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<a href="Bio-module.html">Package Bio</a> ::
<a href="Bio.PDB-module.html">Package PDB</a> ::
Module PSEA
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<h1 class="epydoc">Source Code for <a href="Bio.PDB.PSEA-module.html">Module Bio.PDB.PSEA</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) 2006, 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>
<a name="L7"></a><tt class="py-lineno"> 7</tt> <tt class="py-line"><tt class="py-keyword">import</tt> <tt class="py-name">os</tt> </tt>
<a name="L8"></a><tt class="py-lineno"> 8</tt> <tt class="py-line"><tt class="py-keyword">from</tt> <tt class="py-name">string</tt> <tt class="py-keyword">import</tt> <tt class="py-name">upper</tt> </tt>
<a name="L9"></a><tt class="py-lineno"> 9</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-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>
<a name="run_psea"></a><div id="run_psea-def"><a name="L12"></a><tt class="py-lineno">12</tt> <a class="py-toggle" href="#" id="run_psea-toggle" onclick="return toggle('run_psea');">-</a><tt class="py-line"><tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.PDB.PSEA-module.html#run_psea">run_psea</a><tt class="py-op">(</tt><tt class="py-param">fname</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="run_psea-collapsed" style="display:none;" pad="++" indent="++++"></div><div id="run_psea-expanded"><a name="L13"></a><tt class="py-lineno">13</tt> <tt class="py-line"> <tt class="py-docstring">"""</tt> </tt>
<a name="L14"></a><tt class="py-lineno">14</tt> <tt class="py-line"><tt class="py-docstring"> Run PSEA and return output filename.</tt> </tt>
<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-name">os</tt><tt class="py-op">.</tt><tt class="py-name">system</tt><tt class="py-op">(</tt><tt class="py-string">"psea "</tt><tt class="py-op">+</tt><tt class="py-name">fname</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">last</tt><tt class="py-op">=</tt><tt class="py-name">fname</tt><tt class="py-op">.</tt><tt id="link-2" 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-2', 'split', 'link-2');">split</a></tt><tt class="py-op">(</tt><tt class="py-string">"/"</tt><tt class="py-op">)</tt><tt class="py-op">[</tt><tt class="py-op">-</tt><tt class="py-number">1</tt><tt class="py-op">]</tt> </tt>
<a name="L18"></a><tt class="py-lineno">18</tt> <tt class="py-line"> <tt class="py-name">base</tt><tt class="py-op">=</tt><tt class="py-name">last</tt><tt class="py-op">.</tt><tt id="link-3" class="py-name"><a title="Bio.Nexus.Trees.Tree.split
Bio.Restriction.Restriction.RestrictionBatch.split" class="py-name" href="#" onclick="return doclink('link-3', 'split', 'link-2');">split</a></tt><tt class="py-op">(</tt><tt class="py-string">"."</tt><tt class="py-op">)</tt><tt class="py-op">[</tt><tt class="py-number">0</tt><tt class="py-op">]</tt> </tt>
<a name="L19"></a><tt class="py-lineno">19</tt> <tt class="py-line"> <tt class="py-keyword">return</tt> <tt class="py-name">base</tt><tt class="py-op">+</tt><tt class="py-string">".sea"</tt> </tt>
</div><a name="L20"></a><tt class="py-lineno">20</tt> <tt class="py-line"> </tt>
<a name="psea"></a><div id="psea-def"><a name="L21"></a><tt class="py-lineno">21</tt> <a class="py-toggle" href="#" id="psea-toggle" onclick="return toggle('psea');">-</a><tt class="py-line"><tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.PDB.PSEA-module.html#psea">psea</a><tt class="py-op">(</tt><tt class="py-param">pname</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="psea-collapsed" style="display:none;" pad="++" indent="++++"></div><div id="psea-expanded"><a name="L22"></a><tt class="py-lineno">22</tt> <tt class="py-line"> <tt class="py-docstring">"""</tt> </tt>
<a name="L23"></a><tt class="py-lineno">23</tt> <tt class="py-line"><tt class="py-docstring"> Parse PSEA output file.</tt> </tt>
<a name="L24"></a><tt class="py-lineno">24</tt> <tt class="py-line"><tt class="py-docstring"> """</tt> </tt>
<a name="L25"></a><tt class="py-lineno">25</tt> <tt class="py-line"> <tt class="py-name">fname</tt><tt class="py-op">=</tt><tt id="link-4" class="py-name" targets="Function Bio.PDB.PSEA.run_psea()=Bio.PDB.PSEA-module.html#run_psea"><a title="Bio.PDB.PSEA.run_psea" class="py-name" href="#" onclick="return doclink('link-4', 'run_psea', 'link-4');">run_psea</a></tt><tt class="py-op">(</tt><tt class="py-name">pname</tt><tt class="py-op">)</tt> </tt>
<a name="L26"></a><tt class="py-lineno">26</tt> <tt class="py-line"> <tt id="link-5" 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-5', 'start', 'link-5');">start</a></tt><tt class="py-op">=</tt><tt class="py-number">0</tt> </tt>
<a name="L27"></a><tt class="py-lineno">27</tt> <tt class="py-line"> <tt class="py-name">ss</tt><tt class="py-op">=</tt><tt class="py-string">""</tt> </tt>
<a name="L28"></a><tt class="py-lineno">28</tt> <tt class="py-line"> <tt class="py-name">fp</tt><tt class="py-op">=</tt><tt id="link-6" 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-6', 'open', 'link-6');">open</a></tt><tt class="py-op">(</tt><tt class="py-name">fname</tt><tt class="py-op">,</tt> <tt class="py-string">'r'</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">for</tt> <tt class="py-name">l</tt> <tt class="py-keyword">in</tt> <tt class="py-name">fp</tt><tt class="py-op">.</tt><tt id="link-7" class="py-name" targets="Method Bio.EUtils.ReseekFile.ReseekFile.readlines()=Bio.EUtils.ReseekFile.ReseekFile-class.html#readlines,Method Bio.File.SGMLHandle.readlines()=Bio.File.SGMLHandle-class.html#readlines,Method Bio.File.UndoHandle.readlines()=Bio.File.UndoHandle-class.html#readlines,Method Bio.SGMLExtractor.SGMLExtractorHandle.readlines()=Bio.SGMLExtractor.SGMLExtractorHandle-class.html#readlines"><a title="Bio.EUtils.ReseekFile.ReseekFile.readlines
Bio.File.SGMLHandle.readlines
Bio.File.UndoHandle.readlines
Bio.SGMLExtractor.SGMLExtractorHandle.readlines" class="py-name" href="#" onclick="return doclink('link-7', 'readlines', 'link-7');">readlines</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
<a name="L30"></a><tt class="py-lineno">30</tt> <tt class="py-line"> <tt class="py-keyword">if</tt> <tt class="py-name">l</tt><tt class="py-op">[</tt><tt class="py-number">0</tt><tt class="py-op">:</tt><tt class="py-number">6</tt><tt class="py-op">]</tt><tt class="py-op">==</tt><tt class="py-string">">p-sea"</tt><tt class="py-op">:</tt> </tt>
<a name="L31"></a><tt class="py-lineno">31</tt> <tt class="py-line"> <tt id="link-8" 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-8', 'start', 'link-5');">start</a></tt><tt class="py-op">=</tt><tt class="py-number">1</tt> </tt>
<a name="L32"></a><tt class="py-lineno">32</tt> <tt class="py-line"> <tt class="py-keyword">continue</tt> </tt>
<a name="L33"></a><tt class="py-lineno">33</tt> <tt class="py-line"> <tt class="py-keyword">if</tt> <tt class="py-keyword">not</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-5');">start</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">continue</tt> </tt>
<a name="L35"></a><tt class="py-lineno">35</tt> <tt class="py-line"> <tt class="py-keyword">if</tt> <tt class="py-name">l</tt><tt class="py-op">[</tt><tt class="py-number">0</tt><tt class="py-op">]</tt><tt class="py-op">==</tt><tt class="py-string">"\n"</tt><tt class="py-op">:</tt> </tt>
<a name="L36"></a><tt class="py-lineno">36</tt> <tt class="py-line"> <tt class="py-keyword">break</tt> </tt>
<a name="L37"></a><tt class="py-lineno">37</tt> <tt class="py-line"> <tt class="py-name">ss</tt><tt class="py-op">=</tt><tt class="py-name">ss</tt><tt class="py-op">+</tt><tt class="py-name">l</tt><tt class="py-op">[</tt><tt class="py-number">0</tt><tt class="py-op">:</tt><tt class="py-op">-</tt><tt class="py-number">1</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">fp</tt><tt class="py-op">.</tt><tt id="link-10" class="py-name" targets="Method Bio.FilteredReader.FilteredReader.close()=Bio.FilteredReader.FilteredReader-class.html#close,Method Bio.Mindy.BerkeleyDB.BerkeleyDB.close()=Bio.Mindy.BerkeleyDB.BerkeleyDB-class.html#close,Method Bio.Mindy.FlatDB.MemoryFlatDB.close()=Bio.Mindy.FlatDB.MemoryFlatDB-class.html#close,Method BioSQL.BioSeqDatabase.Adaptor.close()=BioSQL.BioSeqDatabase.Adaptor-class.html#close,Method Martel.Parser.Parser.close()=Martel.Parser.Parser-class.html#close,Method Martel.Parser.RecordParser.close()=Martel.Parser.RecordParser-class.html#close"><a title="Bio.FilteredReader.FilteredReader.close
Bio.Mindy.BerkeleyDB.BerkeleyDB.close
Bio.Mindy.FlatDB.MemoryFlatDB.close
BioSQL.BioSeqDatabase.Adaptor.close
Martel.Parser.Parser.close
Martel.Parser.RecordParser.close" class="py-name" href="#" onclick="return doclink('link-10', 'close', 'link-10');">close</a></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-keyword">return</tt> <tt class="py-name">ss</tt> </tt>
</div><a name="L40"></a><tt class="py-lineno">40</tt> <tt class="py-line"> </tt>
<a name="psea2HEC"></a><div id="psea2HEC-def"><a name="L41"></a><tt class="py-lineno">41</tt> <a class="py-toggle" href="#" id="psea2HEC-toggle" onclick="return toggle('psea2HEC');">-</a><tt class="py-line"><tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.PDB.PSEA-module.html#psea2HEC">psea2HEC</a><tt class="py-op">(</tt><tt class="py-param">pseq</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="psea2HEC-collapsed" style="display:none;" pad="++" indent="++++"></div><div id="psea2HEC-expanded"><a name="L42"></a><tt class="py-lineno">42</tt> <tt class="py-line"> <tt class="py-docstring">"""</tt> </tt>
<a name="L43"></a><tt class="py-lineno">43</tt> <tt class="py-line"><tt class="py-docstring"> Translate PSEA secondary structure string into HEC.</tt> </tt>
<a name="L44"></a><tt class="py-lineno">44</tt> <tt class="py-line"><tt class="py-docstring"> """</tt> </tt>
<a name="L45"></a><tt class="py-lineno">45</tt> <tt class="py-line"> <tt id="link-11" class="py-name" targets="Method Bio.GFF.Feature.seq()=Bio.GFF.Feature-class.html#seq,Method Bio.GFF.FeatureAggregate.seq()=Bio.GFF.FeatureAggregate-class.html#seq,Variable BioSQL.BioSeq.DBSeqRecord.seq=BioSQL.BioSeq.DBSeqRecord-class.html#seq"><a title="Bio.GFF.Feature.seq
Bio.GFF.FeatureAggregate.seq
BioSQL.BioSeq.DBSeqRecord.seq" class="py-name" href="#" onclick="return doclink('link-11', 'seq', 'link-11');">seq</a></tt><tt class="py-op">=</tt><tt class="py-op">[</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">for</tt> <tt class="py-name">ss</tt> <tt class="py-keyword">in</tt> <tt class="py-name">pseq</tt><tt class="py-op">:</tt> </tt>
<a name="L47"></a><tt class="py-lineno">47</tt> <tt class="py-line"> <tt class="py-keyword">if</tt> <tt class="py-name">ss</tt><tt class="py-op">==</tt><tt class="py-string">"a"</tt><tt class="py-op">:</tt> </tt>
<a name="L48"></a><tt class="py-lineno">48</tt> <tt class="py-line"> <tt class="py-name">n</tt><tt class="py-op">=</tt><tt class="py-string">"H"</tt> </tt>
<a name="L49"></a><tt class="py-lineno">49</tt> <tt class="py-line"> <tt class="py-keyword">elif</tt> <tt class="py-name">ss</tt><tt class="py-op">==</tt><tt class="py-string">"b"</tt><tt class="py-op">:</tt> </tt>
<a name="L50"></a><tt class="py-lineno">50</tt> <tt class="py-line"> <tt class="py-name">n</tt><tt class="py-op">=</tt><tt class="py-string">"E"</tt> </tt>
<a name="L51"></a><tt class="py-lineno">51</tt> <tt class="py-line"> <tt class="py-keyword">elif</tt> <tt class="py-name">ss</tt><tt class="py-op">==</tt><tt class="py-string">"c"</tt><tt class="py-op">:</tt> </tt>
<a name="L52"></a><tt class="py-lineno">52</tt> <tt class="py-line"> <tt class="py-name">n</tt><tt class="py-op">=</tt><tt class="py-string">"C"</tt> </tt>
<a name="L53"></a><tt class="py-lineno">53</tt> <tt class="py-line"> <tt id="link-12" class="py-name"><a title="Bio.GFF.Feature.seq
Bio.GFF.FeatureAggregate.seq
BioSQL.BioSeq.DBSeqRecord.seq" class="py-name" href="#" onclick="return doclink('link-12', 'seq', 'link-11');">seq</a></tt><tt class="py-op">.</tt><tt id="link-13" 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-13', 'append', 'link-13');">append</a></tt><tt class="py-op">(</tt><tt class="py-name">n</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">return</tt> <tt id="link-14" class="py-name"><a title="Bio.GFF.Feature.seq
Bio.GFF.FeatureAggregate.seq
BioSQL.BioSeq.DBSeqRecord.seq" class="py-name" href="#" onclick="return doclink('link-14', 'seq', 'link-11');">seq</a></tt> </tt>
</div><a name="L55"></a><tt class="py-lineno">55</tt> <tt class="py-line"> </tt>
<a name="annotate"></a><div id="annotate-def"><a name="L56"></a><tt class="py-lineno">56</tt> <a class="py-toggle" href="#" id="annotate-toggle" onclick="return toggle('annotate');">-</a><tt class="py-line"><tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.PDB.PSEA-module.html#annotate">annotate</a><tt class="py-op">(</tt><tt class="py-param">m</tt><tt class="py-op">,</tt> <tt class="py-param">ss_seq</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><a name="L57"></a><tt class="py-lineno">57</tt> <tt class="py-line"> <tt class="py-name">c</tt><tt class="py-op">=</tt><tt class="py-name">m</tt><tt class="py-op">.</tt><tt id="link-15" class="py-name" targets="Method Bio.PDB.Entity.Entity.get_list()=Bio.PDB.Entity.Entity-class.html#get_list"><a title="Bio.PDB.Entity.Entity.get_list" class="py-name" href="#" onclick="return doclink('link-15', 'get_list', 'link-15');">get_list</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt><tt class="py-op">[</tt><tt class="py-number">0</tt><tt class="py-op">]</tt> </tt>
<a name="L58"></a><tt class="py-lineno">58</tt> <tt class="py-line"> <tt class="py-name">all</tt><tt class="py-op">=</tt><tt class="py-name">c</tt><tt class="py-op">.</tt><tt id="link-16" class="py-name"><a title="Bio.PDB.Entity.Entity.get_list" class="py-name" href="#" onclick="return doclink('link-16', 'get_list', 'link-15');">get_list</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
<a name="L59"></a><tt class="py-lineno">59</tt> <tt class="py-line"> <tt class="py-name">residues</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-comment"># Now remove HOH etc.</tt> </tt>
<a name="L61"></a><tt class="py-lineno">61</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-keyword">for</tt> <tt class="py-name">res</tt> <tt class="py-keyword">in</tt> <tt class="py-name">all</tt><tt class="py-op">:</tt> </tt>
<a name="L62"></a><tt class="py-lineno">62</tt> <tt class="py-line"> <tt class="py-keyword">if</tt> <tt id="link-17" class="py-name" targets="Function Bio.PDB.Polypeptide.is_aa()=Bio.PDB.Polypeptide-module.html#is_aa"><a title="Bio.PDB.Polypeptide.is_aa" class="py-name" href="#" onclick="return doclink('link-17', 'is_aa', 'link-17');">is_aa</a></tt><tt class="py-op">(</tt><tt class="py-name">res</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-name">residues</tt><tt class="py-op">.</tt><tt id="link-18" 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-18', 'append', 'link-13');">append</a></tt><tt class="py-op">(</tt><tt class="py-name">res</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">L</tt><tt class="py-op">=</tt><tt class="py-name">len</tt><tt class="py-op">(</tt><tt class="py-name">residues</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">if</tt> <tt class="py-keyword">not</tt> <tt class="py-op">(</tt><tt class="py-name">L</tt><tt class="py-op">==</tt><tt class="py-name">len</tt><tt class="py-op">(</tt><tt class="py-name">ss_seq</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-keyword">print</tt> <tt class="py-string">"Length mismatch"</tt><tt class="py-op">,</tt> <tt class="py-name">L</tt><tt class="py-op">,</tt> <tt class="py-name">len</tt><tt class="py-op">(</tt><tt class="py-name">ss_seq</tt><tt class="py-op">)</tt> </tt>
<a name="L67"></a><tt class="py-lineno">67</tt> <tt class="py-line"> <tt class="py-keyword">raise</tt> <tt class="py-name">Exception</tt> </tt>
<a name="L68"></a><tt class="py-lineno">68</tt> <tt class="py-line"> <tt class="py-keyword">for</tt> <tt id="link-19" 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-19', 'i', 'link-19');">i</a></tt> <tt class="py-keyword">in</tt> <tt class="py-name">range</tt><tt class="py-op">(</tt><tt class="py-number">0</tt><tt class="py-op">,</tt> <tt class="py-name">L</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-name">residues</tt><tt class="py-op">[</tt><tt id="link-20" class="py-name"><a title="Bio.PDB.Polypeptide.i" class="py-name" href="#" onclick="return doclink('link-20', 'i', 'link-19');">i</a></tt><tt class="py-op">]</tt><tt class="py-op">.</tt><tt class="py-name">xtra</tt><tt class="py-op">[</tt><tt class="py-string">"SS_PSEA"</tt><tt class="py-op">]</tt><tt class="py-op">=</tt><tt class="py-name">ss_seq</tt><tt class="py-op">[</tt><tt id="link-21" class="py-name"><a title="Bio.PDB.Polypeptide.i" class="py-name" href="#" onclick="return doclink('link-21', 'i', 'link-19');">i</a></tt><tt class="py-op">]</tt> </tt>
</div><a name="L70"></a><tt class="py-lineno">70</tt> <tt class="py-line"> <tt class="py-comment">#os.system("rm "+fname)</tt> </tt>
<a name="L71"></a><tt class="py-lineno">71</tt> <tt class="py-line"><tt class="py-comment"></tt> </tt>
<a name="PSEA"></a><div id="PSEA-def"><a name="L72"></a><tt class="py-lineno">72</tt> <a class="py-toggle" href="#" id="PSEA-toggle" onclick="return toggle('PSEA');">-</a><tt class="py-line"><tt class="py-keyword">class</tt> <a class="py-def-name" href="Bio.PDB.PSEA.PSEA-class.html">PSEA</a><tt class="py-op">:</tt> </tt>
</div><div id="PSEA-collapsed" style="display:none;" pad="++" indent="++++"></div><div id="PSEA-expanded"><a name="PSEA.__init__"></a><div id="PSEA.__init__-def"><a name="L73"></a><tt class="py-lineno">73</tt> <a class="py-toggle" href="#" id="PSEA.__init__-toggle" onclick="return toggle('PSEA.__init__');">-</a><tt class="py-line"> <tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.PDB.PSEA.PSEA-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">model</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="PSEA.__init__-collapsed" style="display:none;" pad="++" indent="++++++++"></div><div id="PSEA.__init__-expanded"><a name="L74"></a><tt class="py-lineno">74</tt> <tt class="py-line"> <tt class="py-name">ss_seq</tt><tt class="py-op">=</tt><tt id="link-22" class="py-name" targets="Function Bio.PDB.PSEA.psea()=Bio.PDB.PSEA-module.html#psea"><a title="Bio.PDB.PSEA.psea" class="py-name" href="#" onclick="return doclink('link-22', 'psea', 'link-22');">psea</a></tt><tt class="py-op">(</tt><tt class="py-name">filename</tt><tt class="py-op">)</tt> </tt>
<a name="L75"></a><tt class="py-lineno">75</tt> <tt class="py-line"> <tt class="py-name">ss_seq</tt><tt class="py-op">=</tt><tt id="link-23" class="py-name" targets="Function Bio.PDB.PSEA.psea2HEC()=Bio.PDB.PSEA-module.html#psea2HEC"><a title="Bio.PDB.PSEA.psea2HEC" class="py-name" href="#" onclick="return doclink('link-23', 'psea2HEC', 'link-23');">psea2HEC</a></tt><tt class="py-op">(</tt><tt class="py-name">ss_seq</tt><tt class="py-op">)</tt> </tt>
<a name="L76"></a><tt class="py-lineno">76</tt> <tt class="py-line"> <tt id="link-24" class="py-name" targets="Function Bio.PDB.PSEA.annotate()=Bio.PDB.PSEA-module.html#annotate"><a title="Bio.PDB.PSEA.annotate" class="py-name" href="#" onclick="return doclink('link-24', 'annotate', 'link-24');">annotate</a></tt><tt class="py-op">(</tt><tt class="py-name">model</tt><tt class="py-op">,</tt> <tt class="py-name">ss_seq</tt><tt class="py-op">)</tt> </tt>
<a name="L77"></a><tt class="py-lineno">77</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">ss_seq</tt><tt class="py-op">=</tt><tt class="py-name">ss_seq</tt> </tt>
</div><a name="L78"></a><tt class="py-lineno">78</tt> <tt class="py-line"> </tt>
<a name="PSEA.get_seq"></a><div id="PSEA.get_seq-def"><a name="L79"></a><tt class="py-lineno">79</tt> <a class="py-toggle" href="#" id="PSEA.get_seq-toggle" onclick="return toggle('PSEA.get_seq');">-</a><tt class="py-line"> <tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.PDB.PSEA.PSEA-class.html#get_seq">get_seq</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="PSEA.get_seq-collapsed" style="display:none;" pad="++" indent="++++++++"></div><div id="PSEA.get_seq-expanded"><a name="L80"></a><tt class="py-lineno">80</tt> <tt class="py-line"> <tt class="py-docstring">"""</tt> </tt>
<a name="L81"></a><tt class="py-lineno">81</tt> <tt class="py-line"><tt class="py-docstring"> Return secondary structure string.</tt> </tt>
<a name="L82"></a><tt class="py-lineno">82</tt> <tt class="py-line"><tt class="py-docstring"> """</tt> </tt>
<a name="L83"></a><tt class="py-lineno">83</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">ss_seq</tt> </tt>
</div></div><a name="L84"></a><tt class="py-lineno">84</tt> <tt class="py-line"> </tt>
<a name="L85"></a><tt class="py-lineno">85</tt> <tt class="py-line"> </tt>
<a name="L86"></a><tt class="py-lineno">86</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="L87"></a><tt class="py-lineno">87</tt> <tt class="py-line"> </tt>
<a name="L88"></a><tt class="py-lineno">88</tt> <tt class="py-line"> <tt class="py-keyword">import</tt> <tt class="py-name">sys</tt> </tt>
<a name="L89"></a><tt class="py-lineno">89</tt> <tt class="py-line"> <tt class="py-keyword">from</tt> <tt id="link-25" class="py-name"><a title="Bio" class="py-name" href="#" onclick="return doclink('link-25', 'Bio', 'link-0');">Bio</a></tt><tt class="py-op">.</tt><tt id="link-26" class="py-name"><a title="Bio.PDB" class="py-name" href="#" onclick="return doclink('link-26', 'PDB', 'link-1');">PDB</a></tt> <tt class="py-keyword">import</tt> <tt class="py-op">*</tt> </tt>
<a name="L90"></a><tt class="py-lineno">90</tt> <tt class="py-line"> </tt>
<a name="L91"></a><tt class="py-lineno">91</tt> <tt class="py-line"> <tt class="py-comment"># Parse PDB file</tt> </tt>
<a name="L92"></a><tt class="py-lineno">92</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-name">p</tt><tt class="py-op">=</tt><tt id="link-27" 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-27', 'PDBParser', 'link-27');">PDBParser</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
<a name="L93"></a><tt class="py-lineno">93</tt> <tt class="py-line"> <tt id="link-28" 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-28', 's', 'link-28');">s</a></tt><tt class="py-op">=</tt><tt class="py-name">p</tt><tt class="py-op">.</tt><tt id="link-29" 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-29', 'get_structure', 'link-29');">get_structure</a></tt><tt class="py-op">(</tt><tt class="py-string">'X'</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="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 class="py-comment"># Annotate structure with PSEA sceondary structure info</tt> </tt>
<a name="L96"></a><tt class="py-lineno">96</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt id="link-30" class="py-name" targets="Module Bio.PDB.PSEA=Bio.PDB.PSEA-module.html,Class Bio.PDB.PSEA.PSEA=Bio.PDB.PSEA.PSEA-class.html"><a title="Bio.PDB.PSEA
Bio.PDB.PSEA.PSEA" class="py-name" href="#" onclick="return doclink('link-30', 'PSEA', 'link-30');">PSEA</a></tt><tt class="py-op">(</tt><tt id="link-31" class="py-name"><a title="Martel.test.test_swissprot38.s" class="py-name" href="#" onclick="return doclink('link-31', 's', 'link-28');">s</a></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">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="L97"></a><tt class="py-lineno">97</tt> <tt class="py-line"> </tt><script type="text/javascript">
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