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<h1>Source code for MMTK.Proteins</h1><div class="highlight"><pre>
<span class="c"># This module implements classes for peptide chains and proteins.</span>
<span class="c">#</span>
<span class="c"># Written by Konrad Hinsen</span>
<span class="c">#</span>
<span class="sd">"""</span>
<span class="sd">Peptide chains and proteins</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">Biopolymers</span><span class="p">,</span> <span class="n">Bonds</span><span class="p">,</span> <span class="n">ChemicalObjects</span><span class="p">,</span> <span class="n">Collections</span><span class="p">,</span> \
<span class="n">ConfigIO</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">from</span> <span class="nn">MMTK.Biopolymers</span> <span class="kn">import</span> <span class="n">defineAminoAcidResidue</span>
<span class="c">#</span>
<span class="c"># Residues are special groups</span>
<span class="c">#</span>
<div class="viewcode-block" id="Residue"><a class="viewcode-back" href="../../modules.html#MMTK.Proteins.Residue">[docs]</a><span class="k">class</span> <span class="nc">Residue</span><span class="p">(</span><span class="n">Biopolymers</span><span class="o">.</span><span class="n">Residue</span><span class="p">):</span>
<span class="sd">"""</span>
<span class="sd"> Amino acid residue</span>
<span class="sd"> Amino acid residues are a special kind of group. They are defined</span>
<span class="sd"> in the chemical database. Each residue has two subgroups</span>
<span class="sd"> ('peptide' and 'sidechain') and is usually connected to other</span>
<span class="sd"> residues to form a peptide chain. The database contains three</span>
<span class="sd"> variants of each residue (N-terminal, C-terminal,</span>
<span class="sd"> non-terminal) and various models (all-atom, united-atom,</span>
<span class="sd"> |C_alpha|).</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">name</span> <span class="o">=</span> <span class="bp">None</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"> :param name: the name of the residue in the chemical database. This</span>
<span class="sd"> is the full name of the residue plus the suffix</span>
<span class="sd"> "_nt" or "_ct" for the terminal variants.</span>
<span class="sd"> :type name: str</span>
<span class="sd"> :param model: one of "all" (all-atom), "none" (no hydrogens),</span>
<span class="sd"> "polar" (united-atom with only polar hydrogens),</span>
<span class="sd"> "polar_charmm" (like "polar", but defining</span>
<span class="sd"> polar hydrogens like in the CHARMM force field),</span>
<span class="sd"> "polar_opls" (like "polar", but defining</span>
<span class="sd"> polar hydrogens like in the latest OPLS force field),</span>
<span class="sd"> "calpha" (only the |C_alpha| atom).</span>
<span class="sd"> :type model: str</span>
<span class="sd"> """</span>
<span class="k">if</span> <span class="n">name</span> <span class="ow">is</span> <span class="ow">not</span> <span class="bp">None</span><span class="p">:</span>
<span class="n">blueprint</span> <span class="o">=</span> <span class="n">_residueBlueprint</span><span class="p">(</span><span class="n">name</span><span class="p">,</span> <span class="n">model</span><span class="p">)</span>
<span class="n">ChemicalObjects</span><span class="o">.</span><span class="n">Group</span><span class="o">.</span><span class="n">__init__</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">blueprint</span><span class="p">)</span>
<span class="bp">self</span><span class="o">.</span><span class="n">model</span> <span class="o">=</span> <span class="n">model</span>
<span class="bp">self</span><span class="o">.</span><span class="n">_init</span><span class="p">()</span>
<span class="k">def</span> <span class="nf">_init</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span>
<span class="n">Biopolymers</span><span class="o">.</span><span class="n">Residue</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="c"># create peptide attribute for calpha model</span>
<span class="k">if</span> <span class="bp">self</span><span class="o">.</span><span class="n">model</span> <span class="o">==</span> <span class="s">'calpha'</span><span class="p">:</span>
<span class="bp">self</span><span class="o">.</span><span class="n">peptide</span> <span class="o">=</span> <span class="bp">self</span>
<span class="k">def</span> <span class="nf">isNTerminus</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span>
<span class="k">return</span> <span class="nb">hasattr</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">peptide</span><span class="p">,</span> <span class="s">'H_3'</span><span class="p">)</span>
<span class="k">def</span> <span class="nf">isCTerminus</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span>
<span class="k">return</span> <span class="nb">hasattr</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">peptide</span><span class="p">,</span> <span class="s">'O_2'</span><span class="p">)</span>
<span class="k">def</span> <span class="nf">_makeCystine</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span>
<span class="k">if</span> <span class="bp">self</span><span class="o">.</span><span class="n">model</span> <span class="o">==</span> <span class="s">'calpha'</span><span class="p">:</span>
<span class="k">return</span> <span class="bp">self</span>
<span class="k">if</span> <span class="bp">self</span><span class="o">.</span><span class="n">symbol</span><span class="o">.</span><span class="n">lower</span><span class="p">()</span> <span class="o">!=</span> <span class="s">'cys'</span><span class="p">:</span>
<span class="k">raise</span> <span class="ne">ValueError</span><span class="p">(</span><span class="sb">`self`</span> <span class="o">+</span> <span class="s">" is not cysteine."</span><span class="p">)</span>
<span class="n">new_residue</span> <span class="o">=</span> <span class="s">'cystine_ss'</span>
<span class="k">if</span> <span class="bp">self</span><span class="o">.</span><span class="n">isNTerminus</span><span class="p">():</span>
<span class="n">new_residue</span> <span class="o">=</span> <span class="n">new_residue</span> <span class="o">+</span> <span class="s">'_nt'</span>
<span class="k">elif</span> <span class="bp">self</span><span class="o">.</span><span class="n">isCTerminus</span><span class="p">():</span>
<span class="n">new_residue</span> <span class="o">=</span> <span class="n">new_residue</span> <span class="o">+</span> <span class="s">'_ct'</span>
<span class="n">new_residue</span> <span class="o">=</span> <span class="n">Residue</span><span class="p">(</span><span class="n">new_residue</span><span class="p">,</span> <span class="bp">self</span><span class="o">.</span><span class="n">model</span><span class="p">)</span>
<span class="k">for</span> <span class="n">g</span> <span class="ow">in</span> <span class="p">[</span><span class="s">'peptide'</span><span class="p">,</span> <span class="s">'sidechain'</span><span class="p">]:</span>
<span class="n">g_old</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">g</span><span class="p">)</span>
<span class="n">g_new</span> <span class="o">=</span> <span class="nb">getattr</span><span class="p">(</span><span class="n">new_residue</span><span class="p">,</span> <span class="n">g</span><span class="p">)</span>
<span class="k">for</span> <span class="n">a</span> <span class="ow">in</span> <span class="nb">getattr</span><span class="p">(</span><span class="n">g_new</span><span class="p">,</span> <span class="s">'atoms'</span><span class="p">):</span>
<span class="n">set_method</span> <span class="o">=</span> <span class="nb">getattr</span><span class="p">(</span><span class="nb">getattr</span><span class="p">(</span><span class="n">g_new</span><span class="p">,</span> <span class="n">a</span><span class="o">.</span><span class="n">name</span><span class="p">),</span> <span class="s">'setPosition'</span><span class="p">)</span>
<span class="n">set_method</span><span class="p">(</span><span class="nb">getattr</span><span class="p">(</span><span class="nb">getattr</span><span class="p">(</span><span class="n">g_old</span><span class="p">,</span> <span class="n">a</span><span class="o">.</span><span class="n">name</span><span class="p">),</span> <span class="s">'position'</span><span class="p">)())</span>
<span class="k">return</span> <span class="n">new_residue</span>
<span class="k">def</span> <span class="nf">isSubsetModel</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span>
<span class="k">return</span> <span class="bp">self</span><span class="o">.</span><span class="n">model</span> <span class="o">==</span> <span class="s">'calpha'</span>
<div class="viewcode-block" id="Residue.backbone"><a class="viewcode-back" href="../../modules.html#MMTK.Proteins.Residue.backbone">[docs]</a> <span class="k">def</span> <span class="nf">backbone</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span>
<span class="sd">"""</span>
<span class="sd"> :returns: the peptide group</span>
<span class="sd"> :rtype: :class:`~MMTK.ChemicalObjects.Group`</span>
<span class="sd"> """</span>
<span class="k">return</span> <span class="bp">self</span><span class="o">.</span><span class="n">peptide</span>
</div>
<div class="viewcode-block" id="Residue.sidechains"><a class="viewcode-back" href="../../modules.html#MMTK.Proteins.Residue.sidechains">[docs]</a> <span class="k">def</span> <span class="nf">sidechains</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span>
<span class="sd">"""</span>
<span class="sd"> :returns: the sidechain group</span>
<span class="sd"> :rtype: :class:`~MMTK.ChemicalObjects.Group`</span>
<span class="sd"> """</span>
<span class="k">return</span> <span class="bp">self</span><span class="o">.</span><span class="n">sidechain</span>
</div>
<div class="viewcode-block" id="Residue.phiPsi"><a class="viewcode-back" href="../../modules.html#MMTK.Proteins.Residue.phiPsi">[docs]</a> <span class="k">def</span> <span class="nf">phiPsi</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">conf</span> <span class="o">=</span> <span class="bp">None</span><span class="p">):</span>
<span class="sd">"""</span>
<span class="sd"> :returns: the values of the backbone dihedral angles phi and psi.</span>
<span class="sd"> :rtype: tuple (float, float)</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">universe</span><span class="p">()</span>
<span class="k">if</span> <span class="n">universe</span> <span class="ow">is</span> <span class="bp">None</span><span class="p">:</span>
<span class="n">universe</span> <span class="o">=</span> <span class="n">Universe</span><span class="o">.</span><span class="n">InfiniteUniverse</span><span class="p">()</span>
<span class="n">C</span> <span class="o">=</span> <span class="bp">None</span>
<span class="k">for</span> <span class="n">a</span> <span class="ow">in</span> <span class="bp">self</span><span class="o">.</span><span class="n">peptide</span><span class="o">.</span><span class="n">N</span><span class="o">.</span><span class="n">bondedTo</span><span class="p">():</span>
<span class="k">if</span> <span class="n">a</span><span class="o">.</span><span class="n">parent</span><span class="o">.</span><span class="n">parent</span> <span class="o">!=</span> <span class="bp">self</span><span class="p">:</span>
<span class="n">C</span> <span class="o">=</span> <span class="n">a</span>
<span class="k">break</span>
<span class="k">if</span> <span class="n">C</span> <span class="ow">is</span> <span class="bp">None</span><span class="p">:</span>
<span class="n">phi</span> <span class="o">=</span> <span class="bp">None</span>
<span class="k">else</span><span class="p">:</span>
<span class="n">phi</span> <span class="o">=</span> <span class="n">universe</span><span class="o">.</span><span class="n">dihedral</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">peptide</span><span class="o">.</span><span class="n">C</span><span class="p">,</span> <span class="bp">self</span><span class="o">.</span><span class="n">peptide</span><span class="o">.</span><span class="n">C_alpha</span><span class="p">,</span>
<span class="bp">self</span><span class="o">.</span><span class="n">peptide</span><span class="o">.</span><span class="n">N</span><span class="p">,</span> <span class="n">C</span><span class="p">,</span> <span class="n">conf</span><span class="p">)</span>
<span class="n">N</span> <span class="o">=</span> <span class="bp">None</span>
<span class="k">for</span> <span class="n">a</span> <span class="ow">in</span> <span class="bp">self</span><span class="o">.</span><span class="n">peptide</span><span class="o">.</span><span class="n">C</span><span class="o">.</span><span class="n">bondedTo</span><span class="p">():</span>
<span class="k">if</span> <span class="n">a</span><span class="o">.</span><span class="n">parent</span><span class="o">.</span><span class="n">parent</span> <span class="o">!=</span> <span class="bp">self</span><span class="p">:</span>
<span class="n">N</span> <span class="o">=</span> <span class="n">a</span>
<span class="k">break</span>
<span class="k">if</span> <span class="n">N</span> <span class="ow">is</span> <span class="bp">None</span><span class="p">:</span>
<span class="n">psi</span> <span class="o">=</span> <span class="bp">None</span>
<span class="k">else</span><span class="p">:</span>
<span class="n">psi</span> <span class="o">=</span> <span class="n">universe</span><span class="o">.</span><span class="n">dihedral</span><span class="p">(</span><span class="n">N</span><span class="p">,</span> <span class="bp">self</span><span class="o">.</span><span class="n">peptide</span><span class="o">.</span><span class="n">C</span><span class="p">,</span> <span class="bp">self</span><span class="o">.</span><span class="n">peptide</span><span class="o">.</span><span class="n">C_alpha</span><span class="p">,</span>
<span class="bp">self</span><span class="o">.</span><span class="n">peptide</span><span class="o">.</span><span class="n">N</span><span class="p">,</span> <span class="n">conf</span><span class="p">)</span>
<span class="k">return</span> <span class="n">phi</span><span class="p">,</span> <span class="n">psi</span>
</div>
<div class="viewcode-block" id="Residue.phiAngle"><a class="viewcode-back" href="../../modules.html#MMTK.Proteins.Residue.phiAngle">[docs]</a> <span class="k">def</span> <span class="nf">phiAngle</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span>
<span class="sd">"""</span>
<span class="sd"> :returns: an object representing the phi angle and allowing to modify it</span>
<span class="sd"> :rtype: MMTK.InternalCoordinates.DihedralAngle</span>
<span class="sd"> """</span>
<span class="kn">from</span> <span class="nn">MMTK.InternalCoordinates</span> <span class="kn">import</span> <span class="n">DihedralAngle</span>
<span class="n">C</span> <span class="o">=</span> <span class="bp">None</span>
<span class="k">for</span> <span class="n">a</span> <span class="ow">in</span> <span class="bp">self</span><span class="o">.</span><span class="n">peptide</span><span class="o">.</span><span class="n">N</span><span class="o">.</span><span class="n">bondedTo</span><span class="p">():</span>
<span class="k">if</span> <span class="n">a</span><span class="o">.</span><span class="n">parent</span><span class="o">.</span><span class="n">parent</span> <span class="o">!=</span> <span class="bp">self</span><span class="p">:</span>
<span class="n">C</span> <span class="o">=</span> <span class="n">a</span>
<span class="k">break</span>
<span class="k">if</span> <span class="n">C</span> <span class="ow">is</span> <span class="bp">None</span><span class="p">:</span>
<span class="k">raise</span> <span class="ne">ValueError</span><span class="p">(</span><span class="s">"residue is N-terminus"</span><span class="p">)</span>
<span class="k">return</span> <span class="n">DihedralAngle</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">peptide</span><span class="o">.</span><span class="n">C</span><span class="p">,</span> <span class="bp">self</span><span class="o">.</span><span class="n">peptide</span><span class="o">.</span><span class="n">C_alpha</span><span class="p">,</span>
<span class="bp">self</span><span class="o">.</span><span class="n">peptide</span><span class="o">.</span><span class="n">N</span><span class="p">,</span> <span class="n">C</span><span class="p">)</span>
</div>
<div class="viewcode-block" id="Residue.psiAngle"><a class="viewcode-back" href="../../modules.html#MMTK.Proteins.Residue.psiAngle">[docs]</a> <span class="k">def</span> <span class="nf">psiAngle</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span>
<span class="sd">"""</span>
<span class="sd"> :returns: an object representing the psi angle and allowing to modify it</span>
<span class="sd"> :rtype: MMTK.InternalCoordinates.DihedralAngle</span>
<span class="sd"> """</span>
<span class="kn">from</span> <span class="nn">MMTK.InternalCoordinates</span> <span class="kn">import</span> <span class="n">DihedralAngle</span>
<span class="n">N</span> <span class="o">=</span> <span class="bp">None</span>
<span class="k">for</span> <span class="n">a</span> <span class="ow">in</span> <span class="bp">self</span><span class="o">.</span><span class="n">peptide</span><span class="o">.</span><span class="n">C</span><span class="o">.</span><span class="n">bondedTo</span><span class="p">():</span>
<span class="k">if</span> <span class="n">a</span><span class="o">.</span><span class="n">parent</span><span class="o">.</span><span class="n">parent</span> <span class="o">!=</span> <span class="bp">self</span><span class="p">:</span>
<span class="n">N</span> <span class="o">=</span> <span class="n">a</span>
<span class="k">break</span>
<span class="k">if</span> <span class="n">N</span> <span class="ow">is</span> <span class="bp">None</span><span class="p">:</span>
<span class="k">raise</span> <span class="ne">ValueError</span><span class="p">(</span><span class="s">"residue is C-terminus"</span><span class="p">)</span>
<span class="k">return</span> <span class="n">DihedralAngle</span><span class="p">(</span><span class="n">N</span><span class="p">,</span> <span class="bp">self</span><span class="o">.</span><span class="n">peptide</span><span class="o">.</span><span class="n">C</span><span class="p">,</span> <span class="bp">self</span><span class="o">.</span><span class="n">peptide</span><span class="o">.</span><span class="n">C_alpha</span><span class="p">,</span>
<span class="bp">self</span><span class="o">.</span><span class="n">peptide</span><span class="o">.</span><span class="n">N</span><span class="p">)</span>
</div>
<div class="viewcode-block" id="Residue.chiAngle"><a class="viewcode-back" href="../../modules.html#MMTK.Proteins.Residue.chiAngle">[docs]</a> <span class="k">def</span> <span class="nf">chiAngle</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span>
<span class="sd">"""</span>
<span class="sd"> :returns: an object representing the chi angle and allowing to modify it</span>
<span class="sd"> :rtype: MMTK.InternalCoordinates.DihedralAngle</span>
<span class="sd"> """</span>
<span class="kn">from</span> <span class="nn">MMTK.InternalCoordinates</span> <span class="kn">import</span> <span class="n">DihedralAngle</span>
<span class="k">try</span><span class="p">:</span>
<span class="n">C_beta</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">sidechain</span><span class="o">.</span><span class="n">C_beta</span>
<span class="k">except</span> <span class="ne">AttributeError</span><span class="p">:</span>
<span class="k">raise</span> <span class="ne">ValueError</span><span class="p">(</span><span class="s">"no C_beta in sidechain"</span><span class="p">)</span>
<span class="n">X</span> <span class="o">=</span> <span class="bp">None</span>
<span class="k">for</span> <span class="n">atom_name</span> <span class="ow">in</span> <span class="p">[</span><span class="s">'C_gamma'</span><span class="p">,</span> <span class="s">'C_gamma_1'</span><span class="p">,</span> <span class="s">'S_gamma'</span><span class="p">,</span>
<span class="s">'O_gamma'</span><span class="p">,</span> <span class="s">'O_gamma_1'</span><span class="p">,</span> <span class="s">'H_beta_1'</span><span class="p">]:</span>
<span class="k">try</span><span class="p">:</span>
<span class="n">X</span> <span class="o">=</span> <span class="nb">getattr</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">sidechain</span><span class="p">,</span> <span class="n">atom_name</span><span class="p">)</span>
<span class="k">break</span>
<span class="k">except</span> <span class="ne">AttributeError</span><span class="p">:</span>
<span class="k">pass</span>
<span class="k">if</span> <span class="n">X</span> <span class="ow">is</span> <span class="bp">None</span><span class="p">:</span>
<span class="k">raise</span> <span class="ne">ValueError</span><span class="p">(</span><span class="s">"no sidechain reference atom found"</span><span class="p">)</span>
<span class="k">return</span> <span class="n">DihedralAngle</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">peptide</span><span class="o">.</span><span class="n">N</span><span class="p">,</span> <span class="bp">self</span><span class="o">.</span><span class="n">peptide</span><span class="o">.</span><span class="n">C_alpha</span><span class="p">,</span>
<span class="n">C_beta</span><span class="p">,</span> <span class="n">X</span><span class="p">)</span>
</div></div>
<span class="k">def</span> <span class="nf">_residueBlueprint</span><span class="p">(</span><span class="n">name</span><span class="p">,</span> <span class="n">model</span><span class="p">):</span>
<span class="k">try</span><span class="p">:</span>
<span class="n">blueprint</span> <span class="o">=</span> <span class="n">_residue_blueprints</span><span class="p">[(</span><span class="n">name</span><span class="p">,</span> <span class="n">model</span><span class="p">)]</span>
<span class="k">except</span> <span class="ne">KeyError</span><span class="p">:</span>
<span class="k">if</span> <span class="n">model</span> <span class="o">==</span> <span class="s">'polar'</span><span class="p">:</span>
<span class="n">name</span> <span class="o">=</span> <span class="n">name</span> <span class="o">+</span> <span class="s">'_uni'</span>
<span class="k">elif</span> <span class="n">model</span> <span class="o">==</span> <span class="s">'polar_charmm'</span><span class="p">:</span>
<span class="n">name</span> <span class="o">=</span> <span class="n">name</span> <span class="o">+</span> <span class="s">'_uni2'</span>
<span class="k">elif</span> <span class="n">model</span> <span class="o">==</span> <span class="s">'polar_oldopls'</span><span class="p">:</span>
<span class="n">name</span> <span class="o">=</span> <span class="n">name</span> <span class="o">+</span> <span class="s">'_uni3'</span>
<span class="k">elif</span> <span class="n">model</span> <span class="o">==</span> <span class="s">'none'</span><span class="p">:</span>
<span class="n">name</span> <span class="o">=</span> <span class="n">name</span> <span class="o">+</span> <span class="s">'_noh'</span>
<span class="k">elif</span> <span class="n">model</span> <span class="o">==</span> <span class="s">'calpha'</span><span class="p">:</span>
<span class="n">name</span> <span class="o">=</span> <span class="n">name</span> <span class="o">+</span> <span class="s">'_calpha'</span>
<span class="n">blueprint</span> <span class="o">=</span> <span class="n">Database</span><span class="o">.</span><span class="n">BlueprintGroup</span><span class="p">(</span><span class="n">name</span><span class="p">)</span>
<span class="n">_residue_blueprints</span><span class="p">[(</span><span class="n">name</span><span class="p">,</span> <span class="n">model</span><span class="p">)]</span> <span class="o">=</span> <span class="n">blueprint</span>
<span class="k">return</span> <span class="n">blueprint</span>
<span class="n">_residue_blueprints</span> <span class="o">=</span> <span class="p">{}</span>
<span class="c">#</span>
<span class="c"># Peptide chains are molecules with added features.</span>
<span class="c">#</span>
<div class="viewcode-block" id="PeptideChain"><a class="viewcode-back" href="../../modules.html#MMTK.Proteins.PeptideChain">[docs]</a><span class="k">class</span> <span class="nc">PeptideChain</span><span class="p">(</span><span class="n">Biopolymers</span><span class="o">.</span><span class="n">ResidueChain</span><span class="p">):</span>
<span class="sd">"""</span>
<span class="sd"> Peptide chain</span>
<span class="sd"> Peptide chains consist of amino acid residues that are linked</span>
<span class="sd"> by peptide bonds. They are a special kind of molecule, i.e.</span>
<span class="sd"> all molecule operations are available.</span>
<span class="sd"> Peptide chains act as sequences of residues. If p is a PeptideChain</span>
<span class="sd"> object, then</span>
<span class="sd"> * len(p) yields the number of residues</span>
<span class="sd"> * p[i] yields residue number i</span>
<span class="sd"> * p[i:j] yields the subchain from residue number i up to</span>
<span class="sd"> but excluding residue number j</span>
<span class="sd"> :param sequence: the amino acid sequence. This can be a string</span>
<span class="sd"> containing the one-letter codes, or a list</span>
<span class="sd"> of three-letter codes, or a</span>
<span class="sd"> :class:`~MMTK.PDB.PDBPeptideChain` object.</span>
<span class="sd"> If a PDBPeptideChain object is supplied, the atomic</span>
<span class="sd"> positions it contains are assigned to the atoms</span>
<span class="sd"> of the newly generated peptide chain, otherwise the</span>
<span class="sd"> positions of all atoms are undefined.</span>
<span class="sd"> :keyword model: one of "all" (all-atom), "no_hydrogens" or "none"</span>
<span class="sd"> (no hydrogens), "polar_hydrogens" or "polar"</span>
<span class="sd"> (united-atom with only polar hydrogens),</span>
<span class="sd"> "polar_charmm" (like "polar", but defining</span>
<span class="sd"> polar hydrogens like in the CHARMM force field),</span>
<span class="sd"> "polar_opls" (like "polar", but defining</span>
<span class="sd"> polar hydrogens like in the latest OPLS force field),</span>
<span class="sd"> "calpha" (only the |C_alpha| atom of each residue).</span>
<span class="sd"> Default is "all".</span>
<span class="sd"> :type model: str</span>
<span class="sd"> :keyword n_terminus: if True, the first residue is constructed</span>
<span class="sd"> using the N-terminal variant, if False the</span>
<span class="sd"> non-terminal version is used. Default is True.</span>
<span class="sd"> :type n_terminus: bool</span>
<span class="sd"> :keyword c_terminus: if True, the last residue is constructed</span>
<span class="sd"> using the C-terminal variant, if False the</span>
<span class="sd"> non-terminal version is used. Default is True.</span>
<span class="sd"> :type c_terminus: bool</span>
<span class="sd"> :keyword circular: if True, a peptide bond is constructed</span>
<span class="sd"> between the first and the last residues.</span>
<span class="sd"> Default is False.</span>
<span class="sd"> :type circular: bool</span>
<span class="sd"> :keyword name: a name for the chain (a string)</span>
<span class="sd"> :type name: str</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">sequence</span><span class="p">,</span> <span class="o">**</span><span class="n">properties</span><span class="p">):</span>
<span class="k">if</span> <span class="n">sequence</span> <span class="ow">is</span> <span class="ow">not</span> <span class="bp">None</span><span class="p">:</span>
<span class="n">model</span> <span class="o">=</span> <span class="s">'all'</span>
<span class="k">if</span> <span class="n">properties</span><span class="o">.</span><span class="n">has_key</span><span class="p">(</span><span class="s">'model'</span><span class="p">):</span>
<span class="n">model</span> <span class="o">=</span> <span class="n">properties</span><span class="p">[</span><span class="s">'model'</span><span class="p">]</span><span class="o">.</span><span class="n">lower</span><span class="p">()</span>
<span class="k">elif</span> <span class="n">properties</span><span class="o">.</span><span class="n">has_key</span><span class="p">(</span><span class="s">'hydrogens'</span><span class="p">):</span>
<span class="n">model</span> <span class="o">=</span> <span class="n">properties</span><span class="p">[</span><span class="s">'hydrogens'</span><span class="p">]</span>
<span class="k">if</span> <span class="n">model</span> <span class="o">==</span> <span class="mi">1</span><span class="p">:</span> <span class="n">model</span> <span class="o">=</span> <span class="s">'all'</span>
<span class="k">elif</span> <span class="n">model</span> <span class="o">==</span> <span class="mi">0</span><span class="p">:</span> <span class="n">model</span> <span class="o">=</span> <span class="s">'none'</span>
<span class="k">else</span><span class="p">:</span> <span class="n">model</span> <span class="o">=</span> <span class="n">model</span><span class="o">.</span><span class="n">lower</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">model</span> <span class="o">=</span> <span class="s">'none'</span>
<span class="k">elif</span> <span class="n">model</span> <span class="o">==</span> <span class="s">'polar_hydrogens'</span><span class="p">:</span>
<span class="n">model</span> <span class="o">=</span> <span class="s">'polar'</span>
<span class="n">n_term</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">binaryProperty</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="bp">True</span><span class="p">)</span>
<span class="n">c_term</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">binaryProperty</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="bp">True</span><span class="p">)</span>
<span class="n">circular</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">binaryProperty</span><span class="p">(</span><span class="n">properties</span><span class="p">,</span> <span class="s">'circular'</span><span class="p">,</span> <span class="bp">False</span><span class="p">)</span>
<span class="bp">self</span><span class="o">.</span><span class="n">version_spec</span> <span class="o">=</span> <span class="p">{</span><span class="s">'n_terminus'</span><span class="p">:</span> <span class="n">n_term</span><span class="p">,</span>
<span class="s">'c_terminus'</span><span class="p">:</span> <span class="n">c_term</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="s">'circular'</span><span class="p">:</span> <span class="n">circular</span><span class="p">}</span>
<span class="k">if</span> <span class="nb">type</span><span class="p">(</span><span class="n">sequence</span><span class="p">[</span><span class="mi">0</span><span class="p">])</span> <span class="o">==</span> <span class="nb">type</span><span class="p">(</span><span class="s">''</span><span class="p">):</span>
<span class="n">conf</span> <span class="o">=</span> <span class="bp">None</span>
<span class="n">numbers</span> <span class="o">=</span> <span class="nb">range</span><span class="p">(</span><span class="nb">len</span><span class="p">(</span><span class="n">sequence</span><span class="p">))</span>
<span class="k">else</span><span class="p">:</span>
<span class="n">conf</span> <span class="o">=</span> <span class="n">sequence</span>
<span class="n">sequence</span> <span class="o">=</span> <span class="n">conf</span><span class="o">.</span><span class="n">sequence</span><span class="p">()</span>
<span class="n">numbers</span> <span class="o">=</span> <span class="p">[</span><span class="n">r</span><span class="o">.</span><span class="n">number</span> <span class="k">for</span> <span class="n">r</span> <span class="ow">in</span> <span class="n">conf</span><span class="p">]</span>
<span class="n">sequence</span> <span class="o">=</span> <span class="nb">map</span><span class="p">(</span><span class="n">Biopolymers</span><span class="o">.</span><span class="n">_fullName</span><span class="p">,</span> <span class="n">sequence</span><span class="p">)</span>
<span class="k">if</span> <span class="n">model</span> <span class="o">!=</span> <span class="s">'calpha'</span><span class="p">:</span>
<span class="k">if</span> <span class="n">n_term</span><span class="p">:</span>
<span class="n">sequence</span><span class="p">[</span><span class="mi">0</span><span class="p">]</span> <span class="o">=</span> <span class="n">sequence</span><span class="p">[</span><span class="mi">0</span><span class="p">]</span> <span class="o">+</span> <span class="s">'_nt'</span>
<span class="k">if</span> <span class="n">c_term</span><span class="p">:</span>
<span class="n">sequence</span><span class="p">[</span><span class="o">-</span><span class="mi">1</span><span class="p">]</span> <span class="o">=</span> <span class="n">sequence</span><span class="p">[</span><span class="o">-</span><span class="mi">1</span><span class="p">]</span> <span class="o">+</span> <span class="s">'_ct'</span>
<span class="bp">self</span><span class="o">.</span><span class="n">groups</span> <span class="o">=</span> <span class="p">[]</span>
<span class="n">n</span> <span class="o">=</span> <span class="mi">0</span>
<span class="k">for</span> <span class="n">residue</span><span class="p">,</span> <span class="n">number</span> <span class="ow">in</span> <span class="nb">zip</span><span class="p">(</span><span class="n">sequence</span><span class="p">,</span> <span class="n">numbers</span><span class="p">):</span>
<span class="n">n</span> <span class="o">=</span> <span class="n">n</span> <span class="o">+</span> <span class="mi">1</span>
<span class="n">r</span> <span class="o">=</span> <span class="n">Residue</span><span class="p">(</span><span class="n">residue</span><span class="p">,</span> <span class="n">model</span><span class="p">)</span>
<span class="n">r</span><span class="o">.</span><span class="n">name</span> <span class="o">=</span> <span class="n">r</span><span class="o">.</span><span class="n">symbol</span> <span class="o">+</span> <span class="nb">str</span><span class="p">(</span><span class="n">number</span><span class="p">)</span>
<span class="n">r</span><span class="o">.</span><span class="n">sequence_number</span> <span class="o">=</span> <span class="n">n</span>
<span class="n">r</span><span class="o">.</span><span class="n">parent</span> <span class="o">=</span> <span class="bp">self</span>
<span class="bp">self</span><span class="o">.</span><span class="n">groups</span><span class="o">.</span><span class="n">append</span><span class="p">(</span><span class="n">r</span><span class="p">)</span>
<span class="bp">self</span><span class="o">.</span><span class="n">_setupChain</span><span class="p">(</span><span class="n">circular</span><span class="p">,</span> <span class="n">properties</span><span class="p">,</span> <span class="n">conf</span><span class="p">)</span>
<span class="n">is_peptide_chain</span> <span class="o">=</span> <span class="bp">True</span>
<span class="k">def</span> <span class="nf">__getslice__</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">first</span><span class="p">,</span> <span class="n">last</span><span class="p">):</span>
<span class="k">return</span> <span class="n">SubChain</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="bp">self</span><span class="o">.</span><span class="n">groups</span><span class="p">[</span><span class="n">first</span><span class="p">:</span><span class="n">last</span><span class="p">])</span>
<div class="viewcode-block" id="PeptideChain.sequence"><a class="viewcode-back" href="../../modules.html#MMTK.Proteins.PeptideChain.sequence">[docs]</a> <span class="k">def</span> <span class="nf">sequence</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span>
<span class="sd">"""</span>
<span class="sd"> :returns: the primary sequence as a list of three-letter</span>
<span class="sd"> residue codes.</span>
<span class="sd"> :rtype: list</span>
<span class="sd"> """</span>
<span class="k">return</span> <span class="p">[</span><span class="n">r</span><span class="o">.</span><span class="n">symbol</span> <span class="k">for</span> <span class="n">r</span> <span class="ow">in</span> <span class="bp">self</span><span class="o">.</span><span class="n">groups</span><span class="p">]</span>
</div>
<div class="viewcode-block" id="PeptideChain.backbone"><a class="viewcode-back" href="../../modules.html#MMTK.Proteins.PeptideChain.backbone">[docs]</a> <span class="k">def</span> <span class="nf">backbone</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span>
<span class="sd">"""</span>
<span class="sd"> :returns: the peptide groups of all residues</span>
<span class="sd"> :rtype: :class:`~MMTK.Collections.Collection`</span>
<span class="sd"> """</span>
<span class="n">backbone</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">r</span> <span class="ow">in</span> <span class="bp">self</span><span class="o">.</span><span class="n">groups</span><span class="p">:</span>
<span class="k">try</span><span class="p">:</span>
<span class="n">backbone</span><span class="o">.</span><span class="n">addObject</span><span class="p">(</span><span class="n">r</span><span class="o">.</span><span class="n">peptide</span><span class="p">)</span>
<span class="k">except</span> <span class="ne">AttributeError</span><span class="p">:</span>
<span class="k">pass</span>
<span class="k">return</span> <span class="n">backbone</span>
</div>
<div class="viewcode-block" id="PeptideChain.sidechains"><a class="viewcode-back" href="../../modules.html#MMTK.Proteins.PeptideChain.sidechains">[docs]</a> <span class="k">def</span> <span class="nf">sidechains</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span>
<span class="sd">"""</span>
<span class="sd"> :returns: the sidechain groups of all residues</span>
<span class="sd"> :rtype: :class:`~MMTK.Collections.Collection`</span>
<span class="sd"> """</span>
<span class="n">sidechains</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">r</span> <span class="ow">in</span> <span class="bp">self</span><span class="o">.</span><span class="n">groups</span><span class="p">:</span>
<span class="k">try</span><span class="p">:</span>
<span class="n">sidechains</span><span class="o">.</span><span class="n">addObject</span><span class="p">(</span><span class="n">r</span><span class="o">.</span><span class="n">sidechain</span><span class="p">)</span>
<span class="k">except</span> <span class="ne">AttributeError</span><span class="p">:</span>
<span class="k">pass</span>
<span class="k">return</span> <span class="n">sidechains</span>
</div>
<div class="viewcode-block" id="PeptideChain.phiPsi"><a class="viewcode-back" href="../../modules.html#MMTK.Proteins.PeptideChain.phiPsi">[docs]</a> <span class="k">def</span> <span class="nf">phiPsi</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">conf</span> <span class="o">=</span> <span class="bp">None</span><span class="p">):</span>
<span class="sd">"""</span>
<span class="sd"> :returns: a list of the (phi, psi) backbone angles for each residue</span>
<span class="sd"> :rtype: list of tuple of float</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">universe</span><span class="p">()</span>
<span class="k">if</span> <span class="n">universe</span> <span class="ow">is</span> <span class="bp">None</span><span class="p">:</span>
<span class="n">universe</span> <span class="o">=</span> <span class="n">Universe</span><span class="o">.</span><span class="n">InfiniteUniverse</span><span class="p">()</span>
<span class="n">angles</span> <span class="o">=</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="bp">self</span><span class="p">)):</span>
<span class="n">r</span> <span class="o">=</span> <span class="bp">self</span><span class="p">[</span><span class="n">i</span><span class="p">]</span>
<span class="k">if</span> <span class="n">i</span> <span class="o">==</span> <span class="mi">0</span><span class="p">:</span>
<span class="n">phi</span> <span class="o">=</span> <span class="bp">None</span>
<span class="k">else</span><span class="p">:</span>
<span class="n">phi</span> <span class="o">=</span> <span class="n">universe</span><span class="o">.</span><span class="n">dihedral</span><span class="p">(</span><span class="n">r</span><span class="o">.</span><span class="n">peptide</span><span class="o">.</span><span class="n">C</span><span class="p">,</span> <span class="n">r</span><span class="o">.</span><span class="n">peptide</span><span class="o">.</span><span class="n">C_alpha</span><span class="p">,</span>
<span class="n">r</span><span class="o">.</span><span class="n">peptide</span><span class="o">.</span><span class="n">N</span><span class="p">,</span>
<span class="bp">self</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">peptide</span><span class="o">.</span><span class="n">C</span><span class="p">,</span> <span class="n">conf</span><span class="p">)</span>
<span class="k">if</span> <span class="n">i</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="o">-</span><span class="mi">1</span><span class="p">:</span>
<span class="n">psi</span> <span class="o">=</span> <span class="bp">None</span>
<span class="k">else</span><span class="p">:</span>
<span class="n">psi</span> <span class="o">=</span> <span class="n">universe</span><span class="o">.</span><span class="n">dihedral</span><span class="p">(</span><span class="bp">self</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">peptide</span><span class="o">.</span><span class="n">N</span><span class="p">,</span>
<span class="n">r</span><span class="o">.</span><span class="n">peptide</span><span class="o">.</span><span class="n">C</span><span class="p">,</span> <span class="n">r</span><span class="o">.</span><span class="n">peptide</span><span class="o">.</span><span class="n">C_alpha</span><span class="p">,</span>
<span class="n">r</span><span class="o">.</span><span class="n">peptide</span><span class="o">.</span><span class="n">N</span><span class="p">,</span> <span class="n">conf</span><span class="p">)</span>
<span class="n">angles</span><span class="o">.</span><span class="n">append</span><span class="p">((</span><span class="n">phi</span><span class="p">,</span> <span class="n">psi</span><span class="p">))</span>
<span class="k">return</span> <span class="n">angles</span>
</div>
<div class="viewcode-block" id="PeptideChain.replaceResidue"><a class="viewcode-back" href="../../modules.html#MMTK.Proteins.PeptideChain.replaceResidue">[docs]</a> <span class="k">def</span> <span class="nf">replaceResidue</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">r_old</span><span class="p">,</span> <span class="n">r_new</span><span class="p">):</span>
<span class="sd">"""</span>
<span class="sd"> :param r_old: the residue to be replaced (must be part of the chain)</span>
<span class="sd"> :type r_old: Residue</span>
<span class="sd"> :param r_new: the residue that replaces r_old</span>
<span class="sd"> :type r_new: Residue</span>
<span class="sd"> """</span>
<span class="n">n</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">groups</span><span class="o">.</span><span class="n">index</span><span class="p">(</span><span class="n">r_old</span><span class="p">)</span>
<span class="k">for</span> <span class="n">a</span> <span class="ow">in</span> <span class="n">r_old</span><span class="o">.</span><span class="n">atoms</span><span class="p">:</span>
<span class="bp">self</span><span class="o">.</span><span class="n">atoms</span><span class="o">.</span><span class="n">remove</span><span class="p">(</span><span class="n">a</span><span class="p">)</span>
<span class="n">obsolete_bonds</span> <span class="o">=</span> <span class="p">[]</span>
<span class="k">for</span> <span class="n">b</span> <span class="ow">in</span> <span class="bp">self</span><span class="o">.</span><span class="n">bonds</span><span class="p">:</span>
<span class="k">if</span> <span class="n">b</span><span class="o">.</span><span class="n">a1</span> <span class="ow">in</span> <span class="n">r_old</span><span class="o">.</span><span class="n">atoms</span> <span class="ow">or</span> <span class="n">b</span><span class="o">.</span><span class="n">a2</span> <span class="ow">in</span> <span class="n">r_old</span><span class="o">.</span><span class="n">atoms</span><span class="p">:</span>
<span class="n">obsolete_bonds</span><span class="o">.</span><span class="n">append</span><span class="p">(</span><span class="n">b</span><span class="p">)</span>
<span class="k">for</span> <span class="n">b</span> <span class="ow">in</span> <span class="n">obsolete_bonds</span><span class="p">:</span>
<span class="bp">self</span><span class="o">.</span><span class="n">bonds</span><span class="o">.</span><span class="n">remove</span><span class="p">(</span><span class="n">b</span><span class="p">)</span>
<span class="n">r_old</span><span class="o">.</span><span class="n">parent</span> <span class="o">=</span> <span class="bp">None</span>
<span class="bp">self</span><span class="o">.</span><span class="n">atoms</span><span class="o">.</span><span class="n">extend</span><span class="p">(</span><span class="n">r_new</span><span class="o">.</span><span class="n">atoms</span><span class="p">)</span>
<span class="bp">self</span><span class="o">.</span><span class="n">bonds</span><span class="o">.</span><span class="n">extend</span><span class="p">(</span><span class="n">r_new</span><span class="o">.</span><span class="n">bonds</span><span class="p">)</span>
<span class="n">r_new</span><span class="o">.</span><span class="n">sequence_number</span> <span class="o">=</span> <span class="n">n</span><span class="o">+</span><span class="mi">1</span>
<span class="n">r_new</span><span class="o">.</span><span class="n">name</span> <span class="o">=</span> <span class="n">r_new</span><span class="o">.</span><span class="n">symbol</span><span class="o">+</span><span class="sb">`n+1`</span>
<span class="n">r_new</span><span class="o">.</span><span class="n">parent</span> <span class="o">=</span> <span class="bp">self</span>
<span class="bp">self</span><span class="o">.</span><span class="n">groups</span><span class="p">[</span><span class="n">n</span><span class="p">]</span> <span class="o">=</span> <span class="n">r_new</span>
<span class="k">if</span> <span class="n">n</span> <span class="o">></span> <span class="mi">0</span><span class="p">:</span>
<span class="n">peptide_old</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">bonds</span><span class="o">.</span><span class="n">bondsOf</span><span class="p">(</span><span class="n">r_old</span><span class="o">.</span><span class="n">peptide</span><span class="o">.</span><span class="n">N</span><span class="p">)</span>
<span class="k">if</span> <span class="n">peptide_old</span><span class="p">:</span>
<span class="bp">self</span><span class="o">.</span><span class="n">bonds</span><span class="o">.</span><span class="n">remove</span><span class="p">(</span><span class="n">peptide_old</span><span class="p">[</span><span class="mi">0</span><span class="p">])</span>
<span class="k">if</span> <span class="ow">not</span> <span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">groups</span><span class="p">[</span><span class="n">n</span><span class="o">-</span><span class="mi">1</span><span class="p">]</span><span class="o">.</span><span class="n">isCTerminus</span><span class="p">()</span>
<span class="ow">or</span> <span class="bp">self</span><span class="o">.</span><span class="n">groups</span><span class="p">[</span><span class="n">n</span><span class="p">]</span><span class="o">.</span><span class="n">isNTerminus</span><span class="p">()):</span>
<span class="c"># ConnectedChain objects can have N/C-terminal</span>
<span class="c"># residues inside the (virtual) chain, so the</span>
<span class="c"># test is necessary.</span>
<span class="bp">self</span><span class="o">.</span><span class="n">bonds</span><span class="o">.</span><span class="n">append</span><span class="p">(</span><span class="n">Bonds</span><span class="o">.</span><span class="n">Bond</span><span class="p">((</span><span class="bp">self</span><span class="o">.</span><span class="n">groups</span><span class="p">[</span><span class="n">n</span><span class="o">-</span><span class="mi">1</span><span class="p">]</span><span class="o">.</span><span class="n">peptide</span><span class="o">.</span><span class="n">C</span><span class="p">,</span>
<span class="bp">self</span><span class="o">.</span><span class="n">groups</span><span class="p">[</span><span class="n">n</span><span class="p">]</span><span class="o">.</span><span class="n">peptide</span><span class="o">.</span><span class="n">N</span><span class="p">)))</span>
<span class="k">if</span> <span class="n">n</span> <span class="o"><</span> <span class="nb">len</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">groups</span><span class="p">)</span><span class="o">-</span><span class="mi">1</span><span class="p">:</span>
<span class="n">peptide_old</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">bonds</span><span class="o">.</span><span class="n">bondsOf</span><span class="p">(</span><span class="n">r_old</span><span class="o">.</span><span class="n">peptide</span><span class="o">.</span><span class="n">C</span><span class="p">)</span>
<span class="k">if</span> <span class="n">peptide_old</span><span class="p">:</span>
<span class="bp">self</span><span class="o">.</span><span class="n">bonds</span><span class="o">.</span><span class="n">remove</span><span class="p">(</span><span class="n">peptide_old</span><span class="p">[</span><span class="mi">0</span><span class="p">])</span>
<span class="k">if</span> <span class="ow">not</span> <span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">groups</span><span class="p">[</span><span class="n">n</span><span class="p">]</span><span class="o">.</span><span class="n">isCTerminus</span><span class="p">()</span>
<span class="ow">or</span> <span class="bp">self</span><span class="o">.</span><span class="n">groups</span><span class="p">[</span><span class="n">n</span><span class="o">+</span><span class="mi">1</span><span class="p">]</span><span class="o">.</span><span class="n">isNTerminus</span><span class="p">()):</span>
<span class="bp">self</span><span class="o">.</span><span class="n">bonds</span><span class="o">.</span><span class="n">append</span><span class="p">(</span><span class="n">Bonds</span><span class="o">.</span><span class="n">Bond</span><span class="p">((</span><span class="bp">self</span><span class="o">.</span><span class="n">groups</span><span class="p">[</span><span class="n">n</span><span class="p">]</span><span class="o">.</span><span class="n">peptide</span><span class="o">.</span><span class="n">C</span><span class="p">,</span>
<span class="bp">self</span><span class="o">.</span><span class="n">groups</span><span class="p">[</span><span class="n">n</span><span class="o">+</span><span class="mi">1</span><span class="p">]</span><span class="o">.</span><span class="n">peptide</span><span class="o">.</span><span class="n">N</span><span class="p">)))</span>
<span class="k">if</span> <span class="nb">isinstance</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">parent</span><span class="p">,</span> <span class="n">ChemicalObjects</span><span class="o">.</span><span class="n">Complex</span><span class="p">):</span>
<span class="bp">self</span><span class="o">.</span><span class="n">parent</span><span class="o">.</span><span class="n">recreateAtomList</span><span class="p">()</span>
<span class="n">universe</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">universe</span><span class="p">()</span>
<span class="k">if</span> <span class="n">universe</span> <span class="ow">is</span> <span class="ow">not</span> <span class="bp">None</span><span class="p">:</span>
<span class="n">universe</span><span class="o">.</span><span class="n">_changed</span><span class="p">(</span><span class="bp">True</span><span class="p">)</span>
<span class="c"># add sulfur bridges between cysteine residues</span></div>
<span class="k">def</span> <span class="nf">_addSSBridges</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">bonds</span><span class="p">):</span>
<span class="k">for</span> <span class="n">b</span> <span class="ow">in</span> <span class="n">bonds</span><span class="p">:</span>
<span class="n">cys1</span> <span class="o">=</span> <span class="n">b</span><span class="p">[</span><span class="mi">0</span><span class="p">]</span>
<span class="k">if</span> <span class="n">cys1</span><span class="o">.</span><span class="n">symbol</span><span class="o">.</span><span class="n">lower</span><span class="p">()</span> <span class="o">==</span> <span class="s">'cyx'</span><span class="p">:</span>
<span class="n">cys_ss1</span> <span class="o">=</span> <span class="n">cys1</span>
<span class="k">else</span><span class="p">:</span>
<span class="n">cys_ss1</span> <span class="o">=</span> <span class="n">cys1</span><span class="o">.</span><span class="n">_makeCystine</span><span class="p">()</span>
<span class="bp">self</span><span class="o">.</span><span class="n">replaceResidue</span><span class="p">(</span><span class="n">cys1</span><span class="p">,</span> <span class="n">cys_ss1</span><span class="p">)</span>
<span class="n">cys2</span> <span class="o">=</span> <span class="n">b</span><span class="p">[</span><span class="mi">1</span><span class="p">]</span>
<span class="k">if</span> <span class="n">cys2</span><span class="o">.</span><span class="n">symbol</span><span class="o">.</span><span class="n">lower</span><span class="p">()</span> <span class="o">==</span> <span class="s">'cyx'</span><span class="p">:</span>
<span class="n">cys_ss2</span> <span class="o">=</span> <span class="n">cys2</span>
<span class="k">else</span><span class="p">:</span>
<span class="n">cys_ss2</span> <span class="o">=</span> <span class="n">cys2</span><span class="o">.</span><span class="n">_makeCystine</span><span class="p">()</span>
<span class="bp">self</span><span class="o">.</span><span class="n">replaceResidue</span><span class="p">(</span><span class="n">cys2</span><span class="p">,</span> <span class="n">cys_ss2</span><span class="p">)</span>
<span class="bp">self</span><span class="o">.</span><span class="n">bonds</span><span class="o">.</span><span class="n">append</span><span class="p">(</span><span class="n">Bonds</span><span class="o">.</span><span class="n">Bond</span><span class="p">((</span><span class="n">cys_ss1</span><span class="o">.</span><span class="n">sidechain</span><span class="o">.</span><span class="n">S_gamma</span><span class="p">,</span>
<span class="n">cys_ss2</span><span class="o">.</span><span class="n">sidechain</span><span class="o">.</span><span class="n">S_gamma</span><span class="p">)))</span>
<span class="k">def</span> <span class="nf">_descriptionSpec</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span>
<span class="n">kwargs</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">name</span> <span class="o">+</span> <span class="s">'='</span> <span class="o">+</span> <span class="sb">`self.version_spec[name]`</span>
<span class="k">for</span> <span class="n">name</span> <span class="ow">in</span> <span class="nb">sorted</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">version_spec</span><span class="o">.</span><span class="n">keys</span><span class="p">())])</span>
<span class="k">return</span> <span class="s">"S"</span><span class="p">,</span> <span class="n">kwargs</span>
<span class="k">def</span> <span class="nf">_typeName</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span>
<span class="k">return</span> <span class="s">''</span><span class="o">.</span><span class="n">join</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">sequence</span><span class="p">())</span>
<span class="k">def</span> <span class="nf">_graphics</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">conf</span><span class="p">,</span> <span class="n">distance_fn</span><span class="p">,</span> <span class="n">model</span><span class="p">,</span> <span class="n">module</span><span class="p">,</span> <span class="n">options</span><span class="p">):</span>
<span class="k">if</span> <span class="n">model</span> <span class="o">!=</span> <span class="s">'backbone'</span><span class="p">:</span>
<span class="k">return</span> <span class="n">ChemicalObjects</span><span class="o">.</span><span class="n">Molecule</span><span class="o">.</span><span class="n">_graphics</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">conf</span><span class="p">,</span>
<span class="n">distance_fn</span><span class="p">,</span> <span class="n">model</span><span class="p">,</span>
<span class="n">module</span><span class="p">,</span> <span class="n">options</span><span class="p">)</span>
<span class="n">color</span> <span class="o">=</span> <span class="n">options</span><span class="o">.</span><span class="n">get</span><span class="p">(</span><span class="s">'color'</span><span class="p">,</span> <span class="s">'black'</span><span class="p">)</span>
<span class="n">material</span> <span class="o">=</span> <span class="n">module</span><span class="o">.</span><span class="n">EmissiveMaterial</span><span class="p">(</span><span class="n">color</span><span class="p">)</span>
<span class="n">objects</span> <span class="o">=</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="bp">self</span><span class="o">.</span><span class="n">groups</span><span class="p">)</span><span class="o">-</span><span class="mi">1</span><span class="p">):</span>
<span class="n">a1</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">groups</span><span class="p">[</span><span class="n">i</span><span class="p">]</span><span class="o">.</span><span class="n">peptide</span><span class="o">.</span><span class="n">C_alpha</span>
<span class="n">a2</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">groups</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">peptide</span><span class="o">.</span><span class="n">C_alpha</span>
<span class="n">p1</span> <span class="o">=</span> <span class="n">a1</span><span class="o">.</span><span class="n">position</span><span class="p">(</span><span class="n">conf</span><span class="p">)</span>
<span class="n">p2</span> <span class="o">=</span> <span class="n">a2</span><span class="o">.</span><span class="n">position</span><span class="p">(</span><span class="n">conf</span><span class="p">)</span>
<span class="k">if</span> <span class="n">p1</span> <span class="ow">is</span> <span class="ow">not</span> <span class="bp">None</span> <span class="ow">and</span> <span class="n">p2</span> <span class="ow">is</span> <span class="ow">not</span> <span class="bp">None</span><span class="p">:</span>
<span class="n">bond_vector</span> <span class="o">=</span> <span class="mf">0.5</span><span class="o">*</span><span class="n">distance_fn</span><span class="p">(</span><span class="n">a1</span><span class="p">,</span> <span class="n">a2</span><span class="p">,</span> <span class="n">conf</span><span class="p">)</span>
<span class="n">cut</span> <span class="o">=</span> <span class="n">bond_vector</span> <span class="o">!=</span> <span class="mf">0.5</span><span class="o">*</span><span class="p">(</span><span class="n">p2</span><span class="o">-</span><span class="n">p1</span><span class="p">)</span>
<span class="k">if</span> <span class="ow">not</span> <span class="n">cut</span><span class="p">:</span>
<span class="n">objects</span><span class="o">.</span><span class="n">append</span><span class="p">(</span><span class="n">module</span><span class="o">.</span><span class="n">Line</span><span class="p">(</span><span class="n">p1</span><span class="p">,</span> <span class="n">p2</span><span class="p">,</span> <span class="n">material</span> <span class="o">=</span> <span class="n">material</span><span class="p">))</span>
<span class="k">else</span><span class="p">:</span>
<span class="n">objects</span><span class="o">.</span><span class="n">append</span><span class="p">(</span><span class="n">module</span><span class="o">.</span><span class="n">Line</span><span class="p">(</span><span class="n">p1</span><span class="p">,</span> <span class="n">p1</span><span class="o">+</span><span class="n">bond_vector</span><span class="p">,</span>
<span class="n">material</span> <span class="o">=</span> <span class="n">material</span><span class="p">))</span>
<span class="n">objects</span><span class="o">.</span><span class="n">append</span><span class="p">(</span><span class="n">module</span><span class="o">.</span><span class="n">Line</span><span class="p">(</span><span class="n">p2</span><span class="p">,</span> <span class="n">p2</span><span class="o">-</span><span class="n">bond_vector</span><span class="p">,</span>
<span class="n">material</span> <span class="o">=</span> <span class="n">material</span><span class="p">))</span>
<span class="k">return</span> <span class="n">objects</span>
<span class="c">#</span>
<span class="c"># Subchains are created by slicing chains or extracting a chain from</span>
<span class="c"># a group of connected chains.</span>
<span class="c">#</span></div>
<div class="viewcode-block" id="SubChain"><a class="viewcode-back" href="../../modules.html#MMTK.Proteins.SubChain">[docs]</a><span class="k">class</span> <span class="nc">SubChain</span><span class="p">(</span><span class="n">PeptideChain</span><span class="p">):</span>
<span class="sd">"""</span>
<span class="sd"> A contiguous part of a peptide chain</span>
<span class="sd"> SubChain objects are the result of slicing operations on</span>
<span class="sd"> PeptideChain objects. They cannot be created directly.</span>
<span class="sd"> SubChain objects permit all operations of PeptideChain</span>
<span class="sd"> objects, but cannot be added to a universe.</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">chain</span><span class="o">=</span><span class="bp">None</span><span class="p">,</span> <span class="n">groups</span><span class="o">=</span><span class="bp">None</span><span class="p">,</span> <span class="n">name</span> <span class="o">=</span> <span class="s">''</span><span class="p">):</span>
<span class="k">if</span> <span class="n">chain</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">groups</span> <span class="o">=</span> <span class="n">groups</span>
<span class="bp">self</span><span class="o">.</span><span class="n">atoms</span> <span class="o">=</span> <span class="p">[]</span>
<span class="bp">self</span><span class="o">.</span><span class="n">bonds</span> <span class="o">=</span> <span class="p">[]</span>
<span class="k">for</span> <span class="n">g</span> <span class="ow">in</span> <span class="bp">self</span><span class="o">.</span><span class="n">groups</span><span class="p">:</span>
<span class="bp">self</span><span class="o">.</span><span class="n">atoms</span><span class="o">.</span><span class="n">extend</span><span class="p">(</span><span class="n">g</span><span class="o">.</span><span class="n">atoms</span><span class="p">)</span>
<span class="bp">self</span><span class="o">.</span><span class="n">bonds</span><span class="o">.</span><span class="n">extend</span><span class="p">(</span><span class="n">g</span><span class="o">.</span><span class="n">bonds</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="bp">self</span><span class="o">.</span><span class="n">groups</span><span class="p">)</span><span class="o">-</span><span class="mi">1</span><span class="p">):</span>
<span class="n">link1</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">groups</span><span class="p">[</span><span class="n">i</span><span class="p">]</span><span class="o">.</span><span class="n">chain_links</span><span class="p">[</span><span class="mi">1</span><span class="p">]</span>
<span class="n">link2</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">groups</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">chain_links</span><span class="p">[</span><span class="mi">0</span><span class="p">]</span>
<span class="bp">self</span><span class="o">.</span><span class="n">bonds</span><span class="o">.</span><span class="n">append</span><span class="p">(</span><span class="n">Bonds</span><span class="o">.</span><span class="n">Bond</span><span class="p">((</span><span class="n">link1</span><span class="p">,</span> <span class="n">link2</span><span class="p">)))</span>
<span class="bp">self</span><span class="o">.</span><span class="n">bonds</span> <span class="o">=</span> <span class="n">Bonds</span><span class="o">.</span><span class="n">BondList</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">bonds</span><span class="p">)</span>
<span class="bp">self</span><span class="o">.</span><span class="n">name</span> <span class="o">=</span> <span class="n">name</span>
<span class="bp">self</span><span class="o">.</span><span class="n">model</span> <span class="o">=</span> <span class="n">chain</span><span class="o">.</span><span class="n">model</span>
<span class="bp">self</span><span class="o">.</span><span class="n">parent</span> <span class="o">=</span> <span class="n">chain</span><span class="o">.</span><span class="n">parent</span>
<span class="bp">self</span><span class="o">.</span><span class="n">type</span> <span class="o">=</span> <span class="bp">None</span>
<span class="bp">self</span><span class="o">.</span><span class="n">configurations</span> <span class="o">=</span> <span class="p">{}</span>
<span class="bp">self</span><span class="o">.</span><span class="n">part_of</span> <span class="o">=</span> <span class="n">chain</span>
<span class="n">is_incomplete</span> <span class="o">=</span> <span class="bp">True</span>
<span class="k">def</span> <span class="nf">__repr__</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span>
<span class="k">if</span> <span class="bp">self</span><span class="o">.</span><span class="n">name</span> <span class="o">==</span> <span class="s">''</span><span class="p">:</span>
<span class="k">return</span> <span class="s">'SubChain of '</span> <span class="o">+</span> <span class="nb">repr</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">part_of</span><span class="p">)</span>
<span class="k">else</span><span class="p">:</span>
<span class="k">return</span> <span class="n">ChemicalObjects</span><span class="o">.</span><span class="n">Molecule</span><span class="o">.</span><span class="n">__repr__</span><span class="p">(</span><span class="bp">self</span><span class="p">)</span>
<span class="n">__str__</span> <span class="o">=</span> <span class="n">__repr__</span>
<span class="k">def</span> <span class="nf">replaceResidue</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">r_old</span><span class="p">,</span> <span class="n">r_new</span><span class="p">):</span>
<span class="k">for</span> <span class="n">a</span> <span class="ow">in</span> <span class="n">r_old</span><span class="o">.</span><span class="n">atoms</span><span class="p">:</span>
<span class="bp">self</span><span class="o">.</span><span class="n">atoms</span><span class="o">.</span><span class="n">remove</span><span class="p">(</span><span class="n">a</span><span class="p">)</span>
<span class="n">obsolete_bonds</span> <span class="o">=</span> <span class="p">[]</span>
<span class="k">for</span> <span class="n">b</span> <span class="ow">in</span> <span class="bp">self</span><span class="o">.</span><span class="n">bonds</span><span class="p">:</span>
<span class="k">if</span> <span class="n">b</span><span class="o">.</span><span class="n">a1</span> <span class="ow">in</span> <span class="n">r_old</span><span class="o">.</span><span class="n">atoms</span> <span class="ow">or</span> <span class="n">b</span><span class="o">.</span><span class="n">a2</span> <span class="ow">in</span> <span class="n">r_old</span><span class="o">.</span><span class="n">atoms</span><span class="p">:</span>
<span class="n">obsolete_bonds</span><span class="o">.</span><span class="n">append</span><span class="p">(</span><span class="n">b</span><span class="p">)</span>
<span class="k">for</span> <span class="n">b</span> <span class="ow">in</span> <span class="n">obsolete_bonds</span><span class="p">:</span>
<span class="bp">self</span><span class="o">.</span><span class="n">bonds</span><span class="o">.</span><span class="n">remove</span><span class="p">(</span><span class="n">b</span><span class="p">)</span>
<span class="n">n</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">groups</span><span class="o">.</span><span class="n">index</span><span class="p">(</span><span class="n">r_old</span><span class="p">)</span>
<span class="k">if</span> <span class="n">n</span> <span class="o">></span> <span class="mi">0</span><span class="p">:</span>
<span class="k">for</span> <span class="n">b</span> <span class="ow">in</span> <span class="bp">self</span><span class="o">.</span><span class="n">bonds</span><span class="o">.</span><span class="n">bondsOf</span><span class="p">(</span><span class="n">r_old</span><span class="o">.</span><span class="n">peptide</span><span class="o">.</span><span class="n">N</span><span class="p">):</span>
<span class="bp">self</span><span class="o">.</span><span class="n">bonds</span><span class="o">.</span><span class="n">remove</span><span class="p">(</span><span class="n">b</span><span class="p">)</span>
<span class="k">if</span> <span class="n">n</span> <span class="o"><</span> <span class="nb">len</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">groups</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">b</span> <span class="ow">in</span> <span class="bp">self</span><span class="o">.</span><span class="n">bonds</span><span class="o">.</span><span class="n">bondsOf</span><span class="p">(</span><span class="n">r_old</span><span class="o">.</span><span class="n">peptide</span><span class="o">.</span><span class="n">C</span><span class="p">):</span>
<span class="bp">self</span><span class="o">.</span><span class="n">bonds</span><span class="o">.</span><span class="n">remove</span><span class="p">(</span><span class="n">b</span><span class="p">)</span>
<span class="n">PeptideChain</span><span class="o">.</span><span class="n">replaceResidue</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">part_of</span><span class="p">,</span> <span class="n">r_old</span><span class="p">,</span> <span class="n">r_new</span><span class="p">)</span>
<span class="bp">self</span><span class="o">.</span><span class="n">groups</span><span class="p">[</span><span class="n">n</span><span class="p">]</span> <span class="o">=</span> <span class="n">r_new</span>
<span class="bp">self</span><span class="o">.</span><span class="n">atoms</span><span class="o">.</span><span class="n">extend</span><span class="p">(</span><span class="n">r_new</span><span class="o">.</span><span class="n">atoms</span><span class="p">)</span>
<span class="bp">self</span><span class="o">.</span><span class="n">bonds</span><span class="o">.</span><span class="n">extend</span><span class="p">(</span><span class="n">r_new</span><span class="o">.</span><span class="n">bonds</span><span class="p">)</span>
<span class="k">if</span> <span class="n">n</span> <span class="o">></span> <span class="mi">0</span><span class="p">:</span>
<span class="bp">self</span><span class="o">.</span><span class="n">bonds</span><span class="o">.</span><span class="n">append</span><span class="p">(</span><span class="n">Bonds</span><span class="o">.</span><span class="n">Bond</span><span class="p">((</span><span class="bp">self</span><span class="o">.</span><span class="n">groups</span><span class="p">[</span><span class="n">n</span><span class="o">-</span><span class="mi">1</span><span class="p">]</span><span class="o">.</span><span class="n">peptide</span><span class="o">.</span><span class="n">C</span><span class="p">,</span>
<span class="bp">self</span><span class="o">.</span><span class="n">groups</span><span class="p">[</span><span class="n">n</span><span class="p">]</span><span class="o">.</span><span class="n">peptide</span><span class="o">.</span><span class="n">N</span><span class="p">)))</span>
<span class="k">if</span> <span class="n">n</span> <span class="o"><</span> <span class="nb">len</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">groups</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">bonds</span><span class="o">.</span><span class="n">append</span><span class="p">(</span><span class="n">Bonds</span><span class="o">.</span><span class="n">Bond</span><span class="p">((</span><span class="bp">self</span><span class="o">.</span><span class="n">groups</span><span class="p">[</span><span class="n">n</span><span class="p">]</span><span class="o">.</span><span class="n">peptide</span><span class="o">.</span><span class="n">C</span><span class="p">,</span>
<span class="bp">self</span><span class="o">.</span><span class="n">groups</span><span class="p">[</span><span class="n">n</span><span class="o">+</span><span class="mi">1</span><span class="p">]</span><span class="o">.</span><span class="n">peptide</span><span class="o">.</span><span class="n">N</span><span class="p">)))</span>
<span class="k">def</span> <span class="nf">_distanceConstraintList</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span>
<span class="n">atoms</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">atomList</span><span class="p">()</span>
<span class="k">return</span> <span class="p">[(</span><span class="n">a1</span><span class="p">,</span> <span class="n">a2</span><span class="p">,</span> <span class="n">d</span><span class="p">)</span>
<span class="k">for</span> <span class="n">a1</span><span class="p">,</span> <span class="n">a2</span><span class="p">,</span> <span class="n">d</span> <span class="ow">in</span> <span class="bp">self</span><span class="o">.</span><span class="n">part_of</span><span class="o">.</span><span class="n">_distanceConstraintList</span><span class="p">()</span>
<span class="k">if</span> <span class="n">a1</span> <span class="ow">in</span> <span class="n">atoms</span> <span class="ow">and</span> <span class="n">a2</span> <span class="ow">in</span> <span class="n">atoms</span><span class="p">]</span>
<span class="k">def</span> <span class="nf">addDistanceConstraint</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">atom1</span><span class="p">,</span> <span class="n">atom2</span><span class="p">,</span> <span class="n">distance</span><span class="p">):</span>
<span class="n">chain</span> <span class="o">=</span> <span class="bp">self</span>
<span class="k">while</span> <span class="bp">True</span><span class="p">:</span>
<span class="k">try</span><span class="p">:</span>
<span class="n">chain</span> <span class="o">=</span> <span class="n">chain</span><span class="o">.</span><span class="n">part_of</span>
<span class="k">except</span> <span class="ne">AttributeError</span><span class="p">:</span>
<span class="k">break</span>
<span class="k">try</span><span class="p">:</span>
<span class="n">chain</span><span class="o">.</span><span class="n">distance_constraints</span><span class="o">.</span><span class="n">append</span><span class="p">((</span><span class="n">atom1</span><span class="p">,</span> <span class="n">atom2</span><span class="p">,</span> <span class="n">distance</span><span class="p">))</span>
<span class="k">except</span> <span class="ne">AttributeError</span><span class="p">:</span>
<span class="n">chain</span><span class="o">.</span><span class="n">distance_constraints</span> <span class="o">=</span> <span class="p">[(</span><span class="n">atom1</span><span class="p">,</span> <span class="n">atom2</span><span class="p">,</span> <span class="n">distance</span><span class="p">)]</span>
<span class="k">def</span> <span class="nf">removeDistanceConstraints</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">universe</span><span class="o">=</span><span class="bp">None</span><span class="p">):</span>
<span class="k">raise</span> <span class="ne">NotImplementedError</span>
<span class="c">#</span>
<span class="c"># Connected chains are collections of peptide chains connected by s-s bridges.</span>
<span class="c">#</span></div>
<div class="viewcode-block" id="ConnectedChains"><a class="viewcode-back" href="../../modules.html#MMTK.Proteins.ConnectedChains">[docs]</a><span class="k">class</span> <span class="nc">ConnectedChains</span><span class="p">(</span><span class="n">PeptideChain</span><span class="p">):</span>
<span class="sd">"""</span>
<span class="sd"> Peptide chains connected by disulfide bridges</span>
<span class="sd"> </span>
<span class="sd"> A group of peptide chains connected by disulfide bridges must be considered</span>
<span class="sd"> a single molecule due to the presence of chemical bonds. Such a molecule</span>
<span class="sd"> is represented by a ConnectedChains object. These objects are created</span>
<span class="sd"> automatically when a Protein object is assembled. They are normally</span>
<span class="sd"> not used directly by application programs. When a chain with disulfide</span>
<span class="sd"> bridges to other chains is extracted from a Protein object, the</span>
<span class="sd"> return value is a SubChain object that indirectly refers to a</span>
<span class="sd"> ConnectedChains object.</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">chains</span><span class="o">=</span><span class="bp">None</span><span class="p">):</span>
<span class="k">if</span> <span class="n">chains</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">chains</span> <span class="o">=</span> <span class="p">[]</span>
<span class="bp">self</span><span class="o">.</span><span class="n">groups</span> <span class="o">=</span> <span class="p">[]</span>
<span class="bp">self</span><span class="o">.</span><span class="n">atoms</span> <span class="o">=</span> <span class="p">[]</span>
<span class="bp">self</span><span class="o">.</span><span class="n">bonds</span> <span class="o">=</span> <span class="n">Bonds</span><span class="o">.</span><span class="n">BondList</span><span class="p">([])</span>
<span class="bp">self</span><span class="o">.</span><span class="n">chain_names</span> <span class="o">=</span> <span class="p">[]</span>
<span class="bp">self</span><span class="o">.</span><span class="n">model</span> <span class="o">=</span> <span class="n">chains</span><span class="p">[</span><span class="mi">0</span><span class="p">]</span><span class="o">.</span><span class="n">model</span>
<span class="n">version_spec</span> <span class="o">=</span> <span class="n">chains</span><span class="p">[</span><span class="mi">0</span><span class="p">]</span><span class="o">.</span><span class="n">version_spec</span>
<span class="k">for</span> <span class="n">c</span> <span class="ow">in</span> <span class="n">chains</span><span class="p">:</span>
<span class="k">if</span> <span class="n">c</span><span class="o">.</span><span class="n">version_spec</span><span class="p">[</span><span class="s">'model'</span><span class="p">]</span> <span class="o">!=</span> <span class="n">version_spec</span><span class="p">[</span><span class="s">'model'</span><span class="p">]:</span>
<span class="k">raise</span> <span class="ne">ValueError</span><span class="p">(</span><span class="s">"mixing chains of different model: "</span> <span class="o">+</span>
<span class="n">c</span><span class="o">.</span><span class="n">version_spec</span><span class="p">[</span><span class="s">'model'</span><span class="p">]</span> <span class="o">+</span> <span class="s">"/"</span> <span class="o">+</span>
<span class="n">version_spec</span><span class="p">[</span><span class="s">'model'</span><span class="p">])</span>
<span class="n">ng</span> <span class="o">=</span> <span class="nb">len</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">groups</span><span class="p">)</span>
<span class="bp">self</span><span class="o">.</span><span class="n">chains</span><span class="o">.</span><span class="n">append</span><span class="p">((</span><span class="n">c</span><span class="o">.</span><span class="n">name</span><span class="p">,</span> <span class="n">ng</span><span class="p">,</span> <span class="n">ng</span><span class="o">+</span><span class="nb">len</span><span class="p">(</span><span class="n">c</span><span class="o">.</span><span class="n">groups</span><span class="p">),</span>
<span class="n">c</span><span class="o">.</span><span class="n">version_spec</span><span class="p">))</span>
<span class="bp">self</span><span class="o">.</span><span class="n">groups</span><span class="o">.</span><span class="n">extend</span><span class="p">(</span><span class="n">c</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">atoms</span><span class="o">.</span><span class="n">extend</span><span class="p">(</span><span class="n">c</span><span class="o">.</span><span class="n">atoms</span><span class="p">)</span>
<span class="bp">self</span><span class="o">.</span><span class="n">bonds</span><span class="o">.</span><span class="n">extend</span><span class="p">(</span><span class="n">c</span><span class="o">.</span><span class="n">bonds</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="n">c</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="bp">self</span><span class="o">.</span><span class="n">chain_names</span><span class="o">.</span><span class="n">append</span><span class="p">(</span><span class="n">name</span><span class="p">)</span>
<span class="k">for</span> <span class="n">g</span> <span class="ow">in</span> <span class="bp">self</span><span class="o">.</span><span class="n">groups</span><span class="p">:</span>
<span class="n">g</span><span class="o">.</span><span class="n">parent</span> <span class="o">=</span> <span class="bp">self</span>
<span class="bp">self</span><span class="o">.</span><span class="n">name</span> <span class="o">=</span> <span class="s">''</span>
<span class="bp">self</span><span class="o">.</span><span class="n">parent</span> <span class="o">=</span> <span class="bp">None</span>
<span class="bp">self</span><span class="o">.</span><span class="n">type</span> <span class="o">=</span> <span class="bp">None</span>
<span class="bp">self</span><span class="o">.</span><span class="n">configurations</span> <span class="o">=</span> <span class="p">{}</span>
<span class="n">is_connected_chains</span> <span class="o">=</span> <span class="bp">True</span>
<span class="k">def</span> <span class="nf">_finalize</span><span class="p">(</span><span class="bp">self</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="bp">self</span><span class="o">.</span><span class="n">chains</span><span class="p">)):</span>
<span class="n">c</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">chains</span><span class="p">[</span><span class="n">i</span><span class="p">]</span>
<span class="n">sub_chain</span> <span class="o">=</span> <span class="n">SubChain</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="bp">self</span><span class="o">.</span><span class="n">groups</span><span class="p">[</span><span class="n">c</span><span class="p">[</span><span class="mi">1</span><span class="p">]:</span><span class="n">c</span><span class="p">[</span><span class="mi">2</span><span class="p">]],</span> <span class="n">c</span><span class="p">[</span><span class="mi">0</span><span class="p">])</span>
<span class="n">sub_chain</span><span class="o">.</span><span class="n">version_spec</span> <span class="o">=</span> <span class="n">c</span><span class="p">[</span><span class="mi">3</span><span class="p">]</span>
<span class="k">for</span> <span class="n">g</span> <span class="ow">in</span> <span class="n">sub_chain</span><span class="o">.</span><span class="n">groups</span><span class="p">:</span>
<span class="n">g</span><span class="o">.</span><span class="n">parent</span> <span class="o">=</span> <span class="n">sub_chain</span>
<span class="bp">self</span><span class="o">.</span><span class="n">chains</span><span class="p">[</span><span class="n">i</span><span class="p">]</span> <span class="o">=</span> <span class="n">sub_chain</span>
<span class="k">def</span> <span class="nf">__len__</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span>
<span class="k">return</span> <span class="nb">len</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">chains</span><span class="p">)</span>
<span class="k">def</span> <span class="nf">__getitem__</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">item</span><span class="p">):</span>
<span class="k">return</span> <span class="bp">self</span><span class="o">.</span><span class="n">chains</span><span class="p">[</span><span class="n">item</span><span class="p">]</span>
<span class="k">def</span> <span class="nf">__getslice__</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">first</span><span class="p">,</span> <span class="n">last</span><span class="p">):</span>
<span class="k">raise</span> <span class="ne">TypeError</span><span class="p">(</span><span class="s">"Can't slice connected chains"</span><span class="p">)</span>
<span class="k">def</span> <span class="nf">_graphics</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">conf</span><span class="p">,</span> <span class="n">distance_fn</span><span class="p">,</span> <span class="n">model</span><span class="p">,</span> <span class="n">module</span><span class="p">,</span> <span class="n">options</span><span class="p">):</span>
<span class="k">if</span> <span class="n">model</span> <span class="o">!=</span> <span class="s">'backbone'</span><span class="p">:</span>
<span class="k">return</span> <span class="n">ChemicalObjects</span><span class="o">.</span><span class="n">Molecule</span><span class="o">.</span><span class="n">_graphics</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">conf</span><span class="p">,</span>
<span class="n">distance_fn</span><span class="p">,</span> <span class="n">model</span><span class="p">,</span>
<span class="n">module</span><span class="p">,</span> <span class="n">options</span><span class="p">)</span>
<span class="n">objects</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="p">:</span>
<span class="n">objects</span> <span class="o">=</span> <span class="n">objects</span> <span class="o">+</span> <span class="n">chain</span><span class="o">.</span><span class="n">_graphics</span><span class="p">(</span><span class="n">conf</span><span class="p">,</span> <span class="n">distance_fn</span><span class="p">,</span>
<span class="n">model</span><span class="p">,</span> <span class="n">module</span><span class="p">,</span> <span class="n">options</span><span class="p">)</span>
<span class="k">return</span> <span class="n">objects</span>
<span class="c">#</span>
<span class="c"># Proteins are complexes of peptide chains, connected peptide chains,</span>
<span class="c"># and possibly other things.</span>
<span class="c">#</span></div>
<div class="viewcode-block" id="Protein"><a class="viewcode-back" href="../../modules.html#MMTK.Proteins.Protein">[docs]</a><span class="k">class</span> <span class="nc">Protein</span><span class="p">(</span><span class="n">ChemicalObjects</span><span class="o">.</span><span class="n">Complex</span><span class="p">):</span>
<span class="sd">"""</span>
<span class="sd"> Protein</span>
<span class="sd"> A Protein object is a special kind of :class:`~MMTK.ChemicalObjects.Complex`</span>
<span class="sd"> object which is made up of peptide chains and possibly ligands.</span>
<span class="sd"> If the atoms in the peptide chains that make up a protein have</span>
<span class="sd"> defined positions, sulfur bridges within chains and between</span>
<span class="sd"> chains will be constructed automatically during protein generation</span>
<span class="sd"> based on a distance criterion between cystein sidechains.</span>
<span class="sd"> Proteins act as sequences of chains. If p is a Protein object, then</span>
<span class="sd"> * len(p) yields the number of chains</span>
<span class="sd"> * p[i] yields chain number i</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="o">*</span><span class="n">items</span><span class="p">,</span> <span class="o">**</span><span class="n">properties</span><span class="p">):</span>
<span class="sd">"""</span>
<span class="sd"> :param items: either a sequence of peptide chain objects, or</span>
<span class="sd"> a string, which is interpreted as the name of a</span>
<span class="sd"> database definition for a protein.</span>
<span class="sd"> If that definition does not exist, the string</span>
<span class="sd"> is taken to be the name of a PDB file, from which</span>
<span class="sd"> all peptide chains are constructed and</span>
<span class="sd"> assembled into a protein.</span>
<span class="sd"> :keyword model: one of "all" (all-atom), "no_hydrogens" or "none"</span>
<span class="sd"> (no hydrogens),"polar_hydrogens" or "polar"</span>
<span class="sd"> (united-atom with only polar hydrogens),</span>
<span class="sd"> "polar_charmm" (like "polar", but defining</span>
<span class="sd"> polar hydrogens like in the CHARMM force field),</span>
<span class="sd"> "polar_opls" (like "polar", but defining</span>
<span class="sd"> polar hydrogens like in the latest OPLS force field),</span>
<span class="sd"> "calpha" (only the |C_alpha| atom of each residue).</span>
<span class="sd"> Default is "all".</span>
<span class="sd"> :type model: str</span>
<span class="sd"> :keyword position: the center-of-mass position of the protein</span>
<span class="sd"> :type position: Scientific.Geometry.Vector</span>
<span class="sd"> :keyword name: a name for the protein</span>
<span class="sd"> :type name: str</span>
<span class="sd"> """</span>
<span class="k">if</span> <span class="n">items</span> <span class="o">==</span> <span class="p">(</span><span class="bp">None</span><span class="p">,):</span>
<span class="k">return</span>
<span class="bp">self</span><span class="o">.</span><span class="n">name</span> <span class="o">=</span> <span class="s">''</span>
<span class="k">if</span> <span class="nb">len</span><span class="p">(</span><span class="n">items</span><span class="p">)</span> <span class="o">==</span> <span class="mi">1</span> <span class="ow">and</span> <span class="nb">type</span><span class="p">(</span><span class="n">items</span><span class="p">[</span><span class="mi">0</span><span class="p">])</span> <span class="o">==</span> <span class="nb">type</span><span class="p">(</span><span class="s">''</span><span class="p">):</span>
<span class="k">try</span><span class="p">:</span>
<span class="n">filename</span> <span class="o">=</span> <span class="n">Database</span><span class="o">.</span><span class="n">databasePath</span><span class="p">(</span><span class="n">items</span><span class="p">[</span><span class="mi">0</span><span class="p">],</span> <span class="s">'Proteins'</span><span class="p">)</span>
<span class="n">found</span> <span class="o">=</span> <span class="mi">1</span>
<span class="k">except</span> <span class="ne">IOError</span><span class="p">:</span>
<span class="n">found</span> <span class="o">=</span> <span class="mi">0</span>
<span class="k">if</span> <span class="n">found</span><span class="p">:</span>
<span class="n">blueprint</span> <span class="o">=</span> <span class="n">Database</span><span class="o">.</span><span class="n">BlueprintProtein</span><span class="p">(</span><span class="n">items</span><span class="p">[</span><span class="mi">0</span><span class="p">])</span>
<span class="n">items</span> <span class="o">=</span> <span class="n">blueprint</span><span class="o">.</span><span class="n">chains</span>
<span class="k">for</span> <span class="n">attr</span><span class="p">,</span> <span class="n">value</span> <span class="ow">in</span> <span class="nb">vars</span><span class="p">(</span><span class="n">blueprint</span><span class="p">)</span><span class="o">.</span><span class="n">items</span><span class="p">():</span>
<span class="k">if</span> <span class="n">attr</span> <span class="ow">not</span> <span class="ow">in</span> <span class="p">[</span><span class="s">'type'</span><span class="p">,</span> <span class="s">'chains'</span><span class="p">]:</span>
<span class="nb">setattr</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">attr</span><span class="p">,</span> <span class="n">value</span><span class="p">)</span>
<span class="k">else</span><span class="p">:</span>
<span class="kn">import</span> <span class="nn">PDB</span>
<span class="n">conf</span> <span class="o">=</span> <span class="n">PDB</span><span class="o">.</span><span class="n">PDBConfiguration</span><span class="p">(</span><span class="n">items</span><span class="p">[</span><span class="mi">0</span><span class="p">])</span>
<span class="n">model</span> <span class="o">=</span> <span class="n">properties</span><span class="o">.</span><span class="n">get</span><span class="p">(</span><span class="s">'model'</span><span class="p">,</span> <span class="s">'all'</span><span class="p">)</span>
<span class="n">items</span> <span class="o">=</span> <span class="n">conf</span><span class="o">.</span><span class="n">createPeptideChains</span><span class="p">(</span><span class="n">model</span><span class="p">)</span>
<span class="n">molecules</span> <span class="o">=</span> <span class="p">[]</span>
<span class="k">for</span> <span class="n">i</span> <span class="ow">in</span> <span class="n">items</span><span class="p">:</span>
<span class="k">if</span> <span class="n">ChemicalObjects</span><span class="o">.</span><span class="n">isChemicalObject</span><span class="p">(</span><span class="n">i</span><span class="p">):</span>
<span class="n">molecules</span><span class="o">.</span><span class="n">append</span><span class="p">(</span><span class="n">i</span><span class="p">)</span>
<span class="k">else</span><span class="p">:</span>
<span class="n">molecules</span> <span class="o">=</span> <span class="n">molecules</span> <span class="o">+</span> <span class="nb">list</span><span class="p">(</span><span class="n">i</span><span class="p">)</span>
<span class="k">for</span> <span class="n">m</span><span class="p">,</span> <span class="n">i</span> <span class="ow">in</span> <span class="nb">zip</span><span class="p">(</span><span class="n">molecules</span><span class="p">,</span> <span class="nb">range</span><span class="p">(</span><span class="nb">len</span><span class="p">(</span><span class="n">molecules</span><span class="p">))):</span>
<span class="n">m</span><span class="o">.</span><span class="n">_numbers</span> <span class="o">=</span> <span class="p">[</span><span class="n">i</span><span class="p">]</span>
<span class="k">if</span> <span class="ow">not</span> <span class="n">m</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">name</span> <span class="o">=</span> <span class="s">'chain'</span><span class="o">+</span><span class="sb">`i`</span>
<span class="n">ss</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">_findSSBridges</span><span class="p">(</span><span class="n">molecules</span><span class="p">)</span>
<span class="n">new_mol</span> <span class="o">=</span> <span class="p">{}</span>
<span class="k">for</span> <span class="n">m</span> <span class="ow">in</span> <span class="n">molecules</span><span class="p">:</span>
<span class="n">new_mol</span><span class="p">[</span><span class="n">m</span><span class="p">]</span> <span class="o">=</span> <span class="p">([</span><span class="n">m</span><span class="p">],[])</span>
<span class="k">for</span> <span class="n">bond</span> <span class="ow">in</span> <span class="n">ss</span><span class="p">:</span>
<span class="n">m1</span> <span class="o">=</span> <span class="n">new_mol</span><span class="p">[</span><span class="n">bond</span><span class="p">[</span><span class="mi">0</span><span class="p">]</span><span class="o">.</span><span class="n">topLevelChemicalObject</span><span class="p">()]</span>
<span class="n">m2</span> <span class="o">=</span> <span class="n">new_mol</span><span class="p">[</span><span class="n">bond</span><span class="p">[</span><span class="mi">1</span><span class="p">]</span><span class="o">.</span><span class="n">topLevelChemicalObject</span><span class="p">()]</span>
<span class="k">if</span> <span class="n">m1</span> <span class="o">==</span> <span class="n">m2</span><span class="p">:</span>
<span class="n">m1</span><span class="p">[</span><span class="mi">1</span><span class="p">]</span><span class="o">.</span><span class="n">append</span><span class="p">(</span><span class="n">bond</span><span class="p">)</span>
<span class="k">else</span><span class="p">:</span>
<span class="n">combined</span> <span class="o">=</span> <span class="p">(</span><span class="n">m1</span><span class="p">[</span><span class="mi">0</span><span class="p">]</span> <span class="o">+</span> <span class="n">m2</span><span class="p">[</span><span class="mi">0</span><span class="p">],</span> <span class="n">m1</span><span class="p">[</span><span class="mi">1</span><span class="p">]</span> <span class="o">+</span> <span class="n">m2</span><span class="p">[</span><span class="mi">1</span><span class="p">]</span> <span class="o">+</span> <span class="p">[</span><span class="n">bond</span><span class="p">])</span>
<span class="k">for</span> <span class="n">m</span> <span class="ow">in</span> <span class="n">combined</span><span class="p">[</span><span class="mi">0</span><span class="p">]:</span>
<span class="n">new_mol</span><span class="p">[</span><span class="n">m</span><span class="p">]</span> <span class="o">=</span> <span class="n">combined</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="k">while</span> <span class="n">new_mol</span><span class="p">:</span>
<span class="n">m</span> <span class="o">=</span> <span class="n">new_mol</span><span class="o">.</span><span class="n">values</span><span class="p">()[</span><span class="mi">0</span><span class="p">]</span>
<span class="k">for</span> <span class="n">i</span> <span class="ow">in</span> <span class="n">m</span><span class="p">[</span><span class="mi">0</span><span class="p">]:</span>
<span class="k">del</span> <span class="n">new_mol</span><span class="p">[</span><span class="n">i</span><span class="p">]</span>
<span class="n">bonds</span> <span class="o">=</span> <span class="n">m</span><span class="p">[</span><span class="mi">1</span><span class="p">]</span>
<span class="k">if</span> <span class="nb">len</span><span class="p">(</span><span class="n">m</span><span class="p">[</span><span class="mi">0</span><span class="p">])</span> <span class="o">==</span> <span class="mi">1</span><span class="p">:</span>
<span class="n">m</span> <span class="o">=</span> <span class="n">m</span><span class="p">[</span><span class="mi">0</span><span class="p">][</span><span class="mi">0</span><span class="p">]</span>
<span class="n">m</span><span class="o">.</span><span class="n">_addSSBridges</span><span class="p">(</span><span class="n">bonds</span><span class="p">)</span>
<span class="k">else</span><span class="p">:</span>
<span class="n">numbers</span> <span class="o">=</span> <span class="nb">sum</span><span class="p">((</span><span class="n">i</span><span class="o">.</span><span class="n">_numbers</span> <span class="k">for</span> <span class="n">i</span> <span class="ow">in</span> <span class="n">m</span><span class="p">[</span><span class="mi">0</span><span class="p">]),</span> <span class="p">[])</span>
<span class="n">m</span> <span class="o">=</span> <span class="n">ConnectedChains</span><span class="p">(</span><span class="n">m</span><span class="p">[</span><span class="mi">0</span><span class="p">])</span>
<span class="n">m</span><span class="o">.</span><span class="n">_numbers</span> <span class="o">=</span> <span class="n">numbers</span>
<span class="n">m</span><span class="o">.</span><span class="n">_addSSBridges</span><span class="p">(</span><span class="n">bonds</span><span class="p">)</span>
<span class="n">m</span><span class="o">.</span><span class="n">_finalize</span><span class="p">()</span>
<span class="k">for</span> <span class="n">c</span> <span class="ow">in</span> <span class="n">m</span><span class="p">:</span>
<span class="n">c</span><span class="o">.</span><span class="n">parent</span> <span class="o">=</span> <span class="bp">self</span>
<span class="n">m</span><span class="o">.</span><span class="n">parent</span> <span class="o">=</span> <span class="bp">self</span>
<span class="bp">self</span><span class="o">.</span><span class="n">molecules</span><span class="o">.</span><span class="n">append</span><span class="p">(</span><span class="n">m</span><span class="p">)</span>
<span class="bp">self</span><span class="o">.</span><span class="n">atoms</span> <span class="o">=</span> <span class="p">[]</span>
<span class="bp">self</span><span class="o">.</span><span class="n">chains</span> <span class="o">=</span> <span class="p">[]</span>
<span class="k">for</span> <span class="n">m</span> <span class="ow">in</span> <span class="bp">self</span><span class="o">.</span><span class="n">molecules</span><span class="p">:</span>
<span class="bp">self</span><span class="o">.</span><span class="n">atoms</span><span class="o">.</span><span class="n">extend</span><span class="p">(</span><span class="n">m</span><span class="o">.</span><span class="n">atoms</span><span class="p">)</span>
<span class="k">if</span> <span class="nb">hasattr</span><span class="p">(</span><span class="n">m</span><span class="p">,</span> <span class="s">'is_connected_chains'</span><span class="p">):</span>
<span class="k">for</span> <span class="n">c</span><span class="p">,</span> <span class="n">name</span><span class="p">,</span> <span class="n">i</span> <span class="ow">in</span> <span class="nb">zip</span><span class="p">(</span><span class="nb">range</span><span class="p">(</span><span class="nb">len</span><span class="p">(</span><span class="n">m</span><span class="p">)),</span>
<span class="n">m</span><span class="o">.</span><span class="n">chain_names</span><span class="p">,</span> <span class="n">m</span><span class="o">.</span><span class="n">_numbers</span><span class="p">):</span>
<span class="bp">self</span><span class="o">.</span><span class="n">chains</span><span class="o">.</span><span class="n">append</span><span class="p">((</span><span class="n">m</span><span class="p">,</span> <span class="n">c</span><span class="p">,</span> <span class="n">name</span><span class="p">,</span> <span class="n">i</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="n">m</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="bp">self</span><span class="o">.</span><span class="n">chains</span><span class="o">.</span><span class="n">append</span><span class="p">((</span><span class="n">m</span><span class="p">,</span> <span class="bp">None</span><span class="p">,</span> <span class="n">name</span><span class="p">,</span> <span class="n">m</span><span class="o">.</span><span class="n">_numbers</span><span class="p">[</span><span class="mi">0</span><span class="p">]))</span>
<span class="bp">self</span><span class="o">.</span><span class="n">chains</span><span class="o">.</span><span class="n">sort</span><span class="p">(</span><span class="k">lambda</span> <span class="n">c1</span><span class="p">,</span> <span class="n">c2</span><span class="p">:</span> <span class="nb">cmp</span><span class="p">(</span><span class="n">c1</span><span class="p">[</span><span class="mi">3</span><span class="p">],</span> <span class="n">c2</span><span class="p">[</span><span class="mi">3</span><span class="p">]))</span>
<span class="bp">self</span><span class="o">.</span><span class="n">chains</span> <span class="o">=</span> <span class="nb">map</span><span class="p">(</span><span class="k">lambda</span> <span class="n">c</span><span class="p">:</span> <span class="n">c</span><span class="p">[:</span><span class="mi">3</span><span class="p">],</span> <span class="bp">self</span><span class="o">.</span><span class="n">chains</span><span class="p">)</span>
<span class="bp">self</span><span class="o">.</span><span class="n">parent</span> <span class="o">=</span> <span class="bp">None</span>
<span class="bp">self</span><span class="o">.</span><span class="n">type</span> <span class="o">=</span> <span class="bp">None</span>
<span class="bp">self</span><span class="o">.</span><span class="n">configurations</span> <span class="o">=</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">name</span> <span class="o">=</span> <span class="n">properties</span><span class="p">[</span><span class="s">'name'</span><span class="p">]</span>
<span class="k">del</span> <span class="n">properties</span><span class="p">[</span><span class="s">'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">if</span> <span class="n">properties</span><span class="o">.</span><span class="n">has_key</span><span class="p">(</span><span class="s">'position'</span><span class="p">):</span>
<span class="bp">self</span><span class="o">.</span><span class="n">translateTo</span><span class="p">(</span><span class="n">properties</span><span class="p">[</span><span class="s">'position'</span><span class="p">])</span>
<span class="k">del</span> <span class="n">properties</span><span class="p">[</span><span class="s">'position'</span><span class="p">]</span>
<span class="bp">self</span><span class="o">.</span><span class="n">addProperties</span><span class="p">(</span><span class="n">properties</span><span class="p">)</span>
<span class="n">undefined</span> <span class="o">=</span> <span class="mi">0</span>
<span class="k">for</span> <span class="n">a</span> <span class="ow">in</span> <span class="bp">self</span><span class="o">.</span><span class="n">atoms</span><span class="p">:</span>
<span class="k">if</span> <span class="n">a</span><span class="o">.</span><span class="n">position</span><span class="p">()</span> <span class="ow">is</span> <span class="bp">None</span><span class="p">:</span>
<span class="n">undefined</span> <span class="o">+=</span> <span class="mi">1</span>
<span class="k">if</span> <span class="n">undefined</span> <span class="o">></span> <span class="mi">0</span> <span class="ow">and</span> <span class="n">undefined</span> <span class="o">!=</span> <span class="nb">len</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">atoms</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 in a protein '</span> <span class="o">+</span>
<span class="s">'have undefined positions.'</span><span class="p">)</span>
<span class="n">is_protein</span> <span class="o">=</span> <span class="bp">True</span>
<span class="k">def</span> <span class="nf">__len__</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span>
<span class="k">return</span> <span class="nb">len</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">chains</span><span class="p">)</span>
<span class="k">def</span> <span class="nf">__getitem__</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">item</span><span class="p">):</span>
<span class="k">if</span> <span class="nb">isinstance</span><span class="p">(</span><span class="n">item</span><span class="p">,</span> <span class="nb">int</span><span class="p">):</span>
<span class="n">m</span><span class="p">,</span> <span class="n">c</span><span class="p">,</span> <span class="n">name</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">chains</span><span class="p">[</span><span class="n">item</span><span class="p">]</span>
<span class="k">else</span><span class="p">:</span>
<span class="k">for</span> <span class="n">m</span><span class="p">,</span> <span class="n">c</span><span class="p">,</span> <span class="n">name</span> <span class="ow">in</span> <span class="bp">self</span><span class="o">.</span><span class="n">chains</span><span class="p">:</span>
<span class="k">if</span> <span class="n">name</span> <span class="o">==</span> <span class="n">item</span><span class="p">:</span>
<span class="k">break</span>
<span class="k">if</span> <span class="n">name</span> <span class="o">!=</span> <span class="n">item</span><span class="p">:</span>
<span class="k">raise</span> <span class="ne">ValueError</span><span class="p">(</span><span class="s">'No chain with name '</span> <span class="o">+</span> <span class="n">item</span><span class="p">)</span>
<span class="k">if</span> <span class="n">c</span> <span class="ow">is</span> <span class="bp">None</span><span class="p">:</span>
<span class="k">return</span> <span class="n">m</span>
<span class="k">else</span><span class="p">:</span>
<span class="k">return</span> <span class="n">m</span><span class="p">[</span><span class="n">c</span><span class="p">]</span>
<div class="viewcode-block" id="Protein.residuesOfType"><a class="viewcode-back" href="../../modules.html#MMTK.Proteins.Protein.residuesOfType">[docs]</a> <span class="k">def</span> <span class="nf">residuesOfType</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="o">*</span><span class="n">types</span><span class="p">):</span>
<span class="sd">"""</span>
<span class="sd"> :param types: a sequence of residue codes (one- or three-letter)</span>
<span class="sd"> :type types: sequence of str</span>
<span class="sd"> :returns: all residues whose type (one- or three-letter code)</span>
<span class="sd"> is contained in types</span>
<span class="sd"> :rtype: :class:`~MMTK.Collections.Collection`</span>
<span class="sd"> """</span>
<span class="n">rlist</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">m</span> <span class="ow">in</span> <span class="bp">self</span><span class="o">.</span><span class="n">molecules</span><span class="p">:</span>
<span class="k">if</span> <span class="n">isPeptideChain</span><span class="p">(</span><span class="n">m</span><span class="p">):</span>
<span class="n">rlist</span> <span class="o">=</span> <span class="n">rlist</span> <span class="o">+</span> <span class="nb">apply</span><span class="p">(</span><span class="n">m</span><span class="o">.</span><span class="n">residuesOfType</span><span class="p">,</span> <span class="n">types</span><span class="p">)</span>
<span class="k">return</span> <span class="n">rlist</span>
</div>
<div class="viewcode-block" id="Protein.backbone"><a class="viewcode-back" href="../../modules.html#MMTK.Proteins.Protein.backbone">[docs]</a> <span class="k">def</span> <span class="nf">backbone</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span>
<span class="sd">"""</span>
<span class="sd"> :returns: the peptide groups of all residues in all chains</span>
<span class="sd"> :rtype: :class:`~MMTK.Collections.Collection`</span>
<span class="sd"> """</span>
<span class="n">rlist</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">m</span> <span class="ow">in</span> <span class="bp">self</span><span class="o">.</span><span class="n">molecules</span><span class="p">:</span>
<span class="k">if</span> <span class="n">isPeptideChain</span><span class="p">(</span><span class="n">m</span><span class="p">):</span>
<span class="n">rlist</span> <span class="o">=</span> <span class="n">rlist</span> <span class="o">+</span> <span class="n">m</span><span class="o">.</span><span class="n">backbone</span><span class="p">()</span>
<span class="k">return</span> <span class="n">rlist</span>
</div>
<div class="viewcode-block" id="Protein.sidechains"><a class="viewcode-back" href="../../modules.html#MMTK.Proteins.Protein.sidechains">[docs]</a> <span class="k">def</span> <span class="nf">sidechains</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span>
<span class="sd">"""</span>
<span class="sd"> :returns: the sidechain groups of all residues in all chains</span>
<span class="sd"> :rtype: :class:`~MMTK.Collections.Collection`</span>
<span class="sd"> """</span>
<span class="n">rlist</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">m</span> <span class="ow">in</span> <span class="bp">self</span><span class="o">.</span><span class="n">molecules</span><span class="p">:</span>
<span class="k">if</span> <span class="n">isPeptideChain</span><span class="p">(</span><span class="n">m</span><span class="p">):</span>
<span class="n">rlist</span> <span class="o">=</span> <span class="n">rlist</span> <span class="o">+</span> <span class="n">m</span><span class="o">.</span><span class="n">sidechains</span><span class="p">()</span>
<span class="k">return</span> <span class="n">rlist</span>
</div>
<div class="viewcode-block" id="Protein.residues"><a class="viewcode-back" href="../../modules.html#MMTK.Proteins.Protein.residues">[docs]</a> <span class="k">def</span> <span class="nf">residues</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span>
<span class="sd">"""</span>
<span class="sd"> :returns: all residues in all chains</span>
<span class="sd"> :rtype: :class:`~MMTK.Collections.Collection`</span>
<span class="sd"> """</span>
<span class="n">rlist</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">m</span> <span class="ow">in</span> <span class="bp">self</span><span class="o">.</span><span class="n">molecules</span><span class="p">:</span>
<span class="k">if</span> <span class="n">isPeptideChain</span><span class="p">(</span><span class="n">m</span><span class="p">):</span>
<span class="n">rlist</span> <span class="o">=</span> <span class="n">rlist</span> <span class="o">+</span> <span class="n">m</span><span class="o">.</span><span class="n">residues</span><span class="p">()</span>
<span class="k">return</span> <span class="n">rlist</span>
</div>
<div class="viewcode-block" id="Protein.phiPsi"><a class="viewcode-back" href="../../modules.html#MMTK.Proteins.Protein.phiPsi">[docs]</a> <span class="k">def</span> <span class="nf">phiPsi</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">conf</span> <span class="o">=</span> <span class="bp">None</span><span class="p">):</span>
<span class="sd">"""</span>
<span class="sd"> :returns: a list of the (phi, psi) backbone angles for all residue</span>
<span class="sd"> in all chains</span>
<span class="sd"> :rtype: list of list of tuple of float</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">phiPsi</span><span class="p">(</span><span class="n">conf</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="p">]</span>
</div>
<span class="n">_ss_bond_max</span> <span class="o">=</span> <span class="mf">0.25</span><span class="o">*</span><span class="n">Units</span><span class="o">.</span><span class="n">nm</span>
<span class="k">def</span> <span class="nf">_findSSBridges</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">molecules</span><span class="p">):</span>
<span class="n">molecules</span> <span class="o">=</span> <span class="nb">filter</span><span class="p">(</span><span class="k">lambda</span> <span class="n">m</span><span class="p">:</span> <span class="nb">hasattr</span><span class="p">(</span><span class="n">m</span><span class="p">,</span> <span class="s">'is_peptide_chain'</span><span class="p">),</span> <span class="n">molecules</span><span class="p">)</span>
<span class="n">cys</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">m</span> <span class="ow">in</span> <span class="n">molecules</span><span class="p">:</span>
<span class="k">if</span> <span class="n">m</span><span class="o">.</span><span class="n">version_spec</span><span class="p">[</span><span class="s">'model'</span><span class="p">]</span> <span class="o">!=</span> <span class="s">'calpha'</span><span class="p">:</span>
<span class="n">cys</span> <span class="o">=</span> <span class="n">cys</span> <span class="o">+</span> <span class="n">m</span><span class="o">.</span><span class="n">residuesOfType</span><span class="p">(</span><span class="s">'cys'</span><span class="p">)</span> <span class="o">+</span> <span class="n">m</span><span class="o">.</span><span class="n">residuesOfType</span><span class="p">(</span><span class="s">'cyx'</span><span class="p">)</span>
<span class="n">s</span> <span class="o">=</span> <span class="n">cys</span><span class="o">.</span><span class="n">map</span><span class="p">(</span><span class="k">lambda</span> <span class="n">r</span><span class="p">:</span> <span class="n">r</span><span class="o">.</span><span class="n">sidechain</span><span class="o">.</span><span class="n">S_gamma</span><span class="p">)</span>
<span class="n">ns</span> <span class="o">=</span> <span class="nb">len</span><span class="p">(</span><span class="n">s</span><span class="p">)</span>
<span class="n">ss</span> <span class="o">=</span> <span class="p">[]</span>
<span class="k">for</span> <span class="n">i</span> <span class="ow">in</span> <span class="nb">xrange</span><span class="p">(</span><span class="n">ns</span><span class="o">-</span><span class="mi">1</span><span class="p">):</span>
<span class="k">for</span> <span class="n">j</span> <span class="ow">in</span> <span class="nb">xrange</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="n">ns</span><span class="p">):</span>
<span class="n">r1</span> <span class="o">=</span> <span class="n">s</span><span class="p">[</span><span class="n">i</span><span class="p">]</span><span class="o">.</span><span class="n">position</span><span class="p">()</span>
<span class="n">r2</span> <span class="o">=</span> <span class="n">s</span><span class="p">[</span><span class="n">j</span><span class="p">]</span><span class="o">.</span><span class="n">position</span><span class="p">()</span>
<span class="k">if</span> <span class="n">r1</span> <span class="ow">and</span> <span class="n">r2</span> <span class="ow">and</span> <span class="p">(</span><span class="n">r1</span><span class="o">-</span><span class="n">r2</span><span class="p">)</span><span class="o">.</span><span class="n">length</span><span class="p">()</span> <span class="o"><</span> <span class="bp">self</span><span class="o">.</span><span class="n">_ss_bond_max</span><span class="p">:</span>
<span class="n">ss</span><span class="o">.</span><span class="n">append</span><span class="p">((</span><span class="n">cys</span><span class="p">[</span><span class="n">i</span><span class="p">],</span> <span class="n">cys</span><span class="p">[</span><span class="n">j</span><span class="p">]))</span>
<span class="k">return</span> <span class="n">ss</span>
<span class="k">def</span> <span class="nf">_subunits</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span>
<span class="k">return</span> <span class="nb">list</span><span class="p">(</span><span class="bp">self</span><span class="p">)</span>
<span class="k">def</span> <span class="nf">_description</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">tag</span><span class="p">,</span> <span class="n">index_map</span><span class="p">,</span> <span class="n">toplevel</span><span class="p">):</span>
<span class="k">if</span> <span class="ow">not</span> <span class="n">toplevel</span><span class="p">:</span>
<span class="k">raise</span> <span class="ne">ValueError</span>
<span class="k">return</span> <span class="s">'l('</span> <span class="o">+</span> <span class="sb">`self.__class__.__name__`</span> <span class="o">+</span> <span class="s">','</span> <span class="o">+</span> <span class="sb">`self.name`</span> <span class="o">+</span> <span class="s">',['</span> <span class="o">+</span> \
<span class="s">','</span><span class="o">.</span><span class="n">join</span><span class="p">(</span><span class="n">o</span><span class="o">.</span><span class="n">_description</span><span class="p">(</span><span class="n">tag</span><span class="p">,</span> <span class="n">index_map</span><span class="p">,</span> <span class="bp">True</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="p">)</span> <span class="o">+</span> \
<span class="s">'])'</span>
<span class="k">def</span> <span class="nf">_graphics</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">conf</span><span class="p">,</span> <span class="n">distance_fn</span><span class="p">,</span> <span class="n">model</span><span class="p">,</span> <span class="n">module</span><span class="p">,</span> <span class="n">options</span><span class="p">):</span>
<span class="k">if</span> <span class="n">model</span> <span class="o">!=</span> <span class="s">'backbone'</span><span class="p">:</span>
<span class="k">return</span> <span class="n">ChemicalObjects</span><span class="o">.</span><span class="n">Complex</span><span class="o">.</span><span class="n">_graphics</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">conf</span><span class="p">,</span> <span class="n">distance_fn</span><span class="p">,</span>
<span class="n">model</span><span class="p">,</span> <span class="n">module</span><span class="p">,</span> <span class="n">options</span><span class="p">)</span>
<span class="n">objects</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="p">:</span>
<span class="n">objects</span><span class="o">.</span><span class="n">extend</span><span class="p">(</span><span class="n">chain</span><span class="o">.</span><span class="n">_graphics</span><span class="p">(</span><span class="n">conf</span><span class="p">,</span> <span class="n">distance_fn</span><span class="p">,</span>
<span class="n">model</span><span class="p">,</span> <span class="n">module</span><span class="p">,</span> <span class="n">options</span><span class="p">))</span>
<span class="k">return</span> <span class="n">objects</span>
<span class="c">#</span>
<span class="c"># Type check functions</span>
<span class="c">#</span></div>
<div class="viewcode-block" id="isPeptideChain"><a class="viewcode-back" href="../../modules.html#MMTK.Proteins.isPeptideChain">[docs]</a><span class="k">def</span> <span class="nf">isPeptideChain</span><span class="p">(</span><span class="n">x</span><span class="p">):</span>
<span class="sd">"""</span>
<span class="sd"> :param x: any object</span>
<span class="sd"> :returns: True if x is a peptide chain</span>
<span class="sd"> :rtype: bool</span>
<span class="sd"> """</span>
<span class="k">return</span> <span class="nb">hasattr</span><span class="p">(</span><span class="n">x</span><span class="p">,</span> <span class="s">'is_peptide_chain'</span><span class="p">)</span>
</div>
<div class="viewcode-block" id="isProtein"><a class="viewcode-back" href="../../modules.html#MMTK.Proteins.isProtein">[docs]</a><span class="k">def</span> <span class="nf">isProtein</span><span class="p">(</span><span class="n">x</span><span class="p">):</span>
<span class="sd">"""</span>
<span class="sd"> :param x: any object</span>
<span class="sd"> :returns: True if x is a protein</span>
<span class="sd"> :rtype: bool</span>
<span class="sd"> """</span>
<span class="k">return</span> <span class="nb">hasattr</span><span class="p">(</span><span class="n">x</span><span class="p">,</span> <span class="s">'is_protein'</span><span class="p">)</span></div>
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