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<a href="Bio-module.html">Package Bio</a> ::
Package Ndb
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<h1 class="epydoc">Source Code for <a href="Bio.Ndb-module.html">Package Bio.Ndb</a></h1>
<pre class="py-src">
<a name="L1"></a><tt class="py-lineno"> 1</tt> <tt class="py-line"><tt class="py-comment"># Copyright 2002 by Katharine Lindner. All rights reserved.</tt> </tt>
<a name="L2"></a><tt class="py-lineno"> 2</tt> <tt class="py-line"><tt class="py-comment"></tt><tt class="py-comment"># This code is part of the Biopython distribution and governed by its</tt> </tt>
<a name="L3"></a><tt class="py-lineno"> 3</tt> <tt class="py-line"><tt class="py-comment"></tt><tt class="py-comment"># license. Please see the LICENSE file that should have been included</tt> </tt>
<a name="L4"></a><tt class="py-lineno"> 4</tt> <tt class="py-line"><tt class="py-comment"></tt><tt class="py-comment"># as part of this package.</tt> </tt>
<a name="L5"></a><tt class="py-lineno"> 5</tt> <tt class="py-line"><tt class="py-comment"></tt> </tt>
<a name="L6"></a><tt class="py-lineno"> 6</tt> <tt class="py-line"><tt class="py-docstring">"""</tt> </tt>
<a name="L7"></a><tt class="py-lineno"> 7</tt> <tt class="py-line"><tt class="py-docstring">This module provides code to work with html files from NDB.</tt> </tt>
<a name="L8"></a><tt class="py-lineno"> 8</tt> <tt class="py-line"><tt class="py-docstring">http://ndbserver.rutgers.edu/NDB/structure-finder/ndb/index.html</tt> </tt>
<a name="L9"></a><tt class="py-lineno"> 9</tt> <tt class="py-line"><tt class="py-docstring"></tt> </tt>
<a name="L10"></a><tt class="py-lineno"> 10</tt> <tt class="py-line"><tt class="py-docstring"></tt> </tt>
<a name="L11"></a><tt class="py-lineno"> 11</tt> <tt class="py-line"><tt class="py-docstring">Classes:</tt> </tt>
<a name="L12"></a><tt class="py-lineno"> 12</tt> <tt class="py-line"><tt class="py-docstring">Record Holds NDB sequence data.</tt> </tt>
<a name="L13"></a><tt class="py-lineno"> 13</tt> <tt class="py-line"><tt class="py-docstring">NdbParser Parses NDB sequence data into a Record object.</tt> </tt>
<a name="L14"></a><tt class="py-lineno"> 14</tt> <tt class="py-line"><tt class="py-docstring"></tt> </tt>
<a name="L15"></a><tt class="py-lineno"> 15</tt> <tt class="py-line"><tt class="py-docstring">The algorithm is based on a state machine because the record has multiple </tt> </tt>
<a name="L16"></a><tt class="py-lineno"> 16</tt> <tt class="py-line"><tt class="py-docstring">sections and the handling of tags varies depending on the section. </tt> </tt>
<a name="L17"></a><tt class="py-lineno"> 17</tt> <tt class="py-line"><tt class="py-docstring">Citations have their own state machine.</tt> </tt>
<a name="L18"></a><tt class="py-lineno"> 18</tt> <tt class="py-line"><tt class="py-docstring">"""</tt> </tt>
<a name="L19"></a><tt class="py-lineno"> 19</tt> <tt class="py-line"> </tt>
<a name="L20"></a><tt class="py-lineno"> 20</tt> <tt class="py-line"><tt class="py-keyword">from</tt> <tt class="py-name">types</tt> <tt class="py-keyword">import</tt> <tt class="py-op">*</tt> </tt>
<a name="L21"></a><tt class="py-lineno"> 21</tt> <tt class="py-line"><tt class="py-keyword">import</tt> <tt class="py-name">string</tt> </tt>
<a name="L22"></a><tt class="py-lineno"> 22</tt> <tt class="py-line"><tt class="py-keyword">from</tt> <tt id="link-0" class="py-name" targets="Package Bio=Bio-module.html"><a title="Bio" class="py-name" href="#" onclick="return doclink('link-0', 'Bio', 'link-0');">Bio</a></tt> <tt class="py-keyword">import</tt> <tt id="link-1" class="py-name" targets="Module Bio.File=Bio.File-module.html"><a title="Bio.File" class="py-name" href="#" onclick="return doclink('link-1', 'File', 'link-1');">File</a></tt> </tt>
<a name="L23"></a><tt class="py-lineno"> 23</tt> <tt class="py-line"><tt class="py-keyword">from</tt> <tt id="link-2" class="py-name"><a title="Bio" class="py-name" href="#" onclick="return doclink('link-2', 'Bio', 'link-0');">Bio</a></tt> <tt class="py-keyword">import</tt> <tt id="link-3" class="py-name" targets="Module Bio.Index=Bio.Index-module.html,Class Bio.SCOP.Cla.Index=Bio.SCOP.Cla.Index-class.html"><a title="Bio.Index
Bio.SCOP.Cla.Index" class="py-name" href="#" onclick="return doclink('link-3', 'Index', 'link-3');">Index</a></tt> </tt>
<a name="L24"></a><tt class="py-lineno"> 24</tt> <tt class="py-line"><tt class="py-keyword">from</tt> <tt id="link-4" class="py-name"><a title="Bio" class="py-name" href="#" onclick="return doclink('link-4', 'Bio', 'link-0');">Bio</a></tt><tt class="py-op">.</tt><tt id="link-5" class="py-name" targets="Package Bio.Crystal=Bio.Crystal-module.html,Class Bio.Crystal.Crystal=Bio.Crystal.Crystal-class.html"><a title="Bio.Crystal
Bio.Crystal.Crystal" class="py-name" href="#" onclick="return doclink('link-5', 'Crystal', 'link-5');">Crystal</a></tt> <tt class="py-keyword">import</tt> <tt id="link-6" class="py-name" targets="Class Bio.Crystal.Hetero=Bio.Crystal.Hetero-class.html"><a title="Bio.Crystal.Hetero" class="py-name" href="#" onclick="return doclink('link-6', 'Hetero', 'link-6');">Hetero</a></tt> </tt>
<a name="L25"></a><tt class="py-lineno"> 25</tt> <tt class="py-line"><tt class="py-keyword">from</tt> <tt id="link-7" class="py-name"><a title="Bio" class="py-name" href="#" onclick="return doclink('link-7', 'Bio', 'link-0');">Bio</a></tt><tt class="py-op">.</tt><tt id="link-8" class="py-name"><a title="Bio.Crystal
Bio.Crystal.Crystal" class="py-name" href="#" onclick="return doclink('link-8', 'Crystal', 'link-5');">Crystal</a></tt> <tt class="py-keyword">import</tt> <tt id="link-9" class="py-name" targets="Class Bio.Crystal.Chain=Bio.Crystal.Chain-class.html,Class Bio.Nexus.Nodes.Chain=Bio.Nexus.Nodes.Chain-class.html,Module Bio.PDB.Chain=Bio.PDB.Chain-module.html,Class Bio.PDB.Chain.Chain=Bio.PDB.Chain.Chain-class.html"><a title="Bio.Crystal.Chain
Bio.Nexus.Nodes.Chain
Bio.PDB.Chain
Bio.PDB.Chain.Chain" class="py-name" href="#" onclick="return doclink('link-9', 'Chain', 'link-9');">Chain</a></tt> </tt>
<a name="L26"></a><tt class="py-lineno"> 26</tt> <tt class="py-line"><tt class="py-keyword">from</tt> <tt id="link-10" class="py-name"><a title="Bio" class="py-name" href="#" onclick="return doclink('link-10', 'Bio', 'link-0');">Bio</a></tt><tt class="py-op">.</tt><tt id="link-11" class="py-name"><a title="Bio.Crystal
Bio.Crystal.Crystal" class="py-name" href="#" onclick="return doclink('link-11', 'Crystal', 'link-5');">Crystal</a></tt> <tt class="py-keyword">import</tt> <tt id="link-12" class="py-name"><a title="Bio.Crystal
Bio.Crystal.Crystal" class="py-name" href="#" onclick="return doclink('link-12', 'Crystal', 'link-5');">Crystal</a></tt> </tt>
<a name="L27"></a><tt class="py-lineno"> 27</tt> <tt class="py-line"><tt class="py-keyword">from</tt> <tt id="link-13" class="py-name"><a title="Bio" class="py-name" href="#" onclick="return doclink('link-13', 'Bio', 'link-0');">Bio</a></tt><tt class="py-op">.</tt><tt id="link-14" class="py-name" targets="Module Bio.SeqFeature=Bio.SeqFeature-module.html,Class Bio.SeqFeature.SeqFeature=Bio.SeqFeature.SeqFeature-class.html"><a title="Bio.SeqFeature
Bio.SeqFeature.SeqFeature" class="py-name" href="#" onclick="return doclink('link-14', 'SeqFeature', 'link-14');">SeqFeature</a></tt> <tt class="py-keyword">import</tt> <tt id="link-15" class="py-name" targets="Class Bio.GenBank.Record.Reference=Bio.GenBank.Record.Reference-class.html,Class Bio.Prosite.Prodoc.Reference=Bio.Prosite.Prodoc.Reference-class.html,Class Bio.SeqFeature.Reference=Bio.SeqFeature.Reference-class.html,Class Bio.SwissProt.SProt.Reference=Bio.SwissProt.SProt.Reference-class.html"><a title="Bio.GenBank.Record.Reference
Bio.Prosite.Prodoc.Reference
Bio.SeqFeature.Reference
Bio.SwissProt.SProt.Reference" class="py-name" href="#" onclick="return doclink('link-15', 'Reference', 'link-15');">Reference</a></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">sgmllib</tt> </tt>
<a name="L30"></a><tt class="py-lineno"> 30</tt> <tt class="py-line"><tt class="py-keyword">from</tt> <tt id="link-16" class="py-name"><a title="Bio" class="py-name" href="#" onclick="return doclink('link-16', 'Bio', 'link-0');">Bio</a></tt><tt class="py-op">.</tt><tt id="link-17" class="py-name" targets="Module Bio.ParserSupport=Bio.ParserSupport-module.html"><a title="Bio.ParserSupport" class="py-name" href="#" onclick="return doclink('link-17', 'ParserSupport', 'link-17');">ParserSupport</a></tt> <tt class="py-keyword">import</tt> <tt class="py-op">*</tt> </tt>
<a name="L31"></a><tt class="py-lineno"> 31</tt> <tt class="py-line"><tt class="py-keyword">from</tt> <tt id="link-18" class="py-name"><a title="Bio" class="py-name" href="#" onclick="return doclink('link-18', 'Bio', 'link-0');">Bio</a></tt><tt class="py-op">.</tt><tt id="link-19" class="py-name"><a title="Bio.SeqFeature
Bio.SeqFeature.SeqFeature" class="py-name" href="#" onclick="return doclink('link-19', 'SeqFeature', 'link-14');">SeqFeature</a></tt> <tt class="py-keyword">import</tt> <tt id="link-20" class="py-name"><a title="Bio.GenBank.Record.Reference
Bio.Prosite.Prodoc.Reference
Bio.SeqFeature.Reference
Bio.SwissProt.SProt.Reference" class="py-name" href="#" onclick="return doclink('link-20', 'Reference', 'link-15');">Reference</a></tt> </tt>
<a name="L32"></a><tt class="py-lineno"> 32</tt> <tt class="py-line"> </tt>
<a name="L33"></a><tt class="py-lineno"> 33</tt> <tt class="py-line"> </tt>
<a name="Record"></a><div id="Record-def"><a name="L34"></a><tt class="py-lineno"> 34</tt> <a class="py-toggle" href="#" id="Record-toggle" onclick="return toggle('Record');">-</a><tt class="py-line"><tt class="py-keyword">class</tt> <a class="py-def-name" href="Bio.Ndb.Record-class.html">Record</a><tt class="py-op">(</tt> <tt class="py-base-class">dict</tt> <tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="Record-collapsed" style="display:none;" pad="+++" indent="++++"></div><div id="Record-expanded"><a name="L35"></a><tt class="py-lineno"> 35</tt> <tt class="py-line"> </tt>
<a name="Record.__init__"></a><div id="Record.__init__-def"><a name="L36"></a><tt class="py-lineno"> 36</tt> <a class="py-toggle" href="#" id="Record.__init__-toggle" onclick="return toggle('Record.__init__');">-</a><tt class="py-line"> <tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.Ndb.Record-class.html#__init__">__init__</a><tt class="py-op">(</tt> <tt class="py-param">self</tt> <tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="Record.__init__-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="Record.__init__-expanded"><a name="L37"></a><tt class="py-lineno"> 37</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">[</tt> <tt class="py-string">'Id'</tt> <tt class="py-op">]</tt> <tt class="py-op">=</tt> <tt class="py-string">''</tt> </tt>
<a name="L38"></a><tt class="py-lineno"> 38</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">[</tt> <tt class="py-string">'Features'</tt> <tt class="py-op">]</tt> <tt class="py-op">=</tt> <tt class="py-string">''</tt> </tt>
<a name="L39"></a><tt class="py-lineno"> 39</tt> <tt class="py-line"> <tt class="py-name">self</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>
<a name="L40"></a><tt class="py-lineno"> 40</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">[</tt> <tt class="py-string">'Sequence'</tt> <tt class="py-op">]</tt> <tt class="py-op">=</tt> <tt id="link-21" class="py-name"><a title="Bio.Crystal
Bio.Crystal.Crystal" class="py-name" href="#" onclick="return doclink('link-21', 'Crystal', 'link-5');">Crystal</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="L41"></a><tt class="py-lineno"> 41</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">[</tt> <tt class="py-string">'Citation'</tt> <tt class="py-op">]</tt> <tt class="py-op">=</tt> <tt id="link-22" class="py-name"><a title="Bio.GenBank.Record.Reference
Bio.Prosite.Prodoc.Reference
Bio.SeqFeature.Reference
Bio.SwissProt.SProt.Reference" class="py-name" href="#" onclick="return doclink('link-22', 'Reference', 'link-15');">Reference</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
<a name="L42"></a><tt class="py-lineno"> 42</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">[</tt> <tt class="py-string">'Space Group'</tt> <tt class="py-op">]</tt> <tt class="py-op">=</tt> <tt class="py-string">''</tt> </tt>
<a name="L43"></a><tt class="py-lineno"> 43</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">[</tt> <tt class="py-string">'Cell Constants'</tt> <tt class="py-op">]</tt> <tt class="py-op">=</tt> <tt class="py-op">{</tt><tt class="py-op">}</tt> </tt>
<a name="L44"></a><tt class="py-lineno"> 44</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">[</tt> <tt class="py-string">'Crystallization Conditions'</tt> <tt class="py-op">]</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">self</tt><tt class="py-op">[</tt> <tt class="py-string">'Refinement'</tt> <tt class="py-op">]</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-name">self</tt><tt class="py-op">[</tt> <tt class="py-string">'Coordinates'</tt> <tt class="py-op">]</tt> <tt class="py-op">=</tt> <tt class="py-string">''</tt> </tt>
</div><a name="L47"></a><tt class="py-lineno"> 47</tt> <tt class="py-line"> </tt>
<a name="Record.__str__"></a><div id="Record.__str__-def"><a name="L48"></a><tt class="py-lineno"> 48</tt> <a class="py-toggle" href="#" id="Record.__str__-toggle" onclick="return toggle('Record.__str__');">-</a><tt class="py-line"> <tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.Ndb.Record-class.html#__str__">__str__</a><tt class="py-op">(</tt> <tt class="py-param">self</tt> <tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="Record.__str__-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="Record.__str__-expanded"><a name="L49"></a><tt class="py-lineno"> 49</tt> <tt class="py-line"> <tt id="link-23" 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-23', 'keys', 'link-23');">keys</a></tt> <tt class="py-op">=</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-24" class="py-name"><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-24', 'keys', 'link-23');">keys</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
<a name="L50"></a><tt class="py-lineno"> 50</tt> <tt class="py-line"> <tt id="link-25" class="py-name"><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-25', 'keys', 'link-23');">keys</a></tt><tt class="py-op">.</tt><tt id="link-26" class="py-name" targets="Method Bio.PDB.Residue.DisorderedResidue.sort()=Bio.PDB.Residue.DisorderedResidue-class.html#sort,Method Bio.PDB.Residue.Residue.sort()=Bio.PDB.Residue.Residue-class.html#sort,Method Bio.Sequencing.Ace.ACEFileRecord.sort()=Bio.Sequencing.Ace.ACEFileRecord-class.html#sort"><a title="Bio.PDB.Residue.DisorderedResidue.sort
Bio.PDB.Residue.Residue.sort
Bio.Sequencing.Ace.ACEFileRecord.sort" class="py-name" href="#" onclick="return doclink('link-26', 'sort', 'link-26');">sort</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
<a name="L51"></a><tt class="py-lineno"> 51</tt> <tt class="py-line"> <tt class="py-name">out</tt> <tt class="py-op">=</tt> <tt class="py-string">''</tt> </tt>
<a name="L52"></a><tt class="py-lineno"> 52</tt> <tt class="py-line"> <tt class="py-keyword">for</tt> <tt id="link-27" 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-27', 'key', 'link-27');">key</a></tt> <tt class="py-keyword">in</tt> <tt id="link-28" class="py-name"><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-28', 'keys', 'link-23');">keys</a></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">val</tt> <tt class="py-op">=</tt> <tt class="py-name">self</tt><tt class="py-op">[</tt> <tt id="link-29" class="py-name"><a title="Bio.Translate.key" class="py-name" href="#" onclick="return doclink('link-29', 'key', 'link-27');">key</a></tt> <tt class="py-op">]</tt> </tt>
<a name="L54"></a><tt class="py-lineno"> 54</tt> <tt class="py-line"> <tt class="py-keyword">if</tt><tt class="py-op">(</tt> <tt id="link-30" 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-30', 'type', 'link-30');">type</a></tt><tt class="py-op">(</tt> <tt class="py-name">val</tt> <tt class="py-op">)</tt> <tt class="py-op">==</tt> <tt id="link-31" class="py-name"><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-31', 'type', 'link-30');">type</a></tt><tt class="py-op">(</tt> <tt class="py-op">[</tt><tt class="py-op">]</tt> <tt class="py-op">)</tt> <tt class="py-op">)</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">out</tt> <tt class="py-op">=</tt> <tt class="py-name">out</tt> <tt class="py-op">+</tt> <tt class="py-string">'\n%s\n'</tt> <tt class="py-op">%</tt> <tt id="link-32" class="py-name"><a title="Bio.Translate.key" class="py-name" href="#" onclick="return doclink('link-32', 'key', 'link-27');">key</a></tt> </tt>
<a name="L56"></a><tt class="py-lineno"> 56</tt> <tt class="py-line"> <tt class="py-keyword">for</tt> <tt id="link-33" class="py-name" targets="Method Bio.EUtils.Datatypes.DBIds.item()=Bio.EUtils.Datatypes.DBIds-class.html#item"><a title="Bio.EUtils.Datatypes.DBIds.item" class="py-name" href="#" onclick="return doclink('link-33', 'item', 'link-33');">item</a></tt> <tt class="py-keyword">in</tt> <tt class="py-name">val</tt><tt class="py-op">:</tt> </tt>
<a name="L57"></a><tt class="py-lineno"> 57</tt> <tt class="py-line"> <tt class="py-name">out</tt> <tt class="py-op">=</tt> <tt class="py-name">out</tt> <tt class="py-op">+</tt> <tt class="py-string">'%s\n'</tt> <tt class="py-op">%</tt> <tt id="link-34" class="py-name"><a title="Bio.EUtils.Datatypes.DBIds.item" class="py-name" href="#" onclick="return doclink('link-34', 'item', 'link-33');">item</a></tt> </tt>
<a name="L58"></a><tt class="py-lineno"> 58</tt> <tt class="py-line"> </tt>
<a name="L59"></a><tt class="py-lineno"> 59</tt> <tt class="py-line"> <tt class="py-keyword">elif</tt><tt class="py-op">(</tt> <tt id="link-35" class="py-name"><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-35', 'type', 'link-30');">type</a></tt><tt class="py-op">(</tt> <tt class="py-name">val</tt> <tt class="py-op">)</tt> <tt class="py-op">==</tt> <tt id="link-36" class="py-name"><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-36', 'type', 'link-30');">type</a></tt><tt class="py-op">(</tt> <tt class="py-op">{</tt><tt class="py-op">}</tt> <tt class="py-op">)</tt> <tt class="py-op">)</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">out</tt> <tt class="py-op">=</tt> <tt class="py-name">out</tt> <tt class="py-op">+</tt> <tt class="py-string">'\n%s\n'</tt> <tt class="py-op">%</tt> <tt id="link-37" class="py-name"><a title="Bio.Translate.key" class="py-name" href="#" onclick="return doclink('link-37', 'key', 'link-27');">key</a></tt> </tt>
<a name="L61"></a><tt class="py-lineno"> 61</tt> <tt class="py-line"> <tt class="py-name">subkeys</tt> <tt class="py-op">=</tt> <tt class="py-name">val</tt><tt class="py-op">.</tt><tt id="link-38" class="py-name"><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-38', 'keys', 'link-23');">keys</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
<a name="L62"></a><tt class="py-lineno"> 62</tt> <tt class="py-line"> <tt class="py-name">subkeys</tt><tt class="py-op">.</tt><tt id="link-39" class="py-name"><a title="Bio.PDB.Residue.DisorderedResidue.sort
Bio.PDB.Residue.Residue.sort
Bio.Sequencing.Ace.ACEFileRecord.sort" class="py-name" href="#" onclick="return doclink('link-39', 'sort', 'link-26');">sort</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
<a name="L63"></a><tt class="py-lineno"> 63</tt> <tt class="py-line"> <tt class="py-keyword">for</tt> <tt id="link-40" class="py-name"><a title="Bio.EUtils.Datatypes.DBIds.item" class="py-name" href="#" onclick="return doclink('link-40', 'item', 'link-33');">item</a></tt> <tt class="py-keyword">in</tt> <tt class="py-name">subkeys</tt><tt class="py-op">:</tt> </tt>
<a name="L64"></a><tt class="py-lineno"> 64</tt> <tt class="py-line"> <tt class="py-name">out</tt> <tt class="py-op">=</tt> <tt class="py-name">out</tt> <tt class="py-op">+</tt> <tt class="py-string">'%s : %s\n'</tt> <tt class="py-op">%</tt> <tt class="py-op">(</tt> <tt id="link-41" class="py-name"><a title="Bio.EUtils.Datatypes.DBIds.item" class="py-name" href="#" onclick="return doclink('link-41', 'item', 'link-33');">item</a></tt><tt class="py-op">,</tt> <tt class="py-name">val</tt><tt class="py-op">[</tt> <tt id="link-42" class="py-name"><a title="Bio.EUtils.Datatypes.DBIds.item" class="py-name" href="#" onclick="return doclink('link-42', 'item', 'link-33');">item</a></tt> <tt class="py-op">]</tt> <tt class="py-op">)</tt> </tt>
<a name="L65"></a><tt class="py-lineno"> 65</tt> <tt class="py-line"> <tt class="py-keyword">elif</tt><tt class="py-op">(</tt> <tt class="py-name">isinstance</tt><tt class="py-op">(</tt> <tt class="py-name">val</tt><tt class="py-op">,</tt> <tt class="py-name">dict</tt> <tt class="py-op">)</tt> <tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
<a name="L66"></a><tt class="py-lineno"> 66</tt> <tt class="py-line"> <tt class="py-name">out</tt> <tt class="py-op">=</tt> <tt class="py-name">out</tt> <tt class="py-op">+</tt> <tt class="py-string">'\n%s\n'</tt> <tt class="py-op">%</tt> <tt id="link-43" class="py-name"><a title="Bio.Translate.key" class="py-name" href="#" onclick="return doclink('link-43', 'key', 'link-27');">key</a></tt> </tt>
<a name="L67"></a><tt class="py-lineno"> 67</tt> <tt class="py-line"> <tt class="py-name">subkeys</tt> <tt class="py-op">=</tt> <tt class="py-name">val</tt><tt class="py-op">.</tt><tt id="link-44" class="py-name"><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-44', 'keys', 'link-23');">keys</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
<a name="L68"></a><tt class="py-lineno"> 68</tt> <tt class="py-line"> <tt class="py-name">subkeys</tt><tt class="py-op">.</tt><tt id="link-45" class="py-name"><a title="Bio.PDB.Residue.DisorderedResidue.sort
Bio.PDB.Residue.Residue.sort
Bio.Sequencing.Ace.ACEFileRecord.sort" class="py-name" href="#" onclick="return doclink('link-45', 'sort', 'link-26');">sort</a></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">for</tt> <tt id="link-46" class="py-name"><a title="Bio.EUtils.Datatypes.DBIds.item" class="py-name" href="#" onclick="return doclink('link-46', 'item', 'link-33');">item</a></tt> <tt class="py-keyword">in</tt> <tt class="py-name">subkeys</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">out</tt> <tt class="py-op">=</tt> <tt class="py-name">out</tt> <tt class="py-op">+</tt> <tt class="py-string">'%s : %s\n'</tt> <tt class="py-op">%</tt> <tt class="py-op">(</tt> <tt id="link-47" class="py-name"><a title="Bio.EUtils.Datatypes.DBIds.item" class="py-name" href="#" onclick="return doclink('link-47', 'item', 'link-33');">item</a></tt><tt class="py-op">,</tt> <tt class="py-name">val</tt><tt class="py-op">[</tt> <tt id="link-48" class="py-name"><a title="Bio.EUtils.Datatypes.DBIds.item" class="py-name" href="#" onclick="return doclink('link-48', 'item', 'link-33');">item</a></tt> <tt class="py-op">]</tt> <tt class="py-op">)</tt> </tt>
<a name="L71"></a><tt class="py-lineno"> 71</tt> <tt class="py-line"> </tt>
<a name="L72"></a><tt class="py-lineno"> 72</tt> <tt class="py-line"> <tt class="py-keyword">else</tt><tt class="py-op">:</tt> </tt>
<a name="L73"></a><tt class="py-lineno"> 73</tt> <tt class="py-line"> <tt class="py-name">out</tt> <tt class="py-op">=</tt> <tt class="py-name">out</tt> <tt class="py-op">+</tt> <tt class="py-string">'%s: %s\n'</tt> <tt class="py-op">%</tt> <tt class="py-op">(</tt> <tt id="link-49" class="py-name"><a title="Bio.Translate.key" class="py-name" href="#" onclick="return doclink('link-49', 'key', 'link-27');">key</a></tt><tt class="py-op">,</tt> <tt class="py-name">self</tt><tt class="py-op">[</tt> <tt id="link-50" class="py-name"><a title="Bio.Translate.key" class="py-name" href="#" onclick="return doclink('link-50', 'key', 'link-27');">key</a></tt> <tt class="py-op">]</tt> <tt class="py-op">)</tt> </tt>
<a name="L74"></a><tt class="py-lineno"> 74</tt> <tt class="py-line"> <tt class="py-keyword">return</tt> <tt class="py-name">out</tt> </tt>
</div></div><a name="L75"></a><tt class="py-lineno"> 75</tt> <tt class="py-line"> </tt>
<a name="_parse_constants"></a><div id="_parse_constants-def"><a name="L76"></a><tt class="py-lineno"> 76</tt> <a class="py-toggle" href="#" id="_parse_constants-toggle" onclick="return toggle('_parse_constants');">-</a><tt class="py-line"><tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.Ndb-module.html#_parse_constants">_parse_constants</a><tt class="py-op">(</tt> <tt class="py-param">text</tt> <tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="_parse_constants-collapsed" style="display:none;" pad="+++" indent="++++"></div><div id="_parse_constants-expanded"><a name="L77"></a><tt class="py-lineno"> 77</tt> <tt class="py-line"> <tt id="link-51" class="py-name" targets="Method Bio.Crystal.Crystal.items()=Bio.Crystal.Crystal-class.html#items,Method Bio.EUtils.MultiDict._BaseMultiDict.items()=Bio.EUtils.MultiDict._BaseMultiDict-class.html#items,Variable Bio.Entrez.SerialSet.items=Bio.Entrez.SerialSet-module.html#items,Method Bio.GenBank.NCBIDictionary.items()=Bio.GenBank.NCBIDictionary-class.html#items,Method Bio.Mindy.BaseDB.DictLookup.items()=Bio.Mindy.BaseDB.DictLookup-class.html#items,Method Bio.Prosite.ExPASyDictionary.items()=Bio.Prosite.ExPASyDictionary-class.html#items,Method Bio.Prosite.Prodoc.ExPASyDictionary.items()=Bio.Prosite.Prodoc.ExPASyDictionary-class.html#items,Method Bio.PubMed.Dictionary.items()=Bio.PubMed.Dictionary-class.html#items,Method Bio.SwissProt.SProt.ExPASyDictionary.items()=Bio.SwissProt.SProt.ExPASyDictionary-class.html#items,Method Bio.config.Registry.Registry.items()=Bio.config.Registry.Registry-class.html#items,Function Bio.listfns.items()=Bio.listfns-module.html#items,Method BioSQL.BioSeqDatabase.BioSeqDatabase.items()=BioSQL.BioSeqDatabase.BioSeqDatabase-class.html#items,Method BioSQL.BioSeqDatabase.DBServer.items()=BioSQL.BioSeqDatabase.DBServer-class.html#items,Method Martel.Parser.MartelAttributeList.items()=Martel.Parser.MartelAttributeList-class.html#items"><a title="Bio.Crystal.Crystal.items
Bio.EUtils.MultiDict._BaseMultiDict.items
Bio.Entrez.SerialSet.items
Bio.GenBank.NCBIDictionary.items
Bio.Mindy.BaseDB.DictLookup.items
Bio.Prosite.ExPASyDictionary.items
Bio.Prosite.Prodoc.ExPASyDictionary.items
Bio.PubMed.Dictionary.items
Bio.SwissProt.SProt.ExPASyDictionary.items
Bio.config.Registry.Registry.items
Bio.listfns.items
BioSQL.BioSeqDatabase.BioSeqDatabase.items
BioSQL.BioSeqDatabase.DBServer.items
Martel.Parser.MartelAttributeList.items" class="py-name" href="#" onclick="return doclink('link-51', 'items', 'link-51');">items</a></tt> <tt class="py-op">=</tt> <tt id="link-52" class="py-name" targets="Method Bio.EUtils.POM.ElementNode.text()=Bio.EUtils.POM.ElementNode-class.html#text,Method Bio.Prosite.Prodoc._RecordConsumer.text()=Bio.Prosite.Prodoc._RecordConsumer-class.html#text,Variable Martel.test.test_Iterator.text=Martel.test.test_Iterator-module.html#text,Variable Martel.test.test_ParseRecords.text=Martel.test.test_ParseRecords-module.html#text"><a title="Bio.EUtils.POM.ElementNode.text
Bio.Prosite.Prodoc._RecordConsumer.text
Martel.test.test_Iterator.text
Martel.test.test_ParseRecords.text" class="py-name" href="#" onclick="return doclink('link-52', 'text', 'link-52');">text</a></tt><tt class="py-op">.</tt><tt id="link-53" 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-53', 'split', 'link-53');">split</a></tt><tt class="py-op">(</tt> <tt class="py-string">'='</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">constants</tt> <tt class="py-op">=</tt> <tt class="py-op">{</tt><tt class="py-op">}</tt> </tt>
<a name="L79"></a><tt class="py-lineno"> 79</tt> <tt class="py-line"> <tt id="link-54" class="py-name"><a title="Bio.Translate.key" class="py-name" href="#" onclick="return doclink('link-54', 'key', 'link-27');">key</a></tt> <tt class="py-op">=</tt> <tt class="py-string">''</tt> </tt>
<a name="L80"></a><tt class="py-lineno"> 80</tt> <tt class="py-line"> <tt class="py-keyword">for</tt> <tt id="link-55" 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-55', 'i', 'link-55');">i</a></tt> <tt class="py-keyword">in</tt> <tt class="py-name">range</tt><tt class="py-op">(</tt> <tt class="py-number">0</tt><tt class="py-op">,</tt> <tt class="py-op">(</tt> <tt class="py-name">len</tt><tt class="py-op">(</tt> <tt id="link-56" class="py-name"><a title="Bio.Crystal.Crystal.items
Bio.EUtils.MultiDict._BaseMultiDict.items
Bio.Entrez.SerialSet.items
Bio.GenBank.NCBIDictionary.items
Bio.Mindy.BaseDB.DictLookup.items
Bio.Prosite.ExPASyDictionary.items
Bio.Prosite.Prodoc.ExPASyDictionary.items
Bio.PubMed.Dictionary.items
Bio.SwissProt.SProt.ExPASyDictionary.items
Bio.config.Registry.Registry.items
Bio.listfns.items
BioSQL.BioSeqDatabase.BioSeqDatabase.items
BioSQL.BioSeqDatabase.DBServer.items
Martel.Parser.MartelAttributeList.items" class="py-name" href="#" onclick="return doclink('link-56', 'items', 'link-51');">items</a></tt> <tt class="py-op">)</tt> <tt class="py-op">-</tt> <tt class="py-number">1</tt> <tt class="py-op">)</tt> <tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
<a name="L81"></a><tt class="py-lineno"> 81</tt> <tt class="py-line"> <tt id="link-57" class="py-name"><a title="Bio.EUtils.Datatypes.DBIds.item" class="py-name" href="#" onclick="return doclink('link-57', 'item', 'link-33');">item</a></tt> <tt class="py-op">=</tt> <tt id="link-58" class="py-name"><a title="Bio.Crystal.Crystal.items
Bio.EUtils.MultiDict._BaseMultiDict.items
Bio.Entrez.SerialSet.items
Bio.GenBank.NCBIDictionary.items
Bio.Mindy.BaseDB.DictLookup.items
Bio.Prosite.ExPASyDictionary.items
Bio.Prosite.Prodoc.ExPASyDictionary.items
Bio.PubMed.Dictionary.items
Bio.SwissProt.SProt.ExPASyDictionary.items
Bio.config.Registry.Registry.items
Bio.listfns.items
BioSQL.BioSeqDatabase.BioSeqDatabase.items
BioSQL.BioSeqDatabase.DBServer.items
Martel.Parser.MartelAttributeList.items" class="py-name" href="#" onclick="return doclink('link-58', 'items', 'link-51');">items</a></tt><tt class="py-op">[</tt> <tt id="link-59" class="py-name"><a title="Bio.PDB.Polypeptide.i" class="py-name" href="#" onclick="return doclink('link-59', 'i', 'link-55');">i</a></tt> <tt class="py-op">]</tt> </tt>
<a name="L82"></a><tt class="py-lineno"> 82</tt> <tt class="py-line"> <tt id="link-60" class="py-name"><a title="Bio.EUtils.Datatypes.DBIds.item" class="py-name" href="#" onclick="return doclink('link-60', 'item', 'link-33');">item</a></tt> <tt class="py-op">=</tt> <tt id="link-61" class="py-name"><a title="Bio.EUtils.Datatypes.DBIds.item" class="py-name" href="#" onclick="return doclink('link-61', 'item', 'link-33');">item</a></tt><tt class="py-op">.</tt><tt id="link-62" class="py-name" targets="Class Bio.EUtils.DTDs.LinkOut.strip=Bio.EUtils.DTDs.LinkOut.strip-class.html,Method Bio.File.SGMLStripper.strip()=Bio.File.SGMLStripper-class.html#strip,Method Bio.SGMLExtractor.SGMLExtractor.strip()=Bio.SGMLExtractor.SGMLExtractor-class.html#strip"><a title="Bio.EUtils.DTDs.LinkOut.strip
Bio.File.SGMLStripper.strip
Bio.SGMLExtractor.SGMLExtractor.strip" class="py-name" href="#" onclick="return doclink('link-62', 'strip', 'link-62');">strip</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
<a name="L83"></a><tt class="py-lineno"> 83</tt> <tt class="py-line"> <tt class="py-name">separator</tt> <tt class="py-op">=</tt> <tt id="link-63" class="py-name"><a title="Bio.EUtils.Datatypes.DBIds.item" class="py-name" href="#" onclick="return doclink('link-63', 'item', 'link-33');">item</a></tt><tt class="py-op">.</tt><tt class="py-name">rfind</tt><tt class="py-op">(</tt> <tt class="py-string">' '</tt> <tt class="py-op">)</tt> </tt>
<a name="L84"></a><tt class="py-lineno"> 84</tt> <tt class="py-line"> <tt class="py-keyword">if</tt><tt class="py-op">(</tt> <tt class="py-name">separator</tt> <tt class="py-op"><</tt> <tt class="py-number">0</tt> <tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
<a name="L85"></a><tt class="py-lineno"> 85</tt> <tt class="py-line"> <tt class="py-name">separator</tt> <tt class="py-op">=</tt> <tt class="py-number">0</tt> </tt>
<a name="L86"></a><tt class="py-lineno"> 86</tt> <tt class="py-line"> <tt class="py-name">val</tt> <tt class="py-op">=</tt> <tt id="link-64" class="py-name"><a title="Bio.EUtils.Datatypes.DBIds.item" class="py-name" href="#" onclick="return doclink('link-64', 'item', 'link-33');">item</a></tt><tt class="py-op">[</tt> <tt class="py-op">:</tt><tt class="py-name">separator</tt> <tt class="py-op">]</tt> </tt>
<a name="L87"></a><tt class="py-lineno"> 87</tt> <tt class="py-line"> <tt class="py-name">val</tt> <tt class="py-op">=</tt> <tt class="py-name">val</tt><tt class="py-op">.</tt><tt id="link-65" class="py-name"><a title="Bio.EUtils.DTDs.LinkOut.strip
Bio.File.SGMLStripper.strip
Bio.SGMLExtractor.SGMLExtractor.strip" class="py-name" href="#" onclick="return doclink('link-65', 'strip', 'link-62');">strip</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
<a name="L88"></a><tt class="py-lineno"> 88</tt> <tt class="py-line"> <tt class="py-keyword">if</tt><tt class="py-op">(</tt> <tt id="link-66" class="py-name"><a title="Bio.Translate.key" class="py-name" href="#" onclick="return doclink('link-66', 'key', 'link-27');">key</a></tt> <tt class="py-op">!=</tt> <tt class="py-string">''</tt> <tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
<a name="L89"></a><tt class="py-lineno"> 89</tt> <tt class="py-line"> <tt class="py-name">constants</tt><tt class="py-op">[</tt> <tt id="link-67" class="py-name"><a title="Bio.Translate.key" class="py-name" href="#" onclick="return doclink('link-67', 'key', 'link-27');">key</a></tt> <tt class="py-op">]</tt> <tt class="py-op">=</tt> <tt class="py-name">val</tt> </tt>
<a name="L90"></a><tt class="py-lineno"> 90</tt> <tt class="py-line"> <tt id="link-68" class="py-name"><a title="Bio.Translate.key" class="py-name" href="#" onclick="return doclink('link-68', 'key', 'link-27');">key</a></tt> <tt class="py-op">=</tt> <tt id="link-69" class="py-name"><a title="Bio.EUtils.Datatypes.DBIds.item" class="py-name" href="#" onclick="return doclink('link-69', 'item', 'link-33');">item</a></tt><tt class="py-op">[</tt> <tt class="py-name">separator</tt><tt class="py-op">:</tt> <tt class="py-op">]</tt> </tt>
<a name="L91"></a><tt class="py-lineno"> 91</tt> <tt class="py-line"> <tt id="link-70" class="py-name"><a title="Bio.Translate.key" class="py-name" href="#" onclick="return doclink('link-70', 'key', 'link-27');">key</a></tt> <tt class="py-op">=</tt> <tt id="link-71" class="py-name"><a title="Bio.Translate.key" class="py-name" href="#" onclick="return doclink('link-71', 'key', 'link-27');">key</a></tt><tt class="py-op">.</tt><tt id="link-72" class="py-name"><a title="Bio.EUtils.DTDs.LinkOut.strip
Bio.File.SGMLStripper.strip
Bio.SGMLExtractor.SGMLExtractor.strip" class="py-name" href="#" onclick="return doclink('link-72', 'strip', 'link-62');">strip</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
<a name="L92"></a><tt class="py-lineno"> 92</tt> <tt class="py-line"> <tt class="py-name">constants</tt><tt class="py-op">[</tt> <tt id="link-73" class="py-name"><a title="Bio.Translate.key" class="py-name" href="#" onclick="return doclink('link-73', 'key', 'link-27');">key</a></tt> <tt class="py-op">]</tt> <tt class="py-op">=</tt> <tt id="link-74" class="py-name"><a title="Bio.Crystal.Crystal.items
Bio.EUtils.MultiDict._BaseMultiDict.items
Bio.Entrez.SerialSet.items
Bio.GenBank.NCBIDictionary.items
Bio.Mindy.BaseDB.DictLookup.items
Bio.Prosite.ExPASyDictionary.items
Bio.Prosite.Prodoc.ExPASyDictionary.items
Bio.PubMed.Dictionary.items
Bio.SwissProt.SProt.ExPASyDictionary.items
Bio.config.Registry.Registry.items
Bio.listfns.items
BioSQL.BioSeqDatabase.BioSeqDatabase.items
BioSQL.BioSeqDatabase.DBServer.items
Martel.Parser.MartelAttributeList.items" class="py-name" href="#" onclick="return doclink('link-74', 'items', 'link-51');">items</a></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="L93"></a><tt class="py-lineno"> 93</tt> <tt class="py-line"> <tt class="py-keyword">return</tt> <tt class="py-name">constants</tt> </tt>
</div><a name="L94"></a><tt class="py-lineno"> 94</tt> <tt class="py-line"> </tt>
<a name="L95"></a><tt class="py-lineno"> 95</tt> <tt class="py-line"> </tt>
<a name="L96"></a><tt class="py-lineno"> 96</tt> <tt class="py-line"> </tt>
<a name="L97"></a><tt class="py-lineno"> 97</tt> <tt class="py-line"> </tt>
<a name="L98"></a><tt class="py-lineno"> 98</tt> <tt class="py-line"> </tt>
<a name="NdbParser"></a><div id="NdbParser-def"><a name="L99"></a><tt class="py-lineno"> 99</tt> <a class="py-toggle" href="#" id="NdbParser-toggle" onclick="return toggle('NdbParser');">-</a><tt class="py-line"><tt class="py-keyword">class</tt> <a class="py-def-name" href="Bio.Ndb.NdbParser-class.html">NdbParser</a><tt class="py-op">(</tt> <tt class="py-base-class">sgmllib</tt><tt class="py-op">.</tt><tt class="py-base-class">SGMLParser</tt> <tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="NdbParser-collapsed" style="display:none;" pad="+++" indent="++++"></div><div id="NdbParser-expanded"><a name="L100"></a><tt class="py-lineno">100</tt> <tt class="py-line"> <tt class="py-docstring">"""Parses Ndb sequence data into a Record object.</tt> </tt>
<a name="L101"></a><tt class="py-lineno">101</tt> <tt class="py-line"><tt class="py-docstring"> data available at: http://ndbserver.rutgers.edu/NDB/NDBATLAS/index.html</tt> </tt>
<a name="L102"></a><tt class="py-lineno">102</tt> <tt class="py-line"><tt class="py-docstring"> """</tt> </tt>
<a name="NdbParser.reset"></a><div id="NdbParser.reset-def"><a name="L103"></a><tt class="py-lineno">103</tt> <a class="py-toggle" href="#" id="NdbParser.reset-toggle" onclick="return toggle('NdbParser.reset');">-</a><tt class="py-line"> <tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.Ndb.NdbParser-class.html#reset">reset</a><tt class="py-op">(</tt><tt class="py-param">self</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="NdbParser.reset-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="NdbParser.reset-expanded"><a name="L104"></a><tt class="py-lineno">104</tt> <tt class="py-line"> <tt class="py-name">sgmllib</tt><tt class="py-op">.</tt><tt class="py-name">SGMLParser</tt><tt class="py-op">.</tt><tt id="link-75" class="py-name" targets="Method Bio.Blast.NCBIXML.BlastParser.reset()=Bio.Blast.NCBIXML.BlastParser-class.html#reset,Method Bio.InterPro.InterProParser.reset()=Bio.InterPro.InterProParser-class.html#reset,Method Bio.LocusLink.web_parse.LocusLinkParser.reset()=Bio.LocusLink.web_parse.LocusLinkParser-class.html#reset,Method Bio.Ndb.NdbParser.reset()=Bio.Ndb.NdbParser-class.html#reset,Method Bio.NetCatch.ExtractUrls.reset()=Bio.NetCatch.ExtractUrls-class.html#reset"><a title="Bio.Blast.NCBIXML.BlastParser.reset
Bio.InterPro.InterProParser.reset
Bio.LocusLink.web_parse.LocusLinkParser.reset
Bio.Ndb.NdbParser.reset
Bio.NetCatch.ExtractUrls.reset" class="py-name" href="#" onclick="return doclink('link-75', 'reset', 'link-75');">reset</a></tt><tt class="py-op">(</tt> <tt class="py-name">self</tt> <tt class="py-op">)</tt> </tt>
<a name="L105"></a><tt class="py-lineno">105</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">ndb_dict</tt> <tt class="py-op">=</tt> <tt id="link-76" class="py-name" targets="Module Bio.Blast.Record=Bio.Blast.Record-module.html,Module Bio.CDD.Record=Bio.CDD.Record-module.html,Class Bio.CDD.Record.Record=Bio.CDD.Record.Record-class.html,Class Bio.Cluster.Record=Bio.Cluster.Record-class.html,Class Bio.Compass.Record=Bio.Compass.Record-class.html,Module Bio.ECell.Record=Bio.ECell.Record-module.html,Class Bio.ECell.Record.Record=Bio.ECell.Record.Record-class.html,Class Bio.Fasta.Record=Bio.Fasta.Record-class.html,Module Bio.GenBank.Record=Bio.GenBank.Record-module.html,Class Bio.GenBank.Record.Record=Bio.GenBank.Record.Record-class.html,Module Bio.Geo.Record=Bio.Geo.Record-module.html,Class Bio.Geo.Record.Record=Bio.Geo.Record.Record-class.html,Class Bio.Gobase.Record=Bio.Gobase.Record-class.html,Module Bio.IntelliGenetics.Record=Bio.IntelliGenetics.Record-module.html,Class Bio.IntelliGenetics.Record.Record=Bio.IntelliGenetics.Record.Record-class.html,Class Bio.InterPro.Record=Bio.InterPro.Record-class.html,Class Bio.KEGG.Compound.Record=Bio.KEGG.Compound.Record-class.html,Class Bio.KEGG.Enzyme.Record=Bio.KEGG.Enzyme.Record-class.html,Class Bio.LocusLink.Record=Bio.LocusLink.Record-class.html,Class Bio.LocusLink.web_parse.Record=Bio.LocusLink.web_parse.Record-class.html,Class Bio.Medline.Record=Bio.Medline.Record-class.html,Module Bio.MetaTool.Record=Bio.MetaTool.Record-module.html,Class Bio.MetaTool.Record.Record=Bio.MetaTool.Record.Record-class.html,Module Bio.NBRF.Record=Bio.NBRF.Record-module.html,Class Bio.NBRF.Record.Record=Bio.NBRF.Record.Record-class.html,Class Bio.Ndb.Record=Bio.Ndb.Record-class.html,Class Bio.PopGen.FDist.Record=Bio.PopGen.FDist.Record-class.html,Class Bio.PopGen.GenePop.Record=Bio.PopGen.GenePop.Record-class.html,Class Bio.Prosite.Prodoc.Record=Bio.Prosite.Prodoc.Record-class.html,Class Bio.Prosite.Record=Bio.Prosite.Record-class.html,Class Bio.Rebase.Record=Bio.Rebase.Record-class.html,Class Bio.SCOP.Cla.Record=Bio.SCOP.Cla.Record-class.html,Class Bio.SCOP.Des.Record=Bio.SCOP.Des.Record-class.html,Class Bio.SCOP.Dom.Record=Bio.SCOP.Dom.Record-class.html,Class Bio.SCOP.Hie.Record=Bio.SCOP.Hie.Record-class.html,Module Bio.Saf.Record=Bio.Saf.Record-module.html,Class Bio.Saf.Record.Record=Bio.Saf.Record.Record-class.html,Class Bio.Sequencing.Phd.Record=Bio.Sequencing.Phd.Record-class.html,Class Bio.SwissProt.KeyWList.Record=Bio.SwissProt.KeyWList.Record-class.html,Class Bio.SwissProt.SProt.Record=Bio.SwissProt.SProt.Record-class.html"><a title="Bio.Blast.Record
Bio.CDD.Record
Bio.CDD.Record.Record
Bio.Cluster.Record
Bio.Compass.Record
Bio.ECell.Record
Bio.ECell.Record.Record
Bio.Fasta.Record
Bio.GenBank.Record
Bio.GenBank.Record.Record
Bio.Geo.Record
Bio.Geo.Record.Record
Bio.Gobase.Record
Bio.IntelliGenetics.Record
Bio.IntelliGenetics.Record.Record
Bio.InterPro.Record
Bio.KEGG.Compound.Record
Bio.KEGG.Enzyme.Record
Bio.LocusLink.Record
Bio.LocusLink.web_parse.Record
Bio.Medline.Record
Bio.MetaTool.Record
Bio.MetaTool.Record.Record
Bio.NBRF.Record
Bio.NBRF.Record.Record
Bio.Ndb.Record
Bio.PopGen.FDist.Record
Bio.PopGen.GenePop.Record
Bio.Prosite.Prodoc.Record
Bio.Prosite.Record
Bio.Rebase.Record
Bio.SCOP.Cla.Record
Bio.SCOP.Des.Record
Bio.SCOP.Dom.Record
Bio.SCOP.Hie.Record
Bio.Saf.Record
Bio.Saf.Record.Record
Bio.Sequencing.Phd.Record
Bio.SwissProt.KeyWList.Record
Bio.SwissProt.SProt.Record" class="py-name" href="#" onclick="return doclink('link-76', 'Record', 'link-76');">Record</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
<a name="L106"></a><tt class="py-lineno">106</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-77" class="py-name"><a title="Bio.EUtils.POM.ElementNode.text
Bio.Prosite.Prodoc._RecordConsumer.text
Martel.test.test_Iterator.text
Martel.test.test_ParseRecords.text" class="py-name" href="#" onclick="return doclink('link-77', 'text', 'link-52');">text</a></tt> <tt class="py-op">=</tt> <tt class="py-string">''</tt> </tt>
<a name="L107"></a><tt class="py-lineno">107</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">_space_group</tt> <tt class="py-op">=</tt> <tt class="py-string">''</tt> </tt>
<a name="L108"></a><tt class="py-lineno">108</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">_state</tt> <tt class="py-op">=</tt> <tt class="py-string">'id'</tt> </tt>
<a name="L109"></a><tt class="py-lineno">109</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">_reference_state</tt> <tt class="py-op">=</tt> <tt class="py-string">'authors'</tt> </tt>
<a name="L110"></a><tt class="py-lineno">110</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">_current_reference</tt> <tt class="py-op">=</tt> <tt id="link-78" class="py-name"><a title="Bio.GenBank.Record.Reference
Bio.Prosite.Prodoc.Reference
Bio.SeqFeature.Reference
Bio.SwissProt.SProt.Reference" class="py-name" href="#" onclick="return doclink('link-78', 'Reference', 'link-15');">Reference</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
</div><a name="L111"></a><tt class="py-lineno">111</tt> <tt class="py-line"> </tt>
<a name="NdbParser.parse"></a><div id="NdbParser.parse-def"><a name="L112"></a><tt class="py-lineno">112</tt> <a class="py-toggle" href="#" id="NdbParser.parse-toggle" onclick="return toggle('NdbParser.parse');">-</a><tt class="py-line"> <tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.Ndb.NdbParser-class.html#parse">parse</a><tt class="py-op">(</tt><tt class="py-param">self</tt><tt class="py-op">,</tt> <tt class="py-param">handle</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="NdbParser.parse-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="NdbParser.parse-expanded"><a name="L113"></a><tt class="py-lineno">113</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-79" class="py-name"><a title="Bio.Blast.NCBIXML.BlastParser.reset
Bio.InterPro.InterProParser.reset
Bio.LocusLink.web_parse.LocusLinkParser.reset
Bio.Ndb.NdbParser.reset
Bio.NetCatch.ExtractUrls.reset" class="py-name" href="#" onclick="return doclink('link-79', 'reset', 'link-75');">reset</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
<a name="L114"></a><tt class="py-lineno">114</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-80" class="py-name" targets="Method Bio.Affy.CelFile.CelScanner.feed()=Bio.Affy.CelFile.CelScanner-class.html#feed,Method Bio.AlignAce.Scanner.AlignAceScanner.feed()=Bio.AlignAce.Scanner.AlignAceScanner-class.html#feed,Method Bio.AlignAce.Scanner.CompareAceScanner.feed()=Bio.AlignAce.Scanner.CompareAceScanner-class.html#feed,Method Bio.Blast.NCBIStandalone._Scanner.feed()=Bio.Blast.NCBIStandalone._Scanner-class.html#feed,Method Bio.Blast.NCBIWWW._Scanner.feed()=Bio.Blast.NCBIWWW._Scanner-class.html#feed,Method Bio.CDD._Scanner.feed()=Bio.CDD._Scanner-class.html#feed,Method Bio.Compass._Scanner.feed()=Bio.Compass._Scanner-class.html#feed,Method Bio.ECell._Scanner.feed()=Bio.ECell._Scanner-class.html#feed,Method Bio.Emboss.Primer._Primer3Scanner.feed()=Bio.Emboss.Primer._Primer3Scanner-class.html#feed,Method Bio.Emboss.Primer._PrimerSearchScanner.feed()=Bio.Emboss.Primer._PrimerSearchScanner-class.html#feed,Method Bio.Enzyme._Scanner.feed()=Bio.Enzyme._Scanner-class.html#feed,Method Bio.GenBank.Scanner.InsdcScanner.feed()=Bio.GenBank.Scanner.InsdcScanner-class.html#feed,Method Bio.Gobase._Scanner.feed()=Bio.Gobase._Scanner-class.html#feed,Method Bio.IntelliGenetics._Scanner.feed()=Bio.IntelliGenetics._Scanner-class.html#feed,Method Bio.InterPro.InterProParser.feed()=Bio.InterPro.InterProParser-class.html#feed,Method Bio.LocusLink._Scanner.feed()=Bio.LocusLink._Scanner-class.html#feed,Method Bio.LocusLink.web_parse.LocusLinkParser.feed()=Bio.LocusLink.web_parse.LocusLinkParser-class.html#feed,Method Bio.MEME.Parser._MASTScanner.feed()=Bio.MEME.Parser._MASTScanner-class.html#feed,Method Bio.MEME.Parser._MEMEScanner.feed()=Bio.MEME.Parser._MEMEScanner-class.html#feed,Method Bio.Medline._Scanner.feed()=Bio.Medline._Scanner-class.html#feed,Method Bio.MetaTool._Scanner.feed()=Bio.MetaTool._Scanner-class.html#feed,Method Bio.NBRF._Scanner.feed()=Bio.NBRF._Scanner-class.html#feed,Method Bio.Ndb.NdbParser.feed()=Bio.Ndb.NdbParser-class.html#feed,Method Bio.NetCatch.ExtractUrls.feed()=Bio.NetCatch.ExtractUrls-class.html#feed,Method Bio.PopGen.FDist._Scanner.feed()=Bio.PopGen.FDist._Scanner-class.html#feed,Method Bio.PopGen.GenePop._Scanner.feed()=Bio.PopGen.GenePop._Scanner-class.html#feed,Method Bio.Prosite.Prodoc._Scanner.feed()=Bio.Prosite.Prodoc._Scanner-class.html#feed,Method Bio.Prosite._Scanner.feed()=Bio.Prosite._Scanner-class.html#feed,Method Bio.Rebase._Scanner.feed()=Bio.Rebase._Scanner-class.html#feed,Method Bio.Saf._Scanner.feed()=Bio.Saf._Scanner-class.html#feed,Method Bio.Sequencing.Ace._Scanner.feed()=Bio.Sequencing.Ace._Scanner-class.html#feed,Method Bio.Sequencing.Phd._Scanner.feed()=Bio.Sequencing.Phd._Scanner-class.html#feed,Method Bio.SwissProt.KeyWList._Scanner.feed()=Bio.SwissProt.KeyWList._Scanner-class.html#feed,Method Bio.SwissProt.SProt._Scanner.feed()=Bio.SwissProt.SProt._Scanner-class.html#feed,Method Bio.UniGene._Scanner.feed()=Bio.UniGene._Scanner-class.html#feed"><a title="Bio.Affy.CelFile.CelScanner.feed
Bio.AlignAce.Scanner.AlignAceScanner.feed
Bio.AlignAce.Scanner.CompareAceScanner.feed
Bio.Blast.NCBIStandalone._Scanner.feed
Bio.Blast.NCBIWWW._Scanner.feed
Bio.CDD._Scanner.feed
Bio.Compass._Scanner.feed
Bio.ECell._Scanner.feed
Bio.Emboss.Primer._Primer3Scanner.feed
Bio.Emboss.Primer._PrimerSearchScanner.feed
Bio.Enzyme._Scanner.feed
Bio.GenBank.Scanner.InsdcScanner.feed
Bio.Gobase._Scanner.feed
Bio.IntelliGenetics._Scanner.feed
Bio.InterPro.InterProParser.feed
Bio.LocusLink._Scanner.feed
Bio.LocusLink.web_parse.LocusLinkParser.feed
Bio.MEME.Parser._MASTScanner.feed
Bio.MEME.Parser._MEMEScanner.feed
Bio.Medline._Scanner.feed
Bio.MetaTool._Scanner.feed
Bio.NBRF._Scanner.feed
Bio.Ndb.NdbParser.feed
Bio.NetCatch.ExtractUrls.feed
Bio.PopGen.FDist._Scanner.feed
Bio.PopGen.GenePop._Scanner.feed
Bio.Prosite.Prodoc._Scanner.feed
Bio.Prosite._Scanner.feed
Bio.Rebase._Scanner.feed
Bio.Saf._Scanner.feed
Bio.Sequencing.Ace._Scanner.feed
Bio.Sequencing.Phd._Scanner.feed
Bio.SwissProt.KeyWList._Scanner.feed
Bio.SwissProt.SProt._Scanner.feed
Bio.UniGene._Scanner.feed" class="py-name" href="#" onclick="return doclink('link-80', 'feed', 'link-80');">feed</a></tt><tt class="py-op">(</tt><tt id="link-81" class="py-name" targets="Variable Bio.LocusLink.web_parse.handle=Bio.LocusLink.web_parse-module.html#handle,Variable Bio.Ndb.handle=Bio.Ndb-module.html#handle"><a title="Bio.LocusLink.web_parse.handle
Bio.Ndb.handle" class="py-name" href="#" onclick="return doclink('link-81', 'handle', 'link-81');">handle</a></tt><tt class="py-op">)</tt> </tt>
<a name="L115"></a><tt class="py-lineno">115</tt> <tt class="py-line"> <tt class="py-keyword">return</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">ndb_dict</tt> </tt>
</div><a name="L116"></a><tt class="py-lineno">116</tt> <tt class="py-line"> </tt>
<a name="NdbParser.feed"></a><div id="NdbParser.feed-def"><a name="L117"></a><tt class="py-lineno">117</tt> <a class="py-toggle" href="#" id="NdbParser.feed-toggle" onclick="return toggle('NdbParser.feed');">-</a><tt class="py-line"> <tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.Ndb.NdbParser-class.html#feed">feed</a><tt class="py-op">(</tt><tt class="py-param">self</tt><tt class="py-op">,</tt> <tt class="py-param">handle</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="NdbParser.feed-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="NdbParser.feed-expanded"><a name="L118"></a><tt class="py-lineno">118</tt> <tt class="py-line"> <tt class="py-docstring">"""feed(self, handle )</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 class="py-docstring"> Feed in ndb data for scanning. handle is a file-like object</tt> </tt>
<a name="L121"></a><tt class="py-lineno">121</tt> <tt class="py-line"><tt class="py-docstring"> containing ndb data. consumer is a Consumer object that will</tt> </tt>
<a name="L122"></a><tt class="py-lineno">122</tt> <tt class="py-line"><tt class="py-docstring"> receive events as the ndb data is scanned.</tt> </tt>
<a name="L123"></a><tt class="py-lineno">123</tt> <tt class="py-line"><tt class="py-docstring"></tt> </tt>
<a name="L124"></a><tt class="py-lineno">124</tt> <tt class="py-line"><tt class="py-docstring"> """</tt> </tt>
<a name="L125"></a><tt class="py-lineno">125</tt> <tt class="py-line"> <tt class="py-keyword">if</tt> <tt class="py-name">isinstance</tt><tt class="py-op">(</tt><tt id="link-82" class="py-name"><a title="Bio.LocusLink.web_parse.handle
Bio.Ndb.handle" class="py-name" href="#" onclick="return doclink('link-82', 'handle', 'link-81');">handle</a></tt><tt class="py-op">,</tt> <tt id="link-83" class="py-name"><a title="Bio.File" class="py-name" href="#" onclick="return doclink('link-83', 'File', 'link-1');">File</a></tt><tt class="py-op">.</tt><tt id="link-84" class="py-name" targets="Class Bio.File.UndoHandle=Bio.File.UndoHandle-class.html"><a title="Bio.File.UndoHandle" class="py-name" href="#" onclick="return doclink('link-84', 'UndoHandle', 'link-84');">UndoHandle</a></tt><tt class="py-op">)</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">uhandle</tt> <tt class="py-op">=</tt> <tt id="link-85" class="py-name"><a title="Bio.LocusLink.web_parse.handle
Bio.Ndb.handle" class="py-name" href="#" onclick="return doclink('link-85', 'handle', 'link-81');">handle</a></tt> </tt>
<a name="L127"></a><tt class="py-lineno">127</tt> <tt class="py-line"> <tt class="py-keyword">else</tt><tt class="py-op">:</tt> </tt>
<a name="L128"></a><tt class="py-lineno">128</tt> <tt class="py-line"> <tt class="py-name">uhandle</tt> <tt class="py-op">=</tt> <tt id="link-86" class="py-name"><a title="Bio.File" class="py-name" href="#" onclick="return doclink('link-86', 'File', 'link-1');">File</a></tt><tt class="py-op">.</tt><tt id="link-87" class="py-name"><a title="Bio.File.UndoHandle" class="py-name" href="#" onclick="return doclink('link-87', 'UndoHandle', 'link-84');">UndoHandle</a></tt><tt class="py-op">(</tt><tt id="link-88" class="py-name"><a title="Bio.LocusLink.web_parse.handle
Bio.Ndb.handle" class="py-name" href="#" onclick="return doclink('link-88', 'handle', 'link-81');">handle</a></tt><tt class="py-op">)</tt> </tt>
<a name="L129"></a><tt class="py-lineno">129</tt> <tt class="py-line"> <tt id="link-89" class="py-name"><a title="Bio.EUtils.POM.ElementNode.text
Bio.Prosite.Prodoc._RecordConsumer.text
Martel.test.test_Iterator.text
Martel.test.test_ParseRecords.text" class="py-name" href="#" onclick="return doclink('link-89', 'text', 'link-52');">text</a></tt> <tt class="py-op">=</tt> <tt class="py-string">''</tt> </tt>
<a name="L130"></a><tt class="py-lineno">130</tt> <tt class="py-line"> <tt class="py-keyword">while</tt> <tt class="py-number">1</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">line</tt> <tt class="py-op">=</tt> <tt class="py-name">uhandle</tt><tt class="py-op">.</tt><tt id="link-90" class="py-name" targets="Method Bio.EUtils.ReseekFile.ReseekFile.readline()=Bio.EUtils.ReseekFile.ReseekFile-class.html#readline,Method Bio.File.SGMLHandle.readline()=Bio.File.SGMLHandle-class.html#readline,Method Bio.File.UndoHandle.readline()=Bio.File.UndoHandle-class.html#readline,Method Bio.SGMLExtractor.SGMLExtractorHandle.readline()=Bio.SGMLExtractor.SGMLExtractorHandle-class.html#readline"><a title="Bio.EUtils.ReseekFile.ReseekFile.readline
Bio.File.SGMLHandle.readline
Bio.File.UndoHandle.readline
Bio.SGMLExtractor.SGMLExtractorHandle.readline" class="py-name" href="#" onclick="return doclink('link-90', 'readline', 'link-90');">readline</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">if</tt><tt class="py-op">(</tt> <tt class="py-keyword">not</tt> <tt class="py-name">line</tt> <tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
<a name="L133"></a><tt class="py-lineno">133</tt> <tt class="py-line"> <tt class="py-keyword">break</tt> </tt>
<a name="L134"></a><tt class="py-lineno">134</tt> <tt class="py-line"> <tt class="py-name">line</tt> <tt class="py-op">=</tt> <tt class="py-name">string</tt><tt class="py-op">.</tt><tt id="link-91" class="py-name"><a title="Bio.EUtils.DTDs.LinkOut.strip
Bio.File.SGMLStripper.strip
Bio.SGMLExtractor.SGMLExtractor.strip" class="py-name" href="#" onclick="return doclink('link-91', 'strip', 'link-62');">strip</a></tt><tt class="py-op">(</tt> <tt class="py-name">line</tt> <tt class="py-op">)</tt> </tt>
<a name="L135"></a><tt class="py-lineno">135</tt> <tt class="py-line"> <tt class="py-keyword">if</tt><tt class="py-op">(</tt> <tt class="py-name">line</tt><tt class="py-op">[</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 class="py-string">'</HTML>'</tt> <tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
<a name="L136"></a><tt class="py-lineno">136</tt> <tt class="py-line"> <tt class="py-keyword">break</tt> </tt>
<a name="L137"></a><tt class="py-lineno">137</tt> <tt class="py-line"> <tt id="link-92" class="py-name"><a title="Bio.EUtils.POM.ElementNode.text
Bio.Prosite.Prodoc._RecordConsumer.text
Martel.test.test_Iterator.text
Martel.test.test_ParseRecords.text" class="py-name" href="#" onclick="return doclink('link-92', 'text', 'link-52');">text</a></tt> <tt class="py-op">=</tt> <tt id="link-93" class="py-name"><a title="Bio.EUtils.POM.ElementNode.text
Bio.Prosite.Prodoc._RecordConsumer.text
Martel.test.test_Iterator.text
Martel.test.test_ParseRecords.text" class="py-name" href="#" onclick="return doclink('link-93', 'text', 'link-52');">text</a></tt> <tt class="py-op">+</tt> <tt class="py-string">' '</tt> <tt class="py-op">+</tt> <tt class="py-name">line</tt> </tt>
<a name="L138"></a><tt class="py-lineno">138</tt> <tt class="py-line"> </tt>
<a name="L139"></a><tt class="py-lineno">139</tt> <tt class="py-line"> <tt class="py-name">sgmllib</tt><tt class="py-op">.</tt><tt class="py-name">SGMLParser</tt><tt class="py-op">.</tt><tt id="link-94" class="py-name"><a title="Bio.Affy.CelFile.CelScanner.feed
Bio.AlignAce.Scanner.AlignAceScanner.feed
Bio.AlignAce.Scanner.CompareAceScanner.feed
Bio.Blast.NCBIStandalone._Scanner.feed
Bio.Blast.NCBIWWW._Scanner.feed
Bio.CDD._Scanner.feed
Bio.Compass._Scanner.feed
Bio.ECell._Scanner.feed
Bio.Emboss.Primer._Primer3Scanner.feed
Bio.Emboss.Primer._PrimerSearchScanner.feed
Bio.Enzyme._Scanner.feed
Bio.GenBank.Scanner.InsdcScanner.feed
Bio.Gobase._Scanner.feed
Bio.IntelliGenetics._Scanner.feed
Bio.InterPro.InterProParser.feed
Bio.LocusLink._Scanner.feed
Bio.LocusLink.web_parse.LocusLinkParser.feed
Bio.MEME.Parser._MASTScanner.feed
Bio.MEME.Parser._MEMEScanner.feed
Bio.Medline._Scanner.feed
Bio.MetaTool._Scanner.feed
Bio.NBRF._Scanner.feed
Bio.Ndb.NdbParser.feed
Bio.NetCatch.ExtractUrls.feed
Bio.PopGen.FDist._Scanner.feed
Bio.PopGen.GenePop._Scanner.feed
Bio.Prosite.Prodoc._Scanner.feed
Bio.Prosite._Scanner.feed
Bio.Rebase._Scanner.feed
Bio.Saf._Scanner.feed
Bio.Sequencing.Ace._Scanner.feed
Bio.Sequencing.Phd._Scanner.feed
Bio.SwissProt.KeyWList._Scanner.feed
Bio.SwissProt.SProt._Scanner.feed
Bio.UniGene._Scanner.feed" class="py-name" href="#" onclick="return doclink('link-94', 'feed', 'link-80');">feed</a></tt><tt class="py-op">(</tt> <tt class="py-name">self</tt><tt class="py-op">,</tt> <tt id="link-95" class="py-name"><a title="Bio.EUtils.POM.ElementNode.text
Bio.Prosite.Prodoc._RecordConsumer.text
Martel.test.test_Iterator.text
Martel.test.test_ParseRecords.text" class="py-name" href="#" onclick="return doclink('link-95', 'text', 'link-52');">text</a></tt> <tt class="py-op">)</tt> </tt>
</div><a name="L140"></a><tt class="py-lineno">140</tt> <tt class="py-line"> </tt>
<a name="L141"></a><tt class="py-lineno">141</tt> <tt class="py-line"> </tt>
<a name="NdbParser.handle_data"></a><div id="NdbParser.handle_data-def"><a name="L142"></a><tt class="py-lineno">142</tt> <a class="py-toggle" href="#" id="NdbParser.handle_data-toggle" onclick="return toggle('NdbParser.handle_data');">-</a><tt class="py-line"> <tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.Ndb.NdbParser-class.html#handle_data">handle_data</a><tt class="py-op">(</tt><tt class="py-param">self</tt><tt class="py-op">,</tt> <tt class="py-param">newtext</tt> <tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="NdbParser.handle_data-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="NdbParser.handle_data-expanded"><a name="L143"></a><tt class="py-lineno">143</tt> <tt class="py-line"> <tt class="py-name">newtext</tt> <tt class="py-op">=</tt> <tt class="py-name">string</tt><tt class="py-op">.</tt><tt id="link-96" class="py-name"><a title="Bio.EUtils.DTDs.LinkOut.strip
Bio.File.SGMLStripper.strip
Bio.SGMLExtractor.SGMLExtractor.strip" class="py-name" href="#" onclick="return doclink('link-96', 'strip', 'link-62');">strip</a></tt><tt class="py-op">(</tt> <tt class="py-name">newtext</tt> <tt class="py-op">)</tt> </tt>
<a name="L144"></a><tt class="py-lineno">144</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-97" class="py-name"><a title="Bio.EUtils.POM.ElementNode.text
Bio.Prosite.Prodoc._RecordConsumer.text
Martel.test.test_Iterator.text
Martel.test.test_ParseRecords.text" class="py-name" href="#" onclick="return doclink('link-97', 'text', 'link-52');">text</a></tt> <tt class="py-op">=</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-98" class="py-name"><a title="Bio.EUtils.POM.ElementNode.text
Bio.Prosite.Prodoc._RecordConsumer.text
Martel.test.test_Iterator.text
Martel.test.test_ParseRecords.text" class="py-name" href="#" onclick="return doclink('link-98', 'text', 'link-52');">text</a></tt> <tt class="py-op">+</tt> <tt class="py-name">newtext</tt> </tt>
</div><a name="L145"></a><tt class="py-lineno">145</tt> <tt class="py-line"> </tt>
<a name="NdbParser.start_h1"></a><div id="NdbParser.start_h1-def"><a name="L146"></a><tt class="py-lineno">146</tt> <a class="py-toggle" href="#" id="NdbParser.start_h1-toggle" onclick="return toggle('NdbParser.start_h1');">-</a><tt class="py-line"> <tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.Ndb.NdbParser-class.html#start_h1">start_h1</a><tt class="py-op">(</tt> <tt class="py-param">self</tt><tt class="py-op">,</tt> <tt class="py-param">attrs</tt> <tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="NdbParser.start_h1-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="NdbParser.start_h1-expanded"><a name="L147"></a><tt class="py-lineno">147</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-99" class="py-name" targets="Method Bio.InterPro.InterProParser._flush_text()=Bio.InterPro.InterProParser-class.html#_flush_text,Method Bio.Ndb.NdbParser._flush_text()=Bio.Ndb.NdbParser-class.html#_flush_text"><a title="Bio.InterPro.InterProParser._flush_text
Bio.Ndb.NdbParser._flush_text" class="py-name" href="#" onclick="return doclink('link-99', '_flush_text', 'link-99');">_flush_text</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
</div><a name="L148"></a><tt class="py-lineno">148</tt> <tt class="py-line"> </tt>
<a name="NdbParser.end_h1"></a><div id="NdbParser.end_h1-def"><a name="L149"></a><tt class="py-lineno">149</tt> <a class="py-toggle" href="#" id="NdbParser.end_h1-toggle" onclick="return toggle('NdbParser.end_h1');">-</a><tt class="py-line"> <tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.Ndb.NdbParser-class.html#end_h1">end_h1</a><tt class="py-op">(</tt> <tt class="py-param">self</tt> <tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="NdbParser.end_h1-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="NdbParser.end_h1-expanded"><a name="L150"></a><tt class="py-lineno">150</tt> <tt class="py-line"> <tt id="link-100" class="py-name"><a title="Bio.EUtils.POM.ElementNode.text
Bio.Prosite.Prodoc._RecordConsumer.text
Martel.test.test_Iterator.text
Martel.test.test_ParseRecords.text" class="py-name" href="#" onclick="return doclink('link-100', 'text', 'link-52');">text</a></tt> <tt class="py-op">=</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-101" class="py-name"><a title="Bio.InterPro.InterProParser._flush_text
Bio.Ndb.NdbParser._flush_text" class="py-name" href="#" onclick="return doclink('link-101', '_flush_text', 'link-99');">_flush_text</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
<a name="L151"></a><tt class="py-lineno">151</tt> <tt class="py-line"> <tt class="py-keyword">if</tt><tt class="py-op">(</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">_state</tt> <tt class="py-op">==</tt> <tt class="py-string">'id'</tt> <tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
<a name="L152"></a><tt class="py-lineno">152</tt> <tt class="py-line"> <tt class="py-name">cols</tt> <tt class="py-op">=</tt> <tt id="link-102" class="py-name"><a title="Bio.EUtils.POM.ElementNode.text
Bio.Prosite.Prodoc._RecordConsumer.text
Martel.test.test_Iterator.text
Martel.test.test_ParseRecords.text" class="py-name" href="#" onclick="return doclink('link-102', 'text', 'link-52');">text</a></tt><tt class="py-op">.</tt><tt id="link-103" class="py-name"><a title="Bio.Nexus.Trees.Tree.split
Bio.Restriction.Restriction.RestrictionBatch.split" class="py-name" href="#" onclick="return doclink('link-103', 'split', 'link-53');">split</a></tt><tt class="py-op">(</tt> <tt class="py-string">':'</tt> <tt class="py-op">)</tt> </tt>
<a name="L153"></a><tt class="py-lineno">153</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">ndb_dict</tt><tt class="py-op">[</tt> <tt class="py-string">'Id'</tt> <tt class="py-op">]</tt> <tt class="py-op">=</tt> <tt class="py-op">(</tt> <tt class="py-name">cols</tt><tt class="py-op">[</tt> <tt class="py-number">1</tt> <tt class="py-op">]</tt> <tt class="py-op">)</tt><tt class="py-op">.</tt><tt class="py-name">upper</tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
<a name="L154"></a><tt class="py-lineno">154</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">_state</tt> <tt class="py-op">=</tt> <tt class="py-string">'id_found'</tt> </tt>
</div><a name="L155"></a><tt class="py-lineno">155</tt> <tt class="py-line"> </tt>
<a name="NdbParser.start_h2"></a><div id="NdbParser.start_h2-def"><a name="L156"></a><tt class="py-lineno">156</tt> <a class="py-toggle" href="#" id="NdbParser.start_h2-toggle" onclick="return toggle('NdbParser.start_h2');">-</a><tt class="py-line"> <tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.Ndb.NdbParser-class.html#start_h2">start_h2</a><tt class="py-op">(</tt> <tt class="py-param">self</tt><tt class="py-op">,</tt> <tt class="py-param">attrs</tt> <tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="NdbParser.start_h2-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="NdbParser.start_h2-expanded"><a name="L157"></a><tt class="py-lineno">157</tt> <tt class="py-line"> <tt id="link-104" class="py-name"><a title="Bio.EUtils.POM.ElementNode.text
Bio.Prosite.Prodoc._RecordConsumer.text
Martel.test.test_Iterator.text
Martel.test.test_ParseRecords.text" class="py-name" href="#" onclick="return doclink('link-104', 'text', 'link-52');">text</a></tt> <tt class="py-op">=</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-105" class="py-name"><a title="Bio.InterPro.InterProParser._flush_text
Bio.Ndb.NdbParser._flush_text" class="py-name" href="#" onclick="return doclink('link-105', '_flush_text', 'link-99');">_flush_text</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
<a name="L158"></a><tt class="py-lineno">158</tt> <tt class="py-line"> <tt class="py-keyword">if</tt><tt class="py-op">(</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">_state</tt> <tt class="py-op">==</tt> <tt class="py-string">'features'</tt> <tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
<a name="L159"></a><tt class="py-lineno">159</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">ndb_dict</tt><tt class="py-op">[</tt> <tt class="py-string">'Features'</tt> <tt class="py-op">]</tt> <tt class="py-op">=</tt> <tt id="link-106" class="py-name"><a title="Bio.EUtils.POM.ElementNode.text
Bio.Prosite.Prodoc._RecordConsumer.text
Martel.test.test_Iterator.text
Martel.test.test_ParseRecords.text" class="py-name" href="#" onclick="return doclink('link-106', 'text', 'link-52');">text</a></tt> </tt>
<a name="L160"></a><tt class="py-lineno">160</tt> <tt class="py-line"> <tt class="py-keyword">elif</tt><tt class="py-op">(</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">_state</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="L161"></a><tt class="py-lineno">161</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">ndb_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-107" class="py-name"><a title="Bio.EUtils.POM.ElementNode.text
Bio.Prosite.Prodoc._RecordConsumer.text
Martel.test.test_Iterator.text
Martel.test.test_ParseRecords.text" class="py-name" href="#" onclick="return doclink('link-107', 'text', 'link-52');">text</a></tt> </tt>
<a name="L162"></a><tt class="py-lineno">162</tt> <tt class="py-line"> <tt class="py-keyword">elif</tt><tt class="py-op">(</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">_state</tt> <tt class="py-op">==</tt> <tt class="py-string">'sequence'</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">pass</tt> </tt>
<a name="L164"></a><tt class="py-lineno">164</tt> <tt class="py-line"> <tt class="py-keyword">elif</tt><tt class="py-op">(</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">_state</tt> <tt class="py-op">==</tt> <tt class="py-string">'citation'</tt> <tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
<a name="L165"></a><tt class="py-lineno">165</tt> <tt class="py-line"> <tt class="py-keyword">if</tt><tt class="py-op">(</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">_reference_state</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="L166"></a><tt class="py-lineno">166</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">_current_reference</tt><tt class="py-op">.</tt><tt id="link-108" 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-108', 'journal', 'link-108');">journal</a></tt> <tt class="py-op">=</tt> <tt id="link-109" class="py-name"><a title="Bio.EUtils.POM.ElementNode.text
Bio.Prosite.Prodoc._RecordConsumer.text
Martel.test.test_Iterator.text
Martel.test.test_ParseRecords.text" class="py-name" href="#" onclick="return doclink('link-109', 'text', 'link-52');">text</a></tt> </tt>
<a name="L167"></a><tt class="py-lineno">167</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">ndb_dict</tt><tt class="py-op">[</tt> <tt class="py-string">'Citation'</tt> <tt class="py-op">]</tt> <tt class="py-op">=</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">_current_reference</tt> </tt>
<a name="L168"></a><tt class="py-lineno">168</tt> <tt class="py-line"> <tt class="py-keyword">elif</tt><tt class="py-op">(</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">_state</tt> <tt class="py-op">==</tt> <tt class="py-string">'space'</tt> <tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
<a name="L169"></a><tt class="py-lineno">169</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">_space_group</tt> <tt class="py-op">=</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">_space_group</tt> <tt class="py-op">+</tt> <tt id="link-110" class="py-name"><a title="Bio.EUtils.POM.ElementNode.text
Bio.Prosite.Prodoc._RecordConsumer.text
Martel.test.test_Iterator.text
Martel.test.test_ParseRecords.text" class="py-name" href="#" onclick="return doclink('link-110', 'text', 'link-52');">text</a></tt> </tt>
<a name="L170"></a><tt class="py-lineno">170</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">ndb_dict</tt><tt class="py-op">[</tt> <tt class="py-string">'Space Group'</tt> <tt class="py-op">]</tt> <tt class="py-op">=</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">_space_group</tt> </tt>
<a name="L171"></a><tt class="py-lineno">171</tt> <tt class="py-line"> <tt class="py-keyword">elif</tt><tt class="py-op">(</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">_state</tt> <tt class="py-op">==</tt> <tt class="py-string">'constants'</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">self</tt><tt class="py-op">.</tt><tt class="py-name">ndb_dict</tt><tt class="py-op">[</tt> <tt class="py-string">'Cell Constants'</tt> <tt class="py-op">]</tt> <tt class="py-op">=</tt> <tt id="link-111" class="py-name" targets="Function Bio.Ndb._parse_constants()=Bio.Ndb-module.html#_parse_constants"><a title="Bio.Ndb._parse_constants" class="py-name" href="#" onclick="return doclink('link-111', '_parse_constants', 'link-111');">_parse_constants</a></tt><tt class="py-op">(</tt> <tt id="link-112" class="py-name"><a title="Bio.EUtils.POM.ElementNode.text
Bio.Prosite.Prodoc._RecordConsumer.text
Martel.test.test_Iterator.text
Martel.test.test_ParseRecords.text" class="py-name" href="#" onclick="return doclink('link-112', 'text', 'link-52');">text</a></tt> <tt class="py-op">)</tt> </tt>
<a name="L173"></a><tt class="py-lineno">173</tt> <tt class="py-line"> <tt class="py-keyword">elif</tt><tt class="py-op">(</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">_state</tt> <tt class="py-op">==</tt> <tt class="py-string">'crystallization'</tt> <tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
<a name="L174"></a><tt class="py-lineno">174</tt> <tt class="py-line"> <tt class="py-keyword">pass</tt> </tt>
<a name="L175"></a><tt class="py-lineno">175</tt> <tt class="py-line"> <tt class="py-keyword">elif</tt><tt class="py-op">(</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">_state</tt> <tt class="py-op">==</tt> <tt class="py-string">'refinement'</tt> <tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
<a name="L176"></a><tt class="py-lineno">176</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">ndb_dict</tt><tt class="py-op">[</tt> <tt class="py-string">'Refinement'</tt> <tt class="py-op">]</tt> <tt class="py-op">=</tt> <tt id="link-113" class="py-name"><a title="Bio.EUtils.POM.ElementNode.text
Bio.Prosite.Prodoc._RecordConsumer.text
Martel.test.test_Iterator.text
Martel.test.test_ParseRecords.text" class="py-name" href="#" onclick="return doclink('link-113', 'text', 'link-52');">text</a></tt> </tt>
<a name="L177"></a><tt class="py-lineno">177</tt> <tt class="py-line"> <tt class="py-keyword">elif</tt><tt class="py-op">(</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">_state</tt> <tt class="py-op">==</tt> <tt class="py-string">'coordinates'</tt> <tt class="py-op">)</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">self</tt><tt class="py-op">.</tt><tt class="py-name">ndb_dict</tt><tt class="py-op">[</tt> <tt class="py-string">'Coordinates'</tt> <tt class="py-op">]</tt> <tt class="py-op">=</tt> <tt id="link-114" class="py-name"><a title="Bio.EUtils.POM.ElementNode.text
Bio.Prosite.Prodoc._RecordConsumer.text
Martel.test.test_Iterator.text
Martel.test.test_ParseRecords.text" class="py-name" href="#" onclick="return doclink('link-114', 'text', 'link-52');">text</a></tt> </tt>
</div><a name="L179"></a><tt class="py-lineno">179</tt> <tt class="py-line"> </tt>
<a name="NdbParser.end_h2"></a><div id="NdbParser.end_h2-def"><a name="L180"></a><tt class="py-lineno">180</tt> <a class="py-toggle" href="#" id="NdbParser.end_h2-toggle" onclick="return toggle('NdbParser.end_h2');">-</a><tt class="py-line"> <tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.Ndb.NdbParser-class.html#end_h2">end_h2</a><tt class="py-op">(</tt> <tt class="py-param">self</tt> <tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="NdbParser.end_h2-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="NdbParser.end_h2-expanded"><a name="L181"></a><tt class="py-lineno">181</tt> <tt class="py-line"> <tt id="link-115" class="py-name"><a title="Bio.EUtils.POM.ElementNode.text
Bio.Prosite.Prodoc._RecordConsumer.text
Martel.test.test_Iterator.text
Martel.test.test_ParseRecords.text" class="py-name" href="#" onclick="return doclink('link-115', 'text', 'link-52');">text</a></tt> <tt class="py-op">=</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-116" class="py-name"><a title="Bio.InterPro.InterProParser._flush_text
Bio.Ndb.NdbParser._flush_text" class="py-name" href="#" onclick="return doclink('link-116', '_flush_text', 'link-99');">_flush_text</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
<a name="L182"></a><tt class="py-lineno">182</tt> <tt class="py-line"> <tt id="link-117" class="py-name"><a title="Bio.EUtils.POM.ElementNode.text
Bio.Prosite.Prodoc._RecordConsumer.text
Martel.test.test_Iterator.text
Martel.test.test_ParseRecords.text" class="py-name" href="#" onclick="return doclink('link-117', 'text', 'link-52');">text</a></tt> <tt class="py-op">=</tt> <tt id="link-118" class="py-name"><a title="Bio.EUtils.POM.ElementNode.text
Bio.Prosite.Prodoc._RecordConsumer.text
Martel.test.test_Iterator.text
Martel.test.test_ParseRecords.text" class="py-name" href="#" onclick="return doclink('link-118', 'text', 'link-52');">text</a></tt><tt class="py-op">.</tt><tt class="py-name">lower</tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
<a name="L183"></a><tt class="py-lineno">183</tt> <tt class="py-line"> <tt class="py-keyword">if</tt><tt class="py-op">(</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">_state</tt> <tt class="py-op">==</tt> <tt class="py-string">'id'</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-op">(</tt> <tt id="link-119" class="py-name"><a title="Bio.EUtils.POM.ElementNode.text
Bio.Prosite.Prodoc._RecordConsumer.text
Martel.test.test_Iterator.text
Martel.test.test_ParseRecords.text" class="py-name" href="#" onclick="return doclink('link-119', 'text', 'link-52');">text</a></tt><tt class="py-op">.</tt><tt id="link-120" class="py-name" targets="Method Bio.EUtils.POM.ElementNode.find()=Bio.EUtils.POM.ElementNode-class.html#find,Method Bio.NeuralNetwork.Gene.Motif.MotifFinder.find()=Bio.NeuralNetwork.Gene.Motif.MotifFinder-class.html#find,Method Bio.NeuralNetwork.Gene.Schema.SchemaFinder.find()=Bio.NeuralNetwork.Gene.Schema.SchemaFinder-class.html#find,Method Bio.NeuralNetwork.Gene.Signature.SignatureFinder.find()=Bio.NeuralNetwork.Gene.Signature.SignatureFinder-class.html#find,Method Bio.biblio.Biblio.find()=Bio.biblio.Biblio-class.html#find,Function Bio.triefind.find()=Bio.triefind-module.html#find"><a title="Bio.EUtils.POM.ElementNode.find
Bio.NeuralNetwork.Gene.Motif.MotifFinder.find
Bio.NeuralNetwork.Gene.Schema.SchemaFinder.find
Bio.NeuralNetwork.Gene.Signature.SignatureFinder.find
Bio.biblio.Biblio.find
Bio.triefind.find" class="py-name" href="#" onclick="return doclink('link-120', 'find', 'link-120');">find</a></tt><tt class="py-op">(</tt> <tt class="py-string">'id'</tt> <tt class="py-op">)</tt> <tt class="py-op">>=</tt> <tt class="py-number">0</tt> <tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
<a name="L185"></a><tt class="py-lineno">185</tt> <tt class="py-line"> <tt class="py-name">cols</tt> <tt class="py-op">=</tt> <tt id="link-121" class="py-name"><a title="Bio.EUtils.POM.ElementNode.text
Bio.Prosite.Prodoc._RecordConsumer.text
Martel.test.test_Iterator.text
Martel.test.test_ParseRecords.text" class="py-name" href="#" onclick="return doclink('link-121', 'text', 'link-52');">text</a></tt><tt class="py-op">.</tt><tt id="link-122" class="py-name"><a title="Bio.Nexus.Trees.Tree.split
Bio.Restriction.Restriction.RestrictionBatch.split" class="py-name" href="#" onclick="return doclink('link-122', 'split', 'link-53');">split</a></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">self</tt><tt class="py-op">.</tt><tt class="py-name">ndb_dict</tt><tt class="py-op">[</tt> <tt class="py-string">'Id'</tt> <tt class="py-op">]</tt> <tt class="py-op">=</tt> <tt class="py-op">(</tt> <tt class="py-name">cols</tt><tt class="py-op">[</tt> <tt class="py-number">1</tt> <tt class="py-op">]</tt> <tt class="py-op">)</tt><tt class="py-op">.</tt><tt class="py-name">upper</tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
<a name="L187"></a><tt class="py-lineno">187</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">_state</tt> <tt class="py-op">=</tt> <tt class="py-string">'id_found'</tt> </tt>
<a name="L188"></a><tt class="py-lineno">188</tt> <tt class="py-line"> <tt class="py-keyword">elif</tt><tt class="py-op">(</tt> <tt id="link-123" class="py-name"><a title="Bio.EUtils.POM.ElementNode.text
Bio.Prosite.Prodoc._RecordConsumer.text
Martel.test.test_Iterator.text
Martel.test.test_ParseRecords.text" class="py-name" href="#" onclick="return doclink('link-123', 'text', 'link-52');">text</a></tt><tt class="py-op">.</tt><tt id="link-124" class="py-name"><a title="Bio.EUtils.POM.ElementNode.find
Bio.NeuralNetwork.Gene.Motif.MotifFinder.find
Bio.NeuralNetwork.Gene.Schema.SchemaFinder.find
Bio.NeuralNetwork.Gene.Signature.SignatureFinder.find
Bio.biblio.Biblio.find
Bio.triefind.find" class="py-name" href="#" onclick="return doclink('link-124', 'find', 'link-120');">find</a></tt><tt class="py-op">(</tt> <tt class="py-string">'feature'</tt> <tt class="py-op">)</tt> <tt class="py-op">>=</tt> <tt class="py-number">0</tt> <tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
<a name="L189"></a><tt class="py-lineno">189</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">_state</tt> <tt class="py-op">=</tt> <tt class="py-string">'features'</tt> </tt>
<a name="L190"></a><tt class="py-lineno">190</tt> <tt class="py-line"> <tt class="py-keyword">elif</tt><tt class="py-op">(</tt> <tt id="link-125" class="py-name"><a title="Bio.EUtils.POM.ElementNode.text
Bio.Prosite.Prodoc._RecordConsumer.text
Martel.test.test_Iterator.text
Martel.test.test_ParseRecords.text" class="py-name" href="#" onclick="return doclink('link-125', 'text', 'link-52');">text</a></tt><tt class="py-op">.</tt><tt id="link-126" class="py-name"><a title="Bio.EUtils.POM.ElementNode.find
Bio.NeuralNetwork.Gene.Motif.MotifFinder.find
Bio.NeuralNetwork.Gene.Schema.SchemaFinder.find
Bio.NeuralNetwork.Gene.Signature.SignatureFinder.find
Bio.biblio.Biblio.find
Bio.triefind.find" class="py-name" href="#" onclick="return doclink('link-126', 'find', 'link-120');">find</a></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-number">0</tt> <tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
<a name="L191"></a><tt class="py-lineno">191</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">_state</tt> <tt class="py-op">=</tt> <tt class="py-string">'name'</tt> </tt>
<a name="L192"></a><tt class="py-lineno">192</tt> <tt class="py-line"> <tt class="py-keyword">elif</tt><tt class="py-op">(</tt> <tt id="link-127" class="py-name"><a title="Bio.EUtils.POM.ElementNode.text
Bio.Prosite.Prodoc._RecordConsumer.text
Martel.test.test_Iterator.text
Martel.test.test_ParseRecords.text" class="py-name" href="#" onclick="return doclink('link-127', 'text', 'link-52');">text</a></tt><tt class="py-op">.</tt><tt id="link-128" class="py-name"><a title="Bio.EUtils.POM.ElementNode.find
Bio.NeuralNetwork.Gene.Motif.MotifFinder.find
Bio.NeuralNetwork.Gene.Schema.SchemaFinder.find
Bio.NeuralNetwork.Gene.Signature.SignatureFinder.find
Bio.biblio.Biblio.find
Bio.triefind.find" class="py-name" href="#" onclick="return doclink('link-128', 'find', 'link-120');">find</a></tt><tt class="py-op">(</tt> <tt class="py-string">'sequence'</tt> <tt class="py-op">)</tt> <tt class="py-op">>=</tt> <tt class="py-number">0</tt> <tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
<a name="L193"></a><tt class="py-lineno">193</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">_state</tt> <tt class="py-op">=</tt> <tt class="py-string">'sequence'</tt> </tt>
<a name="L194"></a><tt class="py-lineno">194</tt> <tt class="py-line"> <tt class="py-keyword">elif</tt><tt class="py-op">(</tt> <tt id="link-129" class="py-name"><a title="Bio.EUtils.POM.ElementNode.text
Bio.Prosite.Prodoc._RecordConsumer.text
Martel.test.test_Iterator.text
Martel.test.test_ParseRecords.text" class="py-name" href="#" onclick="return doclink('link-129', 'text', 'link-52');">text</a></tt><tt class="py-op">.</tt><tt id="link-130" class="py-name"><a title="Bio.EUtils.POM.ElementNode.find
Bio.NeuralNetwork.Gene.Motif.MotifFinder.find
Bio.NeuralNetwork.Gene.Schema.SchemaFinder.find
Bio.NeuralNetwork.Gene.Signature.SignatureFinder.find
Bio.biblio.Biblio.find
Bio.triefind.find" class="py-name" href="#" onclick="return doclink('link-130', 'find', 'link-120');">find</a></tt><tt class="py-op">(</tt> <tt class="py-string">'citation'</tt> <tt class="py-op">)</tt> <tt class="py-op">>=</tt> <tt class="py-number">0</tt> <tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
<a name="L195"></a><tt class="py-lineno">195</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">_state</tt> <tt class="py-op">=</tt> <tt class="py-string">'citation'</tt> </tt>
<a name="L196"></a><tt class="py-lineno">196</tt> <tt class="py-line"> <tt class="py-keyword">elif</tt><tt class="py-op">(</tt> <tt id="link-131" class="py-name"><a title="Bio.EUtils.POM.ElementNode.text
Bio.Prosite.Prodoc._RecordConsumer.text
Martel.test.test_Iterator.text
Martel.test.test_ParseRecords.text" class="py-name" href="#" onclick="return doclink('link-131', 'text', 'link-52');">text</a></tt><tt class="py-op">.</tt><tt id="link-132" class="py-name"><a title="Bio.EUtils.POM.ElementNode.find
Bio.NeuralNetwork.Gene.Motif.MotifFinder.find
Bio.NeuralNetwork.Gene.Schema.SchemaFinder.find
Bio.NeuralNetwork.Gene.Signature.SignatureFinder.find
Bio.biblio.Biblio.find
Bio.triefind.find" class="py-name" href="#" onclick="return doclink('link-132', 'find', 'link-120');">find</a></tt><tt class="py-op">(</tt> <tt class="py-string">'space'</tt> <tt class="py-op">)</tt> <tt class="py-op">>=</tt> <tt class="py-number">0</tt> <tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
<a name="L197"></a><tt class="py-lineno">197</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">_state</tt> <tt class="py-op">=</tt> <tt class="py-string">'space'</tt> </tt>
<a name="L198"></a><tt class="py-lineno">198</tt> <tt class="py-line"> <tt class="py-keyword">elif</tt><tt class="py-op">(</tt> <tt id="link-133" class="py-name"><a title="Bio.EUtils.POM.ElementNode.text
Bio.Prosite.Prodoc._RecordConsumer.text
Martel.test.test_Iterator.text
Martel.test.test_ParseRecords.text" class="py-name" href="#" onclick="return doclink('link-133', 'text', 'link-52');">text</a></tt><tt class="py-op">.</tt><tt id="link-134" class="py-name"><a title="Bio.EUtils.POM.ElementNode.find
Bio.NeuralNetwork.Gene.Motif.MotifFinder.find
Bio.NeuralNetwork.Gene.Schema.SchemaFinder.find
Bio.NeuralNetwork.Gene.Signature.SignatureFinder.find
Bio.biblio.Biblio.find
Bio.triefind.find" class="py-name" href="#" onclick="return doclink('link-134', 'find', 'link-120');">find</a></tt><tt class="py-op">(</tt> <tt class="py-string">'constants'</tt> <tt class="py-op">)</tt> <tt class="py-op">>=</tt> <tt class="py-number">0</tt> <tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
<a name="L199"></a><tt class="py-lineno">199</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">_state</tt> <tt class="py-op">=</tt> <tt class="py-string">'constants'</tt> </tt>
<a name="L200"></a><tt class="py-lineno">200</tt> <tt class="py-line"> <tt class="py-keyword">elif</tt><tt class="py-op">(</tt> <tt id="link-135" class="py-name"><a title="Bio.EUtils.POM.ElementNode.text
Bio.Prosite.Prodoc._RecordConsumer.text
Martel.test.test_Iterator.text
Martel.test.test_ParseRecords.text" class="py-name" href="#" onclick="return doclink('link-135', 'text', 'link-52');">text</a></tt><tt class="py-op">.</tt><tt id="link-136" class="py-name"><a title="Bio.EUtils.POM.ElementNode.find
Bio.NeuralNetwork.Gene.Motif.MotifFinder.find
Bio.NeuralNetwork.Gene.Schema.SchemaFinder.find
Bio.NeuralNetwork.Gene.Signature.SignatureFinder.find
Bio.biblio.Biblio.find
Bio.triefind.find" class="py-name" href="#" onclick="return doclink('link-136', 'find', 'link-120');">find</a></tt><tt class="py-op">(</tt> <tt class="py-string">'crystallization'</tt> <tt class="py-op">)</tt> <tt class="py-op">>=</tt> <tt class="py-number">0</tt> <tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
<a name="L201"></a><tt class="py-lineno">201</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">_state</tt> <tt class="py-op">=</tt> <tt class="py-string">'crystallization'</tt> </tt>
<a name="L202"></a><tt class="py-lineno">202</tt> <tt class="py-line"> <tt class="py-keyword">elif</tt><tt class="py-op">(</tt> <tt id="link-137" class="py-name"><a title="Bio.EUtils.POM.ElementNode.text
Bio.Prosite.Prodoc._RecordConsumer.text
Martel.test.test_Iterator.text
Martel.test.test_ParseRecords.text" class="py-name" href="#" onclick="return doclink('link-137', 'text', 'link-52');">text</a></tt><tt class="py-op">.</tt><tt id="link-138" class="py-name"><a title="Bio.EUtils.POM.ElementNode.find
Bio.NeuralNetwork.Gene.Motif.MotifFinder.find
Bio.NeuralNetwork.Gene.Schema.SchemaFinder.find
Bio.NeuralNetwork.Gene.Signature.SignatureFinder.find
Bio.biblio.Biblio.find
Bio.triefind.find" class="py-name" href="#" onclick="return doclink('link-138', 'find', 'link-120');">find</a></tt><tt class="py-op">(</tt> <tt class="py-string">'refinement'</tt> <tt class="py-op">)</tt> <tt class="py-op">>=</tt> <tt class="py-number">0</tt> <tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
<a name="L203"></a><tt class="py-lineno">203</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">_state</tt> <tt class="py-op">=</tt> <tt class="py-string">'refinement'</tt> </tt>
<a name="L204"></a><tt class="py-lineno">204</tt> <tt class="py-line"> <tt class="py-keyword">elif</tt><tt class="py-op">(</tt> <tt id="link-139" class="py-name"><a title="Bio.EUtils.POM.ElementNode.text
Bio.Prosite.Prodoc._RecordConsumer.text
Martel.test.test_Iterator.text
Martel.test.test_ParseRecords.text" class="py-name" href="#" onclick="return doclink('link-139', 'text', 'link-52');">text</a></tt><tt class="py-op">.</tt><tt id="link-140" class="py-name"><a title="Bio.EUtils.POM.ElementNode.find
Bio.NeuralNetwork.Gene.Motif.MotifFinder.find
Bio.NeuralNetwork.Gene.Schema.SchemaFinder.find
Bio.NeuralNetwork.Gene.Signature.SignatureFinder.find
Bio.biblio.Biblio.find
Bio.triefind.find" class="py-name" href="#" onclick="return doclink('link-140', 'find', 'link-120');">find</a></tt><tt class="py-op">(</tt> <tt class="py-string">'coordinates'</tt> <tt class="py-op">)</tt> <tt class="py-op">>=</tt> <tt class="py-number">0</tt> <tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
<a name="L205"></a><tt class="py-lineno">205</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">_state</tt> <tt class="py-op">=</tt> <tt class="py-string">'coordinates'</tt> </tt>
</div><a name="L206"></a><tt class="py-lineno">206</tt> <tt class="py-line"> </tt>
<a name="L207"></a><tt class="py-lineno">207</tt> <tt class="py-line"> </tt>
<a name="NdbParser.start_ul"></a><div id="NdbParser.start_ul-def"><a name="L208"></a><tt class="py-lineno">208</tt> <a class="py-toggle" href="#" id="NdbParser.start_ul-toggle" onclick="return toggle('NdbParser.start_ul');">-</a><tt class="py-line"> <tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.Ndb.NdbParser-class.html#start_ul">start_ul</a><tt class="py-op">(</tt> <tt class="py-param">self</tt><tt class="py-op">,</tt> <tt class="py-param">attrs</tt> <tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="NdbParser.start_ul-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="NdbParser.start_ul-expanded"><a name="L209"></a><tt class="py-lineno">209</tt> <tt class="py-line"> <tt class="py-keyword">if</tt><tt class="py-op">(</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">_state</tt> <tt class="py-op">==</tt> <tt class="py-string">'sequence'</tt> <tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
<a name="L210"></a><tt class="py-lineno">210</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-141" class="py-name"><a title="Bio.InterPro.InterProParser._flush_text
Bio.Ndb.NdbParser._flush_text" class="py-name" href="#" onclick="return doclink('link-141', '_flush_text', 'link-99');">_flush_text</a></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>
<a name="L212"></a><tt class="py-lineno">212</tt> <tt class="py-line"> <tt class="py-keyword">elif</tt><tt class="py-op">(</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">_state</tt> <tt class="py-op">==</tt> <tt class="py-string">'crystallization'</tt> <tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
<a name="L213"></a><tt class="py-lineno">213</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-142" class="py-name"><a title="Bio.InterPro.InterProParser._flush_text
Bio.Ndb.NdbParser._flush_text" class="py-name" href="#" onclick="return doclink('link-142', '_flush_text', 'link-99');">_flush_text</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
</div><a name="L214"></a><tt class="py-lineno">214</tt> <tt class="py-line"> </tt>
<a name="NdbParser.end_ul"></a><div id="NdbParser.end_ul-def"><a name="L215"></a><tt class="py-lineno">215</tt> <a class="py-toggle" href="#" id="NdbParser.end_ul-toggle" onclick="return toggle('NdbParser.end_ul');">-</a><tt class="py-line"> <tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.Ndb.NdbParser-class.html#end_ul">end_ul</a><tt class="py-op">(</tt> <tt class="py-param">self</tt> <tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="NdbParser.end_ul-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="NdbParser.end_ul-expanded"><a name="L216"></a><tt class="py-lineno">216</tt> <tt class="py-line"> <tt class="py-keyword">if</tt><tt class="py-op">(</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">_state</tt> <tt class="py-op">==</tt> <tt class="py-string">'sequence'</tt> <tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
<a name="L217"></a><tt class="py-lineno">217</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-143" class="py-name" targets="Method Bio.Ndb.NdbParser._parse_chain()=Bio.Ndb.NdbParser-class.html#_parse_chain"><a title="Bio.Ndb.NdbParser._parse_chain" class="py-name" href="#" onclick="return doclink('link-143', '_parse_chain', 'link-143');">_parse_chain</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
<a name="L218"></a><tt class="py-lineno">218</tt> <tt class="py-line"> <tt class="py-keyword">elif</tt><tt class="py-op">(</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">_state</tt> <tt class="py-op">==</tt> <tt class="py-string">'crystallization'</tt> <tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
<a name="L219"></a><tt class="py-lineno">219</tt> <tt class="py-line"> <tt id="link-144" class="py-name"><a title="Bio.EUtils.POM.ElementNode.text
Bio.Prosite.Prodoc._RecordConsumer.text
Martel.test.test_Iterator.text
Martel.test.test_ParseRecords.text" class="py-name" href="#" onclick="return doclink('link-144', 'text', 'link-52');">text</a></tt> <tt class="py-op">=</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-145" class="py-name"><a title="Bio.InterPro.InterProParser._flush_text
Bio.Ndb.NdbParser._flush_text" class="py-name" href="#" onclick="return doclink('link-145', '_flush_text', 'link-99');">_flush_text</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
<a name="L220"></a><tt class="py-lineno">220</tt> <tt class="py-line"> <tt class="py-op">(</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">ndb_dict</tt><tt class="py-op">[</tt> <tt class="py-string">'Crystallization Conditions'</tt> <tt class="py-op">]</tt> <tt class="py-op">)</tt><tt class="py-op">.</tt><tt id="link-146" 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-146', 'append', 'link-146');">append</a></tt><tt class="py-op">(</tt> <tt id="link-147" class="py-name"><a title="Bio.EUtils.POM.ElementNode.text
Bio.Prosite.Prodoc._RecordConsumer.text
Martel.test.test_Iterator.text
Martel.test.test_ParseRecords.text" class="py-name" href="#" onclick="return doclink('link-147', 'text', 'link-52');">text</a></tt> <tt class="py-op">)</tt> </tt>
<a name="L221"></a><tt class="py-lineno">221</tt> <tt class="py-line"> <tt class="py-keyword">elif</tt><tt class="py-op">(</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">_state</tt> <tt class="py-op">==</tt> <tt class="py-string">'citation'</tt> <tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
<a name="L222"></a><tt class="py-lineno">222</tt> <tt class="py-line"> <tt class="py-keyword">if</tt><tt class="py-op">(</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">_reference_state</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="L223"></a><tt class="py-lineno">223</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">_current_reference</tt><tt class="py-op">.</tt><tt id="link-148" class="py-name"><a title="Bio.GenBank._FeatureConsumer.journal
Bio.GenBank._RecordConsumer.journal" class="py-name" href="#" onclick="return doclink('link-148', 'journal', 'link-108');">journal</a></tt> <tt class="py-op">=</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-149" class="py-name"><a title="Bio.InterPro.InterProParser._flush_text
Bio.Ndb.NdbParser._flush_text" class="py-name" href="#" onclick="return doclink('link-149', '_flush_text', 'link-99');">_flush_text</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
<a name="L224"></a><tt class="py-lineno">224</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">_reference_state</tt> <tt class="py-op">=</tt> <tt class="py-string">'done'</tt> </tt>
</div><a name="L225"></a><tt class="py-lineno">225</tt> <tt class="py-line"> </tt>
<a name="NdbParser.start_sub"></a><div id="NdbParser.start_sub-def"><a name="L226"></a><tt class="py-lineno">226</tt> <a class="py-toggle" href="#" id="NdbParser.start_sub-toggle" onclick="return toggle('NdbParser.start_sub');">-</a><tt class="py-line"> <tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.Ndb.NdbParser-class.html#start_sub">start_sub</a><tt class="py-op">(</tt> <tt class="py-param">self</tt><tt class="py-op">,</tt> <tt class="py-param">attrs</tt> <tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="NdbParser.start_sub-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="NdbParser.start_sub-expanded"><a name="L227"></a><tt class="py-lineno">227</tt> <tt class="py-line"> <tt class="py-keyword">if</tt><tt class="py-op">(</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">_state</tt> <tt class="py-op">==</tt> <tt class="py-string">'space'</tt> <tt class="py-op">)</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">self</tt><tt class="py-op">.</tt><tt class="py-name">_space_group</tt> <tt class="py-op">=</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">_space_group</tt> <tt class="py-op">+</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-150" class="py-name"><a title="Bio.InterPro.InterProParser._flush_text
Bio.Ndb.NdbParser._flush_text" class="py-name" href="#" onclick="return doclink('link-150', '_flush_text', 'link-99');">_flush_text</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
</div><a name="L229"></a><tt class="py-lineno">229</tt> <tt class="py-line"> </tt>
<a name="NdbParser.end_sub"></a><div id="NdbParser.end_sub-def"><a name="L230"></a><tt class="py-lineno">230</tt> <a class="py-toggle" href="#" id="NdbParser.end_sub-toggle" onclick="return toggle('NdbParser.end_sub');">-</a><tt class="py-line"> <tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.Ndb.NdbParser-class.html#end_sub">end_sub</a><tt class="py-op">(</tt> <tt class="py-param">self</tt> <tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="NdbParser.end_sub-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="NdbParser.end_sub-expanded"><a name="L231"></a><tt class="py-lineno">231</tt> <tt class="py-line"> <tt class="py-keyword">if</tt><tt class="py-op">(</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">_state</tt> <tt class="py-op">==</tt> <tt class="py-string">'space'</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">self</tt><tt class="py-op">.</tt><tt class="py-name">_space_group</tt> <tt class="py-op">=</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">_space_group</tt> <tt class="py-op">+</tt> <tt class="py-string">'(%s) '</tt> <tt class="py-op">%</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-151" class="py-name"><a title="Bio.InterPro.InterProParser._flush_text
Bio.Ndb.NdbParser._flush_text" class="py-name" href="#" onclick="return doclink('link-151', '_flush_text', 'link-99');">_flush_text</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
</div><a name="L233"></a><tt class="py-lineno">233</tt> <tt class="py-line"> </tt>
<a name="NdbParser.start_li"></a><div id="NdbParser.start_li-def"><a name="L234"></a><tt class="py-lineno">234</tt> <a class="py-toggle" href="#" id="NdbParser.start_li-toggle" onclick="return toggle('NdbParser.start_li');">-</a><tt class="py-line"> <tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.Ndb.NdbParser-class.html#start_li">start_li</a><tt class="py-op">(</tt> <tt class="py-param">self</tt><tt class="py-op">,</tt> <tt class="py-param">attrs</tt> <tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="NdbParser.start_li-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="NdbParser.start_li-expanded"><a name="L235"></a><tt class="py-lineno">235</tt> <tt class="py-line"> <tt class="py-keyword">if</tt><tt class="py-op">(</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">_state</tt> <tt class="py-op">==</tt> <tt class="py-string">'sequence'</tt> <tt class="py-op">)</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">self</tt><tt class="py-op">.</tt><tt id="link-152" class="py-name"><a title="Bio.Ndb.NdbParser._parse_chain" class="py-name" href="#" onclick="return doclink('link-152', '_parse_chain', 'link-143');">_parse_chain</a></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">elif</tt><tt class="py-op">(</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">_state</tt> <tt class="py-op">==</tt> <tt class="py-string">'crystallization'</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 id="link-153" class="py-name"><a title="Bio.EUtils.POM.ElementNode.text
Bio.Prosite.Prodoc._RecordConsumer.text
Martel.test.test_Iterator.text
Martel.test.test_ParseRecords.text" class="py-name" href="#" onclick="return doclink('link-153', 'text', 'link-52');">text</a></tt> <tt class="py-op">=</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-154" class="py-name"><a title="Bio.InterPro.InterProParser._flush_text
Bio.Ndb.NdbParser._flush_text" class="py-name" href="#" onclick="return doclink('link-154', '_flush_text', 'link-99');">_flush_text</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
<a name="L239"></a><tt class="py-lineno">239</tt> <tt class="py-line"> <tt class="py-op">(</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">ndb_dict</tt><tt class="py-op">[</tt> <tt class="py-string">'Crystallization Conditions'</tt> <tt class="py-op">]</tt> <tt class="py-op">)</tt><tt class="py-op">.</tt><tt id="link-155" 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-155', 'append', 'link-146');">append</a></tt><tt class="py-op">(</tt> <tt id="link-156" class="py-name"><a title="Bio.EUtils.POM.ElementNode.text
Bio.Prosite.Prodoc._RecordConsumer.text
Martel.test.test_Iterator.text
Martel.test.test_ParseRecords.text" class="py-name" href="#" onclick="return doclink('link-156', 'text', 'link-52');">text</a></tt> <tt class="py-op">)</tt> </tt>
</div><a name="L240"></a><tt class="py-lineno">240</tt> <tt class="py-line"> </tt>
<a name="NdbParser.end_li"></a><div id="NdbParser.end_li-def"><a name="L241"></a><tt class="py-lineno">241</tt> <a class="py-toggle" href="#" id="NdbParser.end_li-toggle" onclick="return toggle('NdbParser.end_li');">-</a><tt class="py-line"> <tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.Ndb.NdbParser-class.html#end_li">end_li</a><tt class="py-op">(</tt> <tt class="py-param">self</tt> <tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="NdbParser.end_li-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="NdbParser.end_li-expanded"><a name="L242"></a><tt class="py-lineno">242</tt> <tt class="py-line"> <tt class="py-keyword">if</tt><tt class="py-op">(</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">_state</tt> <tt class="py-op">==</tt> <tt class="py-string">'sequence'</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">self</tt><tt class="py-op">.</tt><tt id="link-157" class="py-name"><a title="Bio.Ndb.NdbParser._parse_chain" class="py-name" href="#" onclick="return doclink('link-157', '_parse_chain', 'link-143');">_parse_chain</a></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-keyword">elif</tt><tt class="py-op">(</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">_state</tt> <tt class="py-op">==</tt> <tt class="py-string">'crystallization'</tt> <tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
<a name="L245"></a><tt class="py-lineno">245</tt> <tt class="py-line"> <tt id="link-158" class="py-name"><a title="Bio.EUtils.POM.ElementNode.text
Bio.Prosite.Prodoc._RecordConsumer.text
Martel.test.test_Iterator.text
Martel.test.test_ParseRecords.text" class="py-name" href="#" onclick="return doclink('link-158', 'text', 'link-52');">text</a></tt> <tt class="py-op">=</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-159" class="py-name"><a title="Bio.InterPro.InterProParser._flush_text
Bio.Ndb.NdbParser._flush_text" class="py-name" href="#" onclick="return doclink('link-159', '_flush_text', 'link-99');">_flush_text</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
<a name="L246"></a><tt class="py-lineno">246</tt> <tt class="py-line"> <tt class="py-op">(</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">ndb_dict</tt><tt class="py-op">[</tt> <tt class="py-string">'Crystallization Conditions'</tt> <tt class="py-op">]</tt> <tt class="py-op">)</tt><tt class="py-op">.</tt><tt id="link-160" 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-160', 'append', 'link-146');">append</a></tt><tt class="py-op">(</tt> <tt id="link-161" class="py-name"><a title="Bio.EUtils.POM.ElementNode.text
Bio.Prosite.Prodoc._RecordConsumer.text
Martel.test.test_Iterator.text
Martel.test.test_ParseRecords.text" class="py-name" href="#" onclick="return doclink('link-161', 'text', 'link-52');">text</a></tt> <tt class="py-op">)</tt> </tt>
</div><a name="L247"></a><tt class="py-lineno">247</tt> <tt class="py-line"> </tt>
<a name="NdbParser.do_br"></a><div id="NdbParser.do_br-def"><a name="L248"></a><tt class="py-lineno">248</tt> <a class="py-toggle" href="#" id="NdbParser.do_br-toggle" onclick="return toggle('NdbParser.do_br');">-</a><tt class="py-line"> <tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.Ndb.NdbParser-class.html#do_br">do_br</a><tt class="py-op">(</tt> <tt class="py-param">self</tt><tt class="py-op">,</tt> <tt class="py-param">attrs</tt> <tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="NdbParser.do_br-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="NdbParser.do_br-expanded"><a name="L249"></a><tt class="py-lineno">249</tt> <tt class="py-line"> <tt class="py-keyword">if</tt><tt class="py-op">(</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">_state</tt> <tt class="py-op">==</tt> <tt class="py-string">'citation'</tt> <tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
<a name="L250"></a><tt class="py-lineno">250</tt> <tt class="py-line"> <tt class="py-keyword">if</tt><tt class="py-op">(</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">_reference_state</tt> <tt class="py-op">==</tt> <tt class="py-string">'authors'</tt> <tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
<a name="L251"></a><tt class="py-lineno">251</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">_current_reference</tt><tt class="py-op">.</tt><tt id="link-162" class="py-name" targets="Method Bio.GenBank._FeatureConsumer.authors()=Bio.GenBank._FeatureConsumer-class.html#authors,Method Bio.GenBank._RecordConsumer.authors()=Bio.GenBank._RecordConsumer-class.html#authors"><a title="Bio.GenBank._FeatureConsumer.authors
Bio.GenBank._RecordConsumer.authors" class="py-name" href="#" onclick="return doclink('link-162', 'authors', 'link-162');">authors</a></tt> <tt class="py-op">=</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-163" class="py-name"><a title="Bio.InterPro.InterProParser._flush_text
Bio.Ndb.NdbParser._flush_text" class="py-name" href="#" onclick="return doclink('link-163', '_flush_text', 'link-99');">_flush_text</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
<a name="L252"></a><tt class="py-lineno">252</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">_reference_state</tt> <tt class="py-op">=</tt> <tt class="py-string">'title'</tt> </tt>
<a name="L253"></a><tt class="py-lineno">253</tt> <tt class="py-line"> <tt class="py-keyword">elif</tt><tt class="py-op">(</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">_reference_state</tt> <tt class="py-op">==</tt> <tt class="py-string">'title'</tt> <tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
<a name="L254"></a><tt class="py-lineno">254</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">_current_reference</tt><tt class="py-op">.</tt><tt id="link-164" class="py-name" targets="Method Bio.Blast.NCBIStandalone._AlignmentConsumer.title()=Bio.Blast.NCBIStandalone._AlignmentConsumer-class.html#title,Method Bio.GenBank._FeatureConsumer.title()=Bio.GenBank._FeatureConsumer-class.html#title,Method Bio.GenBank._RecordConsumer.title()=Bio.GenBank._RecordConsumer-class.html#title,Method Bio.Medline._RecordConsumer.title()=Bio.Medline._RecordConsumer-class.html#title,Variable Bio.expressions.fasta.title=Bio.expressions.fasta-module.html#title"><a title="Bio.Blast.NCBIStandalone._AlignmentConsumer.title
Bio.GenBank._FeatureConsumer.title
Bio.GenBank._RecordConsumer.title
Bio.Medline._RecordConsumer.title
Bio.expressions.fasta.title" class="py-name" href="#" onclick="return doclink('link-164', 'title', 'link-164');">title</a></tt> <tt class="py-op">=</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-165" class="py-name"><a title="Bio.InterPro.InterProParser._flush_text
Bio.Ndb.NdbParser._flush_text" class="py-name" href="#" onclick="return doclink('link-165', '_flush_text', 'link-99');">_flush_text</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
<a name="L255"></a><tt class="py-lineno">255</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">_reference_state</tt> <tt class="py-op">=</tt> <tt class="py-string">'journal'</tt> </tt>
</div><a name="L256"></a><tt class="py-lineno">256</tt> <tt class="py-line"> </tt>
<a name="NdbParser.start_i"></a><div id="NdbParser.start_i-def"><a name="L257"></a><tt class="py-lineno">257</tt> <a class="py-toggle" href="#" id="NdbParser.start_i-toggle" onclick="return toggle('NdbParser.start_i');">-</a><tt class="py-line"> <tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.Ndb.NdbParser-class.html#start_i">start_i</a><tt class="py-op">(</tt> <tt class="py-param">self</tt><tt class="py-op">,</tt> <tt class="py-param">attrs</tt> <tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="NdbParser.start_i-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="NdbParser.start_i-expanded"><a name="L258"></a><tt class="py-lineno">258</tt> <tt class="py-line"> <tt class="py-keyword">pass</tt> </tt>
</div><a name="L259"></a><tt class="py-lineno">259</tt> <tt class="py-line"> </tt>
<a name="NdbParser.end_i"></a><div id="NdbParser.end_i-def"><a name="L260"></a><tt class="py-lineno">260</tt> <a class="py-toggle" href="#" id="NdbParser.end_i-toggle" onclick="return toggle('NdbParser.end_i');">-</a><tt class="py-line"> <tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.Ndb.NdbParser-class.html#end_i">end_i</a><tt class="py-op">(</tt> <tt class="py-param">self</tt> <tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="NdbParser.end_i-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="NdbParser.end_i-expanded"><a name="L261"></a><tt class="py-lineno">261</tt> <tt class="py-line"> <tt class="py-keyword">if</tt><tt class="py-op">(</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">_state</tt> <tt class="py-op">==</tt> <tt class="py-string">'references'</tt> <tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
<a name="L262"></a><tt class="py-lineno">262</tt> <tt class="py-line"> <tt class="py-keyword">if</tt><tt class="py-op">(</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">_reference_state</tt> <tt class="py-op">==</tt> <tt class="py-string">'title'</tt> <tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
<a name="L263"></a><tt class="py-lineno">263</tt> <tt class="py-line"> <tt id="link-166" class="py-name"><a title="Bio.EUtils.POM.ElementNode.text
Bio.Prosite.Prodoc._RecordConsumer.text
Martel.test.test_Iterator.text
Martel.test.test_ParseRecords.text" class="py-name" href="#" onclick="return doclink('link-166', 'text', 'link-52');">text</a></tt> <tt class="py-op">=</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-167" class="py-name"><a title="Bio.InterPro.InterProParser._flush_text
Bio.Ndb.NdbParser._flush_text" class="py-name" href="#" onclick="return doclink('link-167', '_flush_text', 'link-99');">_flush_text</a></tt><tt class="py-op">(</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">self</tt><tt class="py-op">.</tt><tt class="py-name">_current_reference</tt><tt class="py-op">.</tt><tt id="link-168" class="py-name"><a title="Bio.Blast.NCBIStandalone._AlignmentConsumer.title
Bio.GenBank._FeatureConsumer.title
Bio.GenBank._RecordConsumer.title
Bio.Medline._RecordConsumer.title
Bio.expressions.fasta.title" class="py-name" href="#" onclick="return doclink('link-168', 'title', 'link-164');">title</a></tt> <tt class="py-op">=</tt> <tt id="link-169" class="py-name"><a title="Bio.EUtils.POM.ElementNode.text
Bio.Prosite.Prodoc._RecordConsumer.text
Martel.test.test_Iterator.text
Martel.test.test_ParseRecords.text" class="py-name" href="#" onclick="return doclink('link-169', 'text', 'link-52');">text</a></tt> </tt>
<a name="L265"></a><tt class="py-lineno">265</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">_reference_state</tt> <tt class="py-op">=</tt> <tt class="py-string">'journal'</tt> </tt>
</div><a name="L266"></a><tt class="py-lineno">266</tt> <tt class="py-line"> </tt>
<a name="L267"></a><tt class="py-lineno">267</tt> <tt class="py-line"> </tt>
<a name="NdbParser._parse_chain"></a><div id="NdbParser._parse_chain-def"><a name="L268"></a><tt class="py-lineno">268</tt> <a class="py-toggle" href="#" id="NdbParser._parse_chain-toggle" onclick="return toggle('NdbParser._parse_chain');">-</a><tt class="py-line"> <tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.Ndb.NdbParser-class.html#_parse_chain">_parse_chain</a><tt class="py-op">(</tt> <tt class="py-param">self</tt> <tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="NdbParser._parse_chain-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="NdbParser._parse_chain-expanded"><a name="L269"></a><tt class="py-lineno">269</tt> <tt class="py-line"> <tt id="link-170" class="py-name"><a title="Bio.EUtils.POM.ElementNode.text
Bio.Prosite.Prodoc._RecordConsumer.text
Martel.test.test_Iterator.text
Martel.test.test_ParseRecords.text" class="py-name" href="#" onclick="return doclink('link-170', 'text', 'link-52');">text</a></tt> <tt class="py-op">=</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-171" class="py-name"><a title="Bio.InterPro.InterProParser._flush_text
Bio.Ndb.NdbParser._flush_text" class="py-name" href="#" onclick="return doclink('link-171', '_flush_text', 'link-99');">_flush_text</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
<a name="L270"></a><tt class="py-lineno">270</tt> <tt class="py-line"> <tt id="link-172" class="py-name"><a title="Bio.EUtils.POM.ElementNode.text
Bio.Prosite.Prodoc._RecordConsumer.text
Martel.test.test_Iterator.text
Martel.test.test_ParseRecords.text" class="py-name" href="#" onclick="return doclink('link-172', 'text', 'link-52');">text</a></tt> <tt class="py-op">=</tt> <tt id="link-173" class="py-name"><a title="Bio.EUtils.POM.ElementNode.text
Bio.Prosite.Prodoc._RecordConsumer.text
Martel.test.test_Iterator.text
Martel.test.test_ParseRecords.text" class="py-name" href="#" onclick="return doclink('link-173', 'text', 'link-52');">text</a></tt><tt class="py-op">.</tt><tt id="link-174" class="py-name"><a title="Bio.EUtils.DTDs.LinkOut.strip
Bio.File.SGMLStripper.strip
Bio.SGMLExtractor.SGMLExtractor.strip" class="py-name" href="#" onclick="return doclink('link-174', 'strip', 'link-62');">strip</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
<a name="L271"></a><tt class="py-lineno">271</tt> <tt class="py-line"> <tt class="py-keyword">if</tt><tt class="py-op">(</tt> <tt id="link-175" class="py-name"><a title="Bio.EUtils.POM.ElementNode.text
Bio.Prosite.Prodoc._RecordConsumer.text
Martel.test.test_Iterator.text
Martel.test.test_ParseRecords.text" class="py-name" href="#" onclick="return doclink('link-175', 'text', 'link-52');">text</a></tt><tt class="py-op">.</tt><tt class="py-name">lower</tt><tt class="py-op">(</tt><tt class="py-op">)</tt><tt class="py-op">.</tt><tt class="py-name">startswith</tt><tt class="py-op">(</tt> <tt class="py-string">'chain'</tt> <tt class="py-op">)</tt> <tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
<a name="L272"></a><tt class="py-lineno">272</tt> <tt class="py-line"> <tt class="py-name">fields</tt> <tt class="py-op">=</tt> <tt id="link-176" class="py-name"><a title="Bio.EUtils.POM.ElementNode.text
Bio.Prosite.Prodoc._RecordConsumer.text
Martel.test.test_Iterator.text
Martel.test.test_ParseRecords.text" class="py-name" href="#" onclick="return doclink('link-176', 'text', 'link-52');">text</a></tt><tt class="py-op">.</tt><tt id="link-177" class="py-name"><a title="Bio.Nexus.Trees.Tree.split
Bio.Restriction.Restriction.RestrictionBatch.split" class="py-name" href="#" onclick="return doclink('link-177', 'split', 'link-53');">split</a></tt><tt class="py-op">(</tt> <tt class="py-string">':'</tt> <tt class="py-op">)</tt> </tt>
<a name="L273"></a><tt class="py-lineno">273</tt> <tt class="py-line"> <tt class="py-name">words</tt> <tt class="py-op">=</tt> <tt class="py-name">fields</tt><tt class="py-op">[</tt> <tt class="py-number">0</tt> <tt class="py-op">]</tt><tt class="py-op">.</tt><tt id="link-178" class="py-name"><a title="Bio.Nexus.Trees.Tree.split
Bio.Restriction.Restriction.RestrictionBatch.split" class="py-name" href="#" onclick="return doclink('link-178', 'split', 'link-53');">split</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
<a name="L274"></a><tt class="py-lineno">274</tt> <tt class="py-line"> <tt id="link-179" class="py-name"><a title="Bio.Translate.key" class="py-name" href="#" onclick="return doclink('link-179', 'key', 'link-27');">key</a></tt> <tt class="py-op">=</tt> <tt class="py-name">words</tt><tt class="py-op">[</tt> <tt class="py-number">1</tt> <tt class="py-op">]</tt> </tt>
<a name="L275"></a><tt class="py-lineno">275</tt> <tt class="py-line"> <tt class="py-name">val</tt> <tt class="py-op">=</tt> <tt class="py-name">fields</tt><tt class="py-op">[</tt> <tt class="py-number">1</tt> <tt class="py-op">]</tt> </tt>
<a name="L276"></a><tt class="py-lineno">276</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">ndb_dict</tt><tt class="py-op">[</tt> <tt class="py-string">'Sequence'</tt> <tt class="py-op">]</tt><tt class="py-op">[</tt> <tt id="link-180" class="py-name"><a title="Bio.Translate.key" class="py-name" href="#" onclick="return doclink('link-180', 'key', 'link-27');">key</a></tt> <tt class="py-op">]</tt> <tt class="py-op">=</tt> <tt class="py-name">val</tt> </tt>
</div><a name="L277"></a><tt class="py-lineno">277</tt> <tt class="py-line"> </tt>
<a name="L278"></a><tt class="py-lineno">278</tt> <tt class="py-line"> </tt>
<a name="L279"></a><tt class="py-lineno">279</tt> <tt class="py-line"> </tt>
<a name="NdbParser._flush_text"></a><div id="NdbParser._flush_text-def"><a name="L280"></a><tt class="py-lineno">280</tt> <a class="py-toggle" href="#" id="NdbParser._flush_text-toggle" onclick="return toggle('NdbParser._flush_text');">-</a><tt class="py-line"> <tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.Ndb.NdbParser-class.html#_flush_text">_flush_text</a><tt class="py-op">(</tt> <tt class="py-param">self</tt> <tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="NdbParser._flush_text-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="NdbParser._flush_text-expanded"><a name="L281"></a><tt class="py-lineno">281</tt> <tt class="py-line"> <tt id="link-181" class="py-name"><a title="Bio.EUtils.POM.ElementNode.text
Bio.Prosite.Prodoc._RecordConsumer.text
Martel.test.test_Iterator.text
Martel.test.test_ParseRecords.text" class="py-name" href="#" onclick="return doclink('link-181', 'text', 'link-52');">text</a></tt> <tt class="py-op">=</tt> <tt class="py-name">string</tt><tt class="py-op">.</tt><tt id="link-182" class="py-name"><a title="Bio.EUtils.DTDs.LinkOut.strip
Bio.File.SGMLStripper.strip
Bio.SGMLExtractor.SGMLExtractor.strip" class="py-name" href="#" onclick="return doclink('link-182', 'strip', 'link-62');">strip</a></tt><tt class="py-op">(</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-183" class="py-name"><a title="Bio.EUtils.POM.ElementNode.text
Bio.Prosite.Prodoc._RecordConsumer.text
Martel.test.test_Iterator.text
Martel.test.test_ParseRecords.text" class="py-name" href="#" onclick="return doclink('link-183', 'text', 'link-52');">text</a></tt> <tt class="py-op">)</tt> </tt>
<a name="L282"></a><tt class="py-lineno">282</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-184" class="py-name"><a title="Bio.EUtils.POM.ElementNode.text
Bio.Prosite.Prodoc._RecordConsumer.text
Martel.test.test_Iterator.text
Martel.test.test_ParseRecords.text" class="py-name" href="#" onclick="return doclink('link-184', 'text', 'link-52');">text</a></tt> <tt class="py-op">=</tt> <tt class="py-string">''</tt> </tt>
<a name="L283"></a><tt class="py-lineno">283</tt> <tt class="py-line"> <tt class="py-keyword">return</tt> <tt id="link-185" class="py-name"><a title="Bio.EUtils.POM.ElementNode.text
Bio.Prosite.Prodoc._RecordConsumer.text
Martel.test.test_Iterator.text
Martel.test.test_ParseRecords.text" class="py-name" href="#" onclick="return doclink('link-185', 'text', 'link-52');">text</a></tt><tt class="py-op">[</tt><tt class="py-op">:</tt><tt class="py-op">]</tt> </tt>
</div></div><a name="L284"></a><tt class="py-lineno">284</tt> <tt class="py-line"> </tt>
<a name="L285"></a><tt class="py-lineno">285</tt> <tt class="py-line"> </tt>
<a name="L286"></a><tt class="py-lineno">286</tt> <tt class="py-line"><tt class="py-keyword">if</tt><tt class="py-op">(</tt> <tt class="py-name">__name__</tt> <tt class="py-op">==</tt> <tt class="py-string">'__main__'</tt> <tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
<a name="L287"></a><tt class="py-lineno">287</tt> <tt class="py-line"> <tt id="link-186" class="py-name"><a title="Bio.LocusLink.web_parse.handle
Bio.Ndb.handle" class="py-name" href="#" onclick="return doclink('link-186', 'handle', 'link-81');">handle</a></tt> <tt class="py-op">=</tt> <tt id="link-187" 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-187', 'open', 'link-187');">open</a></tt><tt class="py-op">(</tt> <tt class="py-string">'PR0004.htm'</tt><tt class="py-op">)</tt> </tt>
<a name="L288"></a><tt class="py-lineno">288</tt> <tt class="py-line"> <tt id="link-188" class="py-name" targets="Variable Bio.LocusLink.web_parse.undo_handle=Bio.LocusLink.web_parse-module.html#undo_handle,Variable Bio.Ndb.undo_handle=Bio.Ndb-module.html#undo_handle"><a title="Bio.LocusLink.web_parse.undo_handle
Bio.Ndb.undo_handle" class="py-name" href="#" onclick="return doclink('link-188', 'undo_handle', 'link-188');">undo_handle</a></tt> <tt class="py-op">=</tt> <tt id="link-189" class="py-name"><a title="Bio.File" class="py-name" href="#" onclick="return doclink('link-189', 'File', 'link-1');">File</a></tt><tt class="py-op">.</tt><tt id="link-190" class="py-name"><a title="Bio.File.UndoHandle" class="py-name" href="#" onclick="return doclink('link-190', 'UndoHandle', 'link-84');">UndoHandle</a></tt><tt class="py-op">(</tt> <tt id="link-191" class="py-name"><a title="Bio.LocusLink.web_parse.handle
Bio.Ndb.handle" class="py-name" href="#" onclick="return doclink('link-191', 'handle', 'link-81');">handle</a></tt> <tt class="py-op">)</tt> </tt>
<a name="L289"></a><tt class="py-lineno">289</tt> <tt class="py-line"> <tt id="link-192" class="py-name" targets="Variable Bio.Ndb.ndb_parser=Bio.Ndb-module.html#ndb_parser"><a title="Bio.Ndb.ndb_parser" class="py-name" href="#" onclick="return doclink('link-192', 'ndb_parser', 'link-192');">ndb_parser</a></tt> <tt class="py-op">=</tt> <tt id="link-193" class="py-name" targets="Class Bio.Ndb.NdbParser=Bio.Ndb.NdbParser-class.html"><a title="Bio.Ndb.NdbParser" class="py-name" href="#" onclick="return doclink('link-193', 'NdbParser', 'link-193');">NdbParser</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
<a name="L290"></a><tt class="py-lineno">290</tt> <tt class="py-line"> <tt id="link-194" class="py-name" targets="Variable Bio.Emboss.primer3_format.record=Bio.Emboss.primer3_format-module.html#record,Variable Bio.Emboss.primersearch_format.record=Bio.Emboss.primersearch_format-module.html#record,Method Bio.GFF.Feature.record()=Bio.GFF.Feature-class.html#record,Variable Bio.LocusLink.web_parse.record=Bio.LocusLink.web_parse-module.html#record,Variable Bio.Ndb.record=Bio.Ndb-module.html#record,Function Bio.Std.record()=Bio.Std-module.html#record,Variable Bio.expressions.blocks.record=Bio.expressions.blocks-module.html#record,Variable Bio.expressions.embl.embl65.record=Bio.expressions.embl.embl65-module.html#record,Variable Bio.expressions.fasta.record=Bio.expressions.fasta-module.html#record,Variable Bio.expressions.genbank.record=Bio.expressions.genbank-module.html#record,Variable Bio.expressions.hmmpfam.record=Bio.expressions.hmmpfam-module.html#record,Variable Bio.expressions.swissprot.ipi.record=Bio.expressions.swissprot.ipi-module.html#record,Variable Bio.expressions.swissprot.speclist.record=Bio.expressions.swissprot.speclist-module.html#record,Variable Bio.expressions.swissprot.sprot38.record=Bio.expressions.swissprot.sprot38-module.html#record,Variable Bio.expressions.swissprot.sprot40.record=Bio.expressions.swissprot.sprot40-module.html#record,Variable Martel.test.test_swissprot38.record=Martel.test.test_swissprot38-module.html#record,Variable Martel.test.testformats.swissprot38.record=Martel.test.testformats.swissprot38-module.html#record"><a title="Bio.Emboss.primer3_format.record
Bio.Emboss.primersearch_format.record
Bio.GFF.Feature.record
Bio.LocusLink.web_parse.record
Bio.Ndb.record
Bio.Std.record
Bio.expressions.blocks.record
Bio.expressions.embl.embl65.record
Bio.expressions.fasta.record
Bio.expressions.genbank.record
Bio.expressions.hmmpfam.record
Bio.expressions.swissprot.ipi.record
Bio.expressions.swissprot.speclist.record
Bio.expressions.swissprot.sprot38.record
Bio.expressions.swissprot.sprot40.record
Martel.test.test_swissprot38.record
Martel.test.testformats.swissprot38.record" class="py-name" href="#" onclick="return doclink('link-194', 'record', 'link-194');">record</a></tt> <tt class="py-op">=</tt> <tt id="link-195" class="py-name"><a title="Bio.Ndb.ndb_parser" class="py-name" href="#" onclick="return doclink('link-195', 'ndb_parser', 'link-192');">ndb_parser</a></tt><tt class="py-op">.</tt><tt id="link-196" class="py-name" targets="Method Bio.Affy.CelFile.CelParser.parse()=Bio.Affy.CelFile.CelParser-class.html#parse,Method Bio.AlignAce.Parser.AlignAceParser.parse()=Bio.AlignAce.Parser.AlignAceParser-class.html#parse,Method Bio.AlignAce.Parser.CompareAceParser.parse()=Bio.AlignAce.Parser.CompareAceParser-class.html#parse,Function Bio.AlignIO.parse()=Bio.AlignIO-module.html#parse,Method Bio.Blast.NCBIStandalone.BlastErrorParser.parse()=Bio.Blast.NCBIStandalone.BlastErrorParser-class.html#parse,Method Bio.Blast.NCBIStandalone.BlastParser.parse()=Bio.Blast.NCBIStandalone.BlastParser-class.html#parse,Method Bio.Blast.NCBIStandalone.PSIBlastParser.parse()=Bio.Blast.NCBIStandalone.PSIBlastParser-class.html#parse,Method Bio.Blast.NCBIWWW.BlastParser.parse()=Bio.Blast.NCBIWWW.BlastParser-class.html#parse,Method Bio.Blast.NCBIXML.BlastParser.parse()=Bio.Blast.NCBIXML.BlastParser-class.html#parse,Function Bio.Blast.NCBIXML.parse()=Bio.Blast.NCBIXML-module.html#parse,Method Bio.CDD.RecordParser.parse()=Bio.CDD.RecordParser-class.html#parse,Method Bio.Compass.RecordParser.parse()=Bio.Compass.RecordParser-class.html#parse,Function Bio.Decode.parse()=Bio.Decode-module.html#parse,Method Bio.ECell.RecordParser.parse()=Bio.ECell.RecordParser-class.html#parse,Method Bio.EUtils.POM.POMDocument.parse()=Bio.EUtils.POM.POMDocument-class.html#parse,Module Bio.EUtils.parse=Bio.EUtils.parse-module.html,Method Bio.Emboss.Primer.Primer3Parser.parse()=Bio.Emboss.Primer.Primer3Parser-class.html#parse,Method Bio.Emboss.Primer.PrimerSearchParser.parse()=Bio.Emboss.Primer.PrimerSearchParser-class.html#parse,Method Bio.Enzyme.RecordParser.parse()=Bio.Enzyme.RecordParser-class.html#parse,Method Bio.Fasta.RecordParser.parse()=Bio.Fasta.RecordParser-class.html#parse,Method Bio.Fasta.SequenceParser.parse()=Bio.Fasta.SequenceParser-class.html#parse,Method Bio.GenBank.FeatureParser.parse()=Bio.GenBank.FeatureParser-class.html#parse,Function Bio.GenBank.LocationParser.parse()=Bio.GenBank.LocationParser-module.html#parse,Method Bio.GenBank.RecordParser.parse()=Bio.GenBank.RecordParser-class.html#parse,Method Bio.GenBank.Scanner.InsdcScanner.parse()=Bio.GenBank.Scanner.InsdcScanner-class.html#parse,Function Bio.Geo.parse()=Bio.Geo-module.html#parse,Method Bio.Gobase.RecordParser.parse()=Bio.Gobase.RecordParser-class.html#parse,Method Bio.IntelliGenetics.RecordParser.parse()=Bio.IntelliGenetics.RecordParser-class.html#parse,Method Bio.InterPro.InterProParser.parse()=Bio.InterPro.InterProParser-class.html#parse,Function Bio.KEGG.Compound.parse()=Bio.KEGG.Compound-module.html#parse,Function Bio.KEGG.Enzyme.parse()=Bio.KEGG.Enzyme-module.html#parse,Function Bio.KEGG.Map.parse()=Bio.KEGG.Map-module.html#parse,Method Bio.LocusLink.RecordParser.parse()=Bio.LocusLink.RecordParser-class.html#parse,Method Bio.LocusLink.web_parse.LocusLinkParser.parse()=Bio.LocusLink.web_parse.LocusLinkParser-class.html#parse,Method Bio.MEME.Parser.MASTParser.parse()=Bio.MEME.Parser.MASTParser-class.html#parse,Method Bio.MEME.Parser.MEMEParser.parse()=Bio.MEME.Parser.MEMEParser-class.html#parse,Method Bio.Medline.RecordParser.parse()=Bio.Medline.RecordParser-class.html#parse,Method Bio.MetaTool.RecordParser.parse()=Bio.MetaTool.RecordParser-class.html#parse,Method Bio.NBRF.RecordParser.parse()=Bio.NBRF.RecordParser-class.html#parse,Method Bio.Ndb.NdbParser.parse()=Bio.Ndb.NdbParser-class.html#parse,Method Bio.ParserSupport.AbstractParser.parse()=Bio.ParserSupport.AbstractParser-class.html#parse,Method Bio.Parsers.spark.GenericParser.parse()=Bio.Parsers.spark.GenericParser-class.html#parse,Method Bio.PopGen.FDist.RecordParser.parse()=Bio.PopGen.FDist.RecordParser-class.html#parse,Method Bio.PopGen.GenePop.RecordParser.parse()=Bio.PopGen.GenePop.RecordParser-class.html#parse,Function Bio.PopGen.GenePop.parse()=Bio.PopGen.GenePop-module.html#parse,Method Bio.Prosite.Prodoc.RecordParser.parse()=Bio.Prosite.Prodoc.RecordParser-class.html#parse,Function Bio.Prosite.Prodoc.parse()=Bio.Prosite.Prodoc-module.html#parse,Method Bio.Prosite.RecordParser.parse()=Bio.Prosite.RecordParser-class.html#parse,Function Bio.Prosite.parse()=Bio.Prosite-module.html#parse,Method Bio.Rebase.RecordParser.parse()=Bio.Rebase.RecordParser-class.html#parse,Method Bio.SCOP.Cla.Parser.parse()=Bio.SCOP.Cla.Parser-class.html#parse,Function Bio.SCOP.Cla.parse()=Bio.SCOP.Cla-module.html#parse,Method Bio.SCOP.Des.Parser.parse()=Bio.SCOP.Des.Parser-class.html#parse,Function Bio.SCOP.Des.parse()=Bio.SCOP.Des-module.html#parse,Method Bio.SCOP.Dom.Parser.parse()=Bio.SCOP.Dom.Parser-class.html#parse,Function Bio.SCOP.Dom.parse()=Bio.SCOP.Dom-module.html#parse,Method Bio.SCOP.Hie.Parser.parse()=Bio.SCOP.Hie.Parser-class.html#parse,Function Bio.SCOP.Hie.parse()=Bio.SCOP.Hie-module.html#parse,Method Bio.SCOP.Raf.Parser.parse()=Bio.SCOP.Raf.Parser-class.html#parse,Function Bio.SCOP.Raf.parse()=Bio.SCOP.Raf-module.html#parse,Method Bio.Saf.RecordParser.parse()=Bio.Saf.RecordParser-class.html#parse,Function Bio.SeqIO.parse()=Bio.SeqIO-module.html#parse,Method Bio.Sequencing.Ace.ACEParser.parse()=Bio.Sequencing.Ace.ACEParser-class.html#parse,Method Bio.Sequencing.Ace.RecordParser.parse()=Bio.Sequencing.Ace.RecordParser-class.html#parse,Method Bio.Sequencing.Phd.RecordParser.parse()=Bio.Sequencing.Phd.RecordParser-class.html#parse,Method Bio.SwissProt.KeyWList.ListParser.parse()=Bio.SwissProt.KeyWList.ListParser-class.html#parse,Function Bio.SwissProt.KeyWList.parse()=Bio.SwissProt.KeyWList-module.html#parse,Method Bio.SwissProt.SProt.RecordParser.parse()=Bio.SwissProt.SProt.RecordParser-class.html#parse,Method Bio.SwissProt.SProt.SequenceParser.parse()=Bio.SwissProt.SProt.SequenceParser-class.html#parse,Function Bio.SwissProt.parse()=Bio.SwissProt-module.html#parse,Method Bio.UniGene.RecordParser.parse()=Bio.UniGene.RecordParser-class.html#parse,Function Bio.Wise.psw.parse()=Bio.Wise.psw-module.html#parse,Method Martel.Parser.HeaderFooterParser.parse()=Martel.Parser.HeaderFooterParser-class.html#parse,Method Martel.Parser.Parser.parse()=Martel.Parser.Parser-class.html#parse,Method Martel.Parser.RecordParser.parse()=Martel.Parser.RecordParser-class.html#parse,Function Martel.msre_parse.parse()=Martel.msre_parse-module.html#parse"><a title="Bio.Affy.CelFile.CelParser.parse
Bio.AlignAce.Parser.AlignAceParser.parse
Bio.AlignAce.Parser.CompareAceParser.parse
Bio.AlignIO.parse
Bio.Blast.NCBIStandalone.BlastErrorParser.parse
Bio.Blast.NCBIStandalone.BlastParser.parse
Bio.Blast.NCBIStandalone.PSIBlastParser.parse
Bio.Blast.NCBIWWW.BlastParser.parse
Bio.Blast.NCBIXML.BlastParser.parse
Bio.Blast.NCBIXML.parse
Bio.CDD.RecordParser.parse
Bio.Compass.RecordParser.parse
Bio.Decode.parse
Bio.ECell.RecordParser.parse
Bio.EUtils.POM.POMDocument.parse
Bio.EUtils.parse
Bio.Emboss.Primer.Primer3Parser.parse
Bio.Emboss.Primer.PrimerSearchParser.parse
Bio.Enzyme.RecordParser.parse
Bio.Fasta.RecordParser.parse
Bio.Fasta.SequenceParser.parse
Bio.GenBank.FeatureParser.parse
Bio.GenBank.LocationParser.parse
Bio.GenBank.RecordParser.parse
Bio.GenBank.Scanner.InsdcScanner.parse
Bio.Geo.parse
Bio.Gobase.RecordParser.parse
Bio.IntelliGenetics.RecordParser.parse
Bio.InterPro.InterProParser.parse
Bio.KEGG.Compound.parse
Bio.KEGG.Enzyme.parse
Bio.KEGG.Map.parse
Bio.LocusLink.RecordParser.parse
Bio.LocusLink.web_parse.LocusLinkParser.parse
Bio.MEME.Parser.MASTParser.parse
Bio.MEME.Parser.MEMEParser.parse
Bio.Medline.RecordParser.parse
Bio.MetaTool.RecordParser.parse
Bio.NBRF.RecordParser.parse
Bio.Ndb.NdbParser.parse
Bio.ParserSupport.AbstractParser.parse
Bio.Parsers.spark.GenericParser.parse
Bio.PopGen.FDist.RecordParser.parse
Bio.PopGen.GenePop.RecordParser.parse
Bio.PopGen.GenePop.parse
Bio.Prosite.Prodoc.RecordParser.parse
Bio.Prosite.Prodoc.parse
Bio.Prosite.RecordParser.parse
Bio.Prosite.parse
Bio.Rebase.RecordParser.parse
Bio.SCOP.Cla.Parser.parse
Bio.SCOP.Cla.parse
Bio.SCOP.Des.Parser.parse
Bio.SCOP.Des.parse
Bio.SCOP.Dom.Parser.parse
Bio.SCOP.Dom.parse
Bio.SCOP.Hie.Parser.parse
Bio.SCOP.Hie.parse
Bio.SCOP.Raf.Parser.parse
Bio.SCOP.Raf.parse
Bio.Saf.RecordParser.parse
Bio.SeqIO.parse
Bio.Sequencing.Ace.ACEParser.parse
Bio.Sequencing.Ace.RecordParser.parse
Bio.Sequencing.Phd.RecordParser.parse
Bio.SwissProt.KeyWList.ListParser.parse
Bio.SwissProt.KeyWList.parse
Bio.SwissProt.SProt.RecordParser.parse
Bio.SwissProt.SProt.SequenceParser.parse
Bio.SwissProt.parse
Bio.UniGene.RecordParser.parse
Bio.Wise.psw.parse
Martel.Parser.HeaderFooterParser.parse
Martel.Parser.Parser.parse
Martel.Parser.RecordParser.parse
Martel.msre_parse.parse" class="py-name" href="#" onclick="return doclink('link-196', 'parse', 'link-196');">parse</a></tt><tt class="py-op">(</tt> <tt id="link-197" class="py-name"><a title="Bio.LocusLink.web_parse.handle
Bio.Ndb.handle" class="py-name" href="#" onclick="return doclink('link-197', 'handle', 'link-81');">handle</a></tt> <tt class="py-op">)</tt> </tt>
<a name="L291"></a><tt class="py-lineno">291</tt> <tt class="py-line"> <tt class="py-keyword">print</tt> <tt class="py-name">str</tt><tt class="py-op">(</tt> <tt id="link-198" class="py-name"><a title="Bio.Emboss.primer3_format.record
Bio.Emboss.primersearch_format.record
Bio.GFF.Feature.record
Bio.LocusLink.web_parse.record
Bio.Ndb.record
Bio.Std.record
Bio.expressions.blocks.record
Bio.expressions.embl.embl65.record
Bio.expressions.fasta.record
Bio.expressions.genbank.record
Bio.expressions.hmmpfam.record
Bio.expressions.swissprot.ipi.record
Bio.expressions.swissprot.speclist.record
Bio.expressions.swissprot.sprot38.record
Bio.expressions.swissprot.sprot40.record
Martel.test.test_swissprot38.record
Martel.test.testformats.swissprot38.record" class="py-name" href="#" onclick="return doclink('link-198', 'record', 'link-194');">record</a></tt> <tt class="py-op">)</tt> </tt>
<a name="L292"></a><tt class="py-lineno">292</tt> <tt class="py-line"> </tt><script type="text/javascript">
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