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Module parse_pdb_header'
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<h1 class="epydoc">Source Code for <a href="Bio.PDB.parse_pdb_header%27-module.html">Module Bio.PDB.parse_pdb_header'</a></h1>
<pre class="py-src">
<a name="L1"></a><tt class="py-lineno"> 1</tt> <tt class="py-line"><tt class="py-comment">#!/usr/bin/env python</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">#</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"># parse_pdb_header.py</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"># parses header of PDB files into a python dictionary.</tt> </tt>
<a name="L5"></a><tt class="py-lineno"> 5</tt> <tt class="py-line"><tt class="py-comment"></tt><tt class="py-comment"># emerged from the Columba database project www.columba-db.de.</tt> </tt>
<a name="L6"></a><tt class="py-lineno"> 6</tt> <tt class="py-line"><tt class="py-comment"></tt><tt class="py-comment"># </tt> </tt>
<a name="L7"></a><tt class="py-lineno"> 7</tt> <tt class="py-line"><tt class="py-comment"></tt><tt class="py-comment"># author: Kristian Rother</tt> </tt>
<a name="L8"></a><tt class="py-lineno"> 8</tt> <tt class="py-line"><tt class="py-comment"></tt><tt class="py-comment"># </tt> </tt>
<a name="L9"></a><tt class="py-lineno"> 9</tt> <tt class="py-line"><tt class="py-comment"></tt><tt class="py-comment"># license: same as BioPython, read LICENSE.TXT from current BioPython release.</tt> </tt>
<a name="L10"></a><tt class="py-lineno"> 10</tt> <tt class="py-line"><tt class="py-comment"></tt><tt class="py-comment"># </tt> </tt>
<a name="L11"></a><tt class="py-lineno"> 11</tt> <tt class="py-line"><tt class="py-comment"></tt><tt class="py-comment"># last modified: 9.2.2004</tt> </tt>
<a name="L12"></a><tt class="py-lineno"> 12</tt> <tt class="py-line"><tt class="py-comment"></tt><tt class="py-comment">#</tt> </tt>
<a name="L13"></a><tt class="py-lineno"> 13</tt> <tt class="py-line"><tt class="py-comment"></tt><tt class="py-comment"># Added some small changes: the whole PDB file is not read in anymore, but just</tt> </tt>
<a name="L14"></a><tt class="py-lineno"> 14</tt> <tt class="py-line"><tt class="py-comment"></tt><tt class="py-comment"># until the first ATOM record (faster). I also split parse_pdb_header into </tt> </tt>
<a name="L15"></a><tt class="py-lineno"> 15</tt> <tt class="py-line"><tt class="py-comment"></tt><tt class="py-comment"># parse_pdb_header and parse_pdb_header_list, because parse_pdb_header_list</tt> </tt>
<a name="L16"></a><tt class="py-lineno"> 16</tt> <tt class="py-line"><tt class="py-comment"></tt><tt class="py-comment"># can be more easily reused in PDBParser.</tt> </tt>
<a name="L17"></a><tt class="py-lineno"> 17</tt> <tt class="py-line"><tt class="py-comment"></tt><tt class="py-comment">#</tt> </tt>
<a name="L18"></a><tt class="py-lineno"> 18</tt> <tt class="py-line"><tt class="py-comment"></tt><tt class="py-comment"># Thomas, 19/03/04</tt> </tt>
<a name="L19"></a><tt class="py-lineno"> 19</tt> <tt class="py-line"><tt class="py-comment"></tt><tt class="py-comment">#</tt> </tt>
<a name="L20"></a><tt class="py-lineno"> 20</tt> <tt class="py-line"><tt class="py-comment"></tt><tt class="py-comment"># Renamed some clearly private functions to _something (ie. parse_pdb_header_list</tt> </tt>
<a name="L21"></a><tt class="py-lineno"> 21</tt> <tt class="py-line"><tt class="py-comment"></tt><tt class="py-comment"># is now _parse_pdb_header_list)</tt> </tt>
<a name="L22"></a><tt class="py-lineno"> 22</tt> <tt class="py-line"><tt class="py-comment"></tt><tt class="py-comment"># Thomas 9/05/04</tt> </tt>
<a name="L23"></a><tt class="py-lineno"> 23</tt> <tt class="py-line"><tt class="py-comment"></tt> </tt>
<a name="L24"></a><tt class="py-lineno"> 24</tt> <tt class="py-line"><tt id="link-0" class="py-name" targets="Variable Bio.PDB.AbstractPropertyMap.__doc__=Bio.PDB.AbstractPropertyMap-module.html#__doc__,Variable Bio.PDB.Atom.__doc__=Bio.PDB.Atom-module.html#__doc__,Variable Bio.PDB.Chain.__doc__=Bio.PDB.Chain-module.html#__doc__,Variable Bio.PDB.Entity.__doc__=Bio.PDB.Entity-module.html#__doc__,Variable Bio.PDB.HSExposure.__doc__=Bio.PDB.HSExposure-module.html#__doc__,Variable Bio.PDB.MMCIF2Dict.__doc__=Bio.PDB.MMCIF2Dict-module.html#__doc__,Variable Bio.PDB.MMCIFParser.__doc__=Bio.PDB.MMCIFParser-module.html#__doc__,Variable Bio.PDB.Model.__doc__=Bio.PDB.Model-module.html#__doc__,Variable Bio.PDB.NACCESS.__doc__=Bio.PDB.NACCESS-module.html#__doc__,Variable Bio.PDB.NeighborSearch.__doc__=Bio.PDB.NeighborSearch-module.html#__doc__,Variable Bio.PDB.PDBExceptions.__doc__=Bio.PDB.PDBExceptions-module.html#__doc__,Variable Bio.PDB.Polypeptide.__doc__=Bio.PDB.Polypeptide-module.html#__doc__,Variable Bio.PDB.Residue.__doc__=Bio.PDB.Residue-module.html#__doc__,Variable Bio.PDB.Selection.__doc__=Bio.PDB.Selection-module.html#__doc__,Variable Bio.PDB.Structure.__doc__=Bio.PDB.Structure-module.html#__doc__,Variable Bio.PDB.StructureBuilder.__doc__=Bio.PDB.StructureBuilder-module.html#__doc__,Variable Bio.PDB.__doc__=Bio.PDB-module.html#__doc__"><a title="Bio.PDB.AbstractPropertyMap.__doc__
Bio.PDB.Atom.__doc__
Bio.PDB.Chain.__doc__
Bio.PDB.Entity.__doc__
Bio.PDB.HSExposure.__doc__
Bio.PDB.MMCIF2Dict.__doc__
Bio.PDB.MMCIFParser.__doc__
Bio.PDB.Model.__doc__
Bio.PDB.NACCESS.__doc__
Bio.PDB.NeighborSearch.__doc__
Bio.PDB.PDBExceptions.__doc__
Bio.PDB.Polypeptide.__doc__
Bio.PDB.Residue.__doc__
Bio.PDB.Selection.__doc__
Bio.PDB.Structure.__doc__
Bio.PDB.StructureBuilder.__doc__
Bio.PDB.__doc__" class="py-name" href="#" onclick="return doclink('link-0', '__doc__', 'link-0');">__doc__</a></tt><tt class="py-op">=</tt><tt class="py-docstring">"Parse the header of a PDB file."</tt> </tt>
<a name="L25"></a><tt class="py-lineno"> 25</tt> <tt class="py-line"> </tt>
<a name="L26"></a><tt class="py-lineno"> 26</tt> <tt class="py-line"><tt class="py-keyword">import</tt> <tt class="py-name">sys</tt> </tt>
<a name="L27"></a><tt class="py-lineno"> 27</tt> <tt class="py-line"><tt class="py-keyword">import</tt> <tt class="py-name">os</tt><tt class="py-op">,</tt><tt class="py-name">string</tt><tt class="py-op">,</tt><tt class="py-name">re</tt> </tt>
<a name="L28"></a><tt class="py-lineno"> 28</tt> <tt class="py-line"><tt class="py-keyword">import</tt> <tt class="py-name">urllib</tt> </tt>
<a name="L29"></a><tt class="py-lineno"> 29</tt> <tt class="py-line"><tt class="py-keyword">import</tt> <tt class="py-name">types</tt> </tt>
<a name="L30"></a><tt class="py-lineno"> 30</tt> <tt class="py-line"> </tt>
<a name="L31"></a><tt class="py-lineno"> 31</tt> <tt class="py-line"> </tt>
<a name="_get_journal"></a><div id="_get_journal-def"><a name="L32"></a><tt class="py-lineno"> 32</tt> <a class="py-toggle" href="#" id="_get_journal-toggle" onclick="return toggle('_get_journal');">-</a><tt class="py-line"><tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.PDB.parse_pdb_header'-module.html#_get_journal">_get_journal</a><tt class="py-op">(</tt><tt class="py-param">inl</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="_get_journal-collapsed" style="display:none;" pad="+++" indent="++++"></div><div id="_get_journal-expanded"><a name="L33"></a><tt class="py-lineno"> 33</tt> <tt class="py-line"> <tt class="py-comment"># JRNL AUTH L.CHEN,M.DOI,F.S.MATHEWS,A.Y.CHISTOSERDOV, 2BBK 7</tt> </tt>
<a name="L34"></a><tt class="py-lineno"> 34</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt id="link-1" class="py-name" targets="Method Bio.GenBank._FeatureConsumer.journal()=Bio.GenBank._FeatureConsumer-class.html#journal,Method Bio.GenBank._RecordConsumer.journal()=Bio.GenBank._RecordConsumer-class.html#journal"><a title="Bio.GenBank._FeatureConsumer.journal
Bio.GenBank._RecordConsumer.journal" class="py-name" href="#" onclick="return doclink('link-1', 'journal', 'link-1');">journal</a></tt><tt class="py-op">=</tt><tt class="py-string">""</tt> </tt>
<a name="L35"></a><tt class="py-lineno"> 35</tt> <tt class="py-line"> <tt class="py-keyword">for</tt> <tt class="py-name">l</tt> <tt class="py-keyword">in</tt> <tt class="py-name">inl</tt><tt class="py-op">:</tt> </tt>
<a name="L36"></a><tt class="py-lineno"> 36</tt> <tt class="py-line"> <tt class="py-keyword">if</tt> <tt class="py-name">re</tt><tt class="py-op">.</tt><tt id="link-2" class="py-name" targets="Method Bio.EUtils.DBIdsClient.DBIdsClient.search()=Bio.EUtils.DBIdsClient.DBIdsClient-class.html#search,Method Bio.EUtils.HistoryClient.HistoryClient.search()=Bio.EUtils.HistoryClient.HistoryClient-class.html#search,Method Bio.KDTree.KDTree.KDTree.search()=Bio.KDTree.KDTree.KDTree-class.html#search,Method Bio.PDB.NeighborSearch.NeighborSearch.search()=Bio.PDB.NeighborSearch.NeighborSearch-class.html#search,Method Bio.Prosite.Pattern.Prosite.search()=Bio.Prosite.Pattern.Prosite-class.html#search,Class Method Bio.Restriction.Restriction.AbstractCut.search()=Bio.Restriction.Restriction.AbstractCut-class.html#search,Method Bio.Restriction.Restriction.RestrictionBatch.search()=Bio.Restriction.Restriction.RestrictionBatch-class.html#search,Function Bio.SCOP.search()=Bio.SCOP-module.html#search,Module Bio.builders.Search.search=Bio.builders.Search.search-module.html,Module Bio.formatdefs.search=Bio.formatdefs.search-module.html,Variable Bio.formatdefs.search.search=Bio.formatdefs.search-module.html#search"><a title="Bio.EUtils.DBIdsClient.DBIdsClient.search
Bio.EUtils.HistoryClient.HistoryClient.search
Bio.KDTree.KDTree.KDTree.search
Bio.PDB.NeighborSearch.NeighborSearch.search
Bio.Prosite.Pattern.Prosite.search
Bio.Restriction.Restriction.AbstractCut.search
Bio.Restriction.Restriction.RestrictionBatch.search
Bio.SCOP.search
Bio.builders.Search.search
Bio.formatdefs.search
Bio.formatdefs.search.search" class="py-name" href="#" onclick="return doclink('link-2', 'search', 'link-2');">search</a></tt><tt class="py-op">(</tt><tt class="py-string">"\AJRNL"</tt><tt class="py-op">,</tt><tt class="py-name">l</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
<a name="L37"></a><tt class="py-lineno"> 37</tt> <tt class="py-line"> <tt id="link-3" class="py-name"><a title="Bio.GenBank._FeatureConsumer.journal
Bio.GenBank._RecordConsumer.journal" class="py-name" href="#" onclick="return doclink('link-3', 'journal', 'link-1');">journal</a></tt><tt class="py-op">+=</tt><tt class="py-name">string</tt><tt class="py-op">.</tt><tt class="py-name">lower</tt><tt class="py-op">(</tt><tt class="py-name">l</tt><tt class="py-op">[</tt><tt class="py-number">19</tt><tt class="py-op">:</tt><tt class="py-number">72</tt><tt class="py-op">]</tt><tt class="py-op">)</tt> </tt>
<a name="L38"></a><tt class="py-lineno"> 38</tt> <tt class="py-line"> <tt id="link-4" class="py-name"><a title="Bio.GenBank._FeatureConsumer.journal
Bio.GenBank._RecordConsumer.journal" class="py-name" href="#" onclick="return doclink('link-4', 'journal', 'link-1');">journal</a></tt><tt class="py-op">=</tt><tt class="py-name">re</tt><tt class="py-op">.</tt><tt class="py-name">sub</tt><tt class="py-op">(</tt><tt class="py-string">"\s\s+"</tt><tt class="py-op">,</tt><tt class="py-string">" "</tt><tt class="py-op">,</tt><tt id="link-5" class="py-name"><a title="Bio.GenBank._FeatureConsumer.journal
Bio.GenBank._RecordConsumer.journal" class="py-name" href="#" onclick="return doclink('link-5', 'journal', 'link-1');">journal</a></tt><tt class="py-op">)</tt> </tt>
<a name="L39"></a><tt class="py-lineno"> 39</tt> <tt class="py-line"> <tt class="py-keyword">return</tt> <tt id="link-6" class="py-name"><a title="Bio.GenBank._FeatureConsumer.journal
Bio.GenBank._RecordConsumer.journal" class="py-name" href="#" onclick="return doclink('link-6', 'journal', 'link-1');">journal</a></tt> </tt>
</div><a name="L40"></a><tt class="py-lineno"> 40</tt> <tt class="py-line"> </tt>
<a name="_get_references"></a><div id="_get_references-def"><a name="L41"></a><tt class="py-lineno"> 41</tt> <a class="py-toggle" href="#" id="_get_references-toggle" onclick="return toggle('_get_references');">-</a><tt class="py-line"><tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.PDB.parse_pdb_header'-module.html#_get_references">_get_references</a><tt class="py-op">(</tt><tt class="py-param">inl</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="_get_references-collapsed" style="display:none;" pad="+++" indent="++++"></div><div id="_get_references-expanded"><a name="L42"></a><tt class="py-lineno"> 42</tt> <tt class="py-line"> <tt class="py-comment"># REMARK 1 REFERENCE 1 1CSE 11</tt> </tt>
<a name="L43"></a><tt class="py-lineno"> 43</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-comment"># REMARK 1 AUTH W.BODE,E.PAPAMOKOS,D.MUSIL 1CSE 12</tt> </tt>
<a name="L44"></a><tt class="py-lineno"> 44</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-name">references</tt><tt class="py-op">=</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">actref</tt><tt class="py-op">=</tt><tt class="py-string">""</tt> </tt>
<a name="L46"></a><tt class="py-lineno"> 46</tt> <tt class="py-line"> <tt class="py-keyword">for</tt> <tt class="py-name">l</tt> <tt class="py-keyword">in</tt> <tt class="py-name">inl</tt><tt class="py-op">:</tt> </tt>
<a name="L47"></a><tt class="py-lineno"> 47</tt> <tt class="py-line"> <tt class="py-keyword">if</tt> <tt class="py-name">re</tt><tt class="py-op">.</tt><tt id="link-7" class="py-name"><a title="Bio.EUtils.DBIdsClient.DBIdsClient.search
Bio.EUtils.HistoryClient.HistoryClient.search
Bio.KDTree.KDTree.KDTree.search
Bio.PDB.NeighborSearch.NeighborSearch.search
Bio.Prosite.Pattern.Prosite.search
Bio.Restriction.Restriction.AbstractCut.search
Bio.Restriction.Restriction.RestrictionBatch.search
Bio.SCOP.search
Bio.builders.Search.search
Bio.formatdefs.search
Bio.formatdefs.search.search" class="py-name" href="#" onclick="return doclink('link-7', 'search', 'link-2');">search</a></tt><tt class="py-op">(</tt><tt class="py-string">"\AREMARK 1"</tt><tt class="py-op">,</tt><tt class="py-name">l</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
<a name="L48"></a><tt class="py-lineno"> 48</tt> <tt class="py-line"> <tt class="py-keyword">if</tt> <tt class="py-name">re</tt><tt class="py-op">.</tt><tt id="link-8" class="py-name"><a title="Bio.EUtils.DBIdsClient.DBIdsClient.search
Bio.EUtils.HistoryClient.HistoryClient.search
Bio.KDTree.KDTree.KDTree.search
Bio.PDB.NeighborSearch.NeighborSearch.search
Bio.Prosite.Pattern.Prosite.search
Bio.Restriction.Restriction.AbstractCut.search
Bio.Restriction.Restriction.RestrictionBatch.search
Bio.SCOP.search
Bio.builders.Search.search
Bio.formatdefs.search
Bio.formatdefs.search.search" class="py-name" href="#" onclick="return doclink('link-8', 'search', 'link-2');">search</a></tt><tt class="py-op">(</tt><tt class="py-string">"\AREMARK 1 REFERENCE"</tt><tt class="py-op">,</tt><tt class="py-name">l</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
<a name="L49"></a><tt class="py-lineno"> 49</tt> <tt class="py-line"> <tt class="py-keyword">if</tt> <tt class="py-name">actref</tt><tt class="py-op">!=</tt><tt class="py-string">""</tt><tt class="py-op">:</tt> </tt>
<a name="L50"></a><tt class="py-lineno"> 50</tt> <tt class="py-line"> <tt class="py-name">actref</tt><tt class="py-op">=</tt><tt class="py-name">re</tt><tt class="py-op">.</tt><tt class="py-name">sub</tt><tt class="py-op">(</tt><tt class="py-string">"\s\s+"</tt><tt class="py-op">,</tt><tt class="py-string">" "</tt><tt class="py-op">,</tt><tt class="py-name">actref</tt><tt class="py-op">)</tt> </tt>
<a name="L51"></a><tt class="py-lineno"> 51</tt> <tt class="py-line"> <tt class="py-keyword">if</tt> <tt class="py-name">actref</tt><tt class="py-op">!=</tt><tt class="py-string">" "</tt><tt class="py-op">:</tt> </tt>
<a name="L52"></a><tt class="py-lineno"> 52</tt> <tt class="py-line"> <tt class="py-name">references</tt><tt class="py-op">.</tt><tt id="link-9" class="py-name" targets="Method Bio.Crystal.Chain.append()=Bio.Crystal.Chain-class.html#append,Method Bio.EUtils.POM.ElementNode.append()=Bio.EUtils.POM.ElementNode-class.html#append,Method Bio.EUtils.sourcegen.SourceFile.append()=Bio.EUtils.sourcegen.SourceFile-class.html#append,Method Bio.SCOP.Raf.SeqMap.append()=Bio.SCOP.Raf.SeqMap-class.html#append,Method Bio.Seq.MutableSeq.append()=Bio.Seq.MutableSeq-class.html#append,Method Bio.Wise.psw.Alignment.append()=Bio.Wise.psw.Alignment-class.html#append,Method Bio.Wise.psw.AlignmentColumn.append()=Bio.Wise.psw.AlignmentColumn-class.html#append,Method Martel.msre_parse.SubPattern.append()=Martel.msre_parse.SubPattern-class.html#append"><a title="Bio.Crystal.Chain.append
Bio.EUtils.POM.ElementNode.append
Bio.EUtils.sourcegen.SourceFile.append
Bio.SCOP.Raf.SeqMap.append
Bio.Seq.MutableSeq.append
Bio.Wise.psw.Alignment.append
Bio.Wise.psw.AlignmentColumn.append
Martel.msre_parse.SubPattern.append" class="py-name" href="#" onclick="return doclink('link-9', 'append', 'link-9');">append</a></tt><tt class="py-op">(</tt><tt class="py-name">actref</tt><tt class="py-op">)</tt> </tt>
<a name="L53"></a><tt class="py-lineno"> 53</tt> <tt class="py-line"> <tt class="py-name">actref</tt><tt class="py-op">=</tt><tt class="py-string">""</tt> </tt>
<a name="L54"></a><tt class="py-lineno"> 54</tt> <tt class="py-line"> <tt class="py-keyword">else</tt><tt class="py-op">:</tt> </tt>
<a name="L55"></a><tt class="py-lineno"> 55</tt> <tt class="py-line"> <tt class="py-name">actref</tt><tt class="py-op">+=</tt><tt class="py-name">string</tt><tt class="py-op">.</tt><tt class="py-name">lower</tt><tt class="py-op">(</tt><tt class="py-name">l</tt><tt class="py-op">[</tt><tt class="py-number">19</tt><tt class="py-op">:</tt><tt class="py-number">72</tt><tt class="py-op">]</tt><tt class="py-op">)</tt> </tt>
<a name="L56"></a><tt class="py-lineno"> 56</tt> <tt class="py-line"> </tt>
<a name="L57"></a><tt class="py-lineno"> 57</tt> <tt class="py-line"> <tt class="py-keyword">if</tt> <tt class="py-name">actref</tt><tt class="py-op">!=</tt><tt class="py-string">""</tt><tt class="py-op">:</tt> </tt>
<a name="L58"></a><tt class="py-lineno"> 58</tt> <tt class="py-line"> <tt class="py-name">actref</tt><tt class="py-op">=</tt><tt class="py-name">re</tt><tt class="py-op">.</tt><tt class="py-name">sub</tt><tt class="py-op">(</tt><tt class="py-string">"\s\s+"</tt><tt class="py-op">,</tt><tt class="py-string">" "</tt><tt class="py-op">,</tt><tt class="py-name">actref</tt><tt class="py-op">)</tt> </tt>
<a name="L59"></a><tt class="py-lineno"> 59</tt> <tt class="py-line"> <tt class="py-keyword">if</tt> <tt class="py-name">actref</tt><tt class="py-op">!=</tt><tt class="py-string">" "</tt><tt class="py-op">:</tt> </tt>
<a name="L60"></a><tt class="py-lineno"> 60</tt> <tt class="py-line"> <tt class="py-name">references</tt><tt class="py-op">.</tt><tt id="link-10" class="py-name"><a title="Bio.Crystal.Chain.append
Bio.EUtils.POM.ElementNode.append
Bio.EUtils.sourcegen.SourceFile.append
Bio.SCOP.Raf.SeqMap.append
Bio.Seq.MutableSeq.append
Bio.Wise.psw.Alignment.append
Bio.Wise.psw.AlignmentColumn.append
Martel.msre_parse.SubPattern.append" class="py-name" href="#" onclick="return doclink('link-10', 'append', 'link-9');">append</a></tt><tt class="py-op">(</tt><tt class="py-name">actref</tt><tt class="py-op">)</tt> </tt>
<a name="L61"></a><tt class="py-lineno"> 61</tt> <tt class="py-line"> <tt class="py-keyword">return</tt> <tt class="py-name">references</tt> </tt>
</div><a name="L62"></a><tt class="py-lineno"> 62</tt> <tt class="py-line"> </tt>
<a name="L63"></a><tt class="py-lineno"> 63</tt> <tt class="py-line"> </tt>
<a name="L64"></a><tt class="py-lineno"> 64</tt> <tt class="py-line"><tt class="py-comment"># bring dates to format: 1909-01-08</tt> </tt>
<a name="_format_date"></a><div id="_format_date-def"><a name="L65"></a><tt class="py-lineno"> 65</tt> <a class="py-toggle" href="#" id="_format_date-toggle" onclick="return toggle('_format_date');">-</a><tt class="py-line"><tt class="py-comment"></tt><tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.PDB.parse_pdb_header'-module.html#_format_date">_format_date</a><tt class="py-op">(</tt><tt class="py-param">pdb_date</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="_format_date-collapsed" style="display:none;" pad="+++" indent="++++"></div><div id="_format_date-expanded"><a name="L66"></a><tt class="py-lineno"> 66</tt> <tt class="py-line"> <tt class="py-docstring">"""Converts dates from DD-Mon-YY to YYYY-MM-DD format."""</tt> </tt>
<a name="L67"></a><tt class="py-lineno"> 67</tt> <tt class="py-line"> <tt id="link-11" class="py-name" targets="Method Bio.GenBank._FeatureConsumer.date()=Bio.GenBank._FeatureConsumer-class.html#date,Method Bio.GenBank._RecordConsumer.date()=Bio.GenBank._RecordConsumer-class.html#date,Method Bio.Prosite._RecordConsumer.date()=Bio.Prosite._RecordConsumer-class.html#date,Method Bio.SwissProt.SProt._RecordConsumer.date()=Bio.SwissProt.SProt._RecordConsumer-class.html#date,Method Bio.SwissProt.SProt._SequenceConsumer.date()=Bio.SwissProt.SProt._SequenceConsumer-class.html#date,Variable Bio.expressions.embl.embl65.date=Bio.expressions.embl.embl65-module.html#date,Variable Bio.expressions.genbank.date=Bio.expressions.genbank-module.html#date"><a title="Bio.GenBank._FeatureConsumer.date
Bio.GenBank._RecordConsumer.date
Bio.Prosite._RecordConsumer.date
Bio.SwissProt.SProt._RecordConsumer.date
Bio.SwissProt.SProt._SequenceConsumer.date
Bio.expressions.embl.embl65.date
Bio.expressions.genbank.date" class="py-name" href="#" onclick="return doclink('link-11', 'date', 'link-11');">date</a></tt><tt class="py-op">=</tt><tt class="py-string">""</tt> </tt>
<a name="L68"></a><tt class="py-lineno"> 68</tt> <tt class="py-line"> <tt id="link-12" class="py-name" targets="Method Bio.Medline._RecordConsumer.year()=Bio.Medline._RecordConsumer-class.html#year"><a title="Bio.Medline._RecordConsumer.year" class="py-name" href="#" onclick="return doclink('link-12', 'year', 'link-12');">year</a></tt><tt class="py-op">=</tt><tt class="py-name">int</tt><tt class="py-op">(</tt><tt class="py-name">pdb_date</tt><tt class="py-op">[</tt><tt class="py-number">7</tt><tt class="py-op">:</tt><tt class="py-op">]</tt><tt class="py-op">)</tt> </tt>
<a name="L69"></a><tt class="py-lineno"> 69</tt> <tt class="py-line"> <tt class="py-keyword">if</tt> <tt id="link-13" class="py-name"><a title="Bio.Medline._RecordConsumer.year" class="py-name" href="#" onclick="return doclink('link-13', 'year', 'link-12');">year</a></tt><tt class="py-op"><</tt><tt class="py-number">50</tt><tt class="py-op">:</tt> </tt>
<a name="L70"></a><tt class="py-lineno"> 70</tt> <tt class="py-line"> <tt class="py-name">century</tt><tt class="py-op">=</tt><tt class="py-number">2000</tt> </tt>
<a name="L71"></a><tt class="py-lineno"> 71</tt> <tt class="py-line"> <tt class="py-keyword">else</tt><tt class="py-op">:</tt> </tt>
<a name="L72"></a><tt class="py-lineno"> 72</tt> <tt class="py-line"> <tt class="py-name">century</tt><tt class="py-op">=</tt><tt class="py-number">1900</tt> </tt>
<a name="L73"></a><tt class="py-lineno"> 73</tt> <tt class="py-line"> <tt id="link-14" class="py-name"><a title="Bio.GenBank._FeatureConsumer.date
Bio.GenBank._RecordConsumer.date
Bio.Prosite._RecordConsumer.date
Bio.SwissProt.SProt._RecordConsumer.date
Bio.SwissProt.SProt._SequenceConsumer.date
Bio.expressions.embl.embl65.date
Bio.expressions.genbank.date" class="py-name" href="#" onclick="return doclink('link-14', 'date', 'link-11');">date</a></tt><tt class="py-op">=</tt><tt class="py-name">str</tt><tt class="py-op">(</tt><tt class="py-name">century</tt><tt class="py-op">+</tt><tt id="link-15" class="py-name"><a title="Bio.Medline._RecordConsumer.year" class="py-name" href="#" onclick="return doclink('link-15', 'year', 'link-12');">year</a></tt><tt class="py-op">)</tt><tt class="py-op">+</tt><tt class="py-string">"-"</tt> </tt>
<a name="L74"></a><tt class="py-lineno"> 74</tt> <tt class="py-line"> <tt class="py-name">all_months</tt><tt class="py-op">=</tt><tt class="py-op">[</tt><tt class="py-string">'xxx'</tt><tt class="py-op">,</tt><tt class="py-string">'Jan'</tt><tt class="py-op">,</tt><tt class="py-string">'Feb'</tt><tt class="py-op">,</tt><tt class="py-string">'Mar'</tt><tt class="py-op">,</tt><tt class="py-string">'Apr'</tt><tt class="py-op">,</tt><tt class="py-string">'May'</tt><tt class="py-op">,</tt><tt class="py-string">'Jun'</tt><tt class="py-op">,</tt><tt class="py-string">'Jul'</tt><tt class="py-op">,</tt>\ </tt>
<a name="L75"></a><tt class="py-lineno"> 75</tt> <tt class="py-line"> <tt class="py-string">'Aug'</tt><tt class="py-op">,</tt><tt class="py-string">'Sep'</tt><tt class="py-op">,</tt><tt class="py-string">'Oct'</tt><tt class="py-op">,</tt><tt class="py-string">'Nov'</tt><tt class="py-op">,</tt><tt class="py-string">'Dec'</tt><tt class="py-op">]</tt> </tt>
<a name="L76"></a><tt class="py-lineno"> 76</tt> <tt class="py-line"> <tt class="py-name">month</tt><tt class="py-op">=</tt><tt class="py-name">str</tt><tt class="py-op">(</tt><tt class="py-name">all_months</tt><tt class="py-op">.</tt><tt id="link-16" class="py-name" targets="Method Bio.Crystal.Chain.index()=Bio.Crystal.Chain-class.html#index,Method Bio.EUtils.POM.ElementNode.index()=Bio.EUtils.POM.ElementNode-class.html#index,Method Bio.SCOP.Raf.SeqMap.index()=Bio.SCOP.Raf.SeqMap-class.html#index,Method Bio.Seq.MutableSeq.index()=Bio.Seq.MutableSeq-class.html#index"><a title="Bio.Crystal.Chain.index
Bio.EUtils.POM.ElementNode.index
Bio.SCOP.Raf.SeqMap.index
Bio.Seq.MutableSeq.index" class="py-name" href="#" onclick="return doclink('link-16', 'index', 'link-16');">index</a></tt><tt class="py-op">(</tt><tt class="py-name">pdb_date</tt><tt class="py-op">[</tt><tt class="py-number">3</tt><tt class="py-op">:</tt><tt class="py-number">6</tt><tt class="py-op">]</tt><tt class="py-op">)</tt><tt class="py-op">)</tt> </tt>
<a name="L77"></a><tt class="py-lineno"> 77</tt> <tt class="py-line"> <tt class="py-keyword">if</tt> <tt class="py-name">len</tt><tt class="py-op">(</tt><tt class="py-name">month</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="L78"></a><tt class="py-lineno"> 78</tt> <tt class="py-line"> <tt class="py-name">month</tt> <tt class="py-op">=</tt> <tt class="py-string">'0'</tt><tt class="py-op">+</tt><tt class="py-name">month</tt> </tt>
<a name="L79"></a><tt class="py-lineno"> 79</tt> <tt class="py-line"> <tt id="link-17" class="py-name"><a title="Bio.GenBank._FeatureConsumer.date
Bio.GenBank._RecordConsumer.date
Bio.Prosite._RecordConsumer.date
Bio.SwissProt.SProt._RecordConsumer.date
Bio.SwissProt.SProt._SequenceConsumer.date
Bio.expressions.embl.embl65.date
Bio.expressions.genbank.date" class="py-name" href="#" onclick="return doclink('link-17', 'date', 'link-11');">date</a></tt> <tt class="py-op">=</tt> <tt id="link-18" class="py-name"><a title="Bio.GenBank._FeatureConsumer.date
Bio.GenBank._RecordConsumer.date
Bio.Prosite._RecordConsumer.date
Bio.SwissProt.SProt._RecordConsumer.date
Bio.SwissProt.SProt._SequenceConsumer.date
Bio.expressions.embl.embl65.date
Bio.expressions.genbank.date" class="py-name" href="#" onclick="return doclink('link-18', 'date', 'link-11');">date</a></tt><tt class="py-op">+</tt><tt class="py-name">month</tt><tt class="py-op">+</tt><tt class="py-string">'-'</tt><tt class="py-op">+</tt><tt class="py-name">pdb_date</tt><tt class="py-op">[</tt><tt class="py-op">:</tt><tt class="py-number">2</tt><tt class="py-op">]</tt> </tt>
<a name="L80"></a><tt class="py-lineno"> 80</tt> <tt class="py-line"> <tt class="py-keyword">return</tt> <tt id="link-19" class="py-name"><a title="Bio.GenBank._FeatureConsumer.date
Bio.GenBank._RecordConsumer.date
Bio.Prosite._RecordConsumer.date
Bio.SwissProt.SProt._RecordConsumer.date
Bio.SwissProt.SProt._SequenceConsumer.date
Bio.expressions.embl.embl65.date
Bio.expressions.genbank.date" class="py-name" href="#" onclick="return doclink('link-19', 'date', 'link-11');">date</a></tt> </tt>
</div><a name="L81"></a><tt class="py-lineno"> 81</tt> <tt class="py-line"> </tt>
<a name="L82"></a><tt class="py-lineno"> 82</tt> <tt class="py-line"> </tt>
<a name="_chop_end_codes"></a><div id="_chop_end_codes-def"><a name="L83"></a><tt class="py-lineno"> 83</tt> <a class="py-toggle" href="#" id="_chop_end_codes-toggle" onclick="return toggle('_chop_end_codes');">-</a><tt class="py-line"><tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.PDB.parse_pdb_header'-module.html#_chop_end_codes">_chop_end_codes</a><tt class="py-op">(</tt><tt class="py-param">line</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="_chop_end_codes-collapsed" style="display:none;" pad="+++" indent="++++"></div><div id="_chop_end_codes-expanded"><a name="L84"></a><tt class="py-lineno"> 84</tt> <tt class="py-line"> <tt class="py-docstring">"""Chops lines ending with ' 1CSA 14' and the like."""</tt> </tt>
<a name="L85"></a><tt class="py-lineno"> 85</tt> <tt class="py-line"> <tt class="py-keyword">import</tt> <tt class="py-name">re</tt> </tt>
<a name="L86"></a><tt class="py-lineno"> 86</tt> <tt class="py-line"> <tt class="py-keyword">return</tt> <tt class="py-name">re</tt><tt class="py-op">.</tt><tt class="py-name">sub</tt><tt class="py-op">(</tt><tt class="py-string">"\s\s\s\s+[\w]{4}.\s+\d*\Z"</tt><tt class="py-op">,</tt><tt class="py-string">""</tt><tt class="py-op">,</tt><tt class="py-name">line</tt><tt class="py-op">)</tt> </tt>
</div><a name="L87"></a><tt class="py-lineno"> 87</tt> <tt class="py-line"> </tt>
<a name="_chop_end_misc"></a><div id="_chop_end_misc-def"><a name="L88"></a><tt class="py-lineno"> 88</tt> <a class="py-toggle" href="#" id="_chop_end_misc-toggle" onclick="return toggle('_chop_end_misc');">-</a><tt class="py-line"><tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.PDB.parse_pdb_header'-module.html#_chop_end_misc">_chop_end_misc</a><tt class="py-op">(</tt><tt class="py-param">line</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="_chop_end_misc-collapsed" style="display:none;" pad="+++" indent="++++"></div><div id="_chop_end_misc-expanded"><a name="L89"></a><tt class="py-lineno"> 89</tt> <tt class="py-line"> <tt class="py-docstring">"""Chops lines ending with ' 14-JUL-97 1CSA' and the like."""</tt> </tt>
<a name="L90"></a><tt class="py-lineno"> 90</tt> <tt class="py-line"> <tt class="py-keyword">import</tt> <tt class="py-name">re</tt> </tt>
<a name="L91"></a><tt class="py-lineno"> 91</tt> <tt class="py-line"> <tt class="py-keyword">return</tt> <tt class="py-name">re</tt><tt class="py-op">.</tt><tt class="py-name">sub</tt><tt class="py-op">(</tt><tt class="py-string">"\s\s\s\s+.*\Z"</tt><tt class="py-op">,</tt><tt class="py-string">""</tt><tt class="py-op">,</tt><tt class="py-name">line</tt><tt class="py-op">)</tt> </tt>
</div><a name="L92"></a><tt class="py-lineno"> 92</tt> <tt class="py-line"> </tt>
<a name="_nice_case"></a><div id="_nice_case-def"><a name="L93"></a><tt class="py-lineno"> 93</tt> <a class="py-toggle" href="#" id="_nice_case-toggle" onclick="return toggle('_nice_case');">-</a><tt class="py-line"><tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.PDB.parse_pdb_header'-module.html#_nice_case">_nice_case</a><tt class="py-op">(</tt><tt class="py-param">line</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="_nice_case-collapsed" style="display:none;" pad="+++" indent="++++"></div><div id="_nice_case-expanded"><a name="L94"></a><tt class="py-lineno"> 94</tt> <tt class="py-line"> <tt class="py-docstring">"""Makes A Lowercase String With Capitals."""</tt> </tt>
<a name="L95"></a><tt class="py-lineno"> 95</tt> <tt class="py-line"> <tt class="py-keyword">import</tt> <tt class="py-name">string</tt> </tt>
<a name="L96"></a><tt class="py-lineno"> 96</tt> <tt class="py-line"> <tt class="py-name">l</tt><tt class="py-op">=</tt><tt class="py-name">string</tt><tt class="py-op">.</tt><tt class="py-name">lower</tt><tt class="py-op">(</tt><tt class="py-name">line</tt><tt class="py-op">)</tt> </tt>
<a name="L97"></a><tt class="py-lineno"> 97</tt> <tt class="py-line"> <tt id="link-20" 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-20', 's', 'link-20');">s</a></tt><tt class="py-op">=</tt><tt class="py-string">""</tt> </tt>
<a name="L98"></a><tt class="py-lineno"> 98</tt> <tt class="py-line"> <tt id="link-21" 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-21', 'i', 'link-21');">i</a></tt><tt class="py-op">=</tt><tt class="py-number">0</tt> </tt>
<a name="L99"></a><tt class="py-lineno"> 99</tt> <tt class="py-line"> <tt class="py-name">nextCap</tt><tt class="py-op">=</tt><tt class="py-number">1</tt> </tt>
<a name="L100"></a><tt class="py-lineno">100</tt> <tt class="py-line"> <tt class="py-keyword">while</tt> <tt id="link-22" class="py-name"><a title="Bio.PDB.Polypeptide.i" class="py-name" href="#" onclick="return doclink('link-22', 'i', 'link-21');">i</a></tt><tt class="py-op"><</tt><tt class="py-name">len</tt><tt class="py-op">(</tt><tt class="py-name">l</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
<a name="L101"></a><tt class="py-lineno">101</tt> <tt class="py-line"> <tt class="py-name">c</tt><tt class="py-op">=</tt><tt class="py-name">l</tt><tt class="py-op">[</tt><tt id="link-23" class="py-name"><a title="Bio.PDB.Polypeptide.i" class="py-name" href="#" onclick="return doclink('link-23', 'i', 'link-21');">i</a></tt><tt class="py-op">]</tt> </tt>
<a name="L102"></a><tt class="py-lineno">102</tt> <tt class="py-line"> <tt class="py-keyword">if</tt> <tt class="py-name">c</tt><tt class="py-op">>=</tt><tt class="py-string">'a'</tt> <tt class="py-keyword">and</tt> <tt class="py-name">c</tt><tt class="py-op"><=</tt><tt class="py-string">'z'</tt> <tt class="py-keyword">and</tt> <tt class="py-name">nextCap</tt><tt class="py-op">:</tt> </tt>
<a name="L103"></a><tt class="py-lineno">103</tt> <tt class="py-line"> <tt class="py-name">c</tt><tt class="py-op">=</tt><tt class="py-name">string</tt><tt class="py-op">.</tt><tt class="py-name">upper</tt><tt class="py-op">(</tt><tt class="py-name">c</tt><tt class="py-op">)</tt> </tt>
<a name="L104"></a><tt class="py-lineno">104</tt> <tt class="py-line"> <tt class="py-name">nextCap</tt><tt class="py-op">=</tt><tt class="py-number">0</tt> </tt>
<a name="L105"></a><tt class="py-lineno">105</tt> <tt class="py-line"> <tt class="py-keyword">elif</tt> <tt class="py-name">c</tt><tt class="py-op">==</tt><tt class="py-string">' '</tt> <tt class="py-keyword">or</tt> <tt class="py-name">c</tt><tt class="py-op">==</tt><tt class="py-string">'.'</tt> <tt class="py-keyword">or</tt> <tt class="py-name">c</tt><tt class="py-op">==</tt><tt class="py-string">','</tt> <tt class="py-keyword">or</tt> <tt class="py-name">c</tt><tt class="py-op">==</tt><tt class="py-string">';'</tt> <tt class="py-keyword">or</tt> <tt class="py-name">c</tt><tt class="py-op">==</tt><tt class="py-string">':'</tt> <tt class="py-keyword">or</tt> <tt class="py-name">c</tt><tt class="py-op">==</tt><tt class="py-string">'\t'</tt> <tt class="py-keyword">or</tt>\ </tt>
<a name="L106"></a><tt class="py-lineno">106</tt> <tt class="py-line"> <tt class="py-name">c</tt><tt class="py-op">==</tt><tt class="py-string">'-'</tt> <tt class="py-keyword">or</tt> <tt class="py-name">c</tt><tt class="py-op">==</tt><tt class="py-string">'_'</tt><tt class="py-op">:</tt> </tt>
<a name="L107"></a><tt class="py-lineno">107</tt> <tt class="py-line"> <tt class="py-name">nextCap</tt><tt class="py-op">=</tt><tt class="py-number">1</tt> </tt>
<a name="L108"></a><tt class="py-lineno">108</tt> <tt class="py-line"> <tt id="link-24" class="py-name"><a title="Martel.test.test_swissprot38.s" class="py-name" href="#" onclick="return doclink('link-24', 's', 'link-20');">s</a></tt><tt class="py-op">+=</tt><tt class="py-name">c</tt> </tt>
<a name="L109"></a><tt class="py-lineno">109</tt> <tt class="py-line"> <tt id="link-25" class="py-name"><a title="Bio.PDB.Polypeptide.i" class="py-name" href="#" onclick="return doclink('link-25', 'i', 'link-21');">i</a></tt><tt class="py-op">+=</tt><tt class="py-number">1</tt> </tt>
<a name="L110"></a><tt class="py-lineno">110</tt> <tt class="py-line"> <tt class="py-keyword">return</tt> <tt id="link-26" class="py-name"><a title="Martel.test.test_swissprot38.s" class="py-name" href="#" onclick="return doclink('link-26', 's', 'link-20');">s</a></tt> </tt>
</div><a name="L111"></a><tt class="py-lineno">111</tt> <tt class="py-line"> </tt>
<a name="parse_pdb_header"></a><div id="parse_pdb_header-def"><a name="L112"></a><tt class="py-lineno">112</tt> <a class="py-toggle" href="#" id="parse_pdb_header-toggle" onclick="return toggle('parse_pdb_header');">-</a><tt class="py-line"><tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.PDB.parse_pdb_header'-module.html#parse_pdb_header">parse_pdb_header</a><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="parse_pdb_header-collapsed" style="display:none;" pad="+++" indent="++++"></div><div id="parse_pdb_header-expanded"><a name="L113"></a><tt class="py-lineno">113</tt> <tt class="py-line"> <tt class="py-docstring">"""</tt> </tt>
<a name="L114"></a><tt class="py-lineno">114</tt> <tt class="py-line"><tt class="py-docstring"> Returns the header lines of a pdb file as a dictionary.</tt> </tt>
<a name="L115"></a><tt class="py-lineno">115</tt> <tt class="py-line"><tt class="py-docstring"></tt> </tt>
<a name="L116"></a><tt class="py-lineno">116</tt> <tt class="py-line"><tt class="py-docstring"> Dictionary keys are: head, deposition_date, release_date, structure_method,</tt> </tt>
<a name="L117"></a><tt class="py-lineno">117</tt> <tt class="py-line"><tt class="py-docstring"> resolution, structure_reference, journal_reference, author and</tt> </tt>
<a name="L118"></a><tt class="py-lineno">118</tt> <tt class="py-line"><tt class="py-docstring"> compound.</tt> </tt>
<a name="L119"></a><tt class="py-lineno">119</tt> <tt class="py-line"><tt class="py-docstring"> """</tt> </tt>
<a name="L120"></a><tt class="py-lineno">120</tt> <tt class="py-line"> <tt id="link-27" 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-27', 'header', 'link-27');">header</a></tt><tt class="py-op">=</tt><tt class="py-op">[</tt><tt class="py-op">]</tt> </tt>
<a name="L121"></a><tt class="py-lineno">121</tt> <tt class="py-line"> <tt class="py-keyword">if</tt> <tt id="link-28" class="py-name" targets="Variable Bio.GenBank.LocationParser.Integer.type=Bio.GenBank.LocationParser.Integer-class.html#type,Variable Bio.GenBank.LocationParser.Symbol.type=Bio.GenBank.LocationParser.Symbol-class.html#type,Variable Bio.GenBank.LocationParser.UnsignedInteger.type=Bio.GenBank.LocationParser.UnsignedInteger-class.html#type"><a title="Bio.GenBank.LocationParser.Integer.type
Bio.GenBank.LocationParser.Symbol.type
Bio.GenBank.LocationParser.UnsignedInteger.type" class="py-name" href="#" onclick="return doclink('link-28', 'type', 'link-28');">type</a></tt><tt class="py-op">(</tt><tt class="py-name">file</tt><tt class="py-op">)</tt><tt class="py-op">==</tt><tt class="py-name">types</tt><tt class="py-op">.</tt><tt class="py-name">StringType</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">f</tt><tt class="py-op">=</tt><tt id="link-29" 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-29', 'open', 'link-29');">open</a></tt><tt class="py-op">(</tt><tt class="py-name">file</tt><tt class="py-op">,</tt><tt class="py-string">'r'</tt><tt class="py-op">)</tt> </tt>
<a name="L123"></a><tt class="py-lineno">123</tt> <tt class="py-line"> <tt class="py-keyword">else</tt><tt class="py-op">:</tt> </tt>
<a name="L124"></a><tt class="py-lineno">124</tt> <tt class="py-line"> <tt class="py-name">f</tt><tt class="py-op">=</tt><tt class="py-name">file</tt> </tt>
<a name="L125"></a><tt class="py-lineno">125</tt> <tt class="py-line"> <tt class="py-keyword">for</tt> <tt class="py-name">l</tt> <tt class="py-keyword">in</tt> <tt class="py-name">f</tt><tt class="py-op">:</tt> </tt>
<a name="L126"></a><tt class="py-lineno">126</tt> <tt class="py-line"> <tt class="py-name">record_type</tt><tt class="py-op">=</tt><tt class="py-name">l</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="L127"></a><tt class="py-lineno">127</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">'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>
<a name="L128"></a><tt class="py-lineno">128</tt> <tt class="py-line"> <tt class="py-keyword">break</tt> </tt>
<a name="L129"></a><tt class="py-lineno">129</tt> <tt class="py-line"> <tt class="py-keyword">else</tt><tt class="py-op">:</tt> </tt>
<a name="L130"></a><tt class="py-lineno">130</tt> <tt class="py-line"> <tt id="link-30" 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-30', 'header', 'link-27');">header</a></tt><tt class="py-op">.</tt><tt id="link-31" class="py-name"><a title="Bio.Crystal.Chain.append
Bio.EUtils.POM.ElementNode.append
Bio.EUtils.sourcegen.SourceFile.append
Bio.SCOP.Raf.SeqMap.append
Bio.Seq.MutableSeq.append
Bio.Wise.psw.Alignment.append
Bio.Wise.psw.AlignmentColumn.append
Martel.msre_parse.SubPattern.append" class="py-name" href="#" onclick="return doclink('link-31', 'append', 'link-9');">append</a></tt><tt class="py-op">(</tt><tt class="py-name">l</tt><tt class="py-op">)</tt> </tt>
<a name="L131"></a><tt class="py-lineno">131</tt> <tt class="py-line"> <tt class="py-name">f</tt><tt class="py-op">.</tt><tt id="link-32" class="py-name" targets="Method Bio.FilteredReader.FilteredReader.close()=Bio.FilteredReader.FilteredReader-class.html#close,Method Bio.Mindy.BerkeleyDB.BerkeleyDB.close()=Bio.Mindy.BerkeleyDB.BerkeleyDB-class.html#close,Method Bio.Mindy.FlatDB.MemoryFlatDB.close()=Bio.Mindy.FlatDB.MemoryFlatDB-class.html#close,Method BioSQL.BioSeqDatabase.Adaptor.close()=BioSQL.BioSeqDatabase.Adaptor-class.html#close,Method Martel.Parser.Parser.close()=Martel.Parser.Parser-class.html#close,Method Martel.Parser.RecordParser.close()=Martel.Parser.RecordParser-class.html#close"><a title="Bio.FilteredReader.FilteredReader.close
Bio.Mindy.BerkeleyDB.BerkeleyDB.close
Bio.Mindy.FlatDB.MemoryFlatDB.close
BioSQL.BioSeqDatabase.Adaptor.close
Martel.Parser.Parser.close
Martel.Parser.RecordParser.close" class="py-name" href="#" onclick="return doclink('link-32', 'close', 'link-32');">close</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
<a name="L132"></a><tt class="py-lineno">132</tt> <tt class="py-line"> <tt class="py-keyword">return</tt> <tt id="link-33" 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-33', '_parse_pdb_header_list', 'link-33');">_parse_pdb_header_list</a></tt><tt class="py-op">(</tt><tt id="link-34" 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-34', 'header', 'link-27');">header</a></tt><tt class="py-op">)</tt> </tt>
</div><a name="L133"></a><tt class="py-lineno">133</tt> <tt class="py-line"> </tt>
<a name="_parse_pdb_header_list"></a><div id="_parse_pdb_header_list-def"><a name="L134"></a><tt class="py-lineno">134</tt> <a class="py-toggle" href="#" id="_parse_pdb_header_list-toggle" onclick="return toggle('_parse_pdb_header_list');">-</a><tt class="py-line"><tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.PDB.parse_pdb_header'-module.html#_parse_pdb_header_list">_parse_pdb_header_list</a><tt class="py-op">(</tt><tt class="py-param">header</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="_parse_pdb_header_list-collapsed" style="display:none;" pad="+++" indent="++++"></div><div id="_parse_pdb_header_list-expanded"><a name="L135"></a><tt class="py-lineno">135</tt> <tt class="py-line"> <tt class="py-comment"># database fields</tt> </tt>
<a name="L136"></a><tt class="py-lineno">136</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-name">dict</tt><tt class="py-op">=</tt><tt class="py-op">{</tt><tt class="py-string">'name'</tt><tt class="py-op">:</tt><tt class="py-string">""</tt><tt class="py-op">,</tt> </tt>
<a name="L137"></a><tt class="py-lineno">137</tt> <tt class="py-line"> <tt class="py-string">'head'</tt><tt class="py-op">:</tt><tt class="py-string">''</tt><tt class="py-op">,</tt> </tt>
<a name="L138"></a><tt class="py-lineno">138</tt> <tt class="py-line"> <tt class="py-string">'deposition_date'</tt> <tt class="py-op">:</tt> <tt class="py-string">"1909-01-08"</tt><tt class="py-op">,</tt> </tt>
<a name="L139"></a><tt class="py-lineno">139</tt> <tt class="py-line"> <tt class="py-string">'release_date'</tt> <tt class="py-op">:</tt> <tt class="py-string">"1909-01-08"</tt><tt class="py-op">,</tt> </tt>
<a name="L140"></a><tt class="py-lineno">140</tt> <tt class="py-line"> <tt class="py-string">'structure_method'</tt> <tt class="py-op">:</tt> <tt class="py-string">"unknown"</tt><tt class="py-op">,</tt> </tt>
<a name="L141"></a><tt class="py-lineno">141</tt> <tt class="py-line"> <tt class="py-string">'resolution'</tt> <tt class="py-op">:</tt> <tt class="py-number">0.0</tt><tt class="py-op">,</tt> </tt>
<a name="L142"></a><tt class="py-lineno">142</tt> <tt class="py-line"> <tt class="py-string">'structure_reference'</tt> <tt class="py-op">:</tt> <tt class="py-string">"unknown"</tt><tt class="py-op">,</tt> </tt>
<a name="L143"></a><tt class="py-lineno">143</tt> <tt class="py-line"> <tt class="py-string">'journal_reference'</tt> <tt class="py-op">:</tt> <tt class="py-string">"unknown"</tt><tt class="py-op">,</tt> </tt>
<a name="L144"></a><tt class="py-lineno">144</tt> <tt class="py-line"> <tt class="py-string">'author'</tt> <tt class="py-op">:</tt> <tt class="py-string">""</tt><tt class="py-op">,</tt> </tt>
<a name="L145"></a><tt class="py-lineno">145</tt> <tt class="py-line"> <tt class="py-string">'compound'</tt><tt class="py-op">:</tt><tt class="py-op">{</tt><tt class="py-string">'1'</tt><tt class="py-op">:</tt><tt class="py-op">{</tt><tt class="py-string">'misc'</tt><tt class="py-op">:</tt><tt class="py-string">''</tt><tt class="py-op">}</tt><tt class="py-op">}</tt><tt class="py-op">,</tt><tt class="py-string">'source'</tt><tt class="py-op">:</tt><tt class="py-op">{</tt><tt class="py-string">'1'</tt><tt class="py-op">:</tt><tt class="py-op">{</tt><tt class="py-string">'misc'</tt><tt class="py-op">:</tt><tt class="py-string">''</tt><tt class="py-op">}</tt><tt class="py-op">}</tt><tt class="py-op">}</tt> </tt>
<a name="L146"></a><tt class="py-lineno">146</tt> <tt class="py-line"> </tt>
<a name="L147"></a><tt class="py-lineno">147</tt> <tt class="py-line"> <tt class="py-name">dict</tt><tt class="py-op">[</tt><tt class="py-string">'structure_reference'</tt><tt class="py-op">]</tt> <tt class="py-op">=</tt> <tt id="link-35" class="py-name" targets="Function Bio.PDB.parse_pdb_header'._get_references()=Bio.PDB.parse_pdb_header%27-module.html#_get_references"><a title="Bio.PDB.parse_pdb_header'._get_references" class="py-name" href="#" onclick="return doclink('link-35', '_get_references', 'link-35');">_get_references</a></tt><tt class="py-op">(</tt><tt id="link-36" 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-36', 'header', 'link-27');">header</a></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">dict</tt><tt class="py-op">[</tt><tt class="py-string">'journal_reference'</tt><tt class="py-op">]</tt> <tt class="py-op">=</tt> <tt id="link-37" class="py-name" targets="Function Bio.PDB.parse_pdb_header'._get_journal()=Bio.PDB.parse_pdb_header%27-module.html#_get_journal"><a title="Bio.PDB.parse_pdb_header'._get_journal" class="py-name" href="#" onclick="return doclink('link-37', '_get_journal', 'link-37');">_get_journal</a></tt><tt class="py-op">(</tt><tt id="link-38" 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-38', 'header', 'link-27');">header</a></tt><tt class="py-op">)</tt> </tt>
<a name="L149"></a><tt class="py-lineno">149</tt> <tt class="py-line"> <tt class="py-name">comp_molid</tt><tt class="py-op">=</tt><tt class="py-string">"1"</tt> </tt>
<a name="L150"></a><tt class="py-lineno">150</tt> <tt class="py-line"> <tt class="py-name">src_molid</tt><tt class="py-op">=</tt><tt class="py-string">"1"</tt> </tt>
<a name="L151"></a><tt class="py-lineno">151</tt> <tt class="py-line"> <tt class="py-name">last_comp_key</tt><tt class="py-op">=</tt><tt class="py-string">"misc"</tt> </tt>
<a name="L152"></a><tt class="py-lineno">152</tt> <tt class="py-line"> <tt class="py-name">last_src_key</tt><tt class="py-op">=</tt><tt class="py-string">"misc"</tt> </tt>
<a name="L153"></a><tt class="py-lineno">153</tt> <tt class="py-line"> </tt>
<a name="L154"></a><tt class="py-lineno">154</tt> <tt class="py-line"> <tt class="py-keyword">for</tt> <tt class="py-name">hh</tt> <tt class="py-keyword">in</tt> <tt id="link-39" 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-39', 'header', 'link-27');">header</a></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">h</tt><tt class="py-op">=</tt><tt class="py-name">re</tt><tt class="py-op">.</tt><tt class="py-name">sub</tt><tt class="py-op">(</tt><tt class="py-string">"[\s\n\r]*\Z"</tt><tt class="py-op">,</tt><tt class="py-string">""</tt><tt class="py-op">,</tt><tt class="py-name">hh</tt><tt class="py-op">)</tt> <tt class="py-comment"># chop linebreaks off</tt> </tt>
<a name="L156"></a><tt class="py-lineno">156</tt> <tt class="py-line"> <tt id="link-40" class="py-name" targets="Variable Bio.Translate.key=Bio.Translate-module.html#key"><a title="Bio.Translate.key" class="py-name" href="#" onclick="return doclink('link-40', 'key', 'link-40');">key</a></tt><tt class="py-op">=</tt><tt class="py-name">re</tt><tt class="py-op">.</tt><tt class="py-name">sub</tt><tt class="py-op">(</tt><tt class="py-string">"\s.+\s*"</tt><tt class="py-op">,</tt><tt class="py-string">""</tt><tt class="py-op">,</tt><tt class="py-name">h</tt><tt class="py-op">)</tt> </tt>
<a name="L157"></a><tt class="py-lineno">157</tt> <tt class="py-line"> <tt class="py-name">tail</tt><tt class="py-op">=</tt><tt class="py-name">re</tt><tt class="py-op">.</tt><tt class="py-name">sub</tt><tt class="py-op">(</tt><tt class="py-string">"\A\w+\s+\d*\s*"</tt><tt class="py-op">,</tt><tt class="py-string">""</tt><tt class="py-op">,</tt><tt class="py-name">h</tt><tt class="py-op">)</tt> </tt>
<a name="L158"></a><tt class="py-lineno">158</tt> <tt class="py-line"> <tt class="py-comment"># print key+":"+tail</tt> </tt>
<a name="L159"></a><tt class="py-lineno">159</tt> <tt class="py-line"><tt class="py-comment"></tt> </tt>
<a name="L160"></a><tt class="py-lineno">160</tt> <tt class="py-line"> <tt class="py-comment"># From here, all the keys from the header are being parsed</tt> </tt>
<a name="L161"></a><tt class="py-lineno">161</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-keyword">if</tt> <tt id="link-41" class="py-name"><a title="Bio.Translate.key" class="py-name" href="#" onclick="return doclink('link-41', 'key', 'link-40');">key</a></tt><tt class="py-op">==</tt><tt class="py-string">"TITLE"</tt><tt class="py-op">:</tt> </tt>
<a name="L162"></a><tt class="py-lineno">162</tt> <tt class="py-line"> <tt id="link-42" 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-42', 'name', 'link-42');">name</a></tt><tt class="py-op">=</tt><tt class="py-name">string</tt><tt class="py-op">.</tt><tt class="py-name">lower</tt><tt class="py-op">(</tt><tt id="link-43" class="py-name" targets="Function Bio.PDB.parse_pdb_header'._chop_end_codes()=Bio.PDB.parse_pdb_header%27-module.html#_chop_end_codes"><a title="Bio.PDB.parse_pdb_header'._chop_end_codes" class="py-name" href="#" onclick="return doclink('link-43', '_chop_end_codes', 'link-43');">_chop_end_codes</a></tt><tt class="py-op">(</tt><tt class="py-name">tail</tt><tt class="py-op">)</tt><tt class="py-op">)</tt> </tt>
<a name="L163"></a><tt class="py-lineno">163</tt> <tt class="py-line"> <tt class="py-keyword">if</tt> <tt class="py-name">dict</tt><tt class="py-op">.</tt><tt id="link-44" class="py-name" targets="Method Bio.Crystal.Crystal.has_key()=Bio.Crystal.Crystal-class.html#has_key,Method Bio.EUtils.POM.ElementNode.has_key()=Bio.EUtils.POM.ElementNode-class.html#has_key,Method Bio.GenBank.NCBIDictionary.has_key()=Bio.GenBank.NCBIDictionary-class.html#has_key,Method Bio.PDB.AbstractPropertyMap.AbstractPropertyMap.has_key()=Bio.PDB.AbstractPropertyMap.AbstractPropertyMap-class.html#has_key,Method Bio.PDB.FragmentMapper'.FragmentMapper.has_key()=Bio.PDB.FragmentMapper%27.FragmentMapper-class.html#has_key,Method Bio.Prosite.ExPASyDictionary.has_key()=Bio.Prosite.ExPASyDictionary-class.html#has_key,Method Bio.Prosite.Prodoc.ExPASyDictionary.has_key()=Bio.Prosite.Prodoc.ExPASyDictionary-class.html#has_key,Method Bio.PubMed.Dictionary.has_key()=Bio.PubMed.Dictionary-class.html#has_key,Method Bio.SwissProt.SProt.ExPASyDictionary.has_key()=Bio.SwissProt.SProt.ExPASyDictionary-class.html#has_key,Method Martel.Parser.MartelAttributeList.has_key()=Martel.Parser.MartelAttributeList-class.html#has_key"><a title="Bio.Crystal.Crystal.has_key
Bio.EUtils.POM.ElementNode.has_key
Bio.GenBank.NCBIDictionary.has_key
Bio.PDB.AbstractPropertyMap.AbstractPropertyMap.has_key
Bio.PDB.FragmentMapper'.FragmentMapper.has_key
Bio.Prosite.ExPASyDictionary.has_key
Bio.Prosite.Prodoc.ExPASyDictionary.has_key
Bio.PubMed.Dictionary.has_key
Bio.SwissProt.SProt.ExPASyDictionary.has_key
Martel.Parser.MartelAttributeList.has_key" class="py-name" href="#" onclick="return doclink('link-44', 'has_key', 'link-44');">has_key</a></tt><tt class="py-op">(</tt><tt class="py-string">'name'</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
<a name="L164"></a><tt class="py-lineno">164</tt> <tt class="py-line"> <tt class="py-name">dict</tt><tt class="py-op">[</tt><tt class="py-string">'name'</tt><tt class="py-op">]</tt> <tt class="py-op">+=</tt> <tt class="py-string">" "</tt><tt class="py-op">+</tt><tt id="link-45" class="py-name"><a title="Bio.Encodings.IUPACEncoding.name" class="py-name" href="#" onclick="return doclink('link-45', 'name', 'link-42');">name</a></tt> </tt>
<a name="L165"></a><tt class="py-lineno">165</tt> <tt class="py-line"> <tt class="py-keyword">else</tt><tt class="py-op">:</tt> </tt>
<a name="L166"></a><tt class="py-lineno">166</tt> <tt class="py-line"> <tt class="py-name">dict</tt><tt class="py-op">[</tt><tt class="py-string">'name'</tt><tt class="py-op">]</tt><tt class="py-op">=</tt><tt id="link-46" class="py-name"><a title="Bio.Encodings.IUPACEncoding.name" class="py-name" href="#" onclick="return doclink('link-46', 'name', 'link-42');">name</a></tt> </tt>
<a name="L167"></a><tt class="py-lineno">167</tt> <tt class="py-line"> <tt class="py-keyword">elif</tt> <tt id="link-47" class="py-name"><a title="Bio.Translate.key" class="py-name" href="#" onclick="return doclink('link-47', 'key', 'link-40');">key</a></tt><tt class="py-op">==</tt><tt class="py-string">"HEADER"</tt><tt class="py-op">:</tt> </tt>
<a name="L168"></a><tt class="py-lineno">168</tt> <tt class="py-line"> <tt class="py-name">rr</tt><tt class="py-op">=</tt><tt class="py-name">re</tt><tt class="py-op">.</tt><tt id="link-48" class="py-name"><a title="Bio.EUtils.DBIdsClient.DBIdsClient.search
Bio.EUtils.HistoryClient.HistoryClient.search
Bio.KDTree.KDTree.KDTree.search
Bio.PDB.NeighborSearch.NeighborSearch.search
Bio.Prosite.Pattern.Prosite.search
Bio.Restriction.Restriction.AbstractCut.search
Bio.Restriction.Restriction.RestrictionBatch.search
Bio.SCOP.search
Bio.builders.Search.search
Bio.formatdefs.search
Bio.formatdefs.search.search" class="py-name" href="#" onclick="return doclink('link-48', 'search', 'link-2');">search</a></tt><tt class="py-op">(</tt><tt class="py-string">"\d\d-\w\w\w-\d\d"</tt><tt class="py-op">,</tt><tt class="py-name">tail</tt><tt class="py-op">)</tt> </tt>
<a name="L169"></a><tt class="py-lineno">169</tt> <tt class="py-line"> <tt class="py-keyword">if</tt> <tt class="py-name">rr</tt><tt class="py-op">!=</tt><tt class="py-name">None</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">dict</tt><tt class="py-op">[</tt><tt class="py-string">'deposition_date'</tt><tt class="py-op">]</tt><tt class="py-op">=</tt><tt id="link-49" class="py-name" targets="Function Bio.PDB.parse_pdb_header'._format_date()=Bio.PDB.parse_pdb_header%27-module.html#_format_date"><a title="Bio.PDB.parse_pdb_header'._format_date" class="py-name" href="#" onclick="return doclink('link-49', '_format_date', 'link-49');">_format_date</a></tt><tt class="py-op">(</tt><tt id="link-50" class="py-name" targets="Function Bio.PDB.parse_pdb_header'._nice_case()=Bio.PDB.parse_pdb_header%27-module.html#_nice_case"><a title="Bio.PDB.parse_pdb_header'._nice_case" class="py-name" href="#" onclick="return doclink('link-50', '_nice_case', 'link-50');">_nice_case</a></tt><tt class="py-op">(</tt><tt class="py-name">rr</tt><tt class="py-op">.</tt><tt id="link-51" class="py-name" targets="Method Bio.Prosite.Pattern.PrositeMatch.group()=Bio.Prosite.Pattern.PrositeMatch-class.html#group"><a title="Bio.Prosite.Pattern.PrositeMatch.group" class="py-name" href="#" onclick="return doclink('link-51', 'group', 'link-51');">group</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt><tt class="py-op">)</tt><tt class="py-op">)</tt> </tt>
<a name="L171"></a><tt class="py-lineno">171</tt> <tt class="py-line"> <tt class="py-name">head</tt><tt class="py-op">=</tt><tt class="py-name">string</tt><tt class="py-op">.</tt><tt class="py-name">lower</tt><tt class="py-op">(</tt><tt id="link-52" class="py-name" targets="Function Bio.PDB.parse_pdb_header'._chop_end_misc()=Bio.PDB.parse_pdb_header%27-module.html#_chop_end_misc"><a title="Bio.PDB.parse_pdb_header'._chop_end_misc" class="py-name" href="#" onclick="return doclink('link-52', '_chop_end_misc', 'link-52');">_chop_end_misc</a></tt><tt class="py-op">(</tt><tt class="py-name">tail</tt><tt class="py-op">)</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">dict</tt><tt class="py-op">[</tt><tt class="py-string">'head'</tt><tt class="py-op">]</tt><tt class="py-op">=</tt><tt class="py-name">head</tt> </tt>
<a name="L173"></a><tt class="py-lineno">173</tt> <tt class="py-line"> <tt class="py-keyword">elif</tt> <tt id="link-53" class="py-name"><a title="Bio.Translate.key" class="py-name" href="#" onclick="return doclink('link-53', 'key', 'link-40');">key</a></tt><tt class="py-op">==</tt><tt class="py-string">"COMPND"</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">tt</tt><tt class="py-op">=</tt><tt class="py-name">string</tt><tt class="py-op">.</tt><tt class="py-name">lower</tt><tt class="py-op">(</tt><tt class="py-name">re</tt><tt class="py-op">.</tt><tt class="py-name">sub</tt><tt class="py-op">(</tt><tt class="py-string">"\;\s*\Z"</tt><tt class="py-op">,</tt><tt class="py-string">""</tt><tt class="py-op">,</tt><tt id="link-54" class="py-name"><a title="Bio.PDB.parse_pdb_header'._chop_end_codes" class="py-name" href="#" onclick="return doclink('link-54', '_chop_end_codes', 'link-43');">_chop_end_codes</a></tt><tt class="py-op">(</tt><tt class="py-name">tail</tt><tt class="py-op">)</tt><tt class="py-op">)</tt><tt class="py-op">)</tt> </tt>
<a name="L175"></a><tt class="py-lineno">175</tt> <tt class="py-line"> <tt class="py-comment"># look for E.C. numbers in COMPND lines</tt> </tt>
<a name="L176"></a><tt class="py-lineno">176</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-name">rec</tt> <tt class="py-op">=</tt> <tt class="py-name">re</tt><tt class="py-op">.</tt><tt id="link-55" class="py-name"><a title="Bio.EUtils.DBIdsClient.DBIdsClient.search
Bio.EUtils.HistoryClient.HistoryClient.search
Bio.KDTree.KDTree.KDTree.search
Bio.PDB.NeighborSearch.NeighborSearch.search
Bio.Prosite.Pattern.Prosite.search
Bio.Restriction.Restriction.AbstractCut.search
Bio.Restriction.Restriction.RestrictionBatch.search
Bio.SCOP.search
Bio.builders.Search.search
Bio.formatdefs.search
Bio.formatdefs.search.search" class="py-name" href="#" onclick="return doclink('link-55', 'search', 'link-2');">search</a></tt><tt class="py-op">(</tt><tt class="py-string">'\d+\.\d+\.\d+\.\d+'</tt><tt class="py-op">,</tt><tt class="py-name">tt</tt><tt class="py-op">)</tt> </tt>
<a name="L177"></a><tt class="py-lineno">177</tt> <tt class="py-line"> <tt class="py-keyword">if</tt> <tt class="py-name">rec</tt><tt class="py-op">:</tt> </tt>
<a name="L178"></a><tt class="py-lineno">178</tt> <tt class="py-line"> <tt class="py-name">dict</tt><tt class="py-op">[</tt><tt class="py-string">'compound'</tt><tt class="py-op">]</tt><tt class="py-op">[</tt><tt class="py-name">comp_molid</tt><tt class="py-op">]</tt><tt class="py-op">[</tt><tt class="py-string">'ec_number'</tt><tt class="py-op">]</tt><tt class="py-op">=</tt><tt class="py-name">rec</tt><tt class="py-op">.</tt><tt id="link-56" class="py-name"><a title="Bio.Prosite.Pattern.PrositeMatch.group" class="py-name" href="#" onclick="return doclink('link-56', 'group', 'link-51');">group</a></tt><tt class="py-op">(</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">tt</tt><tt class="py-op">=</tt><tt class="py-name">re</tt><tt class="py-op">.</tt><tt class="py-name">sub</tt><tt class="py-op">(</tt><tt class="py-string">"\((e\.c\.)*\d+\.\d+\.\d+\.\d+\)"</tt><tt class="py-op">,</tt><tt class="py-string">""</tt><tt class="py-op">,</tt><tt class="py-name">tt</tt><tt class="py-op">)</tt> </tt>
<a name="L180"></a><tt class="py-lineno">180</tt> <tt class="py-line"> <tt class="py-name">tok</tt><tt class="py-op">=</tt><tt class="py-name">tt</tt><tt class="py-op">.</tt><tt id="link-57" 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-57', 'split', 'link-57');">split</a></tt><tt class="py-op">(</tt><tt class="py-string">":"</tt><tt class="py-op">)</tt> </tt>
<a name="L181"></a><tt class="py-lineno">181</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">tok</tt><tt class="py-op">)</tt><tt class="py-op">>=</tt><tt class="py-number">2</tt><tt class="py-op">:</tt> </tt>
<a name="L182"></a><tt class="py-lineno">182</tt> <tt class="py-line"> <tt class="py-name">ckey</tt><tt class="py-op">=</tt><tt class="py-name">tok</tt><tt class="py-op">[</tt><tt class="py-number">0</tt><tt class="py-op">]</tt> </tt>
<a name="L183"></a><tt class="py-lineno">183</tt> <tt class="py-line"> <tt class="py-name">cval</tt><tt class="py-op">=</tt><tt class="py-name">re</tt><tt class="py-op">.</tt><tt class="py-name">sub</tt><tt class="py-op">(</tt><tt class="py-string">"\A\s*"</tt><tt class="py-op">,</tt><tt class="py-string">""</tt><tt class="py-op">,</tt><tt class="py-name">tok</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="L184"></a><tt class="py-lineno">184</tt> <tt class="py-line"> <tt class="py-keyword">if</tt> <tt class="py-name">ckey</tt><tt class="py-op">==</tt><tt class="py-string">'mol_id'</tt><tt class="py-op">:</tt> </tt>
<a name="L185"></a><tt class="py-lineno">185</tt> <tt class="py-line"> <tt class="py-name">dict</tt><tt class="py-op">[</tt><tt class="py-string">'compound'</tt><tt class="py-op">]</tt><tt class="py-op">[</tt><tt class="py-name">cval</tt><tt class="py-op">]</tt><tt class="py-op">=</tt><tt class="py-op">{</tt><tt class="py-string">'misc'</tt><tt class="py-op">:</tt><tt class="py-string">''</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">comp_molid</tt><tt class="py-op">=</tt><tt class="py-name">cval</tt> </tt>
<a name="L187"></a><tt class="py-lineno">187</tt> <tt class="py-line"> <tt class="py-name">last_comp_key</tt><tt class="py-op">=</tt><tt class="py-string">"misc"</tt> </tt>
<a name="L188"></a><tt class="py-lineno">188</tt> <tt class="py-line"> <tt class="py-keyword">else</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">dict</tt><tt class="py-op">[</tt><tt class="py-string">'compound'</tt><tt class="py-op">]</tt><tt class="py-op">[</tt><tt class="py-name">comp_molid</tt><tt class="py-op">]</tt><tt class="py-op">[</tt><tt class="py-name">ckey</tt><tt class="py-op">]</tt><tt class="py-op">=</tt><tt class="py-name">cval</tt> </tt>
<a name="L190"></a><tt class="py-lineno">190</tt> <tt class="py-line"> <tt class="py-name">last_comp_key</tt><tt class="py-op">=</tt><tt class="py-name">ckey</tt> </tt>
<a name="L191"></a><tt class="py-lineno">191</tt> <tt class="py-line"> <tt class="py-keyword">else</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">dict</tt><tt class="py-op">[</tt><tt class="py-string">'compound'</tt><tt class="py-op">]</tt><tt class="py-op">[</tt><tt class="py-name">comp_molid</tt><tt class="py-op">]</tt><tt class="py-op">[</tt><tt class="py-name">last_comp_key</tt><tt class="py-op">]</tt><tt class="py-op">+=</tt><tt class="py-name">tok</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-string">" "</tt> </tt>
<a name="L193"></a><tt class="py-lineno">193</tt> <tt class="py-line"> <tt class="py-keyword">elif</tt> <tt id="link-58" class="py-name"><a title="Bio.Translate.key" class="py-name" href="#" onclick="return doclink('link-58', 'key', 'link-40');">key</a></tt><tt class="py-op">==</tt><tt class="py-string">"SOURCE"</tt><tt class="py-op">:</tt> </tt>
<a name="L194"></a><tt class="py-lineno">194</tt> <tt class="py-line"> <tt class="py-name">tt</tt><tt class="py-op">=</tt><tt class="py-name">string</tt><tt class="py-op">.</tt><tt class="py-name">lower</tt><tt class="py-op">(</tt><tt class="py-name">re</tt><tt class="py-op">.</tt><tt class="py-name">sub</tt><tt class="py-op">(</tt><tt class="py-string">"\;\s*\Z"</tt><tt class="py-op">,</tt><tt class="py-string">""</tt><tt class="py-op">,</tt><tt id="link-59" class="py-name"><a title="Bio.PDB.parse_pdb_header'._chop_end_codes" class="py-name" href="#" onclick="return doclink('link-59', '_chop_end_codes', 'link-43');">_chop_end_codes</a></tt><tt class="py-op">(</tt><tt class="py-name">tail</tt><tt class="py-op">)</tt><tt class="py-op">)</tt><tt class="py-op">)</tt> </tt>
<a name="L195"></a><tt class="py-lineno">195</tt> <tt class="py-line"> <tt class="py-name">tok</tt><tt class="py-op">=</tt><tt class="py-name">tt</tt><tt class="py-op">.</tt><tt id="link-60" class="py-name"><a title="Bio.Nexus.Trees.Tree.split
Bio.Restriction.Restriction.RestrictionBatch.split" class="py-name" href="#" onclick="return doclink('link-60', 'split', 'link-57');">split</a></tt><tt class="py-op">(</tt><tt class="py-string">":"</tt><tt class="py-op">)</tt> </tt>
<a name="L196"></a><tt class="py-lineno">196</tt> <tt class="py-line"> <tt class="py-comment"># print tok</tt> </tt>
<a name="L197"></a><tt class="py-lineno">197</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-keyword">if</tt> <tt class="py-name">len</tt><tt class="py-op">(</tt><tt class="py-name">tok</tt><tt class="py-op">)</tt><tt class="py-op">>=</tt><tt class="py-number">2</tt><tt class="py-op">:</tt> </tt>
<a name="L198"></a><tt class="py-lineno">198</tt> <tt class="py-line"> <tt class="py-name">ckey</tt><tt class="py-op">=</tt><tt class="py-name">tok</tt><tt class="py-op">[</tt><tt class="py-number">0</tt><tt class="py-op">]</tt> </tt>
<a name="L199"></a><tt class="py-lineno">199</tt> <tt class="py-line"> <tt class="py-name">cval</tt><tt class="py-op">=</tt><tt class="py-name">re</tt><tt class="py-op">.</tt><tt class="py-name">sub</tt><tt class="py-op">(</tt><tt class="py-string">"\A\s*"</tt><tt class="py-op">,</tt><tt class="py-string">""</tt><tt class="py-op">,</tt><tt class="py-name">tok</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="L200"></a><tt class="py-lineno">200</tt> <tt class="py-line"> <tt class="py-keyword">if</tt> <tt class="py-name">ckey</tt><tt class="py-op">==</tt><tt class="py-string">'mol_id'</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">dict</tt><tt class="py-op">[</tt><tt class="py-string">'source'</tt><tt class="py-op">]</tt><tt class="py-op">[</tt><tt class="py-name">cval</tt><tt class="py-op">]</tt><tt class="py-op">=</tt><tt class="py-op">{</tt><tt class="py-string">'misc'</tt><tt class="py-op">:</tt><tt class="py-string">''</tt><tt class="py-op">}</tt> </tt>
<a name="L202"></a><tt class="py-lineno">202</tt> <tt class="py-line"> <tt class="py-name">comp_molid</tt><tt class="py-op">=</tt><tt class="py-name">cval</tt> </tt>
<a name="L203"></a><tt class="py-lineno">203</tt> <tt class="py-line"> <tt class="py-name">last_src_key</tt><tt class="py-op">=</tt><tt class="py-string">"misc"</tt> </tt>
<a name="L204"></a><tt class="py-lineno">204</tt> <tt class="py-line"> <tt class="py-keyword">else</tt><tt class="py-op">:</tt> </tt>
<a name="L205"></a><tt class="py-lineno">205</tt> <tt class="py-line"> <tt class="py-name">dict</tt><tt class="py-op">[</tt><tt class="py-string">'source'</tt><tt class="py-op">]</tt><tt class="py-op">[</tt><tt class="py-name">comp_molid</tt><tt class="py-op">]</tt><tt class="py-op">[</tt><tt class="py-name">ckey</tt><tt class="py-op">]</tt><tt class="py-op">=</tt><tt class="py-name">cval</tt> </tt>
<a name="L206"></a><tt class="py-lineno">206</tt> <tt class="py-line"> <tt class="py-name">last_src_key</tt><tt class="py-op">=</tt><tt class="py-name">ckey</tt> </tt>
<a name="L207"></a><tt class="py-lineno">207</tt> <tt class="py-line"> <tt class="py-keyword">else</tt><tt class="py-op">:</tt> </tt>
<a name="L208"></a><tt class="py-lineno">208</tt> <tt class="py-line"> <tt class="py-name">dict</tt><tt class="py-op">[</tt><tt class="py-string">'source'</tt><tt class="py-op">]</tt><tt class="py-op">[</tt><tt class="py-name">comp_molid</tt><tt class="py-op">]</tt><tt class="py-op">[</tt><tt class="py-name">last_src_key</tt><tt class="py-op">]</tt><tt class="py-op">+=</tt><tt class="py-name">tok</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-string">" "</tt> </tt>
<a name="L209"></a><tt class="py-lineno">209</tt> <tt class="py-line"> <tt class="py-keyword">elif</tt> <tt id="link-61" class="py-name"><a title="Bio.Translate.key" class="py-name" href="#" onclick="return doclink('link-61', 'key', 'link-40');">key</a></tt><tt class="py-op">==</tt><tt class="py-string">"KEYWDS"</tt><tt class="py-op">:</tt> </tt>
<a name="L210"></a><tt class="py-lineno">210</tt> <tt class="py-line"> <tt class="py-name">kwd</tt><tt class="py-op">=</tt><tt class="py-name">string</tt><tt class="py-op">.</tt><tt class="py-name">lower</tt><tt class="py-op">(</tt><tt id="link-62" class="py-name"><a title="Bio.PDB.parse_pdb_header'._chop_end_codes" class="py-name" href="#" onclick="return doclink('link-62', '_chop_end_codes', 'link-43');">_chop_end_codes</a></tt><tt class="py-op">(</tt><tt class="py-name">tail</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-keyword">if</tt> <tt class="py-name">dict</tt><tt class="py-op">.</tt><tt id="link-63" class="py-name"><a title="Bio.Crystal.Crystal.has_key
Bio.EUtils.POM.ElementNode.has_key
Bio.GenBank.NCBIDictionary.has_key
Bio.PDB.AbstractPropertyMap.AbstractPropertyMap.has_key
Bio.PDB.FragmentMapper'.FragmentMapper.has_key
Bio.Prosite.ExPASyDictionary.has_key
Bio.Prosite.Prodoc.ExPASyDictionary.has_key
Bio.PubMed.Dictionary.has_key
Bio.SwissProt.SProt.ExPASyDictionary.has_key
Martel.Parser.MartelAttributeList.has_key" class="py-name" href="#" onclick="return doclink('link-63', 'has_key', 'link-44');">has_key</a></tt><tt class="py-op">(</tt><tt class="py-string">'keywords'</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
<a name="L212"></a><tt class="py-lineno">212</tt> <tt class="py-line"> <tt class="py-name">dict</tt><tt class="py-op">[</tt><tt class="py-string">'keywords'</tt><tt class="py-op">]</tt><tt class="py-op">+=</tt><tt class="py-string">" "</tt><tt class="py-op">+</tt><tt class="py-name">kwd</tt> </tt>
<a name="L213"></a><tt class="py-lineno">213</tt> <tt class="py-line"> <tt class="py-keyword">else</tt><tt class="py-op">:</tt> </tt>
<a name="L214"></a><tt class="py-lineno">214</tt> <tt class="py-line"> <tt class="py-name">dict</tt><tt class="py-op">[</tt><tt class="py-string">'keywords'</tt><tt class="py-op">]</tt><tt class="py-op">=</tt><tt class="py-name">kwd</tt> </tt>
<a name="L215"></a><tt class="py-lineno">215</tt> <tt class="py-line"> <tt class="py-keyword">elif</tt> <tt id="link-64" class="py-name"><a title="Bio.Translate.key" class="py-name" href="#" onclick="return doclink('link-64', 'key', 'link-40');">key</a></tt><tt class="py-op">==</tt><tt class="py-string">"EXPDTA"</tt><tt class="py-op">:</tt> </tt>
<a name="L216"></a><tt class="py-lineno">216</tt> <tt class="py-line"> <tt class="py-name">expd</tt><tt class="py-op">=</tt><tt id="link-65" class="py-name"><a title="Bio.PDB.parse_pdb_header'._chop_end_codes" class="py-name" href="#" onclick="return doclink('link-65', '_chop_end_codes', 'link-43');">_chop_end_codes</a></tt><tt class="py-op">(</tt><tt class="py-name">tail</tt><tt class="py-op">)</tt> </tt>
<a name="L217"></a><tt class="py-lineno">217</tt> <tt class="py-line"> <tt class="py-comment"># chop junk at end of lines for some structures</tt> </tt>
<a name="L218"></a><tt class="py-lineno">218</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-name">expd</tt><tt class="py-op">=</tt><tt class="py-name">re</tt><tt class="py-op">.</tt><tt class="py-name">sub</tt><tt class="py-op">(</tt><tt class="py-string">'\s\s\s\s\s\s\s.*\Z'</tt><tt class="py-op">,</tt><tt class="py-string">''</tt><tt class="py-op">,</tt><tt class="py-name">expd</tt><tt class="py-op">)</tt> </tt>
<a name="L219"></a><tt class="py-lineno">219</tt> <tt class="py-line"> <tt class="py-comment"># if re.search('\Anmr',expd,re.IGNORECASE): expd='nmr'</tt> </tt>
<a name="L220"></a><tt class="py-lineno">220</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-comment"># if re.search('x-ray diffraction',expd,re.IGNORECASE): expd='x-ray diffraction'</tt> </tt>
<a name="L221"></a><tt class="py-lineno">221</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-name">dict</tt><tt class="py-op">[</tt><tt class="py-string">'structure_method'</tt><tt class="py-op">]</tt><tt class="py-op">=</tt><tt class="py-name">string</tt><tt class="py-op">.</tt><tt class="py-name">lower</tt><tt class="py-op">(</tt><tt class="py-name">expd</tt><tt class="py-op">)</tt> </tt>
<a name="L222"></a><tt class="py-lineno">222</tt> <tt class="py-line"> <tt class="py-keyword">elif</tt> <tt id="link-66" class="py-name"><a title="Bio.Translate.key" class="py-name" href="#" onclick="return doclink('link-66', 'key', 'link-40');">key</a></tt><tt class="py-op">==</tt><tt class="py-string">"CAVEAT"</tt><tt class="py-op">:</tt> </tt>
<a name="L223"></a><tt class="py-lineno">223</tt> <tt class="py-line"> <tt class="py-comment"># make Annotation entries out of these!!!</tt> </tt>
<a name="L224"></a><tt class="py-lineno">224</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-keyword">pass</tt> </tt>
<a name="L225"></a><tt class="py-lineno">225</tt> <tt class="py-line"> <tt class="py-keyword">elif</tt> <tt id="link-67" class="py-name"><a title="Bio.Translate.key" class="py-name" href="#" onclick="return doclink('link-67', 'key', 'link-40');">key</a></tt><tt class="py-op">==</tt><tt class="py-string">"REVDAT"</tt><tt class="py-op">:</tt> </tt>
<a name="L226"></a><tt class="py-lineno">226</tt> <tt class="py-line"> <tt class="py-name">rr</tt><tt class="py-op">=</tt><tt class="py-name">re</tt><tt class="py-op">.</tt><tt id="link-68" class="py-name"><a title="Bio.EUtils.DBIdsClient.DBIdsClient.search
Bio.EUtils.HistoryClient.HistoryClient.search
Bio.KDTree.KDTree.KDTree.search
Bio.PDB.NeighborSearch.NeighborSearch.search
Bio.Prosite.Pattern.Prosite.search
Bio.Restriction.Restriction.AbstractCut.search
Bio.Restriction.Restriction.RestrictionBatch.search
Bio.SCOP.search
Bio.builders.Search.search
Bio.formatdefs.search
Bio.formatdefs.search.search" class="py-name" href="#" onclick="return doclink('link-68', 'search', 'link-2');">search</a></tt><tt class="py-op">(</tt><tt class="py-string">"\d\d-\w\w\w-\d\d"</tt><tt class="py-op">,</tt><tt class="py-name">tail</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">rr</tt><tt class="py-op">!=</tt><tt class="py-name">None</tt><tt class="py-op">:</tt> </tt>
<a name="L228"></a><tt class="py-lineno">228</tt> <tt class="py-line"> <tt class="py-name">dict</tt><tt class="py-op">[</tt><tt class="py-string">'release_date'</tt><tt class="py-op">]</tt><tt class="py-op">=</tt><tt id="link-69" class="py-name"><a title="Bio.PDB.parse_pdb_header'._format_date" class="py-name" href="#" onclick="return doclink('link-69', '_format_date', 'link-49');">_format_date</a></tt><tt class="py-op">(</tt><tt id="link-70" class="py-name"><a title="Bio.PDB.parse_pdb_header'._nice_case" class="py-name" href="#" onclick="return doclink('link-70', '_nice_case', 'link-50');">_nice_case</a></tt><tt class="py-op">(</tt><tt class="py-name">rr</tt><tt class="py-op">.</tt><tt id="link-71" class="py-name"><a title="Bio.Prosite.Pattern.PrositeMatch.group" class="py-name" href="#" onclick="return doclink('link-71', 'group', 'link-51');">group</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt><tt class="py-op">)</tt><tt class="py-op">)</tt> </tt>
<a name="L229"></a><tt class="py-lineno">229</tt> <tt class="py-line"> <tt class="py-keyword">elif</tt> <tt id="link-72" class="py-name"><a title="Bio.Translate.key" class="py-name" href="#" onclick="return doclink('link-72', 'key', 'link-40');">key</a></tt><tt class="py-op">==</tt><tt class="py-string">"JRNL"</tt><tt class="py-op">:</tt> </tt>
<a name="L230"></a><tt class="py-lineno">230</tt> <tt class="py-line"> <tt class="py-comment"># print key,tail</tt> </tt>
<a name="L231"></a><tt class="py-lineno">231</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-keyword">if</tt> <tt class="py-name">dict</tt><tt class="py-op">.</tt><tt id="link-73" class="py-name"><a title="Bio.Crystal.Crystal.has_key
Bio.EUtils.POM.ElementNode.has_key
Bio.GenBank.NCBIDictionary.has_key
Bio.PDB.AbstractPropertyMap.AbstractPropertyMap.has_key
Bio.PDB.FragmentMapper'.FragmentMapper.has_key
Bio.Prosite.ExPASyDictionary.has_key
Bio.Prosite.Prodoc.ExPASyDictionary.has_key
Bio.PubMed.Dictionary.has_key
Bio.SwissProt.SProt.ExPASyDictionary.has_key
Martel.Parser.MartelAttributeList.has_key" class="py-name" href="#" onclick="return doclink('link-73', 'has_key', 'link-44');">has_key</a></tt><tt class="py-op">(</tt><tt class="py-string">'journal'</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
<a name="L232"></a><tt class="py-lineno">232</tt> <tt class="py-line"> <tt class="py-name">dict</tt><tt class="py-op">[</tt><tt class="py-string">'journal'</tt><tt class="py-op">]</tt><tt class="py-op">+=</tt><tt class="py-name">tail</tt> </tt>
<a name="L233"></a><tt class="py-lineno">233</tt> <tt class="py-line"> <tt class="py-keyword">else</tt><tt class="py-op">:</tt> </tt>
<a name="L234"></a><tt class="py-lineno">234</tt> <tt class="py-line"> <tt class="py-name">dict</tt><tt class="py-op">[</tt><tt class="py-string">'journal'</tt><tt class="py-op">]</tt><tt class="py-op">=</tt><tt class="py-name">tail</tt> </tt>
<a name="L235"></a><tt class="py-lineno">235</tt> <tt class="py-line"> <tt class="py-keyword">elif</tt> <tt id="link-74" class="py-name"><a title="Bio.Translate.key" class="py-name" href="#" onclick="return doclink('link-74', 'key', 'link-40');">key</a></tt><tt class="py-op">==</tt><tt class="py-string">"AUTHOR"</tt><tt class="py-op">:</tt> </tt>
<a name="L236"></a><tt class="py-lineno">236</tt> <tt class="py-line"> <tt class="py-name">auth</tt> <tt class="py-op">=</tt> <tt id="link-75" class="py-name"><a title="Bio.PDB.parse_pdb_header'._nice_case" class="py-name" href="#" onclick="return doclink('link-75', '_nice_case', 'link-50');">_nice_case</a></tt><tt class="py-op">(</tt><tt id="link-76" class="py-name"><a title="Bio.PDB.parse_pdb_header'._chop_end_codes" class="py-name" href="#" onclick="return doclink('link-76', '_chop_end_codes', 'link-43');">_chop_end_codes</a></tt><tt class="py-op">(</tt><tt class="py-name">tail</tt><tt class="py-op">)</tt><tt class="py-op">)</tt> </tt>
<a name="L237"></a><tt class="py-lineno">237</tt> <tt class="py-line"> <tt class="py-keyword">if</tt> <tt class="py-name">dict</tt><tt class="py-op">.</tt><tt id="link-77" class="py-name"><a title="Bio.Crystal.Crystal.has_key
Bio.EUtils.POM.ElementNode.has_key
Bio.GenBank.NCBIDictionary.has_key
Bio.PDB.AbstractPropertyMap.AbstractPropertyMap.has_key
Bio.PDB.FragmentMapper'.FragmentMapper.has_key
Bio.Prosite.ExPASyDictionary.has_key
Bio.Prosite.Prodoc.ExPASyDictionary.has_key
Bio.PubMed.Dictionary.has_key
Bio.SwissProt.SProt.ExPASyDictionary.has_key
Martel.Parser.MartelAttributeList.has_key" class="py-name" href="#" onclick="return doclink('link-77', 'has_key', 'link-44');">has_key</a></tt><tt class="py-op">(</tt><tt class="py-string">'author'</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
<a name="L238"></a><tt class="py-lineno">238</tt> <tt class="py-line"> <tt class="py-name">dict</tt><tt class="py-op">[</tt><tt class="py-string">'author'</tt><tt class="py-op">]</tt><tt class="py-op">+=</tt><tt class="py-name">auth</tt> </tt>
<a name="L239"></a><tt class="py-lineno">239</tt> <tt class="py-line"> <tt class="py-keyword">else</tt><tt class="py-op">:</tt> </tt>
<a name="L240"></a><tt class="py-lineno">240</tt> <tt class="py-line"> <tt class="py-name">dict</tt><tt class="py-op">[</tt><tt class="py-string">'author'</tt><tt class="py-op">]</tt><tt class="py-op">=</tt><tt class="py-name">auth</tt> </tt>
<a name="L241"></a><tt class="py-lineno">241</tt> <tt class="py-line"> <tt class="py-keyword">elif</tt> <tt id="link-78" class="py-name"><a title="Bio.Translate.key" class="py-name" href="#" onclick="return doclink('link-78', 'key', 'link-40');">key</a></tt><tt class="py-op">==</tt><tt class="py-string">"REMARK"</tt><tt class="py-op">:</tt> </tt>
<a name="L242"></a><tt class="py-lineno">242</tt> <tt class="py-line"> <tt class="py-keyword">if</tt> <tt class="py-name">re</tt><tt class="py-op">.</tt><tt id="link-79" class="py-name"><a title="Bio.EUtils.DBIdsClient.DBIdsClient.search
Bio.EUtils.HistoryClient.HistoryClient.search
Bio.KDTree.KDTree.KDTree.search
Bio.PDB.NeighborSearch.NeighborSearch.search
Bio.Prosite.Pattern.Prosite.search
Bio.Restriction.Restriction.AbstractCut.search
Bio.Restriction.Restriction.RestrictionBatch.search
Bio.SCOP.search
Bio.builders.Search.search
Bio.formatdefs.search
Bio.formatdefs.search.search" class="py-name" href="#" onclick="return doclink('link-79', 'search', 'link-2');">search</a></tt><tt class="py-op">(</tt><tt class="py-string">"REMARK 2 RESOLUTION."</tt><tt class="py-op">,</tt><tt class="py-name">hh</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 class="py-name">r</tt><tt class="py-op">=</tt><tt id="link-80" class="py-name"><a title="Bio.PDB.parse_pdb_header'._chop_end_codes" class="py-name" href="#" onclick="return doclink('link-80', '_chop_end_codes', 'link-43');">_chop_end_codes</a></tt><tt class="py-op">(</tt><tt class="py-name">re</tt><tt class="py-op">.</tt><tt class="py-name">sub</tt><tt class="py-op">(</tt><tt class="py-string">"REMARK 2 RESOLUTION."</tt><tt class="py-op">,</tt><tt class="py-string">''</tt><tt class="py-op">,</tt><tt class="py-name">hh</tt><tt class="py-op">)</tt><tt class="py-op">)</tt> </tt>
<a name="L244"></a><tt class="py-lineno">244</tt> <tt class="py-line"> <tt class="py-name">r</tt><tt class="py-op">=</tt><tt class="py-name">re</tt><tt class="py-op">.</tt><tt class="py-name">sub</tt><tt class="py-op">(</tt><tt class="py-string">"\s+ANGSTROM.*"</tt><tt class="py-op">,</tt><tt class="py-string">""</tt><tt class="py-op">,</tt><tt class="py-name">r</tt><tt class="py-op">)</tt> </tt>
<a name="L245"></a><tt class="py-lineno">245</tt> <tt class="py-line"> <tt class="py-keyword">try</tt><tt class="py-op">:</tt> </tt>
<a name="L246"></a><tt class="py-lineno">246</tt> <tt class="py-line"> <tt class="py-name">dict</tt><tt class="py-op">[</tt><tt class="py-string">'resolution'</tt><tt class="py-op">]</tt><tt class="py-op">=</tt><tt class="py-name">float</tt><tt class="py-op">(</tt><tt class="py-name">r</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">except</tt><tt class="py-op">:</tt> </tt>
<a name="L248"></a><tt class="py-lineno">248</tt> <tt class="py-line"> <tt class="py-comment">#print 'nonstandard resolution',r</tt> </tt>
<a name="L249"></a><tt class="py-lineno">249</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-name">dict</tt><tt class="py-op">[</tt><tt class="py-string">'resolution'</tt><tt class="py-op">]</tt><tt class="py-op">=</tt><tt class="py-name">None</tt> </tt>
<a name="L250"></a><tt class="py-lineno">250</tt> <tt class="py-line"> <tt class="py-keyword">else</tt><tt class="py-op">:</tt> </tt>
<a name="L251"></a><tt class="py-lineno">251</tt> <tt class="py-line"> <tt class="py-comment"># print key</tt> </tt>
<a name="L252"></a><tt class="py-lineno">252</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-keyword">pass</tt> </tt>
<a name="L253"></a><tt class="py-lineno">253</tt> <tt class="py-line"> <tt class="py-keyword">if</tt> <tt class="py-name">dict</tt><tt class="py-op">[</tt><tt class="py-string">'structure_method'</tt><tt class="py-op">]</tt><tt class="py-op">==</tt><tt class="py-string">'unknown'</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">if</tt> <tt class="py-name">dict</tt><tt class="py-op">[</tt><tt class="py-string">'resolution'</tt><tt class="py-op">]</tt><tt class="py-op">></tt><tt class="py-number">0.0</tt><tt class="py-op">:</tt> <tt class="py-name">dict</tt><tt class="py-op">[</tt><tt class="py-string">'structure_method'</tt><tt class="py-op">]</tt><tt class="py-op">=</tt><tt class="py-string">'x-ray diffraction'</tt> </tt>
<a name="L255"></a><tt class="py-lineno">255</tt> <tt class="py-line"> <tt class="py-keyword">return</tt> <tt class="py-name">dict</tt> </tt>
</div><a name="L256"></a><tt class="py-lineno">256</tt> <tt class="py-line"> </tt>
<a name="L257"></a><tt class="py-lineno">257</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="L258"></a><tt class="py-lineno">258</tt> <tt class="py-line"> <tt class="py-string">"""</tt> </tt>
<a name="L259"></a><tt class="py-lineno">259</tt> <tt class="py-line"><tt class="py-string"> Reads a PDB file passed as argument, parses its header, extracts</tt> </tt>
<a name="L260"></a><tt class="py-lineno">260</tt> <tt class="py-line"><tt class="py-string"> some data and returns it as a dictionary.</tt> </tt>
<a name="L261"></a><tt class="py-lineno">261</tt> <tt class="py-line"><tt class="py-string"> """</tt> </tt>
<a name="L262"></a><tt class="py-lineno">262</tt> <tt class="py-line"> <tt class="py-name">filename</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>
<a name="L263"></a><tt class="py-lineno">263</tt> <tt class="py-line"> <tt class="py-name">file</tt> <tt class="py-op">=</tt> <tt id="link-81" class="py-name"><a title="Bio.Mindy.FlatDB.open
Bio.Mindy.open" class="py-name" href="#" onclick="return doclink('link-81', 'open', 'link-29');">open</a></tt><tt class="py-op">(</tt><tt class="py-name">filename</tt><tt class="py-op">,</tt><tt class="py-string">'r'</tt><tt class="py-op">)</tt> </tt>
<a name="L264"></a><tt class="py-lineno">264</tt> <tt class="py-line"> <tt class="py-name">dict</tt> <tt class="py-op">=</tt> <tt id="link-82" 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-82', 'parse_pdb_header', 'link-82');">parse_pdb_header</a></tt><tt class="py-op">(</tt><tt class="py-name">file</tt><tt class="py-op">)</tt> </tt>
<a name="L265"></a><tt class="py-lineno">265</tt> <tt class="py-line"> </tt>
<a name="L266"></a><tt class="py-lineno">266</tt> <tt class="py-line"> <tt class="py-comment"># print the dictionary</tt> </tt>
<a name="L267"></a><tt class="py-lineno">267</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-keyword">for</tt> <tt id="link-83" class="py-name" targets="Variable Bio.EUtils.setup.d=Bio.EUtils.setup-module.html#d"><a title="Bio.EUtils.setup.d" class="py-name" href="#" onclick="return doclink('link-83', 'd', 'link-83');">d</a></tt> <tt class="py-keyword">in</tt> <tt class="py-name">dict</tt><tt class="py-op">.</tt><tt id="link-84" class="py-name" targets="Method Bio.Crystal.Crystal.keys()=Bio.Crystal.Crystal-class.html#keys,Method Bio.EUtils.MultiDict._BaseMultiDict.keys()=Bio.EUtils.MultiDict._BaseMultiDict-class.html#keys,Method Bio.GenBank.NCBIDictionary.keys()=Bio.GenBank.NCBIDictionary-class.html#keys,Method Bio.Mindy.BaseDB.DictLookup.keys()=Bio.Mindy.BaseDB.DictLookup-class.html#keys,Method Bio.Mindy.BaseDB.OpenDB.keys()=Bio.Mindy.BaseDB.OpenDB-class.html#keys,Method Bio.Mindy.BerkeleyDB.PrimaryNamespace.keys()=Bio.Mindy.BerkeleyDB.PrimaryNamespace-class.html#keys,Method Bio.Mindy.BerkeleyDB.SecondaryNamespace.keys()=Bio.Mindy.BerkeleyDB.SecondaryNamespace-class.html#keys,Method Bio.Mindy.FlatDB.PrimaryNamespace.keys()=Bio.Mindy.FlatDB.PrimaryNamespace-class.html#keys,Method Bio.Mindy.FlatDB.PrimaryTable.keys()=Bio.Mindy.FlatDB.PrimaryTable-class.html#keys,Method Bio.Mindy.FlatDB.SecondaryNamespace.keys()=Bio.Mindy.FlatDB.SecondaryNamespace-class.html#keys,Method Bio.Mindy.FlatDB.SecondaryTable.keys()=Bio.Mindy.FlatDB.SecondaryTable-class.html#keys,Method Bio.PDB.AbstractPropertyMap.AbstractPropertyMap.keys()=Bio.PDB.AbstractPropertyMap.AbstractPropertyMap-class.html#keys,Method Bio.Prosite.ExPASyDictionary.keys()=Bio.Prosite.ExPASyDictionary-class.html#keys,Method Bio.Prosite.Prodoc.ExPASyDictionary.keys()=Bio.Prosite.Prodoc.ExPASyDictionary-class.html#keys,Method Bio.PubMed.Dictionary.keys()=Bio.PubMed.Dictionary-class.html#keys,Method Bio.SwissProt.SProt.Dictionary.keys()=Bio.SwissProt.SProt.Dictionary-class.html#keys,Method Bio.SwissProt.SProt.ExPASyDictionary.keys()=Bio.SwissProt.SProt.ExPASyDictionary-class.html#keys,Method Bio.config.Registry.Registry.keys()=Bio.config.Registry.Registry-class.html#keys,Method BioSQL.BioSeqDatabase.BioSeqDatabase.keys()=BioSQL.BioSeqDatabase.BioSeqDatabase-class.html#keys,Method BioSQL.BioSeqDatabase.DBServer.keys()=BioSQL.BioSeqDatabase.DBServer-class.html#keys,Method Martel.Parser.MartelAttributeList.keys()=Martel.Parser.MartelAttributeList-class.html#keys"><a title="Bio.Crystal.Crystal.keys
Bio.EUtils.MultiDict._BaseMultiDict.keys
Bio.GenBank.NCBIDictionary.keys
Bio.Mindy.BaseDB.DictLookup.keys
Bio.Mindy.BaseDB.OpenDB.keys
Bio.Mindy.BerkeleyDB.PrimaryNamespace.keys
Bio.Mindy.BerkeleyDB.SecondaryNamespace.keys
Bio.Mindy.FlatDB.PrimaryNamespace.keys
Bio.Mindy.FlatDB.PrimaryTable.keys
Bio.Mindy.FlatDB.SecondaryNamespace.keys
Bio.Mindy.FlatDB.SecondaryTable.keys
Bio.PDB.AbstractPropertyMap.AbstractPropertyMap.keys
Bio.Prosite.ExPASyDictionary.keys
Bio.Prosite.Prodoc.ExPASyDictionary.keys
Bio.PubMed.Dictionary.keys
Bio.SwissProt.SProt.Dictionary.keys
Bio.SwissProt.SProt.ExPASyDictionary.keys
Bio.config.Registry.Registry.keys
BioSQL.BioSeqDatabase.BioSeqDatabase.keys
BioSQL.BioSeqDatabase.DBServer.keys
Martel.Parser.MartelAttributeList.keys" class="py-name" href="#" onclick="return doclink('link-84', 'keys', 'link-84');">keys</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
<a name="L268"></a><tt class="py-lineno">268</tt> <tt class="py-line"> <tt class="py-keyword">print</tt> <tt class="py-string">"-"</tt><tt class="py-op">*</tt><tt class="py-number">40</tt> </tt>
<a name="L269"></a><tt class="py-lineno">269</tt> <tt class="py-line"> <tt class="py-keyword">print</tt> <tt id="link-85" class="py-name"><a title="Bio.EUtils.setup.d" class="py-name" href="#" onclick="return doclink('link-85', 'd', 'link-83');">d</a></tt> </tt>
<a name="L270"></a><tt class="py-lineno">270</tt> <tt class="py-line"> <tt class="py-keyword">print</tt> <tt class="py-name">dict</tt><tt class="py-op">[</tt><tt id="link-86" class="py-name"><a title="Bio.EUtils.setup.d" class="py-name" href="#" onclick="return doclink('link-86', 'd', 'link-83');">d</a></tt><tt class="py-op">]</tt> </tt>
<a name="L271"></a><tt class="py-lineno">271</tt> <tt class="py-line"> </tt><script type="text/javascript">
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