span class="mi">1</span>
<span class="n">resname</span> <span class="o">=</span> <span class="n">base_resname</span>
<span class="n">done</span> <span class="o">=</span> <span class="bp">False</span>
<span class="k">while</span> <span class="ow">not</span> <span class="n">done</span><span class="p">:</span>
<span class="k">try</span><span class="p">:</span>
<span class="bp">self</span><span class="o">.</span><span class="n">makeResidue</span><span class="p">(</span><span class="n">residue</span><span class="p">,</span> <span class="n">resname</span><span class="p">)</span>
<span class="n">done</span> <span class="o">=</span> <span class="bp">True</span>
<span class="k">except</span> <span class="ne">ValueError</span><span class="p">,</span> <span class="n">e</span><span class="p">:</span>
<span class="k">if</span> <span class="nb">str</span><span class="p">(</span><span class="n">e</span><span class="p">)</span><span class="o">.</span><span class="n">split</span><span class="p">()[</span><span class="mi">0</span><span class="p">]</span> <span class="o">==</span> <span class="s">"redefinition"</span><span class="p">:</span>
<span class="n">resname</span> <span class="o">=</span> <span class="n">base_resname</span> <span class="o">+</span> <span class="s">"_"</span> <span class="o">+</span> <span class="nb">str</span><span class="p">(</span><span class="n">suffix</span><span class="p">)</span>
<span class="n">suffix</span> <span class="o">+=</span> <span class="mi">1</span>
<span class="k">else</span><span class="p">:</span>
<span class="k">raise</span>
<span class="bp">self</span><span class="o">.</span><span class="n">molecules</span><span class="p">[</span><span class="n">molname</span><span class="p">]</span><span class="o">.</span><span class="n">append</span><span class="p">(</span><span class="n">resname</span><span class="p">)</span>
<span class="k">def</span> <span class="nf">makeChain</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="n">chain_id</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">residue</span> <span class="ow">in</span> <span class="n">chain</span><span class="p">:</span>
<span class="n">resname</span> <span class="o">=</span> <span class="n">chain_id</span> <span class="o">+</span> <span class="s">'_'</span> <span class="o">+</span> <span class="n">residue</span><span class="o">.</span><span class="n">name</span> <span class="o">+</span> <span class="s">'_'</span> <span class="o">+</span> <span class="nb">str</span><span class="p">(</span><span class="n">residue</span><span class="o">.</span><span class="n">number</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">resname</span><span class="p">)</span>
<span class="bp">self</span><span class="o">.</span><span class="n">makeResidue</span><span class="p">(</span><span class="n">residue</span><span class="p">,</span> <span class="n">resname</span><span class="p">)</span>
<span class="bp">self</span><span class="o">.</span><span class="n">createGroup</span><span class="p">(</span><span class="n">chain_id</span><span class="p">)</span>
<span class="n">local_resnames</span> <span class="o">=</span> <span class="p">[]</span>
<span class="k">for</span> <span class="n">resname</span> <span class="ow">in</span> <span class="n">groups</span><span class="p">:</span>
<span class="n">local_resname</span> <span class="o">=</span> <span class="s">'_'</span><span class="o">.</span><span class="n">join</span><span class="p">(</span><span class="n">resname</span><span class="o">.</span><span class="n">split</span><span class="p">(</span><span class="s">'_'</span><span class="p">)[</span><span class="mi">1</span><span class="p">:])</span>
<span class="bp">self</span><span class="o">.</span><span class="n">addSubgroup</span><span class="p">(</span><span class="n">chain_id</span><span class="p">,</span> <span class="n">local_resname</span><span class="p">,</span> <span class="n">resname</span><span class="p">)</span>
<span class="n">local_resnames</span><span class="o">.</span><span class="n">append</span><span class="p">(</span><span class="n">local_resname</span><span class="p">)</span>
<span class="bp">self</span><span class="o">.</span><span class="n">setAttribute</span><span class="p">(</span><span class="n">chain_id</span><span class="p">,</span> <span class="s">'sequence'</span><span class="p">,</span> <span class="n">local_resnames</span><span class="p">)</span>
<span class="k">for</span> <span class="n">i</span> <span class="ow">in</span> <span class="nb">range</span><span class="p">(</span><span class="mi">1</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="k">if</span> <span class="n">chain</span><span class="p">[</span><span class="n">i</span><span class="o">-</span><span class="mi">1</span><span class="p">]</span><span class="o">.</span><span class="n">number</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="o">.</span><span class="n">number</span><span class="o">-</span><span class="mi">1</span><span class="p">:</span>
<span class="k">for</span> <span class="n">atom1</span> <span class="ow">in</span> <span class="n">chain</span><span class="p">[</span><span class="n">i</span><span class="o">-</span><span class="mi">1</span><span class="p">]:</span>
<span class="k">for</span> <span class="n">atom2</span> <span class="ow">in</span> <span class="n">chain</span><span class="p">[</span><span class="n">i</span><span class="p">]:</span>
<span class="k">if</span> <span class="bp">self</span><span class="o">.</span><span class="n">assumeBond</span><span class="p">(</span><span class="n">atom1</span><span class="o">.</span><span class="n">properties</span><span class="p">[</span><span class="s">'element'</span><span class="p">],</span>
<span class="n">atom1</span><span class="o">.</span><span class="n">position</span><span class="p">,</span>
<span class="n">atom2</span><span class="o">.</span><span class="n">properties</span><span class="p">[</span><span class="s">'element'</span><span class="p">],</span>
<span class="n">atom2</span><span class="o">.</span><span class="n">position</span><span class="p">):</span>
<span class="bp">self</span><span class="o">.</span><span class="n">addBond</span><span class="p">(</span><span class="n">chain_id</span><span class="p">,</span>
<span class="n">local_resnames</span><span class="p">[</span><span class="n">i</span><span class="o">-</span><span class="mi">1</span><span class="p">]</span><span class="o">+</span><span class="s">'.'</span><span class="o">+</span><span class="n">atom1</span><span class="o">.</span><span class="n">name</span><span class="p">,</span>
<span class="n">local_resnames</span><span class="p">[</span><span class="n">i</span><span class="p">]</span><span class="o">+</span><span class="s">'.'</span><span class="o">+</span><span class="n">atom2</span><span class="o">.</span><span class="n">name</span><span class="p">)</span>
<span class="k">def</span> <span class="nf">makeResidue</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">residue</span><span class="p">,</span> <span class="n">group_name</span><span class="p">):</span>
<span class="bp">self</span><span class="o">.</span><span class="n">createGroup</span><span class="p">(</span><span class="n">group_name</span><span class="p">)</span>
<span class="bp">self</span><span class="o">.</span><span class="n">setAttribute</span><span class="p">(</span><span class="n">group_name</span><span class="p">,</span> <span class="s">'residue_name'</span><span class="p">,</span> <span class="n">residue</span><span class="o">.</span><span class="n">name</span><span class="p">)</span>
<span class="bp">self</span><span class="o">.</span><span class="n">setAttribute</span><span class="p">(</span><span class="n">group_name</span><span class="p">,</span> <span class="s">'residue_number'</span><span class="p">,</span> <span class="n">residue</span><span class="o">.</span><span class="n">number</span><span class="p">)</span>
<span class="n">atoms</span> <span class="o">=</span> <span class="p">[]</span>
<span class="k">for</span> <span class="n">atom</span> <span class="ow">in</span> <span class="n">residue</span><span class="p">:</span>
<span class="n">atoms</span><span class="o">.</span><span class="n">append</span><span class="p">((</span><span class="n">atom</span><span class="o">.</span><span class="n">name</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">'element'</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="bp">self</span><span class="o">.</span><span class="n">addAtom</span><span class="p">(</span><span class="n">group_name</span><span class="p">,</span> <span class="n">atom</span><span class="o">.</span><span class="n">name</span><span class="p">,</span> <span class="n">atom</span><span class="o">.</span><span class="n">properties</span><span class="p">[</span><span class="s">'element'</span><span class="p">])</span>
<span class="bp">self</span><span class="o">.</span><span class="n">setPosition</span><span class="p">(</span><span class="n">group_name</span><span class="p">,</span> <span class="n">atom</span><span class="o">.</span><span class="n">name</span><span class="p">,</span> <span class="n">atom</span><span class="o">.</span><span class="n">position</span><span class="p">)</span>
<span class="bp">self</span><span class="o">.</span><span class="n">setAttribute</span><span class="p">(</span><span class="n">group_name</span><span class="p">,</span> <span class="n">atom</span><span class="o">.</span><span class="n">name</span><span class="o">+</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="bp">self</span><span class="o">.</span><span class="n">setAttribute</span><span class="p">(</span><span class="n">group_name</span><span class="p">,</span> <span class="n">atom</span><span class="o">.</span><span class="n">name</span><span class="o">+</span><span class="s">'.occupancy'</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">'occupancy'</span><span class="p">])</span>
<span class="bp">self</span><span class="o">.</span><span class="n">setAttribute</span><span class="p">(</span><span class="n">group_name</span><span class="p">,</span> <span class="n">atom</span><span class="o">.</span><span class="n">name</span><span class="o">+</span><span class="s">'.serial_number'</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">'serial_number'</span><span class="p">])</span>
<span class="k">if</span> <span class="n">atom</span><span class="o">.</span><span class="n">properties</span><span class="o">.</span><span class="n">has_key</span><span class="p">(</span><span class="s">'u'</span><span class="p">):</span>
<span class="bp">self</span><span class="o">.</span><span class="n">setAttribute</span><span class="p">(</span><span class="n">group_name</span><span class="p">,</span> <span class="n">atom</span><span class="o">.</span><span class="n">name</span><span class="o">+</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="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">atoms</span><span class="p">)):</span>
<span class="n">atom_i</span><span class="p">,</span> <span class="n">element_i</span><span class="p">,</span> <span class="n">pos_i</span> <span class="o">=</span> <span class="n">atoms</span><span class="p">[</span><span class="n">i</span><span class="p">]</span>
<span class="k">for</span> <span class="n">j</span> <span class="ow">in</span> <span class="nb">range</span><span class="p">(</span><span class="n">i</span><span class="o">+</span><span class="mi">1</span><span class="p">,</span> <span class="nb">len</span><span class="p">(</span><span class="n">atoms</span><span class="p">)):</span>
<span class="n">atom_j</span><span class="p">,</span> <span class="n">element_j</span><span class="p">,</span> <span class="n">pos_j</span> <span class="o">=</span> <span class="n">atoms</span><span class="p">[</span><span class="n">j</span><span class="p">]</span>
<span class="k">if</span> <span class="bp">self</span><span class="o">.</span><span class="n">assumeBond</span><span class="p">(</span><span class="n">element_i</span><span class="p">,</span> <span class="n">pos_i</span><span class="p">,</span> <span class="n">element_j</span><span class="p">,</span> <span class="n">pos_j</span><span class="p">):</span>
<span class="bp">self</span><span class="o">.</span><span class="n">addBond</span><span class="p">(</span><span class="n">group_name</span><span class="p">,</span> <span class="n">atom_i</span><span class="p">,</span> <span class="n">atom_j</span><span class="p">)</span>
<span class="k">def</span> <span class="nf">assumeBond</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">element1</span><span class="p">,</span> <span class="n">pos1</span><span class="p">,</span> <span class="n">element2</span><span class="p">,</span> <span class="n">pos2</span><span class="p">):</span>
<span class="k">if</span> <span class="n">element1</span> <span class="o">></span> <span class="n">element2</span><span class="p">:</span>
<span class="n">element1</span><span class="p">,</span> <span class="n">element2</span> <span class="o">=</span> <span class="n">element2</span><span class="p">,</span> <span class="n">element1</span>
<span class="k">try</span><span class="p">:</span>
<span class="n">d</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">bond_lengths</span><span class="p">[(</span><span class="n">element1</span><span class="p">,</span> <span class="n">element2</span><span class="p">)]</span>
<span class="k">return</span> <span class="p">(</span><span class="n">pos1</span><span class="o">-</span><span class="n">pos2</span><span class="p">)</span><span class="o">.</span><span class="n">length</span><span class="p">()</span> <span class="o"><</span> <span class="n">d</span>
<span class="k">except</span> <span class="ne">KeyError</span><span class="p">:</span>
<span class="k">return</span> <span class="bp">False</span>
<span class="n">bond_lengths</span> <span class="o">=</span> <span class="p">{(</span><span class="s">'C'</span><span class="p">,</span> <span class="s">'C'</span><span class="p">):</span> <span class="mf">0.16</span><span class="p">,</span>
<span class="p">(</span><span class="s">'C'</span><span class="p">,</span> <span class="s">'H'</span><span class="p">):</span> <span class="mf">0.115</span><span class="p">,</span>
<span class="p">(</span><span class="s">'C'</span><span class="p">,</span> <span class="s">'N'</span><span class="p">):</span> <span class="mf">0.215</span><span class="p">,</span>
<span class="p">(</span><span class="s">'C'</span><span class="p">,</span> <span class="s">'O'</span><span class="p">):</span> <span class="mf">0.16</span><span class="p">,</span>
<span class="p">(</span><span class="s">'C'</span><span class="p">,</span> <span class="s">'P'</span><span class="p">):</span> <span class="mf">0.2</span><span class="p">,</span>
<span class="p">(</span><span class="s">'C'</span><span class="p">,</span> <span class="s">'S'</span><span class="p">):</span> <span class="mf">0.2</span><span class="p">,</span>
<span class="p">(</span><span class="s">'H'</span><span class="p">,</span> <span class="s">'H'</span><span class="p">):</span> <span class="mf">0.08</span><span class="p">,</span>
<span class="p">(</span><span class="s">'H'</span><span class="p">,</span> <span class="s">'N'</span><span class="p">):</span> <span class="mf">0.115</span><span class="p">,</span>
<span class="p">(</span><span class="s">'H'</span><span class="p">,</span> <span class="s">'O'</span><span class="p">):</span> <span class="mf">0.115</span><span class="p">,</span>
<span class="p">(</span><span class="s">'H'</span><span class="p">,</span> <span class="s">'P'</span><span class="p">):</span> <span class="mf">0.15</span><span class="p">,</span>
<span class="p">(</span><span class="s">'H'</span><span class="p">,</span> <span class="s">'S'</span><span class="p">):</span> <span class="mf">0.14</span><span class="p">,</span>
<span class="p">(</span><span class="s">'N'</span><span class="p">,</span> <span class="s">'N'</span><span class="p">):</span> <span class="mf">0.155</span><span class="p">,</span>
<span class="p">(</span><span class="s">'N'</span><span class="p">,</span> <span class="s">'O'</span><span class="p">):</span> <span class="mf">0.15</span><span class="p">,</span>
<span class="p">(</span><span class="s">'O'</span><span class="p">,</span> <span class="s">'O'</span><span class="p">):</span> <span class="mf">0.16</span><span class="p">,</span>
<span class="p">(</span><span class="s">'O'</span><span class="p">,</span> <span class="s">'P'</span><span class="p">):</span> <span class="mf">0.17</span><span class="p">,</span>
<span class="p">(</span><span class="s">'O'</span><span class="p">,</span> <span class="s">'S'</span><span class="p">):</span> <span class="mf">0.16</span><span class="p">,</span>
<span class="p">(</span><span class="s">'P'</span><span class="p">,</span> <span class="s">'S'</span><span class="p">):</span> <span class="mf">0.2</span><span class="p">,</span>
<span class="p">(</span><span class="s">'S'</span><span class="p">,</span> <span class="s">'S'</span><span class="p">):</span> <span class="mf">0.25</span><span class="p">,</span>
<span class="p">}</span></div>
</pre></div>
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