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<a href="Bio-module.html">Package Bio</a> ::
<a href="Bio.dbdefs-module.html">Package dbdefs</a> ::
Module pdb
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<h1 class="epydoc">Source Code for <a href="Bio.dbdefs.pdb-module.html">Module Bio.dbdefs.pdb</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 Jeffrey Chang. 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-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-op">.</tt><tt id="link-1" class="py-name" targets="Package Bio.config=Bio.config-module.html"><a title="Bio.config" class="py-name" href="#" onclick="return doclink('link-1', 'config', 'link-1');">config</a></tt><tt class="py-op">.</tt><tt id="link-2" class="py-name" targets="Module Bio.config.DBRegistry=Bio.config.DBRegistry-module.html,Class Bio.config.DBRegistry.DBRegistry=Bio.config.DBRegistry.DBRegistry-class.html"><a title="Bio.config.DBRegistry
Bio.config.DBRegistry.DBRegistry" class="py-name" href="#" onclick="return doclink('link-2', 'DBRegistry', 'link-2');">DBRegistry</a></tt> <tt class="py-keyword">import</tt> <tt id="link-3" class="py-name" targets="Class Bio.config.DBRegistry.CGIDB=Bio.config.DBRegistry.CGIDB-class.html"><a title="Bio.config.DBRegistry.CGIDB" class="py-name" href="#" onclick="return doclink('link-3', 'CGIDB', 'link-3');">CGIDB</a></tt><tt class="py-op">,</tt> <tt id="link-4" class="py-name" targets="Class Bio.config.DBRegistry.DBGroup=Bio.config.DBRegistry.DBGroup-class.html"><a title="Bio.config.DBRegistry.DBGroup" class="py-name" href="#" onclick="return doclink('link-4', 'DBGroup', 'link-4');">DBGroup</a></tt> </tt>
<a name="L7"></a><tt class="py-lineno"> 7</tt> <tt class="py-line"><tt class="py-keyword">from</tt> <tt id="link-5" class="py-name" targets="Module Bio.config._support=Bio.config._support-module.html,Module Bio.dbdefs._support=Bio.dbdefs._support-module.html"><a title="Bio.config._support
Bio.dbdefs._support" class="py-name" href="#" onclick="return doclink('link-5', '_support', 'link-5');">_support</a></tt> <tt class="py-keyword">import</tt> <tt class="py-op">*</tt> </tt>
<a name="L8"></a><tt class="py-lineno"> 8</tt> <tt class="py-line"> </tt>
<a name="L9"></a><tt class="py-lineno"> 9</tt> <tt class="py-line"><tt class="py-keyword">from</tt> <tt id="link-6" class="py-name" targets="Package Martel=Martel-module.html"><a title="Martel" class="py-name" href="#" onclick="return doclink('link-6', 'Martel', 'link-6');">Martel</a></tt> <tt class="py-keyword">import</tt> <tt class="py-op">*</tt> </tt>
<a name="L10"></a><tt class="py-lineno">10</tt> <tt class="py-line"> </tt>
<a name="L11"></a><tt class="py-lineno">11</tt> <tt class="py-line"><tt id="link-7" class="py-name" targets="Variable Bio.dbdefs.pdb.not_header_expr=Bio.dbdefs.pdb-module.html#not_header_expr"><a title="Bio.dbdefs.pdb.not_header_expr" class="py-name" href="#" onclick="return doclink('link-7', 'not_header_expr', 'link-7');">not_header_expr</a></tt> <tt class="py-op">=</tt> <tt id="link-8" class="py-name" targets="Function Martel.AssertNot()=Martel-module.html#AssertNot"><a title="Martel.AssertNot" class="py-name" href="#" onclick="return doclink('link-8', 'AssertNot', 'link-8');">AssertNot</a></tt><tt class="py-op">(</tt><tt id="link-9" class="py-name" targets="Class Martel.Expression.Str=Martel.Expression.Str-class.html,Function Martel.Str()=Martel-module.html#Str"><a title="Martel.Expression.Str
Martel.Str" class="py-name" href="#" onclick="return doclink('link-9', 'Str', 'link-9');">Str</a></tt><tt class="py-op">(</tt><tt class="py-string">"HEADER"</tt><tt class="py-op">)</tt><tt class="py-op">)</tt> </tt>
<a name="L12"></a><tt class="py-lineno">12</tt> <tt class="py-line"><tt id="link-10" class="py-name" targets="Variable Bio.dbdefs.pdb.pdb_rcsb_cgi=Bio.dbdefs.pdb-module.html#pdb_rcsb_cgi"><a title="Bio.dbdefs.pdb.pdb_rcsb_cgi" class="py-name" href="#" onclick="return doclink('link-10', 'pdb_rcsb_cgi', 'link-10');">pdb_rcsb_cgi</a></tt> <tt class="py-op">=</tt> <tt id="link-11" class="py-name"><a title="Bio.config.DBRegistry.CGIDB" class="py-name" href="#" onclick="return doclink('link-11', 'CGIDB', 'link-3');">CGIDB</a></tt><tt class="py-op">(</tt> </tt>
<a name="L13"></a><tt class="py-lineno">13</tt> <tt class="py-line"> <tt id="link-12" class="py-name" targets="Variable Bio.Encodings.IUPACEncoding.name=Bio.Encodings.IUPACEncoding-module.html#name"><a title="Bio.Encodings.IUPACEncoding.name" class="py-name" href="#" onclick="return doclink('link-12', 'name', 'link-12');">name</a></tt><tt class="py-op">=</tt><tt class="py-string">"pdb-rcsb-cgi"</tt><tt class="py-op">,</tt> </tt>
<a name="L14"></a><tt class="py-lineno">14</tt> <tt class="py-line"> <tt class="py-name">cgi</tt><tt class="py-op">=</tt><tt class="py-string">"http://www.rcsb.org/pdb/cgi/export.cgi"</tt><tt class="py-op">,</tt> </tt>
<a name="L15"></a><tt class="py-lineno">15</tt> <tt class="py-line"> <tt class="py-name">url</tt><tt class="py-op">=</tt><tt class="py-string">"XXX PLEASE FILL THIS IN XXX"</tt><tt class="py-op">,</tt> </tt>
<a name="L16"></a><tt class="py-lineno">16</tt> <tt class="py-line"> <tt class="py-name">delay</tt><tt class="py-op">=</tt><tt class="py-number">5.0</tt><tt class="py-op">,</tt> </tt>
<a name="L17"></a><tt class="py-lineno">17</tt> <tt class="py-line"> <tt class="py-name">params</tt><tt class="py-op">=</tt><tt class="py-op">[</tt><tt class="py-op">(</tt><tt class="py-string">"format"</tt><tt class="py-op">,</tt> <tt class="py-string">"PDB"</tt><tt class="py-op">)</tt><tt class="py-op">,</tt> </tt>
<a name="L18"></a><tt class="py-lineno">18</tt> <tt class="py-line"> <tt class="py-op">(</tt><tt class="py-string">"compression"</tt><tt class="py-op">,</tt> <tt class="py-string">"None"</tt><tt class="py-op">)</tt> </tt>
<a name="L19"></a><tt class="py-lineno">19</tt> <tt class="py-line"> <tt class="py-op">]</tt><tt class="py-op">,</tt> </tt>
<a name="L20"></a><tt class="py-lineno">20</tt> <tt class="py-line"> <tt id="link-13" 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-13', 'key', 'link-13');">key</a></tt><tt class="py-op">=</tt><tt class="py-string">"pdbId"</tt><tt class="py-op">,</tt> </tt>
<a name="L21"></a><tt class="py-lineno">21</tt> <tt class="py-line"> <tt class="py-comment"># failure cases for file not found are making retrieval freeze up </tt> </tt>
<a name="L22"></a><tt class="py-lineno">22</tt> <tt class="py-line"> <tt class="py-comment"># while Martel checks for them, for some reason I can't figure</tt> </tt>
<a name="L23"></a><tt class="py-lineno">23</tt> <tt class="py-line"> <tt class="py-comment"># so we go with checking to make sure results look like PDB</tt> </tt>
<a name="L24"></a><tt class="py-lineno">24</tt> <tt class="py-line"> <tt class="py-comment"># failure_cases=[(has_str("File not found"), "ID does not exist")],</tt> </tt>
<a name="L25"></a><tt class="py-lineno">25</tt> <tt class="py-line"> <tt class="py-name">failure_cases</tt><tt class="py-op">=</tt><tt class="py-op">[</tt><tt class="py-op">(</tt><tt id="link-14" class="py-name"><a title="Bio.dbdefs.pdb.not_header_expr" class="py-name" href="#" onclick="return doclink('link-14', 'not_header_expr', 'link-7');">not_header_expr</a></tt><tt class="py-op">,</tt> <tt class="py-string">"results do not look like PDB format"</tt><tt class="py-op">)</tt><tt class="py-op">]</tt> </tt>
<a name="L26"></a><tt class="py-lineno">26</tt> <tt class="py-line"> <tt class="py-op">)</tt> </tt>
<a name="L27"></a><tt class="py-lineno">27</tt> <tt class="py-line"> </tt>
<a name="L28"></a><tt class="py-lineno">28</tt> <tt class="py-line"><tt id="link-15" class="py-name" targets="Variable Bio.dbdefs.pdb.pdb_ebi_cgi=Bio.dbdefs.pdb-module.html#pdb_ebi_cgi"><a title="Bio.dbdefs.pdb.pdb_ebi_cgi" class="py-name" href="#" onclick="return doclink('link-15', 'pdb_ebi_cgi', 'link-15');">pdb_ebi_cgi</a></tt> <tt class="py-op">=</tt> <tt id="link-16" class="py-name"><a title="Bio.config.DBRegistry.CGIDB" class="py-name" href="#" onclick="return doclink('link-16', 'CGIDB', 'link-3');">CGIDB</a></tt><tt class="py-op">(</tt> </tt>
<a name="L29"></a><tt class="py-lineno">29</tt> <tt class="py-line"> <tt id="link-17" class="py-name"><a title="Bio.Encodings.IUPACEncoding.name" class="py-name" href="#" onclick="return doclink('link-17', 'name', 'link-12');">name</a></tt><tt class="py-op">=</tt><tt class="py-string">"pdb-ebi-cgi"</tt><tt class="py-op">,</tt> </tt>
<a name="L30"></a><tt class="py-lineno">30</tt> <tt class="py-line"> <tt class="py-name">cgi</tt><tt class="py-op">=</tt><tt class="py-string">"http://www.ebi.ac.uk/cgi-bin/dbfetch"</tt><tt class="py-op">,</tt> </tt>
<a name="L31"></a><tt class="py-lineno">31</tt> <tt class="py-line"> <tt class="py-name">url</tt><tt class="py-op">=</tt><tt class="py-string">"http://www.ebi.ac.uk/cgi-bin/dbfetch"</tt><tt class="py-op">,</tt> </tt>
<a name="L32"></a><tt class="py-lineno">32</tt> <tt class="py-line"> <tt class="py-name">delay</tt><tt class="py-op">=</tt><tt class="py-number">5.0</tt><tt class="py-op">,</tt> </tt>
<a name="L33"></a><tt class="py-lineno">33</tt> <tt class="py-line"> <tt class="py-name">params</tt><tt class="py-op">=</tt><tt class="py-op">[</tt><tt class="py-op">(</tt><tt class="py-string">"db"</tt><tt class="py-op">,</tt> <tt class="py-string">"PDB"</tt><tt class="py-op">)</tt><tt class="py-op">,</tt> </tt>
<a name="L34"></a><tt class="py-lineno">34</tt> <tt class="py-line"> <tt class="py-op">(</tt><tt class="py-string">"format"</tt><tt class="py-op">,</tt> <tt class="py-string">"default"</tt><tt class="py-op">)</tt><tt class="py-op">,</tt> <tt class="py-comment"># also Fasta, bsml, agave available</tt> </tt>
<a name="L35"></a><tt class="py-lineno">35</tt> <tt class="py-line"> <tt class="py-op">(</tt><tt class="py-string">"style"</tt><tt class="py-op">,</tt> <tt class="py-string">"raw"</tt><tt class="py-op">)</tt><tt class="py-op">,</tt> </tt>
<a name="L36"></a><tt class="py-lineno">36</tt> <tt class="py-line"> <tt class="py-op">]</tt><tt class="py-op">,</tt> </tt>
<a name="L37"></a><tt class="py-lineno">37</tt> <tt class="py-line"> <tt id="link-18" class="py-name"><a title="Bio.Translate.key" class="py-name" href="#" onclick="return doclink('link-18', 'key', 'link-13');">key</a></tt><tt class="py-op">=</tt><tt class="py-string">"id"</tt><tt class="py-op">,</tt> </tt>
<a name="L38"></a><tt class="py-lineno">38</tt> <tt class="py-line"> <tt class="py-name">failure_cases</tt><tt class="py-op">=</tt><tt class="py-op">[</tt><tt class="py-op">(</tt><tt id="link-19" class="py-name"><a title="Bio.dbdefs.pdb.not_header_expr" class="py-name" href="#" onclick="return doclink('link-19', 'not_header_expr', 'link-7');">not_header_expr</a></tt><tt class="py-op">,</tt> <tt class="py-string">"results do not look like PDB format"</tt><tt class="py-op">)</tt><tt class="py-op">]</tt> </tt>
<a name="L39"></a><tt class="py-lineno">39</tt> <tt class="py-line"> <tt class="py-op">)</tt> </tt>
<a name="L40"></a><tt class="py-lineno">40</tt> <tt class="py-line"> </tt>
<a name="L41"></a><tt class="py-lineno">41</tt> <tt class="py-line"><tt id="link-20" class="py-name" targets="Method Bio.FSSP.FSSPAlignDict.pdb()=Bio.FSSP.FSSPAlignDict-class.html#pdb,Module Bio.dbdefs.pdb=Bio.dbdefs.pdb-module.html,Variable Bio.dbdefs.pdb.pdb=Bio.dbdefs.pdb-module.html#pdb"><a title="Bio.FSSP.FSSPAlignDict.pdb
Bio.dbdefs.pdb
Bio.dbdefs.pdb.pdb" class="py-name" href="#" onclick="return doclink('link-20', 'pdb', 'link-20');">pdb</a></tt> <tt class="py-op">=</tt> <tt id="link-21" class="py-name"><a title="Bio.config.DBRegistry.DBGroup" class="py-name" href="#" onclick="return doclink('link-21', 'DBGroup', 'link-4');">DBGroup</a></tt><tt class="py-op">(</tt> </tt>
<a name="L42"></a><tt class="py-lineno">42</tt> <tt class="py-line"> <tt id="link-22" class="py-name"><a title="Bio.Encodings.IUPACEncoding.name" class="py-name" href="#" onclick="return doclink('link-22', 'name', 'link-12');">name</a></tt><tt class="py-op">=</tt><tt class="py-string">"pdb"</tt><tt class="py-op">,</tt> </tt>
<a name="L43"></a><tt class="py-lineno">43</tt> <tt class="py-line"> <tt class="py-name">behavior</tt><tt class="py-op">=</tt><tt class="py-string">"serial"</tt> </tt>
<a name="L44"></a><tt class="py-lineno">44</tt> <tt class="py-line"> <tt class="py-op">)</tt> </tt>
<a name="L45"></a><tt class="py-lineno">45</tt> <tt class="py-line"><tt id="link-23" class="py-name"><a title="Bio.FSSP.FSSPAlignDict.pdb
Bio.dbdefs.pdb
Bio.dbdefs.pdb.pdb" class="py-name" href="#" onclick="return doclink('link-23', 'pdb', 'link-20');">pdb</a></tt><tt class="py-op">.</tt><tt id="link-24" class="py-name" targets="Variable Bio.Affy.CelFile.add=Bio.Affy.CelFile-module.html#add,Method Bio.EUtils.POM.ElementNode.add()=Bio.EUtils.POM.ElementNode-class.html#add,Method Bio.GFF.easy.Location.add()=Bio.GFF.easy.Location-class.html#add,Method Bio.Graphics.BasicChromosome._ChromosomeComponent.add()=Bio.Graphics.BasicChromosome._ChromosomeComponent-class.html#add,Variable Bio.LogisticRegression.add=Bio.LogisticRegression-module.html#add,Variable Bio.MarkovModel.add=Bio.MarkovModel-module.html#add,Variable Bio.MaxEntropy.add=Bio.MaxEntropy-module.html#add,Variable Bio.NaiveBayes.add=Bio.NaiveBayes-module.html#add,Method Bio.Nexus.Nexus.StepMatrix.add()=Bio.Nexus.Nexus.StepMatrix-class.html#add,Method Bio.Nexus.Nodes.Chain.add()=Bio.Nexus.Nodes.Chain-class.html#add,Method Bio.PDB.Entity.Entity.add()=Bio.PDB.Entity.Entity-class.html#add,Method Bio.PDB.Residue.DisorderedResidue.add()=Bio.PDB.Residue.DisorderedResidue-class.html#add,Method Bio.PDB.Residue.Residue.add()=Bio.PDB.Residue.Residue-class.html#add,Method Bio.Pathway.Rep.HashSet.HashSet.add()=Bio.Pathway.Rep.HashSet.HashSet-class.html#add,Method Bio.Restriction.Restriction.RestrictionBatch.add()=Bio.Restriction.Restriction.RestrictionBatch-class.html#add,Variable Bio.Statistics.lowess.add=Bio.Statistics.lowess-module.html#add,Method Bio.config.FormatRegistry.FormatGroup.add()=Bio.config.FormatRegistry.FormatGroup-class.html#add,Method Bio.config.Registry.RegisterableGroup.add()=Bio.config.Registry.RegisterableGroup-class.html#add,Variable Bio.distance.add=Bio.distance-module.html#add,Variable Bio.kNN.add=Bio.kNN-module.html#add,Method Martel.Dispatch.MulticallEnd.add()=Martel.Dispatch.MulticallEnd-class.html#add,Method Martel.Dispatch.MulticallStart.add()=Martel.Dispatch.MulticallStart-class.html#add"><a title="Bio.Affy.CelFile.add
Bio.EUtils.POM.ElementNode.add
Bio.GFF.easy.Location.add
Bio.Graphics.BasicChromosome._ChromosomeComponent.add
Bio.LogisticRegression.add
Bio.MarkovModel.add
Bio.MaxEntropy.add
Bio.NaiveBayes.add
Bio.Nexus.Nexus.StepMatrix.add
Bio.Nexus.Nodes.Chain.add
Bio.PDB.Entity.Entity.add
Bio.PDB.Residue.DisorderedResidue.add
Bio.PDB.Residue.Residue.add
Bio.Pathway.Rep.HashSet.HashSet.add
Bio.Restriction.Restriction.RestrictionBatch.add
Bio.Statistics.lowess.add
Bio.config.FormatRegistry.FormatGroup.add
Bio.config.Registry.RegisterableGroup.add
Bio.distance.add
Bio.kNN.add
Martel.Dispatch.MulticallEnd.add
Martel.Dispatch.MulticallStart.add" class="py-name" href="#" onclick="return doclink('link-24', 'add', 'link-24');">add</a></tt><tt class="py-op">(</tt><tt id="link-25" class="py-name"><a title="Bio.dbdefs.pdb.pdb_rcsb_cgi" class="py-name" href="#" onclick="return doclink('link-25', 'pdb_rcsb_cgi', 'link-10');">pdb_rcsb_cgi</a></tt><tt class="py-op">)</tt> </tt>
<a name="L46"></a><tt class="py-lineno">46</tt> <tt class="py-line"><tt id="link-26" class="py-name"><a title="Bio.FSSP.FSSPAlignDict.pdb
Bio.dbdefs.pdb
Bio.dbdefs.pdb.pdb" class="py-name" href="#" onclick="return doclink('link-26', 'pdb', 'link-20');">pdb</a></tt><tt class="py-op">.</tt><tt id="link-27" class="py-name"><a title="Bio.Affy.CelFile.add
Bio.EUtils.POM.ElementNode.add
Bio.GFF.easy.Location.add
Bio.Graphics.BasicChromosome._ChromosomeComponent.add
Bio.LogisticRegression.add
Bio.MarkovModel.add
Bio.MaxEntropy.add
Bio.NaiveBayes.add
Bio.Nexus.Nexus.StepMatrix.add
Bio.Nexus.Nodes.Chain.add
Bio.PDB.Entity.Entity.add
Bio.PDB.Residue.DisorderedResidue.add
Bio.PDB.Residue.Residue.add
Bio.Pathway.Rep.HashSet.HashSet.add
Bio.Restriction.Restriction.RestrictionBatch.add
Bio.Statistics.lowess.add
Bio.config.FormatRegistry.FormatGroup.add
Bio.config.Registry.RegisterableGroup.add
Bio.distance.add
Bio.kNN.add
Martel.Dispatch.MulticallEnd.add
Martel.Dispatch.MulticallStart.add" class="py-name" href="#" onclick="return doclink('link-27', 'add', 'link-24');">add</a></tt><tt class="py-op">(</tt><tt id="link-28" class="py-name"><a title="Bio.dbdefs.pdb.pdb_ebi_cgi" class="py-name" href="#" onclick="return doclink('link-28', 'pdb_ebi_cgi', 'link-15');">pdb_ebi_cgi</a></tt><tt class="py-op">)</tt> </tt>
<a name="L47"></a><tt class="py-lineno">47</tt> <tt class="py-line"> </tt><script type="text/javascript">
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