<?xml version="1.0" encoding="ascii"?>
<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN"
"DTD/xhtml1-transitional.dtd">
<html xmlns="http://www.w3.org/1999/xhtml" xml:lang="en" lang="en">
<head>
<title>Bio.PDB.PDBParser'</title>
<link rel="stylesheet" href="epydoc.css" type="text/css" />
<script type="text/javascript" src="epydoc.js"></script>
</head>
<body bgcolor="white" text="black" link="blue" vlink="#204080"
alink="#204080">
<!-- ==================== NAVIGATION BAR ==================== -->
<table class="navbar" border="0" width="100%" cellpadding="0"
bgcolor="#a0c0ff" cellspacing="0">
<tr valign="middle">
<!-- Tree link -->
<th> <a
href="module-tree.html">Trees</a> </th>
<!-- Index link -->
<th> <a
href="identifier-index.html">Indices</a> </th>
<!-- Help link -->
<th> <a
href="help.html">Help</a> </th>
<th class="navbar" width="100%"></th>
</tr>
</table>
<table width="100%" cellpadding="0" cellspacing="0">
<tr valign="top">
<td width="100%">
<span class="breadcrumbs">
<a href="Bio-module.html">Package Bio</a> ::
<a href="Bio.PDB-module.html">Package PDB</a> ::
Module PDBParser'
</span>
</td>
<td>
<table cellpadding="0" cellspacing="0">
<!-- hide/show private -->
<tr><td align="right"><span class="options">[<a href="javascript:void(0);" class="privatelink"
onclick="toggle_private();">hide private</a>]</span></td></tr>
<tr><td align="right"><span class="options"
>[<a href="frames.html" target="_top">frames</a
>] | <a href="Bio.PDB.PDBParser%27-pysrc.html"
target="_top">no frames</a>]</span></td></tr>
</table>
</td>
</tr>
</table>
<h1 class="epydoc">Source Code for <a href="Bio.PDB.PDBParser%27-module.html">Module Bio.PDB.PDBParser'</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-comment"># Python stuff</tt> </tt>
<a name="L7"></a><tt class="py-lineno"> 7</tt> <tt class="py-line"><tt class="py-comment"></tt><tt class="py-keyword">import</tt> <tt class="py-name">sys</tt> </tt>
<a name="L8"></a><tt class="py-lineno"> 8</tt> <tt class="py-line"><tt class="py-keyword">from</tt> <tt class="py-name">string</tt> <tt class="py-keyword">import</tt> <tt id="link-0" class="py-name" targets="Method Bio.Nexus.Trees.Tree.split()=Bio.Nexus.Trees.Tree-class.html#split,Method Bio.Restriction.Restriction.RestrictionBatch.split()=Bio.Restriction.Restriction.RestrictionBatch-class.html#split"><a title="Bio.Nexus.Trees.Tree.split
Bio.Restriction.Restriction.RestrictionBatch.split" class="py-name" href="#" onclick="return doclink('link-0', 'split', 'link-0');">split</a></tt> </tt>
<a name="L9"></a><tt class="py-lineno"> 9</tt> <tt class="py-line"><tt class="py-keyword">from</tt> <tt class="py-name">Numeric</tt> <tt class="py-keyword">import</tt> <tt class="py-name">array</tt><tt class="py-op">,</tt> <tt id="link-1" class="py-name" targets="Variable Bio.Affy.CelFile.Float0=Bio.Affy.CelFile-module.html#Float0,Variable Bio.LogisticRegression.Float0=Bio.LogisticRegression-module.html#Float0,Variable Bio.MarkovModel.Float0=Bio.MarkovModel-module.html#Float0,Variable Bio.MaxEntropy.Float0=Bio.MaxEntropy-module.html#Float0,Variable Bio.NaiveBayes.Float0=Bio.NaiveBayes-module.html#Float0,Variable Bio.PDB.FragmentMapper'.Float0=Bio.PDB.FragmentMapper%27-module.html#Float0,Variable Bio.PDB.PDBParser'.Float0=Bio.PDB.PDBParser%27-module.html#Float0,Variable Bio.PDB.Superimposer'.Float0=Bio.PDB.Superimposer%27-module.html#Float0,Variable Bio.Statistics.lowess.Float0=Bio.Statistics.lowess-module.html#Float0,Variable Bio.distance.Float0=Bio.distance-module.html#Float0,Variable Bio.kNN.Float0=Bio.kNN-module.html#Float0"><a title="Bio.Affy.CelFile.Float0
Bio.LogisticRegression.Float0
Bio.MarkovModel.Float0
Bio.MaxEntropy.Float0
Bio.NaiveBayes.Float0
Bio.PDB.FragmentMapper'.Float0
Bio.PDB.PDBParser'.Float0
Bio.PDB.Superimposer'.Float0
Bio.Statistics.lowess.Float0
Bio.distance.Float0
Bio.kNN.Float0" class="py-name" href="#" onclick="return doclink('link-1', 'Float0', 'link-1');">Float0</a></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 class="py-comment"># My stuff</tt> </tt>
<a name="L12"></a><tt class="py-lineno"> 12</tt> <tt class="py-line"><tt class="py-comment"></tt><tt class="py-keyword">from</tt> <tt id="link-2" class="py-name" targets="Module Bio.PDB.StructureBuilder=Bio.PDB.StructureBuilder-module.html,Class Bio.PDB.StructureBuilder.StructureBuilder=Bio.PDB.StructureBuilder.StructureBuilder-class.html"><a title="Bio.PDB.StructureBuilder
Bio.PDB.StructureBuilder.StructureBuilder" class="py-name" href="#" onclick="return doclink('link-2', 'StructureBuilder', 'link-2');">StructureBuilder</a></tt> <tt class="py-keyword">import</tt> <tt id="link-3" class="py-name"><a title="Bio.PDB.StructureBuilder
Bio.PDB.StructureBuilder.StructureBuilder" class="py-name" href="#" onclick="return doclink('link-3', 'StructureBuilder', 'link-2');">StructureBuilder</a></tt> </tt>
<a name="L13"></a><tt class="py-lineno"> 13</tt> <tt class="py-line"><tt class="py-keyword">from</tt> <tt id="link-4" 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-4', 'PDBExceptions', 'link-4');">PDBExceptions</a></tt> <tt class="py-keyword">import</tt> <tt id="link-5" 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-5', 'PDBConstructionException', 'link-5');">PDBConstructionException</a></tt> </tt>
<a name="L14"></a><tt class="py-lineno"> 14</tt> <tt class="py-line"><tt class="py-keyword">from</tt> <tt id="link-6" class="py-name" targets="Function Bio.PDB.parse_pdb_header'.parse_pdb_header()=Bio.PDB.parse_pdb_header%27-module.html#parse_pdb_header"><a title="Bio.PDB.parse_pdb_header'.parse_pdb_header" class="py-name" href="#" onclick="return doclink('link-6', 'parse_pdb_header', 'link-6');">parse_pdb_header</a></tt> <tt class="py-keyword">import</tt> <tt id="link-7" class="py-name" targets="Function Bio.PDB.parse_pdb_header'._parse_pdb_header_list()=Bio.PDB.parse_pdb_header%27-module.html#_parse_pdb_header_list"><a title="Bio.PDB.parse_pdb_header'._parse_pdb_header_list" class="py-name" href="#" onclick="return doclink('link-7', '_parse_pdb_header_list', 'link-7');">_parse_pdb_header_list</a></tt> </tt>
<a name="L15"></a><tt class="py-lineno"> 15</tt> <tt class="py-line"> </tt>
<a name="L16"></a><tt class="py-lineno"> 16</tt> <tt class="py-line"><tt id="link-8" 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-8', '__doc__', 'link-8');">__doc__</a></tt><tt class="py-op">=</tt><tt class="py-string">"Parser for PDB files."</tt> </tt>
<a name="L17"></a><tt class="py-lineno"> 17</tt> <tt class="py-line"> </tt>
<a name="L18"></a><tt class="py-lineno"> 18</tt> <tt class="py-line"> </tt>
<a name="L19"></a><tt class="py-lineno"> 19</tt> <tt class="py-line"><tt class="py-comment"># If PDB spec says "COLUMNS 18-20" this means line[17:20]</tt> </tt>
<a name="L20"></a><tt class="py-lineno"> 20</tt> <tt class="py-line"><tt class="py-comment"></tt> </tt>
<a name="L21"></a><tt class="py-lineno"> 21</tt> <tt class="py-line"> </tt>
<a name="PDBParser"></a><div id="PDBParser-def"><a name="L22"></a><tt class="py-lineno"> 22</tt> <a class="py-toggle" href="#" id="PDBParser-toggle" onclick="return toggle('PDBParser');">-</a><tt class="py-line"><tt class="py-keyword">class</tt> <a class="py-def-name" href="Bio.PDB.PDBParser'.PDBParser-class.html">PDBParser</a><tt class="py-op">:</tt> </tt>
</div><div id="PDBParser-collapsed" style="display:none;" pad="+++" indent="++++"></div><div id="PDBParser-expanded"><a name="L23"></a><tt class="py-lineno"> 23</tt> <tt class="py-line"> <tt class="py-docstring">"""</tt> </tt>
<a name="L24"></a><tt class="py-lineno"> 24</tt> <tt class="py-line"><tt class="py-docstring"> Parse a PDB file and return a Structure object.</tt> </tt>
<a name="L25"></a><tt class="py-lineno"> 25</tt> <tt class="py-line"><tt class="py-docstring"> """</tt> </tt>
<a name="L26"></a><tt class="py-lineno"> 26</tt> <tt class="py-line"> </tt>
<a name="PDBParser.__init__"></a><div id="PDBParser.__init__-def"><a name="L27"></a><tt class="py-lineno"> 27</tt> <a class="py-toggle" href="#" id="PDBParser.__init__-toggle" onclick="return toggle('PDBParser.__init__');">-</a><tt class="py-line"> <tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.PDB.PDBParser'.PDBParser-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">PERMISSIVE</tt><tt class="py-op">=</tt><tt class="py-number">1</tt><tt class="py-op">,</tt> <tt class="py-param">get_header</tt><tt class="py-op">=</tt><tt class="py-number">0</tt><tt class="py-op">,</tt> <tt class="py-param">structure_builder</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="PDBParser.__init__-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="PDBParser.__init__-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"> The PDB parser call a number of standard methods in an aggregated</tt> </tt>
<a name="L30"></a><tt class="py-lineno"> 30</tt> <tt class="py-line"><tt class="py-docstring"> StructureBuilder object. Normally this object is instanciated by the</tt> </tt>
<a name="L31"></a><tt class="py-lineno"> 31</tt> <tt class="py-line"><tt class="py-docstring"> PDBParser object itself, but if the user provides his own StructureBuilder</tt> </tt>
<a name="L32"></a><tt class="py-lineno"> 32</tt> <tt class="py-line"><tt class="py-docstring"> object, the latter is used instead.</tt> </tt>
<a name="L33"></a><tt class="py-lineno"> 33</tt> <tt class="py-line"><tt class="py-docstring"></tt> </tt>
<a name="L34"></a><tt class="py-lineno"> 34</tt> <tt class="py-line"><tt class="py-docstring"> Arguments:</tt> </tt>
<a name="L35"></a><tt class="py-lineno"> 35</tt> <tt class="py-line"><tt class="py-docstring"> o PERMISSIVE - int, if this is 0 exceptions in constructing the</tt> </tt>
<a name="L36"></a><tt class="py-lineno"> 36</tt> <tt class="py-line"><tt class="py-docstring"> SMCRA data structure are fatal. If 1 (DEFAULT), the exceptions are </tt> </tt>
<a name="L37"></a><tt class="py-lineno"> 37</tt> <tt class="py-line"><tt class="py-docstring"> caught, but some residues or atoms will be missing. THESE EXCEPTIONS </tt> </tt>
<a name="L38"></a><tt class="py-lineno"> 38</tt> <tt class="py-line"><tt class="py-docstring"> ARE DUE TO PROBLEMS IN THE PDB FILE!.</tt> </tt>
<a name="L39"></a><tt class="py-lineno"> 39</tt> <tt class="py-line"><tt class="py-docstring"> o structure_builder - an optional user implemented StructureBuilder class. </tt> </tt>
<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-keyword">if</tt> <tt class="py-name">structure_builder</tt><tt class="py-op">!=</tt><tt class="py-name">None</tt><tt class="py-op">:</tt> </tt>
<a name="L42"></a><tt class="py-lineno"> 42</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">structure_builder</tt><tt class="py-op">=</tt><tt class="py-name">structure_builder</tt> </tt>
<a name="L43"></a><tt class="py-lineno"> 43</tt> <tt class="py-line"> <tt class="py-keyword">else</tt><tt class="py-op">:</tt> </tt>
<a name="L44"></a><tt class="py-lineno"> 44</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">structure_builder</tt><tt class="py-op">=</tt><tt id="link-9" class="py-name"><a title="Bio.PDB.StructureBuilder
Bio.PDB.StructureBuilder.StructureBuilder" class="py-name" href="#" onclick="return doclink('link-9', 'StructureBuilder', 'link-2');">StructureBuilder</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
<a name="L45"></a><tt class="py-lineno"> 45</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-10" 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-10', 'header', 'link-10');">header</a></tt><tt class="py-op">=</tt><tt class="py-name">None</tt> </tt>
<a name="L46"></a><tt class="py-lineno"> 46</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">trailer</tt><tt class="py-op">=</tt><tt class="py-name">None</tt> </tt>
<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 class="py-name">line_counter</tt><tt class="py-op">=</tt><tt class="py-number">0</tt> </tt>
<a name="L48"></a><tt class="py-lineno"> 48</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">PERMISSIVE</tt><tt class="py-op">=</tt><tt class="py-name">PERMISSIVE</tt> </tt>
</div><a name="L49"></a><tt class="py-lineno"> 49</tt> <tt class="py-line"> </tt>
<a name="L50"></a><tt class="py-lineno"> 50</tt> <tt class="py-line"> <tt class="py-comment"># Public methods</tt> </tt>
<a name="L51"></a><tt class="py-lineno"> 51</tt> <tt class="py-line"><tt class="py-comment"></tt> </tt>
<a name="PDBParser.get_structure"></a><div id="PDBParser.get_structure-def"><a name="L52"></a><tt class="py-lineno"> 52</tt> <a class="py-toggle" href="#" id="PDBParser.get_structure-toggle" onclick="return toggle('PDBParser.get_structure');">-</a><tt class="py-line"> <tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.PDB.PDBParser'.PDBParser-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-param">id</tt><tt class="py-op">,</tt> <tt class="py-param">file</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="PDBParser.get_structure-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="PDBParser.get_structure-expanded"><a name="L53"></a><tt class="py-lineno"> 53</tt> <tt class="py-line"> <tt class="py-docstring">"""Return the structure.</tt> </tt>
<a name="L54"></a><tt class="py-lineno"> 54</tt> <tt class="py-line"><tt class="py-docstring"></tt> </tt>
<a name="L55"></a><tt class="py-lineno"> 55</tt> <tt class="py-line"><tt class="py-docstring"> Arguments:</tt> </tt>
<a name="L56"></a><tt class="py-lineno"> 56</tt> <tt class="py-line"><tt class="py-docstring"> o id - string, the id that will be used for the structure</tt> </tt>
<a name="L57"></a><tt class="py-lineno"> 57</tt> <tt class="py-line"><tt class="py-docstring"> o file - name of the PDB file OR an open filehandle</tt> </tt>
<a name="L58"></a><tt class="py-lineno"> 58</tt> <tt class="py-line"><tt class="py-docstring"> """</tt> </tt>
<a name="L59"></a><tt class="py-lineno"> 59</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-11" 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-11', 'header', 'link-10');">header</a></tt><tt class="py-op">=</tt><tt class="py-name">None</tt> </tt>
<a name="L60"></a><tt class="py-lineno"> 60</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">trailer</tt><tt class="py-op">=</tt><tt class="py-name">None</tt> </tt>
<a name="L61"></a><tt class="py-lineno"> 61</tt> <tt class="py-line"> <tt class="py-comment"># Make a StructureBuilder instance (pass id of structure as parameter)</tt> </tt>
<a name="L62"></a><tt class="py-lineno"> 62</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">structure_builder</tt><tt class="py-op">.</tt><tt id="link-12" class="py-name" targets="Method Bio.PDB.StructureBuilder.StructureBuilder.init_structure()=Bio.PDB.StructureBuilder.StructureBuilder-class.html#init_structure"><a title="Bio.PDB.StructureBuilder.StructureBuilder.init_structure" class="py-name" href="#" onclick="return doclink('link-12', 'init_structure', 'link-12');">init_structure</a></tt><tt class="py-op">(</tt><tt id="link-13" class="py-name" targets="Variable Bio.Data.CodonTable.id=Bio.Data.CodonTable-module.html#id,Variable Bio.Encodings.IUPACEncoding.id=Bio.Encodings.IUPACEncoding-module.html#id,Method Bio.GFF.Feature.id()=Bio.GFF.Feature-class.html#id"><a title="Bio.Data.CodonTable.id
Bio.Encodings.IUPACEncoding.id
Bio.GFF.Feature.id" class="py-name" href="#" onclick="return doclink('link-13', 'id', 'link-13');">id</a></tt><tt class="py-op">)</tt> </tt>
<a name="L63"></a><tt class="py-lineno"> 63</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="L64"></a><tt class="py-lineno"> 64</tt> <tt class="py-line"> <tt class="py-name">file</tt><tt class="py-op">=</tt><tt id="link-14" 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-14', 'open', 'link-14');">open</a></tt><tt class="py-op">(</tt><tt class="py-name">file</tt><tt class="py-op">)</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-15" class="py-name" targets="Method Bio.Blast.NCBIStandalone._DescriptionConsumer._parse()=Bio.Blast.NCBIStandalone._DescriptionConsumer-class.html#_parse,Method Bio.Nexus.Trees.Tree._parse()=Bio.Nexus.Trees.Tree-class.html#_parse,Method Bio.PDB.PDBParser'.PDBParser._parse()=Bio.PDB.PDBParser%27.PDBParser-class.html#_parse,Method Bio.SCOP.Residues'.Residues._parse()=Bio.SCOP.Residues%27.Residues-class.html#_parse,Function Martel.msre_parse._parse()=Martel.msre_parse-module.html#_parse"><a title="Bio.Blast.NCBIStandalone._DescriptionConsumer._parse
Bio.Nexus.Trees.Tree._parse
Bio.PDB.PDBParser'.PDBParser._parse
Bio.SCOP.Residues'.Residues._parse
Martel.msre_parse._parse" class="py-name" href="#" onclick="return doclink('link-15', '_parse', 'link-15');">_parse</a></tt><tt class="py-op">(</tt><tt class="py-name">file</tt><tt class="py-op">.</tt><tt id="link-16" class="py-name" targets="Method Bio.EUtils.ReseekFile.ReseekFile.readlines()=Bio.EUtils.ReseekFile.ReseekFile-class.html#readlines,Method Bio.File.SGMLHandle.readlines()=Bio.File.SGMLHandle-class.html#readlines,Method Bio.File.UndoHandle.readlines()=Bio.File.UndoHandle-class.html#readlines,Method Bio.SGMLExtractor.SGMLExtractorHandle.readlines()=Bio.SGMLExtractor.SGMLExtractorHandle-class.html#readlines"><a title="Bio.EUtils.ReseekFile.ReseekFile.readlines
Bio.File.SGMLHandle.readlines
Bio.File.UndoHandle.readlines
Bio.SGMLExtractor.SGMLExtractorHandle.readlines" class="py-name" href="#" onclick="return doclink('link-16', 'readlines', 'link-16');">readlines</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt><tt class="py-op">)</tt> </tt>
<a name="L66"></a><tt class="py-lineno"> 66</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">structure_builder</tt><tt class="py-op">.</tt><tt id="link-17" class="py-name" targets="Method Bio.PDB.StructureBuilder.StructureBuilder.set_header()=Bio.PDB.StructureBuilder.StructureBuilder-class.html#set_header"><a title="Bio.PDB.StructureBuilder.StructureBuilder.set_header" class="py-name" href="#" onclick="return doclink('link-17', 'set_header', 'link-17');">set_header</a></tt><tt class="py-op">(</tt><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-10');">header</a></tt><tt class="py-op">)</tt> </tt>
<a name="L67"></a><tt class="py-lineno"> 67</tt> <tt class="py-line"> <tt class="py-comment"># Return the Structure instance</tt> </tt>
<a name="L68"></a><tt class="py-lineno"> 68</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-keyword">return</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">structure_builder</tt><tt class="py-op">.</tt><tt id="link-19" 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-19', 'get_structure', 'link-19');">get_structure</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
</div><a name="L69"></a><tt class="py-lineno"> 69</tt> <tt class="py-line"> </tt>
<a name="PDBParser.get_header"></a><div id="PDBParser.get_header-def"><a name="L70"></a><tt class="py-lineno"> 70</tt> <a class="py-toggle" href="#" id="PDBParser.get_header-toggle" onclick="return toggle('PDBParser.get_header');">-</a><tt class="py-line"> <tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.PDB.PDBParser'.PDBParser-class.html#get_header">get_header</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="PDBParser.get_header-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="PDBParser.get_header-expanded"><a name="L71"></a><tt class="py-lineno"> 71</tt> <tt class="py-line"> <tt class="py-docstring">"Return the header."</tt> </tt>
<a name="L72"></a><tt class="py-lineno"> 72</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-20" 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-20', 'header', 'link-10');">header</a></tt> </tt>
</div><a name="L73"></a><tt class="py-lineno"> 73</tt> <tt class="py-line"> </tt>
<a name="PDBParser.get_trailer"></a><div id="PDBParser.get_trailer-def"><a name="L74"></a><tt class="py-lineno"> 74</tt> <a class="py-toggle" href="#" id="PDBParser.get_trailer-toggle" onclick="return toggle('PDBParser.get_trailer');">-</a><tt class="py-line"> <tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.PDB.PDBParser'.PDBParser-class.html#get_trailer">get_trailer</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="PDBParser.get_trailer-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="PDBParser.get_trailer-expanded"><a name="L75"></a><tt class="py-lineno"> 75</tt> <tt class="py-line"> <tt class="py-docstring">"Return the trailer."</tt> </tt>
<a name="L76"></a><tt class="py-lineno"> 76</tt> <tt class="py-line"> <tt class="py-keyword">return</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">trailer</tt> </tt>
</div><a name="L77"></a><tt class="py-lineno"> 77</tt> <tt class="py-line"> </tt>
<a name="L78"></a><tt class="py-lineno"> 78</tt> <tt class="py-line"> <tt class="py-comment"># Private methods</tt> </tt>
<a name="L79"></a><tt class="py-lineno"> 79</tt> <tt class="py-line"><tt class="py-comment"></tt> </tt>
<a name="PDBParser._parse"></a><div id="PDBParser._parse-def"><a name="L80"></a><tt class="py-lineno"> 80</tt> <a class="py-toggle" href="#" id="PDBParser._parse-toggle" onclick="return toggle('PDBParser._parse');">-</a><tt class="py-line"> <tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.PDB.PDBParser'.PDBParser-class.html#_parse">_parse</a><tt class="py-op">(</tt><tt class="py-param">self</tt><tt class="py-op">,</tt> <tt class="py-param">header_coords_trailer</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="PDBParser._parse-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="PDBParser._parse-expanded"><a name="L81"></a><tt class="py-lineno"> 81</tt> <tt class="py-line"> <tt class="py-docstring">"Parse the PDB file."</tt> </tt>
<a name="L82"></a><tt class="py-lineno"> 82</tt> <tt class="py-line"> <tt class="py-comment"># Extract the header; return the rest of the file</tt> </tt>
<a name="L83"></a><tt class="py-lineno"> 83</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-21" 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-21', 'header', 'link-10');">header</a></tt><tt class="py-op">,</tt> <tt class="py-name">coords_trailer</tt><tt class="py-op">=</tt><tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-22" class="py-name" targets="Method Bio.PDB.PDBParser'.PDBParser._get_header()=Bio.PDB.PDBParser%27.PDBParser-class.html#_get_header"><a title="Bio.PDB.PDBParser'.PDBParser._get_header" class="py-name" href="#" onclick="return doclink('link-22', '_get_header', 'link-22');">_get_header</a></tt><tt class="py-op">(</tt><tt class="py-name">header_coords_trailer</tt><tt class="py-op">)</tt> </tt>
<a name="L84"></a><tt class="py-lineno"> 84</tt> <tt class="py-line"> <tt class="py-comment"># Parse the atomic data; return the PDB file trailer</tt> </tt>
<a name="L85"></a><tt class="py-lineno"> 85</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">trailer</tt><tt class="py-op">=</tt><tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-23" class="py-name" targets="Method Bio.PDB.PDBParser'.PDBParser._parse_coordinates()=Bio.PDB.PDBParser%27.PDBParser-class.html#_parse_coordinates"><a title="Bio.PDB.PDBParser'.PDBParser._parse_coordinates" class="py-name" href="#" onclick="return doclink('link-23', '_parse_coordinates', 'link-23');">_parse_coordinates</a></tt><tt class="py-op">(</tt><tt class="py-name">coords_trailer</tt><tt class="py-op">)</tt> </tt>
</div><a name="L86"></a><tt class="py-lineno"> 86</tt> <tt class="py-line"> </tt>
<a name="PDBParser._get_header"></a><div id="PDBParser._get_header-def"><a name="L87"></a><tt class="py-lineno"> 87</tt> <a class="py-toggle" href="#" id="PDBParser._get_header-toggle" onclick="return toggle('PDBParser._get_header');">-</a><tt class="py-line"> <tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.PDB.PDBParser'.PDBParser-class.html#_get_header">_get_header</a><tt class="py-op">(</tt><tt class="py-param">self</tt><tt class="py-op">,</tt> <tt class="py-param">header_coords_trailer</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="PDBParser._get_header-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="PDBParser._get_header-expanded"><a name="L88"></a><tt class="py-lineno"> 88</tt> <tt class="py-line"> <tt class="py-docstring">"Get the header of the PDB file, return the rest."</tt> </tt>
<a name="L89"></a><tt class="py-lineno"> 89</tt> <tt class="py-line"> <tt class="py-name">structure_builder</tt><tt class="py-op">=</tt><tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">structure_builder</tt> </tt>
<a name="L90"></a><tt class="py-lineno"> 90</tt> <tt class="py-line"> <tt class="py-keyword">for</tt> <tt id="link-24" class="py-name" targets="Variable Bio.PDB.Polypeptide.i=Bio.PDB.Polypeptide-module.html#i"><a title="Bio.PDB.Polypeptide.i" class="py-name" href="#" onclick="return doclink('link-24', 'i', 'link-24');">i</a></tt> <tt class="py-keyword">in</tt> <tt class="py-name">range</tt><tt class="py-op">(</tt><tt class="py-number">0</tt><tt class="py-op">,</tt> <tt class="py-name">len</tt><tt class="py-op">(</tt><tt class="py-name">header_coords_trailer</tt><tt class="py-op">)</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
<a name="L91"></a><tt class="py-lineno"> 91</tt> <tt class="py-line"> <tt class="py-name">structure_builder</tt><tt class="py-op">.</tt><tt id="link-25" class="py-name" targets="Method Bio.PDB.StructureBuilder.StructureBuilder.set_line_counter()=Bio.PDB.StructureBuilder.StructureBuilder-class.html#set_line_counter"><a title="Bio.PDB.StructureBuilder.StructureBuilder.set_line_counter" class="py-name" href="#" onclick="return doclink('link-25', 'set_line_counter', 'link-25');">set_line_counter</a></tt><tt class="py-op">(</tt><tt id="link-26" class="py-name"><a title="Bio.PDB.Polypeptide.i" class="py-name" href="#" onclick="return doclink('link-26', 'i', 'link-24');">i</a></tt><tt class="py-op">+</tt><tt class="py-number">1</tt><tt class="py-op">)</tt> </tt>
<a name="L92"></a><tt class="py-lineno"> 92</tt> <tt class="py-line"> <tt class="py-name">line</tt><tt class="py-op">=</tt><tt class="py-name">header_coords_trailer</tt><tt class="py-op">[</tt><tt id="link-27" class="py-name"><a title="Bio.PDB.Polypeptide.i" class="py-name" href="#" onclick="return doclink('link-27', 'i', 'link-24');">i</a></tt><tt class="py-op">]</tt> </tt>
<a name="L93"></a><tt class="py-lineno"> 93</tt> <tt class="py-line"> <tt class="py-name">record_type</tt><tt class="py-op">=</tt><tt class="py-name">line</tt><tt class="py-op">[</tt><tt class="py-number">0</tt><tt class="py-op">:</tt><tt class="py-number">6</tt><tt class="py-op">]</tt> </tt>
<a name="L94"></a><tt class="py-lineno"> 94</tt> <tt class="py-line"> <tt class="py-keyword">if</tt><tt class="py-op">(</tt><tt class="py-name">record_type</tt><tt class="py-op">==</tt><tt class="py-string">'ATOM '</tt> <tt class="py-keyword">or</tt> <tt class="py-name">record_type</tt><tt class="py-op">==</tt><tt class="py-string">'HETATM'</tt> <tt class="py-keyword">or</tt> <tt class="py-name">record_type</tt><tt class="py-op">==</tt><tt class="py-string">'MODEL '</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
<a name="L95"></a><tt class="py-lineno"> 95</tt> <tt class="py-line"> <tt class="py-keyword">break</tt> </tt>
<a name="L96"></a><tt class="py-lineno"> 96</tt> <tt class="py-line"> <tt id="link-28" 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-28', 'header', 'link-10');">header</a></tt><tt class="py-op">=</tt><tt class="py-name">header_coords_trailer</tt><tt class="py-op">[</tt><tt class="py-number">0</tt><tt class="py-op">:</tt><tt id="link-29" class="py-name"><a title="Bio.PDB.Polypeptide.i" class="py-name" href="#" onclick="return doclink('link-29', 'i', 'link-24');">i</a></tt><tt class="py-op">]</tt> </tt>
<a name="L97"></a><tt class="py-lineno"> 97</tt> <tt class="py-line"> <tt class="py-comment"># Return the rest of the coords+trailer for further processing</tt> </tt>
<a name="L98"></a><tt class="py-lineno"> 98</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">line_counter</tt><tt class="py-op">=</tt><tt id="link-30" class="py-name"><a title="Bio.PDB.Polypeptide.i" class="py-name" href="#" onclick="return doclink('link-30', 'i', 'link-24');">i</a></tt> </tt>
<a name="L99"></a><tt class="py-lineno"> 99</tt> <tt class="py-line"> <tt class="py-name">coords_trailer</tt><tt class="py-op">=</tt><tt class="py-name">header_coords_trailer</tt><tt class="py-op">[</tt><tt id="link-31" class="py-name"><a title="Bio.PDB.Polypeptide.i" class="py-name" href="#" onclick="return doclink('link-31', 'i', 'link-24');">i</a></tt><tt class="py-op">:</tt><tt class="py-op">]</tt> </tt>
<a name="L100"></a><tt class="py-lineno">100</tt> <tt class="py-line"> <tt class="py-name">header_dict</tt><tt class="py-op">=</tt><tt id="link-32" class="py-name"><a title="Bio.PDB.parse_pdb_header'._parse_pdb_header_list" class="py-name" href="#" onclick="return doclink('link-32', '_parse_pdb_header_list', 'link-7');">_parse_pdb_header_list</a></tt><tt class="py-op">(</tt><tt id="link-33" 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-33', 'header', 'link-10');">header</a></tt><tt class="py-op">)</tt> </tt>
<a name="L101"></a><tt class="py-lineno">101</tt> <tt class="py-line"> <tt class="py-keyword">return</tt> <tt class="py-name">header_dict</tt><tt class="py-op">,</tt> <tt class="py-name">coords_trailer</tt> </tt>
</div><a name="L102"></a><tt class="py-lineno">102</tt> <tt class="py-line"> </tt>
<a name="PDBParser._parse_coordinates"></a><div id="PDBParser._parse_coordinates-def"><a name="L103"></a><tt class="py-lineno">103</tt> <a class="py-toggle" href="#" id="PDBParser._parse_coordinates-toggle" onclick="return toggle('PDBParser._parse_coordinates');">-</a><tt class="py-line"> <tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.PDB.PDBParser'.PDBParser-class.html#_parse_coordinates">_parse_coordinates</a><tt class="py-op">(</tt><tt class="py-param">self</tt><tt class="py-op">,</tt> <tt class="py-param">coords_trailer</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="PDBParser._parse_coordinates-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="PDBParser._parse_coordinates-expanded"><a name="L104"></a><tt class="py-lineno">104</tt> <tt class="py-line"> <tt class="py-docstring">"Parse the atomic data in the PDB file."</tt> </tt>
<a name="L105"></a><tt class="py-lineno">105</tt> <tt class="py-line"> <tt class="py-name">local_line_counter</tt><tt class="py-op">=</tt><tt class="py-number">0</tt> </tt>
<a name="L106"></a><tt class="py-lineno">106</tt> <tt class="py-line"> <tt class="py-name">structure_builder</tt><tt class="py-op">=</tt><tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">structure_builder</tt> </tt>
<a name="L107"></a><tt class="py-lineno">107</tt> <tt class="py-line"> <tt class="py-name">current_model_id</tt><tt class="py-op">=</tt><tt class="py-number">0</tt> </tt>
<a name="L108"></a><tt class="py-lineno">108</tt> <tt class="py-line"> <tt class="py-comment"># Flag we have an open model</tt> </tt>
<a name="L109"></a><tt class="py-lineno">109</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-name">model_open</tt><tt class="py-op">=</tt><tt class="py-number">0</tt> </tt>
<a name="L110"></a><tt class="py-lineno">110</tt> <tt class="py-line"> <tt class="py-name">current_chain_id</tt><tt class="py-op">=</tt><tt class="py-name">None</tt> </tt>
<a name="L111"></a><tt class="py-lineno">111</tt> <tt class="py-line"> <tt class="py-name">current_segid</tt><tt class="py-op">=</tt><tt class="py-name">None</tt> </tt>
<a name="L112"></a><tt class="py-lineno">112</tt> <tt class="py-line"> <tt class="py-name">current_residue_id</tt><tt class="py-op">=</tt><tt class="py-name">None</tt> </tt>
<a name="L113"></a><tt class="py-lineno">113</tt> <tt class="py-line"> <tt class="py-name">current_resname</tt><tt class="py-op">=</tt><tt class="py-name">None</tt> </tt>
<a name="L114"></a><tt class="py-lineno">114</tt> <tt class="py-line"> <tt class="py-keyword">for</tt> <tt id="link-34" class="py-name"><a title="Bio.PDB.Polypeptide.i" class="py-name" href="#" onclick="return doclink('link-34', 'i', 'link-24');">i</a></tt> <tt class="py-keyword">in</tt> <tt class="py-name">range</tt><tt class="py-op">(</tt><tt class="py-number">0</tt><tt class="py-op">,</tt> <tt class="py-name">len</tt><tt class="py-op">(</tt><tt class="py-name">coords_trailer</tt><tt class="py-op">)</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
<a name="L115"></a><tt class="py-lineno">115</tt> <tt class="py-line"> <tt class="py-name">line</tt><tt class="py-op">=</tt><tt class="py-name">coords_trailer</tt><tt class="py-op">[</tt><tt id="link-35" class="py-name"><a title="Bio.PDB.Polypeptide.i" class="py-name" href="#" onclick="return doclink('link-35', 'i', 'link-24');">i</a></tt><tt class="py-op">]</tt> </tt>
<a name="L116"></a><tt class="py-lineno">116</tt> <tt class="py-line"> <tt class="py-name">record_type</tt><tt class="py-op">=</tt><tt class="py-name">line</tt><tt class="py-op">[</tt><tt class="py-number">0</tt><tt class="py-op">:</tt><tt class="py-number">6</tt><tt class="py-op">]</tt> </tt>
<a name="L117"></a><tt class="py-lineno">117</tt> <tt class="py-line"> <tt class="py-name">global_line_counter</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-name">local_line_counter</tt><tt class="py-op">+</tt><tt class="py-number">1</tt> </tt>
<a name="L118"></a><tt class="py-lineno">118</tt> <tt class="py-line"> <tt class="py-name">structure_builder</tt><tt class="py-op">.</tt><tt id="link-36" class="py-name"><a title="Bio.PDB.StructureBuilder.StructureBuilder.set_line_counter" class="py-name" href="#" onclick="return doclink('link-36', 'set_line_counter', 'link-25');">set_line_counter</a></tt><tt class="py-op">(</tt><tt class="py-name">global_line_counter</tt><tt class="py-op">)</tt> </tt>
<a name="L119"></a><tt class="py-lineno">119</tt> <tt class="py-line"> <tt class="py-keyword">if</tt><tt class="py-op">(</tt><tt class="py-name">record_type</tt><tt class="py-op">==</tt><tt class="py-string">'ATOM '</tt> <tt class="py-keyword">or</tt> <tt class="py-name">record_type</tt><tt class="py-op">==</tt><tt class="py-string">'HETATM'</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
<a name="L120"></a><tt class="py-lineno">120</tt> <tt class="py-line"> <tt class="py-comment"># Initialize the Model - there was no explicit MODEL record</tt> </tt>
<a name="L121"></a><tt class="py-lineno">121</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">model_open</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">structure_builder</tt><tt class="py-op">.</tt><tt id="link-37" class="py-name" targets="Method Bio.PDB.StructureBuilder.StructureBuilder.init_model()=Bio.PDB.StructureBuilder.StructureBuilder-class.html#init_model"><a title="Bio.PDB.StructureBuilder.StructureBuilder.init_model" class="py-name" href="#" onclick="return doclink('link-37', 'init_model', 'link-37');">init_model</a></tt><tt class="py-op">(</tt><tt class="py-name">current_model_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-name">current_model_id</tt><tt class="py-op">+=</tt><tt class="py-number">1</tt> </tt>
<a name="L124"></a><tt class="py-lineno">124</tt> <tt class="py-line"> <tt class="py-name">model_open</tt><tt class="py-op">=</tt><tt class="py-number">1</tt> </tt>
<a name="L125"></a><tt class="py-lineno">125</tt> <tt class="py-line"> <tt class="py-name">fullname</tt><tt class="py-op">=</tt><tt class="py-name">line</tt><tt class="py-op">[</tt><tt class="py-number">12</tt><tt class="py-op">:</tt><tt class="py-number">16</tt><tt class="py-op">]</tt> </tt>
<a name="L126"></a><tt class="py-lineno">126</tt> <tt class="py-line"> <tt class="py-comment"># get rid of whitespace in atom names</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">split_list</tt><tt class="py-op">=</tt><tt id="link-38" class="py-name"><a title="Bio.Nexus.Trees.Tree.split
Bio.Restriction.Restriction.RestrictionBatch.split" class="py-name" href="#" onclick="return doclink('link-38', 'split', 'link-0');">split</a></tt><tt class="py-op">(</tt><tt class="py-name">fullname</tt><tt class="py-op">)</tt> </tt>
<a name="L128"></a><tt class="py-lineno">128</tt> <tt class="py-line"> <tt class="py-keyword">if</tt> <tt class="py-name">len</tt><tt class="py-op">(</tt><tt class="py-name">split_list</tt><tt class="py-op">)</tt><tt class="py-op">!=</tt><tt class="py-number">1</tt><tt class="py-op">:</tt> </tt>
<a name="L129"></a><tt class="py-lineno">129</tt> <tt class="py-line"> <tt class="py-comment"># atom name has internal spaces, e.g. " N B ", so</tt> </tt>
<a name="L130"></a><tt class="py-lineno">130</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-comment"># we do not strip spaces</tt> </tt>
<a name="L131"></a><tt class="py-lineno">131</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt id="link-39" 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-39', 'name', 'link-39');">name</a></tt><tt class="py-op">=</tt><tt class="py-name">fullname</tt> </tt>
<a name="L132"></a><tt class="py-lineno">132</tt> <tt class="py-line"> <tt class="py-keyword">else</tt><tt class="py-op">:</tt> </tt>
<a name="L133"></a><tt class="py-lineno">133</tt> <tt class="py-line"> <tt class="py-comment"># atom name is like " CA ", so we can strip spaces</tt> </tt>
<a name="L134"></a><tt class="py-lineno">134</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt id="link-40" class="py-name"><a title="Bio.Encodings.IUPACEncoding.name" class="py-name" href="#" onclick="return doclink('link-40', 'name', 'link-39');">name</a></tt><tt class="py-op">=</tt><tt class="py-name">split_list</tt><tt class="py-op">[</tt><tt class="py-number">0</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">altloc</tt><tt class="py-op">=</tt><tt class="py-name">line</tt><tt class="py-op">[</tt><tt class="py-number">16</tt><tt class="py-op">:</tt><tt class="py-number">17</tt><tt class="py-op">]</tt> </tt>
<a name="L136"></a><tt class="py-lineno">136</tt> <tt class="py-line"> <tt class="py-name">resname</tt><tt class="py-op">=</tt><tt class="py-name">line</tt><tt class="py-op">[</tt><tt class="py-number">17</tt><tt class="py-op">:</tt><tt class="py-number">20</tt><tt class="py-op">]</tt> </tt>
<a name="L137"></a><tt class="py-lineno">137</tt> <tt class="py-line"> <tt class="py-name">chainid</tt><tt class="py-op">=</tt><tt class="py-name">line</tt><tt class="py-op">[</tt><tt class="py-number">21</tt><tt class="py-op">:</tt><tt class="py-number">22</tt><tt class="py-op">]</tt> </tt>
<a name="L138"></a><tt class="py-lineno">138</tt> <tt class="py-line"> <tt class="py-keyword">try</tt><tt class="py-op">:</tt> </tt>
<a name="L139"></a><tt class="py-lineno">139</tt> <tt class="py-line"> <tt class="py-name">serial_number</tt><tt class="py-op">=</tt><tt class="py-name">int</tt><tt class="py-op">(</tt><tt class="py-name">line</tt><tt class="py-op">[</tt><tt class="py-number">6</tt><tt class="py-op">:</tt><tt class="py-number">11</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">except</tt><tt class="py-op">:</tt> </tt>
<a name="L141"></a><tt class="py-lineno">141</tt> <tt class="py-line"> <tt class="py-name">serial_number</tt><tt class="py-op">=</tt><tt class="py-number">0</tt> </tt>
<a name="L142"></a><tt class="py-lineno">142</tt> <tt class="py-line"> <tt class="py-name">resseq</tt><tt class="py-op">=</tt><tt class="py-name">int</tt><tt class="py-op">(</tt><tt id="link-41" class="py-name"><a title="Bio.Nexus.Trees.Tree.split
Bio.Restriction.Restriction.RestrictionBatch.split" class="py-name" href="#" onclick="return doclink('link-41', 'split', 'link-0');">split</a></tt><tt class="py-op">(</tt><tt class="py-name">line</tt><tt class="py-op">[</tt><tt class="py-number">22</tt><tt class="py-op">:</tt><tt class="py-number">26</tt><tt class="py-op">]</tt><tt class="py-op">)</tt><tt class="py-op">[</tt><tt class="py-number">0</tt><tt class="py-op">]</tt><tt class="py-op">)</tt> <tt class="py-comment"># sequence identifier </tt> </tt>
<a name="L143"></a><tt class="py-lineno">143</tt> <tt class="py-line"> <tt class="py-name">icode</tt><tt class="py-op">=</tt><tt class="py-name">line</tt><tt class="py-op">[</tt><tt class="py-number">26</tt><tt class="py-op">:</tt><tt class="py-number">27</tt><tt class="py-op">]</tt> <tt class="py-comment"># insertion code</tt> </tt>
<a name="L144"></a><tt class="py-lineno">144</tt> <tt class="py-line"> <tt class="py-keyword">if</tt> <tt class="py-name">record_type</tt><tt class="py-op">==</tt><tt class="py-string">'HETATM'</tt><tt class="py-op">:</tt> <tt class="py-comment"># hetero atom flag</tt> </tt>
<a name="L145"></a><tt class="py-lineno">145</tt> <tt class="py-line"> <tt class="py-keyword">if</tt> <tt class="py-name">resname</tt><tt class="py-op">==</tt><tt class="py-string">"HOH"</tt> <tt class="py-keyword">or</tt> <tt class="py-name">resname</tt><tt class="py-op">==</tt><tt class="py-string">"WAT"</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">hetero_flag</tt><tt class="py-op">=</tt><tt class="py-string">"W"</tt> </tt>
<a name="L147"></a><tt class="py-lineno">147</tt> <tt class="py-line"> <tt class="py-keyword">else</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">hetero_flag</tt><tt class="py-op">=</tt><tt class="py-string">"H"</tt> </tt>
<a name="L149"></a><tt class="py-lineno">149</tt> <tt class="py-line"> <tt class="py-keyword">else</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">hetero_flag</tt><tt class="py-op">=</tt><tt class="py-string">" "</tt> </tt>
<a name="L151"></a><tt class="py-lineno">151</tt> <tt class="py-line"> <tt class="py-name">residue_id</tt><tt class="py-op">=</tt><tt class="py-op">(</tt><tt class="py-name">hetero_flag</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="L152"></a><tt class="py-lineno">152</tt> <tt class="py-line"> <tt class="py-comment"># atomic coordinates</tt> </tt>
<a name="L153"></a><tt class="py-lineno">153</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt id="link-42" 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-42', 'x', 'link-42');">x</a></tt><tt class="py-op">=</tt><tt class="py-name">float</tt><tt class="py-op">(</tt><tt class="py-name">line</tt><tt class="py-op">[</tt><tt class="py-number">30</tt><tt class="py-op">:</tt><tt class="py-number">38</tt><tt class="py-op">]</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">y</tt><tt class="py-op">=</tt><tt class="py-name">float</tt><tt class="py-op">(</tt><tt class="py-name">line</tt><tt class="py-op">[</tt><tt class="py-number">38</tt><tt class="py-op">:</tt><tt class="py-number">46</tt><tt class="py-op">]</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">z</tt><tt class="py-op">=</tt><tt class="py-name">float</tt><tt class="py-op">(</tt><tt class="py-name">line</tt><tt class="py-op">[</tt><tt class="py-number">46</tt><tt class="py-op">:</tt><tt class="py-number">54</tt><tt class="py-op">]</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">coord</tt><tt class="py-op">=</tt><tt class="py-name">array</tt><tt class="py-op">(</tt><tt class="py-op">(</tt><tt id="link-43" class="py-name"><a title="Bio.MarkovModel.x
Bio.Statistics.lowess.x" class="py-name" href="#" onclick="return doclink('link-43', 'x', 'link-42');">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-op">,</tt> <tt id="link-44" class="py-name"><a title="Bio.Affy.CelFile.Float0
Bio.LogisticRegression.Float0
Bio.MarkovModel.Float0
Bio.MaxEntropy.Float0
Bio.NaiveBayes.Float0
Bio.PDB.FragmentMapper'.Float0
Bio.PDB.PDBParser'.Float0
Bio.PDB.Superimposer'.Float0
Bio.Statistics.lowess.Float0
Bio.distance.Float0
Bio.kNN.Float0" class="py-name" href="#" onclick="return doclink('link-44', 'Float0', 'link-1');">Float0</a></tt><tt class="py-op">)</tt> </tt>
<a name="L157"></a><tt class="py-lineno">157</tt> <tt class="py-line"> <tt class="py-comment"># occupancy & B factor</tt> </tt>
<a name="L158"></a><tt class="py-lineno">158</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-name">occupancy</tt><tt class="py-op">=</tt><tt class="py-name">float</tt><tt class="py-op">(</tt><tt class="py-name">line</tt><tt class="py-op">[</tt><tt class="py-number">54</tt><tt class="py-op">:</tt><tt class="py-number">60</tt><tt class="py-op">]</tt><tt class="py-op">)</tt> </tt>
<a name="L159"></a><tt class="py-lineno">159</tt> <tt class="py-line"> <tt class="py-name">bfactor</tt><tt class="py-op">=</tt><tt class="py-name">float</tt><tt class="py-op">(</tt><tt class="py-name">line</tt><tt class="py-op">[</tt><tt class="py-number">60</tt><tt class="py-op">:</tt><tt class="py-number">66</tt><tt class="py-op">]</tt><tt class="py-op">)</tt> </tt>
<a name="L160"></a><tt class="py-lineno">160</tt> <tt class="py-line"> <tt class="py-name">segid</tt><tt class="py-op">=</tt><tt class="py-name">line</tt><tt class="py-op">[</tt><tt class="py-number">72</tt><tt class="py-op">:</tt><tt class="py-number">76</tt><tt class="py-op">]</tt> </tt>
<a name="L161"></a><tt class="py-lineno">161</tt> <tt class="py-line"> <tt class="py-keyword">if</tt> <tt class="py-name">current_segid</tt><tt class="py-op">!=</tt><tt class="py-name">segid</tt><tt class="py-op">:</tt> </tt>
<a name="L162"></a><tt class="py-lineno">162</tt> <tt class="py-line"> <tt class="py-name">current_segid</tt><tt class="py-op">=</tt><tt class="py-name">segid</tt> </tt>
<a name="L163"></a><tt class="py-lineno">163</tt> <tt class="py-line"> <tt class="py-name">structure_builder</tt><tt class="py-op">.</tt><tt id="link-45" class="py-name" targets="Method Bio.PDB.StructureBuilder.StructureBuilder.init_seg()=Bio.PDB.StructureBuilder.StructureBuilder-class.html#init_seg"><a title="Bio.PDB.StructureBuilder.StructureBuilder.init_seg" class="py-name" href="#" onclick="return doclink('link-45', 'init_seg', 'link-45');">init_seg</a></tt><tt class="py-op">(</tt><tt class="py-name">current_segid</tt><tt class="py-op">)</tt> </tt>
<a name="L164"></a><tt class="py-lineno">164</tt> <tt class="py-line"> <tt class="py-keyword">if</tt> <tt class="py-name">current_chain_id</tt><tt class="py-op">!=</tt><tt class="py-name">chainid</tt><tt class="py-op">:</tt> </tt>
<a name="L165"></a><tt class="py-lineno">165</tt> <tt class="py-line"> <tt class="py-name">current_chain_id</tt><tt class="py-op">=</tt><tt class="py-name">chainid</tt> </tt>
<a name="L166"></a><tt class="py-lineno">166</tt> <tt class="py-line"> <tt class="py-name">structure_builder</tt><tt class="py-op">.</tt><tt id="link-46" class="py-name" targets="Method Bio.PDB.StructureBuilder.StructureBuilder.init_chain()=Bio.PDB.StructureBuilder.StructureBuilder-class.html#init_chain"><a title="Bio.PDB.StructureBuilder.StructureBuilder.init_chain" class="py-name" href="#" onclick="return doclink('link-46', 'init_chain', 'link-46');">init_chain</a></tt><tt class="py-op">(</tt><tt class="py-name">current_chain_id</tt><tt class="py-op">)</tt> </tt>
<a name="L167"></a><tt class="py-lineno">167</tt> <tt class="py-line"> <tt class="py-name">current_residue_id</tt><tt class="py-op">=</tt><tt class="py-name">residue_id</tt> </tt>
<a name="L168"></a><tt class="py-lineno">168</tt> <tt class="py-line"> <tt class="py-name">current_resname</tt><tt class="py-op">=</tt><tt class="py-name">resname</tt> </tt>
<a name="L169"></a><tt class="py-lineno">169</tt> <tt class="py-line"> <tt class="py-keyword">try</tt><tt class="py-op">:</tt> </tt>
<a name="L170"></a><tt class="py-lineno">170</tt> <tt class="py-line"> <tt class="py-name">structure_builder</tt><tt class="py-op">.</tt><tt id="link-47" class="py-name" targets="Method Bio.PDB.StructureBuilder.StructureBuilder.init_residue()=Bio.PDB.StructureBuilder.StructureBuilder-class.html#init_residue"><a title="Bio.PDB.StructureBuilder.StructureBuilder.init_residue" class="py-name" href="#" onclick="return doclink('link-47', 'init_residue', 'link-47');">init_residue</a></tt><tt class="py-op">(</tt><tt class="py-name">resname</tt><tt class="py-op">,</tt> <tt class="py-name">hetero_flag</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="L171"></a><tt class="py-lineno">171</tt> <tt class="py-line"> <tt class="py-keyword">except</tt> <tt id="link-48" class="py-name"><a title="Bio.PDB.PDBExceptions.PDBConstructionException
Bio.PDB.PDBParser'.PDBConstructionException" class="py-name" href="#" onclick="return doclink('link-48', 'PDBConstructionException', 'link-5');">PDBConstructionException</a></tt><tt class="py-op">,</tt> <tt id="link-49" class="py-name" targets="Variable Bio.DocSQL.Query.message=Bio.DocSQL.Query-class.html#message"><a title="Bio.DocSQL.Query.message" class="py-name" href="#" onclick="return doclink('link-49', 'message', 'link-49');">message</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">self</tt><tt class="py-op">.</tt><tt id="link-50" class="py-name" targets="Method Bio.PDB.PDBParser'.PDBParser._handle_PDB_exception()=Bio.PDB.PDBParser%27.PDBParser-class.html#_handle_PDB_exception"><a title="Bio.PDB.PDBParser'.PDBParser._handle_PDB_exception" class="py-name" href="#" onclick="return doclink('link-50', '_handle_PDB_exception', 'link-50');">_handle_PDB_exception</a></tt><tt class="py-op">(</tt><tt id="link-51" class="py-name"><a title="Bio.DocSQL.Query.message" class="py-name" href="#" onclick="return doclink('link-51', 'message', 'link-49');">message</a></tt><tt class="py-op">,</tt> <tt class="py-name">global_line_counter</tt><tt class="py-op">)</tt> </tt>
<a name="L173"></a><tt class="py-lineno">173</tt> <tt class="py-line"> <tt class="py-keyword">elif</tt> <tt class="py-name">current_residue_id</tt><tt class="py-op">!=</tt><tt class="py-name">residue_id</tt> <tt class="py-keyword">or</tt> <tt class="py-name">current_resname</tt><tt class="py-op">!=</tt><tt class="py-name">resname</tt><tt class="py-op">:</tt> </tt>
<a name="L174"></a><tt class="py-lineno">174</tt> <tt class="py-line"> <tt class="py-name">current_residue_id</tt><tt class="py-op">=</tt><tt class="py-name">residue_id</tt> </tt>
<a name="L175"></a><tt class="py-lineno">175</tt> <tt class="py-line"> <tt class="py-name">current_resname</tt><tt class="py-op">=</tt><tt class="py-name">resname</tt> </tt>
<a name="L176"></a><tt class="py-lineno">176</tt> <tt class="py-line"> <tt class="py-keyword">try</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">structure_builder</tt><tt class="py-op">.</tt><tt id="link-52" class="py-name"><a title="Bio.PDB.StructureBuilder.StructureBuilder.init_residue" class="py-name" href="#" onclick="return doclink('link-52', 'init_residue', 'link-47');">init_residue</a></tt><tt class="py-op">(</tt><tt class="py-name">resname</tt><tt class="py-op">,</tt> <tt class="py-name">hetero_flag</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="L178"></a><tt class="py-lineno">178</tt> <tt class="py-line"> <tt class="py-keyword">except</tt> <tt id="link-53" class="py-name"><a title="Bio.PDB.PDBExceptions.PDBConstructionException
Bio.PDB.PDBParser'.PDBConstructionException" class="py-name" href="#" onclick="return doclink('link-53', 'PDBConstructionException', 'link-5');">PDBConstructionException</a></tt><tt class="py-op">,</tt> <tt id="link-54" class="py-name"><a title="Bio.DocSQL.Query.message" class="py-name" href="#" onclick="return doclink('link-54', 'message', 'link-49');">message</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">self</tt><tt class="py-op">.</tt><tt id="link-55" class="py-name"><a title="Bio.PDB.PDBParser'.PDBParser._handle_PDB_exception" class="py-name" href="#" onclick="return doclink('link-55', '_handle_PDB_exception', 'link-50');">_handle_PDB_exception</a></tt><tt class="py-op">(</tt><tt id="link-56" class="py-name"><a title="Bio.DocSQL.Query.message" class="py-name" href="#" onclick="return doclink('link-56', 'message', 'link-49');">message</a></tt><tt class="py-op">,</tt> <tt class="py-name">global_line_counter</tt><tt class="py-op">)</tt> </tt>
<a name="L180"></a><tt class="py-lineno">180</tt> <tt class="py-line"> <tt class="py-comment"># init atom</tt> </tt>
<a name="L181"></a><tt class="py-lineno">181</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-keyword">try</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">structure_builder</tt><tt class="py-op">.</tt><tt id="link-57" class="py-name" targets="Method Bio.PDB.StructureBuilder.StructureBuilder.init_atom()=Bio.PDB.StructureBuilder.StructureBuilder-class.html#init_atom"><a title="Bio.PDB.StructureBuilder.StructureBuilder.init_atom" class="py-name" href="#" onclick="return doclink('link-57', 'init_atom', 'link-57');">init_atom</a></tt><tt class="py-op">(</tt><tt id="link-58" class="py-name"><a title="Bio.Encodings.IUPACEncoding.name" class="py-name" href="#" onclick="return doclink('link-58', 'name', 'link-39');">name</a></tt><tt class="py-op">,</tt> <tt class="py-name">coord</tt><tt class="py-op">,</tt> <tt class="py-name">bfactor</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="L183"></a><tt class="py-lineno">183</tt> <tt class="py-line"> <tt class="py-keyword">except</tt> <tt id="link-59" class="py-name"><a title="Bio.PDB.PDBExceptions.PDBConstructionException
Bio.PDB.PDBParser'.PDBConstructionException" class="py-name" href="#" onclick="return doclink('link-59', 'PDBConstructionException', 'link-5');">PDBConstructionException</a></tt><tt class="py-op">,</tt> <tt id="link-60" class="py-name"><a title="Bio.DocSQL.Query.message" class="py-name" href="#" onclick="return doclink('link-60', 'message', 'link-49');">message</a></tt><tt class="py-op">:</tt> </tt>
<a name="L184"></a><tt class="py-lineno">184</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-61" class="py-name"><a title="Bio.PDB.PDBParser'.PDBParser._handle_PDB_exception" class="py-name" href="#" onclick="return doclink('link-61', '_handle_PDB_exception', 'link-50');">_handle_PDB_exception</a></tt><tt class="py-op">(</tt><tt id="link-62" class="py-name"><a title="Bio.DocSQL.Query.message" class="py-name" href="#" onclick="return doclink('link-62', 'message', 'link-49');">message</a></tt><tt class="py-op">,</tt> <tt class="py-name">global_line_counter</tt><tt class="py-op">)</tt> </tt>
<a name="L185"></a><tt class="py-lineno">185</tt> <tt class="py-line"> <tt class="py-keyword">elif</tt><tt class="py-op">(</tt><tt class="py-name">record_type</tt><tt class="py-op">==</tt><tt class="py-string">'ANISOU'</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
<a name="L186"></a><tt class="py-lineno">186</tt> <tt class="py-line"> <tt class="py-name">anisou</tt><tt class="py-op">=</tt><tt id="link-63" class="py-name" targets="Method Bio.GFF.FeatureAggregate.map()=Bio.GFF.FeatureAggregate-class.html#map"><a title="Bio.GFF.FeatureAggregate.map" class="py-name" href="#" onclick="return doclink('link-63', 'map', 'link-63');">map</a></tt><tt class="py-op">(</tt><tt class="py-name">float</tt><tt class="py-op">,</tt> <tt class="py-op">(</tt><tt class="py-name">line</tt><tt class="py-op">[</tt><tt class="py-number">28</tt><tt class="py-op">:</tt><tt class="py-number">35</tt><tt class="py-op">]</tt><tt class="py-op">,</tt> <tt class="py-name">line</tt><tt class="py-op">[</tt><tt class="py-number">35</tt><tt class="py-op">:</tt><tt class="py-number">42</tt><tt class="py-op">]</tt><tt class="py-op">,</tt> <tt class="py-name">line</tt><tt class="py-op">[</tt><tt class="py-number">43</tt><tt class="py-op">:</tt><tt class="py-number">49</tt><tt class="py-op">]</tt><tt class="py-op">,</tt> <tt class="py-name">line</tt><tt class="py-op">[</tt><tt class="py-number">49</tt><tt class="py-op">:</tt><tt class="py-number">56</tt><tt class="py-op">]</tt><tt class="py-op">,</tt> <tt class="py-name">line</tt><tt class="py-op">[</tt><tt class="py-number">56</tt><tt class="py-op">:</tt><tt class="py-number">63</tt><tt class="py-op">]</tt><tt class="py-op">,</tt> <tt class="py-name">line</tt><tt class="py-op">[</tt><tt class="py-number">63</tt><tt class="py-op">:</tt><tt class="py-number">70</tt><tt class="py-op">]</tt><tt class="py-op">)</tt><tt class="py-op">)</tt> </tt>
<a name="L187"></a><tt class="py-lineno">187</tt> <tt class="py-line"> <tt class="py-comment"># U's are scaled by 10^4 </tt> </tt>
<a name="L188"></a><tt class="py-lineno">188</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-name">anisou_array</tt><tt class="py-op">=</tt><tt class="py-op">(</tt><tt class="py-name">array</tt><tt class="py-op">(</tt><tt class="py-name">anisou</tt><tt class="py-op">,</tt> <tt id="link-64" class="py-name"><a title="Bio.Affy.CelFile.Float0
Bio.LogisticRegression.Float0
Bio.MarkovModel.Float0
Bio.MaxEntropy.Float0
Bio.NaiveBayes.Float0
Bio.PDB.FragmentMapper'.Float0
Bio.PDB.PDBParser'.Float0
Bio.PDB.Superimposer'.Float0
Bio.Statistics.lowess.Float0
Bio.distance.Float0
Bio.kNN.Float0" class="py-name" href="#" onclick="return doclink('link-64', 'Float0', 'link-1');">Float0</a></tt><tt class="py-op">)</tt><tt class="py-op">/</tt><tt class="py-number">10000.0</tt><tt class="py-op">)</tt><tt class="py-op">.</tt><tt class="py-name">astype</tt><tt class="py-op">(</tt><tt id="link-65" class="py-name"><a title="Bio.Affy.CelFile.Float0
Bio.LogisticRegression.Float0
Bio.MarkovModel.Float0
Bio.MaxEntropy.Float0
Bio.NaiveBayes.Float0
Bio.PDB.FragmentMapper'.Float0
Bio.PDB.PDBParser'.Float0
Bio.PDB.Superimposer'.Float0
Bio.Statistics.lowess.Float0
Bio.distance.Float0
Bio.kNN.Float0" class="py-name" href="#" onclick="return doclink('link-65', 'Float0', 'link-1');">Float0</a></tt><tt class="py-op">)</tt> </tt>
<a name="L189"></a><tt class="py-lineno">189</tt> <tt class="py-line"> <tt class="py-name">structure_builder</tt><tt class="py-op">.</tt><tt id="link-66" 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-66', 'set_anisou', 'link-66');">set_anisou</a></tt><tt class="py-op">(</tt><tt class="py-name">anisou_array</tt><tt class="py-op">)</tt> </tt>
<a name="L190"></a><tt class="py-lineno">190</tt> <tt class="py-line"> <tt class="py-keyword">elif</tt><tt class="py-op">(</tt><tt class="py-name">record_type</tt><tt class="py-op">==</tt><tt class="py-string">'MODEL '</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
<a name="L191"></a><tt class="py-lineno">191</tt> <tt class="py-line"> <tt class="py-name">structure_builder</tt><tt class="py-op">.</tt><tt id="link-67" class="py-name"><a title="Bio.PDB.StructureBuilder.StructureBuilder.init_model" class="py-name" href="#" onclick="return doclink('link-67', 'init_model', 'link-37');">init_model</a></tt><tt class="py-op">(</tt><tt class="py-name">current_model_id</tt><tt class="py-op">)</tt> </tt>
<a name="L192"></a><tt class="py-lineno">192</tt> <tt class="py-line"> <tt class="py-name">current_model_id</tt><tt class="py-op">+=</tt><tt class="py-number">1</tt> </tt>
<a name="L193"></a><tt class="py-lineno">193</tt> <tt class="py-line"> <tt class="py-name">model_open</tt><tt class="py-op">=</tt><tt class="py-number">1</tt> </tt>
<a name="L194"></a><tt class="py-lineno">194</tt> <tt class="py-line"> <tt class="py-name">current_chain_id</tt><tt class="py-op">=</tt><tt class="py-name">None</tt> </tt>
<a name="L195"></a><tt class="py-lineno">195</tt> <tt class="py-line"> <tt class="py-name">current_residue_id</tt><tt class="py-op">=</tt><tt class="py-name">None</tt> </tt>
<a name="L196"></a><tt class="py-lineno">196</tt> <tt class="py-line"> <tt class="py-keyword">elif</tt><tt class="py-op">(</tt><tt class="py-name">record_type</tt><tt class="py-op">==</tt><tt class="py-string">'END '</tt> <tt class="py-keyword">or</tt> <tt class="py-name">record_type</tt><tt class="py-op">==</tt><tt class="py-string">'CONECT'</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
<a name="L197"></a><tt class="py-lineno">197</tt> <tt class="py-line"> <tt class="py-comment"># End of atomic data, return the trailer</tt> </tt>
<a name="L198"></a><tt class="py-lineno">198</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">line_counter</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-name">local_line_counter</tt> </tt>
<a name="L199"></a><tt class="py-lineno">199</tt> <tt class="py-line"> <tt class="py-keyword">return</tt> <tt class="py-name">coords_trailer</tt><tt class="py-op">[</tt><tt class="py-name">local_line_counter</tt><tt class="py-op">:</tt><tt class="py-op">]</tt> </tt>
<a name="L200"></a><tt class="py-lineno">200</tt> <tt class="py-line"> <tt class="py-keyword">elif</tt><tt class="py-op">(</tt><tt class="py-name">record_type</tt><tt class="py-op">==</tt><tt class="py-string">'ENDMDL'</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
<a name="L201"></a><tt class="py-lineno">201</tt> <tt class="py-line"> <tt class="py-name">model_open</tt><tt class="py-op">=</tt><tt class="py-number">0</tt> </tt>
<a name="L202"></a><tt class="py-lineno">202</tt> <tt class="py-line"> <tt class="py-name">current_chain_id</tt><tt class="py-op">=</tt><tt class="py-name">None</tt> </tt>
<a name="L203"></a><tt class="py-lineno">203</tt> <tt class="py-line"> <tt class="py-name">current_residue_id</tt><tt class="py-op">=</tt><tt class="py-name">None</tt> </tt>
<a name="L204"></a><tt class="py-lineno">204</tt> <tt class="py-line"> <tt class="py-keyword">elif</tt><tt class="py-op">(</tt><tt class="py-name">record_type</tt><tt class="py-op">==</tt><tt class="py-string">'SIGUIJ'</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
<a name="L205"></a><tt class="py-lineno">205</tt> <tt class="py-line"> <tt class="py-comment"># standard deviation of anisotropic B factor</tt> </tt>
<a name="L206"></a><tt class="py-lineno">206</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-name">siguij</tt><tt class="py-op">=</tt><tt id="link-68" class="py-name"><a title="Bio.GFF.FeatureAggregate.map" class="py-name" href="#" onclick="return doclink('link-68', 'map', 'link-63');">map</a></tt><tt class="py-op">(</tt><tt class="py-name">float</tt><tt class="py-op">,</tt> <tt class="py-op">(</tt><tt class="py-name">line</tt><tt class="py-op">[</tt><tt class="py-number">28</tt><tt class="py-op">:</tt><tt class="py-number">35</tt><tt class="py-op">]</tt><tt class="py-op">,</tt> <tt class="py-name">line</tt><tt class="py-op">[</tt><tt class="py-number">35</tt><tt class="py-op">:</tt><tt class="py-number">42</tt><tt class="py-op">]</tt><tt class="py-op">,</tt> <tt class="py-name">line</tt><tt class="py-op">[</tt><tt class="py-number">42</tt><tt class="py-op">:</tt><tt class="py-number">49</tt><tt class="py-op">]</tt><tt class="py-op">,</tt> <tt class="py-name">line</tt><tt class="py-op">[</tt><tt class="py-number">49</tt><tt class="py-op">:</tt><tt class="py-number">56</tt><tt class="py-op">]</tt><tt class="py-op">,</tt> <tt class="py-name">line</tt><tt class="py-op">[</tt><tt class="py-number">56</tt><tt class="py-op">:</tt><tt class="py-number">63</tt><tt class="py-op">]</tt><tt class="py-op">,</tt> <tt class="py-name">line</tt><tt class="py-op">[</tt><tt class="py-number">63</tt><tt class="py-op">:</tt><tt class="py-number">70</tt><tt class="py-op">]</tt><tt class="py-op">)</tt><tt class="py-op">)</tt> </tt>
<a name="L207"></a><tt class="py-lineno">207</tt> <tt class="py-line"> <tt class="py-comment"># U sigma's are scaled by 10^4</tt> </tt>
<a name="L208"></a><tt class="py-lineno">208</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-name">siguij_array</tt><tt class="py-op">=</tt><tt class="py-op">(</tt><tt class="py-name">array</tt><tt class="py-op">(</tt><tt class="py-name">siguij</tt><tt class="py-op">,</tt> <tt id="link-69" class="py-name"><a title="Bio.Affy.CelFile.Float0
Bio.LogisticRegression.Float0
Bio.MarkovModel.Float0
Bio.MaxEntropy.Float0
Bio.NaiveBayes.Float0
Bio.PDB.FragmentMapper'.Float0
Bio.PDB.PDBParser'.Float0
Bio.PDB.Superimposer'.Float0
Bio.Statistics.lowess.Float0
Bio.distance.Float0
Bio.kNN.Float0" class="py-name" href="#" onclick="return doclink('link-69', 'Float0', 'link-1');">Float0</a></tt><tt class="py-op">)</tt><tt class="py-op">/</tt><tt class="py-number">10000.0</tt><tt class="py-op">)</tt><tt class="py-op">.</tt><tt class="py-name">astype</tt><tt class="py-op">(</tt><tt id="link-70" class="py-name"><a title="Bio.Affy.CelFile.Float0
Bio.LogisticRegression.Float0
Bio.MarkovModel.Float0
Bio.MaxEntropy.Float0
Bio.NaiveBayes.Float0
Bio.PDB.FragmentMapper'.Float0
Bio.PDB.PDBParser'.Float0
Bio.PDB.Superimposer'.Float0
Bio.Statistics.lowess.Float0
Bio.distance.Float0
Bio.kNN.Float0" class="py-name" href="#" onclick="return doclink('link-70', 'Float0', 'link-1');">Float0</a></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">structure_builder</tt><tt class="py-op">.</tt><tt id="link-71" 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-71', 'set_siguij', 'link-71');">set_siguij</a></tt><tt class="py-op">(</tt><tt class="py-name">siguij_array</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">elif</tt><tt class="py-op">(</tt><tt class="py-name">record_type</tt><tt class="py-op">==</tt><tt class="py-string">'SIGATM'</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
<a name="L211"></a><tt class="py-lineno">211</tt> <tt class="py-line"> <tt class="py-comment"># standard deviation of atomic positions</tt> </tt>
<a name="L212"></a><tt class="py-lineno">212</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-name">sigatm</tt><tt class="py-op">=</tt><tt id="link-72" class="py-name"><a title="Bio.GFF.FeatureAggregate.map" class="py-name" href="#" onclick="return doclink('link-72', 'map', 'link-63');">map</a></tt><tt class="py-op">(</tt><tt class="py-name">float</tt><tt class="py-op">,</tt> <tt class="py-op">(</tt><tt class="py-name">line</tt><tt class="py-op">[</tt><tt class="py-number">30</tt><tt class="py-op">:</tt><tt class="py-number">38</tt><tt class="py-op">]</tt><tt class="py-op">,</tt> <tt class="py-name">line</tt><tt class="py-op">[</tt><tt class="py-number">38</tt><tt class="py-op">:</tt><tt class="py-number">45</tt><tt class="py-op">]</tt><tt class="py-op">,</tt> <tt class="py-name">line</tt><tt class="py-op">[</tt><tt class="py-number">46</tt><tt class="py-op">:</tt><tt class="py-number">54</tt><tt class="py-op">]</tt><tt class="py-op">,</tt> <tt class="py-name">line</tt><tt class="py-op">[</tt><tt class="py-number">54</tt><tt class="py-op">:</tt><tt class="py-number">60</tt><tt class="py-op">]</tt><tt class="py-op">,</tt> <tt class="py-name">line</tt><tt class="py-op">[</tt><tt class="py-number">60</tt><tt class="py-op">:</tt><tt class="py-number">66</tt><tt class="py-op">]</tt><tt class="py-op">)</tt><tt class="py-op">)</tt> </tt>
<a name="L213"></a><tt class="py-lineno">213</tt> <tt class="py-line"> <tt class="py-name">sigatm_array</tt><tt class="py-op">=</tt><tt class="py-name">array</tt><tt class="py-op">(</tt><tt class="py-name">sigatm</tt><tt class="py-op">,</tt> <tt id="link-73" class="py-name"><a title="Bio.Affy.CelFile.Float0
Bio.LogisticRegression.Float0
Bio.MarkovModel.Float0
Bio.MaxEntropy.Float0
Bio.NaiveBayes.Float0
Bio.PDB.FragmentMapper'.Float0
Bio.PDB.PDBParser'.Float0
Bio.PDB.Superimposer'.Float0
Bio.Statistics.lowess.Float0
Bio.distance.Float0
Bio.kNN.Float0" class="py-name" href="#" onclick="return doclink('link-73', 'Float0', 'link-1');">Float0</a></tt><tt class="py-op">)</tt> </tt>
<a name="L214"></a><tt class="py-lineno">214</tt> <tt class="py-line"> <tt class="py-name">structure_builder</tt><tt class="py-op">.</tt><tt id="link-74" 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-74', 'set_sigatm', 'link-74');">set_sigatm</a></tt><tt class="py-op">(</tt><tt class="py-name">sigatm_array</tt><tt class="py-op">)</tt> </tt>
<a name="L215"></a><tt class="py-lineno">215</tt> <tt class="py-line"> <tt class="py-name">local_line_counter</tt><tt class="py-op">=</tt><tt class="py-name">local_line_counter</tt><tt class="py-op">+</tt><tt class="py-number">1</tt> </tt>
<a name="L216"></a><tt class="py-lineno">216</tt> <tt class="py-line"> <tt class="py-comment"># EOF (does not end in END or CONECT)</tt> </tt>
<a name="L217"></a><tt class="py-lineno">217</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">line_counter</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-name">local_line_counter</tt> </tt>
<a name="L218"></a><tt class="py-lineno">218</tt> <tt class="py-line"> <tt class="py-keyword">return</tt> <tt class="py-op">[</tt><tt class="py-op">]</tt> </tt>
</div><a name="L219"></a><tt class="py-lineno">219</tt> <tt class="py-line"> </tt>
<a name="PDBParser._handle_PDB_exception"></a><div id="PDBParser._handle_PDB_exception-def"><a name="L220"></a><tt class="py-lineno">220</tt> <a class="py-toggle" href="#" id="PDBParser._handle_PDB_exception-toggle" onclick="return toggle('PDBParser._handle_PDB_exception');">-</a><tt class="py-line"> <tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.PDB.PDBParser'.PDBParser-class.html#_handle_PDB_exception">_handle_PDB_exception</a><tt class="py-op">(</tt><tt class="py-param">self</tt><tt class="py-op">,</tt> <tt class="py-param">message</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="PDBParser._handle_PDB_exception-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="PDBParser._handle_PDB_exception-expanded"><a name="L221"></a><tt class="py-lineno">221</tt> <tt class="py-line"> <tt class="py-docstring">"""</tt> </tt>
<a name="L222"></a><tt class="py-lineno">222</tt> <tt class="py-line"><tt class="py-docstring"> This method catches an exception that occurs in the StructureBuilder</tt> </tt>
<a name="L223"></a><tt class="py-lineno">223</tt> <tt class="py-line"><tt class="py-docstring"> object (if PERMISSIVE==1), or raises it again, this time adding the </tt> </tt>
<a name="L224"></a><tt class="py-lineno">224</tt> <tt class="py-line"><tt class="py-docstring"> PDB line number to the error message.</tt> </tt>
<a name="L225"></a><tt class="py-lineno">225</tt> <tt class="py-line"><tt class="py-docstring"> """</tt> </tt>
<a name="L226"></a><tt class="py-lineno">226</tt> <tt class="py-line"> <tt id="link-75" class="py-name"><a title="Bio.DocSQL.Query.message" class="py-name" href="#" onclick="return doclink('link-75', 'message', 'link-49');">message</a></tt><tt class="py-op">=</tt><tt class="py-string">"%s at line %i."</tt> <tt class="py-op">%</tt> <tt class="py-op">(</tt><tt id="link-76" class="py-name"><a title="Bio.DocSQL.Query.message" class="py-name" href="#" onclick="return doclink('link-76', 'message', 'link-49');">message</a></tt><tt class="py-op">,</tt> <tt class="py-name">line_counter</tt><tt class="py-op">)</tt> </tt>
<a name="L227"></a><tt class="py-lineno">227</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">PERMISSIVE</tt><tt class="py-op">:</tt> </tt>
<a name="L228"></a><tt class="py-lineno">228</tt> <tt class="py-line"> <tt class="py-comment"># just print a warning - some residues/atoms will be missing</tt> </tt>
<a name="L229"></a><tt class="py-lineno">229</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-keyword">print</tt> <tt class="py-string">"PDBConstructionException: %s"</tt> <tt class="py-op">%</tt> <tt id="link-77" class="py-name"><a title="Bio.DocSQL.Query.message" class="py-name" href="#" onclick="return doclink('link-77', 'message', 'link-49');">message</a></tt> </tt>
<a name="L230"></a><tt class="py-lineno">230</tt> <tt class="py-line"> <tt class="py-keyword">print</tt> <tt class="py-string">"Exception ignored.\nSome atoms or residues will be missing in the data structure."</tt> </tt>
<a name="L231"></a><tt class="py-lineno">231</tt> <tt class="py-line"> <tt class="py-keyword">else</tt><tt class="py-op">:</tt> </tt>
<a name="L232"></a><tt class="py-lineno">232</tt> <tt class="py-line"> <tt class="py-comment"># exceptions are fatal - raise again with new message (including line nr)</tt> </tt>
<a name="L233"></a><tt class="py-lineno">233</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-keyword">raise</tt> <tt id="link-78" class="py-name"><a title="Bio.PDB.PDBExceptions.PDBConstructionException
Bio.PDB.PDBParser'.PDBConstructionException" class="py-name" href="#" onclick="return doclink('link-78', 'PDBConstructionException', 'link-5');">PDBConstructionException</a></tt><tt class="py-op">,</tt> <tt id="link-79" class="py-name"><a title="Bio.DocSQL.Query.message" class="py-name" href="#" onclick="return doclink('link-79', 'message', 'link-49');">message</a></tt> </tt>
</div></div><a name="L234"></a><tt class="py-lineno">234</tt> <tt class="py-line"> </tt>
<a name="L235"></a><tt class="py-lineno">235</tt> <tt class="py-line"> </tt>
<a name="L236"></a><tt class="py-lineno">236</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="L237"></a><tt class="py-lineno">237</tt> <tt class="py-line"> </tt>
<a name="L238"></a><tt class="py-lineno">238</tt> <tt class="py-line"> <tt class="py-keyword">import</tt> <tt class="py-name">sys</tt> </tt>
<a name="L239"></a><tt class="py-lineno">239</tt> <tt class="py-line"> </tt>
<a name="L240"></a><tt class="py-lineno">240</tt> <tt class="py-line"> <tt class="py-name">p</tt><tt class="py-op">=</tt><tt id="link-80" 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-80', 'PDBParser', 'link-80');">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="L241"></a><tt class="py-lineno">241</tt> <tt class="py-line"> </tt>
<a name="L242"></a><tt class="py-lineno">242</tt> <tt class="py-line"> <tt id="link-81" 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-81', 's', 'link-81');">s</a></tt><tt class="py-op">=</tt><tt class="py-name">p</tt><tt class="py-op">.</tt><tt id="link-82" 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-82', 'get_structure', 'link-19');">get_structure</a></tt><tt class="py-op">(</tt><tt class="py-string">"scr"</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="L243"></a><tt class="py-lineno">243</tt> <tt class="py-line"> </tt>
<a name="L244"></a><tt class="py-lineno">244</tt> <tt class="py-line"> <tt class="py-keyword">for</tt> <tt class="py-name">m</tt> <tt class="py-keyword">in</tt> <tt id="link-83" class="py-name"><a title="Martel.test.test_swissprot38.s" class="py-name" href="#" onclick="return doclink('link-83', 's', 'link-81');">s</a></tt><tt class="py-op">:</tt> </tt>
<a name="L245"></a><tt class="py-lineno">245</tt> <tt class="py-line"> <tt class="py-name">p</tt><tt class="py-op">=</tt><tt class="py-name">m</tt><tt class="py-op">.</tt><tt id="link-84" class="py-name" targets="Method Bio.EUtils.POM.ElementNode.get_parent()=Bio.EUtils.POM.ElementNode-class.html#get_parent,Method Bio.PDB.Atom.Atom.get_parent()=Bio.PDB.Atom.Atom-class.html#get_parent,Method Bio.PDB.Entity.DisorderedEntityWrapper.get_parent()=Bio.PDB.Entity.DisorderedEntityWrapper-class.html#get_parent,Method Bio.PDB.Entity.Entity.get_parent()=Bio.PDB.Entity.Entity-class.html#get_parent"><a title="Bio.EUtils.POM.ElementNode.get_parent
Bio.PDB.Atom.Atom.get_parent
Bio.PDB.Entity.DisorderedEntityWrapper.get_parent
Bio.PDB.Entity.Entity.get_parent" class="py-name" href="#" onclick="return doclink('link-84', 'get_parent', 'link-84');">get_parent</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
<a name="L246"></a><tt class="py-lineno">246</tt> <tt class="py-line"> <tt class="py-keyword">assert</tt><tt class="py-op">(</tt><tt class="py-name">p</tt> <tt class="py-keyword">is</tt> <tt id="link-85" class="py-name"><a title="Martel.test.test_swissprot38.s" class="py-name" href="#" onclick="return doclink('link-85', 's', 'link-81');">s</a></tt><tt class="py-op">)</tt> </tt>
<a name="L247"></a><tt class="py-lineno">247</tt> <tt class="py-line"> <tt class="py-keyword">for</tt> <tt class="py-name">c</tt> <tt class="py-keyword">in</tt> <tt class="py-name">m</tt><tt class="py-op">:</tt> </tt>
<a name="L248"></a><tt class="py-lineno">248</tt> <tt class="py-line"> <tt class="py-name">p</tt><tt class="py-op">=</tt><tt class="py-name">c</tt><tt class="py-op">.</tt><tt id="link-86" class="py-name"><a title="Bio.EUtils.POM.ElementNode.get_parent
Bio.PDB.Atom.Atom.get_parent
Bio.PDB.Entity.DisorderedEntityWrapper.get_parent
Bio.PDB.Entity.Entity.get_parent" class="py-name" href="#" onclick="return doclink('link-86', 'get_parent', 'link-84');">get_parent</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
<a name="L249"></a><tt class="py-lineno">249</tt> <tt class="py-line"> <tt class="py-keyword">assert</tt><tt class="py-op">(</tt><tt class="py-name">p</tt> <tt class="py-keyword">is</tt> <tt class="py-name">m</tt><tt class="py-op">)</tt> </tt>
<a name="L250"></a><tt class="py-lineno">250</tt> <tt class="py-line"> <tt class="py-keyword">for</tt> <tt class="py-name">r</tt> <tt class="py-keyword">in</tt> <tt class="py-name">c</tt><tt class="py-op">:</tt> </tt>
<a name="L251"></a><tt class="py-lineno">251</tt> <tt class="py-line"> <tt class="py-keyword">print</tt> <tt class="py-name">r</tt> </tt>
<a name="L252"></a><tt class="py-lineno">252</tt> <tt class="py-line"> <tt class="py-name">p</tt><tt class="py-op">=</tt><tt class="py-name">r</tt><tt class="py-op">.</tt><tt id="link-87" class="py-name"><a title="Bio.EUtils.POM.ElementNode.get_parent
Bio.PDB.Atom.Atom.get_parent
Bio.PDB.Entity.DisorderedEntityWrapper.get_parent
Bio.PDB.Entity.Entity.get_parent" class="py-name" href="#" onclick="return doclink('link-87', 'get_parent', 'link-84');">get_parent</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
<a name="L253"></a><tt class="py-lineno">253</tt> <tt class="py-line"> <tt class="py-keyword">assert</tt><tt class="py-op">(</tt><tt class="py-name">p</tt> <tt class="py-keyword">is</tt> <tt class="py-name">c</tt><tt class="py-op">)</tt> </tt>
<a name="L254"></a><tt class="py-lineno">254</tt> <tt class="py-line"> <tt class="py-keyword">for</tt> <tt class="py-name">a</tt> <tt class="py-keyword">in</tt> <tt class="py-name">r</tt><tt class="py-op">:</tt> </tt>
<a name="L255"></a><tt class="py-lineno">255</tt> <tt class="py-line"> <tt class="py-name">p</tt><tt class="py-op">=</tt><tt class="py-name">a</tt><tt class="py-op">.</tt><tt id="link-88" class="py-name"><a title="Bio.EUtils.POM.ElementNode.get_parent
Bio.PDB.Atom.Atom.get_parent
Bio.PDB.Entity.DisorderedEntityWrapper.get_parent
Bio.PDB.Entity.Entity.get_parent" class="py-name" href="#" onclick="return doclink('link-88', 'get_parent', 'link-84');">get_parent</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
<a name="L256"></a><tt class="py-lineno">256</tt> <tt class="py-line"> <tt class="py-keyword">if</tt> <tt class="py-keyword">not</tt> <tt class="py-name">p</tt> <tt class="py-keyword">is</tt> <tt class="py-name">r</tt><tt class="py-op">:</tt> </tt>
<a name="L257"></a><tt class="py-lineno">257</tt> <tt class="py-line"> <tt class="py-keyword">print</tt> <tt class="py-name">p</tt><tt class="py-op">,</tt> <tt class="py-name">r</tt> </tt>
<a name="L258"></a><tt class="py-lineno">258</tt> <tt class="py-line"> </tt><script type="text/javascript">
<!--
expandto(location.href);
// -->
</script>
</pre>
<br />
<!-- ==================== NAVIGATION BAR ==================== -->
<table class="navbar" border="0" width="100%" cellpadding="0"
bgcolor="#a0c0ff" cellspacing="0">
<tr valign="middle">
<!-- Tree link -->
<th> <a
href="module-tree.html">Trees</a> </th>
<!-- Index link -->
<th> <a
href="identifier-index.html">Indices</a> </th>
<!-- Help link -->
<th> <a
href="help.html">Help</a> </th>
<th class="navbar" width="100%"></th>
</tr>
</table>
<table border="0" cellpadding="0" cellspacing="0" width="100%%">
<tr>
<td align="left" class="footer">
Generated by Epydoc 3.0.1 on Mon Sep 15 09:26:41 2008
</td>
<td align="right" class="footer">
<a target="mainFrame" href="http://epydoc.sourceforge.net"
>http://epydoc.sourceforge.net</a>
</td>
</tr>
</table>
<script type="text/javascript">
<!--
// Private objects are initially displayed (because if
// javascript is turned off then we want them to be
// visible); but by default, we want to hide them. So hide
// them unless we have a cookie that says to show them.
checkCookie();
// -->
</script>
</body>
</html>
