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<a href="Bio-module.html">Package Bio</a> ::
<a href="Bio.PDB-module.html">Package PDB</a> ::
Module Dice
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<h1 class="epydoc">Source Code for <a href="Bio.PDB.Dice-module.html">Module Bio.PDB.Dice</a></h1>
<pre class="py-src">
<a name="L1"></a><tt class="py-lineno"> 1</tt> <tt class="py-line"><tt class="py-comment"># Copyright (C) 2002, Thomas Hamelryck (thamelry@binf.ku.dk)</tt> </tt>
<a name="L2"></a><tt class="py-lineno"> 2</tt> <tt class="py-line"><tt class="py-comment"></tt><tt class="py-comment"># This code is part of the Biopython distribution and governed by its</tt> </tt>
<a name="L3"></a><tt class="py-lineno"> 3</tt> <tt class="py-line"><tt class="py-comment"></tt><tt class="py-comment"># license. Please see the LICENSE file that should have been included</tt> </tt>
<a name="L4"></a><tt class="py-lineno"> 4</tt> <tt class="py-line"><tt class="py-comment"></tt><tt class="py-comment"># as part of this package.</tt> </tt>
<a name="L5"></a><tt class="py-lineno"> 5</tt> <tt class="py-line"><tt class="py-comment"></tt> </tt>
<a name="L6"></a><tt class="py-lineno"> 6</tt> <tt class="py-line"><tt class="py-keyword">import</tt> <tt class="py-name">re</tt> </tt>
<a name="L7"></a><tt class="py-lineno"> 7</tt> <tt class="py-line"> </tt>
<a name="L8"></a><tt class="py-lineno"> 8</tt> <tt class="py-line"><tt 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.PDB=Bio.PDB-module.html"><a title="Bio.PDB" class="py-name" href="#" onclick="return doclink('link-1', 'PDB', 'link-1');">PDB</a></tt><tt class="py-op">.</tt><tt id="link-2" class="py-name" targets="Class Bio.PDB.PDBIO'.PDBIO=Bio.PDB.PDBIO%27.PDBIO-class.html"><a title="Bio.PDB.PDBIO'.PDBIO" class="py-name" href="#" onclick="return doclink('link-2', 'PDBIO', 'link-2');">PDBIO</a></tt> <tt class="py-keyword">import</tt> <tt id="link-3" class="py-name"><a title="Bio.PDB.PDBIO'.PDBIO" class="py-name" href="#" onclick="return doclink('link-3', 'PDBIO', 'link-2');">PDBIO</a></tt> </tt>
<a name="L9"></a><tt class="py-lineno"> 9</tt> <tt class="py-line"> </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-4" class="py-name" targets="Variable Bio.PDB.Dice._hydrogen=Bio.PDB.Dice-module.html#_hydrogen"><a title="Bio.PDB.Dice._hydrogen" class="py-name" href="#" onclick="return doclink('link-4', '_hydrogen', 'link-4');">_hydrogen</a></tt><tt class="py-op">=</tt><tt class="py-name">re</tt><tt class="py-op">.</tt><tt id="link-5" class="py-name" targets="Function Bio.Prosite.Pattern.compile()=Bio.Prosite.Pattern-module.html#compile"><a title="Bio.Prosite.Pattern.compile" class="py-name" href="#" onclick="return doclink('link-5', 'compile', 'link-5');">compile</a></tt><tt class="py-op">(</tt><tt class="py-string">"[123 ]*H.*"</tt><tt class="py-op">)</tt> </tt>
<a name="L12"></a><tt class="py-lineno">12</tt> <tt class="py-line"> </tt>
<a name="L13"></a><tt class="py-lineno">13</tt> <tt class="py-line"> </tt>
<a name="ChainSelector"></a><div id="ChainSelector-def"><a name="L14"></a><tt class="py-lineno">14</tt> <a class="py-toggle" href="#" id="ChainSelector-toggle" onclick="return toggle('ChainSelector');">-</a><tt class="py-line"><tt class="py-keyword">class</tt> <a class="py-def-name" href="Bio.PDB.Dice.ChainSelector-class.html">ChainSelector</a><tt class="py-op">:</tt> </tt>
</div><div id="ChainSelector-collapsed" style="display:none;" pad="++" indent="++++"></div><div id="ChainSelector-expanded"><a name="L15"></a><tt class="py-lineno">15</tt> <tt class="py-line"> <tt class="py-docstring">"""</tt> </tt>
<a name="L16"></a><tt class="py-lineno">16</tt> <tt class="py-line"><tt class="py-docstring"> Only accepts residues with right chainid</tt> </tt>
<a name="L17"></a><tt class="py-lineno">17</tt> <tt class="py-line"><tt class="py-docstring"> and between start and end. Remove hydrogens, waters and ligands.</tt> </tt>
<a name="L18"></a><tt class="py-lineno">18</tt> <tt class="py-line"><tt class="py-docstring"> Only use model 0 by default.</tt> </tt>
<a name="L19"></a><tt class="py-lineno">19</tt> <tt class="py-line"><tt class="py-docstring"> """</tt> </tt>
<a name="ChainSelector.__init__"></a><div id="ChainSelector.__init__-def"><a name="L20"></a><tt class="py-lineno">20</tt> <a class="py-toggle" href="#" id="ChainSelector.__init__-toggle" onclick="return toggle('ChainSelector.__init__');">-</a><tt class="py-line"> <tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.PDB.Dice.ChainSelector-class.html#__init__">__init__</a><tt class="py-op">(</tt><tt class="py-param">self</tt><tt class="py-op">,</tt> <tt class="py-param">chain_id</tt><tt class="py-op">,</tt> <tt class="py-param">start</tt><tt class="py-op">,</tt> <tt class="py-param">end</tt><tt class="py-op">,</tt> <tt class="py-param">model_id</tt><tt class="py-op">=</tt><tt class="py-number">0</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="ChainSelector.__init__-collapsed" style="display:none;" pad="++" indent="++++++++"></div><div id="ChainSelector.__init__-expanded"><a name="L21"></a><tt class="py-lineno">21</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-6" class="py-name" targets="Variable Bio.FSSP.fssp_rec.align.chain_id=Bio.FSSP.fssp_rec.align-class.html#chain_id"><a title="Bio.FSSP.fssp_rec.align.chain_id" class="py-name" href="#" onclick="return doclink('link-6', 'chain_id', 'link-6');">chain_id</a></tt><tt class="py-op">=</tt><tt id="link-7" class="py-name"><a title="Bio.FSSP.fssp_rec.align.chain_id" class="py-name" href="#" onclick="return doclink('link-7', 'chain_id', 'link-6');">chain_id</a></tt> </tt>
<a name="L22"></a><tt class="py-lineno">22</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-8" class="py-name" targets="Method Bio.GFF.easy.Location.start()=Bio.GFF.easy.Location-class.html#start,Method Bio.Prosite.Pattern.PrositeMatch.start()=Bio.Prosite.Pattern.PrositeMatch-class.html#start,Variable Bio.Restriction._Update.RestrictionCompiler.start=Bio.Restriction._Update.RestrictionCompiler-module.html#start,Method Martel.LAX.LAX.start()=Martel.LAX.LAX-class.html#start"><a title="Bio.GFF.easy.Location.start
Bio.Prosite.Pattern.PrositeMatch.start
Bio.Restriction._Update.RestrictionCompiler.start
Martel.LAX.LAX.start" class="py-name" href="#" onclick="return doclink('link-8', 'start', 'link-8');">start</a></tt><tt class="py-op">=</tt><tt id="link-9" class="py-name"><a title="Bio.GFF.easy.Location.start
Bio.Prosite.Pattern.PrositeMatch.start
Bio.Restriction._Update.RestrictionCompiler.start
Martel.LAX.LAX.start" class="py-name" href="#" onclick="return doclink('link-9', 'start', 'link-8');">start</a></tt> </tt>
<a name="L23"></a><tt class="py-lineno">23</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-10" class="py-name" targets="Method Bio.GFF.easy.Location.end()=Bio.GFF.easy.Location-class.html#end,Method Bio.Prosite.Pattern.PrositeMatch.end()=Bio.Prosite.Pattern.PrositeMatch-class.html#end,Variable Bio.expressions.blocks.end=Bio.expressions.blocks-module.html#end,Variable Bio.expressions.embl.embl65.end=Bio.expressions.embl.embl65-module.html#end,Variable Bio.expressions.swissprot.sprot38.end=Bio.expressions.swissprot.sprot38-module.html#end,Method Martel.LAX.LAX.end()=Martel.LAX.LAX-class.html#end,Variable Martel.test.test_swissprot38.end=Martel.test.test_swissprot38-module.html#end,Variable Martel.test.testformats.swissprot38.end=Martel.test.testformats.swissprot38-module.html#end"><a title="Bio.GFF.easy.Location.end
Bio.Prosite.Pattern.PrositeMatch.end
Bio.expressions.blocks.end
Bio.expressions.embl.embl65.end
Bio.expressions.swissprot.sprot38.end
Martel.LAX.LAX.end
Martel.test.test_swissprot38.end
Martel.test.testformats.swissprot38.end" class="py-name" href="#" onclick="return doclink('link-10', 'end', 'link-10');">end</a></tt><tt class="py-op">=</tt><tt id="link-11" class="py-name"><a title="Bio.GFF.easy.Location.end
Bio.Prosite.Pattern.PrositeMatch.end
Bio.expressions.blocks.end
Bio.expressions.embl.embl65.end
Bio.expressions.swissprot.sprot38.end
Martel.LAX.LAX.end
Martel.test.test_swissprot38.end
Martel.test.testformats.swissprot38.end" class="py-name" href="#" onclick="return doclink('link-11', 'end', 'link-10');">end</a></tt> </tt>
<a name="L24"></a><tt class="py-lineno">24</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">model_id</tt><tt class="py-op">=</tt><tt class="py-number">0</tt> </tt>
</div><a name="L25"></a><tt class="py-lineno">25</tt> <tt class="py-line"> </tt>
<a name="ChainSelector.accept_model"></a><div id="ChainSelector.accept_model-def"><a name="L26"></a><tt class="py-lineno">26</tt> <a class="py-toggle" href="#" id="ChainSelector.accept_model-toggle" onclick="return toggle('ChainSelector.accept_model');">-</a><tt class="py-line"> <tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.PDB.Dice.ChainSelector-class.html#accept_model">accept_model</a><tt class="py-op">(</tt><tt class="py-param">self</tt><tt class="py-op">,</tt> <tt class="py-param">model</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="ChainSelector.accept_model-collapsed" style="display:none;" pad="++" indent="++++++++"></div><div id="ChainSelector.accept_model-expanded"><a name="L27"></a><tt class="py-lineno">27</tt> <tt class="py-line"> <tt class="py-comment"># model - only keep model 0</tt> </tt>
<a name="L28"></a><tt class="py-lineno">28</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-keyword">if</tt> <tt class="py-name">model</tt><tt class="py-op">.</tt><tt id="link-12" class="py-name" targets="Method Bio.Nexus.Nodes.Node.get_id()=Bio.Nexus.Nodes.Node-class.html#get_id,Method Bio.PDB.Atom.Atom.get_id()=Bio.PDB.Atom.Atom-class.html#get_id,Method Bio.PDB.Entity.DisorderedEntityWrapper.get_id()=Bio.PDB.Entity.DisorderedEntityWrapper-class.html#get_id,Method Bio.PDB.Entity.Entity.get_id()=Bio.PDB.Entity.Entity-class.html#get_id,Method Bio.PDB.FragmentMapper'.Fragment.get_id()=Bio.PDB.FragmentMapper%27.Fragment-class.html#get_id"><a title="Bio.Nexus.Nodes.Node.get_id
Bio.PDB.Atom.Atom.get_id
Bio.PDB.Entity.DisorderedEntityWrapper.get_id
Bio.PDB.Entity.Entity.get_id
Bio.PDB.FragmentMapper'.Fragment.get_id" class="py-name" href="#" onclick="return doclink('link-12', 'get_id', 'link-12');">get_id</a></tt><tt class="py-op">(</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">model_id</tt><tt class="py-op">:</tt> </tt>
<a name="L29"></a><tt class="py-lineno">29</tt> <tt class="py-line"> <tt class="py-keyword">return</tt> <tt class="py-number">1</tt> </tt>
<a name="L30"></a><tt class="py-lineno">30</tt> <tt class="py-line"> <tt class="py-keyword">return</tt> <tt class="py-number">0</tt> </tt>
</div><a name="L31"></a><tt class="py-lineno">31</tt> <tt class="py-line"> </tt>
<a name="ChainSelector.accept_chain"></a><div id="ChainSelector.accept_chain-def"><a name="L32"></a><tt class="py-lineno">32</tt> <a class="py-toggle" href="#" id="ChainSelector.accept_chain-toggle" onclick="return toggle('ChainSelector.accept_chain');">-</a><tt class="py-line"> <tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.PDB.Dice.ChainSelector-class.html#accept_chain">accept_chain</a><tt class="py-op">(</tt><tt class="py-param">self</tt><tt class="py-op">,</tt> <tt class="py-param">chain</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="ChainSelector.accept_chain-collapsed" style="display:none;" pad="++" indent="++++++++"></div><div id="ChainSelector.accept_chain-expanded"><a name="L33"></a><tt class="py-lineno">33</tt> <tt class="py-line"> <tt class="py-keyword">if</tt> <tt class="py-name">chain</tt><tt class="py-op">.</tt><tt id="link-13" class="py-name"><a title="Bio.Nexus.Nodes.Node.get_id
Bio.PDB.Atom.Atom.get_id
Bio.PDB.Entity.DisorderedEntityWrapper.get_id
Bio.PDB.Entity.Entity.get_id
Bio.PDB.FragmentMapper'.Fragment.get_id" class="py-name" href="#" onclick="return doclink('link-13', 'get_id', 'link-12');">get_id</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt><tt class="py-op">==</tt><tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-14" class="py-name"><a title="Bio.FSSP.fssp_rec.align.chain_id" class="py-name" href="#" onclick="return doclink('link-14', 'chain_id', 'link-6');">chain_id</a></tt><tt class="py-op">:</tt> </tt>
<a name="L34"></a><tt class="py-lineno">34</tt> <tt class="py-line"> <tt class="py-keyword">return</tt> <tt class="py-number">1</tt> </tt>
<a name="L35"></a><tt class="py-lineno">35</tt> <tt class="py-line"> <tt class="py-keyword">return</tt> <tt class="py-number">0</tt> </tt>
</div><a name="L36"></a><tt class="py-lineno">36</tt> <tt class="py-line"> </tt>
<a name="ChainSelector.accept_residue"></a><div id="ChainSelector.accept_residue-def"><a name="L37"></a><tt class="py-lineno">37</tt> <a class="py-toggle" href="#" id="ChainSelector.accept_residue-toggle" onclick="return toggle('ChainSelector.accept_residue');">-</a><tt class="py-line"> <tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.PDB.Dice.ChainSelector-class.html#accept_residue">accept_residue</a><tt class="py-op">(</tt><tt class="py-param">self</tt><tt class="py-op">,</tt> <tt class="py-param">residue</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="ChainSelector.accept_residue-collapsed" style="display:none;" pad="++" indent="++++++++"></div><div id="ChainSelector.accept_residue-expanded"><a name="L38"></a><tt class="py-lineno">38</tt> <tt class="py-line"> <tt class="py-comment"># residue - between start and end</tt> </tt>
<a name="L39"></a><tt class="py-lineno">39</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-name">hetatm_flag</tt><tt class="py-op">,</tt> <tt class="py-name">resseq</tt><tt class="py-op">,</tt> <tt class="py-name">icode</tt><tt class="py-op">=</tt><tt class="py-name">residue</tt><tt class="py-op">.</tt><tt id="link-15" class="py-name"><a title="Bio.Nexus.Nodes.Node.get_id
Bio.PDB.Atom.Atom.get_id
Bio.PDB.Entity.DisorderedEntityWrapper.get_id
Bio.PDB.Entity.Entity.get_id
Bio.PDB.FragmentMapper'.Fragment.get_id" class="py-name" href="#" onclick="return doclink('link-15', 'get_id', 'link-12');">get_id</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
<a name="L40"></a><tt class="py-lineno">40</tt> <tt class="py-line"> <tt class="py-keyword">if</tt> <tt class="py-name">hetatm_flag</tt><tt class="py-op">!=</tt><tt class="py-string">" "</tt><tt class="py-op">:</tt> </tt>
<a name="L41"></a><tt class="py-lineno">41</tt> <tt class="py-line"> <tt class="py-comment"># skip HETATMS</tt> </tt>
<a name="L42"></a><tt class="py-lineno">42</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-keyword">return</tt> <tt class="py-number">0</tt> </tt>
<a name="L43"></a><tt class="py-lineno">43</tt> <tt class="py-line"> <tt class="py-keyword">if</tt> <tt class="py-name">icode</tt><tt class="py-op">!=</tt><tt class="py-string">" "</tt><tt class="py-op">:</tt> </tt>
<a name="L44"></a><tt class="py-lineno">44</tt> <tt class="py-line"> <tt class="py-keyword">print</tt> <tt class="py-string">"WARNING: Icode at "</tt><tt class="py-op">,</tt> <tt class="py-name">residue</tt><tt class="py-op">.</tt><tt id="link-16" class="py-name"><a title="Bio.Nexus.Nodes.Node.get_id
Bio.PDB.Atom.Atom.get_id
Bio.PDB.Entity.DisorderedEntityWrapper.get_id
Bio.PDB.Entity.Entity.get_id
Bio.PDB.FragmentMapper'.Fragment.get_id" class="py-name" href="#" onclick="return doclink('link-16', 'get_id', 'link-12');">get_id</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
<a name="L45"></a><tt class="py-lineno">45</tt> <tt class="py-line"> <tt class="py-keyword">if</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-17" class="py-name"><a title="Bio.GFF.easy.Location.start
Bio.Prosite.Pattern.PrositeMatch.start
Bio.Restriction._Update.RestrictionCompiler.start
Martel.LAX.LAX.start" class="py-name" href="#" onclick="return doclink('link-17', 'start', 'link-8');">start</a></tt><tt class="py-op"><=</tt><tt class="py-name">resseq</tt><tt class="py-op"><=</tt><tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-18" class="py-name"><a title="Bio.GFF.easy.Location.end
Bio.Prosite.Pattern.PrositeMatch.end
Bio.expressions.blocks.end
Bio.expressions.embl.embl65.end
Bio.expressions.swissprot.sprot38.end
Martel.LAX.LAX.end
Martel.test.test_swissprot38.end
Martel.test.testformats.swissprot38.end" class="py-name" href="#" onclick="return doclink('link-18', 'end', 'link-10');">end</a></tt><tt class="py-op">:</tt> </tt>
<a name="L46"></a><tt class="py-lineno">46</tt> <tt class="py-line"> <tt class="py-keyword">return</tt> <tt class="py-number">1</tt> </tt>
<a name="L47"></a><tt class="py-lineno">47</tt> <tt class="py-line"> <tt class="py-keyword">return</tt> <tt class="py-number">0</tt> </tt>
</div><a name="L48"></a><tt class="py-lineno">48</tt> <tt class="py-line"> </tt>
<a name="ChainSelector.accept_atom"></a><div id="ChainSelector.accept_atom-def"><a name="L49"></a><tt class="py-lineno">49</tt> <a class="py-toggle" href="#" id="ChainSelector.accept_atom-toggle" onclick="return toggle('ChainSelector.accept_atom');">-</a><tt class="py-line"> <tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.PDB.Dice.ChainSelector-class.html#accept_atom">accept_atom</a><tt class="py-op">(</tt><tt class="py-param">self</tt><tt class="py-op">,</tt> <tt class="py-param">atom</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="ChainSelector.accept_atom-collapsed" style="display:none;" pad="++" indent="++++++++"></div><div id="ChainSelector.accept_atom-expanded"><a name="L50"></a><tt class="py-lineno">50</tt> <tt class="py-line"> <tt class="py-comment"># atoms - get rid of hydrogens</tt> </tt>
<a name="L51"></a><tt class="py-lineno">51</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt id="link-19" 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-19', 'name', 'link-19');">name</a></tt><tt class="py-op">=</tt><tt class="py-name">atom</tt><tt class="py-op">.</tt><tt id="link-20" class="py-name"><a title="Bio.Nexus.Nodes.Node.get_id
Bio.PDB.Atom.Atom.get_id
Bio.PDB.Entity.DisorderedEntityWrapper.get_id
Bio.PDB.Entity.Entity.get_id
Bio.PDB.FragmentMapper'.Fragment.get_id" class="py-name" href="#" onclick="return doclink('link-20', 'get_id', 'link-12');">get_id</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
<a name="L52"></a><tt class="py-lineno">52</tt> <tt class="py-line"> <tt class="py-keyword">if</tt> <tt id="link-21" class="py-name"><a title="Bio.PDB.Dice._hydrogen" class="py-name" href="#" onclick="return doclink('link-21', '_hydrogen', 'link-4');">_hydrogen</a></tt><tt class="py-op">.</tt><tt id="link-22" class="py-name" targets="Method Bio.Parsers.spark.GenericASTMatcher.match()=Bio.Parsers.spark.GenericASTMatcher-class.html#match,Method Bio.Prosite.Pattern.Prosite.match()=Bio.Prosite.Pattern.Prosite-class.html#match,Function Bio.triefind.match()=Bio.triefind-module.html#match,Method Martel.msre_parse.Tokenizer.match()=Martel.msre_parse.Tokenizer-class.html#match"><a title="Bio.Parsers.spark.GenericASTMatcher.match
Bio.Prosite.Pattern.Prosite.match
Bio.triefind.match
Martel.msre_parse.Tokenizer.match" class="py-name" href="#" onclick="return doclink('link-22', 'match', 'link-22');">match</a></tt><tt class="py-op">(</tt><tt id="link-23" class="py-name"><a title="Bio.Encodings.IUPACEncoding.name" class="py-name" href="#" onclick="return doclink('link-23', 'name', 'link-19');">name</a></tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
<a name="L53"></a><tt class="py-lineno">53</tt> <tt class="py-line"> <tt class="py-keyword">return</tt> <tt class="py-number">0</tt> </tt>
<a name="L54"></a><tt class="py-lineno">54</tt> <tt class="py-line"> <tt class="py-keyword">else</tt><tt class="py-op">:</tt> </tt>
<a name="L55"></a><tt class="py-lineno">55</tt> <tt class="py-line"> <tt class="py-keyword">return</tt> <tt class="py-number">1</tt> </tt>
</div></div><a name="L56"></a><tt class="py-lineno">56</tt> <tt class="py-line"> </tt>
<a name="L57"></a><tt class="py-lineno">57</tt> <tt class="py-line"> </tt>
<a name="extract"></a><div id="extract-def"><a name="L58"></a><tt class="py-lineno">58</tt> <a class="py-toggle" href="#" id="extract-toggle" onclick="return toggle('extract');">-</a><tt class="py-line"><tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.PDB.Dice-module.html#extract">extract</a><tt class="py-op">(</tt><tt class="py-param">structure</tt><tt class="py-op">,</tt> <tt class="py-param">chain_id</tt><tt class="py-op">,</tt> <tt class="py-param">start</tt><tt class="py-op">,</tt> <tt class="py-param">end</tt><tt class="py-op">,</tt> <tt class="py-param">filename</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="extract-collapsed" style="display:none;" pad="++" indent="++++"></div><div id="extract-expanded"><a name="L59"></a><tt class="py-lineno">59</tt> <tt class="py-line"> <tt class="py-docstring">"""</tt> </tt>
<a name="L60"></a><tt class="py-lineno">60</tt> <tt class="py-line"><tt class="py-docstring"> Write out selected portion to filename.</tt> </tt>
<a name="L61"></a><tt class="py-lineno">61</tt> <tt class="py-line"><tt class="py-docstring"> """</tt> </tt>
<a name="L62"></a><tt class="py-lineno">62</tt> <tt class="py-line"> <tt class="py-name">sel</tt><tt class="py-op">=</tt><tt id="link-24" class="py-name" targets="Class Bio.PDB.Dice.ChainSelector=Bio.PDB.Dice.ChainSelector-class.html"><a title="Bio.PDB.Dice.ChainSelector" class="py-name" href="#" onclick="return doclink('link-24', 'ChainSelector', 'link-24');">ChainSelector</a></tt><tt class="py-op">(</tt><tt id="link-25" class="py-name"><a title="Bio.FSSP.fssp_rec.align.chain_id" class="py-name" href="#" onclick="return doclink('link-25', 'chain_id', 'link-6');">chain_id</a></tt><tt class="py-op">,</tt> <tt id="link-26" class="py-name"><a title="Bio.GFF.easy.Location.start
Bio.Prosite.Pattern.PrositeMatch.start
Bio.Restriction._Update.RestrictionCompiler.start
Martel.LAX.LAX.start" class="py-name" href="#" onclick="return doclink('link-26', 'start', 'link-8');">start</a></tt><tt class="py-op">,</tt> <tt id="link-27" class="py-name"><a title="Bio.GFF.easy.Location.end
Bio.Prosite.Pattern.PrositeMatch.end
Bio.expressions.blocks.end
Bio.expressions.embl.embl65.end
Bio.expressions.swissprot.sprot38.end
Martel.LAX.LAX.end
Martel.test.test_swissprot38.end
Martel.test.testformats.swissprot38.end" class="py-name" href="#" onclick="return doclink('link-27', 'end', 'link-10');">end</a></tt><tt class="py-op">)</tt> </tt>
<a name="L63"></a><tt class="py-lineno">63</tt> <tt class="py-line"> <tt class="py-name">io</tt><tt class="py-op">=</tt><tt id="link-28" class="py-name"><a title="Bio.PDB.PDBIO'.PDBIO" class="py-name" href="#" onclick="return doclink('link-28', 'PDBIO', 'link-2');">PDBIO</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
<a name="L64"></a><tt class="py-lineno">64</tt> <tt class="py-line"> <tt class="py-name">io</tt><tt class="py-op">.</tt><tt id="link-29" class="py-name" targets="Method Bio.PDB.PDBIO'.PDBIO.set_structure()=Bio.PDB.PDBIO%27.PDBIO-class.html#set_structure"><a title="Bio.PDB.PDBIO'.PDBIO.set_structure" class="py-name" href="#" onclick="return doclink('link-29', 'set_structure', 'link-29');">set_structure</a></tt><tt class="py-op">(</tt><tt id="link-30" class="py-name" targets="Variable Bio.SubsMat.MatrixInfo.structure=Bio.SubsMat.MatrixInfo-module.html#structure"><a title="Bio.SubsMat.MatrixInfo.structure" class="py-name" href="#" onclick="return doclink('link-30', 'structure', 'link-30');">structure</a></tt><tt class="py-op">)</tt> </tt>
<a name="L65"></a><tt class="py-lineno">65</tt> <tt class="py-line"> <tt class="py-name">io</tt><tt class="py-op">.</tt><tt id="link-31" class="py-name" targets="Method Bio.Cluster.Record.save()=Bio.Cluster.Record-class.html#save,Function Bio.MarkovModel.save()=Bio.MarkovModel-module.html#save,Method Bio.PDB.PDBIO'.PDBIO.save()=Bio.PDB.PDBIO%27.PDBIO-class.html#save"><a title="Bio.Cluster.Record.save
Bio.MarkovModel.save
Bio.PDB.PDBIO'.PDBIO.save" class="py-name" href="#" onclick="return doclink('link-31', 'save', 'link-31');">save</a></tt><tt class="py-op">(</tt><tt class="py-name">filename</tt><tt class="py-op">,</tt> <tt class="py-name">sel</tt><tt class="py-op">)</tt> </tt>
</div><a name="L66"></a><tt class="py-lineno">66</tt> <tt class="py-line"> </tt>
<a name="L67"></a><tt class="py-lineno">67</tt> <tt class="py-line"> </tt>
<a name="L68"></a><tt class="py-lineno">68</tt> <tt class="py-line"> </tt>
<a name="L69"></a><tt class="py-lineno">69</tt> <tt class="py-line"><tt class="py-keyword">if</tt> <tt class="py-name">__name__</tt><tt class="py-op">==</tt><tt class="py-string">"__main__"</tt><tt class="py-op">:</tt> </tt>
<a name="L70"></a><tt class="py-lineno">70</tt> <tt class="py-line"> </tt>
<a name="L71"></a><tt class="py-lineno">71</tt> <tt class="py-line"> <tt class="py-keyword">from</tt> <tt id="link-32" class="py-name"><a title="Bio" class="py-name" href="#" onclick="return doclink('link-32', 'Bio', 'link-0');">Bio</a></tt><tt class="py-op">.</tt><tt id="link-33" class="py-name"><a title="Bio.PDB" class="py-name" href="#" onclick="return doclink('link-33', 'PDB', 'link-1');">PDB</a></tt><tt class="py-op">.</tt><tt id="link-34" class="py-name" targets="Class Bio.PDB.PDBParser'.PDBParser=Bio.PDB.PDBParser%27.PDBParser-class.html"><a title="Bio.PDB.PDBParser'.PDBParser" class="py-name" href="#" onclick="return doclink('link-34', 'PDBParser', 'link-34');">PDBParser</a></tt> <tt class="py-keyword">import</tt> <tt id="link-35" class="py-name"><a title="Bio.PDB.PDBParser'.PDBParser" class="py-name" href="#" onclick="return doclink('link-35', 'PDBParser', 'link-34');">PDBParser</a></tt> </tt>
<a name="L72"></a><tt class="py-lineno">72</tt> <tt class="py-line"> </tt>
<a name="L73"></a><tt class="py-lineno">73</tt> <tt class="py-line"> <tt class="py-keyword">import</tt> <tt class="py-name">sys</tt> </tt>
<a name="L74"></a><tt class="py-lineno">74</tt> <tt class="py-line"> </tt>
<a name="L75"></a><tt class="py-lineno">75</tt> <tt class="py-line"> <tt class="py-name">p</tt><tt class="py-op">=</tt><tt id="link-36" class="py-name"><a title="Bio.PDB.PDBParser'.PDBParser" class="py-name" href="#" onclick="return doclink('link-36', 'PDBParser', 'link-34');">PDBParser</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
<a name="L76"></a><tt class="py-lineno">76</tt> <tt class="py-line"> <tt id="link-37" class="py-name" targets="Variable Martel.test.test_swissprot38.s=Martel.test.test_swissprot38-module.html#s"><a title="Martel.test.test_swissprot38.s" class="py-name" href="#" onclick="return doclink('link-37', 's', 'link-37');">s</a></tt><tt class="py-op">=</tt><tt class="py-name">p</tt><tt class="py-op">.</tt><tt id="link-38" class="py-name" targets="Method Bio.PDB.MMCIFParser.MMCIFParser.get_structure()=Bio.PDB.MMCIFParser.MMCIFParser-class.html#get_structure,Method Bio.PDB.PDBParser'.PDBParser.get_structure()=Bio.PDB.PDBParser%27.PDBParser-class.html#get_structure,Method Bio.PDB.StructureBuilder.StructureBuilder.get_structure()=Bio.PDB.StructureBuilder.StructureBuilder-class.html#get_structure"><a title="Bio.PDB.MMCIFParser.MMCIFParser.get_structure
Bio.PDB.PDBParser'.PDBParser.get_structure
Bio.PDB.StructureBuilder.StructureBuilder.get_structure" class="py-name" href="#" onclick="return doclink('link-38', 'get_structure', 'link-38');">get_structure</a></tt><tt class="py-op">(</tt><tt class="py-string">"scr"</tt><tt class="py-op">,</tt> <tt class="py-name">sys</tt><tt class="py-op">.</tt><tt class="py-name">argv</tt><tt class="py-op">[</tt><tt class="py-number">1</tt><tt class="py-op">]</tt><tt class="py-op">)</tt> </tt>
<a name="L77"></a><tt class="py-lineno">77</tt> <tt class="py-line"> </tt>
<a name="L78"></a><tt class="py-lineno">78</tt> <tt class="py-line"> <tt id="link-39" class="py-name" targets="Function Bio.PDB.Dice.extract()=Bio.PDB.Dice-module.html#extract"><a title="Bio.PDB.Dice.extract" class="py-name" href="#" onclick="return doclink('link-39', 'extract', 'link-39');">extract</a></tt><tt class="py-op">(</tt><tt id="link-40" class="py-name"><a title="Martel.test.test_swissprot38.s" class="py-name" href="#" onclick="return doclink('link-40', 's', 'link-37');">s</a></tt><tt class="py-op">,</tt> <tt class="py-string">" "</tt><tt class="py-op">,</tt> <tt class="py-number">1</tt><tt class="py-op">,</tt> <tt class="py-number">100</tt><tt class="py-op">,</tt> <tt class="py-string">"out.pdb"</tt><tt class="py-op">)</tt> </tt>
<a name="L79"></a><tt class="py-lineno">79</tt> <tt class="py-line"> </tt><script type="text/javascript">
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