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<a href="Bio-module.html">Package Bio</a> ::
<a href="Bio.PDB-module.html">Package PDB</a> ::
Module PDBIO'
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<h1 class="epydoc">Source Code for <a href="Bio.PDB.PDBIO%27-module.html">Module Bio.PDB.PDBIO'</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 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-docstring">"Output of PDB files."</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-1" class="py-name" targets="Variable Bio.PDB.PDBIO'._ATOM_FORMAT_STRING=Bio.PDB.PDBIO%27-module.html#_ATOM_FORMAT_STRING"><a title="Bio.PDB.PDBIO'._ATOM_FORMAT_STRING" class="py-name" href="#" onclick="return doclink('link-1', '_ATOM_FORMAT_STRING', 'link-1');">_ATOM_FORMAT_STRING</a></tt><tt class="py-op">=</tt><tt class="py-string">"%s%5i %-4s%c%3s %c%4i%c %8.3f%8.3f%8.3f%6.2f%6.2f %4s%2s%2s\n"</tt> </tt>
<a name="L10"></a><tt class="py-lineno"> 10</tt> <tt class="py-line"> </tt>
<a name="L11"></a><tt class="py-lineno"> 11</tt> <tt class="py-line"> </tt>
<a name="Select"></a><div id="Select-def"><a name="L12"></a><tt class="py-lineno"> 12</tt> <a class="py-toggle" href="#" id="Select-toggle" onclick="return toggle('Select');">-</a><tt class="py-line"><tt class="py-keyword">class</tt> <a class="py-def-name" href="Bio.PDB.PDBIO'.Select-class.html">Select</a><tt class="py-op">:</tt> </tt>
</div><div id="Select-collapsed" style="display:none;" pad="+++" indent="++++"></div><div id="Select-expanded"><a name="L13"></a><tt class="py-lineno"> 13</tt> <tt class="py-line"> <tt class="py-docstring">"""</tt> </tt>
<a name="L14"></a><tt class="py-lineno"> 14</tt> <tt class="py-line"><tt class="py-docstring"> Default selection (everything) during writing - can be used as base class</tt> </tt>
<a name="L15"></a><tt class="py-lineno"> 15</tt> <tt class="py-line"><tt class="py-docstring"> to implement selective output. This selects which entities will be written out.</tt> </tt>
<a name="L16"></a><tt class="py-lineno"> 16</tt> <tt class="py-line"><tt class="py-docstring"> """</tt> </tt>
<a name="L17"></a><tt class="py-lineno"> 17</tt> <tt class="py-line"> </tt>
<a name="Select.__repr__"></a><div id="Select.__repr__-def"><a name="L18"></a><tt class="py-lineno"> 18</tt> <a class="py-toggle" href="#" id="Select.__repr__-toggle" onclick="return toggle('Select.__repr__');">-</a><tt class="py-line"> <tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.PDB.PDBIO'.Select-class.html#__repr__">__repr__</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="Select.__repr__-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="Select.__repr__-expanded"><a name="L19"></a><tt class="py-lineno"> 19</tt> <tt class="py-line"> <tt class="py-keyword">return</tt> <tt class="py-string">"<Select all>"</tt> </tt>
</div><a name="L20"></a><tt class="py-lineno"> 20</tt> <tt class="py-line"> </tt>
<a name="Select.accept_model"></a><div id="Select.accept_model-def"><a name="L21"></a><tt class="py-lineno"> 21</tt> <a class="py-toggle" href="#" id="Select.accept_model-toggle" onclick="return toggle('Select.accept_model');">-</a><tt class="py-line"> <tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.PDB.PDBIO'.Select-class.html#accept_model">accept_model</a><tt class="py-op">(</tt><tt class="py-param">self</tt><tt class="py-op">,</tt> <tt class="py-param">model</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="Select.accept_model-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="Select.accept_model-expanded"><a name="L22"></a><tt class="py-lineno"> 22</tt> <tt class="py-line"> <tt class="py-docstring">"""</tt> </tt>
<a name="L23"></a><tt class="py-lineno"> 23</tt> <tt class="py-line"><tt class="py-docstring"> Overload this to reject models for output.</tt> </tt>
<a name="L24"></a><tt class="py-lineno"> 24</tt> <tt class="py-line"><tt class="py-docstring"> """</tt> </tt>
<a name="L25"></a><tt class="py-lineno"> 25</tt> <tt class="py-line"> <tt class="py-keyword">return</tt> <tt class="py-number">1</tt> </tt>
</div><a name="L26"></a><tt class="py-lineno"> 26</tt> <tt class="py-line"> </tt>
<a name="Select.accept_chain"></a><div id="Select.accept_chain-def"><a name="L27"></a><tt class="py-lineno"> 27</tt> <a class="py-toggle" href="#" id="Select.accept_chain-toggle" onclick="return toggle('Select.accept_chain');">-</a><tt class="py-line"> <tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.PDB.PDBIO'.Select-class.html#accept_chain">accept_chain</a><tt class="py-op">(</tt><tt class="py-param">self</tt><tt class="py-op">,</tt> <tt class="py-param">chain</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="Select.accept_chain-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="Select.accept_chain-expanded"><a name="L28"></a><tt class="py-lineno"> 28</tt> <tt class="py-line"> <tt class="py-docstring">"""</tt> </tt>
<a name="L29"></a><tt class="py-lineno"> 29</tt> <tt class="py-line"><tt class="py-docstring"> Overload this to reject chains for output.</tt> </tt>
<a name="L30"></a><tt class="py-lineno"> 30</tt> <tt class="py-line"><tt class="py-docstring"> """</tt> </tt>
<a name="L31"></a><tt class="py-lineno"> 31</tt> <tt class="py-line"> <tt class="py-keyword">return</tt> <tt class="py-number">1</tt> </tt>
</div><a name="L32"></a><tt class="py-lineno"> 32</tt> <tt class="py-line"> </tt>
<a name="Select.accept_residue"></a><div id="Select.accept_residue-def"><a name="L33"></a><tt class="py-lineno"> 33</tt> <a class="py-toggle" href="#" id="Select.accept_residue-toggle" onclick="return toggle('Select.accept_residue');">-</a><tt class="py-line"> <tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.PDB.PDBIO'.Select-class.html#accept_residue">accept_residue</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="Select.accept_residue-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="Select.accept_residue-expanded"><a name="L34"></a><tt class="py-lineno"> 34</tt> <tt class="py-line"> <tt class="py-docstring">"""</tt> </tt>
<a name="L35"></a><tt class="py-lineno"> 35</tt> <tt class="py-line"><tt class="py-docstring"> Overload this to reject residues for output.</tt> </tt>
<a name="L36"></a><tt class="py-lineno"> 36</tt> <tt class="py-line"><tt class="py-docstring"> """</tt> </tt>
<a name="L37"></a><tt class="py-lineno"> 37</tt> <tt class="py-line"> <tt class="py-keyword">return</tt> <tt class="py-number">1</tt> </tt>
</div><a name="L38"></a><tt class="py-lineno"> 38</tt> <tt class="py-line"> </tt>
<a name="Select.accept_atom"></a><div id="Select.accept_atom-def"><a name="L39"></a><tt class="py-lineno"> 39</tt> <a class="py-toggle" href="#" id="Select.accept_atom-toggle" onclick="return toggle('Select.accept_atom');">-</a><tt class="py-line"> <tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.PDB.PDBIO'.Select-class.html#accept_atom">accept_atom</a><tt class="py-op">(</tt><tt class="py-param">self</tt><tt class="py-op">,</tt> <tt class="py-param">atom</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="Select.accept_atom-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="Select.accept_atom-expanded"><a name="L40"></a><tt class="py-lineno"> 40</tt> <tt class="py-line"> <tt class="py-docstring">"""</tt> </tt>
<a name="L41"></a><tt class="py-lineno"> 41</tt> <tt class="py-line"><tt class="py-docstring"> Overload this to reject atoms for output.</tt> </tt>
<a name="L42"></a><tt class="py-lineno"> 42</tt> <tt class="py-line"><tt class="py-docstring"> """</tt> </tt>
<a name="L43"></a><tt class="py-lineno"> 43</tt> <tt class="py-line"> <tt class="py-keyword">return</tt> <tt class="py-number">1</tt> </tt>
</div></div><a name="L44"></a><tt class="py-lineno"> 44</tt> <tt class="py-line"> </tt>
<a name="L45"></a><tt class="py-lineno"> 45</tt> <tt class="py-line"> </tt>
<a name="PDBIO"></a><div id="PDBIO-def"><a name="L46"></a><tt class="py-lineno"> 46</tt> <a class="py-toggle" href="#" id="PDBIO-toggle" onclick="return toggle('PDBIO');">-</a><tt class="py-line"><tt class="py-keyword">class</tt> <a class="py-def-name" href="Bio.PDB.PDBIO'.PDBIO-class.html">PDBIO</a><tt class="py-op">:</tt> </tt>
</div><div id="PDBIO-collapsed" style="display:none;" pad="+++" indent="++++"></div><div id="PDBIO-expanded"><a name="L47"></a><tt class="py-lineno"> 47</tt> <tt class="py-line"> <tt class="py-docstring">"""</tt> </tt>
<a name="L48"></a><tt class="py-lineno"> 48</tt> <tt class="py-line"><tt class="py-docstring"> Write a Structure object (or a subset of a Structure object) as a PDB file.</tt> </tt>
<a name="L49"></a><tt class="py-lineno"> 49</tt> <tt class="py-line"><tt class="py-docstring"></tt> </tt>
<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"> Example:</tt> </tt>
<a name="L52"></a><tt class="py-lineno"> 52</tt> <tt class="py-line"><tt class="py-docstring"> >>> p=PDBParser()</tt> </tt>
<a name="L53"></a><tt class="py-lineno"> 53</tt> <tt class="py-line"><tt class="py-docstring"> >>> s=p.get_structure("1fat", "1fat.pdb")</tt> </tt>
<a name="L54"></a><tt class="py-lineno"> 54</tt> <tt class="py-line"><tt class="py-docstring"> >>> io=PDBIO()</tt> </tt>
<a name="L55"></a><tt class="py-lineno"> 55</tt> <tt class="py-line"><tt class="py-docstring"> >>> io.set_structure(s)</tt> </tt>
<a name="L56"></a><tt class="py-lineno"> 56</tt> <tt class="py-line"><tt class="py-docstring"> >>> io.save("out.pdb")</tt> </tt>
<a name="L57"></a><tt class="py-lineno"> 57</tt> <tt class="py-line"><tt class="py-docstring"> """</tt> </tt>
<a name="PDBIO.__init__"></a><div id="PDBIO.__init__-def"><a name="L58"></a><tt class="py-lineno"> 58</tt> <a class="py-toggle" href="#" id="PDBIO.__init__-toggle" onclick="return toggle('PDBIO.__init__');">-</a><tt class="py-line"> <tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.PDB.PDBIO'.PDBIO-class.html#__init__">__init__</a><tt class="py-op">(</tt><tt class="py-param">self</tt><tt class="py-op">,</tt> <tt class="py-param">use_model_flag</tt><tt class="py-op">=</tt><tt class="py-number">0</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="PDBIO.__init__-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="PDBIO.__init__-expanded"><a name="L59"></a><tt class="py-lineno"> 59</tt> <tt class="py-line"> <tt class="py-docstring">"""</tt> </tt>
<a name="L60"></a><tt class="py-lineno"> 60</tt> <tt class="py-line"><tt class="py-docstring"> @param use_model_flag: if 1, force use of the MODEL record in output.</tt> </tt>
<a name="L61"></a><tt class="py-lineno"> 61</tt> <tt class="py-line"><tt class="py-docstring"> @type use_model_flag: int</tt> </tt>
<a name="L62"></a><tt class="py-lineno"> 62</tt> <tt class="py-line"><tt class="py-docstring"> """</tt> </tt>
<a name="L63"></a><tt class="py-lineno"> 63</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">use_model_flag</tt><tt class="py-op">=</tt><tt class="py-name">use_model_flag</tt> </tt>
</div><a name="L64"></a><tt class="py-lineno"> 64</tt> <tt class="py-line"> </tt>
<a name="L65"></a><tt class="py-lineno"> 65</tt> <tt class="py-line"> <tt class="py-comment"># private mathods</tt> </tt>
<a name="L66"></a><tt class="py-lineno"> 66</tt> <tt class="py-line"><tt class="py-comment"></tt> </tt>
<a name="PDBIO._get_atom_line"></a><div id="PDBIO._get_atom_line-def"><a name="L67"></a><tt class="py-lineno"> 67</tt> <a class="py-toggle" href="#" id="PDBIO._get_atom_line-toggle" onclick="return toggle('PDBIO._get_atom_line');">-</a><tt class="py-line"> <tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.PDB.PDBIO'.PDBIO-class.html#_get_atom_line">_get_atom_line</a><tt class="py-op">(</tt><tt class="py-param">self</tt><tt class="py-op">,</tt> <tt class="py-param">atom</tt><tt class="py-op">,</tt> <tt class="py-param">hetfield</tt><tt class="py-op">,</tt> <tt class="py-param">segid</tt><tt class="py-op">,</tt> <tt class="py-param">atom_number</tt><tt class="py-op">,</tt> <tt class="py-param">resname</tt><tt class="py-op">,</tt> </tt>
<a name="L68"></a><tt class="py-lineno"> 68</tt> <tt class="py-line"> <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-param">chain_id</tt><tt class="py-op">,</tt> <tt class="py-param">element</tt><tt class="py-op">=</tt><tt class="py-string">" "</tt><tt class="py-op">,</tt> <tt class="py-param">charge</tt><tt class="py-op">=</tt><tt class="py-string">" "</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="PDBIO._get_atom_line-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="PDBIO._get_atom_line-expanded"><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"> Returns an ATOM PDB string.</tt> </tt>
<a name="L71"></a><tt class="py-lineno"> 71</tt> <tt class="py-line"><tt class="py-docstring"> """</tt> </tt>
<a name="L72"></a><tt class="py-lineno"> 72</tt> <tt class="py-line"> <tt class="py-keyword">if</tt> <tt class="py-name">hetfield</tt><tt class="py-op">!=</tt><tt class="py-string">" "</tt><tt class="py-op">:</tt> </tt>
<a name="L73"></a><tt class="py-lineno"> 73</tt> <tt class="py-line"> <tt class="py-name">record_type</tt><tt class="py-op">=</tt><tt class="py-string">"HETATM"</tt> </tt>
<a name="L74"></a><tt class="py-lineno"> 74</tt> <tt class="py-line"> <tt class="py-keyword">else</tt><tt class="py-op">:</tt> </tt>
<a name="L75"></a><tt class="py-lineno"> 75</tt> <tt class="py-line"> <tt class="py-name">record_type</tt><tt class="py-op">=</tt><tt class="py-string">"ATOM "</tt> </tt>
<a name="L76"></a><tt class="py-lineno"> 76</tt> <tt class="py-line"> <tt id="link-2" 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-2', 'name', 'link-2');">name</a></tt><tt class="py-op">=</tt><tt class="py-name">atom</tt><tt class="py-op">.</tt><tt id="link-3" 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-3', 'get_fullname', 'link-3');">get_fullname</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
<a name="L77"></a><tt class="py-lineno"> 77</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-4" 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-4', 'get_altloc', 'link-4');">get_altloc</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
<a name="L78"></a><tt class="py-lineno"> 78</tt> <tt class="py-line"> <tt id="link-5" class="py-name" targets="Variable Bio.MarkovModel.x=Bio.MarkovModel-module.html#x,Variable Bio.Statistics.lowess.x=Bio.Statistics.lowess-module.html#x"><a title="Bio.MarkovModel.x
Bio.Statistics.lowess.x" class="py-name" href="#" onclick="return doclink('link-5', 'x', 'link-5');">x</a></tt><tt class="py-op">,</tt> <tt class="py-name">y</tt><tt class="py-op">,</tt> <tt class="py-name">z</tt><tt class="py-op">=</tt><tt class="py-name">atom</tt><tt class="py-op">.</tt><tt id="link-6" class="py-name" targets="Method Bio.PDB.Atom.Atom.get_coord()=Bio.PDB.Atom.Atom-class.html#get_coord"><a title="Bio.PDB.Atom.Atom.get_coord" class="py-name" href="#" onclick="return doclink('link-6', 'get_coord', 'link-6');">get_coord</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
<a name="L79"></a><tt class="py-lineno"> 79</tt> <tt class="py-line"> <tt class="py-name">bfactor</tt><tt class="py-op">=</tt><tt class="py-name">atom</tt><tt class="py-op">.</tt><tt id="link-7" class="py-name" targets="Method Bio.PDB.Atom.Atom.get_bfactor()=Bio.PDB.Atom.Atom-class.html#get_bfactor"><a title="Bio.PDB.Atom.Atom.get_bfactor" class="py-name" href="#" onclick="return doclink('link-7', 'get_bfactor', 'link-7');">get_bfactor</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
<a name="L80"></a><tt class="py-lineno"> 80</tt> <tt class="py-line"> <tt class="py-name">occupancy</tt><tt class="py-op">=</tt><tt class="py-name">atom</tt><tt class="py-op">.</tt><tt id="link-8" class="py-name" targets="Method Bio.PDB.Atom.Atom.get_occupancy()=Bio.PDB.Atom.Atom-class.html#get_occupancy"><a title="Bio.PDB.Atom.Atom.get_occupancy" class="py-name" href="#" onclick="return doclink('link-8', 'get_occupancy', 'link-8');">get_occupancy</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
<a name="L81"></a><tt class="py-lineno"> 81</tt> <tt class="py-line"> <tt class="py-name">args</tt><tt class="py-op">=</tt><tt class="py-op">(</tt><tt class="py-name">record_type</tt><tt class="py-op">,</tt> <tt class="py-name">atom_number</tt><tt class="py-op">,</tt> <tt id="link-9" class="py-name"><a title="Bio.Encodings.IUPACEncoding.name" class="py-name" href="#" onclick="return doclink('link-9', 'name', 'link-2');">name</a></tt><tt class="py-op">,</tt> <tt class="py-name">altloc</tt><tt class="py-op">,</tt> <tt class="py-name">resname</tt><tt class="py-op">,</tt> <tt id="link-10" 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-10', 'chain_id', 'link-10');">chain_id</a></tt><tt class="py-op">,</tt> </tt>
<a name="L82"></a><tt class="py-lineno"> 82</tt> <tt class="py-line"> <tt class="py-name">resseq</tt><tt class="py-op">,</tt> <tt class="py-name">icode</tt><tt class="py-op">,</tt> <tt id="link-11" class="py-name"><a title="Bio.MarkovModel.x
Bio.Statistics.lowess.x" class="py-name" href="#" onclick="return doclink('link-11', 'x', 'link-5');">x</a></tt><tt class="py-op">,</tt> <tt class="py-name">y</tt><tt class="py-op">,</tt> <tt class="py-name">z</tt><tt class="py-op">,</tt> <tt class="py-name">occupancy</tt><tt class="py-op">,</tt> <tt class="py-name">bfactor</tt><tt class="py-op">,</tt> <tt class="py-name">segid</tt><tt class="py-op">,</tt> </tt>
<a name="L83"></a><tt class="py-lineno"> 83</tt> <tt class="py-line"> <tt id="link-12" class="py-name" targets="Method Martel.LAX.LAX.element()=Martel.LAX.LAX-class.html#element,Method Martel.LAX.LAXAttrs.element()=Martel.LAX.LAXAttrs-class.html#element,Method Martel.LAX.LAXPositions.element()=Martel.LAX.LAXPositions-class.html#element"><a title="Martel.LAX.LAX.element
Martel.LAX.LAXAttrs.element
Martel.LAX.LAXPositions.element" class="py-name" href="#" onclick="return doclink('link-12', 'element', 'link-12');">element</a></tt><tt class="py-op">,</tt> <tt class="py-name">charge</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">return</tt> <tt id="link-13" class="py-name"><a title="Bio.PDB.PDBIO'._ATOM_FORMAT_STRING" class="py-name" href="#" onclick="return doclink('link-13', '_ATOM_FORMAT_STRING', 'link-1');">_ATOM_FORMAT_STRING</a></tt> <tt class="py-op">%</tt> <tt class="py-name">args</tt> </tt>
</div><a name="L85"></a><tt class="py-lineno"> 85</tt> <tt class="py-line"> </tt>
<a name="L86"></a><tt class="py-lineno"> 86</tt> <tt class="py-line"> <tt class="py-comment"># Public methods</tt> </tt>
<a name="L87"></a><tt class="py-lineno"> 87</tt> <tt class="py-line"><tt class="py-comment"></tt> </tt>
<a name="PDBIO.set_structure"></a><div id="PDBIO.set_structure-def"><a name="L88"></a><tt class="py-lineno"> 88</tt> <a class="py-toggle" href="#" id="PDBIO.set_structure-toggle" onclick="return toggle('PDBIO.set_structure');">-</a><tt class="py-line"> <tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.PDB.PDBIO'.PDBIO-class.html#set_structure">set_structure</a><tt class="py-op">(</tt><tt class="py-param">self</tt><tt class="py-op">,</tt> <tt class="py-param">structure</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="PDBIO.set_structure-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="PDBIO.set_structure-expanded"><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 id="link-14" 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-14', 'structure', 'link-14');">structure</a></tt><tt class="py-op">=</tt><tt id="link-15" class="py-name"><a title="Bio.SubsMat.MatrixInfo.structure" class="py-name" href="#" onclick="return doclink('link-15', 'structure', 'link-14');">structure</a></tt> </tt>
</div><a name="L90"></a><tt class="py-lineno"> 90</tt> <tt class="py-line"> </tt>
<a name="PDBIO.save"></a><div id="PDBIO.save-def"><a name="L91"></a><tt class="py-lineno"> 91</tt> <a class="py-toggle" href="#" id="PDBIO.save-toggle" onclick="return toggle('PDBIO.save');">-</a><tt class="py-line"> <tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.PDB.PDBIO'.PDBIO-class.html#save">save</a><tt class="py-op">(</tt><tt class="py-param">self</tt><tt class="py-op">,</tt> <tt class="py-param">file</tt><tt class="py-op">,</tt> <tt class="py-param">select</tt><tt class="py-op">=</tt><tt id="link-16" class="py-name" targets="Class Bio.PDB.PDBIO'.Select=Bio.PDB.PDBIO%27.Select-class.html"><a title="Bio.PDB.PDBIO'.Select" class="py-name" href="#" onclick="return doclink('link-16', 'Select', 'link-16');">Select</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="PDBIO.save-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="PDBIO.save-expanded"><a name="L92"></a><tt class="py-lineno"> 92</tt> <tt class="py-line"> <tt class="py-docstring">"""</tt> </tt>
<a name="L93"></a><tt class="py-lineno"> 93</tt> <tt class="py-line"><tt class="py-docstring"> @param file: output file</tt> </tt>
<a name="L94"></a><tt class="py-lineno"> 94</tt> <tt class="py-line"><tt class="py-docstring"> @type file: string or filehandle </tt> </tt>
<a name="L95"></a><tt class="py-lineno"> 95</tt> <tt class="py-line"><tt class="py-docstring"></tt> </tt>
<a name="L96"></a><tt class="py-lineno"> 96</tt> <tt class="py-line"><tt class="py-docstring"> @param select: selects which entities will be written.</tt> </tt>
<a name="L97"></a><tt class="py-lineno"> 97</tt> <tt class="py-line"><tt class="py-docstring"> @type select: </tt> </tt>
<a name="L98"></a><tt class="py-lineno"> 98</tt> <tt class="py-line"><tt class="py-docstring"> select hould have the following methods:</tt> </tt>
<a name="L99"></a><tt class="py-lineno"> 99</tt> <tt class="py-line"><tt class="py-docstring"> - accept_model(model)</tt> </tt>
<a name="L100"></a><tt class="py-lineno">100</tt> <tt class="py-line"><tt class="py-docstring"> - accept_chain(chain)</tt> </tt>
<a name="L101"></a><tt class="py-lineno">101</tt> <tt class="py-line"><tt class="py-docstring"> - accept_residue(residue)</tt> </tt>
<a name="L102"></a><tt class="py-lineno">102</tt> <tt class="py-line"><tt class="py-docstring"> - accept_atom(atom)</tt> </tt>
<a name="L103"></a><tt class="py-lineno">103</tt> <tt class="py-line"><tt class="py-docstring"> These methods should return 1 if the entity</tt> </tt>
<a name="L104"></a><tt class="py-lineno">104</tt> <tt class="py-line"><tt class="py-docstring"> is to be written out, 0 otherwise.</tt> </tt>
<a name="L105"></a><tt class="py-lineno">105</tt> <tt class="py-line"><tt class="py-docstring"></tt> </tt>
<a name="L106"></a><tt class="py-lineno">106</tt> <tt class="py-line"><tt class="py-docstring"> Typically select is a subclass of L{Select}.</tt> </tt>
<a name="L107"></a><tt class="py-lineno">107</tt> <tt class="py-line"><tt class="py-docstring"> """</tt> </tt>
<a name="L108"></a><tt class="py-lineno">108</tt> <tt class="py-line"> <tt class="py-name">get_atom_line</tt><tt class="py-op">=</tt><tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-17" class="py-name" targets="Method Bio.PDB.PDBIO'.PDBIO._get_atom_line()=Bio.PDB.PDBIO%27.PDBIO-class.html#_get_atom_line"><a title="Bio.PDB.PDBIO'.PDBIO._get_atom_line" class="py-name" href="#" onclick="return doclink('link-17', '_get_atom_line', 'link-17');">_get_atom_line</a></tt> </tt>
<a name="L109"></a><tt class="py-lineno">109</tt> <tt class="py-line"> <tt class="py-keyword">if</tt> <tt class="py-name">isinstance</tt><tt class="py-op">(</tt><tt class="py-name">file</tt><tt class="py-op">,</tt> <tt class="py-name">basestring</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
<a name="L110"></a><tt class="py-lineno">110</tt> <tt class="py-line"> <tt class="py-name">fp</tt><tt class="py-op">=</tt><tt id="link-18" class="py-name" targets="Function Bio.Mindy.FlatDB.open()=Bio.Mindy.FlatDB-module.html#open,Function Bio.Mindy.open()=Bio.Mindy-module.html#open"><a title="Bio.Mindy.FlatDB.open
Bio.Mindy.open" class="py-name" href="#" onclick="return doclink('link-18', 'open', 'link-18');">open</a></tt><tt class="py-op">(</tt><tt class="py-name">file</tt><tt class="py-op">,</tt> <tt class="py-string">"w"</tt><tt class="py-op">)</tt> </tt>
<a name="L111"></a><tt class="py-lineno">111</tt> <tt class="py-line"> <tt class="py-name">close_file</tt><tt class="py-op">=</tt><tt class="py-number">1</tt> </tt>
<a name="L112"></a><tt class="py-lineno">112</tt> <tt class="py-line"> <tt class="py-keyword">else</tt><tt class="py-op">:</tt> </tt>
<a name="L113"></a><tt class="py-lineno">113</tt> <tt class="py-line"> <tt class="py-comment"># filehandle, I hope :-)</tt> </tt>
<a name="L114"></a><tt class="py-lineno">114</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-name">fp</tt><tt class="py-op">=</tt><tt class="py-name">file</tt> </tt>
<a name="L115"></a><tt class="py-lineno">115</tt> <tt class="py-line"> <tt class="py-name">close_file</tt><tt class="py-op">=</tt><tt class="py-number">0</tt> </tt>
<a name="L116"></a><tt class="py-lineno">116</tt> <tt class="py-line"> <tt class="py-comment"># multiple models?</tt> </tt>
<a name="L117"></a><tt class="py-lineno">117</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-keyword">if</tt> <tt class="py-name">len</tt><tt class="py-op">(</tt><tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-19" class="py-name"><a title="Bio.SubsMat.MatrixInfo.structure" class="py-name" href="#" onclick="return doclink('link-19', 'structure', 'link-14');">structure</a></tt><tt class="py-op">)</tt><tt class="py-op">></tt><tt class="py-number">1</tt> <tt class="py-keyword">or</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">use_model_flag</tt><tt class="py-op">:</tt> </tt>
<a name="L118"></a><tt class="py-lineno">118</tt> <tt class="py-line"> <tt class="py-name">model_flag</tt><tt class="py-op">=</tt><tt class="py-number">1</tt> </tt>
<a name="L119"></a><tt class="py-lineno">119</tt> <tt class="py-line"> <tt class="py-keyword">else</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">model_flag</tt><tt class="py-op">=</tt><tt class="py-number">0</tt> </tt>
<a name="L121"></a><tt class="py-lineno">121</tt> <tt class="py-line"> <tt class="py-keyword">for</tt> <tt class="py-name">model</tt> <tt class="py-keyword">in</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-20" class="py-name"><a title="Bio.SubsMat.MatrixInfo.structure" class="py-name" href="#" onclick="return doclink('link-20', 'structure', 'link-14');">structure</a></tt><tt class="py-op">.</tt><tt id="link-21" class="py-name" targets="Method Bio.PDB.Entity.Entity.get_list()=Bio.PDB.Entity.Entity-class.html#get_list"><a title="Bio.PDB.Entity.Entity.get_list" class="py-name" href="#" onclick="return doclink('link-21', 'get_list', 'link-21');">get_list</a></tt><tt class="py-op">(</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-keyword">if</tt> <tt class="py-keyword">not</tt> <tt id="link-22" class="py-name" targets="Method Bio.GA.Selection.Abstract.AbstractSelection.select()=Bio.GA.Selection.Abstract.AbstractSelection-class.html#select,Method Bio.GA.Selection.Diversity.DiversitySelection.select()=Bio.GA.Selection.Diversity.DiversitySelection-class.html#select,Method Bio.GA.Selection.RouletteWheel.RouletteWheelSelection.select()=Bio.GA.Selection.RouletteWheel.RouletteWheelSelection-class.html#select,Method Bio.GA.Selection.Tournament.TournamentSelection.select()=Bio.GA.Selection.Tournament.TournamentSelection-class.html#select"><a title="Bio.GA.Selection.Abstract.AbstractSelection.select
Bio.GA.Selection.Diversity.DiversitySelection.select
Bio.GA.Selection.RouletteWheel.RouletteWheelSelection.select
Bio.GA.Selection.Tournament.TournamentSelection.select" class="py-name" href="#" onclick="return doclink('link-22', 'select', 'link-22');">select</a></tt><tt class="py-op">.</tt><tt id="link-23" class="py-name" targets="Method Bio.PDB.Dice.ChainSelector.accept_model()=Bio.PDB.Dice.ChainSelector-class.html#accept_model,Method Bio.PDB.PDBIO'.Select.accept_model()=Bio.PDB.PDBIO%27.Select-class.html#accept_model"><a title="Bio.PDB.Dice.ChainSelector.accept_model
Bio.PDB.PDBIO'.Select.accept_model" class="py-name" href="#" onclick="return doclink('link-23', 'accept_model', 'link-23');">accept_model</a></tt><tt class="py-op">(</tt><tt class="py-name">model</tt><tt class="py-op">)</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">continue</tt> </tt>
<a name="L124"></a><tt class="py-lineno">124</tt> <tt class="py-line"> <tt class="py-comment"># necessary for ENDMDL </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"># do not write ENDMDL if no residues were written</tt> </tt>
<a name="L126"></a><tt class="py-lineno">126</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-comment"># for this model</tt> </tt>
<a name="L127"></a><tt class="py-lineno">127</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-name">model_residues_written</tt><tt class="py-op">=</tt><tt class="py-number">0</tt> </tt>
<a name="L128"></a><tt class="py-lineno">128</tt> <tt class="py-line"> <tt class="py-name">atom_number</tt><tt class="py-op">=</tt><tt class="py-number">1</tt> </tt>
<a name="L129"></a><tt class="py-lineno">129</tt> <tt class="py-line"> <tt class="py-keyword">if</tt> <tt class="py-name">model_flag</tt><tt class="py-op">:</tt> </tt>
<a name="L130"></a><tt class="py-lineno">130</tt> <tt class="py-line"> <tt class="py-name">fp</tt><tt class="py-op">.</tt><tt id="link-24" 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-24', 'write', 'link-24');">write</a></tt><tt class="py-op">(</tt><tt class="py-string">"MODEL \n"</tt><tt class="py-op">)</tt> </tt>
<a name="L131"></a><tt class="py-lineno">131</tt> <tt class="py-line"> <tt class="py-keyword">for</tt> <tt class="py-name">chain</tt> <tt class="py-keyword">in</tt> <tt class="py-name">model</tt><tt class="py-op">.</tt><tt id="link-25" class="py-name"><a title="Bio.PDB.Entity.Entity.get_list" class="py-name" href="#" onclick="return doclink('link-25', 'get_list', 'link-21');">get_list</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
<a name="L132"></a><tt class="py-lineno">132</tt> <tt class="py-line"> <tt class="py-keyword">if</tt> <tt class="py-keyword">not</tt> <tt id="link-26" class="py-name"><a title="Bio.GA.Selection.Abstract.AbstractSelection.select
Bio.GA.Selection.Diversity.DiversitySelection.select
Bio.GA.Selection.RouletteWheel.RouletteWheelSelection.select
Bio.GA.Selection.Tournament.TournamentSelection.select" class="py-name" href="#" onclick="return doclink('link-26', 'select', 'link-22');">select</a></tt><tt class="py-op">.</tt><tt id="link-27" class="py-name" targets="Method Bio.PDB.Dice.ChainSelector.accept_chain()=Bio.PDB.Dice.ChainSelector-class.html#accept_chain,Method Bio.PDB.PDBIO'.Select.accept_chain()=Bio.PDB.PDBIO%27.Select-class.html#accept_chain"><a title="Bio.PDB.Dice.ChainSelector.accept_chain
Bio.PDB.PDBIO'.Select.accept_chain" class="py-name" href="#" onclick="return doclink('link-27', 'accept_chain', 'link-27');">accept_chain</a></tt><tt class="py-op">(</tt><tt class="py-name">chain</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
<a name="L133"></a><tt class="py-lineno">133</tt> <tt class="py-line"> <tt class="py-keyword">continue</tt> </tt>
<a name="L134"></a><tt class="py-lineno">134</tt> <tt class="py-line"> <tt id="link-28" class="py-name"><a title="Bio.FSSP.fssp_rec.align.chain_id" class="py-name" href="#" onclick="return doclink('link-28', 'chain_id', 'link-10');">chain_id</a></tt><tt class="py-op">=</tt><tt class="py-name">chain</tt><tt class="py-op">.</tt><tt id="link-29" class="py-name" targets="Method Bio.Nexus.Nodes.Node.get_id()=Bio.Nexus.Nodes.Node-class.html#get_id,Method Bio.PDB.Atom.Atom.get_id()=Bio.PDB.Atom.Atom-class.html#get_id,Method Bio.PDB.Entity.DisorderedEntityWrapper.get_id()=Bio.PDB.Entity.DisorderedEntityWrapper-class.html#get_id,Method Bio.PDB.Entity.Entity.get_id()=Bio.PDB.Entity.Entity-class.html#get_id,Method Bio.PDB.FragmentMapper'.Fragment.get_id()=Bio.PDB.FragmentMapper%27.Fragment-class.html#get_id"><a title="Bio.Nexus.Nodes.Node.get_id
Bio.PDB.Atom.Atom.get_id
Bio.PDB.Entity.DisorderedEntityWrapper.get_id
Bio.PDB.Entity.Entity.get_id
Bio.PDB.FragmentMapper'.Fragment.get_id" class="py-name" href="#" onclick="return doclink('link-29', 'get_id', 'link-29');">get_id</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
<a name="L135"></a><tt class="py-lineno">135</tt> <tt class="py-line"> <tt class="py-comment"># necessary for TER </tt> </tt>
<a name="L136"></a><tt class="py-lineno">136</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-comment"># do not write TER if no residues were written</tt> </tt>
<a name="L137"></a><tt class="py-lineno">137</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-comment"># for this chain</tt> </tt>
<a name="L138"></a><tt class="py-lineno">138</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-name">chain_residues_written</tt><tt class="py-op">=</tt><tt class="py-number">0</tt> </tt>
<a name="L139"></a><tt class="py-lineno">139</tt> <tt class="py-line"> <tt class="py-keyword">for</tt> <tt class="py-name">residue</tt> <tt class="py-keyword">in</tt> <tt class="py-name">chain</tt><tt class="py-op">.</tt><tt id="link-30" 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-30', 'get_unpacked_list', 'link-30');">get_unpacked_list</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
<a name="L140"></a><tt class="py-lineno">140</tt> <tt class="py-line"> <tt class="py-keyword">if</tt> <tt class="py-keyword">not</tt> <tt id="link-31" class="py-name"><a title="Bio.GA.Selection.Abstract.AbstractSelection.select
Bio.GA.Selection.Diversity.DiversitySelection.select
Bio.GA.Selection.RouletteWheel.RouletteWheelSelection.select
Bio.GA.Selection.Tournament.TournamentSelection.select" class="py-name" href="#" onclick="return doclink('link-31', 'select', 'link-22');">select</a></tt><tt class="py-op">.</tt><tt id="link-32" class="py-name" targets="Method Bio.PDB.Dice.ChainSelector.accept_residue()=Bio.PDB.Dice.ChainSelector-class.html#accept_residue,Method Bio.PDB.PDBIO'.Select.accept_residue()=Bio.PDB.PDBIO%27.Select-class.html#accept_residue"><a title="Bio.PDB.Dice.ChainSelector.accept_residue
Bio.PDB.PDBIO'.Select.accept_residue" class="py-name" href="#" onclick="return doclink('link-32', 'accept_residue', 'link-32');">accept_residue</a></tt><tt class="py-op">(</tt><tt class="py-name">residue</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
<a name="L141"></a><tt class="py-lineno">141</tt> <tt class="py-line"> <tt class="py-keyword">continue</tt> </tt>
<a name="L142"></a><tt class="py-lineno">142</tt> <tt class="py-line"> <tt class="py-name">hetfield</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">residue</tt><tt class="py-op">.</tt><tt id="link-33" class="py-name"><a title="Bio.Nexus.Nodes.Node.get_id
Bio.PDB.Atom.Atom.get_id
Bio.PDB.Entity.DisorderedEntityWrapper.get_id
Bio.PDB.Entity.Entity.get_id
Bio.PDB.FragmentMapper'.Fragment.get_id" class="py-name" href="#" onclick="return doclink('link-33', 'get_id', 'link-29');">get_id</a></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-name">resname</tt><tt class="py-op">=</tt><tt class="py-name">residue</tt><tt class="py-op">.</tt><tt id="link-34" class="py-name" targets="Method Bio.PDB.Residue.Residue.get_resname()=Bio.PDB.Residue.Residue-class.html#get_resname"><a title="Bio.PDB.Residue.Residue.get_resname" class="py-name" href="#" onclick="return doclink('link-34', 'get_resname', 'link-34');">get_resname</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
<a name="L144"></a><tt class="py-lineno">144</tt> <tt class="py-line"> <tt class="py-name">segid</tt><tt class="py-op">=</tt><tt class="py-name">residue</tt><tt class="py-op">.</tt><tt id="link-35" class="py-name" targets="Method Bio.PDB.Residue.Residue.get_segid()=Bio.PDB.Residue.Residue-class.html#get_segid"><a title="Bio.PDB.Residue.Residue.get_segid" class="py-name" href="#" onclick="return doclink('link-35', 'get_segid', 'link-35');">get_segid</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
<a name="L145"></a><tt class="py-lineno">145</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">residue</tt><tt class="py-op">.</tt><tt id="link-36" class="py-name"><a title="Bio.PDB.Chain.Chain.get_unpacked_list
Bio.PDB.Residue.Residue.get_unpacked_list" class="py-name" href="#" onclick="return doclink('link-36', 'get_unpacked_list', 'link-30');">get_unpacked_list</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
<a name="L146"></a><tt class="py-lineno">146</tt> <tt class="py-line"> <tt class="py-keyword">if</tt> <tt id="link-37" class="py-name"><a title="Bio.GA.Selection.Abstract.AbstractSelection.select
Bio.GA.Selection.Diversity.DiversitySelection.select
Bio.GA.Selection.RouletteWheel.RouletteWheelSelection.select
Bio.GA.Selection.Tournament.TournamentSelection.select" class="py-name" href="#" onclick="return doclink('link-37', 'select', 'link-22');">select</a></tt><tt class="py-op">.</tt><tt id="link-38" class="py-name" targets="Method Bio.PDB.Dice.ChainSelector.accept_atom()=Bio.PDB.Dice.ChainSelector-class.html#accept_atom,Method Bio.PDB.PDBIO'.Select.accept_atom()=Bio.PDB.PDBIO%27.Select-class.html#accept_atom"><a title="Bio.PDB.Dice.ChainSelector.accept_atom
Bio.PDB.PDBIO'.Select.accept_atom" class="py-name" href="#" onclick="return doclink('link-38', 'accept_atom', 'link-38');">accept_atom</a></tt><tt class="py-op">(</tt><tt class="py-name">atom</tt><tt class="py-op">)</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">chain_residues_written</tt><tt class="py-op">=</tt><tt class="py-number">1</tt> </tt>
<a name="L148"></a><tt class="py-lineno">148</tt> <tt class="py-line"> <tt class="py-name">model_residues_written</tt><tt class="py-op">=</tt><tt class="py-number">1</tt> </tt>
<a name="L149"></a><tt class="py-lineno">149</tt> <tt class="py-line"> <tt id="link-39" class="py-name" targets="Variable Martel.test.test_swissprot38.s=Martel.test.test_swissprot38-module.html#s"><a title="Martel.test.test_swissprot38.s" class="py-name" href="#" onclick="return doclink('link-39', 's', 'link-39');">s</a></tt><tt class="py-op">=</tt><tt class="py-name">get_atom_line</tt><tt class="py-op">(</tt><tt class="py-name">atom</tt><tt class="py-op">,</tt> <tt class="py-name">hetfield</tt><tt class="py-op">,</tt> <tt class="py-name">segid</tt><tt class="py-op">,</tt> <tt class="py-name">atom_number</tt><tt class="py-op">,</tt> <tt class="py-name">resname</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">resseq</tt><tt class="py-op">,</tt> <tt class="py-name">icode</tt><tt class="py-op">,</tt> <tt id="link-40" class="py-name"><a title="Bio.FSSP.fssp_rec.align.chain_id" class="py-name" href="#" onclick="return doclink('link-40', 'chain_id', 'link-10');">chain_id</a></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">fp</tt><tt class="py-op">.</tt><tt id="link-41" 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-41', 'write', 'link-24');">write</a></tt><tt class="py-op">(</tt><tt id="link-42" class="py-name"><a title="Martel.test.test_swissprot38.s" class="py-name" href="#" onclick="return doclink('link-42', 's', 'link-39');">s</a></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">atom_number</tt><tt class="py-op">=</tt><tt class="py-name">atom_number</tt><tt class="py-op">+</tt><tt class="py-number">1</tt> </tt>
<a name="L153"></a><tt class="py-lineno">153</tt> <tt class="py-line"> <tt class="py-keyword">if</tt> <tt class="py-name">chain_residues_written</tt><tt class="py-op">:</tt> </tt>
<a name="L154"></a><tt class="py-lineno">154</tt> <tt class="py-line"> <tt class="py-name">fp</tt><tt class="py-op">.</tt><tt id="link-43" 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-43', 'write', 'link-24');">write</a></tt><tt class="py-op">(</tt><tt class="py-string">"TER\n"</tt><tt class="py-op">)</tt> </tt>
<a name="L155"></a><tt class="py-lineno">155</tt> <tt class="py-line"> <tt class="py-keyword">if</tt> <tt class="py-name">model_flag</tt> <tt class="py-keyword">and</tt> <tt class="py-name">model_residues_written</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">fp</tt><tt class="py-op">.</tt><tt id="link-44" 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-44', 'write', 'link-24');">write</a></tt><tt class="py-op">(</tt><tt class="py-string">"ENDMDL\n"</tt><tt class="py-op">)</tt> </tt>
<a name="L157"></a><tt class="py-lineno">157</tt> <tt class="py-line"> <tt class="py-keyword">if</tt> <tt class="py-name">close_file</tt><tt class="py-op">:</tt> </tt>
<a name="L158"></a><tt class="py-lineno">158</tt> <tt class="py-line"> <tt class="py-name">fp</tt><tt class="py-op">.</tt><tt id="link-45" class="py-name" targets="Method Bio.FilteredReader.FilteredReader.close()=Bio.FilteredReader.FilteredReader-class.html#close,Method Bio.Mindy.BerkeleyDB.BerkeleyDB.close()=Bio.Mindy.BerkeleyDB.BerkeleyDB-class.html#close,Method Bio.Mindy.FlatDB.MemoryFlatDB.close()=Bio.Mindy.FlatDB.MemoryFlatDB-class.html#close,Method BioSQL.BioSeqDatabase.Adaptor.close()=BioSQL.BioSeqDatabase.Adaptor-class.html#close,Method Martel.Parser.Parser.close()=Martel.Parser.Parser-class.html#close,Method Martel.Parser.RecordParser.close()=Martel.Parser.RecordParser-class.html#close"><a title="Bio.FilteredReader.FilteredReader.close
Bio.Mindy.BerkeleyDB.BerkeleyDB.close
Bio.Mindy.FlatDB.MemoryFlatDB.close
BioSQL.BioSeqDatabase.Adaptor.close
Martel.Parser.Parser.close
Martel.Parser.RecordParser.close" class="py-name" href="#" onclick="return doclink('link-45', 'close', 'link-45');">close</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
</div></div><a name="L159"></a><tt class="py-lineno">159</tt> <tt class="py-line"> </tt>
<a name="L160"></a><tt class="py-lineno">160</tt> <tt class="py-line"><tt class="py-keyword">if</tt> <tt class="py-name">__name__</tt><tt class="py-op">==</tt><tt class="py-string">"__main__"</tt><tt class="py-op">:</tt> </tt>
<a name="L161"></a><tt class="py-lineno">161</tt> <tt class="py-line"> </tt>
<a name="L162"></a><tt class="py-lineno">162</tt> <tt class="py-line"> <tt class="py-keyword">from</tt> <tt id="link-46" class="py-name" targets="Package Bio=Bio-module.html"><a title="Bio" class="py-name" href="#" onclick="return doclink('link-46', 'Bio', 'link-46');">Bio</a></tt><tt class="py-op">.</tt><tt id="link-47" class="py-name" targets="Package Bio.PDB=Bio.PDB-module.html"><a title="Bio.PDB" class="py-name" href="#" onclick="return doclink('link-47', 'PDB', 'link-47');">PDB</a></tt><tt class="py-op">.</tt><tt id="link-48" class="py-name" targets="Class Bio.PDB.PDBParser'.PDBParser=Bio.PDB.PDBParser%27.PDBParser-class.html"><a title="Bio.PDB.PDBParser'.PDBParser" class="py-name" href="#" onclick="return doclink('link-48', 'PDBParser', 'link-48');">PDBParser</a></tt> <tt class="py-keyword">import</tt> <tt id="link-49" class="py-name"><a title="Bio.PDB.PDBParser'.PDBParser" class="py-name" href="#" onclick="return doclink('link-49', 'PDBParser', 'link-48');">PDBParser</a></tt> </tt>
<a name="L163"></a><tt class="py-lineno">163</tt> <tt class="py-line"> </tt>
<a name="L164"></a><tt class="py-lineno">164</tt> <tt class="py-line"> <tt class="py-keyword">import</tt> <tt class="py-name">sys</tt> </tt>
<a name="L165"></a><tt class="py-lineno">165</tt> <tt class="py-line"> </tt>
<a name="L166"></a><tt class="py-lineno">166</tt> <tt class="py-line"> <tt class="py-name">p</tt><tt class="py-op">=</tt><tt id="link-50" class="py-name"><a title="Bio.PDB.PDBParser'.PDBParser" class="py-name" href="#" onclick="return doclink('link-50', 'PDBParser', 'link-48');">PDBParser</a></tt><tt class="py-op">(</tt><tt class="py-name">PERMISSIVE</tt><tt class="py-op">=</tt><tt class="py-number">1</tt><tt class="py-op">)</tt> </tt>
<a name="L167"></a><tt class="py-lineno">167</tt> <tt class="py-line"> </tt>
<a name="L168"></a><tt class="py-lineno">168</tt> <tt class="py-line"> <tt id="link-51" class="py-name"><a title="Martel.test.test_swissprot38.s" class="py-name" href="#" onclick="return doclink('link-51', 's', 'link-39');">s</a></tt><tt class="py-op">=</tt><tt class="py-name">p</tt><tt class="py-op">.</tt><tt id="link-52" class="py-name" targets="Method Bio.PDB.MMCIFParser.MMCIFParser.get_structure()=Bio.PDB.MMCIFParser.MMCIFParser-class.html#get_structure,Method Bio.PDB.PDBParser'.PDBParser.get_structure()=Bio.PDB.PDBParser%27.PDBParser-class.html#get_structure,Method Bio.PDB.StructureBuilder.StructureBuilder.get_structure()=Bio.PDB.StructureBuilder.StructureBuilder-class.html#get_structure"><a title="Bio.PDB.MMCIFParser.MMCIFParser.get_structure
Bio.PDB.PDBParser'.PDBParser.get_structure
Bio.PDB.StructureBuilder.StructureBuilder.get_structure" class="py-name" href="#" onclick="return doclink('link-52', 'get_structure', 'link-52');">get_structure</a></tt><tt class="py-op">(</tt><tt class="py-string">"test"</tt><tt class="py-op">,</tt> <tt class="py-name">sys</tt><tt class="py-op">.</tt><tt class="py-name">argv</tt><tt class="py-op">[</tt><tt class="py-number">1</tt><tt class="py-op">]</tt><tt class="py-op">)</tt> </tt>
<a name="L169"></a><tt class="py-lineno">169</tt> <tt class="py-line"> </tt>
<a name="L170"></a><tt class="py-lineno">170</tt> <tt class="py-line"> <tt class="py-name">io</tt><tt class="py-op">=</tt><tt id="link-53" class="py-name" targets="Class Bio.PDB.PDBIO'.PDBIO=Bio.PDB.PDBIO%27.PDBIO-class.html"><a title="Bio.PDB.PDBIO'.PDBIO" class="py-name" href="#" onclick="return doclink('link-53', 'PDBIO', 'link-53');">PDBIO</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
<a name="L171"></a><tt class="py-lineno">171</tt> <tt class="py-line"> <tt class="py-name">io</tt><tt class="py-op">.</tt><tt id="link-54" class="py-name" targets="Method Bio.PDB.PDBIO'.PDBIO.set_structure()=Bio.PDB.PDBIO%27.PDBIO-class.html#set_structure"><a title="Bio.PDB.PDBIO'.PDBIO.set_structure" class="py-name" href="#" onclick="return doclink('link-54', 'set_structure', 'link-54');">set_structure</a></tt><tt class="py-op">(</tt><tt id="link-55" class="py-name"><a title="Martel.test.test_swissprot38.s" class="py-name" href="#" onclick="return doclink('link-55', 's', 'link-39');">s</a></tt><tt class="py-op">)</tt> </tt>
<a name="L172"></a><tt class="py-lineno">172</tt> <tt class="py-line"> <tt class="py-name">io</tt><tt class="py-op">.</tt><tt id="link-56" class="py-name" targets="Method Bio.Cluster.Record.save()=Bio.Cluster.Record-class.html#save,Function Bio.MarkovModel.save()=Bio.MarkovModel-module.html#save,Method Bio.PDB.PDBIO'.PDBIO.save()=Bio.PDB.PDBIO%27.PDBIO-class.html#save"><a title="Bio.Cluster.Record.save
Bio.MarkovModel.save
Bio.PDB.PDBIO'.PDBIO.save" class="py-name" href="#" onclick="return doclink('link-56', 'save', 'link-56');">save</a></tt><tt class="py-op">(</tt><tt class="py-string">"out1.pdb"</tt><tt class="py-op">)</tt> </tt>
<a name="L173"></a><tt class="py-lineno">173</tt> <tt class="py-line"> </tt>
<a name="L174"></a><tt class="py-lineno">174</tt> <tt class="py-line"> <tt class="py-name">fp</tt><tt class="py-op">=</tt><tt id="link-57" class="py-name"><a title="Bio.Mindy.FlatDB.open
Bio.Mindy.open" class="py-name" href="#" onclick="return doclink('link-57', 'open', 'link-18');">open</a></tt><tt class="py-op">(</tt><tt class="py-string">"out2.pdb"</tt><tt class="py-op">,</tt> <tt class="py-string">"w"</tt><tt class="py-op">)</tt> </tt>
<a name="L175"></a><tt class="py-lineno">175</tt> <tt class="py-line"> <tt id="link-58" class="py-name" targets="Variable Martel.test.test_swissprot38.s1=Martel.test.test_swissprot38-module.html#s1"><a title="Martel.test.test_swissprot38.s1" class="py-name" href="#" onclick="return doclink('link-58', 's1', 'link-58');">s1</a></tt><tt class="py-op">=</tt><tt class="py-name">p</tt><tt class="py-op">.</tt><tt id="link-59" class="py-name"><a title="Bio.PDB.MMCIFParser.MMCIFParser.get_structure
Bio.PDB.PDBParser'.PDBParser.get_structure
Bio.PDB.StructureBuilder.StructureBuilder.get_structure" class="py-name" href="#" onclick="return doclink('link-59', 'get_structure', 'link-52');">get_structure</a></tt><tt class="py-op">(</tt><tt class="py-string">"test1"</tt><tt class="py-op">,</tt> <tt class="py-name">sys</tt><tt class="py-op">.</tt><tt class="py-name">argv</tt><tt class="py-op">[</tt><tt class="py-number">1</tt><tt class="py-op">]</tt><tt class="py-op">)</tt> </tt>
<a name="L176"></a><tt class="py-lineno">176</tt> <tt class="py-line"> <tt id="link-60" class="py-name" targets="Variable Martel.test.test_swissprot38.s2=Martel.test.test_swissprot38-module.html#s2"><a title="Martel.test.test_swissprot38.s2" class="py-name" href="#" onclick="return doclink('link-60', 's2', 'link-60');">s2</a></tt><tt class="py-op">=</tt><tt class="py-name">p</tt><tt class="py-op">.</tt><tt id="link-61" class="py-name"><a title="Bio.PDB.MMCIFParser.MMCIFParser.get_structure
Bio.PDB.PDBParser'.PDBParser.get_structure
Bio.PDB.StructureBuilder.StructureBuilder.get_structure" class="py-name" href="#" onclick="return doclink('link-61', 'get_structure', 'link-52');">get_structure</a></tt><tt class="py-op">(</tt><tt class="py-string">"test2"</tt><tt class="py-op">,</tt> <tt class="py-name">sys</tt><tt class="py-op">.</tt><tt class="py-name">argv</tt><tt class="py-op">[</tt><tt class="py-number">2</tt><tt class="py-op">]</tt><tt class="py-op">)</tt> </tt>
<a name="L177"></a><tt class="py-lineno">177</tt> <tt class="py-line"> <tt class="py-name">io</tt><tt class="py-op">=</tt><tt id="link-62" class="py-name"><a title="Bio.PDB.PDBIO'.PDBIO" class="py-name" href="#" onclick="return doclink('link-62', 'PDBIO', 'link-53');">PDBIO</a></tt><tt class="py-op">(</tt><tt class="py-number">1</tt><tt class="py-op">)</tt> </tt>
<a name="L178"></a><tt class="py-lineno">178</tt> <tt class="py-line"> <tt class="py-name">io</tt><tt class="py-op">.</tt><tt id="link-63" class="py-name"><a title="Bio.PDB.PDBIO'.PDBIO.set_structure" class="py-name" href="#" onclick="return doclink('link-63', 'set_structure', 'link-54');">set_structure</a></tt><tt class="py-op">(</tt><tt id="link-64" class="py-name"><a title="Martel.test.test_swissprot38.s1" class="py-name" href="#" onclick="return doclink('link-64', 's1', 'link-58');">s1</a></tt><tt class="py-op">)</tt> </tt>
<a name="L179"></a><tt class="py-lineno">179</tt> <tt class="py-line"> <tt class="py-name">io</tt><tt class="py-op">.</tt><tt id="link-65" class="py-name"><a title="Bio.Cluster.Record.save
Bio.MarkovModel.save
Bio.PDB.PDBIO'.PDBIO.save" class="py-name" href="#" onclick="return doclink('link-65', 'save', 'link-56');">save</a></tt><tt class="py-op">(</tt><tt class="py-name">fp</tt><tt class="py-op">)</tt> </tt>
<a name="L180"></a><tt class="py-lineno">180</tt> <tt class="py-line"> <tt class="py-name">io</tt><tt class="py-op">.</tt><tt id="link-66" class="py-name"><a title="Bio.PDB.PDBIO'.PDBIO.set_structure" class="py-name" href="#" onclick="return doclink('link-66', 'set_structure', 'link-54');">set_structure</a></tt><tt class="py-op">(</tt><tt id="link-67" class="py-name"><a title="Martel.test.test_swissprot38.s2" class="py-name" href="#" onclick="return doclink('link-67', 's2', 'link-60');">s2</a></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">io</tt><tt class="py-op">.</tt><tt id="link-68" class="py-name"><a title="Bio.Cluster.Record.save
Bio.MarkovModel.save
Bio.PDB.PDBIO'.PDBIO.save" class="py-name" href="#" onclick="return doclink('link-68', 'save', 'link-56');">save</a></tt><tt class="py-op">(</tt><tt class="py-name">fp</tt><tt class="py-op">)</tt> </tt>
<a name="L182"></a><tt class="py-lineno">182</tt> <tt class="py-line"> <tt class="py-name">fp</tt><tt class="py-op">.</tt><tt id="link-69" class="py-name"><a title="Bio.FilteredReader.FilteredReader.close
Bio.Mindy.BerkeleyDB.BerkeleyDB.close
Bio.Mindy.FlatDB.MemoryFlatDB.close
BioSQL.BioSeqDatabase.Adaptor.close
Martel.Parser.Parser.close
Martel.Parser.RecordParser.close" class="py-name" href="#" onclick="return doclink('link-69', 'close', 'link-45');">close</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
<a name="L183"></a><tt class="py-lineno">183</tt> <tt class="py-line"> </tt><script type="text/javascript">
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