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<a href="Bio-module.html">Package Bio</a> ::
<a href="Bio.PDB-module.html">Package PDB</a> ::
Module StructureBuilder
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<h1 class="epydoc">Source Code for <a href="Bio.PDB.StructureBuilder-module.html">Module Bio.PDB.StructureBuilder</a></h1>
<pre class="py-src">
<a name="L1"></a><tt class="py-lineno"> 1</tt> <tt class="py-line"><tt class="py-comment"># Copyright (C) 2002, Thomas Hamelryck (thamelry@binf.ku.dk)</tt> </tt>
<a name="L2"></a><tt class="py-lineno"> 2</tt> <tt class="py-line"><tt class="py-comment"></tt><tt class="py-comment"># This code is part of the Biopython distribution and governed by its</tt> </tt>
<a name="L3"></a><tt class="py-lineno"> 3</tt> <tt class="py-line"><tt class="py-comment"></tt><tt class="py-comment"># license. Please see the LICENSE file that should have been included</tt> </tt>
<a name="L4"></a><tt class="py-lineno"> 4</tt> <tt class="py-line"><tt class="py-comment"></tt><tt class="py-comment"># as part of this package. </tt> </tt>
<a name="L5"></a><tt class="py-lineno"> 5</tt> <tt class="py-line"><tt class="py-comment"></tt> </tt>
<a name="L6"></a><tt class="py-lineno"> 6</tt> <tt class="py-line"><tt class="py-keyword">import</tt> <tt class="py-name">sys</tt> </tt>
<a name="L7"></a><tt class="py-lineno"> 7</tt> <tt class="py-line"> </tt>
<a name="L8"></a><tt class="py-lineno"> 8</tt> <tt class="py-line"> </tt>
<a name="L9"></a><tt class="py-lineno"> 9</tt> <tt class="py-line"><tt id="link-0" class="py-name" targets="Variable Bio.PDB.AbstractPropertyMap.__doc__=Bio.PDB.AbstractPropertyMap-module.html#__doc__,Variable Bio.PDB.Atom.__doc__=Bio.PDB.Atom-module.html#__doc__,Variable Bio.PDB.Chain.__doc__=Bio.PDB.Chain-module.html#__doc__,Variable Bio.PDB.Entity.__doc__=Bio.PDB.Entity-module.html#__doc__,Variable Bio.PDB.HSExposure.__doc__=Bio.PDB.HSExposure-module.html#__doc__,Variable Bio.PDB.MMCIF2Dict.__doc__=Bio.PDB.MMCIF2Dict-module.html#__doc__,Variable Bio.PDB.MMCIFParser.__doc__=Bio.PDB.MMCIFParser-module.html#__doc__,Variable Bio.PDB.Model.__doc__=Bio.PDB.Model-module.html#__doc__,Variable Bio.PDB.NACCESS.__doc__=Bio.PDB.NACCESS-module.html#__doc__,Variable Bio.PDB.NeighborSearch.__doc__=Bio.PDB.NeighborSearch-module.html#__doc__,Variable Bio.PDB.PDBExceptions.__doc__=Bio.PDB.PDBExceptions-module.html#__doc__,Variable Bio.PDB.Polypeptide.__doc__=Bio.PDB.Polypeptide-module.html#__doc__,Variable Bio.PDB.Residue.__doc__=Bio.PDB.Residue-module.html#__doc__,Variable Bio.PDB.Selection.__doc__=Bio.PDB.Selection-module.html#__doc__,Variable Bio.PDB.Structure.__doc__=Bio.PDB.Structure-module.html#__doc__,Variable Bio.PDB.StructureBuilder.__doc__=Bio.PDB.StructureBuilder-module.html#__doc__,Variable Bio.PDB.__doc__=Bio.PDB-module.html#__doc__"><a title="Bio.PDB.AbstractPropertyMap.__doc__
Bio.PDB.Atom.__doc__
Bio.PDB.Chain.__doc__
Bio.PDB.Entity.__doc__
Bio.PDB.HSExposure.__doc__
Bio.PDB.MMCIF2Dict.__doc__
Bio.PDB.MMCIFParser.__doc__
Bio.PDB.Model.__doc__
Bio.PDB.NACCESS.__doc__
Bio.PDB.NeighborSearch.__doc__
Bio.PDB.PDBExceptions.__doc__
Bio.PDB.Polypeptide.__doc__
Bio.PDB.Residue.__doc__
Bio.PDB.Selection.__doc__
Bio.PDB.Structure.__doc__
Bio.PDB.StructureBuilder.__doc__
Bio.PDB.__doc__" class="py-name" href="#" onclick="return doclink('link-0', '__doc__', 'link-0');">__doc__</a></tt><tt class="py-op">=</tt><tt class="py-string">"""</tt> </tt>
<a name="L10"></a><tt class="py-lineno"> 10</tt> <tt class="py-line"><tt class="py-string">Consumer class that builds a Structure object. This is used by </tt> </tt>
<a name="L11"></a><tt class="py-lineno"> 11</tt> <tt class="py-line"><tt class="py-string">the PDBParser and MMCIFparser classes.</tt> </tt>
<a name="L12"></a><tt class="py-lineno"> 12</tt> <tt class="py-line"><tt class="py-string">"""</tt> </tt>
<a name="L13"></a><tt class="py-lineno"> 13</tt> <tt class="py-line"> </tt>
<a name="L14"></a><tt class="py-lineno"> 14</tt> <tt class="py-line"> </tt>
<a name="L15"></a><tt class="py-lineno"> 15</tt> <tt class="py-line"><tt class="py-comment"># My stuff </tt> </tt>
<a name="L16"></a><tt class="py-lineno"> 16</tt> <tt class="py-line"><tt class="py-comment"></tt><tt class="py-comment"># SMCRA hierarchy</tt> </tt>
<a name="L17"></a><tt class="py-lineno"> 17</tt> <tt class="py-line"><tt class="py-comment"></tt><tt class="py-keyword">from</tt> <tt id="link-1" class="py-name" targets="Module Bio.PDB.Structure=Bio.PDB.Structure-module.html,Class Bio.PDB.Structure.Structure=Bio.PDB.Structure.Structure-class.html"><a title="Bio.PDB.Structure
Bio.PDB.Structure.Structure" class="py-name" href="#" onclick="return doclink('link-1', 'Structure', 'link-1');">Structure</a></tt> <tt class="py-keyword">import</tt> <tt id="link-2" class="py-name"><a title="Bio.PDB.Structure
Bio.PDB.Structure.Structure" class="py-name" href="#" onclick="return doclink('link-2', 'Structure', 'link-1');">Structure</a></tt> </tt>
<a name="L18"></a><tt class="py-lineno"> 18</tt> <tt class="py-line"><tt class="py-keyword">from</tt> <tt id="link-3" class="py-name" targets="Module Bio.PDB.Model=Bio.PDB.Model-module.html,Class Bio.PDB.Model.Model=Bio.PDB.Model.Model-class.html"><a title="Bio.PDB.Model
Bio.PDB.Model.Model" class="py-name" href="#" onclick="return doclink('link-3', 'Model', 'link-3');">Model</a></tt> <tt class="py-keyword">import</tt> <tt id="link-4" class="py-name"><a title="Bio.PDB.Model
Bio.PDB.Model.Model" class="py-name" href="#" onclick="return doclink('link-4', 'Model', 'link-3');">Model</a></tt> </tt>
<a name="L19"></a><tt class="py-lineno"> 19</tt> <tt class="py-line"><tt class="py-keyword">from</tt> <tt id="link-5" class="py-name" targets="Class Bio.Crystal.Chain=Bio.Crystal.Chain-class.html,Class Bio.Nexus.Nodes.Chain=Bio.Nexus.Nodes.Chain-class.html,Module Bio.PDB.Chain=Bio.PDB.Chain-module.html,Class Bio.PDB.Chain.Chain=Bio.PDB.Chain.Chain-class.html"><a title="Bio.Crystal.Chain
Bio.Nexus.Nodes.Chain
Bio.PDB.Chain
Bio.PDB.Chain.Chain" class="py-name" href="#" onclick="return doclink('link-5', 'Chain', 'link-5');">Chain</a></tt> <tt class="py-keyword">import</tt> <tt id="link-6" class="py-name"><a title="Bio.Crystal.Chain
Bio.Nexus.Nodes.Chain
Bio.PDB.Chain
Bio.PDB.Chain.Chain" class="py-name" href="#" onclick="return doclink('link-6', 'Chain', 'link-5');">Chain</a></tt> </tt>
<a name="L20"></a><tt class="py-lineno"> 20</tt> <tt class="py-line"><tt class="py-keyword">from</tt> <tt id="link-7" class="py-name" targets="Module Bio.PDB.Residue=Bio.PDB.Residue-module.html,Class Bio.PDB.Residue.Residue=Bio.PDB.Residue.Residue-class.html"><a title="Bio.PDB.Residue
Bio.PDB.Residue.Residue" class="py-name" href="#" onclick="return doclink('link-7', 'Residue', 'link-7');">Residue</a></tt> <tt class="py-keyword">import</tt> <tt id="link-8" class="py-name"><a title="Bio.PDB.Residue
Bio.PDB.Residue.Residue" class="py-name" href="#" onclick="return doclink('link-8', 'Residue', 'link-7');">Residue</a></tt><tt class="py-op">,</tt> <tt id="link-9" class="py-name" targets="Class Bio.PDB.Residue.DisorderedResidue=Bio.PDB.Residue.DisorderedResidue-class.html"><a title="Bio.PDB.Residue.DisorderedResidue" class="py-name" href="#" onclick="return doclink('link-9', 'DisorderedResidue', 'link-9');">DisorderedResidue</a></tt> </tt>
<a name="L21"></a><tt class="py-lineno"> 21</tt> <tt class="py-line"><tt class="py-keyword">from</tt> <tt id="link-10" class="py-name" targets="Module Bio.PDB.Atom=Bio.PDB.Atom-module.html,Class Bio.PDB.Atom.Atom=Bio.PDB.Atom.Atom-class.html"><a title="Bio.PDB.Atom
Bio.PDB.Atom.Atom" class="py-name" href="#" onclick="return doclink('link-10', 'Atom', 'link-10');">Atom</a></tt> <tt class="py-keyword">import</tt> <tt id="link-11" class="py-name"><a title="Bio.PDB.Atom
Bio.PDB.Atom.Atom" class="py-name" href="#" onclick="return doclink('link-11', 'Atom', 'link-10');">Atom</a></tt><tt class="py-op">,</tt> <tt id="link-12" class="py-name" targets="Class Bio.PDB.Atom.DisorderedAtom=Bio.PDB.Atom.DisorderedAtom-class.html"><a title="Bio.PDB.Atom.DisorderedAtom" class="py-name" href="#" onclick="return doclink('link-12', 'DisorderedAtom', 'link-12');">DisorderedAtom</a></tt> </tt>
<a name="L22"></a><tt class="py-lineno"> 22</tt> <tt class="py-line"> </tt>
<a name="L23"></a><tt class="py-lineno"> 23</tt> <tt class="py-line"><tt class="py-keyword">from</tt> <tt id="link-13" class="py-name" targets="Module Bio.PDB.PDBExceptions=Bio.PDB.PDBExceptions-module.html"><a title="Bio.PDB.PDBExceptions" class="py-name" href="#" onclick="return doclink('link-13', 'PDBExceptions', 'link-13');">PDBExceptions</a></tt> <tt class="py-keyword">import</tt> <tt id="link-14" class="py-name" targets="Variable Bio.PDB.PDBExceptions.PDBConstructionException=Bio.PDB.PDBExceptions-module.html#PDBConstructionException,Variable Bio.PDB.PDBParser'.PDBConstructionException=Bio.PDB.PDBParser%27-module.html#PDBConstructionException"><a title="Bio.PDB.PDBExceptions.PDBConstructionException
Bio.PDB.PDBParser'.PDBConstructionException" class="py-name" href="#" onclick="return doclink('link-14', 'PDBConstructionException', 'link-14');">PDBConstructionException</a></tt> </tt>
<a name="L24"></a><tt class="py-lineno"> 24</tt> <tt class="py-line"> </tt>
<a name="L25"></a><tt class="py-lineno"> 25</tt> <tt class="py-line"> </tt>
<a name="StructureBuilder"></a><div id="StructureBuilder-def"><a name="L26"></a><tt class="py-lineno"> 26</tt> <a class="py-toggle" href="#" id="StructureBuilder-toggle" onclick="return toggle('StructureBuilder');">-</a><tt class="py-line"><tt class="py-keyword">class</tt> <a class="py-def-name" href="Bio.PDB.StructureBuilder.StructureBuilder-class.html">StructureBuilder</a><tt class="py-op">:</tt> </tt>
</div><div id="StructureBuilder-collapsed" style="display:none;" pad="+++" indent="++++"></div><div id="StructureBuilder-expanded"><a name="L27"></a><tt class="py-lineno"> 27</tt> <tt class="py-line"> <tt class="py-docstring">"""</tt> </tt>
<a name="L28"></a><tt class="py-lineno"> 28</tt> <tt class="py-line"><tt class="py-docstring"> Deals with contructing the Structure object. The StructureBuilder class is used</tt> </tt>
<a name="L29"></a><tt class="py-lineno"> 29</tt> <tt class="py-line"><tt class="py-docstring"> by the PDBParser classes to translate a file to a Structure object.</tt> </tt>
<a name="L30"></a><tt class="py-lineno"> 30</tt> <tt class="py-line"><tt class="py-docstring"> """</tt> </tt>
<a name="StructureBuilder.__init__"></a><div id="StructureBuilder.__init__-def"><a name="L31"></a><tt class="py-lineno"> 31</tt> <a class="py-toggle" href="#" id="StructureBuilder.__init__-toggle" onclick="return toggle('StructureBuilder.__init__');">-</a><tt class="py-line"> <tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.PDB.StructureBuilder.StructureBuilder-class.html#__init__">__init__</a><tt class="py-op">(</tt><tt class="py-param">self</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="StructureBuilder.__init__-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="StructureBuilder.__init__-expanded"><a name="L32"></a><tt class="py-lineno"> 32</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">line_counter</tt><tt class="py-op">=</tt><tt class="py-number">0</tt> </tt>
<a name="L33"></a><tt class="py-lineno"> 33</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-15" class="py-name" targets="Variable Bio.Wise.dnal.Statistics.header=Bio.Wise.dnal.Statistics-class.html#header,Variable Bio.expressions.blast.ncbiblast.header=Bio.expressions.blast.ncbiblast-module.html#header,Variable Bio.expressions.blast.wublast.header=Bio.expressions.blast.wublast-module.html#header,Variable Bio.expressions.blocks.header=Bio.expressions.blocks-module.html#header,Variable Bio.expressions.genbank.header=Bio.expressions.genbank-module.html#header,Variable Bio.expressions.hmmpfam.header=Bio.expressions.hmmpfam-module.html#header"><a title="Bio.Wise.dnal.Statistics.header
Bio.expressions.blast.ncbiblast.header
Bio.expressions.blast.wublast.header
Bio.expressions.blocks.header
Bio.expressions.genbank.header
Bio.expressions.hmmpfam.header" class="py-name" href="#" onclick="return doclink('link-15', 'header', 'link-15');">header</a></tt><tt class="py-op">=</tt><tt class="py-op">{</tt><tt class="py-op">}</tt> </tt>
</div><a name="L34"></a><tt class="py-lineno"> 34</tt> <tt class="py-line"> </tt>
<a name="StructureBuilder._is_completely_disordered"></a><div id="StructureBuilder._is_completely_disordered-def"><a name="L35"></a><tt class="py-lineno"> 35</tt> <a class="py-toggle" href="#" id="StructureBuilder._is_completely_disordered-toggle" onclick="return toggle('StructureBuilder._is_completely_disordered');">-</a><tt class="py-line"> <tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.PDB.StructureBuilder.StructureBuilder-class.html#_is_completely_disordered">_is_completely_disordered</a><tt class="py-op">(</tt><tt class="py-param">self</tt><tt class="py-op">,</tt> <tt class="py-param">residue</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="StructureBuilder._is_completely_disordered-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="StructureBuilder._is_completely_disordered-expanded"><a name="L36"></a><tt class="py-lineno"> 36</tt> <tt class="py-line"> <tt class="py-docstring">"Return 1 if all atoms in the residue have a non blanc altloc."</tt> </tt>
<a name="L37"></a><tt class="py-lineno"> 37</tt> <tt class="py-line"> <tt class="py-name">atom_list</tt><tt class="py-op">=</tt><tt class="py-name">residue</tt><tt class="py-op">.</tt><tt id="link-16" class="py-name" targets="Method Bio.PDB.Chain.Chain.get_unpacked_list()=Bio.PDB.Chain.Chain-class.html#get_unpacked_list,Method Bio.PDB.Residue.Residue.get_unpacked_list()=Bio.PDB.Residue.Residue-class.html#get_unpacked_list"><a title="Bio.PDB.Chain.Chain.get_unpacked_list
Bio.PDB.Residue.Residue.get_unpacked_list" class="py-name" href="#" onclick="return doclink('link-16', 'get_unpacked_list', 'link-16');">get_unpacked_list</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
<a name="L38"></a><tt class="py-lineno"> 38</tt> <tt class="py-line"> <tt class="py-keyword">for</tt> <tt class="py-name">atom</tt> <tt class="py-keyword">in</tt> <tt class="py-name">atom_list</tt><tt class="py-op">:</tt> </tt>
<a name="L39"></a><tt class="py-lineno"> 39</tt> <tt class="py-line"> <tt class="py-name">altloc</tt><tt class="py-op">=</tt><tt class="py-name">atom</tt><tt class="py-op">.</tt><tt id="link-17" class="py-name" targets="Method Bio.PDB.Atom.Atom.get_altloc()=Bio.PDB.Atom.Atom-class.html#get_altloc"><a title="Bio.PDB.Atom.Atom.get_altloc" class="py-name" href="#" onclick="return doclink('link-17', 'get_altloc', 'link-17');">get_altloc</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
<a name="L40"></a><tt class="py-lineno"> 40</tt> <tt class="py-line"> <tt class="py-keyword">if</tt> <tt class="py-name">altloc</tt><tt class="py-op">==</tt><tt class="py-string">" "</tt><tt class="py-op">:</tt> </tt>
<a name="L41"></a><tt class="py-lineno"> 41</tt> <tt class="py-line"> <tt class="py-keyword">return</tt> <tt class="py-number">0</tt> </tt>
<a name="L42"></a><tt class="py-lineno"> 42</tt> <tt class="py-line"> <tt class="py-keyword">return</tt> <tt class="py-number">1</tt> </tt>
</div><a name="L43"></a><tt class="py-lineno"> 43</tt> <tt class="py-line"> </tt>
<a name="L44"></a><tt class="py-lineno"> 44</tt> <tt class="py-line"> <tt class="py-comment"># Public methods called by the Parser classes</tt> </tt>
<a name="L45"></a><tt class="py-lineno"> 45</tt> <tt class="py-line"><tt class="py-comment"></tt> </tt>
<a name="StructureBuilder.set_header"></a><div id="StructureBuilder.set_header-def"><a name="L46"></a><tt class="py-lineno"> 46</tt> <a class="py-toggle" href="#" id="StructureBuilder.set_header-toggle" onclick="return toggle('StructureBuilder.set_header');">-</a><tt class="py-line"> <tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.PDB.StructureBuilder.StructureBuilder-class.html#set_header">set_header</a><tt class="py-op">(</tt><tt class="py-param">self</tt><tt class="py-op">,</tt> <tt class="py-param">header</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="StructureBuilder.set_header-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="StructureBuilder.set_header-expanded"><a name="L47"></a><tt class="py-lineno"> 47</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-18" class="py-name"><a title="Bio.Wise.dnal.Statistics.header
Bio.expressions.blast.ncbiblast.header
Bio.expressions.blast.wublast.header
Bio.expressions.blocks.header
Bio.expressions.genbank.header
Bio.expressions.hmmpfam.header" class="py-name" href="#" onclick="return doclink('link-18', 'header', 'link-15');">header</a></tt><tt class="py-op">=</tt><tt id="link-19" class="py-name"><a title="Bio.Wise.dnal.Statistics.header
Bio.expressions.blast.ncbiblast.header
Bio.expressions.blast.wublast.header
Bio.expressions.blocks.header
Bio.expressions.genbank.header
Bio.expressions.hmmpfam.header" class="py-name" href="#" onclick="return doclink('link-19', 'header', 'link-15');">header</a></tt> </tt>
</div><a name="L48"></a><tt class="py-lineno"> 48</tt> <tt class="py-line"> </tt>
<a name="StructureBuilder.set_line_counter"></a><div id="StructureBuilder.set_line_counter-def"><a name="L49"></a><tt class="py-lineno"> 49</tt> <a class="py-toggle" href="#" id="StructureBuilder.set_line_counter-toggle" onclick="return toggle('StructureBuilder.set_line_counter');">-</a><tt class="py-line"> <tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.PDB.StructureBuilder.StructureBuilder-class.html#set_line_counter">set_line_counter</a><tt class="py-op">(</tt><tt class="py-param">self</tt><tt class="py-op">,</tt> <tt class="py-param">line_counter</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="StructureBuilder.set_line_counter-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="StructureBuilder.set_line_counter-expanded"><a name="L50"></a><tt class="py-lineno"> 50</tt> <tt class="py-line"> <tt class="py-docstring">"""</tt> </tt>
<a name="L51"></a><tt class="py-lineno"> 51</tt> <tt class="py-line"><tt class="py-docstring"> The line counter keeps track of the line in the PDB file that </tt> </tt>
<a name="L52"></a><tt class="py-lineno"> 52</tt> <tt class="py-line"><tt class="py-docstring"> is being parsed.</tt> </tt>
<a name="L53"></a><tt class="py-lineno"> 53</tt> <tt class="py-line"><tt class="py-docstring"> </tt> </tt>
<a name="L54"></a><tt class="py-lineno"> 54</tt> <tt class="py-line"><tt class="py-docstring"> Arguments:</tt> </tt>
<a name="L55"></a><tt class="py-lineno"> 55</tt> <tt class="py-line"><tt class="py-docstring"> o line_counter - int</tt> </tt>
<a name="L56"></a><tt class="py-lineno"> 56</tt> <tt class="py-line"><tt class="py-docstring"> """</tt> </tt>
<a name="L57"></a><tt class="py-lineno"> 57</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">line_counter</tt><tt class="py-op">=</tt><tt class="py-name">line_counter</tt> </tt>
</div><a name="L58"></a><tt class="py-lineno"> 58</tt> <tt class="py-line"> </tt>
<a name="StructureBuilder.init_structure"></a><div id="StructureBuilder.init_structure-def"><a name="L59"></a><tt class="py-lineno"> 59</tt> <a class="py-toggle" href="#" id="StructureBuilder.init_structure-toggle" onclick="return toggle('StructureBuilder.init_structure');">-</a><tt class="py-line"> <tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.PDB.StructureBuilder.StructureBuilder-class.html#init_structure">init_structure</a><tt class="py-op">(</tt><tt class="py-param">self</tt><tt class="py-op">,</tt> <tt class="py-param">structure_id</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="StructureBuilder.init_structure-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="StructureBuilder.init_structure-expanded"><a name="L60"></a><tt class="py-lineno"> 60</tt> <tt class="py-line"> <tt class="py-docstring">"""Initiate a new Structure object with given id.</tt> </tt>
<a name="L61"></a><tt class="py-lineno"> 61</tt> <tt class="py-line"><tt class="py-docstring"></tt> </tt>
<a name="L62"></a><tt class="py-lineno"> 62</tt> <tt class="py-line"><tt class="py-docstring"> Arguments:</tt> </tt>
<a name="L63"></a><tt class="py-lineno"> 63</tt> <tt class="py-line"><tt class="py-docstring"> o id - string</tt> </tt>
<a name="L64"></a><tt class="py-lineno"> 64</tt> <tt class="py-line"><tt class="py-docstring"> """</tt> </tt>
<a name="L65"></a><tt class="py-lineno"> 65</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-20" class="py-name" targets="Variable Bio.SubsMat.MatrixInfo.structure=Bio.SubsMat.MatrixInfo-module.html#structure"><a title="Bio.SubsMat.MatrixInfo.structure" class="py-name" href="#" onclick="return doclink('link-20', 'structure', 'link-20');">structure</a></tt><tt class="py-op">=</tt><tt id="link-21" class="py-name"><a title="Bio.PDB.Structure
Bio.PDB.Structure.Structure" class="py-name" href="#" onclick="return doclink('link-21', 'Structure', 'link-1');">Structure</a></tt><tt class="py-op">(</tt><tt class="py-name">structure_id</tt><tt class="py-op">)</tt> </tt>
</div><a name="L66"></a><tt class="py-lineno"> 66</tt> <tt class="py-line"> </tt>
<a name="StructureBuilder.init_model"></a><div id="StructureBuilder.init_model-def"><a name="L67"></a><tt class="py-lineno"> 67</tt> <a class="py-toggle" href="#" id="StructureBuilder.init_model-toggle" onclick="return toggle('StructureBuilder.init_model');">-</a><tt class="py-line"> <tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.PDB.StructureBuilder.StructureBuilder-class.html#init_model">init_model</a><tt class="py-op">(</tt><tt class="py-param">self</tt><tt class="py-op">,</tt> <tt class="py-param">model_id</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="StructureBuilder.init_model-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="StructureBuilder.init_model-expanded"><a name="L68"></a><tt class="py-lineno"> 68</tt> <tt class="py-line"> <tt class="py-docstring">"""Initiate a new Model object with given id.</tt> </tt>
<a name="L69"></a><tt class="py-lineno"> 69</tt> <tt class="py-line"><tt class="py-docstring"> </tt> </tt>
<a name="L70"></a><tt class="py-lineno"> 70</tt> <tt class="py-line"><tt class="py-docstring"> Arguments:</tt> </tt>
<a name="L71"></a><tt class="py-lineno"> 71</tt> <tt class="py-line"><tt class="py-docstring"> o id - int</tt> </tt>
<a name="L72"></a><tt class="py-lineno"> 72</tt> <tt class="py-line"><tt class="py-docstring"> """</tt> </tt>
<a name="L73"></a><tt class="py-lineno"> 73</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">model</tt><tt class="py-op">=</tt><tt id="link-22" class="py-name"><a title="Bio.PDB.Model
Bio.PDB.Model.Model" class="py-name" href="#" onclick="return doclink('link-22', 'Model', 'link-3');">Model</a></tt><tt class="py-op">(</tt><tt class="py-name">model_id</tt><tt class="py-op">)</tt> </tt>
<a name="L74"></a><tt class="py-lineno"> 74</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-23" class="py-name"><a title="Bio.SubsMat.MatrixInfo.structure" class="py-name" href="#" onclick="return doclink('link-23', 'structure', 'link-20');">structure</a></tt><tt class="py-op">.</tt><tt id="link-24" class="py-name" targets="Variable Bio.Affy.CelFile.add=Bio.Affy.CelFile-module.html#add,Method Bio.EUtils.POM.ElementNode.add()=Bio.EUtils.POM.ElementNode-class.html#add,Method Bio.GFF.easy.Location.add()=Bio.GFF.easy.Location-class.html#add,Method Bio.Graphics.BasicChromosome._ChromosomeComponent.add()=Bio.Graphics.BasicChromosome._ChromosomeComponent-class.html#add,Variable Bio.LogisticRegression.add=Bio.LogisticRegression-module.html#add,Variable Bio.MarkovModel.add=Bio.MarkovModel-module.html#add,Variable Bio.MaxEntropy.add=Bio.MaxEntropy-module.html#add,Variable Bio.NaiveBayes.add=Bio.NaiveBayes-module.html#add,Method Bio.Nexus.Nexus.StepMatrix.add()=Bio.Nexus.Nexus.StepMatrix-class.html#add,Method Bio.Nexus.Nodes.Chain.add()=Bio.Nexus.Nodes.Chain-class.html#add,Method Bio.PDB.Entity.Entity.add()=Bio.PDB.Entity.Entity-class.html#add,Method Bio.PDB.Residue.DisorderedResidue.add()=Bio.PDB.Residue.DisorderedResidue-class.html#add,Method Bio.PDB.Residue.Residue.add()=Bio.PDB.Residue.Residue-class.html#add,Method Bio.Pathway.Rep.HashSet.HashSet.add()=Bio.Pathway.Rep.HashSet.HashSet-class.html#add,Method Bio.Restriction.Restriction.RestrictionBatch.add()=Bio.Restriction.Restriction.RestrictionBatch-class.html#add,Variable Bio.Statistics.lowess.add=Bio.Statistics.lowess-module.html#add,Method Bio.config.FormatRegistry.FormatGroup.add()=Bio.config.FormatRegistry.FormatGroup-class.html#add,Method Bio.config.Registry.RegisterableGroup.add()=Bio.config.Registry.RegisterableGroup-class.html#add,Variable Bio.distance.add=Bio.distance-module.html#add,Variable Bio.kNN.add=Bio.kNN-module.html#add,Method Martel.Dispatch.MulticallEnd.add()=Martel.Dispatch.MulticallEnd-class.html#add,Method Martel.Dispatch.MulticallStart.add()=Martel.Dispatch.MulticallStart-class.html#add"><a title="Bio.Affy.CelFile.add
Bio.EUtils.POM.ElementNode.add
Bio.GFF.easy.Location.add
Bio.Graphics.BasicChromosome._ChromosomeComponent.add
Bio.LogisticRegression.add
Bio.MarkovModel.add
Bio.MaxEntropy.add
Bio.NaiveBayes.add
Bio.Nexus.Nexus.StepMatrix.add
Bio.Nexus.Nodes.Chain.add
Bio.PDB.Entity.Entity.add
Bio.PDB.Residue.DisorderedResidue.add
Bio.PDB.Residue.Residue.add
Bio.Pathway.Rep.HashSet.HashSet.add
Bio.Restriction.Restriction.RestrictionBatch.add
Bio.Statistics.lowess.add
Bio.config.FormatRegistry.FormatGroup.add
Bio.config.Registry.RegisterableGroup.add
Bio.distance.add
Bio.kNN.add
Martel.Dispatch.MulticallEnd.add
Martel.Dispatch.MulticallStart.add" class="py-name" href="#" onclick="return doclink('link-24', 'add', 'link-24');">add</a></tt><tt class="py-op">(</tt><tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">model</tt><tt class="py-op">)</tt> </tt>
</div><a name="L75"></a><tt class="py-lineno"> 75</tt> <tt class="py-line"> </tt>
<a name="StructureBuilder.init_chain"></a><div id="StructureBuilder.init_chain-def"><a name="L76"></a><tt class="py-lineno"> 76</tt> <a class="py-toggle" href="#" id="StructureBuilder.init_chain-toggle" onclick="return toggle('StructureBuilder.init_chain');">-</a><tt class="py-line"> <tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.PDB.StructureBuilder.StructureBuilder-class.html#init_chain">init_chain</a><tt class="py-op">(</tt><tt class="py-param">self</tt><tt class="py-op">,</tt> <tt class="py-param">chain_id</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="StructureBuilder.init_chain-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="StructureBuilder.init_chain-expanded"><a name="L77"></a><tt class="py-lineno"> 77</tt> <tt class="py-line"> <tt class="py-docstring">"""Initiate a new Chain object with given id.</tt> </tt>
<a name="L78"></a><tt class="py-lineno"> 78</tt> <tt class="py-line"><tt class="py-docstring"></tt> </tt>
<a name="L79"></a><tt class="py-lineno"> 79</tt> <tt class="py-line"><tt class="py-docstring"> Arguments:</tt> </tt>
<a name="L80"></a><tt class="py-lineno"> 80</tt> <tt class="py-line"><tt class="py-docstring"> o chain_id - string</tt> </tt>
<a name="L81"></a><tt class="py-lineno"> 81</tt> <tt class="py-line"><tt class="py-docstring"> """</tt> </tt>
<a name="L82"></a><tt class="py-lineno"> 82</tt> <tt class="py-line"> <tt class="py-keyword">if</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">model</tt><tt class="py-op">.</tt><tt id="link-25" class="py-name" targets="Method Bio.PDB.Chain.Chain.has_id()=Bio.PDB.Chain.Chain-class.html#has_id,Method Bio.PDB.Entity.Entity.has_id()=Bio.PDB.Entity.Entity-class.html#has_id"><a title="Bio.PDB.Chain.Chain.has_id
Bio.PDB.Entity.Entity.has_id" class="py-name" href="#" onclick="return doclink('link-25', 'has_id', 'link-25');">has_id</a></tt><tt class="py-op">(</tt><tt id="link-26" class="py-name" targets="Variable Bio.FSSP.fssp_rec.align.chain_id=Bio.FSSP.fssp_rec.align-class.html#chain_id"><a title="Bio.FSSP.fssp_rec.align.chain_id" class="py-name" href="#" onclick="return doclink('link-26', 'chain_id', 'link-26');">chain_id</a></tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
<a name="L83"></a><tt class="py-lineno"> 83</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">chain</tt><tt class="py-op">=</tt><tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">model</tt><tt class="py-op">[</tt><tt id="link-27" class="py-name"><a title="Bio.FSSP.fssp_rec.align.chain_id" class="py-name" href="#" onclick="return doclink('link-27', 'chain_id', 'link-26');">chain_id</a></tt><tt class="py-op">]</tt> </tt>
<a name="L84"></a><tt class="py-lineno"> 84</tt> <tt class="py-line"> <tt class="py-keyword">if</tt> <tt class="py-name">__debug__</tt><tt class="py-op">:</tt> </tt>
<a name="L85"></a><tt class="py-lineno"> 85</tt> <tt class="py-line"> <tt class="py-name">sys</tt><tt class="py-op">.</tt><tt class="py-name">stderr</tt><tt class="py-op">.</tt><tt id="link-28" class="py-name" targets="Method Bio.AlignAce.Motif.Motif.write()=Bio.AlignAce.Motif.Motif-class.html#write,Function Bio.AlignIO.write()=Bio.AlignIO-module.html#write,Method Bio.EUtils.sourcegen.SourceFile.write()=Bio.EUtils.sourcegen.SourceFile-class.html#write,Method Bio.EUtils.sourcegen.SourceGen.write()=Bio.EUtils.sourcegen.SourceGen-class.html#write,Method Bio.NeuralNetwork.Gene.Pattern.PatternIO.write()=Bio.NeuralNetwork.Gene.Pattern.PatternIO-class.html#write,Function Bio.SeqIO.write()=Bio.SeqIO-module.html#write,Method Bio.Writer.Writer.write()=Bio.Writer.Writer-class.html#write,Method Bio.writers.SeqRecord.embl.WriteEmbl.write()=Bio.writers.SeqRecord.embl.WriteEmbl-class.html#write,Method Bio.writers.SeqRecord.fasta.WriteFasta.write()=Bio.writers.SeqRecord.fasta.WriteFasta-class.html#write"><a title="Bio.AlignAce.Motif.Motif.write
Bio.AlignIO.write
Bio.EUtils.sourcegen.SourceFile.write
Bio.EUtils.sourcegen.SourceGen.write
Bio.NeuralNetwork.Gene.Pattern.PatternIO.write
Bio.SeqIO.write
Bio.Writer.Writer.write
Bio.writers.SeqRecord.embl.WriteEmbl.write
Bio.writers.SeqRecord.fasta.WriteFasta.write" class="py-name" href="#" onclick="return doclink('link-28', 'write', 'link-28');">write</a></tt><tt class="py-op">(</tt><tt class="py-string">"WARNING: Chain %s is discontinuous at line %i.\n"</tt> </tt>
<a name="L86"></a><tt class="py-lineno"> 86</tt> <tt class="py-line"> <tt class="py-op">%</tt> <tt class="py-op">(</tt><tt id="link-29" class="py-name"><a title="Bio.FSSP.fssp_rec.align.chain_id" class="py-name" href="#" onclick="return doclink('link-29', 'chain_id', 'link-26');">chain_id</a></tt><tt class="py-op">,</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">line_counter</tt><tt class="py-op">)</tt><tt class="py-op">)</tt> </tt>
<a name="L87"></a><tt class="py-lineno"> 87</tt> <tt class="py-line"> <tt class="py-keyword">else</tt><tt class="py-op">:</tt> </tt>
<a name="L88"></a><tt class="py-lineno"> 88</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">chain</tt><tt class="py-op">=</tt><tt id="link-30" class="py-name"><a title="Bio.Crystal.Chain
Bio.Nexus.Nodes.Chain
Bio.PDB.Chain
Bio.PDB.Chain.Chain" class="py-name" href="#" onclick="return doclink('link-30', 'Chain', 'link-5');">Chain</a></tt><tt class="py-op">(</tt><tt id="link-31" class="py-name"><a title="Bio.FSSP.fssp_rec.align.chain_id" class="py-name" href="#" onclick="return doclink('link-31', 'chain_id', 'link-26');">chain_id</a></tt><tt class="py-op">)</tt> </tt>
<a name="L89"></a><tt class="py-lineno"> 89</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">model</tt><tt class="py-op">.</tt><tt id="link-32" class="py-name"><a title="Bio.Affy.CelFile.add
Bio.EUtils.POM.ElementNode.add
Bio.GFF.easy.Location.add
Bio.Graphics.BasicChromosome._ChromosomeComponent.add
Bio.LogisticRegression.add
Bio.MarkovModel.add
Bio.MaxEntropy.add
Bio.NaiveBayes.add
Bio.Nexus.Nexus.StepMatrix.add
Bio.Nexus.Nodes.Chain.add
Bio.PDB.Entity.Entity.add
Bio.PDB.Residue.DisorderedResidue.add
Bio.PDB.Residue.Residue.add
Bio.Pathway.Rep.HashSet.HashSet.add
Bio.Restriction.Restriction.RestrictionBatch.add
Bio.Statistics.lowess.add
Bio.config.FormatRegistry.FormatGroup.add
Bio.config.Registry.RegisterableGroup.add
Bio.distance.add
Bio.kNN.add
Martel.Dispatch.MulticallEnd.add
Martel.Dispatch.MulticallStart.add" class="py-name" href="#" onclick="return doclink('link-32', 'add', 'link-24');">add</a></tt><tt class="py-op">(</tt><tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">chain</tt><tt class="py-op">)</tt> </tt>
</div><a name="L90"></a><tt class="py-lineno"> 90</tt> <tt class="py-line"> </tt>
<a name="StructureBuilder.init_seg"></a><div id="StructureBuilder.init_seg-def"><a name="L91"></a><tt class="py-lineno"> 91</tt> <a class="py-toggle" href="#" id="StructureBuilder.init_seg-toggle" onclick="return toggle('StructureBuilder.init_seg');">-</a><tt class="py-line"> <tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.PDB.StructureBuilder.StructureBuilder-class.html#init_seg">init_seg</a><tt class="py-op">(</tt><tt class="py-param">self</tt><tt class="py-op">,</tt> <tt class="py-param">segid</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="StructureBuilder.init_seg-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="StructureBuilder.init_seg-expanded"><a name="L92"></a><tt class="py-lineno"> 92</tt> <tt class="py-line"> <tt class="py-docstring">"""Flag a change in segid.</tt> </tt>
<a name="L93"></a><tt class="py-lineno"> 93</tt> <tt class="py-line"><tt class="py-docstring"> </tt> </tt>
<a name="L94"></a><tt class="py-lineno"> 94</tt> <tt class="py-line"><tt class="py-docstring"> Arguments:</tt> </tt>
<a name="L95"></a><tt class="py-lineno"> 95</tt> <tt class="py-line"><tt class="py-docstring"> o segid - string</tt> </tt>
<a name="L96"></a><tt class="py-lineno"> 96</tt> <tt class="py-line"><tt class="py-docstring"> """</tt> </tt>
<a name="L97"></a><tt class="py-lineno"> 97</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">segid</tt><tt class="py-op">=</tt><tt class="py-name">segid</tt> </tt>
</div><a name="L98"></a><tt class="py-lineno"> 98</tt> <tt class="py-line"> </tt>
<a name="StructureBuilder.init_residue"></a><div id="StructureBuilder.init_residue-def"><a name="L99"></a><tt class="py-lineno"> 99</tt> <a class="py-toggle" href="#" id="StructureBuilder.init_residue-toggle" onclick="return toggle('StructureBuilder.init_residue');">-</a><tt class="py-line"> <tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.PDB.StructureBuilder.StructureBuilder-class.html#init_residue">init_residue</a><tt class="py-op">(</tt><tt class="py-param">self</tt><tt class="py-op">,</tt> <tt class="py-param">resname</tt><tt class="py-op">,</tt> <tt class="py-param">field</tt><tt class="py-op">,</tt> <tt class="py-param">resseq</tt><tt class="py-op">,</tt> <tt class="py-param">icode</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="StructureBuilder.init_residue-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="StructureBuilder.init_residue-expanded"><a name="L100"></a><tt class="py-lineno">100</tt> <tt class="py-line"> <tt class="py-docstring">"""</tt> </tt>
<a name="L101"></a><tt class="py-lineno">101</tt> <tt class="py-line"><tt class="py-docstring"> Initiate a new Residue object.</tt> </tt>
<a name="L102"></a><tt class="py-lineno">102</tt> <tt class="py-line"><tt class="py-docstring"></tt> </tt>
<a name="L103"></a><tt class="py-lineno">103</tt> <tt class="py-line"><tt class="py-docstring"> Arguments:</tt> </tt>
<a name="L104"></a><tt class="py-lineno">104</tt> <tt class="py-line"><tt class="py-docstring"> o resname - string, e.g. "ASN"</tt> </tt>
<a name="L105"></a><tt class="py-lineno">105</tt> <tt class="py-line"><tt class="py-docstring"> o field - hetero flag, "W" for waters, "H" for </tt> </tt>
<a name="L106"></a><tt class="py-lineno">106</tt> <tt class="py-line"><tt class="py-docstring"> hetero residues, otherwise blanc.</tt> </tt>
<a name="L107"></a><tt class="py-lineno">107</tt> <tt class="py-line"><tt class="py-docstring"> o resseq - int, sequence identifier</tt> </tt>
<a name="L108"></a><tt class="py-lineno">108</tt> <tt class="py-line"><tt class="py-docstring"> o icode - string, insertion code</tt> </tt>
<a name="L109"></a><tt class="py-lineno">109</tt> <tt class="py-line"><tt class="py-docstring"> """</tt> </tt>
<a name="L110"></a><tt class="py-lineno">110</tt> <tt class="py-line"> <tt class="py-keyword">if</tt> <tt class="py-name">field</tt><tt class="py-op">!=</tt><tt class="py-string">" "</tt><tt class="py-op">:</tt> </tt>
<a name="L111"></a><tt class="py-lineno">111</tt> <tt class="py-line"> <tt class="py-keyword">if</tt> <tt class="py-name">field</tt><tt class="py-op">==</tt><tt class="py-string">"H"</tt><tt class="py-op">:</tt> </tt>
<a name="L112"></a><tt class="py-lineno">112</tt> <tt class="py-line"> <tt class="py-comment"># The hetero field consists of H_ + the residue name (e.g. H_FUC)</tt> </tt>
<a name="L113"></a><tt class="py-lineno">113</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-name">field</tt><tt class="py-op">=</tt><tt class="py-string">"H_"</tt><tt class="py-op">+</tt><tt class="py-name">resname</tt> </tt>
<a name="L114"></a><tt class="py-lineno">114</tt> <tt class="py-line"> <tt class="py-name">res_id</tt><tt class="py-op">=</tt><tt class="py-op">(</tt><tt class="py-name">field</tt><tt class="py-op">,</tt> <tt class="py-name">resseq</tt><tt class="py-op">,</tt> <tt class="py-name">icode</tt><tt class="py-op">)</tt> </tt>
<a name="L115"></a><tt class="py-lineno">115</tt> <tt class="py-line"> <tt class="py-keyword">if</tt> <tt class="py-name">field</tt><tt class="py-op">==</tt><tt class="py-string">" "</tt><tt class="py-op">:</tt> </tt>
<a name="L116"></a><tt class="py-lineno">116</tt> <tt class="py-line"> <tt class="py-keyword">if</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">chain</tt><tt class="py-op">.</tt><tt id="link-33" class="py-name"><a title="Bio.PDB.Chain.Chain.has_id
Bio.PDB.Entity.Entity.has_id" class="py-name" href="#" onclick="return doclink('link-33', 'has_id', 'link-25');">has_id</a></tt><tt class="py-op">(</tt><tt class="py-name">res_id</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
<a name="L117"></a><tt class="py-lineno">117</tt> <tt class="py-line"> <tt class="py-comment"># There already is a residue with the id (field, resseq, icode).</tt> </tt>
<a name="L118"></a><tt class="py-lineno">118</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-comment"># This only makes sense in the case of a point mutation.</tt> </tt>
<a name="L119"></a><tt class="py-lineno">119</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-keyword">if</tt> <tt class="py-name">__debug__</tt><tt class="py-op">:</tt> </tt>
<a name="L120"></a><tt class="py-lineno">120</tt> <tt class="py-line"> <tt class="py-name">sys</tt><tt class="py-op">.</tt><tt class="py-name">stderr</tt><tt class="py-op">.</tt><tt id="link-34" class="py-name"><a title="Bio.AlignAce.Motif.Motif.write
Bio.AlignIO.write
Bio.EUtils.sourcegen.SourceFile.write
Bio.EUtils.sourcegen.SourceGen.write
Bio.NeuralNetwork.Gene.Pattern.PatternIO.write
Bio.SeqIO.write
Bio.Writer.Writer.write
Bio.writers.SeqRecord.embl.WriteEmbl.write
Bio.writers.SeqRecord.fasta.WriteFasta.write" class="py-name" href="#" onclick="return doclink('link-34', 'write', 'link-28');">write</a></tt><tt class="py-op">(</tt><tt class="py-string">"WARNING: Residue ('%s', %i, '%s') redefined at line %i.\n"</tt> </tt>
<a name="L121"></a><tt class="py-lineno">121</tt> <tt class="py-line"> <tt class="py-op">%</tt> <tt class="py-op">(</tt><tt class="py-name">field</tt><tt class="py-op">,</tt> <tt class="py-name">resseq</tt><tt class="py-op">,</tt> <tt class="py-name">icode</tt><tt class="py-op">,</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">line_counter</tt><tt class="py-op">)</tt><tt class="py-op">)</tt> </tt>
<a name="L122"></a><tt class="py-lineno">122</tt> <tt class="py-line"> <tt class="py-name">duplicate_residue</tt><tt class="py-op">=</tt><tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">chain</tt><tt class="py-op">[</tt><tt class="py-name">res_id</tt><tt class="py-op">]</tt> </tt>
<a name="L123"></a><tt class="py-lineno">123</tt> <tt class="py-line"> <tt class="py-keyword">if</tt> <tt class="py-name">duplicate_residue</tt><tt class="py-op">.</tt><tt id="link-35" class="py-name" targets="Method Bio.PDB.Atom.Atom.is_disordered()=Bio.PDB.Atom.Atom-class.html#is_disordered,Method Bio.PDB.Entity.DisorderedEntityWrapper.is_disordered()=Bio.PDB.Entity.DisorderedEntityWrapper-class.html#is_disordered,Method Bio.PDB.Residue.Residue.is_disordered()=Bio.PDB.Residue.Residue-class.html#is_disordered"><a title="Bio.PDB.Atom.Atom.is_disordered
Bio.PDB.Entity.DisorderedEntityWrapper.is_disordered
Bio.PDB.Residue.Residue.is_disordered" class="py-name" href="#" onclick="return doclink('link-35', 'is_disordered', 'link-35');">is_disordered</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt><tt class="py-op">==</tt><tt class="py-number">2</tt><tt class="py-op">:</tt> </tt>
<a name="L124"></a><tt class="py-lineno">124</tt> <tt class="py-line"> <tt class="py-comment"># The residue in the chain is a DisorderedResidue object.</tt> </tt>
<a name="L125"></a><tt class="py-lineno">125</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-comment"># So just add the last Residue object. </tt> </tt>
<a name="L126"></a><tt class="py-lineno">126</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-keyword">if</tt> <tt class="py-name">duplicate_residue</tt><tt class="py-op">.</tt><tt id="link-36" class="py-name" targets="Method Bio.PDB.Entity.DisorderedEntityWrapper.disordered_has_id()=Bio.PDB.Entity.DisorderedEntityWrapper-class.html#disordered_has_id"><a title="Bio.PDB.Entity.DisorderedEntityWrapper.disordered_has_id" class="py-name" href="#" onclick="return doclink('link-36', 'disordered_has_id', 'link-36');">disordered_has_id</a></tt><tt class="py-op">(</tt><tt class="py-name">resname</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
<a name="L127"></a><tt class="py-lineno">127</tt> <tt class="py-line"> <tt class="py-comment"># The residue was already made</tt> </tt>
<a name="L128"></a><tt class="py-lineno">128</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">residue</tt><tt class="py-op">=</tt><tt class="py-name">duplicate_residue</tt> </tt>
<a name="L129"></a><tt class="py-lineno">129</tt> <tt class="py-line"> <tt class="py-name">duplicate_residue</tt><tt class="py-op">.</tt><tt id="link-37" class="py-name" targets="Method Bio.PDB.Entity.DisorderedEntityWrapper.disordered_select()=Bio.PDB.Entity.DisorderedEntityWrapper-class.html#disordered_select"><a title="Bio.PDB.Entity.DisorderedEntityWrapper.disordered_select" class="py-name" href="#" onclick="return doclink('link-37', 'disordered_select', 'link-37');">disordered_select</a></tt><tt class="py-op">(</tt><tt class="py-name">resname</tt><tt class="py-op">)</tt> </tt>
<a name="L130"></a><tt class="py-lineno">130</tt> <tt class="py-line"> <tt class="py-keyword">else</tt><tt class="py-op">:</tt> </tt>
<a name="L131"></a><tt class="py-lineno">131</tt> <tt class="py-line"> <tt class="py-comment"># Make a new residue and add it to the already</tt> </tt>
<a name="L132"></a><tt class="py-lineno">132</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-comment"># present DisorderedResidue</tt> </tt>
<a name="L133"></a><tt class="py-lineno">133</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-name">new_residue</tt><tt class="py-op">=</tt><tt id="link-38" class="py-name"><a title="Bio.PDB.Residue
Bio.PDB.Residue.Residue" class="py-name" href="#" onclick="return doclink('link-38', 'Residue', 'link-7');">Residue</a></tt><tt class="py-op">(</tt><tt class="py-name">res_id</tt><tt class="py-op">,</tt> <tt class="py-name">resname</tt><tt class="py-op">,</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">segid</tt><tt class="py-op">)</tt> </tt>
<a name="L134"></a><tt class="py-lineno">134</tt> <tt class="py-line"> <tt class="py-name">duplicate_residue</tt><tt class="py-op">.</tt><tt id="link-39" class="py-name" targets="Method Bio.PDB.Atom.DisorderedAtom.disordered_add()=Bio.PDB.Atom.DisorderedAtom-class.html#disordered_add,Method Bio.PDB.Entity.DisorderedEntityWrapper.disordered_add()=Bio.PDB.Entity.DisorderedEntityWrapper-class.html#disordered_add,Method Bio.PDB.Residue.DisorderedResidue.disordered_add()=Bio.PDB.Residue.DisorderedResidue-class.html#disordered_add"><a title="Bio.PDB.Atom.DisorderedAtom.disordered_add
Bio.PDB.Entity.DisorderedEntityWrapper.disordered_add
Bio.PDB.Residue.DisorderedResidue.disordered_add" class="py-name" href="#" onclick="return doclink('link-39', 'disordered_add', 'link-39');">disordered_add</a></tt><tt class="py-op">(</tt><tt class="py-name">new_residue</tt><tt class="py-op">)</tt> </tt>
<a name="L135"></a><tt class="py-lineno">135</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">residue</tt><tt class="py-op">=</tt><tt class="py-name">duplicate_residue</tt> </tt>
<a name="L136"></a><tt class="py-lineno">136</tt> <tt class="py-line"> <tt class="py-keyword">return</tt> </tt>
<a name="L137"></a><tt class="py-lineno">137</tt> <tt class="py-line"> <tt class="py-keyword">else</tt><tt class="py-op">:</tt> </tt>
<a name="L138"></a><tt class="py-lineno">138</tt> <tt class="py-line"> <tt class="py-comment"># Make a new DisorderedResidue object and put all</tt> </tt>
<a name="L139"></a><tt class="py-lineno">139</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-comment"># the Residue objects with the id (field, resseq, icode) in it.</tt> </tt>
<a name="L140"></a><tt class="py-lineno">140</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-comment"># These residues each should have non-blanc altlocs for all their atoms.</tt> </tt>
<a name="L141"></a><tt class="py-lineno">141</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-comment"># If not, the PDB file probably contains an error. </tt> </tt>
<a name="L142"></a><tt class="py-lineno">142</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-keyword">if</tt> <tt class="py-keyword">not</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-40" class="py-name" targets="Method Bio.PDB.StructureBuilder.StructureBuilder._is_completely_disordered()=Bio.PDB.StructureBuilder.StructureBuilder-class.html#_is_completely_disordered"><a title="Bio.PDB.StructureBuilder.StructureBuilder._is_completely_disordered" class="py-name" href="#" onclick="return doclink('link-40', '_is_completely_disordered', 'link-40');">_is_completely_disordered</a></tt><tt class="py-op">(</tt><tt class="py-name">duplicate_residue</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
<a name="L143"></a><tt class="py-lineno">143</tt> <tt class="py-line"> <tt class="py-comment"># if this exception is ignored, a residue will be missing</tt> </tt>
<a name="L144"></a><tt class="py-lineno">144</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">residue</tt><tt class="py-op">=</tt><tt class="py-name">None</tt> </tt>
<a name="L145"></a><tt class="py-lineno">145</tt> <tt class="py-line"> <tt class="py-keyword">raise</tt> <tt id="link-41" class="py-name"><a title="Bio.PDB.PDBExceptions.PDBConstructionException
Bio.PDB.PDBParser'.PDBConstructionException" class="py-name" href="#" onclick="return doclink('link-41', 'PDBConstructionException', 'link-14');">PDBConstructionException</a></tt><tt class="py-op">,</tt> <tt class="py-string">"Blank altlocs in duplicate residue %s ('%s', %i, '%s')"</tt> <tt class="py-op">%</tt> <tt class="py-op">(</tt><tt class="py-name">resname</tt><tt class="py-op">,</tt> <tt class="py-name">field</tt><tt class="py-op">,</tt> <tt class="py-name">resseq</tt><tt class="py-op">,</tt> <tt class="py-name">icode</tt><tt class="py-op">)</tt> </tt>
<a name="L146"></a><tt class="py-lineno">146</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">chain</tt><tt class="py-op">.</tt><tt id="link-42" class="py-name" targets="Method Bio.PDB.Entity.Entity.detach_child()=Bio.PDB.Entity.Entity-class.html#detach_child"><a title="Bio.PDB.Entity.Entity.detach_child" class="py-name" href="#" onclick="return doclink('link-42', 'detach_child', 'link-42');">detach_child</a></tt><tt class="py-op">(</tt><tt class="py-name">res_id</tt><tt class="py-op">)</tt> </tt>
<a name="L147"></a><tt class="py-lineno">147</tt> <tt class="py-line"> <tt class="py-name">new_residue</tt><tt class="py-op">=</tt><tt id="link-43" class="py-name"><a title="Bio.PDB.Residue
Bio.PDB.Residue.Residue" class="py-name" href="#" onclick="return doclink('link-43', 'Residue', 'link-7');">Residue</a></tt><tt class="py-op">(</tt><tt class="py-name">res_id</tt><tt class="py-op">,</tt> <tt class="py-name">resname</tt><tt class="py-op">,</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">segid</tt><tt class="py-op">)</tt> </tt>
<a name="L148"></a><tt class="py-lineno">148</tt> <tt class="py-line"> <tt class="py-name">disordered_residue</tt><tt class="py-op">=</tt><tt id="link-44" class="py-name"><a title="Bio.PDB.Residue.DisorderedResidue" class="py-name" href="#" onclick="return doclink('link-44', 'DisorderedResidue', 'link-9');">DisorderedResidue</a></tt><tt class="py-op">(</tt><tt class="py-name">res_id</tt><tt class="py-op">)</tt> </tt>
<a name="L149"></a><tt class="py-lineno">149</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">chain</tt><tt class="py-op">.</tt><tt id="link-45" class="py-name"><a title="Bio.Affy.CelFile.add
Bio.EUtils.POM.ElementNode.add
Bio.GFF.easy.Location.add
Bio.Graphics.BasicChromosome._ChromosomeComponent.add
Bio.LogisticRegression.add
Bio.MarkovModel.add
Bio.MaxEntropy.add
Bio.NaiveBayes.add
Bio.Nexus.Nexus.StepMatrix.add
Bio.Nexus.Nodes.Chain.add
Bio.PDB.Entity.Entity.add
Bio.PDB.Residue.DisorderedResidue.add
Bio.PDB.Residue.Residue.add
Bio.Pathway.Rep.HashSet.HashSet.add
Bio.Restriction.Restriction.RestrictionBatch.add
Bio.Statistics.lowess.add
Bio.config.FormatRegistry.FormatGroup.add
Bio.config.Registry.RegisterableGroup.add
Bio.distance.add
Bio.kNN.add
Martel.Dispatch.MulticallEnd.add
Martel.Dispatch.MulticallStart.add" class="py-name" href="#" onclick="return doclink('link-45', 'add', 'link-24');">add</a></tt><tt class="py-op">(</tt><tt class="py-name">disordered_residue</tt><tt class="py-op">)</tt> </tt>
<a name="L150"></a><tt class="py-lineno">150</tt> <tt class="py-line"> <tt class="py-name">disordered_residue</tt><tt class="py-op">.</tt><tt id="link-46" class="py-name"><a title="Bio.PDB.Atom.DisorderedAtom.disordered_add
Bio.PDB.Entity.DisorderedEntityWrapper.disordered_add
Bio.PDB.Residue.DisorderedResidue.disordered_add" class="py-name" href="#" onclick="return doclink('link-46', 'disordered_add', 'link-39');">disordered_add</a></tt><tt class="py-op">(</tt><tt class="py-name">duplicate_residue</tt><tt class="py-op">)</tt> </tt>
<a name="L151"></a><tt class="py-lineno">151</tt> <tt class="py-line"> <tt class="py-name">disordered_residue</tt><tt class="py-op">.</tt><tt id="link-47" class="py-name"><a title="Bio.PDB.Atom.DisorderedAtom.disordered_add
Bio.PDB.Entity.DisorderedEntityWrapper.disordered_add
Bio.PDB.Residue.DisorderedResidue.disordered_add" class="py-name" href="#" onclick="return doclink('link-47', 'disordered_add', 'link-39');">disordered_add</a></tt><tt class="py-op">(</tt><tt class="py-name">new_residue</tt><tt class="py-op">)</tt> </tt>
<a name="L152"></a><tt class="py-lineno">152</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">residue</tt><tt class="py-op">=</tt><tt class="py-name">disordered_residue</tt> </tt>
<a name="L153"></a><tt class="py-lineno">153</tt> <tt class="py-line"> <tt class="py-keyword">return</tt> </tt>
<a name="L154"></a><tt class="py-lineno">154</tt> <tt class="py-line"> <tt class="py-name">residue</tt><tt class="py-op">=</tt><tt id="link-48" class="py-name"><a title="Bio.PDB.Residue
Bio.PDB.Residue.Residue" class="py-name" href="#" onclick="return doclink('link-48', 'Residue', 'link-7');">Residue</a></tt><tt class="py-op">(</tt><tt class="py-name">res_id</tt><tt class="py-op">,</tt> <tt class="py-name">resname</tt><tt class="py-op">,</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">segid</tt><tt class="py-op">)</tt> </tt>
<a name="L155"></a><tt class="py-lineno">155</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">chain</tt><tt class="py-op">.</tt><tt id="link-49" class="py-name"><a title="Bio.Affy.CelFile.add
Bio.EUtils.POM.ElementNode.add
Bio.GFF.easy.Location.add
Bio.Graphics.BasicChromosome._ChromosomeComponent.add
Bio.LogisticRegression.add
Bio.MarkovModel.add
Bio.MaxEntropy.add
Bio.NaiveBayes.add
Bio.Nexus.Nexus.StepMatrix.add
Bio.Nexus.Nodes.Chain.add
Bio.PDB.Entity.Entity.add
Bio.PDB.Residue.DisorderedResidue.add
Bio.PDB.Residue.Residue.add
Bio.Pathway.Rep.HashSet.HashSet.add
Bio.Restriction.Restriction.RestrictionBatch.add
Bio.Statistics.lowess.add
Bio.config.FormatRegistry.FormatGroup.add
Bio.config.Registry.RegisterableGroup.add
Bio.distance.add
Bio.kNN.add
Martel.Dispatch.MulticallEnd.add
Martel.Dispatch.MulticallStart.add" class="py-name" href="#" onclick="return doclink('link-49', 'add', 'link-24');">add</a></tt><tt class="py-op">(</tt><tt class="py-name">residue</tt><tt class="py-op">)</tt> </tt>
<a name="L156"></a><tt class="py-lineno">156</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">residue</tt><tt class="py-op">=</tt><tt class="py-name">residue</tt> </tt>
</div><a name="L157"></a><tt class="py-lineno">157</tt> <tt class="py-line"> </tt>
<a name="StructureBuilder.init_atom"></a><div id="StructureBuilder.init_atom-def"><a name="L158"></a><tt class="py-lineno">158</tt> <a class="py-toggle" href="#" id="StructureBuilder.init_atom-toggle" onclick="return toggle('StructureBuilder.init_atom');">-</a><tt class="py-line"> <tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.PDB.StructureBuilder.StructureBuilder-class.html#init_atom">init_atom</a><tt class="py-op">(</tt><tt class="py-param">self</tt><tt class="py-op">,</tt> <tt class="py-param">name</tt><tt class="py-op">,</tt> <tt class="py-param">coord</tt><tt class="py-op">,</tt> <tt class="py-param">b_factor</tt><tt class="py-op">,</tt> <tt class="py-param">occupancy</tt><tt class="py-op">,</tt> <tt class="py-param">altloc</tt><tt class="py-op">,</tt> <tt class="py-param">fullname</tt><tt class="py-op">,</tt> <tt class="py-param">serial_number</tt><tt class="py-op">=</tt><tt class="py-name">None</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="StructureBuilder.init_atom-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="StructureBuilder.init_atom-expanded"><a name="L159"></a><tt class="py-lineno">159</tt> <tt class="py-line"> <tt class="py-docstring">"""</tt> </tt>
<a name="L160"></a><tt class="py-lineno">160</tt> <tt class="py-line"><tt class="py-docstring"> Initiate a new Atom object.</tt> </tt>
<a name="L161"></a><tt class="py-lineno">161</tt> <tt class="py-line"><tt class="py-docstring"></tt> </tt>
<a name="L162"></a><tt class="py-lineno">162</tt> <tt class="py-line"><tt class="py-docstring"> Arguments:</tt> </tt>
<a name="L163"></a><tt class="py-lineno">163</tt> <tt class="py-line"><tt class="py-docstring"> o name - string, atom name, e.g. CA, spaces should be stripped</tt> </tt>
<a name="L164"></a><tt class="py-lineno">164</tt> <tt class="py-line"><tt class="py-docstring"> o coord - Numeric array (Float0, size 3), atomic coordinates</tt> </tt>
<a name="L165"></a><tt class="py-lineno">165</tt> <tt class="py-line"><tt class="py-docstring"> o b_factor - float, B factor</tt> </tt>
<a name="L166"></a><tt class="py-lineno">166</tt> <tt class="py-line"><tt class="py-docstring"> o occupancy - float</tt> </tt>
<a name="L167"></a><tt class="py-lineno">167</tt> <tt class="py-line"><tt class="py-docstring"> o altloc - string, alternative location specifier</tt> </tt>
<a name="L168"></a><tt class="py-lineno">168</tt> <tt class="py-line"><tt class="py-docstring"> o fullname - string, atom name including spaces, e.g. " CA "</tt> </tt>
<a name="L169"></a><tt class="py-lineno">169</tt> <tt class="py-line"><tt class="py-docstring"> """</tt> </tt>
<a name="L170"></a><tt class="py-lineno">170</tt> <tt class="py-line"> <tt class="py-name">residue</tt><tt class="py-op">=</tt><tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">residue</tt> </tt>
<a name="L171"></a><tt class="py-lineno">171</tt> <tt class="py-line"> <tt class="py-comment"># if residue is None, an exception was generated during</tt> </tt>
<a name="L172"></a><tt class="py-lineno">172</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-comment"># the construction of the residue</tt> </tt>
<a name="L173"></a><tt class="py-lineno">173</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-keyword">if</tt> <tt class="py-name">residue</tt> <tt class="py-keyword">is</tt> <tt class="py-name">None</tt><tt class="py-op">:</tt> </tt>
<a name="L174"></a><tt class="py-lineno">174</tt> <tt class="py-line"> <tt class="py-keyword">return</tt> </tt>
<a name="L175"></a><tt class="py-lineno">175</tt> <tt class="py-line"> <tt class="py-comment"># First check if this atom is already present in the residue. </tt> </tt>
<a name="L176"></a><tt class="py-lineno">176</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-comment"># If it is, it might be due to the fact that the two atoms have atom </tt> </tt>
<a name="L177"></a><tt class="py-lineno">177</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-comment"># names that differ only in spaces (e.g. "CA.." and ".CA.",</tt> </tt>
<a name="L178"></a><tt class="py-lineno">178</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-comment"># where the dots are spaces). If that is so, use all spaces</tt> </tt>
<a name="L179"></a><tt class="py-lineno">179</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-comment"># in the atom name of the current atom. </tt> </tt>
<a name="L180"></a><tt class="py-lineno">180</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-keyword">if</tt> <tt class="py-name">residue</tt><tt class="py-op">.</tt><tt id="link-50" class="py-name"><a title="Bio.PDB.Chain.Chain.has_id
Bio.PDB.Entity.Entity.has_id" class="py-name" href="#" onclick="return doclink('link-50', 'has_id', 'link-25');">has_id</a></tt><tt class="py-op">(</tt><tt id="link-51" class="py-name" targets="Variable Bio.Encodings.IUPACEncoding.name=Bio.Encodings.IUPACEncoding-module.html#name"><a title="Bio.Encodings.IUPACEncoding.name" class="py-name" href="#" onclick="return doclink('link-51', 'name', 'link-51');">name</a></tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
<a name="L181"></a><tt class="py-lineno">181</tt> <tt class="py-line"> <tt class="py-name">duplicate_atom</tt><tt class="py-op">=</tt><tt class="py-name">residue</tt><tt class="py-op">[</tt><tt id="link-52" class="py-name"><a title="Bio.Encodings.IUPACEncoding.name" class="py-name" href="#" onclick="return doclink('link-52', 'name', 'link-51');">name</a></tt><tt class="py-op">]</tt> </tt>
<a name="L182"></a><tt class="py-lineno">182</tt> <tt class="py-line"> <tt class="py-comment"># atom name with spaces of duplicate atom</tt> </tt>
<a name="L183"></a><tt class="py-lineno">183</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-name">duplicate_fullname</tt><tt class="py-op">=</tt><tt class="py-name">duplicate_atom</tt><tt class="py-op">.</tt><tt id="link-53" class="py-name" targets="Method Bio.PDB.Atom.Atom.get_fullname()=Bio.PDB.Atom.Atom-class.html#get_fullname"><a title="Bio.PDB.Atom.Atom.get_fullname" class="py-name" href="#" onclick="return doclink('link-53', 'get_fullname', 'link-53');">get_fullname</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
<a name="L184"></a><tt class="py-lineno">184</tt> <tt class="py-line"> <tt class="py-keyword">if</tt> <tt class="py-name">duplicate_fullname</tt><tt class="py-op">!=</tt><tt class="py-name">fullname</tt><tt class="py-op">:</tt> </tt>
<a name="L185"></a><tt class="py-lineno">185</tt> <tt class="py-line"> <tt class="py-comment"># name of current atom now includes spaces</tt> </tt>
<a name="L186"></a><tt class="py-lineno">186</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt id="link-54" class="py-name"><a title="Bio.Encodings.IUPACEncoding.name" class="py-name" href="#" onclick="return doclink('link-54', 'name', 'link-51');">name</a></tt><tt class="py-op">=</tt><tt class="py-name">fullname</tt> </tt>
<a name="L187"></a><tt class="py-lineno">187</tt> <tt class="py-line"> <tt class="py-keyword">if</tt> <tt class="py-name">__debug__</tt><tt class="py-op">:</tt> </tt>
<a name="L188"></a><tt class="py-lineno">188</tt> <tt class="py-line"> <tt class="py-name">sys</tt><tt class="py-op">.</tt><tt class="py-name">stderr</tt><tt class="py-op">.</tt><tt id="link-55" class="py-name"><a title="Bio.AlignAce.Motif.Motif.write
Bio.AlignIO.write
Bio.EUtils.sourcegen.SourceFile.write
Bio.EUtils.sourcegen.SourceGen.write
Bio.NeuralNetwork.Gene.Pattern.PatternIO.write
Bio.SeqIO.write
Bio.Writer.Writer.write
Bio.writers.SeqRecord.embl.WriteEmbl.write
Bio.writers.SeqRecord.fasta.WriteFasta.write" class="py-name" href="#" onclick="return doclink('link-55', 'write', 'link-28');">write</a></tt><tt class="py-op">(</tt><tt class="py-string">"WARNING: atom names %s and %s differ only in spaces at line %i.\n"</tt> </tt>
<a name="L189"></a><tt class="py-lineno">189</tt> <tt class="py-line"> <tt class="py-op">%</tt> <tt class="py-op">(</tt><tt class="py-name">duplicate_fullname</tt><tt class="py-op">,</tt> <tt class="py-name">fullname</tt><tt class="py-op">,</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">line_counter</tt><tt class="py-op">)</tt><tt class="py-op">)</tt> </tt>
<a name="L190"></a><tt class="py-lineno">190</tt> <tt class="py-line"> <tt class="py-name">atom</tt><tt class="py-op">=</tt><tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">atom</tt><tt class="py-op">=</tt><tt id="link-56" class="py-name"><a title="Bio.PDB.Atom
Bio.PDB.Atom.Atom" class="py-name" href="#" onclick="return doclink('link-56', 'Atom', 'link-10');">Atom</a></tt><tt class="py-op">(</tt><tt id="link-57" class="py-name"><a title="Bio.Encodings.IUPACEncoding.name" class="py-name" href="#" onclick="return doclink('link-57', 'name', 'link-51');">name</a></tt><tt class="py-op">,</tt> <tt class="py-name">coord</tt><tt class="py-op">,</tt> <tt class="py-name">b_factor</tt><tt class="py-op">,</tt> <tt class="py-name">occupancy</tt><tt class="py-op">,</tt> <tt class="py-name">altloc</tt><tt class="py-op">,</tt> <tt class="py-name">fullname</tt><tt class="py-op">,</tt> <tt class="py-name">serial_number</tt><tt class="py-op">)</tt> </tt>
<a name="L191"></a><tt class="py-lineno">191</tt> <tt class="py-line"> <tt class="py-keyword">if</tt> <tt class="py-name">altloc</tt><tt class="py-op">!=</tt><tt class="py-string">" "</tt><tt class="py-op">:</tt> </tt>
<a name="L192"></a><tt class="py-lineno">192</tt> <tt class="py-line"> <tt class="py-comment"># The atom is disordered</tt> </tt>
<a name="L193"></a><tt class="py-lineno">193</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-keyword">if</tt> <tt class="py-name">residue</tt><tt class="py-op">.</tt><tt id="link-58" class="py-name"><a title="Bio.PDB.Chain.Chain.has_id
Bio.PDB.Entity.Entity.has_id" class="py-name" href="#" onclick="return doclink('link-58', 'has_id', 'link-25');">has_id</a></tt><tt class="py-op">(</tt><tt id="link-59" class="py-name"><a title="Bio.Encodings.IUPACEncoding.name" class="py-name" href="#" onclick="return doclink('link-59', 'name', 'link-51');">name</a></tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
<a name="L194"></a><tt class="py-lineno">194</tt> <tt class="py-line"> <tt class="py-comment"># Residue already contains this atom</tt> </tt>
<a name="L195"></a><tt class="py-lineno">195</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-name">duplicate_atom</tt><tt class="py-op">=</tt><tt class="py-name">residue</tt><tt class="py-op">[</tt><tt id="link-60" class="py-name"><a title="Bio.Encodings.IUPACEncoding.name" class="py-name" href="#" onclick="return doclink('link-60', 'name', 'link-51');">name</a></tt><tt class="py-op">]</tt> </tt>
<a name="L196"></a><tt class="py-lineno">196</tt> <tt class="py-line"> <tt class="py-keyword">if</tt> <tt class="py-name">duplicate_atom</tt><tt class="py-op">.</tt><tt id="link-61" class="py-name"><a title="Bio.PDB.Atom.Atom.is_disordered
Bio.PDB.Entity.DisorderedEntityWrapper.is_disordered
Bio.PDB.Residue.Residue.is_disordered" class="py-name" href="#" onclick="return doclink('link-61', 'is_disordered', 'link-35');">is_disordered</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt><tt class="py-op">==</tt><tt class="py-number">2</tt><tt class="py-op">:</tt> </tt>
<a name="L197"></a><tt class="py-lineno">197</tt> <tt class="py-line"> <tt class="py-name">duplicate_atom</tt><tt class="py-op">.</tt><tt id="link-62" class="py-name"><a title="Bio.PDB.Atom.DisorderedAtom.disordered_add
Bio.PDB.Entity.DisorderedEntityWrapper.disordered_add
Bio.PDB.Residue.DisorderedResidue.disordered_add" class="py-name" href="#" onclick="return doclink('link-62', 'disordered_add', 'link-39');">disordered_add</a></tt><tt class="py-op">(</tt><tt class="py-name">atom</tt><tt class="py-op">)</tt> </tt>
<a name="L198"></a><tt class="py-lineno">198</tt> <tt class="py-line"> <tt class="py-keyword">else</tt><tt class="py-op">:</tt> </tt>
<a name="L199"></a><tt class="py-lineno">199</tt> <tt class="py-line"> <tt class="py-comment"># This is an error in the PDB file:</tt> </tt>
<a name="L200"></a><tt class="py-lineno">200</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-comment"># a disordered atom is found with a blanc altloc</tt> </tt>
<a name="L201"></a><tt class="py-lineno">201</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-comment"># Detach the duplicate atom, and put it in a </tt> </tt>
<a name="L202"></a><tt class="py-lineno">202</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-comment"># DisorderedAtom object together with the current </tt> </tt>
<a name="L203"></a><tt class="py-lineno">203</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-comment"># atom.</tt> </tt>
<a name="L204"></a><tt class="py-lineno">204</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-name">residue</tt><tt class="py-op">.</tt><tt id="link-63" class="py-name"><a title="Bio.PDB.Entity.Entity.detach_child" class="py-name" href="#" onclick="return doclink('link-63', 'detach_child', 'link-42');">detach_child</a></tt><tt class="py-op">(</tt><tt id="link-64" class="py-name"><a title="Bio.Encodings.IUPACEncoding.name" class="py-name" href="#" onclick="return doclink('link-64', 'name', 'link-51');">name</a></tt><tt class="py-op">)</tt> </tt>
<a name="L205"></a><tt class="py-lineno">205</tt> <tt class="py-line"> <tt class="py-name">disordered_atom</tt><tt class="py-op">=</tt><tt id="link-65" class="py-name"><a title="Bio.PDB.Atom.DisorderedAtom" class="py-name" href="#" onclick="return doclink('link-65', 'DisorderedAtom', 'link-12');">DisorderedAtom</a></tt><tt class="py-op">(</tt><tt id="link-66" class="py-name"><a title="Bio.Encodings.IUPACEncoding.name" class="py-name" href="#" onclick="return doclink('link-66', 'name', 'link-51');">name</a></tt><tt class="py-op">)</tt> </tt>
<a name="L206"></a><tt class="py-lineno">206</tt> <tt class="py-line"> <tt class="py-name">residue</tt><tt class="py-op">.</tt><tt id="link-67" class="py-name"><a title="Bio.Affy.CelFile.add
Bio.EUtils.POM.ElementNode.add
Bio.GFF.easy.Location.add
Bio.Graphics.BasicChromosome._ChromosomeComponent.add
Bio.LogisticRegression.add
Bio.MarkovModel.add
Bio.MaxEntropy.add
Bio.NaiveBayes.add
Bio.Nexus.Nexus.StepMatrix.add
Bio.Nexus.Nodes.Chain.add
Bio.PDB.Entity.Entity.add
Bio.PDB.Residue.DisorderedResidue.add
Bio.PDB.Residue.Residue.add
Bio.Pathway.Rep.HashSet.HashSet.add
Bio.Restriction.Restriction.RestrictionBatch.add
Bio.Statistics.lowess.add
Bio.config.FormatRegistry.FormatGroup.add
Bio.config.Registry.RegisterableGroup.add
Bio.distance.add
Bio.kNN.add
Martel.Dispatch.MulticallEnd.add
Martel.Dispatch.MulticallStart.add" class="py-name" href="#" onclick="return doclink('link-67', 'add', 'link-24');">add</a></tt><tt class="py-op">(</tt><tt class="py-name">disordered_atom</tt><tt class="py-op">)</tt> </tt>
<a name="L207"></a><tt class="py-lineno">207</tt> <tt class="py-line"> <tt class="py-name">disordered_atom</tt><tt class="py-op">.</tt><tt id="link-68" class="py-name"><a title="Bio.PDB.Atom.DisorderedAtom.disordered_add
Bio.PDB.Entity.DisorderedEntityWrapper.disordered_add
Bio.PDB.Residue.DisorderedResidue.disordered_add" class="py-name" href="#" onclick="return doclink('link-68', 'disordered_add', 'link-39');">disordered_add</a></tt><tt class="py-op">(</tt><tt class="py-name">atom</tt><tt class="py-op">)</tt> </tt>
<a name="L208"></a><tt class="py-lineno">208</tt> <tt class="py-line"> <tt class="py-name">disordered_atom</tt><tt class="py-op">.</tt><tt id="link-69" class="py-name"><a title="Bio.PDB.Atom.DisorderedAtom.disordered_add
Bio.PDB.Entity.DisorderedEntityWrapper.disordered_add
Bio.PDB.Residue.DisorderedResidue.disordered_add" class="py-name" href="#" onclick="return doclink('link-69', 'disordered_add', 'link-39');">disordered_add</a></tt><tt class="py-op">(</tt><tt class="py-name">duplicate_atom</tt><tt class="py-op">)</tt> </tt>
<a name="L209"></a><tt class="py-lineno">209</tt> <tt class="py-line"> <tt class="py-name">residue</tt><tt class="py-op">.</tt><tt id="link-70" class="py-name" targets="Method Bio.PDB.Residue.Residue.flag_disordered()=Bio.PDB.Residue.Residue-class.html#flag_disordered"><a title="Bio.PDB.Residue.Residue.flag_disordered" class="py-name" href="#" onclick="return doclink('link-70', 'flag_disordered', 'link-70');">flag_disordered</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
<a name="L210"></a><tt class="py-lineno">210</tt> <tt class="py-line"> <tt class="py-keyword">if</tt> <tt class="py-name">__debug__</tt><tt class="py-op">:</tt> </tt>
<a name="L211"></a><tt class="py-lineno">211</tt> <tt class="py-line"> <tt class="py-name">sys</tt><tt class="py-op">.</tt><tt class="py-name">stderr</tt><tt class="py-op">.</tt><tt id="link-71" class="py-name"><a title="Bio.AlignAce.Motif.Motif.write
Bio.AlignIO.write
Bio.EUtils.sourcegen.SourceFile.write
Bio.EUtils.sourcegen.SourceGen.write
Bio.NeuralNetwork.Gene.Pattern.PatternIO.write
Bio.SeqIO.write
Bio.Writer.Writer.write
Bio.writers.SeqRecord.embl.WriteEmbl.write
Bio.writers.SeqRecord.fasta.WriteFasta.write" class="py-name" href="#" onclick="return doclink('link-71', 'write', 'link-28');">write</a></tt><tt class="py-op">(</tt><tt class="py-string">"WARNING: disordered atom found with blanc altloc before line %i.\n"</tt> </tt>
<a name="L212"></a><tt class="py-lineno">212</tt> <tt class="py-line"> <tt class="py-op">%</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">line_counter</tt><tt class="py-op">)</tt> </tt>
<a name="L213"></a><tt class="py-lineno">213</tt> <tt class="py-line"> <tt class="py-keyword">else</tt><tt class="py-op">:</tt> </tt>
<a name="L214"></a><tt class="py-lineno">214</tt> <tt class="py-line"> <tt class="py-comment"># The residue does not contain this disordered atom</tt> </tt>
<a name="L215"></a><tt class="py-lineno">215</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-comment"># so we create a new one.</tt> </tt>
<a name="L216"></a><tt class="py-lineno">216</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-name">disordered_atom</tt><tt class="py-op">=</tt><tt id="link-72" class="py-name"><a title="Bio.PDB.Atom.DisorderedAtom" class="py-name" href="#" onclick="return doclink('link-72', 'DisorderedAtom', 'link-12');">DisorderedAtom</a></tt><tt class="py-op">(</tt><tt id="link-73" class="py-name"><a title="Bio.Encodings.IUPACEncoding.name" class="py-name" href="#" onclick="return doclink('link-73', 'name', 'link-51');">name</a></tt><tt class="py-op">)</tt> </tt>
<a name="L217"></a><tt class="py-lineno">217</tt> <tt class="py-line"> <tt class="py-name">residue</tt><tt class="py-op">.</tt><tt id="link-74" class="py-name"><a title="Bio.Affy.CelFile.add
Bio.EUtils.POM.ElementNode.add
Bio.GFF.easy.Location.add
Bio.Graphics.BasicChromosome._ChromosomeComponent.add
Bio.LogisticRegression.add
Bio.MarkovModel.add
Bio.MaxEntropy.add
Bio.NaiveBayes.add
Bio.Nexus.Nexus.StepMatrix.add
Bio.Nexus.Nodes.Chain.add
Bio.PDB.Entity.Entity.add
Bio.PDB.Residue.DisorderedResidue.add
Bio.PDB.Residue.Residue.add
Bio.Pathway.Rep.HashSet.HashSet.add
Bio.Restriction.Restriction.RestrictionBatch.add
Bio.Statistics.lowess.add
Bio.config.FormatRegistry.FormatGroup.add
Bio.config.Registry.RegisterableGroup.add
Bio.distance.add
Bio.kNN.add
Martel.Dispatch.MulticallEnd.add
Martel.Dispatch.MulticallStart.add" class="py-name" href="#" onclick="return doclink('link-74', 'add', 'link-24');">add</a></tt><tt class="py-op">(</tt><tt class="py-name">disordered_atom</tt><tt class="py-op">)</tt> </tt>
<a name="L218"></a><tt class="py-lineno">218</tt> <tt class="py-line"> <tt class="py-comment"># Add the real atom to the disordered atom, and the </tt> </tt>
<a name="L219"></a><tt class="py-lineno">219</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-comment"># disordered atom to the residue</tt> </tt>
<a name="L220"></a><tt class="py-lineno">220</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-name">disordered_atom</tt><tt class="py-op">.</tt><tt id="link-75" class="py-name"><a title="Bio.PDB.Atom.DisorderedAtom.disordered_add
Bio.PDB.Entity.DisorderedEntityWrapper.disordered_add
Bio.PDB.Residue.DisorderedResidue.disordered_add" class="py-name" href="#" onclick="return doclink('link-75', 'disordered_add', 'link-39');">disordered_add</a></tt><tt class="py-op">(</tt><tt class="py-name">atom</tt><tt class="py-op">)</tt> </tt>
<a name="L221"></a><tt class="py-lineno">221</tt> <tt class="py-line"> <tt class="py-name">residue</tt><tt class="py-op">.</tt><tt id="link-76" class="py-name"><a title="Bio.PDB.Residue.Residue.flag_disordered" class="py-name" href="#" onclick="return doclink('link-76', 'flag_disordered', 'link-70');">flag_disordered</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
<a name="L222"></a><tt class="py-lineno">222</tt> <tt class="py-line"> <tt class="py-keyword">else</tt><tt class="py-op">:</tt> </tt>
<a name="L223"></a><tt class="py-lineno">223</tt> <tt class="py-line"> <tt class="py-comment"># The atom is not disordered</tt> </tt>
<a name="L224"></a><tt class="py-lineno">224</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-name">residue</tt><tt class="py-op">.</tt><tt id="link-77" class="py-name"><a title="Bio.Affy.CelFile.add
Bio.EUtils.POM.ElementNode.add
Bio.GFF.easy.Location.add
Bio.Graphics.BasicChromosome._ChromosomeComponent.add
Bio.LogisticRegression.add
Bio.MarkovModel.add
Bio.MaxEntropy.add
Bio.NaiveBayes.add
Bio.Nexus.Nexus.StepMatrix.add
Bio.Nexus.Nodes.Chain.add
Bio.PDB.Entity.Entity.add
Bio.PDB.Residue.DisorderedResidue.add
Bio.PDB.Residue.Residue.add
Bio.Pathway.Rep.HashSet.HashSet.add
Bio.Restriction.Restriction.RestrictionBatch.add
Bio.Statistics.lowess.add
Bio.config.FormatRegistry.FormatGroup.add
Bio.config.Registry.RegisterableGroup.add
Bio.distance.add
Bio.kNN.add
Martel.Dispatch.MulticallEnd.add
Martel.Dispatch.MulticallStart.add" class="py-name" href="#" onclick="return doclink('link-77', 'add', 'link-24');">add</a></tt><tt class="py-op">(</tt><tt class="py-name">atom</tt><tt class="py-op">)</tt> </tt>
</div><a name="L225"></a><tt class="py-lineno">225</tt> <tt class="py-line"> </tt>
<a name="StructureBuilder.set_anisou"></a><div id="StructureBuilder.set_anisou-def"><a name="L226"></a><tt class="py-lineno">226</tt> <a class="py-toggle" href="#" id="StructureBuilder.set_anisou-toggle" onclick="return toggle('StructureBuilder.set_anisou');">-</a><tt class="py-line"> <tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.PDB.StructureBuilder.StructureBuilder-class.html#set_anisou">set_anisou</a><tt class="py-op">(</tt><tt class="py-param">self</tt><tt class="py-op">,</tt> <tt class="py-param">anisou_array</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="StructureBuilder.set_anisou-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="StructureBuilder.set_anisou-expanded"><a name="L227"></a><tt class="py-lineno">227</tt> <tt class="py-line"> <tt class="py-docstring">"Set anisotropic B factor of current Atom."</tt> </tt>
<a name="L228"></a><tt class="py-lineno">228</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">atom</tt><tt class="py-op">.</tt><tt id="link-78" class="py-name" targets="Method Bio.PDB.Atom.Atom.set_anisou()=Bio.PDB.Atom.Atom-class.html#set_anisou,Method Bio.PDB.StructureBuilder.StructureBuilder.set_anisou()=Bio.PDB.StructureBuilder.StructureBuilder-class.html#set_anisou"><a title="Bio.PDB.Atom.Atom.set_anisou
Bio.PDB.StructureBuilder.StructureBuilder.set_anisou" class="py-name" href="#" onclick="return doclink('link-78', 'set_anisou', 'link-78');">set_anisou</a></tt><tt class="py-op">(</tt><tt class="py-name">anisou_array</tt><tt class="py-op">)</tt> </tt>
</div><a name="L229"></a><tt class="py-lineno">229</tt> <tt class="py-line"> </tt>
<a name="StructureBuilder.set_siguij"></a><div id="StructureBuilder.set_siguij-def"><a name="L230"></a><tt class="py-lineno">230</tt> <a class="py-toggle" href="#" id="StructureBuilder.set_siguij-toggle" onclick="return toggle('StructureBuilder.set_siguij');">-</a><tt class="py-line"> <tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.PDB.StructureBuilder.StructureBuilder-class.html#set_siguij">set_siguij</a><tt class="py-op">(</tt><tt class="py-param">self</tt><tt class="py-op">,</tt> <tt class="py-param">siguij_array</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="StructureBuilder.set_siguij-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="StructureBuilder.set_siguij-expanded"><a name="L231"></a><tt class="py-lineno">231</tt> <tt class="py-line"> <tt class="py-docstring">"Set standard deviation of anisotropic B factor of current Atom."</tt> </tt>
<a name="L232"></a><tt class="py-lineno">232</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">atom</tt><tt class="py-op">.</tt><tt id="link-79" class="py-name" targets="Method Bio.PDB.Atom.Atom.set_siguij()=Bio.PDB.Atom.Atom-class.html#set_siguij,Method Bio.PDB.StructureBuilder.StructureBuilder.set_siguij()=Bio.PDB.StructureBuilder.StructureBuilder-class.html#set_siguij"><a title="Bio.PDB.Atom.Atom.set_siguij
Bio.PDB.StructureBuilder.StructureBuilder.set_siguij" class="py-name" href="#" onclick="return doclink('link-79', 'set_siguij', 'link-79');">set_siguij</a></tt><tt class="py-op">(</tt><tt class="py-name">siguij_array</tt><tt class="py-op">)</tt> </tt>
</div><a name="L233"></a><tt class="py-lineno">233</tt> <tt class="py-line"> </tt>
<a name="StructureBuilder.set_sigatm"></a><div id="StructureBuilder.set_sigatm-def"><a name="L234"></a><tt class="py-lineno">234</tt> <a class="py-toggle" href="#" id="StructureBuilder.set_sigatm-toggle" onclick="return toggle('StructureBuilder.set_sigatm');">-</a><tt class="py-line"> <tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.PDB.StructureBuilder.StructureBuilder-class.html#set_sigatm">set_sigatm</a><tt class="py-op">(</tt><tt class="py-param">self</tt><tt class="py-op">,</tt> <tt class="py-param">sigatm_array</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="StructureBuilder.set_sigatm-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="StructureBuilder.set_sigatm-expanded"><a name="L235"></a><tt class="py-lineno">235</tt> <tt class="py-line"> <tt class="py-docstring">"Set standard deviation of atom position of current Atom."</tt> </tt>
<a name="L236"></a><tt class="py-lineno">236</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">atom</tt><tt class="py-op">.</tt><tt id="link-80" class="py-name" targets="Method Bio.PDB.Atom.Atom.set_sigatm()=Bio.PDB.Atom.Atom-class.html#set_sigatm,Method Bio.PDB.StructureBuilder.StructureBuilder.set_sigatm()=Bio.PDB.StructureBuilder.StructureBuilder-class.html#set_sigatm"><a title="Bio.PDB.Atom.Atom.set_sigatm
Bio.PDB.StructureBuilder.StructureBuilder.set_sigatm" class="py-name" href="#" onclick="return doclink('link-80', 'set_sigatm', 'link-80');">set_sigatm</a></tt><tt class="py-op">(</tt><tt class="py-name">sigatm_array</tt><tt class="py-op">)</tt> </tt>
</div><a name="L237"></a><tt class="py-lineno">237</tt> <tt class="py-line"> </tt>
<a name="StructureBuilder.get_structure"></a><div id="StructureBuilder.get_structure-def"><a name="L238"></a><tt class="py-lineno">238</tt> <a class="py-toggle" href="#" id="StructureBuilder.get_structure-toggle" onclick="return toggle('StructureBuilder.get_structure');">-</a><tt class="py-line"> <tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.PDB.StructureBuilder.StructureBuilder-class.html#get_structure">get_structure</a><tt class="py-op">(</tt><tt class="py-param">self</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="StructureBuilder.get_structure-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="StructureBuilder.get_structure-expanded"><a name="L239"></a><tt class="py-lineno">239</tt> <tt class="py-line"> <tt class="py-docstring">"Return the structure."</tt> </tt>
<a name="L240"></a><tt class="py-lineno">240</tt> <tt class="py-line"> <tt class="py-comment"># first sort everything</tt> </tt>
<a name="L241"></a><tt class="py-lineno">241</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-comment"># self.structure.sort()</tt> </tt>
<a name="L242"></a><tt class="py-lineno">242</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-comment"># Add the header dict</tt> </tt>
<a name="L243"></a><tt class="py-lineno">243</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-81" class="py-name"><a title="Bio.SubsMat.MatrixInfo.structure" class="py-name" href="#" onclick="return doclink('link-81', 'structure', 'link-20');">structure</a></tt><tt class="py-op">.</tt><tt id="link-82" class="py-name"><a title="Bio.Wise.dnal.Statistics.header
Bio.expressions.blast.ncbiblast.header
Bio.expressions.blast.wublast.header
Bio.expressions.blocks.header
Bio.expressions.genbank.header
Bio.expressions.hmmpfam.header" class="py-name" href="#" onclick="return doclink('link-82', 'header', 'link-15');">header</a></tt><tt class="py-op">=</tt><tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-83" class="py-name"><a title="Bio.Wise.dnal.Statistics.header
Bio.expressions.blast.ncbiblast.header
Bio.expressions.blast.wublast.header
Bio.expressions.blocks.header
Bio.expressions.genbank.header
Bio.expressions.hmmpfam.header" class="py-name" href="#" onclick="return doclink('link-83', 'header', 'link-15');">header</a></tt> </tt>
<a name="L244"></a><tt class="py-lineno">244</tt> <tt class="py-line"> <tt class="py-keyword">return</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-84" class="py-name"><a title="Bio.SubsMat.MatrixInfo.structure" class="py-name" href="#" onclick="return doclink('link-84', 'structure', 'link-20');">structure</a></tt> </tt>
</div><a name="L245"></a><tt class="py-lineno">245</tt> <tt class="py-line"> </tt>
<a name="StructureBuilder.set_symmetry"></a><div id="StructureBuilder.set_symmetry-def"><a name="L246"></a><tt class="py-lineno">246</tt> <a class="py-toggle" href="#" id="StructureBuilder.set_symmetry-toggle" onclick="return toggle('StructureBuilder.set_symmetry');">-</a><tt class="py-line"> <tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.PDB.StructureBuilder.StructureBuilder-class.html#set_symmetry">set_symmetry</a><tt class="py-op">(</tt><tt class="py-param">self</tt><tt class="py-op">,</tt> <tt class="py-param">spacegroup</tt><tt class="py-op">,</tt> <tt class="py-param">cell</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="StructureBuilder.set_symmetry-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="StructureBuilder.set_symmetry-expanded"><a name="L247"></a><tt class="py-lineno">247</tt> <tt class="py-line"> <tt class="py-keyword">pass</tt> </tt>
</div></div><a name="L248"></a><tt class="py-lineno">248</tt> <tt class="py-line"> </tt><script type="text/javascript">
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