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<h1>Source code for MMTK.NucleicAcids</h1><div class="highlight"><pre>
<span class="c"># This module implements classes for nucleotide chains.</span>
<span class="c">#</span>
<span class="c"># Written by Konrad Hinsen</span>
<span class="c">#</span>
<span class="sd">"""</span>
<span class="sd">Nucleic acid chains</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">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">defineNucleicAcidResidue</span>
<span class="c">#</span>
<span class="c"># Nucleotides are special groups</span>
<span class="c">#</span>
<div class="viewcode-block" id="Nucleotide"><a class="viewcode-back" href="../../modules.html#MMTK.NucleicAcids.Nucleotide">[docs]</a><span class="k">class</span> <span class="nc">Nucleotide</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"> Nucleic acid residue</span>
<span class="sd"> Nucleotides are a special kind of group. Like any other</span>
<span class="sd"> group, they are defined in the chemical database. Each residue</span>
<span class="sd"> has two or three subgroups ('sugar' and 'base', plus 'phosphate'</span>
<span class="sd"> except for 5'-terminal residues) and is usually</span>
<span class="sd"> connected to other residues to form a nucleotide chain. The database</span>
<span class="sd"> contains three variants of each residue (5'-terminal, 3'-terminal,</span>
<span class="sd"> non-terminal).</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 nucleotide in the chemical database. This</span>
<span class="sd"> is the full name of the residue plus the suffix</span>
<span class="sd"> "_5ter" or "_3ter" 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"> Currently the database has definitions only for "all".</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>
<div class="viewcode-block" id="Nucleotide.backbone"><a class="viewcode-back" href="../../modules.html#MMTK.NucleicAcids.Nucleotide.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 sugar and phosphate groups</span>
<span class="sd"> :rtype: :class:`~MMTK.ChemicalObjects.Group`</span>
<span class="sd"> """</span>
<span class="n">bb</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">sugar</span>
<span class="k">if</span> <span class="nb">hasattr</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="s">'phosphate'</span><span class="p">):</span>
<span class="n">bb</span> <span class="o">=</span> <span class="n">Collections</span><span class="o">.</span><span class="n">Collection</span><span class="p">([</span><span class="n">bb</span><span class="p">,</span> <span class="bp">self</span><span class="o">.</span><span class="n">phosphate</span><span class="p">])</span>
<span class="k">return</span> <span class="n">bb</span>
</div>
<div class="viewcode-block" id="Nucleotide.bases"><a class="viewcode-back" href="../../modules.html#MMTK.NucleicAcids.Nucleotide.bases">[docs]</a> <span class="k">def</span> <span class="nf">bases</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span>
<span class="sd">"""</span>
<span class="sd"> :returns: the base 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">base</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">'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="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"># Nucleotide chains are molecules with added features.</span>
<span class="c">#</span>
<div class="viewcode-block" id="NucleotideChain"><a class="viewcode-back" href="../../modules.html#MMTK.NucleicAcids.NucleotideChain">[docs]</a><span class="k">class</span> <span class="nc">NucleotideChain</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"> Nucleotide chain</span>
<span class="sd"> Nucleotide chains consist of nucleotides that are linked together.</span>
<span class="sd"> They are a special kind of molecule, i.e. all molecule operations</span>
<span class="sd"> are available.</span>
<span class="sd"> Nucleotide chains act as sequences of residues. If n is a NucleotideChain</span>
<span class="sd"> object, then</span>
<span class="sd"> * len(n) yields the number of nucleotides</span>
<span class="sd"> * n[i] yields nucleotide number i</span>
<span class="sd"> * n[i:j] yields the subchain from nucleotide number i up to but</span>
<span class="sd"> excluding nucleotide number j</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="sd">"""</span>
<span class="sd"> :param sequence: the nucleotide sequence. This can be a string</span>
<span class="sd"> containing the one-letter codes, or a list</span>
<span class="sd"> of two-letter codes (a "d" or "r" for the type of</span>
<span class="sd"> sugar, and the one-letter base code), or a</span>
<span class="sd"> :class:`~MMTK.PDB.PDBNucleotideChain` object.</span>
<span class="sd"> If a PDBNucleotideChain object is supplied, the</span>
<span class="sd"> atomic positions it contains are assigned to the</span>
<span class="sd"> atoms of the newly generated nucleotide chain,</span>
<span class="sd"> otherwise the 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"> Default is "all". Currently the database contains</span>
<span class="sd"> definitions only for "all".</span>
<span class="sd"> :type model: str</span>
<span class="sd"> :keyword terminus_5: if True, the first residue is constructed</span>
<span class="sd"> using the 5'-terminal variant, if False the</span>
<span class="sd"> non-terminal version is used. Default is True.</span>
<span class="sd"> :type terminus_5: bool</span>
<span class="sd"> :keyword terminus_3: if True, the last residue is constructed</span>
<span class="sd"> using the 3'-terminal variant, if False the</span>
<span class="sd"> non-terminal version is used. Default is True.</span>
<span class="sd"> :type terminus_3: bool</span>
<span class="sd"> :keyword circular: if True, a bond is constructed</span>
<span class="sd"> between the first and the last residue.</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">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">hydrogens</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">'hydrogens'</span><span class="p">,</span> <span class="s">'all'</span><span class="p">)</span>
<span class="k">if</span> <span class="n">hydrogens</span> <span class="o">==</span> <span class="mi">1</span><span class="p">:</span>
<span class="n">hydrogens</span> <span class="o">=</span> <span class="s">'all'</span>
<span class="k">elif</span> <span class="n">hydrogens</span> <span class="o">==</span> <span class="mi">0</span><span class="p">:</span>
<span class="n">hydrogens</span> <span class="o">=</span> <span class="s">'none'</span>
<span class="n">term5</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">'terminus_5'</span><span class="p">,</span> <span class="bp">True</span><span class="p">)</span>
<span class="n">term3</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">'terminus_3'</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="k">try</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">except</span> <span class="ne">KeyError</span><span class="p">:</span>
<span class="n">model</span> <span class="o">=</span> <span class="n">hydrogens</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">'hydrogens'</span><span class="p">:</span> <span class="n">hydrogens</span><span class="p">,</span>
<span class="s">'terminus_5'</span><span class="p">:</span> <span class="n">term5</span><span class="p">,</span>
<span class="s">'terminus_3'</span><span class="p">:</span> <span class="n">term3</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">isinstance</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="nb">basestring</span><span class="p">):</span>
<span class="n">conf</span> <span class="o">=</span> <span class="bp">None</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="p">[</span><span class="n">r</span><span class="o">.</span><span class="n">name</span> <span class="k">for</span> <span class="n">r</span> <span class="ow">in</span> <span class="n">sequence</span><span class="p">]</span>
<span class="n">sequence</span> <span class="o">=</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">r</span><span class="p">)</span> <span class="k">for</span> <span class="n">r</span> <span class="ow">in</span> <span class="n">sequence</span><span class="p">]</span>
<span class="k">if</span> <span class="n">term5</span><span class="p">:</span>
<span class="k">if</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">find</span><span class="p">(</span><span class="s">'5ter'</span><span class="p">)</span> <span class="o">==</span> <span class="o">-</span><span class="mi">1</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="s">'_5ter'</span>
<span class="k">if</span> <span class="n">term3</span><span class="p">:</span>
<span class="k">if</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">find</span><span class="p">(</span><span class="s">'3ter'</span><span class="p">)</span> <span class="o">==</span> <span class="o">-</span><span class="mi">1</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="s">'_3ter'</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="ow">in</span> <span class="n">sequence</span><span class="p">:</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">Nucleotide</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="s">'_'</span> <span class="o">+</span> <span class="sb">`n`</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_nucleotide_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">NucleotideSubChain</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="NucleotideChain.backbone"><a class="viewcode-back" href="../../modules.html#MMTK.NucleicAcids.NucleotideChain.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 sugar and phosphate groups of all nucleotides</span>
<span class="sd"> :rtype: :class:`~MMTK.Collections.Collection`</span>
<span class="sd"> """</span>
<span class="n">bb</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">residue</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">bb</span><span class="o">.</span><span class="n">addObject</span><span class="p">(</span><span class="n">residue</span><span class="o">.</span><span class="n">phosphate</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="n">bb</span><span class="o">.</span><span class="n">addObject</span><span class="p">(</span><span class="n">residue</span><span class="o">.</span><span class="n">sugar</span><span class="p">)</span>
<span class="k">return</span> <span class="n">bb</span>
</div>
<div class="viewcode-block" id="NucleotideChain.bases"><a class="viewcode-back" href="../../modules.html#MMTK.NucleicAcids.NucleotideChain.bases">[docs]</a> <span class="k">def</span> <span class="nf">bases</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span>
<span class="sd">"""</span>
<span class="sd"> :returns: the base groups of all nucleotides</span>
<span class="sd"> :rtype: :class:`~MMTK.Collections.Collection`</span>
<span class="sd"> """</span>
<span class="k">return</span> <span class="n">Collections</span><span class="o">.</span><span class="n">Collection</span><span class="p">([</span><span class="n">r</span><span class="o">.</span><span class="n">base</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>
<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">"N"</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="n">s</span><span class="o">.</span><span class="n">ljust</span><span class="p">(</span><span class="mi">3</span><span class="p">)</span> <span class="k">for</span> <span class="n">s</span> <span class="ow">in</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="mi">1</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">phosphate</span><span class="o">.</span><span class="n">P</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">phosphate</span><span class="o">.</span><span class="n">P</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="NucleotideSubChain"><a class="viewcode-back" href="../../modules.html#MMTK.NucleicAcids.NucleotideSubChain">[docs]</a><span class="k">class</span> <span class="nc">NucleotideSubChain</span><span class="p">(</span><span class="n">NucleotideChain</span><span class="p">):</span>
<span class="sd">"""</span>
<span class="sd"> A contiguous part of a nucleotide chain</span>
<span class="sd"> NucleotideSubChain objects are the result of slicing operations on</span>
<span class="sd"> NucleotideChain objects. They cannot be created directly.</span>
<span class="sd"> NucleotideSubChain objects permit all operations of NucleotideChain</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="p">,</span> <span class="n">groups</span><span class="p">,</span> <span class="n">name</span> <span class="o">=</span> <span class="s">''</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="bp">self</span><span class="o">.</span><span class="n">atoms</span> <span class="o">+</span> <span class="n">g</span><span class="o">.</span><span class="n">atoms</span>
<span class="bp">self</span><span class="o">.</span><span class="n">bonds</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">g</span><span class="o">.</span><span class="n">bonds</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="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">i</span><span class="p">]</span><span class="o">.</span><span class="n">sugar</span><span class="o">.</span><span class="n">O_3</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">i</span><span class="o">+</span><span class="mi">1</span><span class="p">]</span><span class="o">.</span><span class="n">phosphate</span><span class="o">.</span><span class="n">P</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">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="c">#</span>
<span class="c"># Type check functions</span>
<span class="c">#</span></div>
<div class="viewcode-block" id="isNucleotideChain"><a class="viewcode-back" href="../../modules.html#MMTK.NucleicAcids.isNucleotideChain">[docs]</a><span class="k">def</span> <span class="nf">isNucleotideChain</span><span class="p">(</span><span class="n">x</span><span class="p">):</span>
<span class="s">"Returns True if x is a NucleotideChain."</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_nucleotide_chain'</span><span class="p">)</span></div>
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