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<a href="Bio-module.html">Package Bio</a> ::
<a href="Bio.SCOP-module.html">Package SCOP</a> ::
Module Residues'
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<h1 class="epydoc">Source Code for <a href="Bio.SCOP.Residues%27-module.html">Module Bio.SCOP.Residues'</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 2000 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-comment"># Gavin E. Crooks 2001-11-03</tt> </tt>
<a name="L7"></a><tt class="py-lineno"> 7</tt> <tt class="py-line"><tt class="py-comment"></tt><tt class="py-comment"># Minor extensions, some bug fixes, and major changes to the interface </tt> </tt>
<a name="L8"></a><tt class="py-lineno"> 8</tt> <tt class="py-line"><tt class="py-comment"></tt> </tt>
<a name="L9"></a><tt class="py-lineno"> 9</tt> <tt class="py-line"><tt class="py-keyword">import</tt> <tt class="py-name">re</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 class="py-string">"""A collection of residues from a PDB structure."""</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 id="link-0" class="py-name" targets="Variable Bio.SCOP.Residues'._pdbid_re=Bio.SCOP.Residues%27-module.html#_pdbid_re"><a title="Bio.SCOP.Residues'._pdbid_re" class="py-name" href="#" onclick="return doclink('link-0', '_pdbid_re', 'link-0');">_pdbid_re</a></tt> <tt class="py-op">=</tt> <tt class="py-name">re</tt><tt class="py-op">.</tt><tt id="link-1" 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-1', 'compile', 'link-1');">compile</a></tt><tt class="py-op">(</tt><tt class="py-string">r"^(\w\w\w\w)(?:$|\s+|_)(.*)"</tt><tt class="py-op">)</tt> </tt>
<a name="L14"></a><tt class="py-lineno">14</tt> <tt class="py-line"><tt id="link-2" class="py-name" targets="Variable Bio.SCOP.Residues'._fragment_re=Bio.SCOP.Residues%27-module.html#_fragment_re"><a title="Bio.SCOP.Residues'._fragment_re" class="py-name" href="#" onclick="return doclink('link-2', '_fragment_re', 'link-2');">_fragment_re</a></tt> <tt class="py-op">=</tt> <tt class="py-name">re</tt><tt class="py-op">.</tt><tt id="link-3" class="py-name"><a title="Bio.Prosite.Pattern.compile" class="py-name" href="#" onclick="return doclink('link-3', 'compile', 'link-1');">compile</a></tt><tt class="py-op">(</tt><tt class="py-string">r"\(?(\w:)?(-?\w*)-?(-?\w*)\)?(.*)"</tt><tt class="py-op">)</tt> </tt>
<a name="L15"></a><tt class="py-lineno">15</tt> <tt class="py-line"> </tt>
<a name="Residues"></a><div id="Residues-def"><a name="L16"></a><tt class="py-lineno">16</tt> <a class="py-toggle" href="#" id="Residues-toggle" onclick="return toggle('Residues');">-</a><tt class="py-line"><tt class="py-keyword">class</tt> <a class="py-def-name" href="Bio.SCOP.Residues'.Residues-class.html">Residues</a> <tt class="py-op">:</tt> </tt>
</div><div id="Residues-collapsed" style="display:none;" pad="++" indent="++++"></div><div id="Residues-expanded"><a name="L17"></a><tt class="py-lineno">17</tt> <tt class="py-line"> <tt class="py-docstring">"""A collection of residues from a PDB structure.</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 class="py-docstring"> This class provides code to work with SCOP domain definitions. These</tt> </tt>
<a name="L20"></a><tt class="py-lineno">20</tt> <tt class="py-line"><tt class="py-docstring"> are concisely expressed as a one or more chain fragments. For example,</tt> </tt>
<a name="L21"></a><tt class="py-lineno">21</tt> <tt class="py-line"><tt class="py-docstring"> "(1bba A:10-20,B:)" indicates residue 10 through 20 (inclusive) of</tt> </tt>
<a name="L22"></a><tt class="py-lineno">22</tt> <tt class="py-line"><tt class="py-docstring"> chain A, and every residue of chain B in the pdb structure 1bba. The pdb</tt> </tt>
<a name="L23"></a><tt class="py-lineno">23</tt> <tt class="py-line"><tt class="py-docstring"> id and brackets are optional. In addition "-" indicates every residue of</tt> </tt>
<a name="L24"></a><tt class="py-lineno">24</tt> <tt class="py-line"><tt class="py-docstring"> a pbd structure with one unnamed chain.</tt> </tt>
<a name="L25"></a><tt class="py-lineno">25</tt> <tt class="py-line"><tt class="py-docstring"></tt> </tt>
<a name="L26"></a><tt class="py-lineno">26</tt> <tt class="py-line"><tt class="py-docstring"> Start and end residue ids consist of the residue sequence number and an</tt> </tt>
<a name="L27"></a><tt class="py-lineno">27</tt> <tt class="py-line"><tt class="py-docstring"> optional single letter insertion code. e.g. "12", "-1", "1a", "1000"</tt> </tt>
<a name="L28"></a><tt class="py-lineno">28</tt> <tt class="py-line"><tt class="py-docstring"></tt> </tt>
<a name="L29"></a><tt class="py-lineno">29</tt> <tt class="py-line"><tt class="py-docstring"></tt> </tt>
<a name="L30"></a><tt class="py-lineno">30</tt> <tt class="py-line"><tt class="py-docstring"> pdbid -- An optional PDB id, e.g. "1bba"</tt> </tt>
<a name="L31"></a><tt class="py-lineno">31</tt> <tt class="py-line"><tt class="py-docstring"></tt> </tt>
<a name="L32"></a><tt class="py-lineno">32</tt> <tt class="py-line"><tt class="py-docstring"> fragments -- A sequence of tuples (chainID, startResID, endResID)</tt> </tt>
<a name="L33"></a><tt class="py-lineno">33</tt> <tt class="py-line"><tt class="py-docstring"> </tt> </tt>
<a name="L34"></a><tt class="py-lineno">34</tt> <tt class="py-line"><tt class="py-docstring"> """</tt> </tt>
<a name="L35"></a><tt class="py-lineno">35</tt> <tt class="py-line"> </tt>
<a name="L36"></a><tt class="py-lineno">36</tt> <tt class="py-line"> </tt>
<a name="Residues.__init__"></a><div id="Residues.__init__-def"><a name="L37"></a><tt class="py-lineno">37</tt> <a class="py-toggle" href="#" id="Residues.__init__-toggle" onclick="return toggle('Residues.__init__');">-</a><tt class="py-line"> <tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.SCOP.Residues'.Residues-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">str</tt><tt class="py-op">=</tt><tt class="py-name">None</tt><tt class="py-op">)</tt> <tt class="py-op">:</tt> </tt>
</div><div id="Residues.__init__-collapsed" style="display:none;" pad="++" indent="++++++++"></div><div id="Residues.__init__-expanded"><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-name">pdbid</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-name">fragments</tt> <tt class="py-op">=</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">str</tt> <tt class="py-keyword">is</tt> <tt class="py-keyword">not</tt> <tt class="py-name">None</tt> <tt class="py-op">:</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-4" class="py-name" targets="Method Bio.Blast.NCBIStandalone._DescriptionConsumer._parse()=Bio.Blast.NCBIStandalone._DescriptionConsumer-class.html#_parse,Method Bio.Nexus.Trees.Tree._parse()=Bio.Nexus.Trees.Tree-class.html#_parse,Method Bio.PDB.PDBParser'.PDBParser._parse()=Bio.PDB.PDBParser%27.PDBParser-class.html#_parse,Method Bio.SCOP.Residues'.Residues._parse()=Bio.SCOP.Residues%27.Residues-class.html#_parse,Function Martel.msre_parse._parse()=Martel.msre_parse-module.html#_parse"><a title="Bio.Blast.NCBIStandalone._DescriptionConsumer._parse
Bio.Nexus.Trees.Tree._parse
Bio.PDB.PDBParser'.PDBParser._parse
Bio.SCOP.Residues'.Residues._parse
Martel.msre_parse._parse" class="py-name" href="#" onclick="return doclink('link-4', '_parse', 'link-4');">_parse</a></tt><tt class="py-op">(</tt><tt class="py-name">str</tt><tt class="py-op">)</tt> </tt>
</div><a name="L41"></a><tt class="py-lineno">41</tt> <tt class="py-line"> </tt>
<a name="L42"></a><tt class="py-lineno">42</tt> <tt class="py-line"> </tt>
<a name="Residues._parse"></a><div id="Residues._parse-def"><a name="L43"></a><tt class="py-lineno">43</tt> <a class="py-toggle" href="#" id="Residues._parse-toggle" onclick="return toggle('Residues._parse');">-</a><tt class="py-line"> <tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.SCOP.Residues'.Residues-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">str</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="Residues._parse-collapsed" style="display:none;" pad="++" indent="++++++++"></div><div id="Residues._parse-expanded"><a name="L44"></a><tt class="py-lineno">44</tt> <tt class="py-line"> <tt class="py-name">str</tt> <tt class="py-op">=</tt> <tt class="py-name">str</tt><tt class="py-op">.</tt><tt id="link-5" 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-5', 'strip', 'link-5');">strip</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>
<a name="L46"></a><tt class="py-lineno">46</tt> <tt class="py-line"> <tt class="py-comment">#Is there a pdbid at the front? e.g. 1bba A:1-100</tt> </tt>
<a name="L47"></a><tt class="py-lineno">47</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-name">m</tt> <tt class="py-op">=</tt> <tt id="link-6" class="py-name"><a title="Bio.SCOP.Residues'._pdbid_re" class="py-name" href="#" onclick="return doclink('link-6', '_pdbid_re', 'link-0');">_pdbid_re</a></tt><tt class="py-op">.</tt><tt id="link-7" 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-7', 'match', 'link-7');">match</a></tt><tt class="py-op">(</tt><tt class="py-name">str</tt><tt class="py-op">)</tt> </tt>
<a name="L48"></a><tt class="py-lineno">48</tt> <tt class="py-line"> <tt class="py-keyword">if</tt> <tt class="py-name">m</tt> <tt class="py-keyword">is</tt> <tt class="py-keyword">not</tt> <tt class="py-name">None</tt> <tt class="py-op">:</tt> </tt>
<a name="L49"></a><tt class="py-lineno">49</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">pdbid</tt> <tt class="py-op">=</tt> <tt class="py-name">m</tt><tt class="py-op">.</tt><tt id="link-8" class="py-name" targets="Method Bio.Prosite.Pattern.PrositeMatch.group()=Bio.Prosite.Pattern.PrositeMatch-class.html#group"><a title="Bio.Prosite.Pattern.PrositeMatch.group" class="py-name" href="#" onclick="return doclink('link-8', 'group', 'link-8');">group</a></tt><tt class="py-op">(</tt><tt class="py-number">1</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">str</tt> <tt class="py-op">=</tt> <tt class="py-name">m</tt><tt class="py-op">.</tt><tt id="link-9" class="py-name"><a title="Bio.Prosite.Pattern.PrositeMatch.group" class="py-name" href="#" onclick="return doclink('link-9', 'group', 'link-8');">group</a></tt><tt class="py-op">(</tt><tt class="py-number">2</tt><tt class="py-op">)</tt> <tt class="py-comment"># Everything else</tt> </tt>
<a name="L51"></a><tt class="py-lineno">51</tt> <tt class="py-line"> </tt>
<a name="L52"></a><tt class="py-lineno">52</tt> <tt class="py-line"> <tt class="py-keyword">if</tt> <tt class="py-name">str</tt><tt class="py-op">==</tt><tt class="py-string">''</tt> <tt class="py-keyword">or</tt> <tt class="py-name">str</tt> <tt class="py-op">==</tt> <tt class="py-string">'-'</tt> <tt class="py-keyword">or</tt> <tt class="py-name">str</tt><tt class="py-op">==</tt><tt class="py-string">'(-)'</tt><tt class="py-op">:</tt> <tt class="py-comment"># no fragments, whole sequence</tt> </tt>
<a name="L53"></a><tt class="py-lineno">53</tt> <tt class="py-line"> <tt class="py-keyword">return</tt> </tt>
<a name="L54"></a><tt class="py-lineno">54</tt> <tt class="py-line"> </tt>
<a name="L55"></a><tt class="py-lineno">55</tt> <tt class="py-line"> <tt class="py-name">fragments</tt> <tt class="py-op">=</tt> <tt class="py-op">[</tt><tt class="py-op">]</tt> </tt>
<a name="L56"></a><tt class="py-lineno">56</tt> <tt class="py-line"> <tt class="py-keyword">for</tt> <tt class="py-name">l</tt> <tt class="py-keyword">in</tt> <tt class="py-name">str</tt><tt class="py-op">.</tt><tt id="link-10" 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-10', 'split', 'link-10');">split</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="L57"></a><tt class="py-lineno">57</tt> <tt class="py-line"> <tt class="py-name">m</tt> <tt class="py-op">=</tt> <tt id="link-11" class="py-name"><a title="Bio.SCOP.Residues'._fragment_re" class="py-name" href="#" onclick="return doclink('link-11', '_fragment_re', 'link-2');">_fragment_re</a></tt><tt class="py-op">.</tt><tt id="link-12" class="py-name"><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-12', 'match', 'link-7');">match</a></tt><tt class="py-op">(</tt><tt class="py-name">l</tt><tt class="py-op">)</tt> </tt>
<a name="L58"></a><tt class="py-lineno">58</tt> <tt class="py-line"> <tt class="py-keyword">if</tt> <tt class="py-name">m</tt> <tt class="py-keyword">is</tt> <tt class="py-name">None</tt><tt class="py-op">:</tt> </tt>
<a name="L59"></a><tt class="py-lineno">59</tt> <tt class="py-line"> <tt class="py-keyword">raise</tt> <tt class="py-name">ValueError</tt><tt class="py-op">,</tt> <tt class="py-string">"I don't understand the format of %s"</tt> <tt class="py-op">%</tt> <tt class="py-name">l</tt> </tt>
<a name="L60"></a><tt class="py-lineno">60</tt> <tt class="py-line"> <tt class="py-name">chain</tt><tt class="py-op">,</tt> <tt id="link-13" 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-13', 'start', 'link-13');">start</a></tt><tt class="py-op">,</tt> <tt id="link-14" 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-14', 'end', 'link-14');">end</a></tt><tt class="py-op">,</tt> <tt class="py-name">postfix</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.Prosite.Pattern.PrositeMatch.groups()=Bio.Prosite.Pattern.PrositeMatch-class.html#groups"><a title="Bio.Prosite.Pattern.PrositeMatch.groups" class="py-name" href="#" onclick="return doclink('link-15', 'groups', 'link-15');">groups</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
<a name="L61"></a><tt class="py-lineno">61</tt> <tt class="py-line"> </tt>
<a name="L62"></a><tt class="py-lineno">62</tt> <tt class="py-line"> <tt class="py-keyword">if</tt> <tt class="py-name">postfix</tt> <tt class="py-op">!=</tt> <tt class="py-string">""</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">raise</tt> <tt class="py-name">ValueError</tt><tt class="py-op">,</tt> <tt class="py-string">"I don't understand the format of %s"</tt> <tt class="py-op">%</tt> <tt class="py-name">l</tt> </tt>
<a name="L64"></a><tt class="py-lineno">64</tt> <tt class="py-line"> </tt>
<a name="L65"></a><tt class="py-lineno">65</tt> <tt class="py-line"> <tt class="py-keyword">if</tt> <tt class="py-name">chain</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">if</tt> <tt class="py-name">chain</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-string">':'</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">ValueError</tt><tt class="py-op">,</tt> <tt class="py-string">"I don't understand the chain in %s"</tt> <tt class="py-op">%</tt> <tt class="py-name">l</tt> </tt>
<a name="L68"></a><tt class="py-lineno">68</tt> <tt class="py-line"> <tt class="py-name">chain</tt> <tt class="py-op">=</tt> <tt class="py-name">chain</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 class="py-comment"># chop off the ':'</tt> </tt>
<a name="L69"></a><tt class="py-lineno">69</tt> <tt class="py-line"> <tt class="py-keyword">else</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">chain</tt> <tt class="py-op">=</tt><tt class="py-string">""</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-name">fragments</tt><tt class="py-op">.</tt><tt id="link-16" 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-16', 'append', 'link-16');">append</a></tt><tt class="py-op">(</tt><tt class="py-op">(</tt><tt class="py-name">chain</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-13');">start</a></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-14');">end</a></tt><tt class="py-op">)</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">self</tt><tt class="py-op">.</tt><tt class="py-name">fragments</tt> <tt class="py-op">=</tt> <tt class="py-name">tuple</tt><tt class="py-op">(</tt><tt class="py-name">fragments</tt><tt class="py-op">)</tt> </tt>
</div><a name="L74"></a><tt class="py-lineno">74</tt> <tt class="py-line"> </tt>
<a name="Residues.__str__"></a><div id="Residues.__str__-def"><a name="L75"></a><tt class="py-lineno">75</tt> <a class="py-toggle" href="#" id="Residues.__str__-toggle" onclick="return toggle('Residues.__str__');">-</a><tt class="py-line"> <tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.SCOP.Residues'.Residues-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="Residues.__str__-collapsed" style="display:none;" pad="++" indent="++++++++"></div><div id="Residues.__str__-expanded"><a name="L76"></a><tt class="py-lineno">76</tt> <tt class="py-line"> <tt id="link-19" class="py-name" targets="Variable Bio.DocSQL.Query.prefix=Bio.DocSQL.Query-class.html#prefix"><a title="Bio.DocSQL.Query.prefix" class="py-name" href="#" onclick="return doclink('link-19', 'prefix', 'link-19');">prefix</a></tt> <tt class="py-op">=</tt><tt class="py-string">""</tt> </tt>
<a name="L77"></a><tt class="py-lineno">77</tt> <tt class="py-line"> <tt class="py-keyword">if</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">pdbid</tt> <tt class="py-op">:</tt> </tt>
<a name="L78"></a><tt class="py-lineno">78</tt> <tt class="py-line"> <tt id="link-20" class="py-name"><a title="Bio.DocSQL.Query.prefix" class="py-name" href="#" onclick="return doclink('link-20', 'prefix', 'link-19');">prefix</a></tt> <tt class="py-op">=</tt><tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">pdbid</tt> <tt class="py-op">+</tt><tt class="py-string">' '</tt> </tt>
<a name="L79"></a><tt class="py-lineno">79</tt> <tt class="py-line"> </tt>
<a name="L80"></a><tt class="py-lineno">80</tt> <tt class="py-line"> <tt class="py-keyword">if</tt> <tt class="py-keyword">not</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">fragments</tt><tt class="py-op">:</tt> <tt class="py-keyword">return</tt> <tt id="link-21" class="py-name"><a title="Bio.DocSQL.Query.prefix" class="py-name" href="#" onclick="return doclink('link-21', 'prefix', 'link-19');">prefix</a></tt><tt class="py-op">+</tt><tt class="py-string">'-'</tt> </tt>
<a name="L81"></a><tt class="py-lineno">81</tt> <tt class="py-line"> <tt class="py-name">strs</tt> <tt class="py-op">=</tt> <tt class="py-op">[</tt><tt class="py-op">]</tt> </tt>
<a name="L82"></a><tt class="py-lineno">82</tt> <tt class="py-line"> <tt class="py-keyword">for</tt> <tt class="py-name">chain</tt><tt class="py-op">,</tt> <tt id="link-22" 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-22', 'start', 'link-13');">start</a></tt><tt class="py-op">,</tt> <tt id="link-23" 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-23', 'end', 'link-14');">end</a></tt> <tt class="py-keyword">in</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">fragments</tt><tt class="py-op">:</tt> </tt>
<a name="L83"></a><tt class="py-lineno">83</tt> <tt class="py-line"> <tt id="link-24" 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-24', 's', 'link-24');">s</a></tt> <tt class="py-op">=</tt> <tt class="py-op">[</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-name">chain</tt><tt class="py-op">:</tt> <tt id="link-25" class="py-name"><a title="Martel.test.test_swissprot38.s" class="py-name" href="#" onclick="return doclink('link-25', 's', 'link-24');">s</a></tt><tt class="py-op">.</tt><tt id="link-26" 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-26', 'append', 'link-16');">append</a></tt><tt class="py-op">(</tt><tt class="py-string">"%s:"</tt> <tt class="py-op">%</tt> <tt class="py-name">chain</tt><tt class="py-op">)</tt> </tt>
<a name="L85"></a><tt class="py-lineno">85</tt> <tt class="py-line"> <tt class="py-keyword">if</tt> <tt id="link-27" 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-27', 'start', 'link-13');">start</a></tt><tt class="py-op">:</tt> <tt id="link-28" class="py-name"><a title="Martel.test.test_swissprot38.s" class="py-name" href="#" onclick="return doclink('link-28', 's', 'link-24');">s</a></tt><tt class="py-op">.</tt><tt id="link-29" 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-29', 'append', 'link-16');">append</a></tt><tt class="py-op">(</tt><tt class="py-string">"%s-%s"</tt> <tt class="py-op">%</tt> <tt class="py-op">(</tt><tt id="link-30" 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-30', 'start', 'link-13');">start</a></tt><tt class="py-op">,</tt> <tt id="link-31" 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-31', 'end', 'link-14');">end</a></tt><tt class="py-op">)</tt><tt class="py-op">)</tt> </tt>
<a name="L86"></a><tt class="py-lineno">86</tt> <tt class="py-line"> <tt class="py-name">strs</tt><tt class="py-op">.</tt><tt id="link-32" 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-32', 'append', 'link-16');">append</a></tt><tt class="py-op">(</tt><tt class="py-string">""</tt><tt class="py-op">.</tt><tt class="py-name">join</tt><tt class="py-op">(</tt><tt id="link-33" class="py-name"><a title="Martel.test.test_swissprot38.s" class="py-name" href="#" onclick="return doclink('link-33', 's', 'link-24');">s</a></tt><tt class="py-op">)</tt><tt class="py-op">)</tt> </tt>
<a name="L87"></a><tt class="py-lineno">87</tt> <tt class="py-line"> <tt class="py-keyword">return</tt> <tt id="link-34" class="py-name"><a title="Bio.DocSQL.Query.prefix" class="py-name" href="#" onclick="return doclink('link-34', 'prefix', 'link-19');">prefix</a></tt><tt class="py-op">+</tt> <tt class="py-string">","</tt><tt class="py-op">.</tt><tt class="py-name">join</tt><tt class="py-op">(</tt><tt class="py-name">strs</tt><tt class="py-op">)</tt> </tt>
</div></div><a name="L88"></a><tt class="py-lineno">88</tt> <tt class="py-line"> </tt><script type="text/javascript">
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