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<a href="Bio-module.html">Package Bio</a> ::
Package SCOP
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<h1 class="epydoc">Source Code for <a href="Bio.SCOP-module.html">Package Bio.SCOP</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 2001 by Gavin E. Crooks. 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"># Modifications Copyright 2004/2005 James Casbon. All rights Reserved.</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">#</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"># This code is part of the Biopython distribution and governed by its</tt> </tt>
<a name="L5"></a><tt class="py-lineno"> 5</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="L6"></a><tt class="py-lineno"> 6</tt> <tt class="py-line"><tt class="py-comment"></tt><tt class="py-comment"># as part of this package.</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">#</tt> </tt>
<a name="L8"></a><tt class="py-lineno"> 8</tt> <tt class="py-line"><tt class="py-comment"></tt><tt class="py-comment"># Changes made by James Casbon:</tt> </tt>
<a name="L9"></a><tt class="py-lineno"> 9</tt> <tt class="py-line"><tt class="py-comment"></tt><tt class="py-comment"># - New Astral class</tt> </tt>
<a name="L10"></a><tt class="py-lineno"> 10</tt> <tt class="py-line"><tt class="py-comment"></tt><tt class="py-comment"># - SQL functionality for both Scop and Astral classes</tt> </tt>
<a name="L11"></a><tt class="py-lineno"> 11</tt> <tt class="py-line"><tt class="py-comment"></tt><tt class="py-comment"># - All sunids are int not strings</tt> </tt>
<a name="L12"></a><tt class="py-lineno"> 12</tt> <tt class="py-line"><tt class="py-comment"></tt><tt class="py-comment">#</tt> </tt>
<a name="L13"></a><tt class="py-lineno"> 13</tt> <tt class="py-line"><tt class="py-comment"></tt><tt class="py-comment"># Code written by Jeffrey Chang to access SCOP over the internet, which</tt> </tt>
<a name="L14"></a><tt class="py-lineno"> 14</tt> <tt class="py-line"><tt class="py-comment"></tt><tt class="py-comment"># was previously in Bio.WWW.SCOP, has now been merged into this module.</tt> </tt>
<a name="L15"></a><tt class="py-lineno"> 15</tt> <tt class="py-line"><tt class="py-comment"></tt> </tt>
<a name="L16"></a><tt class="py-lineno"> 16</tt> <tt class="py-line"><tt class="py-docstring">""" SCOP: Structural Classification of Proteins.</tt> </tt>
<a name="L17"></a><tt class="py-lineno"> 17</tt> <tt class="py-line"><tt class="py-docstring"></tt> </tt>
<a name="L18"></a><tt class="py-lineno"> 18</tt> <tt class="py-line"><tt class="py-docstring">The SCOP database aims to provide a manually constructed classification of</tt> </tt>
<a name="L19"></a><tt class="py-lineno"> 19</tt> <tt class="py-line"><tt class="py-docstring">all know protein structures into a hierarchy, the main levels of which</tt> </tt>
<a name="L20"></a><tt class="py-lineno"> 20</tt> <tt class="py-line"><tt class="py-docstring">are family, superfamily and fold.</tt> </tt>
<a name="L21"></a><tt class="py-lineno"> 21</tt> <tt class="py-line"><tt class="py-docstring"></tt> </tt>
<a name="L22"></a><tt class="py-lineno"> 22</tt> <tt class="py-line"><tt class="py-docstring">* "SCOP":http://scop.mrc-lmb.cam.ac.uk/scop/</tt> </tt>
<a name="L23"></a><tt class="py-lineno"> 23</tt> <tt class="py-line"><tt class="py-docstring"></tt> </tt>
<a name="L24"></a><tt class="py-lineno"> 24</tt> <tt class="py-line"><tt class="py-docstring">* "Introduction":http://scop.mrc-lmb.cam.ac.uk/scop/intro.html</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">* "SCOP parsable files":http://scop.mrc-lmb.cam.ac.uk/scop/parse/</tt> </tt>
<a name="L27"></a><tt class="py-lineno"> 27</tt> <tt class="py-line"><tt class="py-docstring"></tt> </tt>
<a name="L28"></a><tt class="py-lineno"> 28</tt> <tt class="py-line"><tt class="py-docstring">The Scop object in this module represents the entire SCOP classification. It</tt> </tt>
<a name="L29"></a><tt class="py-lineno"> 29</tt> <tt class="py-line"><tt class="py-docstring">can be built from the three SCOP parsable files, modified is so desired, and</tt> </tt>
<a name="L30"></a><tt class="py-lineno"> 30</tt> <tt class="py-line"><tt class="py-docstring">converted back to the same file formats. A single SCOP domain (represented</tt> </tt>
<a name="L31"></a><tt class="py-lineno"> 31</tt> <tt class="py-line"><tt class="py-docstring">by the Domain class) can be obtained from Scop using the domain's SCOP</tt> </tt>
<a name="L32"></a><tt class="py-lineno"> 32</tt> <tt class="py-line"><tt class="py-docstring">identifier (sid).</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 class="py-docstring">nodeCodeDict -- A mapping between known 2 letter node codes and a longer</tt> </tt>
<a name="L36"></a><tt class="py-lineno"> 36</tt> <tt class="py-line"><tt class="py-docstring"> description. The known node types are 'cl' (class), 'cf'</tt> </tt>
<a name="L37"></a><tt class="py-lineno"> 37</tt> <tt class="py-line"><tt class="py-docstring"> (fold), 'sf' (superfamily), 'fa' (family), 'dm' (domain), </tt> </tt>
<a name="L38"></a><tt class="py-lineno"> 38</tt> <tt class="py-line"><tt class="py-docstring"> 'sp' (species), 'px' (domain). Additional node types may</tt> </tt>
<a name="L39"></a><tt class="py-lineno"> 39</tt> <tt class="py-line"><tt class="py-docstring"> be added in the future.</tt> </tt>
<a name="L40"></a><tt class="py-lineno"> 40</tt> <tt class="py-line"><tt class="py-docstring"></tt> </tt>
<a name="L41"></a><tt class="py-lineno"> 41</tt> <tt class="py-line"><tt class="py-docstring">This module also provides code to access SCOP over the WWW.</tt> </tt>
<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">Functions:</tt> </tt>
<a name="L44"></a><tt class="py-lineno"> 44</tt> <tt class="py-line"><tt class="py-docstring">search -- Access the main CGI script.</tt> </tt>
<a name="L45"></a><tt class="py-lineno"> 45</tt> <tt class="py-line"><tt class="py-docstring">_open -- Internally used function.</tt> </tt>
<a name="L46"></a><tt class="py-lineno"> 46</tt> <tt class="py-line"><tt class="py-docstring"></tt> </tt>
<a name="L47"></a><tt class="py-lineno"> 47</tt> <tt class="py-line"><tt class="py-docstring">"""</tt> </tt>
<a name="L48"></a><tt class="py-lineno"> 48</tt> <tt class="py-line"> </tt>
<a name="L49"></a><tt class="py-lineno"> 49</tt> <tt class="py-line"><tt class="py-keyword">from</tt> <tt class="py-name">types</tt> <tt class="py-keyword">import</tt> <tt class="py-op">*</tt> </tt>
<a name="L50"></a><tt class="py-lineno"> 50</tt> <tt class="py-line"><tt class="py-keyword">import</tt> <tt class="py-name">os</tt><tt class="py-op">,</tt> <tt class="py-name">string</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">import</tt> <tt id="link-0" class="py-name" targets="Module Bio.SCOP.Des=Bio.SCOP.Des-module.html"><a title="Bio.SCOP.Des" class="py-name" href="#" onclick="return doclink('link-0', 'Des', 'link-0');">Des</a></tt> </tt>
<a name="L53"></a><tt class="py-lineno"> 53</tt> <tt class="py-line"><tt class="py-keyword">import</tt> <tt id="link-1" class="py-name" targets="Module Bio.SCOP.Cla=Bio.SCOP.Cla-module.html"><a title="Bio.SCOP.Cla" class="py-name" href="#" onclick="return doclink('link-1', 'Cla', 'link-1');">Cla</a></tt> </tt>
<a name="L54"></a><tt class="py-lineno"> 54</tt> <tt class="py-line"><tt class="py-keyword">import</tt> <tt id="link-2" class="py-name" targets="Module Bio.SCOP.Hie=Bio.SCOP.Hie-module.html"><a title="Bio.SCOP.Hie" class="py-name" href="#" onclick="return doclink('link-2', 'Hie', 'link-2');">Hie</a></tt> </tt>
<a name="L55"></a><tt class="py-lineno"> 55</tt> <tt class="py-line"><tt class="py-keyword">from</tt> <tt id="link-3" class="py-name" targets="Class Bio.SCOP.Residues'.Residues=Bio.SCOP.Residues%27.Residues-class.html"><a title="Bio.SCOP.Residues'.Residues" class="py-name" href="#" onclick="return doclink('link-3', 'Residues', 'link-3');">Residues</a></tt> <tt class="py-keyword">import</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">from</tt> <tt id="link-4" class="py-name" targets="Package Bio=Bio-module.html"><a title="Bio" class="py-name" href="#" onclick="return doclink('link-4', 'Bio', 'link-4');">Bio</a></tt> <tt class="py-keyword">import</tt> <tt id="link-5" class="py-name" targets="Package Bio.SeqIO=Bio.SeqIO-module.html"><a title="Bio.SeqIO" class="py-name" href="#" onclick="return doclink('link-5', 'SeqIO', 'link-5');">SeqIO</a></tt> </tt>
<a name="L57"></a><tt class="py-lineno"> 57</tt> <tt class="py-line"><tt class="py-keyword">from</tt> <tt id="link-6" class="py-name"><a title="Bio" class="py-name" href="#" onclick="return doclink('link-6', 'Bio', 'link-4');">Bio</a></tt><tt class="py-op">.</tt><tt id="link-7" class="py-name" targets="Package Bio.Alphabet=Bio.Alphabet-module.html,Class Bio.Alphabet.Alphabet=Bio.Alphabet.Alphabet-class.html"><a title="Bio.Alphabet
Bio.Alphabet.Alphabet" class="py-name" href="#" onclick="return doclink('link-7', 'Alphabet', 'link-7');">Alphabet</a></tt> <tt class="py-keyword">import</tt> <tt id="link-8" class="py-name" targets="Module Bio.Alphabet.IUPAC=Bio.Alphabet.IUPAC-module.html"><a title="Bio.Alphabet.IUPAC" class="py-name" href="#" onclick="return doclink('link-8', 'IUPAC', 'link-8');">IUPAC</a></tt> </tt>
<a name="L58"></a><tt class="py-lineno"> 58</tt> <tt class="py-line"><tt class="py-keyword">from</tt> <tt id="link-9" class="py-name"><a title="Bio" class="py-name" href="#" onclick="return doclink('link-9', 'Bio', 'link-4');">Bio</a></tt><tt class="py-op">.</tt><tt id="link-10" class="py-name" targets="Module Bio.Seq=Bio.Seq-module.html,Class Bio.Seq.Seq=Bio.Seq.Seq-class.html,Class Martel.Expression.Seq=Martel.Expression.Seq-class.html,Function Martel.Seq()=Martel-module.html#Seq"><a title="Bio.Seq
Bio.Seq.Seq
Martel.Expression.Seq
Martel.Seq" class="py-name" href="#" onclick="return doclink('link-10', 'Seq', 'link-10');">Seq</a></tt> <tt class="py-keyword">import</tt> <tt id="link-11" class="py-name"><a title="Bio.Seq
Bio.Seq.Seq
Martel.Expression.Seq
Martel.Seq" class="py-name" href="#" onclick="return doclink('link-11', 'Seq', 'link-10');">Seq</a></tt> </tt>
<a name="L59"></a><tt class="py-lineno"> 59</tt> <tt class="py-line"> </tt>
<a name="L60"></a><tt class="py-lineno"> 60</tt> <tt class="py-line"> </tt>
<a name="L61"></a><tt class="py-lineno"> 61</tt> <tt class="py-line"><tt id="link-12" class="py-name" targets="Variable Bio.SCOP.nodeCodeDict=Bio.SCOP-module.html#nodeCodeDict"><a title="Bio.SCOP.nodeCodeDict" class="py-name" href="#" onclick="return doclink('link-12', 'nodeCodeDict', 'link-12');">nodeCodeDict</a></tt> <tt class="py-op">=</tt> <tt class="py-op">{</tt> <tt class="py-string">'cl'</tt><tt class="py-op">:</tt><tt class="py-string">'class'</tt><tt class="py-op">,</tt> <tt class="py-string">'cf'</tt><tt class="py-op">:</tt><tt class="py-string">'fold'</tt><tt class="py-op">,</tt> <tt class="py-string">'sf'</tt><tt class="py-op">:</tt><tt class="py-string">'superfamily'</tt><tt class="py-op">,</tt> </tt>
<a name="L62"></a><tt class="py-lineno"> 62</tt> <tt class="py-line"> <tt class="py-string">'fa'</tt><tt class="py-op">:</tt><tt class="py-string">'family'</tt><tt class="py-op">,</tt> <tt class="py-string">'dm'</tt><tt class="py-op">:</tt><tt class="py-string">'protein'</tt><tt class="py-op">,</tt> <tt class="py-string">'sp'</tt><tt class="py-op">:</tt><tt class="py-string">'species'</tt><tt class="py-op">,</tt> <tt class="py-string">'px'</tt><tt class="py-op">:</tt><tt class="py-string">'domain'</tt><tt class="py-op">}</tt> </tt>
<a name="L63"></a><tt class="py-lineno"> 63</tt> <tt class="py-line"> </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 id="link-13" class="py-name" targets="Variable Bio.SCOP._nodetype_to_code=Bio.SCOP-module.html#_nodetype_to_code"><a title="Bio.SCOP._nodetype_to_code" class="py-name" href="#" onclick="return doclink('link-13', '_nodetype_to_code', 'link-13');">_nodetype_to_code</a></tt><tt class="py-op">=</tt> <tt class="py-op">{</tt> <tt class="py-string">'class'</tt><tt class="py-op">:</tt> <tt class="py-string">'cl'</tt><tt class="py-op">,</tt> <tt class="py-string">'fold'</tt><tt class="py-op">:</tt> <tt class="py-string">'cf'</tt><tt class="py-op">,</tt> <tt class="py-string">'superfamily'</tt><tt class="py-op">:</tt> <tt class="py-string">'sf'</tt><tt class="py-op">,</tt> </tt>
<a name="L66"></a><tt class="py-lineno"> 66</tt> <tt class="py-line"> <tt class="py-string">'family'</tt><tt class="py-op">:</tt> <tt class="py-string">'fa'</tt><tt class="py-op">,</tt> <tt class="py-string">'protein'</tt><tt class="py-op">:</tt> <tt class="py-string">'dm'</tt><tt class="py-op">,</tt> <tt class="py-string">'species'</tt><tt class="py-op">:</tt> <tt class="py-string">'sp'</tt><tt class="py-op">,</tt> <tt class="py-string">'domain'</tt><tt class="py-op">:</tt> <tt class="py-string">'px'</tt><tt class="py-op">}</tt> </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 id="link-14" class="py-name" targets="Variable Bio.SCOP.nodeCodeOrder=Bio.SCOP-module.html#nodeCodeOrder"><a title="Bio.SCOP.nodeCodeOrder" class="py-name" href="#" onclick="return doclink('link-14', 'nodeCodeOrder', 'link-14');">nodeCodeOrder</a></tt> <tt class="py-op">=</tt> <tt class="py-op">[</tt> <tt class="py-string">'ro'</tt><tt class="py-op">,</tt> <tt class="py-string">'cl'</tt><tt class="py-op">,</tt> <tt class="py-string">'cf'</tt><tt class="py-op">,</tt> <tt class="py-string">'sf'</tt><tt class="py-op">,</tt> <tt class="py-string">'fa'</tt><tt class="py-op">,</tt> <tt class="py-string">'dm'</tt><tt class="py-op">,</tt> <tt class="py-string">'sp'</tt><tt class="py-op">,</tt> <tt class="py-string">'px'</tt> <tt class="py-op">]</tt> </tt>
<a name="L69"></a><tt class="py-lineno"> 69</tt> <tt class="py-line"> </tt>
<a name="L70"></a><tt class="py-lineno"> 70</tt> <tt class="py-line"><tt id="link-15" class="py-name" targets="Variable Bio.SCOP.astralBibIds=Bio.SCOP-module.html#astralBibIds"><a title="Bio.SCOP.astralBibIds" class="py-name" href="#" onclick="return doclink('link-15', 'astralBibIds', 'link-15');">astralBibIds</a></tt> <tt class="py-op">=</tt> <tt class="py-op">[</tt><tt class="py-number">10</tt><tt class="py-op">,</tt><tt class="py-number">20</tt><tt class="py-op">,</tt><tt class="py-number">25</tt><tt class="py-op">,</tt><tt class="py-number">30</tt><tt class="py-op">,</tt><tt class="py-number">35</tt><tt class="py-op">,</tt><tt class="py-number">40</tt><tt class="py-op">,</tt><tt class="py-number">50</tt><tt class="py-op">,</tt><tt class="py-number">70</tt><tt class="py-op">,</tt><tt class="py-number">90</tt><tt class="py-op">,</tt><tt class="py-number">95</tt><tt class="py-op">,</tt><tt class="py-number">100</tt><tt class="py-op">]</tt> </tt>
<a name="L71"></a><tt class="py-lineno"> 71</tt> <tt class="py-line"> </tt>
<a name="L72"></a><tt class="py-lineno"> 72</tt> <tt class="py-line"><tt id="link-16" class="py-name" targets="Variable Bio.SCOP.astralEvs=Bio.SCOP-module.html#astralEvs"><a title="Bio.SCOP.astralEvs" class="py-name" href="#" onclick="return doclink('link-16', 'astralEvs', 'link-16');">astralEvs</a></tt> <tt class="py-op">=</tt> <tt class="py-op">[</tt><tt class="py-number">10</tt><tt class="py-op">,</tt> <tt class="py-number">5</tt><tt class="py-op">,</tt> <tt class="py-number">1</tt><tt class="py-op">,</tt> <tt class="py-number">0.5</tt><tt class="py-op">,</tt> <tt class="py-number">0.1</tt><tt class="py-op">,</tt> <tt class="py-number">0.05</tt><tt class="py-op">,</tt> <tt class="py-number">0.01</tt><tt class="py-op">,</tt> <tt class="py-number">0.005</tt><tt class="py-op">,</tt> <tt class="py-number">0.001</tt><tt class="py-op">,</tt> <tt class="py-number">1e-4</tt><tt class="py-op">,</tt> <tt class="py-number">1e-5</tt><tt class="py-op">,</tt> <tt class="py-number">1e-10</tt><tt class="py-op">,</tt> <tt class="py-number">1e-15</tt><tt class="py-op">,</tt> </tt>
<a name="L73"></a><tt class="py-lineno"> 73</tt> <tt class="py-line"> <tt class="py-number">1e-20</tt><tt class="py-op">,</tt> <tt class="py-number">1e-25</tt><tt class="py-op">,</tt> <tt class="py-number">1e-50</tt><tt class="py-op">]</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 id="link-17" class="py-name" targets="Variable Bio.SCOP.astralEv_to_file=Bio.SCOP-module.html#astralEv_to_file"><a title="Bio.SCOP.astralEv_to_file" class="py-name" href="#" onclick="return doclink('link-17', 'astralEv_to_file', 'link-17');">astralEv_to_file</a></tt> <tt class="py-op">=</tt> <tt class="py-op">{</tt> <tt class="py-number">10</tt><tt class="py-op">:</tt> <tt class="py-string">'e+1'</tt><tt class="py-op">,</tt> <tt class="py-number">5</tt><tt class="py-op">:</tt> <tt class="py-string">'e+0,7'</tt><tt class="py-op">,</tt> <tt class="py-number">1</tt><tt class="py-op">:</tt> <tt class="py-string">'e+0'</tt><tt class="py-op">,</tt> <tt class="py-number">0.5</tt><tt class="py-op">:</tt> <tt class="py-string">'e-0,3'</tt><tt class="py-op">,</tt> <tt class="py-number">0.1</tt><tt class="py-op">:</tt> <tt class="py-string">'e-1'</tt><tt class="py-op">,</tt> </tt>
<a name="L76"></a><tt class="py-lineno"> 76</tt> <tt class="py-line"> <tt class="py-number">0.05</tt><tt class="py-op">:</tt> <tt class="py-string">'e-1,3'</tt><tt class="py-op">,</tt> <tt class="py-number">0.01</tt><tt class="py-op">:</tt> <tt class="py-string">'e-2'</tt><tt class="py-op">,</tt> <tt class="py-number">0.005</tt><tt class="py-op">:</tt> <tt class="py-string">'e-2,3'</tt><tt class="py-op">,</tt> <tt class="py-number">0.001</tt><tt class="py-op">:</tt> <tt class="py-string">'e-3'</tt><tt class="py-op">,</tt> </tt>
<a name="L77"></a><tt class="py-lineno"> 77</tt> <tt class="py-line"> <tt class="py-number">1e-4</tt><tt class="py-op">:</tt> <tt class="py-string">'e-4'</tt><tt class="py-op">,</tt> <tt class="py-number">1e-5</tt><tt class="py-op">:</tt> <tt class="py-string">'e-5'</tt><tt class="py-op">,</tt> <tt class="py-number">1e-10</tt><tt class="py-op">:</tt> <tt class="py-string">'e-10'</tt><tt class="py-op">,</tt> <tt class="py-number">1e-15</tt><tt class="py-op">:</tt> <tt class="py-string">'e-15'</tt><tt class="py-op">,</tt> </tt>
<a name="L78"></a><tt class="py-lineno"> 78</tt> <tt class="py-line"> <tt class="py-number">1e-20</tt><tt class="py-op">:</tt> <tt class="py-string">'e-20'</tt><tt class="py-op">,</tt> <tt class="py-number">1e-25</tt><tt class="py-op">:</tt> <tt class="py-string">'e-25'</tt><tt class="py-op">,</tt> <tt class="py-number">1e-50</tt><tt class="py-op">:</tt> <tt class="py-string">'e-50'</tt> <tt class="py-op">}</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 id="link-18" class="py-name" targets="Variable Bio.SCOP.astralEv_to_sql=Bio.SCOP-module.html#astralEv_to_sql"><a title="Bio.SCOP.astralEv_to_sql" class="py-name" href="#" onclick="return doclink('link-18', 'astralEv_to_sql', 'link-18');">astralEv_to_sql</a></tt> <tt class="py-op">=</tt> <tt class="py-op">{</tt> <tt class="py-number">10</tt><tt class="py-op">:</tt> <tt class="py-string">'e1'</tt><tt class="py-op">,</tt> <tt class="py-number">5</tt><tt class="py-op">:</tt> <tt class="py-string">'e0_7'</tt><tt class="py-op">,</tt> <tt class="py-number">1</tt><tt class="py-op">:</tt> <tt class="py-string">'e0'</tt><tt class="py-op">,</tt> <tt class="py-number">0.5</tt><tt class="py-op">:</tt> <tt class="py-string">'e_0_3'</tt><tt class="py-op">,</tt> <tt class="py-number">0.1</tt><tt class="py-op">:</tt> <tt class="py-string">'e_1'</tt><tt class="py-op">,</tt> </tt>
<a name="L81"></a><tt class="py-lineno"> 81</tt> <tt class="py-line"> <tt class="py-number">0.05</tt><tt class="py-op">:</tt> <tt class="py-string">'e_1_3'</tt><tt class="py-op">,</tt> <tt class="py-number">0.01</tt><tt class="py-op">:</tt> <tt class="py-string">'e_2'</tt><tt class="py-op">,</tt> <tt class="py-number">0.005</tt><tt class="py-op">:</tt> <tt class="py-string">'e_2_3'</tt><tt class="py-op">,</tt> <tt class="py-number">0.001</tt><tt class="py-op">:</tt> <tt class="py-string">'e_3'</tt><tt class="py-op">,</tt> </tt>
<a name="L82"></a><tt class="py-lineno"> 82</tt> <tt class="py-line"> <tt class="py-number">1e-4</tt><tt class="py-op">:</tt> <tt class="py-string">'e_4'</tt><tt class="py-op">,</tt> <tt class="py-number">1e-5</tt><tt class="py-op">:</tt> <tt class="py-string">'e_5'</tt><tt class="py-op">,</tt> <tt class="py-number">1e-10</tt><tt class="py-op">:</tt> <tt class="py-string">'e_10'</tt><tt class="py-op">,</tt> <tt class="py-number">1e-15</tt><tt class="py-op">:</tt> <tt class="py-string">'e_15'</tt><tt class="py-op">,</tt> </tt>
<a name="L83"></a><tt class="py-lineno"> 83</tt> <tt class="py-line"> <tt class="py-number">1e-20</tt><tt class="py-op">:</tt> <tt class="py-string">'e_20'</tt><tt class="py-op">,</tt> <tt class="py-number">1e-25</tt><tt class="py-op">:</tt> <tt class="py-string">'e_25'</tt><tt class="py-op">,</tt> <tt class="py-number">1e-50</tt><tt class="py-op">:</tt> <tt class="py-string">'e_50'</tt> <tt class="py-op">}</tt> </tt>
<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="cmp_sccs"></a><div id="cmp_sccs-def"><a name="L86"></a><tt class="py-lineno"> 86</tt> <a class="py-toggle" href="#" id="cmp_sccs-toggle" onclick="return toggle('cmp_sccs');">-</a><tt class="py-line"><tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.SCOP-module.html#cmp_sccs">cmp_sccs</a><tt class="py-op">(</tt><tt class="py-param">sccs1</tt><tt class="py-op">,</tt> <tt class="py-param">sccs2</tt><tt class="py-op">)</tt> <tt class="py-op">:</tt> </tt>
</div><div id="cmp_sccs-collapsed" style="display:none;" pad="+++" indent="++++"></div><div id="cmp_sccs-expanded"><a name="L87"></a><tt class="py-lineno"> 87</tt> <tt class="py-line"> <tt class="py-docstring">"""Order SCOP concise classification strings (sccs).</tt> </tt>
<a name="L88"></a><tt class="py-lineno"> 88</tt> <tt class="py-line"><tt class="py-docstring"></tt> </tt>
<a name="L89"></a><tt class="py-lineno"> 89</tt> <tt class="py-line"><tt class="py-docstring"> a.4.5.1 < a.4.5.11 < b.1.1.1 </tt> </tt>
<a name="L90"></a><tt class="py-lineno"> 90</tt> <tt class="py-line"><tt class="py-docstring"></tt> </tt>
<a name="L91"></a><tt class="py-lineno"> 91</tt> <tt class="py-line"><tt class="py-docstring"> A sccs (e.g. a.4.5.11) compactly represents a domain's classification.</tt> </tt>
<a name="L92"></a><tt class="py-lineno"> 92</tt> <tt class="py-line"><tt class="py-docstring"> The letter represents the class, and the numbers are the fold,</tt> </tt>
<a name="L93"></a><tt class="py-lineno"> 93</tt> <tt class="py-line"><tt class="py-docstring"> superfamily, and family, respectively.</tt> </tt>
<a name="L94"></a><tt class="py-lineno"> 94</tt> <tt class="py-line"><tt class="py-docstring"></tt> </tt>
<a name="L95"></a><tt class="py-lineno"> 95</tt> <tt class="py-line"><tt class="py-docstring"> """</tt> </tt>
<a name="L96"></a><tt class="py-lineno"> 96</tt> <tt class="py-line"> </tt>
<a name="L97"></a><tt class="py-lineno"> 97</tt> <tt class="py-line"> <tt id="link-19" class="py-name" targets="Variable Martel.test.test_swissprot38.s1=Martel.test.test_swissprot38-module.html#s1"><a title="Martel.test.test_swissprot38.s1" class="py-name" href="#" onclick="return doclink('link-19', 's1', 'link-19');">s1</a></tt> <tt class="py-op">=</tt> <tt class="py-name">sccs1</tt><tt class="py-op">.</tt><tt id="link-20" 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-20', 'split', 'link-20');">split</a></tt><tt class="py-op">(</tt><tt class="py-string">"."</tt><tt class="py-op">)</tt> </tt>
<a name="L98"></a><tt class="py-lineno"> 98</tt> <tt class="py-line"> <tt id="link-21" class="py-name" targets="Variable Martel.test.test_swissprot38.s2=Martel.test.test_swissprot38-module.html#s2"><a title="Martel.test.test_swissprot38.s2" class="py-name" href="#" onclick="return doclink('link-21', 's2', 'link-21');">s2</a></tt> <tt class="py-op">=</tt> <tt class="py-name">sccs2</tt><tt class="py-op">.</tt><tt id="link-22" class="py-name"><a title="Bio.Nexus.Trees.Tree.split
Bio.Restriction.Restriction.RestrictionBatch.split" class="py-name" href="#" onclick="return doclink('link-22', 'split', 'link-20');">split</a></tt><tt class="py-op">(</tt><tt class="py-string">"."</tt><tt class="py-op">)</tt> </tt>
<a name="L99"></a><tt class="py-lineno"> 99</tt> <tt class="py-line"> </tt>
<a name="L100"></a><tt class="py-lineno">100</tt> <tt class="py-line"> <tt class="py-keyword">if</tt> <tt id="link-23" class="py-name"><a title="Martel.test.test_swissprot38.s1" class="py-name" href="#" onclick="return doclink('link-23', 's1', 'link-19');">s1</a></tt><tt class="py-op">[</tt><tt class="py-number">0</tt><tt class="py-op">]</tt> <tt class="py-op">!=</tt> <tt id="link-24" class="py-name"><a title="Martel.test.test_swissprot38.s2" class="py-name" href="#" onclick="return doclink('link-24', 's2', 'link-21');">s2</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-keyword">return</tt> <tt class="py-name">cmp</tt><tt class="py-op">(</tt><tt id="link-25" class="py-name"><a title="Martel.test.test_swissprot38.s1" class="py-name" href="#" onclick="return doclink('link-25', 's1', 'link-19');">s1</a></tt><tt class="py-op">[</tt><tt class="py-number">0</tt><tt class="py-op">]</tt><tt class="py-op">,</tt> <tt id="link-26" class="py-name"><a title="Martel.test.test_swissprot38.s2" class="py-name" href="#" onclick="return doclink('link-26', 's2', 'link-21');">s2</a></tt><tt class="py-op">[</tt><tt class="py-number">0</tt><tt class="py-op">]</tt><tt class="py-op">)</tt> </tt>
<a name="L101"></a><tt class="py-lineno">101</tt> <tt class="py-line"> </tt>
<a name="L102"></a><tt class="py-lineno">102</tt> <tt class="py-line"> <tt id="link-27" class="py-name"><a title="Martel.test.test_swissprot38.s1" class="py-name" href="#" onclick="return doclink('link-27', 's1', 'link-19');">s1</a></tt> <tt class="py-op">=</tt> <tt id="link-28" class="py-name" targets="Method Bio.GFF.FeatureAggregate.map()=Bio.GFF.FeatureAggregate-class.html#map"><a title="Bio.GFF.FeatureAggregate.map" class="py-name" href="#" onclick="return doclink('link-28', 'map', 'link-28');">map</a></tt><tt class="py-op">(</tt><tt class="py-name">int</tt><tt class="py-op">,</tt> <tt id="link-29" class="py-name"><a title="Martel.test.test_swissprot38.s1" class="py-name" href="#" onclick="return doclink('link-29', 's1', 'link-19');">s1</a></tt><tt class="py-op">[</tt><tt class="py-number">1</tt><tt class="py-op">:</tt><tt class="py-op">]</tt><tt class="py-op">)</tt> </tt>
<a name="L103"></a><tt class="py-lineno">103</tt> <tt class="py-line"> <tt id="link-30" class="py-name"><a title="Martel.test.test_swissprot38.s2" class="py-name" href="#" onclick="return doclink('link-30', 's2', 'link-21');">s2</a></tt> <tt class="py-op">=</tt> <tt id="link-31" class="py-name"><a title="Bio.GFF.FeatureAggregate.map" class="py-name" href="#" onclick="return doclink('link-31', 'map', 'link-28');">map</a></tt><tt class="py-op">(</tt><tt class="py-name">int</tt><tt class="py-op">,</tt> <tt id="link-32" class="py-name"><a title="Martel.test.test_swissprot38.s2" class="py-name" href="#" onclick="return doclink('link-32', 's2', 'link-21');">s2</a></tt><tt class="py-op">[</tt><tt class="py-number">1</tt><tt class="py-op">:</tt><tt class="py-op">]</tt><tt class="py-op">)</tt> </tt>
<a name="L104"></a><tt class="py-lineno">104</tt> <tt class="py-line"> </tt>
<a name="L105"></a><tt class="py-lineno">105</tt> <tt class="py-line"> <tt class="py-keyword">return</tt> <tt class="py-name">cmp</tt><tt class="py-op">(</tt><tt id="link-33" class="py-name"><a title="Martel.test.test_swissprot38.s1" class="py-name" href="#" onclick="return doclink('link-33', 's1', 'link-19');">s1</a></tt><tt class="py-op">,</tt><tt id="link-34" class="py-name"><a title="Martel.test.test_swissprot38.s2" class="py-name" href="#" onclick="return doclink('link-34', 's2', 'link-21');">s2</a></tt><tt class="py-op">)</tt> </tt>
</div><a name="L106"></a><tt class="py-lineno">106</tt> <tt class="py-line"> </tt>
<a name="L107"></a><tt class="py-lineno">107</tt> <tt class="py-line"> </tt>
<a name="L108"></a><tt class="py-lineno">108</tt> <tt class="py-line"><tt id="link-35" class="py-name" targets="Variable Bio.SCOP._domain_re=Bio.SCOP-module.html#_domain_re"><a title="Bio.SCOP._domain_re" class="py-name" href="#" onclick="return doclink('link-35', '_domain_re', 'link-35');">_domain_re</a></tt> <tt class="py-op">=</tt> <tt class="py-name">re</tt><tt class="py-op">.</tt><tt id="link-36" 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-36', 'compile', 'link-36');">compile</a></tt><tt class="py-op">(</tt><tt class="py-string">r">?([\w_\.]*)\s+([\w\.]*)\s+\(([^)]*)\) (.*)"</tt><tt class="py-op">)</tt> </tt>
<a name="L109"></a><tt class="py-lineno">109</tt> <tt class="py-line"> </tt>
<a name="parse_domain"></a><div id="parse_domain-def"><a name="L110"></a><tt class="py-lineno">110</tt> <a class="py-toggle" href="#" id="parse_domain-toggle" onclick="return toggle('parse_domain');">-</a><tt class="py-line"><tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.SCOP-module.html#parse_domain">parse_domain</a><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="parse_domain-collapsed" style="display:none;" pad="+++" indent="++++"></div><div id="parse_domain-expanded"><a name="L111"></a><tt class="py-lineno">111</tt> <tt class="py-line"> <tt class="py-docstring">"""Convert an ASTRAL header string into a Scop domain.</tt> </tt>
<a name="L112"></a><tt class="py-lineno">112</tt> <tt class="py-line"><tt class="py-docstring"></tt> </tt>
<a name="L113"></a><tt class="py-lineno">113</tt> <tt class="py-line"><tt class="py-docstring"> An ASTRAL (http://astral.stanford.edu/) header contains a concise</tt> </tt>
<a name="L114"></a><tt class="py-lineno">114</tt> <tt class="py-line"><tt class="py-docstring"> description of a SCOP domain. A very similar format is used when a</tt> </tt>
<a name="L115"></a><tt class="py-lineno">115</tt> <tt class="py-line"><tt class="py-docstring"> Domain object is converted into a string. The Domain returned by this</tt> </tt>
<a name="L116"></a><tt class="py-lineno">116</tt> <tt class="py-line"><tt class="py-docstring"> method contains most of the SCOP information, but it will not be located</tt> </tt>
<a name="L117"></a><tt class="py-lineno">117</tt> <tt class="py-line"><tt class="py-docstring"> within the SCOP hierarchy (i.e. The parent node will be None). The</tt> </tt>
<a name="L118"></a><tt class="py-lineno">118</tt> <tt class="py-line"><tt class="py-docstring"> description is composed of the SCOP protein and species descriptions.</tt> </tt>
<a name="L119"></a><tt class="py-lineno">119</tt> <tt class="py-line"><tt class="py-docstring"></tt> </tt>
<a name="L120"></a><tt class="py-lineno">120</tt> <tt class="py-line"><tt class="py-docstring"> A typical ASTRAL header looks like --</tt> </tt>
<a name="L121"></a><tt class="py-lineno">121</tt> <tt class="py-line"><tt class="py-docstring"> >d1tpt_1 a.46.2.1 (1-70) Thymidine phosphorylase {Escherichia coli}</tt> </tt>
<a name="L122"></a><tt class="py-lineno">122</tt> <tt class="py-line"><tt class="py-docstring"> """</tt> </tt>
<a name="L123"></a><tt class="py-lineno">123</tt> <tt class="py-line"> </tt>
<a name="L124"></a><tt class="py-lineno">124</tt> <tt class="py-line"> <tt class="py-name">m</tt> <tt class="py-op">=</tt> <tt id="link-37" class="py-name"><a title="Bio.SCOP._domain_re" class="py-name" href="#" onclick="return doclink('link-37', '_domain_re', 'link-35');">_domain_re</a></tt><tt class="py-op">.</tt><tt id="link-38" 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-38', 'match', 'link-38');">match</a></tt><tt class="py-op">(</tt><tt class="py-name">str</tt><tt class="py-op">)</tt> </tt>
<a name="L125"></a><tt class="py-lineno">125</tt> <tt class="py-line"> <tt class="py-keyword">if</tt> <tt class="py-op">(</tt><tt class="py-keyword">not</tt> <tt class="py-name">m</tt><tt class="py-op">)</tt> <tt class="py-op">:</tt> <tt class="py-keyword">raise</tt> <tt class="py-name">ValueError</tt><tt class="py-op">,</tt> <tt class="py-string">"Domain: "</tt><tt class="py-op">+</tt> <tt class="py-name">str</tt> </tt>
<a name="L126"></a><tt class="py-lineno">126</tt> <tt class="py-line"> </tt>
<a name="L127"></a><tt class="py-lineno">127</tt> <tt class="py-line"> <tt class="py-name">dom</tt> <tt class="py-op">=</tt> <tt id="link-39" class="py-name" targets="Class Bio.SCOP.Domain=Bio.SCOP.Domain-class.html"><a title="Bio.SCOP.Domain" class="py-name" href="#" onclick="return doclink('link-39', 'Domain', 'link-39');">Domain</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
<a name="L128"></a><tt class="py-lineno">128</tt> <tt class="py-line"> <tt class="py-name">dom</tt><tt class="py-op">.</tt><tt class="py-name">sid</tt> <tt class="py-op">=</tt> <tt class="py-name">m</tt><tt class="py-op">.</tt><tt id="link-40" 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-40', 'group', 'link-40');">group</a></tt><tt class="py-op">(</tt><tt class="py-number">1</tt><tt class="py-op">)</tt> </tt>
<a name="L129"></a><tt class="py-lineno">129</tt> <tt class="py-line"> <tt class="py-name">dom</tt><tt class="py-op">.</tt><tt class="py-name">sccs</tt> <tt class="py-op">=</tt> <tt class="py-name">m</tt><tt class="py-op">.</tt><tt id="link-41" class="py-name"><a title="Bio.Prosite.Pattern.PrositeMatch.group" class="py-name" href="#" onclick="return doclink('link-41', 'group', 'link-40');">group</a></tt><tt class="py-op">(</tt><tt class="py-number">2</tt><tt class="py-op">)</tt> </tt>
<a name="L130"></a><tt class="py-lineno">130</tt> <tt class="py-line"> <tt class="py-name">dom</tt><tt class="py-op">.</tt><tt class="py-name">residues</tt> <tt class="py-op">=</tt> <tt id="link-42" class="py-name"><a title="Bio.SCOP.Residues'.Residues" class="py-name" href="#" onclick="return doclink('link-42', 'Residues', 'link-3');">Residues</a></tt><tt class="py-op">(</tt><tt class="py-name">m</tt><tt class="py-op">.</tt><tt id="link-43" class="py-name"><a title="Bio.Prosite.Pattern.PrositeMatch.group" class="py-name" href="#" onclick="return doclink('link-43', 'group', 'link-40');">group</a></tt><tt class="py-op">(</tt><tt class="py-number">3</tt><tt class="py-op">)</tt><tt class="py-op">)</tt> </tt>
<a name="L131"></a><tt class="py-lineno">131</tt> <tt class="py-line"> <tt class="py-keyword">if</tt> <tt class="py-keyword">not</tt> <tt class="py-name">dom</tt><tt class="py-op">.</tt><tt class="py-name">residues</tt><tt class="py-op">.</tt><tt class="py-name">pdbid</tt> <tt class="py-op">:</tt> </tt>
<a name="L132"></a><tt class="py-lineno">132</tt> <tt class="py-line"> <tt class="py-name">dom</tt><tt class="py-op">.</tt><tt class="py-name">residues</tt><tt class="py-op">.</tt><tt class="py-name">pdbid</tt><tt class="py-op">=</tt> <tt class="py-name">dom</tt><tt class="py-op">.</tt><tt class="py-name">sid</tt><tt class="py-op">[</tt><tt class="py-number">1</tt><tt class="py-op">:</tt><tt class="py-number">5</tt><tt class="py-op">]</tt> </tt>
<a name="L133"></a><tt class="py-lineno">133</tt> <tt class="py-line"> <tt class="py-name">dom</tt><tt class="py-op">.</tt><tt id="link-44" class="py-name" targets="Method Bio.Blast.NCBIStandalone._DescriptionConsumer.description()=Bio.Blast.NCBIStandalone._DescriptionConsumer-class.html#description,Method Bio.Enzyme._RecordConsumer.description()=Bio.Enzyme._RecordConsumer-class.html#description,Method Bio.Prosite._RecordConsumer.description()=Bio.Prosite._RecordConsumer-class.html#description,Function Bio.Std.description()=Bio.Std-module.html#description,Method Bio.SwissProt.SProt._RecordConsumer.description()=Bio.SwissProt.SProt._RecordConsumer-class.html#description,Method Bio.SwissProt.SProt._SequenceConsumer.description()=Bio.SwissProt.SProt._SequenceConsumer-class.html#description,Variable Martel.setup.run_local_tests.description=Martel.setup.run_local_tests-class.html#description"><a title="Bio.Blast.NCBIStandalone._DescriptionConsumer.description
Bio.Enzyme._RecordConsumer.description
Bio.Prosite._RecordConsumer.description
Bio.Std.description
Bio.SwissProt.SProt._RecordConsumer.description
Bio.SwissProt.SProt._SequenceConsumer.description
Martel.setup.run_local_tests.description" class="py-name" href="#" onclick="return doclink('link-44', 'description', 'link-44');">description</a></tt> <tt class="py-op">=</tt> <tt class="py-name">m</tt><tt class="py-op">.</tt><tt id="link-45" class="py-name"><a title="Bio.Prosite.Pattern.PrositeMatch.group" class="py-name" href="#" onclick="return doclink('link-45', 'group', 'link-40');">group</a></tt><tt class="py-op">(</tt><tt class="py-number">4</tt><tt class="py-op">)</tt><tt class="py-op">.</tt><tt id="link-46" 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-46', 'strip', 'link-46');">strip</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
<a name="L134"></a><tt class="py-lineno">134</tt> <tt class="py-line"> </tt>
<a name="L135"></a><tt class="py-lineno">135</tt> <tt class="py-line"> <tt class="py-keyword">return</tt> <tt class="py-name">dom</tt> </tt>
</div><a name="L136"></a><tt class="py-lineno">136</tt> <tt class="py-line"> </tt>
<a name="_open_scop_file"></a><div id="_open_scop_file-def"><a name="L137"></a><tt class="py-lineno">137</tt> <a class="py-toggle" href="#" id="_open_scop_file-toggle" onclick="return toggle('_open_scop_file');">-</a><tt class="py-line"><tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.SCOP-module.html#_open_scop_file">_open_scop_file</a><tt class="py-op">(</tt><tt class="py-param">scop_dir_path</tt><tt class="py-op">,</tt> <tt class="py-param">version</tt><tt class="py-op">,</tt> <tt class="py-param">filetype</tt><tt class="py-op">)</tt> <tt class="py-op">:</tt> </tt>
</div><div id="_open_scop_file-collapsed" style="display:none;" pad="+++" indent="++++"></div><div id="_open_scop_file-expanded"><a name="L138"></a><tt class="py-lineno">138</tt> <tt class="py-line"> <tt class="py-name">filename</tt> <tt class="py-op">=</tt> <tt class="py-string">"dir.%s.scop.txt_%s"</tt> <tt class="py-op">%</tt> <tt class="py-op">(</tt><tt class="py-name">filetype</tt><tt class="py-op">,</tt><tt id="link-47" class="py-name" targets="Method Bio.AlignAce.Parser.AlignAceConsumer.version()=Bio.AlignAce.Parser.AlignAceConsumer-class.html#version,Method Bio.Blast.NCBIStandalone._HeaderConsumer.version()=Bio.Blast.NCBIStandalone._HeaderConsumer-class.html#version,Method Bio.GenBank._FeatureConsumer.version()=Bio.GenBank._FeatureConsumer-class.html#version,Method Bio.GenBank._RecordConsumer.version()=Bio.GenBank._RecordConsumer-class.html#version,Variable Bio.MetaTool.metatool_format.version=Bio.MetaTool.metatool_format-module.html#version,Variable Bio.expressions.genbank.version=Bio.expressions.genbank-module.html#version"><a title="Bio.AlignAce.Parser.AlignAceConsumer.version
Bio.Blast.NCBIStandalone._HeaderConsumer.version
Bio.GenBank._FeatureConsumer.version
Bio.GenBank._RecordConsumer.version
Bio.MetaTool.metatool_format.version
Bio.expressions.genbank.version" class="py-name" href="#" onclick="return doclink('link-47', 'version', 'link-47');">version</a></tt><tt class="py-op">)</tt> </tt>
<a name="L139"></a><tt class="py-lineno">139</tt> <tt class="py-line"> <tt id="link-48" class="py-name" targets="Variable Bio.LocusLink.web_parse.handle=Bio.LocusLink.web_parse-module.html#handle,Variable Bio.Ndb.handle=Bio.Ndb-module.html#handle"><a title="Bio.LocusLink.web_parse.handle
Bio.Ndb.handle" class="py-name" href="#" onclick="return doclink('link-48', 'handle', 'link-48');">handle</a></tt> <tt class="py-op">=</tt> <tt id="link-49" 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-49', 'open', 'link-49');">open</a></tt><tt class="py-op">(</tt><tt class="py-name">os</tt><tt class="py-op">.</tt><tt class="py-name">path</tt><tt class="py-op">.</tt><tt class="py-name">join</tt><tt class="py-op">(</tt> <tt class="py-name">scop_dir_path</tt><tt class="py-op">,</tt> <tt class="py-name">filename</tt><tt class="py-op">)</tt><tt class="py-op">)</tt> </tt>
<a name="L140"></a><tt class="py-lineno">140</tt> <tt class="py-line"> <tt class="py-keyword">return</tt> <tt id="link-50" class="py-name"><a title="Bio.LocusLink.web_parse.handle
Bio.Ndb.handle" class="py-name" href="#" onclick="return doclink('link-50', 'handle', 'link-48');">handle</a></tt> </tt>
</div><a name="L141"></a><tt class="py-lineno">141</tt> <tt class="py-line"> </tt>
<a name="L142"></a><tt class="py-lineno">142</tt> <tt class="py-line"> </tt>
<a name="Scop"></a><div id="Scop-def"><a name="L143"></a><tt class="py-lineno">143</tt> <a class="py-toggle" href="#" id="Scop-toggle" onclick="return toggle('Scop');">-</a><tt class="py-line"><tt class="py-keyword">class</tt> <a class="py-def-name" href="Bio.SCOP.Scop-class.html">Scop</a><tt class="py-op">:</tt> </tt>
</div><div id="Scop-collapsed" style="display:none;" pad="+++" indent="++++"></div><div id="Scop-expanded"><a name="L144"></a><tt class="py-lineno">144</tt> <tt class="py-line"> <tt class="py-docstring">"""The entire SCOP hierarchy.</tt> </tt>
<a name="L145"></a><tt class="py-lineno">145</tt> <tt class="py-line"><tt class="py-docstring"></tt> </tt>
<a name="L146"></a><tt class="py-lineno">146</tt> <tt class="py-line"><tt class="py-docstring"> root -- The root node of the hierarchy </tt> </tt>
<a name="L147"></a><tt class="py-lineno">147</tt> <tt class="py-line"><tt class="py-docstring"> """</tt> </tt>
<a name="Scop.__init__"></a><div id="Scop.__init__-def"><a name="L148"></a><tt class="py-lineno">148</tt> <a class="py-toggle" href="#" id="Scop.__init__-toggle" onclick="return toggle('Scop.__init__');">-</a><tt class="py-line"> <tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.SCOP.Scop-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">cla_handle</tt><tt class="py-op">=</tt><tt class="py-name">None</tt><tt class="py-op">,</tt> <tt class="py-param">des_handle</tt><tt class="py-op">=</tt><tt class="py-name">None</tt><tt class="py-op">,</tt> <tt class="py-param">hie_handle</tt><tt class="py-op">=</tt><tt class="py-name">None</tt><tt class="py-op">,</tt> </tt>
<a name="L149"></a><tt class="py-lineno">149</tt> <tt class="py-line"> <tt class="py-param">dir_path</tt><tt class="py-op">=</tt><tt class="py-name">None</tt><tt class="py-op">,</tt> <tt class="py-param">db_handle</tt><tt class="py-op">=</tt><tt class="py-name">None</tt><tt class="py-op">,</tt> <tt class="py-param">version</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="Scop.__init__-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="Scop.__init__-expanded"><a name="L150"></a><tt class="py-lineno">150</tt> <tt class="py-line"> <tt class="py-docstring">"""Build the SCOP hierarchy from the SCOP parsable files, or a sql backend.</tt> </tt>
<a name="L151"></a><tt class="py-lineno">151</tt> <tt class="py-line"><tt class="py-docstring"></tt> </tt>
<a name="L152"></a><tt class="py-lineno">152</tt> <tt class="py-line"><tt class="py-docstring"> If no file handles are given, then a Scop object with a single</tt> </tt>
<a name="L153"></a><tt class="py-lineno">153</tt> <tt class="py-line"><tt class="py-docstring"> empty root node is returned.</tt> </tt>
<a name="L154"></a><tt class="py-lineno">154</tt> <tt class="py-line"><tt class="py-docstring"></tt> </tt>
<a name="L155"></a><tt class="py-lineno">155</tt> <tt class="py-line"><tt class="py-docstring"> If a directory and version are given (with dir_path=.., version=...) or</tt> </tt>
<a name="L156"></a><tt class="py-lineno">156</tt> <tt class="py-line"><tt class="py-docstring"> file handles for each file, the whole scop tree will be built in memory.</tt> </tt>
<a name="L157"></a><tt class="py-lineno">157</tt> <tt class="py-line"><tt class="py-docstring"></tt> </tt>
<a name="L158"></a><tt class="py-lineno">158</tt> <tt class="py-line"><tt class="py-docstring"> If a MySQLdb database handle is given, the tree will be built as needed,</tt> </tt>
<a name="L159"></a><tt class="py-lineno">159</tt> <tt class="py-line"><tt class="py-docstring"> minimising construction times. To build the SQL database to the methods</tt> </tt>
<a name="L160"></a><tt class="py-lineno">160</tt> <tt class="py-line"><tt class="py-docstring"> write_xxx_sql to create the tables.</tt> </tt>
<a name="L161"></a><tt class="py-lineno">161</tt> <tt class="py-line"><tt class="py-docstring"> </tt> </tt>
<a name="L162"></a><tt class="py-lineno">162</tt> <tt class="py-line"><tt class="py-docstring"> """</tt> </tt>
<a name="L163"></a><tt class="py-lineno">163</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">_sidDict</tt> <tt class="py-op">=</tt> <tt class="py-op">{</tt><tt class="py-op">}</tt> </tt>
<a name="L164"></a><tt class="py-lineno">164</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">_sunidDict</tt> <tt class="py-op">=</tt> <tt class="py-op">{</tt><tt class="py-op">}</tt> </tt>
<a name="L165"></a><tt class="py-lineno">165</tt> <tt class="py-line"> </tt>
<a name="L166"></a><tt class="py-lineno">166</tt> <tt class="py-line"> <tt class="py-keyword">if</tt> <tt class="py-name">cla_handle</tt><tt class="py-op">==</tt><tt class="py-name">des_handle</tt><tt class="py-op">==</tt><tt class="py-name">hie_handle</tt><tt class="py-op">==</tt><tt class="py-name">dir_path</tt><tt class="py-op">==</tt><tt class="py-name">db_handle</tt><tt class="py-op">==</tt><tt class="py-name">None</tt><tt class="py-op">:</tt> <tt class="py-keyword">return</tt> </tt>
<a name="L167"></a><tt class="py-lineno">167</tt> <tt class="py-line"> </tt>
<a name="L168"></a><tt class="py-lineno">168</tt> <tt class="py-line"> <tt class="py-keyword">if</tt> <tt class="py-name">dir_path</tt> <tt class="py-keyword">is</tt> <tt class="py-name">None</tt> <tt class="py-keyword">and</tt> <tt class="py-name">db_handle</tt> <tt class="py-keyword">is</tt> <tt class="py-name">None</tt><tt class="py-op">:</tt> </tt>
<a name="L169"></a><tt class="py-lineno">169</tt> <tt class="py-line"> <tt class="py-keyword">if</tt> <tt class="py-name">cla_handle</tt> <tt class="py-op">==</tt> <tt class="py-name">None</tt> <tt class="py-keyword">or</tt> <tt class="py-name">des_handle</tt><tt class="py-op">==</tt><tt class="py-name">None</tt> <tt class="py-keyword">or</tt> <tt class="py-name">hie_handle</tt><tt class="py-op">==</tt><tt class="py-name">None</tt><tt class="py-op">:</tt> </tt>
<a name="L170"></a><tt class="py-lineno">170</tt> <tt class="py-line"> <tt class="py-keyword">raise</tt> <tt class="py-name">RuntimeError</tt><tt class="py-op">,</tt><tt class="py-string">"Need CLA, DES and HIE files to build SCOP"</tt> </tt>
<a name="L171"></a><tt class="py-lineno">171</tt> <tt class="py-line"> </tt>
<a name="L172"></a><tt class="py-lineno">172</tt> <tt class="py-line"> <tt class="py-name">sunidDict</tt> <tt class="py-op">=</tt> <tt class="py-op">{</tt><tt class="py-op">}</tt> </tt>
<a name="L173"></a><tt class="py-lineno">173</tt> <tt class="py-line"> </tt>
<a name="L174"></a><tt class="py-lineno">174</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">db_handle</tt> <tt class="py-op">=</tt> <tt class="py-name">db_handle</tt> </tt>
<a name="L175"></a><tt class="py-lineno">175</tt> <tt class="py-line"> <tt class="py-keyword">try</tt><tt class="py-op">:</tt> </tt>
<a name="L176"></a><tt class="py-lineno">176</tt> <tt class="py-line"> </tt>
<a name="L177"></a><tt class="py-lineno">177</tt> <tt class="py-line"> <tt class="py-keyword">if</tt> <tt class="py-name">db_handle</tt><tt class="py-op">:</tt> </tt>
<a name="L178"></a><tt class="py-lineno">178</tt> <tt class="py-line"> <tt class="py-comment"># do nothing if we have a db handle, we'll do it all on the fly</tt> </tt>
<a name="L179"></a><tt class="py-lineno">179</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-keyword">pass</tt> </tt>
<a name="L180"></a><tt class="py-lineno">180</tt> <tt class="py-line"> </tt>
<a name="L181"></a><tt class="py-lineno">181</tt> <tt class="py-line"> <tt class="py-keyword">else</tt><tt class="py-op">:</tt> </tt>
<a name="L182"></a><tt class="py-lineno">182</tt> <tt class="py-line"> <tt class="py-comment"># open SCOP parseable files </tt> </tt>
<a name="L183"></a><tt class="py-lineno">183</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-keyword">if</tt> <tt class="py-name">dir_path</tt><tt class="py-op">:</tt> </tt>
<a name="L184"></a><tt class="py-lineno">184</tt> <tt class="py-line"> <tt class="py-keyword">if</tt> <tt class="py-keyword">not</tt> <tt id="link-51" class="py-name"><a title="Bio.AlignAce.Parser.AlignAceConsumer.version
Bio.Blast.NCBIStandalone._HeaderConsumer.version
Bio.GenBank._FeatureConsumer.version
Bio.GenBank._RecordConsumer.version
Bio.MetaTool.metatool_format.version
Bio.expressions.genbank.version" class="py-name" href="#" onclick="return doclink('link-51', 'version', 'link-47');">version</a></tt> <tt class="py-op">:</tt> </tt>
<a name="L185"></a><tt class="py-lineno">185</tt> <tt class="py-line"> <tt class="py-keyword">raise</tt> <tt class="py-name">RuntimeError</tt><tt class="py-op">,</tt> <tt class="py-string">"Need SCOP version to find parsable files in directory"</tt> </tt>
<a name="L186"></a><tt class="py-lineno">186</tt> <tt class="py-line"> <tt class="py-keyword">if</tt> <tt class="py-name">cla_handle</tt> <tt class="py-keyword">or</tt> <tt class="py-name">des_handle</tt> <tt class="py-keyword">or</tt> <tt class="py-name">hie_handle</tt><tt class="py-op">:</tt> </tt>
<a name="L187"></a><tt class="py-lineno">187</tt> <tt class="py-line"> <tt class="py-keyword">raise</tt> <tt class="py-name">RuntimeError</tt><tt class="py-op">,</tt><tt class="py-string">"Cannot specify SCOP directory and specific files"</tt> </tt>
<a name="L188"></a><tt class="py-lineno">188</tt> <tt class="py-line"> </tt>
<a name="L189"></a><tt class="py-lineno">189</tt> <tt class="py-line"> <tt class="py-name">cla_handle</tt> <tt class="py-op">=</tt> <tt id="link-52" class="py-name" targets="Function Bio.SCOP._open_scop_file()=Bio.SCOP-module.html#_open_scop_file"><a title="Bio.SCOP._open_scop_file" class="py-name" href="#" onclick="return doclink('link-52', '_open_scop_file', 'link-52');">_open_scop_file</a></tt><tt class="py-op">(</tt> <tt class="py-name">dir_path</tt><tt class="py-op">,</tt> <tt id="link-53" class="py-name"><a title="Bio.AlignAce.Parser.AlignAceConsumer.version
Bio.Blast.NCBIStandalone._HeaderConsumer.version
Bio.GenBank._FeatureConsumer.version
Bio.GenBank._RecordConsumer.version
Bio.MetaTool.metatool_format.version
Bio.expressions.genbank.version" class="py-name" href="#" onclick="return doclink('link-53', 'version', 'link-47');">version</a></tt><tt class="py-op">,</tt> <tt class="py-string">'cla'</tt><tt class="py-op">)</tt> </tt>
<a name="L190"></a><tt class="py-lineno">190</tt> <tt class="py-line"> <tt class="py-name">des_handle</tt> <tt class="py-op">=</tt> <tt id="link-54" class="py-name"><a title="Bio.SCOP._open_scop_file" class="py-name" href="#" onclick="return doclink('link-54', '_open_scop_file', 'link-52');">_open_scop_file</a></tt><tt class="py-op">(</tt> <tt class="py-name">dir_path</tt><tt class="py-op">,</tt> <tt id="link-55" class="py-name"><a title="Bio.AlignAce.Parser.AlignAceConsumer.version
Bio.Blast.NCBIStandalone._HeaderConsumer.version
Bio.GenBank._FeatureConsumer.version
Bio.GenBank._RecordConsumer.version
Bio.MetaTool.metatool_format.version
Bio.expressions.genbank.version" class="py-name" href="#" onclick="return doclink('link-55', 'version', 'link-47');">version</a></tt><tt class="py-op">,</tt> <tt class="py-string">'des'</tt><tt class="py-op">)</tt> </tt>
<a name="L191"></a><tt class="py-lineno">191</tt> <tt class="py-line"> <tt class="py-name">hie_handle</tt> <tt class="py-op">=</tt> <tt id="link-56" class="py-name"><a title="Bio.SCOP._open_scop_file" class="py-name" href="#" onclick="return doclink('link-56', '_open_scop_file', 'link-52');">_open_scop_file</a></tt><tt class="py-op">(</tt> <tt class="py-name">dir_path</tt><tt class="py-op">,</tt> <tt id="link-57" class="py-name"><a title="Bio.AlignAce.Parser.AlignAceConsumer.version
Bio.Blast.NCBIStandalone._HeaderConsumer.version
Bio.GenBank._FeatureConsumer.version
Bio.GenBank._RecordConsumer.version
Bio.MetaTool.metatool_format.version
Bio.expressions.genbank.version" class="py-name" href="#" onclick="return doclink('link-57', 'version', 'link-47');">version</a></tt><tt class="py-op">,</tt> <tt class="py-string">'hie'</tt><tt class="py-op">)</tt> </tt>
<a name="L192"></a><tt class="py-lineno">192</tt> <tt class="py-line"> </tt>
<a name="L193"></a><tt class="py-lineno">193</tt> <tt class="py-line"> <tt class="py-name">root</tt> <tt class="py-op">=</tt> <tt id="link-58" class="py-name" targets="Class Bio.Nexus.Nodes.Node=Bio.Nexus.Nodes.Node-class.html,Class Bio.SCOP.Node=Bio.SCOP.Node-class.html"><a title="Bio.Nexus.Nodes.Node
Bio.SCOP.Node" class="py-name" href="#" onclick="return doclink('link-58', 'Node', 'link-58');">Node</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
<a name="L194"></a><tt class="py-lineno">194</tt> <tt class="py-line"> <tt class="py-name">domains</tt> <tt class="py-op">=</tt> <tt class="py-op">[</tt><tt class="py-op">]</tt> </tt>
<a name="L195"></a><tt class="py-lineno">195</tt> <tt class="py-line"> <tt class="py-name">root</tt><tt class="py-op">.</tt><tt class="py-name">sunid</tt><tt class="py-op">=</tt><tt class="py-number">0</tt> </tt>
<a name="L196"></a><tt class="py-lineno">196</tt> <tt class="py-line"> <tt class="py-name">root</tt><tt class="py-op">.</tt><tt id="link-59" class="py-name" targets="Variable Bio.GenBank.LocationParser.Integer.type=Bio.GenBank.LocationParser.Integer-class.html#type,Variable Bio.GenBank.LocationParser.Symbol.type=Bio.GenBank.LocationParser.Symbol-class.html#type,Variable Bio.GenBank.LocationParser.UnsignedInteger.type=Bio.GenBank.LocationParser.UnsignedInteger-class.html#type"><a title="Bio.GenBank.LocationParser.Integer.type
Bio.GenBank.LocationParser.Symbol.type
Bio.GenBank.LocationParser.UnsignedInteger.type" class="py-name" href="#" onclick="return doclink('link-59', 'type', 'link-59');">type</a></tt><tt class="py-op">=</tt><tt class="py-string">'ro'</tt> </tt>
<a name="L197"></a><tt class="py-lineno">197</tt> <tt class="py-line"> <tt class="py-name">sunidDict</tt><tt class="py-op">[</tt><tt class="py-name">root</tt><tt class="py-op">.</tt><tt class="py-name">sunid</tt><tt class="py-op">]</tt> <tt class="py-op">=</tt> <tt class="py-name">root</tt> </tt>
<a name="L198"></a><tt class="py-lineno">198</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">root</tt> <tt class="py-op">=</tt> <tt class="py-name">root</tt> </tt>
<a name="L199"></a><tt class="py-lineno">199</tt> <tt class="py-line"> <tt class="py-name">root</tt><tt class="py-op">.</tt><tt id="link-60" class="py-name"><a title="Bio.Blast.NCBIStandalone._DescriptionConsumer.description
Bio.Enzyme._RecordConsumer.description
Bio.Prosite._RecordConsumer.description
Bio.Std.description
Bio.SwissProt.SProt._RecordConsumer.description
Bio.SwissProt.SProt._SequenceConsumer.description
Martel.setup.run_local_tests.description" class="py-name" href="#" onclick="return doclink('link-60', 'description', 'link-44');">description</a></tt> <tt class="py-op">=</tt> <tt class="py-string">'SCOP Root'</tt> </tt>
<a name="L200"></a><tt class="py-lineno">200</tt> <tt class="py-line"> </tt>
<a name="L201"></a><tt class="py-lineno">201</tt> <tt class="py-line"> <tt class="py-comment"># Build the rest of the nodes using the DES file</tt> </tt>
<a name="L202"></a><tt class="py-lineno">202</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-name">records</tt> <tt class="py-op">=</tt> <tt id="link-61" class="py-name"><a title="Bio.SCOP.Des" class="py-name" href="#" onclick="return doclink('link-61', 'Des', 'link-0');">Des</a></tt><tt class="py-op">.</tt><tt id="link-62" class="py-name" targets="Method Bio.Affy.CelFile.CelParser.parse()=Bio.Affy.CelFile.CelParser-class.html#parse,Method Bio.AlignAce.Parser.AlignAceParser.parse()=Bio.AlignAce.Parser.AlignAceParser-class.html#parse,Method Bio.AlignAce.Parser.CompareAceParser.parse()=Bio.AlignAce.Parser.CompareAceParser-class.html#parse,Function Bio.AlignIO.parse()=Bio.AlignIO-module.html#parse,Method Bio.Blast.NCBIStandalone.BlastErrorParser.parse()=Bio.Blast.NCBIStandalone.BlastErrorParser-class.html#parse,Method Bio.Blast.NCBIStandalone.BlastParser.parse()=Bio.Blast.NCBIStandalone.BlastParser-class.html#parse,Method Bio.Blast.NCBIStandalone.PSIBlastParser.parse()=Bio.Blast.NCBIStandalone.PSIBlastParser-class.html#parse,Method Bio.Blast.NCBIWWW.BlastParser.parse()=Bio.Blast.NCBIWWW.BlastParser-class.html#parse,Method Bio.Blast.NCBIXML.BlastParser.parse()=Bio.Blast.NCBIXML.BlastParser-class.html#parse,Function Bio.Blast.NCBIXML.parse()=Bio.Blast.NCBIXML-module.html#parse,Method Bio.CDD.RecordParser.parse()=Bio.CDD.RecordParser-class.html#parse,Method Bio.Compass.RecordParser.parse()=Bio.Compass.RecordParser-class.html#parse,Function Bio.Decode.parse()=Bio.Decode-module.html#parse,Method Bio.ECell.RecordParser.parse()=Bio.ECell.RecordParser-class.html#parse,Method Bio.EUtils.POM.POMDocument.parse()=Bio.EUtils.POM.POMDocument-class.html#parse,Module Bio.EUtils.parse=Bio.EUtils.parse-module.html,Method Bio.Emboss.Primer.Primer3Parser.parse()=Bio.Emboss.Primer.Primer3Parser-class.html#parse,Method Bio.Emboss.Primer.PrimerSearchParser.parse()=Bio.Emboss.Primer.PrimerSearchParser-class.html#parse,Method Bio.Enzyme.RecordParser.parse()=Bio.Enzyme.RecordParser-class.html#parse,Method Bio.Fasta.RecordParser.parse()=Bio.Fasta.RecordParser-class.html#parse,Method Bio.Fasta.SequenceParser.parse()=Bio.Fasta.SequenceParser-class.html#parse,Method Bio.GenBank.FeatureParser.parse()=Bio.GenBank.FeatureParser-class.html#parse,Function Bio.GenBank.LocationParser.parse()=Bio.GenBank.LocationParser-module.html#parse,Method Bio.GenBank.RecordParser.parse()=Bio.GenBank.RecordParser-class.html#parse,Method Bio.GenBank.Scanner.InsdcScanner.parse()=Bio.GenBank.Scanner.InsdcScanner-class.html#parse,Function Bio.Geo.parse()=Bio.Geo-module.html#parse,Method Bio.Gobase.RecordParser.parse()=Bio.Gobase.RecordParser-class.html#parse,Method Bio.IntelliGenetics.RecordParser.parse()=Bio.IntelliGenetics.RecordParser-class.html#parse,Method Bio.InterPro.InterProParser.parse()=Bio.InterPro.InterProParser-class.html#parse,Function Bio.KEGG.Compound.parse()=Bio.KEGG.Compound-module.html#parse,Function Bio.KEGG.Enzyme.parse()=Bio.KEGG.Enzyme-module.html#parse,Function Bio.KEGG.Map.parse()=Bio.KEGG.Map-module.html#parse,Method Bio.LocusLink.RecordParser.parse()=Bio.LocusLink.RecordParser-class.html#parse,Method Bio.LocusLink.web_parse.LocusLinkParser.parse()=Bio.LocusLink.web_parse.LocusLinkParser-class.html#parse,Method Bio.MEME.Parser.MASTParser.parse()=Bio.MEME.Parser.MASTParser-class.html#parse,Method Bio.MEME.Parser.MEMEParser.parse()=Bio.MEME.Parser.MEMEParser-class.html#parse,Method Bio.Medline.RecordParser.parse()=Bio.Medline.RecordParser-class.html#parse,Method Bio.MetaTool.RecordParser.parse()=Bio.MetaTool.RecordParser-class.html#parse,Method Bio.NBRF.RecordParser.parse()=Bio.NBRF.RecordParser-class.html#parse,Method Bio.Ndb.NdbParser.parse()=Bio.Ndb.NdbParser-class.html#parse,Method Bio.ParserSupport.AbstractParser.parse()=Bio.ParserSupport.AbstractParser-class.html#parse,Method Bio.Parsers.spark.GenericParser.parse()=Bio.Parsers.spark.GenericParser-class.html#parse,Method Bio.PopGen.FDist.RecordParser.parse()=Bio.PopGen.FDist.RecordParser-class.html#parse,Method Bio.PopGen.GenePop.RecordParser.parse()=Bio.PopGen.GenePop.RecordParser-class.html#parse,Function Bio.PopGen.GenePop.parse()=Bio.PopGen.GenePop-module.html#parse,Method Bio.Prosite.Prodoc.RecordParser.parse()=Bio.Prosite.Prodoc.RecordParser-class.html#parse,Function Bio.Prosite.Prodoc.parse()=Bio.Prosite.Prodoc-module.html#parse,Method Bio.Prosite.RecordParser.parse()=Bio.Prosite.RecordParser-class.html#parse,Function Bio.Prosite.parse()=Bio.Prosite-module.html#parse,Method Bio.Rebase.RecordParser.parse()=Bio.Rebase.RecordParser-class.html#parse,Method Bio.SCOP.Cla.Parser.parse()=Bio.SCOP.Cla.Parser-class.html#parse,Function Bio.SCOP.Cla.parse()=Bio.SCOP.Cla-module.html#parse,Method Bio.SCOP.Des.Parser.parse()=Bio.SCOP.Des.Parser-class.html#parse,Function Bio.SCOP.Des.parse()=Bio.SCOP.Des-module.html#parse,Method Bio.SCOP.Dom.Parser.parse()=Bio.SCOP.Dom.Parser-class.html#parse,Function Bio.SCOP.Dom.parse()=Bio.SCOP.Dom-module.html#parse,Method Bio.SCOP.Hie.Parser.parse()=Bio.SCOP.Hie.Parser-class.html#parse,Function Bio.SCOP.Hie.parse()=Bio.SCOP.Hie-module.html#parse,Method Bio.SCOP.Raf.Parser.parse()=Bio.SCOP.Raf.Parser-class.html#parse,Function Bio.SCOP.Raf.parse()=Bio.SCOP.Raf-module.html#parse,Method Bio.Saf.RecordParser.parse()=Bio.Saf.RecordParser-class.html#parse,Function Bio.SeqIO.parse()=Bio.SeqIO-module.html#parse,Method Bio.Sequencing.Ace.ACEParser.parse()=Bio.Sequencing.Ace.ACEParser-class.html#parse,Method Bio.Sequencing.Ace.RecordParser.parse()=Bio.Sequencing.Ace.RecordParser-class.html#parse,Method Bio.Sequencing.Phd.RecordParser.parse()=Bio.Sequencing.Phd.RecordParser-class.html#parse,Method Bio.SwissProt.KeyWList.ListParser.parse()=Bio.SwissProt.KeyWList.ListParser-class.html#parse,Function Bio.SwissProt.KeyWList.parse()=Bio.SwissProt.KeyWList-module.html#parse,Method Bio.SwissProt.SProt.RecordParser.parse()=Bio.SwissProt.SProt.RecordParser-class.html#parse,Method Bio.SwissProt.SProt.SequenceParser.parse()=Bio.SwissProt.SProt.SequenceParser-class.html#parse,Function Bio.SwissProt.parse()=Bio.SwissProt-module.html#parse,Method Bio.UniGene.RecordParser.parse()=Bio.UniGene.RecordParser-class.html#parse,Function Bio.Wise.psw.parse()=Bio.Wise.psw-module.html#parse,Method Martel.Parser.HeaderFooterParser.parse()=Martel.Parser.HeaderFooterParser-class.html#parse,Method Martel.Parser.Parser.parse()=Martel.Parser.Parser-class.html#parse,Method Martel.Parser.RecordParser.parse()=Martel.Parser.RecordParser-class.html#parse,Function Martel.msre_parse.parse()=Martel.msre_parse-module.html#parse"><a title="Bio.Affy.CelFile.CelParser.parse
Bio.AlignAce.Parser.AlignAceParser.parse
Bio.AlignAce.Parser.CompareAceParser.parse
Bio.AlignIO.parse
Bio.Blast.NCBIStandalone.BlastErrorParser.parse
Bio.Blast.NCBIStandalone.BlastParser.parse
Bio.Blast.NCBIStandalone.PSIBlastParser.parse
Bio.Blast.NCBIWWW.BlastParser.parse
Bio.Blast.NCBIXML.BlastParser.parse
Bio.Blast.NCBIXML.parse
Bio.CDD.RecordParser.parse
Bio.Compass.RecordParser.parse
Bio.Decode.parse
Bio.ECell.RecordParser.parse
Bio.EUtils.POM.POMDocument.parse
Bio.EUtils.parse
Bio.Emboss.Primer.Primer3Parser.parse
Bio.Emboss.Primer.PrimerSearchParser.parse
Bio.Enzyme.RecordParser.parse
Bio.Fasta.RecordParser.parse
Bio.Fasta.SequenceParser.parse
Bio.GenBank.FeatureParser.parse
Bio.GenBank.LocationParser.parse
Bio.GenBank.RecordParser.parse
Bio.GenBank.Scanner.InsdcScanner.parse
Bio.Geo.parse
Bio.Gobase.RecordParser.parse
Bio.IntelliGenetics.RecordParser.parse
Bio.InterPro.InterProParser.parse
Bio.KEGG.Compound.parse
Bio.KEGG.Enzyme.parse
Bio.KEGG.Map.parse
Bio.LocusLink.RecordParser.parse
Bio.LocusLink.web_parse.LocusLinkParser.parse
Bio.MEME.Parser.MASTParser.parse
Bio.MEME.Parser.MEMEParser.parse
Bio.Medline.RecordParser.parse
Bio.MetaTool.RecordParser.parse
Bio.NBRF.RecordParser.parse
Bio.Ndb.NdbParser.parse
Bio.ParserSupport.AbstractParser.parse
Bio.Parsers.spark.GenericParser.parse
Bio.PopGen.FDist.RecordParser.parse
Bio.PopGen.GenePop.RecordParser.parse
Bio.PopGen.GenePop.parse
Bio.Prosite.Prodoc.RecordParser.parse
Bio.Prosite.Prodoc.parse
Bio.Prosite.RecordParser.parse
Bio.Prosite.parse
Bio.Rebase.RecordParser.parse
Bio.SCOP.Cla.Parser.parse
Bio.SCOP.Cla.parse
Bio.SCOP.Des.Parser.parse
Bio.SCOP.Des.parse
Bio.SCOP.Dom.Parser.parse
Bio.SCOP.Dom.parse
Bio.SCOP.Hie.Parser.parse
Bio.SCOP.Hie.parse
Bio.SCOP.Raf.Parser.parse
Bio.SCOP.Raf.parse
Bio.Saf.RecordParser.parse
Bio.SeqIO.parse
Bio.Sequencing.Ace.ACEParser.parse
Bio.Sequencing.Ace.RecordParser.parse
Bio.Sequencing.Phd.RecordParser.parse
Bio.SwissProt.KeyWList.ListParser.parse
Bio.SwissProt.KeyWList.parse
Bio.SwissProt.SProt.RecordParser.parse
Bio.SwissProt.SProt.SequenceParser.parse
Bio.SwissProt.parse
Bio.UniGene.RecordParser.parse
Bio.Wise.psw.parse
Martel.Parser.HeaderFooterParser.parse
Martel.Parser.Parser.parse
Martel.Parser.RecordParser.parse
Martel.msre_parse.parse" class="py-name" href="#" onclick="return doclink('link-62', 'parse', 'link-62');">parse</a></tt><tt class="py-op">(</tt><tt class="py-name">des_handle</tt><tt class="py-op">)</tt> </tt>
<a name="L203"></a><tt class="py-lineno">203</tt> <tt class="py-line"> <tt class="py-keyword">for</tt> <tt id="link-63" class="py-name" targets="Variable Bio.Emboss.primer3_format.record=Bio.Emboss.primer3_format-module.html#record,Variable Bio.Emboss.primersearch_format.record=Bio.Emboss.primersearch_format-module.html#record,Method Bio.GFF.Feature.record()=Bio.GFF.Feature-class.html#record,Variable Bio.LocusLink.web_parse.record=Bio.LocusLink.web_parse-module.html#record,Variable Bio.Ndb.record=Bio.Ndb-module.html#record,Function Bio.Std.record()=Bio.Std-module.html#record,Variable Bio.expressions.blocks.record=Bio.expressions.blocks-module.html#record,Variable Bio.expressions.embl.embl65.record=Bio.expressions.embl.embl65-module.html#record,Variable Bio.expressions.fasta.record=Bio.expressions.fasta-module.html#record,Variable Bio.expressions.genbank.record=Bio.expressions.genbank-module.html#record,Variable Bio.expressions.hmmpfam.record=Bio.expressions.hmmpfam-module.html#record,Variable Bio.expressions.swissprot.ipi.record=Bio.expressions.swissprot.ipi-module.html#record,Variable Bio.expressions.swissprot.speclist.record=Bio.expressions.swissprot.speclist-module.html#record,Variable Bio.expressions.swissprot.sprot38.record=Bio.expressions.swissprot.sprot38-module.html#record,Variable Bio.expressions.swissprot.sprot40.record=Bio.expressions.swissprot.sprot40-module.html#record,Variable Martel.test.test_swissprot38.record=Martel.test.test_swissprot38-module.html#record,Variable Martel.test.testformats.swissprot38.record=Martel.test.testformats.swissprot38-module.html#record"><a title="Bio.Emboss.primer3_format.record
Bio.Emboss.primersearch_format.record
Bio.GFF.Feature.record
Bio.LocusLink.web_parse.record
Bio.Ndb.record
Bio.Std.record
Bio.expressions.blocks.record
Bio.expressions.embl.embl65.record
Bio.expressions.fasta.record
Bio.expressions.genbank.record
Bio.expressions.hmmpfam.record
Bio.expressions.swissprot.ipi.record
Bio.expressions.swissprot.speclist.record
Bio.expressions.swissprot.sprot38.record
Bio.expressions.swissprot.sprot40.record
Martel.test.test_swissprot38.record
Martel.test.testformats.swissprot38.record" class="py-name" href="#" onclick="return doclink('link-63', 'record', 'link-63');">record</a></tt> <tt class="py-keyword">in</tt> <tt class="py-name">records</tt><tt class="py-op">:</tt> </tt>
<a name="L204"></a><tt class="py-lineno">204</tt> <tt class="py-line"> <tt class="py-keyword">if</tt> <tt id="link-64" class="py-name"><a title="Bio.Emboss.primer3_format.record
Bio.Emboss.primersearch_format.record
Bio.GFF.Feature.record
Bio.LocusLink.web_parse.record
Bio.Ndb.record
Bio.Std.record
Bio.expressions.blocks.record
Bio.expressions.embl.embl65.record
Bio.expressions.fasta.record
Bio.expressions.genbank.record
Bio.expressions.hmmpfam.record
Bio.expressions.swissprot.ipi.record
Bio.expressions.swissprot.speclist.record
Bio.expressions.swissprot.sprot38.record
Bio.expressions.swissprot.sprot40.record
Martel.test.test_swissprot38.record
Martel.test.testformats.swissprot38.record" class="py-name" href="#" onclick="return doclink('link-64', 'record', 'link-63');">record</a></tt><tt class="py-op">.</tt><tt class="py-name">nodetype</tt> <tt class="py-op">==</tt><tt class="py-string">'px'</tt> <tt class="py-op">:</tt> </tt>
<a name="L205"></a><tt class="py-lineno">205</tt> <tt class="py-line"> <tt class="py-name">n</tt> <tt class="py-op">=</tt> <tt id="link-65" class="py-name"><a title="Bio.SCOP.Domain" class="py-name" href="#" onclick="return doclink('link-65', 'Domain', 'link-39');">Domain</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
<a name="L206"></a><tt class="py-lineno">206</tt> <tt class="py-line"> <tt class="py-name">n</tt><tt class="py-op">.</tt><tt class="py-name">sid</tt> <tt class="py-op">=</tt> <tt id="link-66" class="py-name"><a title="Bio.Emboss.primer3_format.record
Bio.Emboss.primersearch_format.record
Bio.GFF.Feature.record
Bio.LocusLink.web_parse.record
Bio.Ndb.record
Bio.Std.record
Bio.expressions.blocks.record
Bio.expressions.embl.embl65.record
Bio.expressions.fasta.record
Bio.expressions.genbank.record
Bio.expressions.hmmpfam.record
Bio.expressions.swissprot.ipi.record
Bio.expressions.swissprot.speclist.record
Bio.expressions.swissprot.sprot38.record
Bio.expressions.swissprot.sprot40.record
Martel.test.test_swissprot38.record
Martel.test.testformats.swissprot38.record" class="py-name" href="#" onclick="return doclink('link-66', 'record', 'link-63');">record</a></tt><tt class="py-op">.</tt><tt id="link-67" 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-67', 'name', 'link-67');">name</a></tt> </tt>
<a name="L207"></a><tt class="py-lineno">207</tt> <tt class="py-line"> <tt class="py-name">domains</tt><tt class="py-op">.</tt><tt id="link-68" 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-68', 'append', 'link-68');">append</a></tt><tt class="py-op">(</tt><tt class="py-name">n</tt><tt class="py-op">)</tt> </tt>
<a name="L208"></a><tt class="py-lineno">208</tt> <tt class="py-line"> <tt class="py-keyword">else</tt> <tt class="py-op">:</tt> </tt>
<a name="L209"></a><tt class="py-lineno">209</tt> <tt class="py-line"> <tt class="py-name">n</tt> <tt class="py-op">=</tt> <tt id="link-69" class="py-name"><a title="Bio.Nexus.Nodes.Node
Bio.SCOP.Node" class="py-name" href="#" onclick="return doclink('link-69', 'Node', 'link-58');">Node</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
<a name="L210"></a><tt class="py-lineno">210</tt> <tt class="py-line"> <tt class="py-name">n</tt><tt class="py-op">.</tt><tt class="py-name">sunid</tt> <tt class="py-op">=</tt> <tt id="link-70" class="py-name"><a title="Bio.Emboss.primer3_format.record
Bio.Emboss.primersearch_format.record
Bio.GFF.Feature.record
Bio.LocusLink.web_parse.record
Bio.Ndb.record
Bio.Std.record
Bio.expressions.blocks.record
Bio.expressions.embl.embl65.record
Bio.expressions.fasta.record
Bio.expressions.genbank.record
Bio.expressions.hmmpfam.record
Bio.expressions.swissprot.ipi.record
Bio.expressions.swissprot.speclist.record
Bio.expressions.swissprot.sprot38.record
Bio.expressions.swissprot.sprot40.record
Martel.test.test_swissprot38.record
Martel.test.testformats.swissprot38.record" class="py-name" href="#" onclick="return doclink('link-70', 'record', 'link-63');">record</a></tt><tt class="py-op">.</tt><tt class="py-name">sunid</tt> </tt>
<a name="L211"></a><tt class="py-lineno">211</tt> <tt class="py-line"> <tt class="py-name">n</tt><tt class="py-op">.</tt><tt id="link-71" class="py-name"><a title="Bio.GenBank.LocationParser.Integer.type
Bio.GenBank.LocationParser.Symbol.type
Bio.GenBank.LocationParser.UnsignedInteger.type" class="py-name" href="#" onclick="return doclink('link-71', 'type', 'link-59');">type</a></tt> <tt class="py-op">=</tt> <tt id="link-72" class="py-name"><a title="Bio.Emboss.primer3_format.record
Bio.Emboss.primersearch_format.record
Bio.GFF.Feature.record
Bio.LocusLink.web_parse.record
Bio.Ndb.record
Bio.Std.record
Bio.expressions.blocks.record
Bio.expressions.embl.embl65.record
Bio.expressions.fasta.record
Bio.expressions.genbank.record
Bio.expressions.hmmpfam.record
Bio.expressions.swissprot.ipi.record
Bio.expressions.swissprot.speclist.record
Bio.expressions.swissprot.sprot38.record
Bio.expressions.swissprot.sprot40.record
Martel.test.test_swissprot38.record
Martel.test.testformats.swissprot38.record" class="py-name" href="#" onclick="return doclink('link-72', 'record', 'link-63');">record</a></tt><tt class="py-op">.</tt><tt class="py-name">nodetype</tt> </tt>
<a name="L212"></a><tt class="py-lineno">212</tt> <tt class="py-line"> <tt class="py-name">n</tt><tt class="py-op">.</tt><tt class="py-name">sccs</tt> <tt class="py-op">=</tt> <tt id="link-73" class="py-name"><a title="Bio.Emboss.primer3_format.record
Bio.Emboss.primersearch_format.record
Bio.GFF.Feature.record
Bio.LocusLink.web_parse.record
Bio.Ndb.record
Bio.Std.record
Bio.expressions.blocks.record
Bio.expressions.embl.embl65.record
Bio.expressions.fasta.record
Bio.expressions.genbank.record
Bio.expressions.hmmpfam.record
Bio.expressions.swissprot.ipi.record
Bio.expressions.swissprot.speclist.record
Bio.expressions.swissprot.sprot38.record
Bio.expressions.swissprot.sprot40.record
Martel.test.test_swissprot38.record
Martel.test.testformats.swissprot38.record" class="py-name" href="#" onclick="return doclink('link-73', 'record', 'link-63');">record</a></tt><tt class="py-op">.</tt><tt class="py-name">sccs</tt> </tt>
<a name="L213"></a><tt class="py-lineno">213</tt> <tt class="py-line"> <tt class="py-name">n</tt><tt class="py-op">.</tt><tt id="link-74" class="py-name"><a title="Bio.Blast.NCBIStandalone._DescriptionConsumer.description
Bio.Enzyme._RecordConsumer.description
Bio.Prosite._RecordConsumer.description
Bio.Std.description
Bio.SwissProt.SProt._RecordConsumer.description
Bio.SwissProt.SProt._SequenceConsumer.description
Martel.setup.run_local_tests.description" class="py-name" href="#" onclick="return doclink('link-74', 'description', 'link-44');">description</a></tt> <tt class="py-op">=</tt> <tt id="link-75" class="py-name"><a title="Bio.Emboss.primer3_format.record
Bio.Emboss.primersearch_format.record
Bio.GFF.Feature.record
Bio.LocusLink.web_parse.record
Bio.Ndb.record
Bio.Std.record
Bio.expressions.blocks.record
Bio.expressions.embl.embl65.record
Bio.expressions.fasta.record
Bio.expressions.genbank.record
Bio.expressions.hmmpfam.record
Bio.expressions.swissprot.ipi.record
Bio.expressions.swissprot.speclist.record
Bio.expressions.swissprot.sprot38.record
Bio.expressions.swissprot.sprot40.record
Martel.test.test_swissprot38.record
Martel.test.testformats.swissprot38.record" class="py-name" href="#" onclick="return doclink('link-75', 'record', 'link-63');">record</a></tt><tt class="py-op">.</tt><tt id="link-76" class="py-name"><a title="Bio.Blast.NCBIStandalone._DescriptionConsumer.description
Bio.Enzyme._RecordConsumer.description
Bio.Prosite._RecordConsumer.description
Bio.Std.description
Bio.SwissProt.SProt._RecordConsumer.description
Bio.SwissProt.SProt._SequenceConsumer.description
Martel.setup.run_local_tests.description" class="py-name" href="#" onclick="return doclink('link-76', 'description', 'link-44');">description</a></tt> </tt>
<a name="L214"></a><tt class="py-lineno">214</tt> <tt class="py-line"> </tt>
<a name="L215"></a><tt class="py-lineno">215</tt> <tt class="py-line"> <tt class="py-name">sunidDict</tt><tt class="py-op">[</tt><tt class="py-name">n</tt><tt class="py-op">.</tt><tt class="py-name">sunid</tt><tt class="py-op">]</tt> <tt class="py-op">=</tt> <tt class="py-name">n</tt> </tt>
<a name="L216"></a><tt class="py-lineno">216</tt> <tt class="py-line"> </tt>
<a name="L217"></a><tt class="py-lineno">217</tt> <tt class="py-line"> <tt class="py-comment"># Glue all of the Nodes together using the HIE file</tt> </tt>
<a name="L218"></a><tt class="py-lineno">218</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-name">records</tt> <tt class="py-op">=</tt> <tt id="link-77" class="py-name"><a title="Bio.SCOP.Hie" class="py-name" href="#" onclick="return doclink('link-77', 'Hie', 'link-2');">Hie</a></tt><tt class="py-op">.</tt><tt id="link-78" class="py-name"><a title="Bio.Affy.CelFile.CelParser.parse
Bio.AlignAce.Parser.AlignAceParser.parse
Bio.AlignAce.Parser.CompareAceParser.parse
Bio.AlignIO.parse
Bio.Blast.NCBIStandalone.BlastErrorParser.parse
Bio.Blast.NCBIStandalone.BlastParser.parse
Bio.Blast.NCBIStandalone.PSIBlastParser.parse
Bio.Blast.NCBIWWW.BlastParser.parse
Bio.Blast.NCBIXML.BlastParser.parse
Bio.Blast.NCBIXML.parse
Bio.CDD.RecordParser.parse
Bio.Compass.RecordParser.parse
Bio.Decode.parse
Bio.ECell.RecordParser.parse
Bio.EUtils.POM.POMDocument.parse
Bio.EUtils.parse
Bio.Emboss.Primer.Primer3Parser.parse
Bio.Emboss.Primer.PrimerSearchParser.parse
Bio.Enzyme.RecordParser.parse
Bio.Fasta.RecordParser.parse
Bio.Fasta.SequenceParser.parse
Bio.GenBank.FeatureParser.parse
Bio.GenBank.LocationParser.parse
Bio.GenBank.RecordParser.parse
Bio.GenBank.Scanner.InsdcScanner.parse
Bio.Geo.parse
Bio.Gobase.RecordParser.parse
Bio.IntelliGenetics.RecordParser.parse
Bio.InterPro.InterProParser.parse
Bio.KEGG.Compound.parse
Bio.KEGG.Enzyme.parse
Bio.KEGG.Map.parse
Bio.LocusLink.RecordParser.parse
Bio.LocusLink.web_parse.LocusLinkParser.parse
Bio.MEME.Parser.MASTParser.parse
Bio.MEME.Parser.MEMEParser.parse
Bio.Medline.RecordParser.parse
Bio.MetaTool.RecordParser.parse
Bio.NBRF.RecordParser.parse
Bio.Ndb.NdbParser.parse
Bio.ParserSupport.AbstractParser.parse
Bio.Parsers.spark.GenericParser.parse
Bio.PopGen.FDist.RecordParser.parse
Bio.PopGen.GenePop.RecordParser.parse
Bio.PopGen.GenePop.parse
Bio.Prosite.Prodoc.RecordParser.parse
Bio.Prosite.Prodoc.parse
Bio.Prosite.RecordParser.parse
Bio.Prosite.parse
Bio.Rebase.RecordParser.parse
Bio.SCOP.Cla.Parser.parse
Bio.SCOP.Cla.parse
Bio.SCOP.Des.Parser.parse
Bio.SCOP.Des.parse
Bio.SCOP.Dom.Parser.parse
Bio.SCOP.Dom.parse
Bio.SCOP.Hie.Parser.parse
Bio.SCOP.Hie.parse
Bio.SCOP.Raf.Parser.parse
Bio.SCOP.Raf.parse
Bio.Saf.RecordParser.parse
Bio.SeqIO.parse
Bio.Sequencing.Ace.ACEParser.parse
Bio.Sequencing.Ace.RecordParser.parse
Bio.Sequencing.Phd.RecordParser.parse
Bio.SwissProt.KeyWList.ListParser.parse
Bio.SwissProt.KeyWList.parse
Bio.SwissProt.SProt.RecordParser.parse
Bio.SwissProt.SProt.SequenceParser.parse
Bio.SwissProt.parse
Bio.UniGene.RecordParser.parse
Bio.Wise.psw.parse
Martel.Parser.HeaderFooterParser.parse
Martel.Parser.Parser.parse
Martel.Parser.RecordParser.parse
Martel.msre_parse.parse" class="py-name" href="#" onclick="return doclink('link-78', 'parse', 'link-62');">parse</a></tt><tt class="py-op">(</tt><tt class="py-name">hie_handle</tt><tt class="py-op">)</tt> </tt>
<a name="L219"></a><tt class="py-lineno">219</tt> <tt class="py-line"> <tt class="py-keyword">for</tt> <tt id="link-79" class="py-name"><a title="Bio.Emboss.primer3_format.record
Bio.Emboss.primersearch_format.record
Bio.GFF.Feature.record
Bio.LocusLink.web_parse.record
Bio.Ndb.record
Bio.Std.record
Bio.expressions.blocks.record
Bio.expressions.embl.embl65.record
Bio.expressions.fasta.record
Bio.expressions.genbank.record
Bio.expressions.hmmpfam.record
Bio.expressions.swissprot.ipi.record
Bio.expressions.swissprot.speclist.record
Bio.expressions.swissprot.sprot38.record
Bio.expressions.swissprot.sprot40.record
Martel.test.test_swissprot38.record
Martel.test.testformats.swissprot38.record" class="py-name" href="#" onclick="return doclink('link-79', 'record', 'link-63');">record</a></tt> <tt class="py-keyword">in</tt> <tt class="py-name">records</tt><tt class="py-op">:</tt> </tt>
<a name="L220"></a><tt class="py-lineno">220</tt> <tt class="py-line"> <tt class="py-keyword">if</tt> <tt class="py-keyword">not</tt> <tt class="py-name">sunidDict</tt><tt class="py-op">.</tt><tt id="link-80" class="py-name" targets="Method Bio.Crystal.Crystal.has_key()=Bio.Crystal.Crystal-class.html#has_key,Method Bio.EUtils.POM.ElementNode.has_key()=Bio.EUtils.POM.ElementNode-class.html#has_key,Method Bio.GenBank.NCBIDictionary.has_key()=Bio.GenBank.NCBIDictionary-class.html#has_key,Method Bio.PDB.AbstractPropertyMap.AbstractPropertyMap.has_key()=Bio.PDB.AbstractPropertyMap.AbstractPropertyMap-class.html#has_key,Method Bio.PDB.FragmentMapper'.FragmentMapper.has_key()=Bio.PDB.FragmentMapper%27.FragmentMapper-class.html#has_key,Method Bio.Prosite.ExPASyDictionary.has_key()=Bio.Prosite.ExPASyDictionary-class.html#has_key,Method Bio.Prosite.Prodoc.ExPASyDictionary.has_key()=Bio.Prosite.Prodoc.ExPASyDictionary-class.html#has_key,Method Bio.PubMed.Dictionary.has_key()=Bio.PubMed.Dictionary-class.html#has_key,Method Bio.SwissProt.SProt.ExPASyDictionary.has_key()=Bio.SwissProt.SProt.ExPASyDictionary-class.html#has_key,Method Martel.Parser.MartelAttributeList.has_key()=Martel.Parser.MartelAttributeList-class.html#has_key"><a title="Bio.Crystal.Crystal.has_key
Bio.EUtils.POM.ElementNode.has_key
Bio.GenBank.NCBIDictionary.has_key
Bio.PDB.AbstractPropertyMap.AbstractPropertyMap.has_key
Bio.PDB.FragmentMapper'.FragmentMapper.has_key
Bio.Prosite.ExPASyDictionary.has_key
Bio.Prosite.Prodoc.ExPASyDictionary.has_key
Bio.PubMed.Dictionary.has_key
Bio.SwissProt.SProt.ExPASyDictionary.has_key
Martel.Parser.MartelAttributeList.has_key" class="py-name" href="#" onclick="return doclink('link-80', 'has_key', 'link-80');">has_key</a></tt><tt class="py-op">(</tt><tt id="link-81" class="py-name"><a title="Bio.Emboss.primer3_format.record
Bio.Emboss.primersearch_format.record
Bio.GFF.Feature.record
Bio.LocusLink.web_parse.record
Bio.Ndb.record
Bio.Std.record
Bio.expressions.blocks.record
Bio.expressions.embl.embl65.record
Bio.expressions.fasta.record
Bio.expressions.genbank.record
Bio.expressions.hmmpfam.record
Bio.expressions.swissprot.ipi.record
Bio.expressions.swissprot.speclist.record
Bio.expressions.swissprot.sprot38.record
Bio.expressions.swissprot.sprot40.record
Martel.test.test_swissprot38.record
Martel.test.testformats.swissprot38.record" class="py-name" href="#" onclick="return doclink('link-81', 'record', 'link-63');">record</a></tt><tt class="py-op">.</tt><tt class="py-name">sunid</tt><tt class="py-op">)</tt> <tt class="py-op">:</tt> </tt>
<a name="L221"></a><tt class="py-lineno">221</tt> <tt class="py-line"> <tt class="py-keyword">print</tt> <tt id="link-82" class="py-name"><a title="Bio.Emboss.primer3_format.record
Bio.Emboss.primersearch_format.record
Bio.GFF.Feature.record
Bio.LocusLink.web_parse.record
Bio.Ndb.record
Bio.Std.record
Bio.expressions.blocks.record
Bio.expressions.embl.embl65.record
Bio.expressions.fasta.record
Bio.expressions.genbank.record
Bio.expressions.hmmpfam.record
Bio.expressions.swissprot.ipi.record
Bio.expressions.swissprot.speclist.record
Bio.expressions.swissprot.sprot38.record
Bio.expressions.swissprot.sprot40.record
Martel.test.test_swissprot38.record
Martel.test.testformats.swissprot38.record" class="py-name" href="#" onclick="return doclink('link-82', 'record', 'link-63');">record</a></tt><tt class="py-op">.</tt><tt class="py-name">sunid</tt> </tt>
<a name="L222"></a><tt class="py-lineno">222</tt> <tt class="py-line"> </tt>
<a name="L223"></a><tt class="py-lineno">223</tt> <tt class="py-line"> <tt class="py-name">n</tt> <tt class="py-op">=</tt> <tt class="py-name">sunidDict</tt><tt class="py-op">[</tt><tt id="link-83" class="py-name"><a title="Bio.Emboss.primer3_format.record
Bio.Emboss.primersearch_format.record
Bio.GFF.Feature.record
Bio.LocusLink.web_parse.record
Bio.Ndb.record
Bio.Std.record
Bio.expressions.blocks.record
Bio.expressions.embl.embl65.record
Bio.expressions.fasta.record
Bio.expressions.genbank.record
Bio.expressions.hmmpfam.record
Bio.expressions.swissprot.ipi.record
Bio.expressions.swissprot.speclist.record
Bio.expressions.swissprot.sprot38.record
Bio.expressions.swissprot.sprot40.record
Martel.test.test_swissprot38.record
Martel.test.testformats.swissprot38.record" class="py-name" href="#" onclick="return doclink('link-83', 'record', 'link-63');">record</a></tt><tt class="py-op">.</tt><tt class="py-name">sunid</tt><tt class="py-op">]</tt> </tt>
<a name="L224"></a><tt class="py-lineno">224</tt> <tt class="py-line"> </tt>
<a name="L225"></a><tt class="py-lineno">225</tt> <tt class="py-line"> <tt class="py-keyword">if</tt> <tt id="link-84" class="py-name"><a title="Bio.Emboss.primer3_format.record
Bio.Emboss.primersearch_format.record
Bio.GFF.Feature.record
Bio.LocusLink.web_parse.record
Bio.Ndb.record
Bio.Std.record
Bio.expressions.blocks.record
Bio.expressions.embl.embl65.record
Bio.expressions.fasta.record
Bio.expressions.genbank.record
Bio.expressions.hmmpfam.record
Bio.expressions.swissprot.ipi.record
Bio.expressions.swissprot.speclist.record
Bio.expressions.swissprot.sprot38.record
Bio.expressions.swissprot.sprot40.record
Martel.test.test_swissprot38.record
Martel.test.testformats.swissprot38.record" class="py-name" href="#" onclick="return doclink('link-84', 'record', 'link-63');">record</a></tt><tt class="py-op">.</tt><tt class="py-name">parent</tt> <tt class="py-op">!=</tt> <tt class="py-string">''</tt> <tt class="py-op">:</tt> <tt class="py-comment"># Not root node</tt> </tt>
<a name="L226"></a><tt class="py-lineno">226</tt> <tt class="py-line"> </tt>
<a name="L227"></a><tt class="py-lineno">227</tt> <tt class="py-line"> <tt class="py-keyword">if</tt> <tt class="py-keyword">not</tt> <tt class="py-name">sunidDict</tt><tt class="py-op">.</tt><tt id="link-85" class="py-name"><a title="Bio.Crystal.Crystal.has_key
Bio.EUtils.POM.ElementNode.has_key
Bio.GenBank.NCBIDictionary.has_key
Bio.PDB.AbstractPropertyMap.AbstractPropertyMap.has_key
Bio.PDB.FragmentMapper'.FragmentMapper.has_key
Bio.Prosite.ExPASyDictionary.has_key
Bio.Prosite.Prodoc.ExPASyDictionary.has_key
Bio.PubMed.Dictionary.has_key
Bio.SwissProt.SProt.ExPASyDictionary.has_key
Martel.Parser.MartelAttributeList.has_key" class="py-name" href="#" onclick="return doclink('link-85', 'has_key', 'link-80');">has_key</a></tt><tt class="py-op">(</tt><tt id="link-86" class="py-name"><a title="Bio.Emboss.primer3_format.record
Bio.Emboss.primersearch_format.record
Bio.GFF.Feature.record
Bio.LocusLink.web_parse.record
Bio.Ndb.record
Bio.Std.record
Bio.expressions.blocks.record
Bio.expressions.embl.embl65.record
Bio.expressions.fasta.record
Bio.expressions.genbank.record
Bio.expressions.hmmpfam.record
Bio.expressions.swissprot.ipi.record
Bio.expressions.swissprot.speclist.record
Bio.expressions.swissprot.sprot38.record
Bio.expressions.swissprot.sprot40.record
Martel.test.test_swissprot38.record
Martel.test.testformats.swissprot38.record" class="py-name" href="#" onclick="return doclink('link-86', 'record', 'link-63');">record</a></tt><tt class="py-op">.</tt><tt class="py-name">parent</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
<a name="L228"></a><tt class="py-lineno">228</tt> <tt class="py-line"> <tt class="py-keyword">raise</tt> <tt class="py-name">ValueError</tt><tt class="py-op">,</tt> <tt class="py-string">"Incomplete data?"</tt> </tt>
<a name="L229"></a><tt class="py-lineno">229</tt> <tt class="py-line"> </tt>
<a name="L230"></a><tt class="py-lineno">230</tt> <tt class="py-line"> <tt class="py-name">n</tt><tt class="py-op">.</tt><tt class="py-name">parent</tt> <tt class="py-op">=</tt> <tt class="py-name">sunidDict</tt><tt class="py-op">[</tt><tt id="link-87" class="py-name"><a title="Bio.Emboss.primer3_format.record
Bio.Emboss.primersearch_format.record
Bio.GFF.Feature.record
Bio.LocusLink.web_parse.record
Bio.Ndb.record
Bio.Std.record
Bio.expressions.blocks.record
Bio.expressions.embl.embl65.record
Bio.expressions.fasta.record
Bio.expressions.genbank.record
Bio.expressions.hmmpfam.record
Bio.expressions.swissprot.ipi.record
Bio.expressions.swissprot.speclist.record
Bio.expressions.swissprot.sprot38.record
Bio.expressions.swissprot.sprot40.record
Martel.test.test_swissprot38.record
Martel.test.testformats.swissprot38.record" class="py-name" href="#" onclick="return doclink('link-87', 'record', 'link-63');">record</a></tt><tt class="py-op">.</tt><tt class="py-name">parent</tt><tt class="py-op">]</tt> </tt>
<a name="L231"></a><tt class="py-lineno">231</tt> <tt class="py-line"> </tt>
<a name="L232"></a><tt class="py-lineno">232</tt> <tt class="py-line"> <tt class="py-keyword">for</tt> <tt class="py-name">c</tt> <tt class="py-keyword">in</tt> <tt id="link-88" class="py-name"><a title="Bio.Emboss.primer3_format.record
Bio.Emboss.primersearch_format.record
Bio.GFF.Feature.record
Bio.LocusLink.web_parse.record
Bio.Ndb.record
Bio.Std.record
Bio.expressions.blocks.record
Bio.expressions.embl.embl65.record
Bio.expressions.fasta.record
Bio.expressions.genbank.record
Bio.expressions.hmmpfam.record
Bio.expressions.swissprot.ipi.record
Bio.expressions.swissprot.speclist.record
Bio.expressions.swissprot.sprot38.record
Bio.expressions.swissprot.sprot40.record
Martel.test.test_swissprot38.record
Martel.test.testformats.swissprot38.record" class="py-name" href="#" onclick="return doclink('link-88', 'record', 'link-63');">record</a></tt><tt class="py-op">.</tt><tt id="link-89" class="py-name" targets="Method Bio.Pathway.Rep.Graph.Graph.children()=Bio.Pathway.Rep.Graph.Graph-class.html#children,Method Bio.Pathway.Rep.MultiGraph.MultiGraph.children()=Bio.Pathway.Rep.MultiGraph.MultiGraph-class.html#children"><a title="Bio.Pathway.Rep.Graph.Graph.children
Bio.Pathway.Rep.MultiGraph.MultiGraph.children" class="py-name" href="#" onclick="return doclink('link-89', 'children', 'link-89');">children</a></tt><tt class="py-op">:</tt> </tt>
<a name="L233"></a><tt class="py-lineno">233</tt> <tt class="py-line"> <tt class="py-keyword">if</tt> <tt class="py-keyword">not</tt> <tt class="py-name">sunidDict</tt><tt class="py-op">.</tt><tt id="link-90" class="py-name"><a title="Bio.Crystal.Crystal.has_key
Bio.EUtils.POM.ElementNode.has_key
Bio.GenBank.NCBIDictionary.has_key
Bio.PDB.AbstractPropertyMap.AbstractPropertyMap.has_key
Bio.PDB.FragmentMapper'.FragmentMapper.has_key
Bio.Prosite.ExPASyDictionary.has_key
Bio.Prosite.Prodoc.ExPASyDictionary.has_key
Bio.PubMed.Dictionary.has_key
Bio.SwissProt.SProt.ExPASyDictionary.has_key
Martel.Parser.MartelAttributeList.has_key" class="py-name" href="#" onclick="return doclink('link-90', 'has_key', 'link-80');">has_key</a></tt><tt class="py-op">(</tt><tt class="py-name">c</tt><tt class="py-op">)</tt> <tt class="py-op">:</tt> </tt>
<a name="L234"></a><tt class="py-lineno">234</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">"Incomplete data?"</tt> </tt>
<a name="L235"></a><tt class="py-lineno">235</tt> <tt class="py-line"> <tt class="py-name">n</tt><tt class="py-op">.</tt><tt id="link-91" class="py-name"><a title="Bio.Pathway.Rep.Graph.Graph.children
Bio.Pathway.Rep.MultiGraph.MultiGraph.children" class="py-name" href="#" onclick="return doclink('link-91', 'children', 'link-89');">children</a></tt><tt class="py-op">.</tt><tt id="link-92" 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-92', 'append', 'link-68');">append</a></tt><tt class="py-op">(</tt><tt class="py-name">sunidDict</tt><tt class="py-op">[</tt><tt class="py-name">c</tt><tt class="py-op">]</tt><tt class="py-op">)</tt> </tt>
<a name="L236"></a><tt class="py-lineno">236</tt> <tt class="py-line"> </tt>
<a name="L237"></a><tt class="py-lineno">237</tt> <tt class="py-line"> </tt>
<a name="L238"></a><tt class="py-lineno">238</tt> <tt class="py-line"> <tt class="py-comment"># Fill in the gaps with information from the CLA file</tt> </tt>
<a name="L239"></a><tt class="py-lineno">239</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-name">sidDict</tt> <tt class="py-op">=</tt> <tt class="py-op">{</tt><tt class="py-op">}</tt> </tt>
<a name="L240"></a><tt class="py-lineno">240</tt> <tt class="py-line"> <tt class="py-name">records</tt> <tt class="py-op">=</tt> <tt id="link-93" class="py-name"><a title="Bio.SCOP.Cla" class="py-name" href="#" onclick="return doclink('link-93', 'Cla', 'link-1');">Cla</a></tt><tt class="py-op">.</tt><tt id="link-94" class="py-name"><a title="Bio.Affy.CelFile.CelParser.parse
Bio.AlignAce.Parser.AlignAceParser.parse
Bio.AlignAce.Parser.CompareAceParser.parse
Bio.AlignIO.parse
Bio.Blast.NCBIStandalone.BlastErrorParser.parse
Bio.Blast.NCBIStandalone.BlastParser.parse
Bio.Blast.NCBIStandalone.PSIBlastParser.parse
Bio.Blast.NCBIWWW.BlastParser.parse
Bio.Blast.NCBIXML.BlastParser.parse
Bio.Blast.NCBIXML.parse
Bio.CDD.RecordParser.parse
Bio.Compass.RecordParser.parse
Bio.Decode.parse
Bio.ECell.RecordParser.parse
Bio.EUtils.POM.POMDocument.parse
Bio.EUtils.parse
Bio.Emboss.Primer.Primer3Parser.parse
Bio.Emboss.Primer.PrimerSearchParser.parse
Bio.Enzyme.RecordParser.parse
Bio.Fasta.RecordParser.parse
Bio.Fasta.SequenceParser.parse
Bio.GenBank.FeatureParser.parse
Bio.GenBank.LocationParser.parse
Bio.GenBank.RecordParser.parse
Bio.GenBank.Scanner.InsdcScanner.parse
Bio.Geo.parse
Bio.Gobase.RecordParser.parse
Bio.IntelliGenetics.RecordParser.parse
Bio.InterPro.InterProParser.parse
Bio.KEGG.Compound.parse
Bio.KEGG.Enzyme.parse
Bio.KEGG.Map.parse
Bio.LocusLink.RecordParser.parse
Bio.LocusLink.web_parse.LocusLinkParser.parse
Bio.MEME.Parser.MASTParser.parse
Bio.MEME.Parser.MEMEParser.parse
Bio.Medline.RecordParser.parse
Bio.MetaTool.RecordParser.parse
Bio.NBRF.RecordParser.parse
Bio.Ndb.NdbParser.parse
Bio.ParserSupport.AbstractParser.parse
Bio.Parsers.spark.GenericParser.parse
Bio.PopGen.FDist.RecordParser.parse
Bio.PopGen.GenePop.RecordParser.parse
Bio.PopGen.GenePop.parse
Bio.Prosite.Prodoc.RecordParser.parse
Bio.Prosite.Prodoc.parse
Bio.Prosite.RecordParser.parse
Bio.Prosite.parse
Bio.Rebase.RecordParser.parse
Bio.SCOP.Cla.Parser.parse
Bio.SCOP.Cla.parse
Bio.SCOP.Des.Parser.parse
Bio.SCOP.Des.parse
Bio.SCOP.Dom.Parser.parse
Bio.SCOP.Dom.parse
Bio.SCOP.Hie.Parser.parse
Bio.SCOP.Hie.parse
Bio.SCOP.Raf.Parser.parse
Bio.SCOP.Raf.parse
Bio.Saf.RecordParser.parse
Bio.SeqIO.parse
Bio.Sequencing.Ace.ACEParser.parse
Bio.Sequencing.Ace.RecordParser.parse
Bio.Sequencing.Phd.RecordParser.parse
Bio.SwissProt.KeyWList.ListParser.parse
Bio.SwissProt.KeyWList.parse
Bio.SwissProt.SProt.RecordParser.parse
Bio.SwissProt.SProt.SequenceParser.parse
Bio.SwissProt.parse
Bio.UniGene.RecordParser.parse
Bio.Wise.psw.parse
Martel.Parser.HeaderFooterParser.parse
Martel.Parser.Parser.parse
Martel.Parser.RecordParser.parse
Martel.msre_parse.parse" class="py-name" href="#" onclick="return doclink('link-94', 'parse', 'link-62');">parse</a></tt><tt class="py-op">(</tt><tt class="py-name">cla_handle</tt><tt class="py-op">)</tt> </tt>
<a name="L241"></a><tt class="py-lineno">241</tt> <tt class="py-line"> <tt class="py-keyword">for</tt> <tt id="link-95" class="py-name"><a title="Bio.Emboss.primer3_format.record
Bio.Emboss.primersearch_format.record
Bio.GFF.Feature.record
Bio.LocusLink.web_parse.record
Bio.Ndb.record
Bio.Std.record
Bio.expressions.blocks.record
Bio.expressions.embl.embl65.record
Bio.expressions.fasta.record
Bio.expressions.genbank.record
Bio.expressions.hmmpfam.record
Bio.expressions.swissprot.ipi.record
Bio.expressions.swissprot.speclist.record
Bio.expressions.swissprot.sprot38.record
Bio.expressions.swissprot.sprot40.record
Martel.test.test_swissprot38.record
Martel.test.testformats.swissprot38.record" class="py-name" href="#" onclick="return doclink('link-95', 'record', 'link-63');">record</a></tt> <tt class="py-keyword">in</tt> <tt class="py-name">records</tt><tt class="py-op">:</tt> </tt>
<a name="L242"></a><tt class="py-lineno">242</tt> <tt class="py-line"> <tt class="py-name">n</tt> <tt class="py-op">=</tt> <tt class="py-name">sunidDict</tt><tt class="py-op">[</tt><tt id="link-96" class="py-name"><a title="Bio.Emboss.primer3_format.record
Bio.Emboss.primersearch_format.record
Bio.GFF.Feature.record
Bio.LocusLink.web_parse.record
Bio.Ndb.record
Bio.Std.record
Bio.expressions.blocks.record
Bio.expressions.embl.embl65.record
Bio.expressions.fasta.record
Bio.expressions.genbank.record
Bio.expressions.hmmpfam.record
Bio.expressions.swissprot.ipi.record
Bio.expressions.swissprot.speclist.record
Bio.expressions.swissprot.sprot38.record
Bio.expressions.swissprot.sprot40.record
Martel.test.test_swissprot38.record
Martel.test.testformats.swissprot38.record" class="py-name" href="#" onclick="return doclink('link-96', 'record', 'link-63');">record</a></tt><tt class="py-op">.</tt><tt class="py-name">sunid</tt><tt class="py-op">]</tt> </tt>
<a name="L243"></a><tt class="py-lineno">243</tt> <tt class="py-line"> <tt class="py-keyword">assert</tt> <tt class="py-name">n</tt><tt class="py-op">.</tt><tt class="py-name">sccs</tt> <tt class="py-op">==</tt> <tt id="link-97" class="py-name"><a title="Bio.Emboss.primer3_format.record
Bio.Emboss.primersearch_format.record
Bio.GFF.Feature.record
Bio.LocusLink.web_parse.record
Bio.Ndb.record
Bio.Std.record
Bio.expressions.blocks.record
Bio.expressions.embl.embl65.record
Bio.expressions.fasta.record
Bio.expressions.genbank.record
Bio.expressions.hmmpfam.record
Bio.expressions.swissprot.ipi.record
Bio.expressions.swissprot.speclist.record
Bio.expressions.swissprot.sprot38.record
Bio.expressions.swissprot.sprot40.record
Martel.test.test_swissprot38.record
Martel.test.testformats.swissprot38.record" class="py-name" href="#" onclick="return doclink('link-97', 'record', 'link-63');">record</a></tt><tt class="py-op">.</tt><tt class="py-name">sccs</tt> </tt>
<a name="L244"></a><tt class="py-lineno">244</tt> <tt class="py-line"> <tt class="py-keyword">assert</tt> <tt class="py-name">n</tt><tt class="py-op">.</tt><tt class="py-name">sid</tt> <tt class="py-op">==</tt> <tt id="link-98" class="py-name"><a title="Bio.Emboss.primer3_format.record
Bio.Emboss.primersearch_format.record
Bio.GFF.Feature.record
Bio.LocusLink.web_parse.record
Bio.Ndb.record
Bio.Std.record
Bio.expressions.blocks.record
Bio.expressions.embl.embl65.record
Bio.expressions.fasta.record
Bio.expressions.genbank.record
Bio.expressions.hmmpfam.record
Bio.expressions.swissprot.ipi.record
Bio.expressions.swissprot.speclist.record
Bio.expressions.swissprot.sprot38.record
Bio.expressions.swissprot.sprot40.record
Martel.test.test_swissprot38.record
Martel.test.testformats.swissprot38.record" class="py-name" href="#" onclick="return doclink('link-98', 'record', 'link-63');">record</a></tt><tt class="py-op">.</tt><tt class="py-name">sid</tt> </tt>
<a name="L245"></a><tt class="py-lineno">245</tt> <tt class="py-line"> <tt class="py-name">n</tt><tt class="py-op">.</tt><tt class="py-name">residues</tt> <tt class="py-op">=</tt> <tt id="link-99" class="py-name"><a title="Bio.Emboss.primer3_format.record
Bio.Emboss.primersearch_format.record
Bio.GFF.Feature.record
Bio.LocusLink.web_parse.record
Bio.Ndb.record
Bio.Std.record
Bio.expressions.blocks.record
Bio.expressions.embl.embl65.record
Bio.expressions.fasta.record
Bio.expressions.genbank.record
Bio.expressions.hmmpfam.record
Bio.expressions.swissprot.ipi.record
Bio.expressions.swissprot.speclist.record
Bio.expressions.swissprot.sprot38.record
Bio.expressions.swissprot.sprot40.record
Martel.test.test_swissprot38.record
Martel.test.testformats.swissprot38.record" class="py-name" href="#" onclick="return doclink('link-99', 'record', 'link-63');">record</a></tt><tt class="py-op">.</tt><tt class="py-name">residues</tt> </tt>
<a name="L246"></a><tt class="py-lineno">246</tt> <tt class="py-line"> <tt class="py-name">sidDict</tt><tt class="py-op">[</tt><tt class="py-name">n</tt><tt class="py-op">.</tt><tt class="py-name">sid</tt><tt class="py-op">]</tt> <tt class="py-op">=</tt> <tt class="py-name">n</tt> </tt>
<a name="L247"></a><tt class="py-lineno">247</tt> <tt class="py-line"> </tt>
<a name="L248"></a><tt class="py-lineno">248</tt> <tt class="py-line"> <tt class="py-comment"># Clean up</tt> </tt>
<a name="L249"></a><tt class="py-lineno">249</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">_sunidDict</tt> <tt class="py-op">=</tt> <tt class="py-name">sunidDict</tt> </tt>
<a name="L250"></a><tt class="py-lineno">250</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">_sidDict</tt> <tt class="py-op">=</tt> <tt class="py-name">sidDict</tt> </tt>
<a name="L251"></a><tt class="py-lineno">251</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">_domains</tt> <tt class="py-op">=</tt> <tt class="py-name">tuple</tt><tt class="py-op">(</tt><tt class="py-name">domains</tt><tt class="py-op">)</tt> </tt>
<a name="L252"></a><tt class="py-lineno">252</tt> <tt class="py-line"> </tt>
<a name="L253"></a><tt class="py-lineno">253</tt> <tt class="py-line"> <tt class="py-keyword">finally</tt><tt class="py-op">:</tt> </tt>
<a name="L254"></a><tt class="py-lineno">254</tt> <tt class="py-line"> <tt class="py-keyword">if</tt> <tt class="py-name">dir_path</tt> <tt class="py-op">:</tt> </tt>
<a name="L255"></a><tt class="py-lineno">255</tt> <tt class="py-line"> <tt class="py-comment"># If we opened the files, we close the files</tt> </tt>
<a name="L256"></a><tt class="py-lineno">256</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-keyword">if</tt> <tt class="py-name">cla_handle</tt> <tt class="py-op">:</tt> <tt class="py-name">cla_handle</tt><tt class="py-op">.</tt><tt id="link-100" 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-100', 'close', 'link-100');">close</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
<a name="L257"></a><tt class="py-lineno">257</tt> <tt class="py-line"> <tt class="py-keyword">if</tt> <tt class="py-name">des_handle</tt> <tt class="py-op">:</tt> <tt class="py-name">des_handle</tt><tt class="py-op">.</tt><tt id="link-101" class="py-name"><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-101', 'close', 'link-100');">close</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
<a name="L258"></a><tt class="py-lineno">258</tt> <tt class="py-line"> <tt class="py-keyword">if</tt> <tt class="py-name">hie_handle</tt> <tt class="py-op">:</tt> <tt class="py-name">hie_handle</tt><tt class="py-op">.</tt><tt id="link-102" class="py-name"><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-102', 'close', 'link-100');">close</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
</div><a name="L259"></a><tt class="py-lineno">259</tt> <tt class="py-line"> </tt>
<a name="L260"></a><tt class="py-lineno">260</tt> <tt class="py-line"> </tt>
<a name="Scop.getRoot"></a><div id="Scop.getRoot-def"><a name="L261"></a><tt class="py-lineno">261</tt> <a class="py-toggle" href="#" id="Scop.getRoot-toggle" onclick="return toggle('Scop.getRoot');">-</a><tt class="py-line"> <tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.SCOP.Scop-class.html#getRoot">getRoot</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="Scop.getRoot-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="Scop.getRoot-expanded"><a name="L262"></a><tt class="py-lineno">262</tt> <tt class="py-line"> <tt class="py-keyword">return</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-103" class="py-name" targets="Method Bio.SCOP.Scop.getNodeBySunid()=Bio.SCOP.Scop-class.html#getNodeBySunid"><a title="Bio.SCOP.Scop.getNodeBySunid" class="py-name" href="#" onclick="return doclink('link-103', 'getNodeBySunid', 'link-103');">getNodeBySunid</a></tt><tt class="py-op">(</tt><tt class="py-number">0</tt><tt class="py-op">)</tt> </tt>
</div><a name="L263"></a><tt class="py-lineno">263</tt> <tt class="py-line"> </tt>
<a name="L264"></a><tt class="py-lineno">264</tt> <tt class="py-line"> </tt>
<a name="Scop.getDomainBySid"></a><div id="Scop.getDomainBySid-def"><a name="L265"></a><tt class="py-lineno">265</tt> <a class="py-toggle" href="#" id="Scop.getDomainBySid-toggle" onclick="return toggle('Scop.getDomainBySid');">-</a><tt class="py-line"> <tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.SCOP.Scop-class.html#getDomainBySid">getDomainBySid</a><tt class="py-op">(</tt><tt class="py-param">self</tt><tt class="py-op">,</tt> <tt class="py-param">sid</tt><tt class="py-op">)</tt> <tt class="py-op">:</tt> </tt>
</div><div id="Scop.getDomainBySid-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="Scop.getDomainBySid-expanded"><a name="L266"></a><tt class="py-lineno">266</tt> <tt class="py-line"> <tt class="py-docstring">"""Return a domain from its sid"""</tt> </tt>
<a name="L267"></a><tt class="py-lineno">267</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">_sidDict</tt><tt class="py-op">.</tt><tt id="link-104" class="py-name"><a title="Bio.Crystal.Crystal.has_key
Bio.EUtils.POM.ElementNode.has_key
Bio.GenBank.NCBIDictionary.has_key
Bio.PDB.AbstractPropertyMap.AbstractPropertyMap.has_key
Bio.PDB.FragmentMapper'.FragmentMapper.has_key
Bio.Prosite.ExPASyDictionary.has_key
Bio.Prosite.Prodoc.ExPASyDictionary.has_key
Bio.PubMed.Dictionary.has_key
Bio.SwissProt.SProt.ExPASyDictionary.has_key
Martel.Parser.MartelAttributeList.has_key" class="py-name" href="#" onclick="return doclink('link-104', 'has_key', 'link-80');">has_key</a></tt><tt class="py-op">(</tt><tt class="py-name">sid</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
<a name="L268"></a><tt class="py-lineno">268</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">_sidDict</tt><tt class="py-op">[</tt><tt class="py-name">sid</tt><tt class="py-op">]</tt> </tt>
<a name="L269"></a><tt class="py-lineno">269</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">db_handle</tt><tt class="py-op">:</tt> </tt>
<a name="L270"></a><tt class="py-lineno">270</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-105" class="py-name" targets="Method Bio.SCOP.Scop.getDomainFromSQL()=Bio.SCOP.Scop-class.html#getDomainFromSQL"><a title="Bio.SCOP.Scop.getDomainFromSQL" class="py-name" href="#" onclick="return doclink('link-105', 'getDomainFromSQL', 'link-105');">getDomainFromSQL</a></tt><tt class="py-op">(</tt><tt class="py-name">sid</tt><tt class="py-op">=</tt><tt class="py-name">sid</tt><tt class="py-op">)</tt> </tt>
<a name="L271"></a><tt class="py-lineno">271</tt> <tt class="py-line"> <tt class="py-keyword">if</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">_sidDict</tt><tt class="py-op">.</tt><tt id="link-106" class="py-name"><a title="Bio.Crystal.Crystal.has_key
Bio.EUtils.POM.ElementNode.has_key
Bio.GenBank.NCBIDictionary.has_key
Bio.PDB.AbstractPropertyMap.AbstractPropertyMap.has_key
Bio.PDB.FragmentMapper'.FragmentMapper.has_key
Bio.Prosite.ExPASyDictionary.has_key
Bio.Prosite.Prodoc.ExPASyDictionary.has_key
Bio.PubMed.Dictionary.has_key
Bio.SwissProt.SProt.ExPASyDictionary.has_key
Martel.Parser.MartelAttributeList.has_key" class="py-name" href="#" onclick="return doclink('link-106', 'has_key', 'link-80');">has_key</a></tt><tt class="py-op">(</tt><tt class="py-name">sid</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
<a name="L272"></a><tt class="py-lineno">272</tt> <tt class="py-line"> <tt class="py-keyword">return</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">_sidDict</tt><tt class="py-op">[</tt><tt class="py-name">sid</tt><tt class="py-op">]</tt> </tt>
<a name="L273"></a><tt class="py-lineno">273</tt> <tt class="py-line"> <tt class="py-keyword">else</tt><tt class="py-op">:</tt> </tt>
<a name="L274"></a><tt class="py-lineno">274</tt> <tt class="py-line"> <tt class="py-keyword">return</tt> <tt class="py-name">None</tt> </tt>
</div><a name="L275"></a><tt class="py-lineno">275</tt> <tt class="py-line"> </tt>
<a name="L276"></a><tt class="py-lineno">276</tt> <tt class="py-line"> </tt>
<a name="Scop.getNodeBySunid"></a><div id="Scop.getNodeBySunid-def"><a name="L277"></a><tt class="py-lineno">277</tt> <a class="py-toggle" href="#" id="Scop.getNodeBySunid-toggle" onclick="return toggle('Scop.getNodeBySunid');">-</a><tt class="py-line"> <tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.SCOP.Scop-class.html#getNodeBySunid">getNodeBySunid</a><tt class="py-op">(</tt><tt class="py-param">self</tt><tt class="py-op">,</tt> <tt class="py-param">sunid</tt><tt class="py-op">)</tt> <tt class="py-op">:</tt> </tt>
</div><div id="Scop.getNodeBySunid-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="Scop.getNodeBySunid-expanded"><a name="L278"></a><tt class="py-lineno">278</tt> <tt class="py-line"> <tt class="py-docstring">"""Return a node from its sunid"""</tt> </tt>
<a name="L279"></a><tt class="py-lineno">279</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">_sunidDict</tt><tt class="py-op">.</tt><tt id="link-107" class="py-name"><a title="Bio.Crystal.Crystal.has_key
Bio.EUtils.POM.ElementNode.has_key
Bio.GenBank.NCBIDictionary.has_key
Bio.PDB.AbstractPropertyMap.AbstractPropertyMap.has_key
Bio.PDB.FragmentMapper'.FragmentMapper.has_key
Bio.Prosite.ExPASyDictionary.has_key
Bio.Prosite.Prodoc.ExPASyDictionary.has_key
Bio.PubMed.Dictionary.has_key
Bio.SwissProt.SProt.ExPASyDictionary.has_key
Martel.Parser.MartelAttributeList.has_key" class="py-name" href="#" onclick="return doclink('link-107', 'has_key', 'link-80');">has_key</a></tt><tt class="py-op">(</tt><tt class="py-name">sunid</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
<a name="L280"></a><tt class="py-lineno">280</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">_sunidDict</tt><tt class="py-op">[</tt><tt class="py-name">sunid</tt><tt class="py-op">]</tt> </tt>
<a name="L281"></a><tt class="py-lineno">281</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">db_handle</tt><tt class="py-op">:</tt> </tt>
<a name="L282"></a><tt class="py-lineno">282</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-108" class="py-name"><a title="Bio.SCOP.Scop.getDomainFromSQL" class="py-name" href="#" onclick="return doclink('link-108', 'getDomainFromSQL', 'link-105');">getDomainFromSQL</a></tt><tt class="py-op">(</tt><tt class="py-name">sunid</tt><tt class="py-op">=</tt><tt class="py-name">sunid</tt><tt class="py-op">)</tt> </tt>
<a name="L283"></a><tt class="py-lineno">283</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">_sunidDict</tt><tt class="py-op">.</tt><tt id="link-109" class="py-name"><a title="Bio.Crystal.Crystal.has_key
Bio.EUtils.POM.ElementNode.has_key
Bio.GenBank.NCBIDictionary.has_key
Bio.PDB.AbstractPropertyMap.AbstractPropertyMap.has_key
Bio.PDB.FragmentMapper'.FragmentMapper.has_key
Bio.Prosite.ExPASyDictionary.has_key
Bio.Prosite.Prodoc.ExPASyDictionary.has_key
Bio.PubMed.Dictionary.has_key
Bio.SwissProt.SProt.ExPASyDictionary.has_key
Martel.Parser.MartelAttributeList.has_key" class="py-name" href="#" onclick="return doclink('link-109', 'has_key', 'link-80');">has_key</a></tt><tt class="py-op">(</tt><tt class="py-name">sunid</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
<a name="L284"></a><tt class="py-lineno">284</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">_sunidDict</tt><tt class="py-op">[</tt><tt class="py-name">sunid</tt><tt class="py-op">]</tt> </tt>
<a name="L285"></a><tt class="py-lineno">285</tt> <tt class="py-line"> <tt class="py-keyword">else</tt><tt class="py-op">:</tt> </tt>
<a name="L286"></a><tt class="py-lineno">286</tt> <tt class="py-line"> <tt class="py-keyword">return</tt> <tt class="py-name">None</tt> </tt>
</div><a name="L287"></a><tt class="py-lineno">287</tt> <tt class="py-line"> </tt>
<a name="L288"></a><tt class="py-lineno">288</tt> <tt class="py-line"> </tt>
<a name="Scop.getDomains"></a><div id="Scop.getDomains-def"><a name="L289"></a><tt class="py-lineno">289</tt> <a class="py-toggle" href="#" id="Scop.getDomains-toggle" onclick="return toggle('Scop.getDomains');">-</a><tt class="py-line"> <tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.SCOP.Scop-class.html#getDomains">getDomains</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="Scop.getDomains-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="Scop.getDomains-expanded"><a name="L290"></a><tt class="py-lineno">290</tt> <tt class="py-line"> <tt class="py-docstring">"""Returns an ordered tuple of all SCOP Domains"""</tt> </tt>
<a name="L291"></a><tt class="py-lineno">291</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">db_handle</tt><tt class="py-op">:</tt> </tt>
<a name="L292"></a><tt class="py-lineno">292</tt> <tt class="py-line"> <tt class="py-keyword">return</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-110" class="py-name" targets="Method Bio.SCOP.Scop.getRoot()=Bio.SCOP.Scop-class.html#getRoot"><a title="Bio.SCOP.Scop.getRoot" class="py-name" href="#" onclick="return doclink('link-110', 'getRoot', 'link-110');">getRoot</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt><tt class="py-op">.</tt><tt id="link-111" class="py-name" targets="Method Bio.SCOP.Node.getDescendents()=Bio.SCOP.Node-class.html#getDescendents"><a title="Bio.SCOP.Node.getDescendents" class="py-name" href="#" onclick="return doclink('link-111', 'getDescendents', 'link-111');">getDescendents</a></tt><tt class="py-op">(</tt><tt class="py-string">'px'</tt><tt class="py-op">)</tt> </tt>
<a name="L293"></a><tt class="py-lineno">293</tt> <tt class="py-line"> <tt class="py-keyword">else</tt><tt class="py-op">:</tt> </tt>
<a name="L294"></a><tt class="py-lineno">294</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">_domains</tt> </tt>
</div><a name="L295"></a><tt class="py-lineno">295</tt> <tt class="py-line"> </tt>
<a name="L296"></a><tt class="py-lineno">296</tt> <tt class="py-line"> </tt>
<a name="L297"></a><tt class="py-lineno">297</tt> <tt class="py-line"> </tt>
<a name="Scop.write_hie"></a><div id="Scop.write_hie-def"><a name="L298"></a><tt class="py-lineno">298</tt> <a class="py-toggle" href="#" id="Scop.write_hie-toggle" onclick="return toggle('Scop.write_hie');">-</a><tt class="py-line"> <tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.SCOP.Scop-class.html#write_hie">write_hie</a><tt class="py-op">(</tt><tt class="py-param">self</tt><tt class="py-op">,</tt> <tt class="py-param">handle</tt><tt class="py-op">)</tt> <tt class="py-op">:</tt> </tt>
</div><div id="Scop.write_hie-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="Scop.write_hie-expanded"><a name="L299"></a><tt class="py-lineno">299</tt> <tt class="py-line"> <tt class="py-docstring">"""Build an HIE SCOP parsable file from this object"""</tt> </tt>
<a name="L300"></a><tt class="py-lineno">300</tt> <tt class="py-line"> <tt id="link-112" class="py-name" targets="Method Bio.Pathway.Rep.Graph.Graph.nodes()=Bio.Pathway.Rep.Graph.Graph-class.html#nodes,Method Bio.Pathway.Rep.MultiGraph.MultiGraph.nodes()=Bio.Pathway.Rep.MultiGraph.MultiGraph-class.html#nodes"><a title="Bio.Pathway.Rep.Graph.Graph.nodes
Bio.Pathway.Rep.MultiGraph.MultiGraph.nodes" class="py-name" href="#" onclick="return doclink('link-112', 'nodes', 'link-112');">nodes</a></tt> <tt class="py-op">=</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">_sunidDict</tt><tt class="py-op">.</tt><tt id="link-113" class="py-name" targets="Method Bio.Crystal.Crystal.values()=Bio.Crystal.Crystal-class.html#values,Method Bio.EUtils.MultiDict._BaseMultiDict.values()=Bio.EUtils.MultiDict._BaseMultiDict-class.html#values,Method Bio.GenBank.NCBIDictionary.values()=Bio.GenBank.NCBIDictionary-class.html#values,Method Bio.Mindy.BaseDB.DictLookup.values()=Bio.Mindy.BaseDB.DictLookup-class.html#values,Method Bio.Prosite.ExPASyDictionary.values()=Bio.Prosite.ExPASyDictionary-class.html#values,Method Bio.Prosite.Prodoc.ExPASyDictionary.values()=Bio.Prosite.Prodoc.ExPASyDictionary-class.html#values,Method Bio.PubMed.Dictionary.values()=Bio.PubMed.Dictionary-class.html#values,Method Bio.SwissProt.SProt.ExPASyDictionary.values()=Bio.SwissProt.SProt.ExPASyDictionary-class.html#values,Method Bio.config.Registry.Registry.values()=Bio.config.Registry.Registry-class.html#values,Method BioSQL.BioSeqDatabase.BioSeqDatabase.values()=BioSQL.BioSeqDatabase.BioSeqDatabase-class.html#values,Method BioSQL.BioSeqDatabase.DBServer.values()=BioSQL.BioSeqDatabase.DBServer-class.html#values,Method Martel.Parser.MartelAttributeList.values()=Martel.Parser.MartelAttributeList-class.html#values"><a title="Bio.Crystal.Crystal.values
Bio.EUtils.MultiDict._BaseMultiDict.values
Bio.GenBank.NCBIDictionary.values
Bio.Mindy.BaseDB.DictLookup.values
Bio.Prosite.ExPASyDictionary.values
Bio.Prosite.Prodoc.ExPASyDictionary.values
Bio.PubMed.Dictionary.values
Bio.SwissProt.SProt.ExPASyDictionary.values
Bio.config.Registry.Registry.values
BioSQL.BioSeqDatabase.BioSeqDatabase.values
BioSQL.BioSeqDatabase.DBServer.values
Martel.Parser.MartelAttributeList.values" class="py-name" href="#" onclick="return doclink('link-113', 'values', 'link-113');">values</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
<a name="L301"></a><tt class="py-lineno">301</tt> <tt class="py-line"> <tt class="py-comment"># We order nodes to ease comparison with original file</tt> </tt>
<a name="L302"></a><tt class="py-lineno">302</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt id="link-114" class="py-name"><a title="Bio.Pathway.Rep.Graph.Graph.nodes
Bio.Pathway.Rep.MultiGraph.MultiGraph.nodes" class="py-name" href="#" onclick="return doclink('link-114', 'nodes', 'link-112');">nodes</a></tt><tt class="py-op">.</tt><tt id="link-115" class="py-name" targets="Method Bio.PDB.Residue.DisorderedResidue.sort()=Bio.PDB.Residue.DisorderedResidue-class.html#sort,Method Bio.PDB.Residue.Residue.sort()=Bio.PDB.Residue.Residue-class.html#sort,Method Bio.Sequencing.Ace.ACEFileRecord.sort()=Bio.Sequencing.Ace.ACEFileRecord-class.html#sort"><a title="Bio.PDB.Residue.DisorderedResidue.sort
Bio.PDB.Residue.Residue.sort
Bio.Sequencing.Ace.ACEFileRecord.sort" class="py-name" href="#" onclick="return doclink('link-115', 'sort', 'link-115');">sort</a></tt><tt class="py-op">(</tt><tt class="py-keyword">lambda</tt> <tt id="link-116" class="py-name" targets="Variable Bio.PDB.Polypeptide.n1=Bio.PDB.Polypeptide-module.html#n1"><a title="Bio.PDB.Polypeptide.n1" class="py-name" href="#" onclick="return doclink('link-116', 'n1', 'link-116');">n1</a></tt><tt class="py-op">,</tt><tt class="py-name">n2</tt><tt class="py-op">:</tt> <tt class="py-name">cmp</tt><tt class="py-op">(</tt><tt id="link-117" class="py-name"><a title="Bio.PDB.Polypeptide.n1" class="py-name" href="#" onclick="return doclink('link-117', 'n1', 'link-116');">n1</a></tt><tt class="py-op">.</tt><tt class="py-name">sunid</tt><tt class="py-op">,</tt> <tt class="py-name">n2</tt><tt class="py-op">.</tt><tt class="py-name">sunid</tt><tt class="py-op">)</tt><tt class="py-op">)</tt> </tt>
<a name="L303"></a><tt class="py-lineno">303</tt> <tt class="py-line"> </tt>
<a name="L304"></a><tt class="py-lineno">304</tt> <tt class="py-line"> <tt class="py-keyword">for</tt> <tt class="py-name">n</tt> <tt class="py-keyword">in</tt> <tt id="link-118" class="py-name"><a title="Bio.Pathway.Rep.Graph.Graph.nodes
Bio.Pathway.Rep.MultiGraph.MultiGraph.nodes" class="py-name" href="#" onclick="return doclink('link-118', 'nodes', 'link-112');">nodes</a></tt> <tt class="py-op">:</tt> </tt>
<a name="L305"></a><tt class="py-lineno">305</tt> <tt class="py-line"> <tt id="link-119" class="py-name"><a title="Bio.LocusLink.web_parse.handle
Bio.Ndb.handle" class="py-name" href="#" onclick="return doclink('link-119', 'handle', 'link-48');">handle</a></tt><tt class="py-op">.</tt><tt id="link-120" class="py-name" targets="Method Bio.AlignAce.Motif.Motif.write()=Bio.AlignAce.Motif.Motif-class.html#write,Function Bio.AlignIO.write()=Bio.AlignIO-module.html#write,Method Bio.EUtils.sourcegen.SourceFile.write()=Bio.EUtils.sourcegen.SourceFile-class.html#write,Method Bio.EUtils.sourcegen.SourceGen.write()=Bio.EUtils.sourcegen.SourceGen-class.html#write,Method Bio.NeuralNetwork.Gene.Pattern.PatternIO.write()=Bio.NeuralNetwork.Gene.Pattern.PatternIO-class.html#write,Function Bio.SeqIO.write()=Bio.SeqIO-module.html#write,Method Bio.Writer.Writer.write()=Bio.Writer.Writer-class.html#write,Method Bio.writers.SeqRecord.embl.WriteEmbl.write()=Bio.writers.SeqRecord.embl.WriteEmbl-class.html#write,Method Bio.writers.SeqRecord.fasta.WriteFasta.write()=Bio.writers.SeqRecord.fasta.WriteFasta-class.html#write"><a title="Bio.AlignAce.Motif.Motif.write
Bio.AlignIO.write
Bio.EUtils.sourcegen.SourceFile.write
Bio.EUtils.sourcegen.SourceGen.write
Bio.NeuralNetwork.Gene.Pattern.PatternIO.write
Bio.SeqIO.write
Bio.Writer.Writer.write
Bio.writers.SeqRecord.embl.WriteEmbl.write
Bio.writers.SeqRecord.fasta.WriteFasta.write" class="py-name" href="#" onclick="return doclink('link-120', 'write', 'link-120');">write</a></tt><tt class="py-op">(</tt><tt class="py-name">str</tt><tt class="py-op">(</tt><tt class="py-name">n</tt><tt class="py-op">.</tt><tt id="link-121" class="py-name" targets="Method Bio.SCOP.Node.toHieRecord()=Bio.SCOP.Node-class.html#toHieRecord"><a title="Bio.SCOP.Node.toHieRecord" class="py-name" href="#" onclick="return doclink('link-121', 'toHieRecord', 'link-121');">toHieRecord</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt><tt class="py-op">)</tt><tt class="py-op">)</tt> </tt>
</div><a name="L306"></a><tt class="py-lineno">306</tt> <tt class="py-line"> </tt>
<a name="L307"></a><tt class="py-lineno">307</tt> <tt class="py-line"> </tt>
<a name="Scop.write_des"></a><div id="Scop.write_des-def"><a name="L308"></a><tt class="py-lineno">308</tt> <a class="py-toggle" href="#" id="Scop.write_des-toggle" onclick="return toggle('Scop.write_des');">-</a><tt class="py-line"> <tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.SCOP.Scop-class.html#write_des">write_des</a><tt class="py-op">(</tt><tt class="py-param">self</tt><tt class="py-op">,</tt> <tt class="py-param">handle</tt><tt class="py-op">)</tt> <tt class="py-op">:</tt> </tt>
</div><div id="Scop.write_des-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="Scop.write_des-expanded"><a name="L309"></a><tt class="py-lineno">309</tt> <tt class="py-line"> <tt class="py-docstring">"""Build a DES SCOP parsable file from this object"""</tt> </tt>
<a name="L310"></a><tt class="py-lineno">310</tt> <tt class="py-line"> <tt id="link-122" class="py-name"><a title="Bio.Pathway.Rep.Graph.Graph.nodes
Bio.Pathway.Rep.MultiGraph.MultiGraph.nodes" class="py-name" href="#" onclick="return doclink('link-122', 'nodes', 'link-112');">nodes</a></tt> <tt class="py-op">=</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">_sunidDict</tt><tt class="py-op">.</tt><tt id="link-123" class="py-name"><a title="Bio.Crystal.Crystal.values
Bio.EUtils.MultiDict._BaseMultiDict.values
Bio.GenBank.NCBIDictionary.values
Bio.Mindy.BaseDB.DictLookup.values
Bio.Prosite.ExPASyDictionary.values
Bio.Prosite.Prodoc.ExPASyDictionary.values
Bio.PubMed.Dictionary.values
Bio.SwissProt.SProt.ExPASyDictionary.values
Bio.config.Registry.Registry.values
BioSQL.BioSeqDatabase.BioSeqDatabase.values
BioSQL.BioSeqDatabase.DBServer.values
Martel.Parser.MartelAttributeList.values" class="py-name" href="#" onclick="return doclink('link-123', 'values', 'link-113');">values</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
<a name="L311"></a><tt class="py-lineno">311</tt> <tt class="py-line"> <tt class="py-comment"># Origional SCOP file is not ordered?</tt> </tt>
<a name="L312"></a><tt class="py-lineno">312</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt id="link-124" class="py-name"><a title="Bio.Pathway.Rep.Graph.Graph.nodes
Bio.Pathway.Rep.MultiGraph.MultiGraph.nodes" class="py-name" href="#" onclick="return doclink('link-124', 'nodes', 'link-112');">nodes</a></tt><tt class="py-op">.</tt><tt id="link-125" class="py-name"><a title="Bio.PDB.Residue.DisorderedResidue.sort
Bio.PDB.Residue.Residue.sort
Bio.Sequencing.Ace.ACEFileRecord.sort" class="py-name" href="#" onclick="return doclink('link-125', 'sort', 'link-115');">sort</a></tt><tt class="py-op">(</tt><tt class="py-keyword">lambda</tt> <tt id="link-126" class="py-name"><a title="Bio.PDB.Polypeptide.n1" class="py-name" href="#" onclick="return doclink('link-126', 'n1', 'link-116');">n1</a></tt><tt class="py-op">,</tt><tt class="py-name">n2</tt><tt class="py-op">:</tt> <tt class="py-name">cmp</tt><tt class="py-op">(</tt><tt id="link-127" class="py-name"><a title="Bio.PDB.Polypeptide.n1" class="py-name" href="#" onclick="return doclink('link-127', 'n1', 'link-116');">n1</a></tt><tt class="py-op">.</tt><tt class="py-name">sunid</tt><tt class="py-op">,</tt> <tt class="py-name">n2</tt><tt class="py-op">.</tt><tt class="py-name">sunid</tt><tt class="py-op">)</tt><tt class="py-op">)</tt> </tt>
<a name="L313"></a><tt class="py-lineno">313</tt> <tt class="py-line"> </tt>
<a name="L314"></a><tt class="py-lineno">314</tt> <tt class="py-line"> <tt class="py-keyword">for</tt> <tt class="py-name">n</tt> <tt class="py-keyword">in</tt> <tt id="link-128" class="py-name"><a title="Bio.Pathway.Rep.Graph.Graph.nodes
Bio.Pathway.Rep.MultiGraph.MultiGraph.nodes" class="py-name" href="#" onclick="return doclink('link-128', 'nodes', 'link-112');">nodes</a></tt> <tt class="py-op">:</tt> </tt>
<a name="L315"></a><tt class="py-lineno">315</tt> <tt class="py-line"> <tt class="py-keyword">if</tt> <tt class="py-name">n</tt> <tt class="py-op">!=</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">root</tt> <tt class="py-op">:</tt> </tt>
<a name="L316"></a><tt class="py-lineno">316</tt> <tt class="py-line"> <tt id="link-129" class="py-name"><a title="Bio.LocusLink.web_parse.handle
Bio.Ndb.handle" class="py-name" href="#" onclick="return doclink('link-129', 'handle', 'link-48');">handle</a></tt><tt class="py-op">.</tt><tt id="link-130" class="py-name"><a title="Bio.AlignAce.Motif.Motif.write
Bio.AlignIO.write
Bio.EUtils.sourcegen.SourceFile.write
Bio.EUtils.sourcegen.SourceGen.write
Bio.NeuralNetwork.Gene.Pattern.PatternIO.write
Bio.SeqIO.write
Bio.Writer.Writer.write
Bio.writers.SeqRecord.embl.WriteEmbl.write
Bio.writers.SeqRecord.fasta.WriteFasta.write" class="py-name" href="#" onclick="return doclink('link-130', 'write', 'link-120');">write</a></tt><tt class="py-op">(</tt><tt class="py-name">str</tt><tt class="py-op">(</tt><tt class="py-name">n</tt><tt class="py-op">.</tt><tt id="link-131" class="py-name" targets="Method Bio.SCOP.Domain.toDesRecord()=Bio.SCOP.Domain-class.html#toDesRecord,Method Bio.SCOP.Node.toDesRecord()=Bio.SCOP.Node-class.html#toDesRecord"><a title="Bio.SCOP.Domain.toDesRecord
Bio.SCOP.Node.toDesRecord" class="py-name" href="#" onclick="return doclink('link-131', 'toDesRecord', 'link-131');">toDesRecord</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt><tt class="py-op">)</tt><tt class="py-op">)</tt> </tt>
</div><a name="L317"></a><tt class="py-lineno">317</tt> <tt class="py-line"> </tt>
<a name="L318"></a><tt class="py-lineno">318</tt> <tt class="py-line"> </tt>
<a name="Scop.write_cla"></a><div id="Scop.write_cla-def"><a name="L319"></a><tt class="py-lineno">319</tt> <a class="py-toggle" href="#" id="Scop.write_cla-toggle" onclick="return toggle('Scop.write_cla');">-</a><tt class="py-line"> <tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.SCOP.Scop-class.html#write_cla">write_cla</a><tt class="py-op">(</tt><tt class="py-param">self</tt><tt class="py-op">,</tt> <tt class="py-param">handle</tt><tt class="py-op">)</tt> <tt class="py-op">:</tt> </tt>
</div><div id="Scop.write_cla-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="Scop.write_cla-expanded"><a name="L320"></a><tt class="py-lineno">320</tt> <tt class="py-line"> <tt class="py-docstring">"""Build a CLA SCOP parsable file from this object"""</tt> </tt>
<a name="L321"></a><tt class="py-lineno">321</tt> <tt class="py-line"> <tt id="link-132" class="py-name"><a title="Bio.Pathway.Rep.Graph.Graph.nodes
Bio.Pathway.Rep.MultiGraph.MultiGraph.nodes" class="py-name" href="#" onclick="return doclink('link-132', 'nodes', 'link-112');">nodes</a></tt> <tt class="py-op">=</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">_sidDict</tt><tt class="py-op">.</tt><tt id="link-133" class="py-name"><a title="Bio.Crystal.Crystal.values
Bio.EUtils.MultiDict._BaseMultiDict.values
Bio.GenBank.NCBIDictionary.values
Bio.Mindy.BaseDB.DictLookup.values
Bio.Prosite.ExPASyDictionary.values
Bio.Prosite.Prodoc.ExPASyDictionary.values
Bio.PubMed.Dictionary.values
Bio.SwissProt.SProt.ExPASyDictionary.values
Bio.config.Registry.Registry.values
BioSQL.BioSeqDatabase.BioSeqDatabase.values
BioSQL.BioSeqDatabase.DBServer.values
Martel.Parser.MartelAttributeList.values" class="py-name" href="#" onclick="return doclink('link-133', 'values', 'link-113');">values</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
<a name="L322"></a><tt class="py-lineno">322</tt> <tt class="py-line"> <tt class="py-comment"># We order nodes to ease comparison with original file</tt> </tt>
<a name="L323"></a><tt class="py-lineno">323</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt id="link-134" class="py-name"><a title="Bio.Pathway.Rep.Graph.Graph.nodes
Bio.Pathway.Rep.MultiGraph.MultiGraph.nodes" class="py-name" href="#" onclick="return doclink('link-134', 'nodes', 'link-112');">nodes</a></tt><tt class="py-op">.</tt><tt id="link-135" class="py-name"><a title="Bio.PDB.Residue.DisorderedResidue.sort
Bio.PDB.Residue.Residue.sort
Bio.Sequencing.Ace.ACEFileRecord.sort" class="py-name" href="#" onclick="return doclink('link-135', 'sort', 'link-115');">sort</a></tt><tt class="py-op">(</tt><tt class="py-keyword">lambda</tt> <tt id="link-136" class="py-name"><a title="Bio.PDB.Polypeptide.n1" class="py-name" href="#" onclick="return doclink('link-136', 'n1', 'link-116');">n1</a></tt><tt class="py-op">,</tt><tt class="py-name">n2</tt><tt class="py-op">:</tt> <tt class="py-name">cmp</tt><tt class="py-op">(</tt><tt id="link-137" class="py-name"><a title="Bio.PDB.Polypeptide.n1" class="py-name" href="#" onclick="return doclink('link-137', 'n1', 'link-116');">n1</a></tt><tt class="py-op">.</tt><tt class="py-name">sunid</tt><tt class="py-op">,</tt> <tt class="py-name">n2</tt><tt class="py-op">.</tt><tt class="py-name">sunid</tt><tt class="py-op">)</tt><tt class="py-op">)</tt> </tt>
<a name="L324"></a><tt class="py-lineno">324</tt> <tt class="py-line"> </tt>
<a name="L325"></a><tt class="py-lineno">325</tt> <tt class="py-line"> <tt class="py-keyword">for</tt> <tt class="py-name">n</tt> <tt class="py-keyword">in</tt> <tt id="link-138" class="py-name"><a title="Bio.Pathway.Rep.Graph.Graph.nodes
Bio.Pathway.Rep.MultiGraph.MultiGraph.nodes" class="py-name" href="#" onclick="return doclink('link-138', 'nodes', 'link-112');">nodes</a></tt> <tt class="py-op">:</tt> </tt>
<a name="L326"></a><tt class="py-lineno">326</tt> <tt class="py-line"> <tt id="link-139" class="py-name"><a title="Bio.LocusLink.web_parse.handle
Bio.Ndb.handle" class="py-name" href="#" onclick="return doclink('link-139', 'handle', 'link-48');">handle</a></tt><tt class="py-op">.</tt><tt id="link-140" class="py-name"><a title="Bio.AlignAce.Motif.Motif.write
Bio.AlignIO.write
Bio.EUtils.sourcegen.SourceFile.write
Bio.EUtils.sourcegen.SourceGen.write
Bio.NeuralNetwork.Gene.Pattern.PatternIO.write
Bio.SeqIO.write
Bio.Writer.Writer.write
Bio.writers.SeqRecord.embl.WriteEmbl.write
Bio.writers.SeqRecord.fasta.WriteFasta.write" class="py-name" href="#" onclick="return doclink('link-140', 'write', 'link-120');">write</a></tt><tt class="py-op">(</tt><tt class="py-name">str</tt><tt class="py-op">(</tt><tt class="py-name">n</tt><tt class="py-op">.</tt><tt id="link-141" class="py-name" targets="Method Bio.SCOP.Domain.toClaRecord()=Bio.SCOP.Domain-class.html#toClaRecord"><a title="Bio.SCOP.Domain.toClaRecord" class="py-name" href="#" onclick="return doclink('link-141', 'toClaRecord', 'link-141');">toClaRecord</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt><tt class="py-op">)</tt><tt class="py-op">)</tt> </tt>
</div><a name="L327"></a><tt class="py-lineno">327</tt> <tt class="py-line"> </tt>
<a name="L328"></a><tt class="py-lineno">328</tt> <tt class="py-line"> </tt>
<a name="Scop.getDomainFromSQL"></a><div id="Scop.getDomainFromSQL-def"><a name="L329"></a><tt class="py-lineno">329</tt> <a class="py-toggle" href="#" id="Scop.getDomainFromSQL-toggle" onclick="return toggle('Scop.getDomainFromSQL');">-</a><tt class="py-line"> <tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.SCOP.Scop-class.html#getDomainFromSQL">getDomainFromSQL</a><tt class="py-op">(</tt><tt class="py-param">self</tt><tt class="py-op">,</tt> <tt class="py-param">sunid</tt><tt class="py-op">=</tt><tt class="py-name">None</tt><tt class="py-op">,</tt> <tt class="py-param">sid</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="Scop.getDomainFromSQL-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="Scop.getDomainFromSQL-expanded"><a name="L330"></a><tt class="py-lineno">330</tt> <tt class="py-line"> <tt class="py-docstring">"""Load a node from the SQL backend using sunid or sid"""</tt> </tt>
<a name="L331"></a><tt class="py-lineno">331</tt> <tt class="py-line"> <tt class="py-keyword">if</tt> <tt class="py-name">sunid</tt><tt class="py-op">==</tt><tt class="py-name">sid</tt><tt class="py-op">==</tt><tt class="py-name">None</tt><tt class="py-op">:</tt> <tt class="py-keyword">return</tt> <tt class="py-name">None</tt> </tt>
<a name="L332"></a><tt class="py-lineno">332</tt> <tt class="py-line"> </tt>
<a name="L333"></a><tt class="py-lineno">333</tt> <tt class="py-line"> <tt class="py-name">cur</tt> <tt class="py-op">=</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">db_handle</tt><tt class="py-op">.</tt><tt id="link-142" class="py-name" targets="Method Bio.DocSQL.Query.cursor()=Bio.DocSQL.Query-class.html#cursor,Method Bio.DocSQL.QuerySingle.cursor()=Bio.DocSQL.QuerySingle-class.html#cursor"><a title="Bio.DocSQL.Query.cursor
Bio.DocSQL.QuerySingle.cursor" class="py-name" href="#" onclick="return doclink('link-142', 'cursor', 'link-142');">cursor</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
<a name="L334"></a><tt class="py-lineno">334</tt> <tt class="py-line"> </tt>
<a name="L335"></a><tt class="py-lineno">335</tt> <tt class="py-line"> <tt class="py-keyword">if</tt> <tt class="py-name">sid</tt><tt class="py-op">:</tt> </tt>
<a name="L336"></a><tt class="py-lineno">336</tt> <tt class="py-line"> <tt class="py-name">cur</tt><tt class="py-op">.</tt><tt id="link-143" class="py-name" targets="Method BioSQL.BioSeqDatabase.Adaptor.execute()=BioSQL.BioSeqDatabase.Adaptor-class.html#execute"><a title="BioSQL.BioSeqDatabase.Adaptor.execute" class="py-name" href="#" onclick="return doclink('link-143', 'execute', 'link-143');">execute</a></tt><tt class="py-op">(</tt><tt class="py-string">"SELECT sunid FROM cla WHERE sid=%s"</tt><tt class="py-op">,</tt> <tt class="py-name">sid</tt><tt class="py-op">)</tt> </tt>
<a name="L337"></a><tt class="py-lineno">337</tt> <tt class="py-line"> <tt class="py-name">res</tt> <tt class="py-op">=</tt> <tt class="py-name">cur</tt><tt class="py-op">.</tt><tt class="py-name">fetchone</tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
<a name="L338"></a><tt class="py-lineno">338</tt> <tt class="py-line"> <tt class="py-keyword">if</tt> <tt class="py-name">res</tt> <tt class="py-keyword">is</tt> <tt class="py-name">None</tt><tt class="py-op">:</tt> </tt>
<a name="L339"></a><tt class="py-lineno">339</tt> <tt class="py-line"> <tt class="py-keyword">return</tt> <tt class="py-name">None</tt> </tt>
<a name="L340"></a><tt class="py-lineno">340</tt> <tt class="py-line"> <tt class="py-name">sunid</tt> <tt class="py-op">=</tt> <tt class="py-name">res</tt><tt class="py-op">[</tt><tt class="py-number">0</tt><tt class="py-op">]</tt> </tt>
<a name="L341"></a><tt class="py-lineno">341</tt> <tt class="py-line"> </tt>
<a name="L342"></a><tt class="py-lineno">342</tt> <tt class="py-line"> <tt class="py-name">cur</tt><tt class="py-op">.</tt><tt id="link-144" class="py-name"><a title="BioSQL.BioSeqDatabase.Adaptor.execute" class="py-name" href="#" onclick="return doclink('link-144', 'execute', 'link-143');">execute</a></tt><tt class="py-op">(</tt><tt class="py-string">"SELECT * FROM des WHERE sunid=%s"</tt><tt class="py-op">,</tt> <tt class="py-name">sunid</tt><tt class="py-op">)</tt> </tt>
<a name="L343"></a><tt class="py-lineno">343</tt> <tt class="py-line"> <tt id="link-145" class="py-name" targets="Variable BioSQL.BioSeq.DBSeq.data=BioSQL.BioSeq.DBSeq-class.html#data"><a title="BioSQL.BioSeq.DBSeq.data" class="py-name" href="#" onclick="return doclink('link-145', 'data', 'link-145');">data</a></tt> <tt class="py-op">=</tt> <tt class="py-name">cur</tt><tt class="py-op">.</tt><tt class="py-name">fetchone</tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
<a name="L344"></a><tt class="py-lineno">344</tt> <tt class="py-line"> </tt>
<a name="L345"></a><tt class="py-lineno">345</tt> <tt class="py-line"> <tt class="py-keyword">if</tt> <tt id="link-146" class="py-name"><a title="BioSQL.BioSeq.DBSeq.data" class="py-name" href="#" onclick="return doclink('link-146', 'data', 'link-145');">data</a></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="L346"></a><tt class="py-lineno">346</tt> <tt class="py-line"> <tt class="py-name">n</tt> <tt class="py-op">=</tt> <tt class="py-name">None</tt> </tt>
<a name="L347"></a><tt class="py-lineno">347</tt> <tt class="py-line"> </tt>
<a name="L348"></a><tt class="py-lineno">348</tt> <tt class="py-line"> <tt class="py-comment">#determine if Node or Domain</tt> </tt>
<a name="L349"></a><tt class="py-lineno">349</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-keyword">if</tt> <tt id="link-147" class="py-name"><a title="BioSQL.BioSeq.DBSeq.data" class="py-name" href="#" onclick="return doclink('link-147', 'data', 'link-145');">data</a></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">"px"</tt><tt class="py-op">:</tt> </tt>
<a name="L350"></a><tt class="py-lineno">350</tt> <tt class="py-line"> <tt class="py-name">n</tt> <tt class="py-op">=</tt> <tt id="link-148" class="py-name"><a title="Bio.Nexus.Nodes.Node
Bio.SCOP.Node" class="py-name" href="#" onclick="return doclink('link-148', 'Node', 'link-58');">Node</a></tt><tt class="py-op">(</tt><tt class="py-name">scop</tt><tt class="py-op">=</tt><tt class="py-name">self</tt><tt class="py-op">)</tt> </tt>
<a name="L351"></a><tt class="py-lineno">351</tt> <tt class="py-line"> </tt>
<a name="L352"></a><tt class="py-lineno">352</tt> <tt class="py-line"> <tt class="py-name">cur</tt><tt class="py-op">.</tt><tt id="link-149" class="py-name"><a title="BioSQL.BioSeqDatabase.Adaptor.execute" class="py-name" href="#" onclick="return doclink('link-149', 'execute', 'link-143');">execute</a></tt><tt class="py-op">(</tt><tt class="py-string">"SELECT child FROM hie WHERE parent=%s"</tt><tt class="py-op">,</tt> <tt class="py-name">sunid</tt><tt class="py-op">)</tt> </tt>
<a name="L353"></a><tt class="py-lineno">353</tt> <tt class="py-line"> <tt id="link-150" class="py-name"><a title="Bio.Pathway.Rep.Graph.Graph.children
Bio.Pathway.Rep.MultiGraph.MultiGraph.children" class="py-name" href="#" onclick="return doclink('link-150', 'children', 'link-89');">children</a></tt> <tt class="py-op">=</tt> <tt class="py-op">[</tt><tt class="py-op">]</tt> </tt>
<a name="L354"></a><tt class="py-lineno">354</tt> <tt class="py-line"> <tt class="py-keyword">for</tt> <tt class="py-name">c</tt> <tt class="py-keyword">in</tt> <tt class="py-name">cur</tt><tt class="py-op">.</tt><tt class="py-name">fetchall</tt><tt class="py-op">(</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
<a name="L355"></a><tt class="py-lineno">355</tt> <tt class="py-line"> <tt id="link-151" class="py-name"><a title="Bio.Pathway.Rep.Graph.Graph.children
Bio.Pathway.Rep.MultiGraph.MultiGraph.children" class="py-name" href="#" onclick="return doclink('link-151', 'children', 'link-89');">children</a></tt><tt class="py-op">.</tt><tt id="link-152" 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-152', 'append', 'link-68');">append</a></tt><tt class="py-op">(</tt><tt class="py-name">c</tt><tt class="py-op">[</tt><tt class="py-number">0</tt><tt class="py-op">]</tt><tt class="py-op">)</tt> </tt>
<a name="L356"></a><tt class="py-lineno">356</tt> <tt class="py-line"> <tt class="py-name">n</tt><tt class="py-op">.</tt><tt id="link-153" class="py-name"><a title="Bio.Pathway.Rep.Graph.Graph.children
Bio.Pathway.Rep.MultiGraph.MultiGraph.children" class="py-name" href="#" onclick="return doclink('link-153', 'children', 'link-89');">children</a></tt> <tt class="py-op">=</tt> <tt id="link-154" class="py-name"><a title="Bio.Pathway.Rep.Graph.Graph.children
Bio.Pathway.Rep.MultiGraph.MultiGraph.children" class="py-name" href="#" onclick="return doclink('link-154', 'children', 'link-89');">children</a></tt> </tt>
<a name="L357"></a><tt class="py-lineno">357</tt> <tt class="py-line"> </tt>
<a name="L358"></a><tt class="py-lineno">358</tt> <tt class="py-line"> </tt>
<a name="L359"></a><tt class="py-lineno">359</tt> <tt class="py-line"> <tt class="py-keyword">else</tt><tt class="py-op">:</tt> </tt>
<a name="L360"></a><tt class="py-lineno">360</tt> <tt class="py-line"> <tt class="py-name">n</tt> <tt class="py-op">=</tt> <tt id="link-155" class="py-name"><a title="Bio.SCOP.Domain" class="py-name" href="#" onclick="return doclink('link-155', 'Domain', 'link-39');">Domain</a></tt><tt class="py-op">(</tt><tt class="py-name">scop</tt><tt class="py-op">=</tt><tt class="py-name">self</tt><tt class="py-op">)</tt> </tt>
<a name="L361"></a><tt class="py-lineno">361</tt> <tt class="py-line"> <tt class="py-name">cur</tt><tt class="py-op">.</tt><tt id="link-156" class="py-name"><a title="BioSQL.BioSeqDatabase.Adaptor.execute" class="py-name" href="#" onclick="return doclink('link-156', 'execute', 'link-143');">execute</a></tt><tt class="py-op">(</tt><tt class="py-string">"select sid, residues, pdbid from cla where sunid=%s"</tt><tt class="py-op">,</tt> </tt>
<a name="L362"></a><tt class="py-lineno">362</tt> <tt class="py-line"> <tt class="py-name">sunid</tt><tt class="py-op">)</tt> </tt>
<a name="L363"></a><tt class="py-lineno">363</tt> <tt class="py-line"> </tt>
<a name="L364"></a><tt class="py-lineno">364</tt> <tt class="py-line"> <tt class="py-op">[</tt><tt class="py-name">n</tt><tt class="py-op">.</tt><tt class="py-name">sid</tt><tt class="py-op">,</tt><tt class="py-name">n</tt><tt class="py-op">.</tt><tt class="py-name">residues</tt><tt class="py-op">,</tt><tt class="py-name">pdbid</tt><tt class="py-op">]</tt> <tt class="py-op">=</tt> <tt class="py-name">cur</tt><tt class="py-op">.</tt><tt class="py-name">fetchone</tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
<a name="L365"></a><tt class="py-lineno">365</tt> <tt class="py-line"> <tt class="py-name">n</tt><tt class="py-op">.</tt><tt class="py-name">residues</tt> <tt class="py-op">=</tt> <tt id="link-157" class="py-name"><a title="Bio.SCOP.Residues'.Residues" class="py-name" href="#" onclick="return doclink('link-157', 'Residues', 'link-3');">Residues</a></tt><tt class="py-op">(</tt><tt class="py-name">n</tt><tt class="py-op">.</tt><tt class="py-name">residues</tt><tt class="py-op">)</tt> </tt>
<a name="L366"></a><tt class="py-lineno">366</tt> <tt class="py-line"> <tt class="py-name">n</tt><tt class="py-op">.</tt><tt class="py-name">residues</tt><tt class="py-op">.</tt><tt class="py-name">pdbid</tt><tt class="py-op">=</tt><tt class="py-name">pdbid</tt> </tt>
<a name="L367"></a><tt class="py-lineno">367</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">_sidDict</tt><tt class="py-op">[</tt><tt class="py-name">n</tt><tt class="py-op">.</tt><tt class="py-name">sid</tt><tt class="py-op">]</tt> <tt class="py-op">=</tt> <tt class="py-name">n</tt> </tt>
<a name="L368"></a><tt class="py-lineno">368</tt> <tt class="py-line"> </tt>
<a name="L369"></a><tt class="py-lineno">369</tt> <tt class="py-line"> <tt class="py-op">[</tt><tt class="py-name">n</tt><tt class="py-op">.</tt><tt class="py-name">sunid</tt><tt class="py-op">,</tt><tt class="py-name">n</tt><tt class="py-op">.</tt><tt id="link-158" class="py-name"><a title="Bio.GenBank.LocationParser.Integer.type
Bio.GenBank.LocationParser.Symbol.type
Bio.GenBank.LocationParser.UnsignedInteger.type" class="py-name" href="#" onclick="return doclink('link-158', 'type', 'link-59');">type</a></tt><tt class="py-op">,</tt><tt class="py-name">n</tt><tt class="py-op">.</tt><tt class="py-name">sccs</tt><tt class="py-op">,</tt><tt class="py-name">n</tt><tt class="py-op">.</tt><tt id="link-159" class="py-name"><a title="Bio.Blast.NCBIStandalone._DescriptionConsumer.description
Bio.Enzyme._RecordConsumer.description
Bio.Prosite._RecordConsumer.description
Bio.Std.description
Bio.SwissProt.SProt._RecordConsumer.description
Bio.SwissProt.SProt._SequenceConsumer.description
Martel.setup.run_local_tests.description" class="py-name" href="#" onclick="return doclink('link-159', 'description', 'link-44');">description</a></tt><tt class="py-op">]</tt> <tt class="py-op">=</tt> <tt id="link-160" class="py-name"><a title="BioSQL.BioSeq.DBSeq.data" class="py-name" href="#" onclick="return doclink('link-160', 'data', 'link-145');">data</a></tt> </tt>
<a name="L370"></a><tt class="py-lineno">370</tt> <tt class="py-line"> </tt>
<a name="L371"></a><tt class="py-lineno">371</tt> <tt class="py-line"> <tt class="py-keyword">if</tt> <tt id="link-161" class="py-name"><a title="BioSQL.BioSeq.DBSeq.data" class="py-name" href="#" onclick="return doclink('link-161', 'data', 'link-145');">data</a></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">'ro'</tt><tt class="py-op">:</tt> </tt>
<a name="L372"></a><tt class="py-lineno">372</tt> <tt class="py-line"> <tt class="py-name">cur</tt><tt class="py-op">.</tt><tt id="link-162" class="py-name"><a title="BioSQL.BioSeqDatabase.Adaptor.execute" class="py-name" href="#" onclick="return doclink('link-162', 'execute', 'link-143');">execute</a></tt><tt class="py-op">(</tt><tt class="py-string">"SELECT parent FROM hie WHERE child=%s"</tt><tt class="py-op">,</tt> <tt class="py-name">sunid</tt><tt class="py-op">)</tt> </tt>
<a name="L373"></a><tt class="py-lineno">373</tt> <tt class="py-line"> <tt class="py-name">n</tt><tt class="py-op">.</tt><tt class="py-name">parent</tt> <tt class="py-op">=</tt> <tt class="py-name">cur</tt><tt class="py-op">.</tt><tt class="py-name">fetchone</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="L374"></a><tt class="py-lineno">374</tt> <tt class="py-line"> </tt>
<a name="L375"></a><tt class="py-lineno">375</tt> <tt class="py-line"> <tt class="py-name">n</tt><tt class="py-op">.</tt><tt class="py-name">sunid</tt> <tt class="py-op">=</tt> <tt class="py-name">int</tt><tt class="py-op">(</tt><tt class="py-name">n</tt><tt class="py-op">.</tt><tt class="py-name">sunid</tt><tt class="py-op">)</tt> </tt>
<a name="L376"></a><tt class="py-lineno">376</tt> <tt class="py-line"> </tt>
<a name="L377"></a><tt class="py-lineno">377</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">_sunidDict</tt><tt class="py-op">[</tt><tt class="py-name">n</tt><tt class="py-op">.</tt><tt class="py-name">sunid</tt><tt class="py-op">]</tt> <tt class="py-op">=</tt> <tt class="py-name">n</tt> </tt>
</div><a name="L378"></a><tt class="py-lineno">378</tt> <tt class="py-line"> </tt>
<a name="L379"></a><tt class="py-lineno">379</tt> <tt class="py-line"> </tt>
<a name="Scop.getAscendentFromSQL"></a><div id="Scop.getAscendentFromSQL-def"><a name="L380"></a><tt class="py-lineno">380</tt> <a class="py-toggle" href="#" id="Scop.getAscendentFromSQL-toggle" onclick="return toggle('Scop.getAscendentFromSQL');">-</a><tt class="py-line"> <tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.SCOP.Scop-class.html#getAscendentFromSQL">getAscendentFromSQL</a><tt class="py-op">(</tt><tt class="py-param">self</tt><tt class="py-op">,</tt> <tt class="py-param">node</tt><tt class="py-op">,</tt> <tt class="py-param">type</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="Scop.getAscendentFromSQL-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="Scop.getAscendentFromSQL-expanded"><a name="L381"></a><tt class="py-lineno">381</tt> <tt class="py-line"> <tt class="py-docstring">"""Get ascendents using SQL backend"""</tt> </tt>
<a name="L382"></a><tt class="py-lineno">382</tt> <tt class="py-line"> <tt class="py-keyword">if</tt> <tt id="link-163" class="py-name"><a title="Bio.SCOP.nodeCodeOrder" class="py-name" href="#" onclick="return doclink('link-163', 'nodeCodeOrder', 'link-14');">nodeCodeOrder</a></tt><tt class="py-op">.</tt><tt id="link-164" class="py-name" targets="Method Bio.Crystal.Chain.index()=Bio.Crystal.Chain-class.html#index,Method Bio.EUtils.POM.ElementNode.index()=Bio.EUtils.POM.ElementNode-class.html#index,Method Bio.SCOP.Raf.SeqMap.index()=Bio.SCOP.Raf.SeqMap-class.html#index,Method Bio.Seq.MutableSeq.index()=Bio.Seq.MutableSeq-class.html#index"><a title="Bio.Crystal.Chain.index
Bio.EUtils.POM.ElementNode.index
Bio.SCOP.Raf.SeqMap.index
Bio.Seq.MutableSeq.index" class="py-name" href="#" onclick="return doclink('link-164', 'index', 'link-164');">index</a></tt><tt class="py-op">(</tt><tt id="link-165" class="py-name"><a title="Bio.GenBank.LocationParser.Integer.type
Bio.GenBank.LocationParser.Symbol.type
Bio.GenBank.LocationParser.UnsignedInteger.type" class="py-name" href="#" onclick="return doclink('link-165', 'type', 'link-59');">type</a></tt><tt class="py-op">)</tt> <tt class="py-op">>=</tt> <tt id="link-166" class="py-name"><a title="Bio.SCOP.nodeCodeOrder" class="py-name" href="#" onclick="return doclink('link-166', 'nodeCodeOrder', 'link-14');">nodeCodeOrder</a></tt><tt class="py-op">.</tt><tt id="link-167" class="py-name"><a title="Bio.Crystal.Chain.index
Bio.EUtils.POM.ElementNode.index
Bio.SCOP.Raf.SeqMap.index
Bio.Seq.MutableSeq.index" class="py-name" href="#" onclick="return doclink('link-167', 'index', 'link-164');">index</a></tt><tt class="py-op">(</tt><tt id="link-168" class="py-name" targets="Method Bio.EUtils.POM.ElementNode.node()=Bio.EUtils.POM.ElementNode-class.html#node,Method Bio.Nexus.Trees.Tree.node()=Bio.Nexus.Trees.Tree-class.html#node"><a title="Bio.EUtils.POM.ElementNode.node
Bio.Nexus.Trees.Tree.node" class="py-name" href="#" onclick="return doclink('link-168', 'node', 'link-168');">node</a></tt><tt class="py-op">.</tt><tt id="link-169" class="py-name"><a title="Bio.GenBank.LocationParser.Integer.type
Bio.GenBank.LocationParser.Symbol.type
Bio.GenBank.LocationParser.UnsignedInteger.type" class="py-name" href="#" onclick="return doclink('link-169', 'type', 'link-59');">type</a></tt><tt class="py-op">)</tt><tt class="py-op">:</tt> <tt class="py-keyword">return</tt> <tt class="py-name">None</tt> </tt>
<a name="L383"></a><tt class="py-lineno">383</tt> <tt class="py-line"> </tt>
<a name="L384"></a><tt class="py-lineno">384</tt> <tt class="py-line"> <tt class="py-name">cur</tt> <tt class="py-op">=</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">db_handle</tt><tt class="py-op">.</tt><tt id="link-170" class="py-name"><a title="Bio.DocSQL.Query.cursor
Bio.DocSQL.QuerySingle.cursor" class="py-name" href="#" onclick="return doclink('link-170', 'cursor', 'link-142');">cursor</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
<a name="L385"></a><tt class="py-lineno">385</tt> <tt class="py-line"> <tt class="py-name">cur</tt><tt class="py-op">.</tt><tt id="link-171" class="py-name"><a title="BioSQL.BioSeqDatabase.Adaptor.execute" class="py-name" href="#" onclick="return doclink('link-171', 'execute', 'link-143');">execute</a></tt><tt class="py-op">(</tt><tt class="py-string">"SELECT "</tt><tt class="py-op">+</tt><tt id="link-172" class="py-name"><a title="Bio.GenBank.LocationParser.Integer.type
Bio.GenBank.LocationParser.Symbol.type
Bio.GenBank.LocationParser.UnsignedInteger.type" class="py-name" href="#" onclick="return doclink('link-172', 'type', 'link-59');">type</a></tt><tt class="py-op">+</tt><tt class="py-string">" from cla WHERE "</tt><tt class="py-op">+</tt><tt id="link-173" class="py-name"><a title="Bio.EUtils.POM.ElementNode.node
Bio.Nexus.Trees.Tree.node" class="py-name" href="#" onclick="return doclink('link-173', 'node', 'link-168');">node</a></tt><tt class="py-op">.</tt><tt id="link-174" class="py-name"><a title="Bio.GenBank.LocationParser.Integer.type
Bio.GenBank.LocationParser.Symbol.type
Bio.GenBank.LocationParser.UnsignedInteger.type" class="py-name" href="#" onclick="return doclink('link-174', 'type', 'link-59');">type</a></tt><tt class="py-op">+</tt><tt class="py-string">"=%s"</tt><tt class="py-op">,</tt> <tt class="py-op">(</tt><tt id="link-175" class="py-name"><a title="Bio.EUtils.POM.ElementNode.node
Bio.Nexus.Trees.Tree.node" class="py-name" href="#" onclick="return doclink('link-175', 'node', 'link-168');">node</a></tt><tt class="py-op">.</tt><tt class="py-name">sunid</tt><tt class="py-op">)</tt><tt class="py-op">)</tt> </tt>
<a name="L386"></a><tt class="py-lineno">386</tt> <tt class="py-line"> <tt class="py-name">result</tt> <tt class="py-op">=</tt> <tt class="py-name">cur</tt><tt class="py-op">.</tt><tt class="py-name">fetchone</tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
<a name="L387"></a><tt class="py-lineno">387</tt> <tt class="py-line"> <tt class="py-keyword">if</tt> <tt class="py-name">result</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="L388"></a><tt class="py-lineno">388</tt> <tt class="py-line"> <tt class="py-keyword">return</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-176" class="py-name"><a title="Bio.SCOP.Scop.getNodeBySunid" class="py-name" href="#" onclick="return doclink('link-176', 'getNodeBySunid', 'link-103');">getNodeBySunid</a></tt><tt class="py-op">(</tt><tt class="py-name">result</tt><tt class="py-op">[</tt><tt class="py-number">0</tt><tt class="py-op">]</tt><tt class="py-op">)</tt> </tt>
<a name="L389"></a><tt class="py-lineno">389</tt> <tt class="py-line"> <tt class="py-keyword">else</tt><tt class="py-op">:</tt> </tt>
<a name="L390"></a><tt class="py-lineno">390</tt> <tt class="py-line"> <tt class="py-keyword">return</tt> <tt class="py-name">None</tt> </tt>
</div><a name="L391"></a><tt class="py-lineno">391</tt> <tt class="py-line"> </tt>
<a name="L392"></a><tt class="py-lineno">392</tt> <tt class="py-line"> </tt>
<a name="Scop.getDescendentsFromSQL"></a><div id="Scop.getDescendentsFromSQL-def"><a name="L393"></a><tt class="py-lineno">393</tt> <a class="py-toggle" href="#" id="Scop.getDescendentsFromSQL-toggle" onclick="return toggle('Scop.getDescendentsFromSQL');">-</a><tt class="py-line"> <tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.SCOP.Scop-class.html#getDescendentsFromSQL">getDescendentsFromSQL</a><tt class="py-op">(</tt><tt class="py-param">self</tt><tt class="py-op">,</tt> <tt class="py-param">node</tt><tt class="py-op">,</tt> <tt class="py-param">type</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="Scop.getDescendentsFromSQL-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="Scop.getDescendentsFromSQL-expanded"><a name="L394"></a><tt class="py-lineno">394</tt> <tt class="py-line"> <tt class="py-docstring">"""Get descendents of a node using the database backend. This avoids</tt> </tt>
<a name="L395"></a><tt class="py-lineno">395</tt> <tt class="py-line"><tt class="py-docstring"> repeated iteration of SQL calls and is therefore much quicker than</tt> </tt>
<a name="L396"></a><tt class="py-lineno">396</tt> <tt class="py-line"><tt class="py-docstring"> repeatedly calling node.getChildren().</tt> </tt>
<a name="L397"></a><tt class="py-lineno">397</tt> <tt class="py-line"><tt class="py-docstring"> """</tt> </tt>
<a name="L398"></a><tt class="py-lineno">398</tt> <tt class="py-line"> <tt class="py-keyword">if</tt> <tt id="link-177" class="py-name"><a title="Bio.SCOP.nodeCodeOrder" class="py-name" href="#" onclick="return doclink('link-177', 'nodeCodeOrder', 'link-14');">nodeCodeOrder</a></tt><tt class="py-op">.</tt><tt id="link-178" class="py-name"><a title="Bio.Crystal.Chain.index
Bio.EUtils.POM.ElementNode.index
Bio.SCOP.Raf.SeqMap.index
Bio.Seq.MutableSeq.index" class="py-name" href="#" onclick="return doclink('link-178', 'index', 'link-164');">index</a></tt><tt class="py-op">(</tt><tt id="link-179" class="py-name"><a title="Bio.GenBank.LocationParser.Integer.type
Bio.GenBank.LocationParser.Symbol.type
Bio.GenBank.LocationParser.UnsignedInteger.type" class="py-name" href="#" onclick="return doclink('link-179', 'type', 'link-59');">type</a></tt><tt class="py-op">)</tt> <tt class="py-op"><=</tt> <tt id="link-180" class="py-name"><a title="Bio.SCOP.nodeCodeOrder" class="py-name" href="#" onclick="return doclink('link-180', 'nodeCodeOrder', 'link-14');">nodeCodeOrder</a></tt><tt class="py-op">.</tt><tt id="link-181" class="py-name"><a title="Bio.Crystal.Chain.index
Bio.EUtils.POM.ElementNode.index
Bio.SCOP.Raf.SeqMap.index
Bio.Seq.MutableSeq.index" class="py-name" href="#" onclick="return doclink('link-181', 'index', 'link-164');">index</a></tt><tt class="py-op">(</tt><tt id="link-182" class="py-name"><a title="Bio.EUtils.POM.ElementNode.node
Bio.Nexus.Trees.Tree.node" class="py-name" href="#" onclick="return doclink('link-182', 'node', 'link-168');">node</a></tt><tt class="py-op">.</tt><tt id="link-183" class="py-name"><a title="Bio.GenBank.LocationParser.Integer.type
Bio.GenBank.LocationParser.Symbol.type
Bio.GenBank.LocationParser.UnsignedInteger.type" class="py-name" href="#" onclick="return doclink('link-183', 'type', 'link-59');">type</a></tt><tt class="py-op">)</tt><tt class="py-op">:</tt> <tt class="py-keyword">return</tt> <tt class="py-op">[</tt><tt class="py-op">]</tt> </tt>
<a name="L399"></a><tt class="py-lineno">399</tt> <tt class="py-line"> </tt>
<a name="L400"></a><tt class="py-lineno">400</tt> <tt class="py-line"> <tt class="py-name">des_list</tt> <tt class="py-op">=</tt> <tt class="py-op">[</tt><tt class="py-op">]</tt> </tt>
<a name="L401"></a><tt class="py-lineno">401</tt> <tt class="py-line"> </tt>
<a name="L402"></a><tt class="py-lineno">402</tt> <tt class="py-line"> </tt>
<a name="L403"></a><tt class="py-lineno">403</tt> <tt class="py-line"> <tt class="py-comment"># SQL cla table knows nothing about 'ro'</tt> </tt>
<a name="L404"></a><tt class="py-lineno">404</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-keyword">if</tt> <tt id="link-184" class="py-name"><a title="Bio.EUtils.POM.ElementNode.node
Bio.Nexus.Trees.Tree.node" class="py-name" href="#" onclick="return doclink('link-184', 'node', 'link-168');">node</a></tt><tt class="py-op">.</tt><tt id="link-185" class="py-name"><a title="Bio.GenBank.LocationParser.Integer.type
Bio.GenBank.LocationParser.Symbol.type
Bio.GenBank.LocationParser.UnsignedInteger.type" class="py-name" href="#" onclick="return doclink('link-185', 'type', 'link-59');">type</a></tt> <tt class="py-op">==</tt> <tt class="py-string">'ro'</tt><tt class="py-op">:</tt> </tt>
<a name="L405"></a><tt class="py-lineno">405</tt> <tt class="py-line"> <tt class="py-keyword">for</tt> <tt class="py-name">c</tt> <tt class="py-keyword">in</tt> <tt id="link-186" class="py-name"><a title="Bio.EUtils.POM.ElementNode.node
Bio.Nexus.Trees.Tree.node" class="py-name" href="#" onclick="return doclink('link-186', 'node', 'link-168');">node</a></tt><tt class="py-op">.</tt><tt id="link-187" class="py-name" targets="Method Bio.SCOP.Node.getChildren()=Bio.SCOP.Node-class.html#getChildren"><a title="Bio.SCOP.Node.getChildren" class="py-name" href="#" onclick="return doclink('link-187', 'getChildren', 'link-187');">getChildren</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
<a name="L406"></a><tt class="py-lineno">406</tt> <tt class="py-line"> <tt class="py-keyword">for</tt> <tt id="link-188" class="py-name" targets="Variable Bio.EUtils.setup.d=Bio.EUtils.setup-module.html#d"><a title="Bio.EUtils.setup.d" class="py-name" href="#" onclick="return doclink('link-188', 'd', 'link-188');">d</a></tt> <tt class="py-keyword">in</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-189" class="py-name" targets="Method Bio.SCOP.Scop.getDescendentsFromSQL()=Bio.SCOP.Scop-class.html#getDescendentsFromSQL"><a title="Bio.SCOP.Scop.getDescendentsFromSQL" class="py-name" href="#" onclick="return doclink('link-189', 'getDescendentsFromSQL', 'link-189');">getDescendentsFromSQL</a></tt><tt class="py-op">(</tt><tt class="py-name">c</tt><tt class="py-op">,</tt><tt id="link-190" class="py-name"><a title="Bio.GenBank.LocationParser.Integer.type
Bio.GenBank.LocationParser.Symbol.type
Bio.GenBank.LocationParser.UnsignedInteger.type" class="py-name" href="#" onclick="return doclink('link-190', 'type', 'link-59');">type</a></tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
<a name="L407"></a><tt class="py-lineno">407</tt> <tt class="py-line"> <tt class="py-name">des_list</tt><tt class="py-op">.</tt><tt id="link-191" 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-191', 'append', 'link-68');">append</a></tt><tt class="py-op">(</tt><tt id="link-192" class="py-name"><a title="Bio.EUtils.setup.d" class="py-name" href="#" onclick="return doclink('link-192', 'd', 'link-188');">d</a></tt><tt class="py-op">)</tt> </tt>
<a name="L408"></a><tt class="py-lineno">408</tt> <tt class="py-line"> <tt class="py-keyword">return</tt> <tt class="py-name">des_list</tt> </tt>
<a name="L409"></a><tt class="py-lineno">409</tt> <tt class="py-line"> </tt>
<a name="L410"></a><tt class="py-lineno">410</tt> <tt class="py-line"> <tt class="py-name">cur</tt> <tt class="py-op">=</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">db_handle</tt><tt class="py-op">.</tt><tt id="link-193" class="py-name"><a title="Bio.DocSQL.Query.cursor
Bio.DocSQL.QuerySingle.cursor" class="py-name" href="#" onclick="return doclink('link-193', 'cursor', 'link-142');">cursor</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
<a name="L411"></a><tt class="py-lineno">411</tt> <tt class="py-line"> </tt>
<a name="L412"></a><tt class="py-lineno">412</tt> <tt class="py-line"> </tt>
<a name="L413"></a><tt class="py-lineno">413</tt> <tt class="py-line"> <tt class="py-keyword">if</tt> <tt id="link-194" class="py-name"><a title="Bio.GenBank.LocationParser.Integer.type
Bio.GenBank.LocationParser.Symbol.type
Bio.GenBank.LocationParser.UnsignedInteger.type" class="py-name" href="#" onclick="return doclink('link-194', 'type', 'link-59');">type</a></tt> <tt class="py-op">!=</tt> <tt class="py-string">'px'</tt><tt class="py-op">:</tt> </tt>
<a name="L414"></a><tt class="py-lineno">414</tt> <tt class="py-line"> <tt class="py-name">cur</tt><tt class="py-op">.</tt><tt id="link-195" class="py-name"><a title="BioSQL.BioSeqDatabase.Adaptor.execute" class="py-name" href="#" onclick="return doclink('link-195', 'execute', 'link-143');">execute</a></tt><tt class="py-op">(</tt><tt class="py-string">"SELECT DISTINCT des.sunid,des.type,des.sccs,description FROM \</tt> </tt>
<a name="L415"></a><tt class="py-lineno">415</tt> <tt class="py-line"><tt class="py-string"> cla,des WHERE cla."</tt><tt class="py-op">+</tt><tt id="link-196" class="py-name"><a title="Bio.EUtils.POM.ElementNode.node
Bio.Nexus.Trees.Tree.node" class="py-name" href="#" onclick="return doclink('link-196', 'node', 'link-168');">node</a></tt><tt class="py-op">.</tt><tt id="link-197" class="py-name"><a title="Bio.GenBank.LocationParser.Integer.type
Bio.GenBank.LocationParser.Symbol.type
Bio.GenBank.LocationParser.UnsignedInteger.type" class="py-name" href="#" onclick="return doclink('link-197', 'type', 'link-59');">type</a></tt><tt class="py-op">+</tt><tt class="py-string">"=%s AND cla."</tt><tt class="py-op">+</tt><tt id="link-198" class="py-name"><a title="Bio.GenBank.LocationParser.Integer.type
Bio.GenBank.LocationParser.Symbol.type
Bio.GenBank.LocationParser.UnsignedInteger.type" class="py-name" href="#" onclick="return doclink('link-198', 'type', 'link-59');">type</a></tt><tt class="py-op">+</tt><tt class="py-string">"=des.sunid"</tt><tt class="py-op">,</tt> <tt class="py-op">(</tt><tt id="link-199" class="py-name"><a title="Bio.EUtils.POM.ElementNode.node
Bio.Nexus.Trees.Tree.node" class="py-name" href="#" onclick="return doclink('link-199', 'node', 'link-168');">node</a></tt><tt class="py-op">.</tt><tt class="py-name">sunid</tt><tt class="py-op">)</tt><tt class="py-op">)</tt> </tt>
<a name="L416"></a><tt class="py-lineno">416</tt> <tt class="py-line"> <tt id="link-200" class="py-name"><a title="BioSQL.BioSeq.DBSeq.data" class="py-name" href="#" onclick="return doclink('link-200', 'data', 'link-145');">data</a></tt> <tt class="py-op">=</tt> <tt class="py-name">cur</tt><tt class="py-op">.</tt><tt class="py-name">fetchall</tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
<a name="L417"></a><tt class="py-lineno">417</tt> <tt class="py-line"> <tt class="py-keyword">for</tt> <tt id="link-201" class="py-name"><a title="Bio.EUtils.setup.d" class="py-name" href="#" onclick="return doclink('link-201', 'd', 'link-188');">d</a></tt> <tt class="py-keyword">in</tt> <tt id="link-202" class="py-name"><a title="BioSQL.BioSeq.DBSeq.data" class="py-name" href="#" onclick="return doclink('link-202', 'data', 'link-145');">data</a></tt><tt class="py-op">:</tt> </tt>
<a name="L418"></a><tt class="py-lineno">418</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">_sunidDict</tt><tt class="py-op">.</tt><tt id="link-203" class="py-name"><a title="Bio.Crystal.Crystal.has_key
Bio.EUtils.POM.ElementNode.has_key
Bio.GenBank.NCBIDictionary.has_key
Bio.PDB.AbstractPropertyMap.AbstractPropertyMap.has_key
Bio.PDB.FragmentMapper'.FragmentMapper.has_key
Bio.Prosite.ExPASyDictionary.has_key
Bio.Prosite.Prodoc.ExPASyDictionary.has_key
Bio.PubMed.Dictionary.has_key
Bio.SwissProt.SProt.ExPASyDictionary.has_key
Martel.Parser.MartelAttributeList.has_key" class="py-name" href="#" onclick="return doclink('link-203', 'has_key', 'link-80');">has_key</a></tt><tt class="py-op">(</tt><tt class="py-name">int</tt><tt class="py-op">(</tt><tt id="link-204" class="py-name"><a title="Bio.EUtils.setup.d" class="py-name" href="#" onclick="return doclink('link-204', 'd', 'link-188');">d</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-op">)</tt><tt class="py-op">:</tt> </tt>
<a name="L419"></a><tt class="py-lineno">419</tt> <tt class="py-line"> <tt class="py-name">n</tt> <tt class="py-op">=</tt> <tt id="link-205" class="py-name"><a title="Bio.Nexus.Nodes.Node
Bio.SCOP.Node" class="py-name" href="#" onclick="return doclink('link-205', 'Node', 'link-58');">Node</a></tt><tt class="py-op">(</tt><tt class="py-name">scop</tt><tt class="py-op">=</tt><tt class="py-name">self</tt><tt class="py-op">)</tt> </tt>
<a name="L420"></a><tt class="py-lineno">420</tt> <tt class="py-line"> <tt class="py-op">[</tt><tt class="py-name">n</tt><tt class="py-op">.</tt><tt class="py-name">sunid</tt><tt class="py-op">,</tt><tt class="py-name">n</tt><tt class="py-op">.</tt><tt id="link-206" class="py-name"><a title="Bio.GenBank.LocationParser.Integer.type
Bio.GenBank.LocationParser.Symbol.type
Bio.GenBank.LocationParser.UnsignedInteger.type" class="py-name" href="#" onclick="return doclink('link-206', 'type', 'link-59');">type</a></tt><tt class="py-op">,</tt><tt class="py-name">n</tt><tt class="py-op">.</tt><tt class="py-name">sccs</tt><tt class="py-op">,</tt><tt class="py-name">n</tt><tt class="py-op">.</tt><tt id="link-207" class="py-name"><a title="Bio.Blast.NCBIStandalone._DescriptionConsumer.description
Bio.Enzyme._RecordConsumer.description
Bio.Prosite._RecordConsumer.description
Bio.Std.description
Bio.SwissProt.SProt._RecordConsumer.description
Bio.SwissProt.SProt._SequenceConsumer.description
Martel.setup.run_local_tests.description" class="py-name" href="#" onclick="return doclink('link-207', 'description', 'link-44');">description</a></tt><tt class="py-op">]</tt> <tt class="py-op">=</tt> <tt id="link-208" class="py-name"><a title="Bio.EUtils.setup.d" class="py-name" href="#" onclick="return doclink('link-208', 'd', 'link-188');">d</a></tt> </tt>
<a name="L421"></a><tt class="py-lineno">421</tt> <tt class="py-line"> <tt class="py-name">n</tt><tt class="py-op">.</tt><tt class="py-name">sunid</tt><tt class="py-op">=</tt><tt class="py-name">int</tt><tt class="py-op">(</tt><tt class="py-name">n</tt><tt class="py-op">.</tt><tt class="py-name">sunid</tt><tt class="py-op">)</tt> </tt>
<a name="L422"></a><tt class="py-lineno">422</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">_sunidDict</tt><tt class="py-op">[</tt><tt class="py-name">n</tt><tt class="py-op">.</tt><tt class="py-name">sunid</tt><tt class="py-op">]</tt> <tt class="py-op">=</tt> <tt class="py-name">n</tt> </tt>
<a name="L423"></a><tt class="py-lineno">423</tt> <tt class="py-line"> </tt>
<a name="L424"></a><tt class="py-lineno">424</tt> <tt class="py-line"> <tt class="py-name">cur</tt><tt class="py-op">.</tt><tt id="link-209" class="py-name"><a title="BioSQL.BioSeqDatabase.Adaptor.execute" class="py-name" href="#" onclick="return doclink('link-209', 'execute', 'link-143');">execute</a></tt><tt class="py-op">(</tt><tt class="py-string">"SELECT parent FROM hie WHERE child=%s"</tt><tt class="py-op">,</tt> <tt class="py-name">n</tt><tt class="py-op">.</tt><tt class="py-name">sunid</tt><tt class="py-op">)</tt> </tt>
<a name="L425"></a><tt class="py-lineno">425</tt> <tt class="py-line"> <tt class="py-name">n</tt><tt class="py-op">.</tt><tt class="py-name">parent</tt> <tt class="py-op">=</tt> <tt class="py-name">cur</tt><tt class="py-op">.</tt><tt class="py-name">fetchone</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="L426"></a><tt class="py-lineno">426</tt> <tt class="py-line"> </tt>
<a name="L427"></a><tt class="py-lineno">427</tt> <tt class="py-line"> <tt class="py-name">cur</tt><tt class="py-op">.</tt><tt id="link-210" class="py-name"><a title="BioSQL.BioSeqDatabase.Adaptor.execute" class="py-name" href="#" onclick="return doclink('link-210', 'execute', 'link-143');">execute</a></tt><tt class="py-op">(</tt><tt class="py-string">"SELECT child FROM hie WHERE parent=%s"</tt><tt class="py-op">,</tt> <tt class="py-name">n</tt><tt class="py-op">.</tt><tt class="py-name">sunid</tt><tt class="py-op">)</tt> </tt>
<a name="L428"></a><tt class="py-lineno">428</tt> <tt class="py-line"> <tt id="link-211" class="py-name"><a title="Bio.Pathway.Rep.Graph.Graph.children
Bio.Pathway.Rep.MultiGraph.MultiGraph.children" class="py-name" href="#" onclick="return doclink('link-211', 'children', 'link-89');">children</a></tt> <tt class="py-op">=</tt> <tt class="py-op">[</tt><tt class="py-op">]</tt> </tt>
<a name="L429"></a><tt class="py-lineno">429</tt> <tt class="py-line"> <tt class="py-keyword">for</tt> <tt class="py-name">c</tt> <tt class="py-keyword">in</tt> <tt class="py-name">cur</tt><tt class="py-op">.</tt><tt class="py-name">fetchall</tt><tt class="py-op">(</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
<a name="L430"></a><tt class="py-lineno">430</tt> <tt class="py-line"> <tt id="link-212" class="py-name"><a title="Bio.Pathway.Rep.Graph.Graph.children
Bio.Pathway.Rep.MultiGraph.MultiGraph.children" class="py-name" href="#" onclick="return doclink('link-212', 'children', 'link-89');">children</a></tt><tt class="py-op">.</tt><tt id="link-213" 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-213', 'append', 'link-68');">append</a></tt><tt class="py-op">(</tt><tt class="py-name">c</tt><tt class="py-op">[</tt><tt class="py-number">0</tt><tt class="py-op">]</tt><tt class="py-op">)</tt> </tt>
<a name="L431"></a><tt class="py-lineno">431</tt> <tt class="py-line"> <tt class="py-name">n</tt><tt class="py-op">.</tt><tt id="link-214" class="py-name"><a title="Bio.Pathway.Rep.Graph.Graph.children
Bio.Pathway.Rep.MultiGraph.MultiGraph.children" class="py-name" href="#" onclick="return doclink('link-214', 'children', 'link-89');">children</a></tt> <tt class="py-op">=</tt> <tt id="link-215" class="py-name"><a title="Bio.Pathway.Rep.Graph.Graph.children
Bio.Pathway.Rep.MultiGraph.MultiGraph.children" class="py-name" href="#" onclick="return doclink('link-215', 'children', 'link-89');">children</a></tt> </tt>
<a name="L432"></a><tt class="py-lineno">432</tt> <tt class="py-line"> </tt>
<a name="L433"></a><tt class="py-lineno">433</tt> <tt class="py-line"> </tt>
<a name="L434"></a><tt class="py-lineno">434</tt> <tt class="py-line"> <tt class="py-name">des_list</tt><tt class="py-op">.</tt><tt id="link-216" 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-216', 'append', 'link-68');">append</a></tt><tt class="py-op">(</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">_sunidDict</tt><tt class="py-op">[</tt><tt class="py-name">int</tt><tt class="py-op">(</tt><tt id="link-217" class="py-name"><a title="Bio.EUtils.setup.d" class="py-name" href="#" onclick="return doclink('link-217', 'd', 'link-188');">d</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-op">]</tt> <tt class="py-op">)</tt> </tt>
<a name="L435"></a><tt class="py-lineno">435</tt> <tt class="py-line"> </tt>
<a name="L436"></a><tt class="py-lineno">436</tt> <tt class="py-line"> <tt class="py-keyword">else</tt><tt class="py-op">:</tt> </tt>
<a name="L437"></a><tt class="py-lineno">437</tt> <tt class="py-line"> <tt class="py-name">cur</tt><tt class="py-op">.</tt><tt id="link-218" class="py-name"><a title="BioSQL.BioSeqDatabase.Adaptor.execute" class="py-name" href="#" onclick="return doclink('link-218', 'execute', 'link-143');">execute</a></tt><tt class="py-op">(</tt><tt class="py-string">"SELECT cla.sunid,sid,pdbid,residues,cla.sccs,type,description,sp\</tt> </tt>
<a name="L438"></a><tt class="py-lineno">438</tt> <tt class="py-line"><tt class="py-string"> FROM cla,des where cla.sunid=des.sunid and cla."</tt><tt class="py-op">+</tt><tt id="link-219" class="py-name"><a title="Bio.EUtils.POM.ElementNode.node
Bio.Nexus.Trees.Tree.node" class="py-name" href="#" onclick="return doclink('link-219', 'node', 'link-168');">node</a></tt><tt class="py-op">.</tt><tt id="link-220" class="py-name"><a title="Bio.GenBank.LocationParser.Integer.type
Bio.GenBank.LocationParser.Symbol.type
Bio.GenBank.LocationParser.UnsignedInteger.type" class="py-name" href="#" onclick="return doclink('link-220', 'type', 'link-59');">type</a></tt><tt class="py-op">+</tt><tt class="py-string">"=%s"</tt><tt class="py-op">,</tt> </tt>
<a name="L439"></a><tt class="py-lineno">439</tt> <tt class="py-line"> <tt id="link-221" class="py-name"><a title="Bio.EUtils.POM.ElementNode.node
Bio.Nexus.Trees.Tree.node" class="py-name" href="#" onclick="return doclink('link-221', 'node', 'link-168');">node</a></tt><tt class="py-op">.</tt><tt class="py-name">sunid</tt><tt class="py-op">)</tt> </tt>
<a name="L440"></a><tt class="py-lineno">440</tt> <tt class="py-line"> </tt>
<a name="L441"></a><tt class="py-lineno">441</tt> <tt class="py-line"> <tt id="link-222" class="py-name"><a title="BioSQL.BioSeq.DBSeq.data" class="py-name" href="#" onclick="return doclink('link-222', 'data', 'link-145');">data</a></tt> <tt class="py-op">=</tt> <tt class="py-name">cur</tt><tt class="py-op">.</tt><tt class="py-name">fetchall</tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
<a name="L442"></a><tt class="py-lineno">442</tt> <tt class="py-line"> <tt class="py-keyword">for</tt> <tt id="link-223" class="py-name"><a title="Bio.EUtils.setup.d" class="py-name" href="#" onclick="return doclink('link-223', 'd', 'link-188');">d</a></tt> <tt class="py-keyword">in</tt> <tt id="link-224" class="py-name"><a title="BioSQL.BioSeq.DBSeq.data" class="py-name" href="#" onclick="return doclink('link-224', 'data', 'link-145');">data</a></tt><tt class="py-op">:</tt> </tt>
<a name="L443"></a><tt class="py-lineno">443</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">_sunidDict</tt><tt class="py-op">.</tt><tt id="link-225" class="py-name"><a title="Bio.Crystal.Crystal.has_key
Bio.EUtils.POM.ElementNode.has_key
Bio.GenBank.NCBIDictionary.has_key
Bio.PDB.AbstractPropertyMap.AbstractPropertyMap.has_key
Bio.PDB.FragmentMapper'.FragmentMapper.has_key
Bio.Prosite.ExPASyDictionary.has_key
Bio.Prosite.Prodoc.ExPASyDictionary.has_key
Bio.PubMed.Dictionary.has_key
Bio.SwissProt.SProt.ExPASyDictionary.has_key
Martel.Parser.MartelAttributeList.has_key" class="py-name" href="#" onclick="return doclink('link-225', 'has_key', 'link-80');">has_key</a></tt><tt class="py-op">(</tt><tt class="py-name">int</tt><tt class="py-op">(</tt><tt id="link-226" class="py-name"><a title="Bio.EUtils.setup.d" class="py-name" href="#" onclick="return doclink('link-226', 'd', 'link-188');">d</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-op">)</tt><tt class="py-op">:</tt> </tt>
<a name="L444"></a><tt class="py-lineno">444</tt> <tt class="py-line"> <tt class="py-name">n</tt> <tt class="py-op">=</tt> <tt id="link-227" class="py-name"><a title="Bio.SCOP.Domain" class="py-name" href="#" onclick="return doclink('link-227', 'Domain', 'link-39');">Domain</a></tt><tt class="py-op">(</tt><tt class="py-name">scop</tt><tt class="py-op">=</tt><tt class="py-name">self</tt><tt class="py-op">)</tt> </tt>
<a name="L445"></a><tt class="py-lineno">445</tt> <tt class="py-line"> <tt class="py-comment">#[n.sunid, n.sid, n.pdbid, n.residues, n.sccs, n.type,</tt> </tt>
<a name="L446"></a><tt class="py-lineno">446</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-comment">#n.description,n.parent] = data</tt> </tt>
<a name="L447"></a><tt class="py-lineno">447</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-op">[</tt><tt class="py-name">n</tt><tt class="py-op">.</tt><tt class="py-name">sunid</tt><tt class="py-op">,</tt><tt class="py-name">n</tt><tt class="py-op">.</tt><tt class="py-name">sid</tt><tt class="py-op">,</tt> <tt class="py-name">pdbid</tt><tt class="py-op">,</tt><tt class="py-name">n</tt><tt class="py-op">.</tt><tt class="py-name">residues</tt><tt class="py-op">,</tt><tt class="py-name">n</tt><tt class="py-op">.</tt><tt class="py-name">sccs</tt><tt class="py-op">,</tt><tt class="py-name">n</tt><tt class="py-op">.</tt><tt id="link-228" class="py-name"><a title="Bio.GenBank.LocationParser.Integer.type
Bio.GenBank.LocationParser.Symbol.type
Bio.GenBank.LocationParser.UnsignedInteger.type" class="py-name" href="#" onclick="return doclink('link-228', 'type', 'link-59');">type</a></tt><tt class="py-op">,</tt><tt class="py-name">n</tt><tt class="py-op">.</tt><tt id="link-229" class="py-name"><a title="Bio.Blast.NCBIStandalone._DescriptionConsumer.description
Bio.Enzyme._RecordConsumer.description
Bio.Prosite._RecordConsumer.description
Bio.Std.description
Bio.SwissProt.SProt._RecordConsumer.description
Bio.SwissProt.SProt._SequenceConsumer.description
Martel.setup.run_local_tests.description" class="py-name" href="#" onclick="return doclink('link-229', 'description', 'link-44');">description</a></tt><tt class="py-op">,</tt> </tt>
<a name="L448"></a><tt class="py-lineno">448</tt> <tt class="py-line"> <tt class="py-name">n</tt><tt class="py-op">.</tt><tt class="py-name">parent</tt><tt class="py-op">]</tt> <tt class="py-op">=</tt> <tt id="link-230" class="py-name"><a title="Bio.EUtils.setup.d" class="py-name" href="#" onclick="return doclink('link-230', 'd', 'link-188');">d</a></tt><tt class="py-op">[</tt><tt class="py-number">0</tt><tt class="py-op">:</tt><tt class="py-number">8</tt><tt class="py-op">]</tt> </tt>
<a name="L449"></a><tt class="py-lineno">449</tt> <tt class="py-line"> <tt class="py-name">n</tt><tt class="py-op">.</tt><tt class="py-name">residues</tt> <tt class="py-op">=</tt> <tt id="link-231" class="py-name"><a title="Bio.SCOP.Residues'.Residues" class="py-name" href="#" onclick="return doclink('link-231', 'Residues', 'link-3');">Residues</a></tt><tt class="py-op">(</tt><tt class="py-name">n</tt><tt class="py-op">.</tt><tt class="py-name">residues</tt><tt class="py-op">)</tt> </tt>
<a name="L450"></a><tt class="py-lineno">450</tt> <tt class="py-line"> <tt class="py-name">n</tt><tt class="py-op">.</tt><tt class="py-name">residues</tt><tt class="py-op">.</tt><tt class="py-name">pdbid</tt> <tt class="py-op">=</tt> <tt class="py-name">pdbid</tt> </tt>
<a name="L451"></a><tt class="py-lineno">451</tt> <tt class="py-line"> <tt class="py-name">n</tt><tt class="py-op">.</tt><tt class="py-name">sunid</tt> <tt class="py-op">=</tt> <tt class="py-name">int</tt><tt class="py-op">(</tt><tt class="py-name">n</tt><tt class="py-op">.</tt><tt class="py-name">sunid</tt><tt class="py-op">)</tt> </tt>
<a name="L452"></a><tt class="py-lineno">452</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">_sunidDict</tt><tt class="py-op">[</tt><tt class="py-name">n</tt><tt class="py-op">.</tt><tt class="py-name">sunid</tt><tt class="py-op">]</tt> <tt class="py-op">=</tt> <tt class="py-name">n</tt> </tt>
<a name="L453"></a><tt class="py-lineno">453</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">_sidDict</tt><tt class="py-op">[</tt><tt class="py-name">n</tt><tt class="py-op">.</tt><tt class="py-name">sid</tt><tt class="py-op">]</tt> <tt class="py-op">=</tt> <tt class="py-name">n</tt> </tt>
<a name="L454"></a><tt class="py-lineno">454</tt> <tt class="py-line"> </tt>
<a name="L455"></a><tt class="py-lineno">455</tt> <tt class="py-line"> </tt>
<a name="L456"></a><tt class="py-lineno">456</tt> <tt class="py-line"> <tt class="py-name">des_list</tt><tt class="py-op">.</tt><tt id="link-232" 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-232', 'append', 'link-68');">append</a></tt><tt class="py-op">(</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">_sunidDict</tt><tt class="py-op">[</tt><tt class="py-name">int</tt><tt class="py-op">(</tt><tt id="link-233" class="py-name"><a title="Bio.EUtils.setup.d" class="py-name" href="#" onclick="return doclink('link-233', 'd', 'link-188');">d</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-op">]</tt> <tt class="py-op">)</tt> </tt>
<a name="L457"></a><tt class="py-lineno">457</tt> <tt class="py-line"> </tt>
<a name="L458"></a><tt class="py-lineno">458</tt> <tt class="py-line"> <tt class="py-keyword">return</tt> <tt class="py-name">des_list</tt> </tt>
</div><a name="L459"></a><tt class="py-lineno">459</tt> <tt class="py-line"> </tt>
<a name="L460"></a><tt class="py-lineno">460</tt> <tt class="py-line"> </tt>
<a name="L461"></a><tt class="py-lineno">461</tt> <tt class="py-line"> </tt>
<a name="L462"></a><tt class="py-lineno">462</tt> <tt class="py-line"> </tt>
<a name="Scop.write_hie_sql"></a><div id="Scop.write_hie_sql-def"><a name="L463"></a><tt class="py-lineno">463</tt> <a class="py-toggle" href="#" id="Scop.write_hie_sql-toggle" onclick="return toggle('Scop.write_hie_sql');">-</a><tt class="py-line"> <tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.SCOP.Scop-class.html#write_hie_sql">write_hie_sql</a><tt class="py-op">(</tt><tt class="py-param">self</tt><tt class="py-op">,</tt> <tt class="py-param">handle</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="Scop.write_hie_sql-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="Scop.write_hie_sql-expanded"><a name="L464"></a><tt class="py-lineno">464</tt> <tt class="py-line"> <tt class="py-docstring">"""Write HIE data to SQL database"""</tt> </tt>
<a name="L465"></a><tt class="py-lineno">465</tt> <tt class="py-line"> <tt class="py-name">cur</tt> <tt class="py-op">=</tt> <tt id="link-234" class="py-name"><a title="Bio.LocusLink.web_parse.handle
Bio.Ndb.handle" class="py-name" href="#" onclick="return doclink('link-234', 'handle', 'link-48');">handle</a></tt><tt class="py-op">.</tt><tt id="link-235" class="py-name"><a title="Bio.DocSQL.Query.cursor
Bio.DocSQL.QuerySingle.cursor" class="py-name" href="#" onclick="return doclink('link-235', 'cursor', 'link-142');">cursor</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
<a name="L466"></a><tt class="py-lineno">466</tt> <tt class="py-line"> </tt>
<a name="L467"></a><tt class="py-lineno">467</tt> <tt class="py-line"> <tt class="py-name">cur</tt><tt class="py-op">.</tt><tt id="link-236" class="py-name"><a title="BioSQL.BioSeqDatabase.Adaptor.execute" class="py-name" href="#" onclick="return doclink('link-236', 'execute', 'link-143');">execute</a></tt><tt class="py-op">(</tt><tt class="py-string">"DROP TABLE IF EXISTS hie"</tt><tt class="py-op">)</tt> </tt>
<a name="L468"></a><tt class="py-lineno">468</tt> <tt class="py-line"> <tt class="py-name">cur</tt><tt class="py-op">.</tt><tt id="link-237" class="py-name"><a title="BioSQL.BioSeqDatabase.Adaptor.execute" class="py-name" href="#" onclick="return doclink('link-237', 'execute', 'link-143');">execute</a></tt><tt class="py-op">(</tt><tt class="py-string">"CREATE TABLE hie (parent INT, child INT, PRIMARY KEY (child),\</tt> </tt>
<a name="L469"></a><tt class="py-lineno">469</tt> <tt class="py-line"><tt class="py-string"> INDEX (parent) )"</tt><tt class="py-op">)</tt> </tt>
<a name="L470"></a><tt class="py-lineno">470</tt> <tt class="py-line"> </tt>
<a name="L471"></a><tt class="py-lineno">471</tt> <tt class="py-line"> <tt class="py-keyword">for</tt> <tt class="py-name">p</tt> <tt class="py-keyword">in</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">_sunidDict</tt><tt class="py-op">.</tt><tt id="link-238" class="py-name"><a title="Bio.Crystal.Crystal.values
Bio.EUtils.MultiDict._BaseMultiDict.values
Bio.GenBank.NCBIDictionary.values
Bio.Mindy.BaseDB.DictLookup.values
Bio.Prosite.ExPASyDictionary.values
Bio.Prosite.Prodoc.ExPASyDictionary.values
Bio.PubMed.Dictionary.values
Bio.SwissProt.SProt.ExPASyDictionary.values
Bio.config.Registry.Registry.values
BioSQL.BioSeqDatabase.BioSeqDatabase.values
BioSQL.BioSeqDatabase.DBServer.values
Martel.Parser.MartelAttributeList.values" class="py-name" href="#" onclick="return doclink('link-238', 'values', 'link-113');">values</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
<a name="L472"></a><tt class="py-lineno">472</tt> <tt class="py-line"> <tt class="py-keyword">for</tt> <tt class="py-name">c</tt> <tt class="py-keyword">in</tt> <tt class="py-name">p</tt><tt class="py-op">.</tt><tt id="link-239" class="py-name"><a title="Bio.Pathway.Rep.Graph.Graph.children
Bio.Pathway.Rep.MultiGraph.MultiGraph.children" class="py-name" href="#" onclick="return doclink('link-239', 'children', 'link-89');">children</a></tt><tt class="py-op">:</tt> </tt>
<a name="L473"></a><tt class="py-lineno">473</tt> <tt class="py-line"> <tt class="py-name">cur</tt><tt class="py-op">.</tt><tt id="link-240" class="py-name"><a title="BioSQL.BioSeqDatabase.Adaptor.execute" class="py-name" href="#" onclick="return doclink('link-240', 'execute', 'link-143');">execute</a></tt><tt class="py-op">(</tt><tt class="py-string">"INSERT INTO hie VALUES (%s,%s)"</tt> <tt class="py-op">%</tt> <tt class="py-op">(</tt><tt class="py-name">p</tt><tt class="py-op">.</tt><tt class="py-name">sunid</tt><tt class="py-op">,</tt> <tt class="py-name">c</tt><tt class="py-op">.</tt><tt class="py-name">sunid</tt><tt class="py-op">)</tt><tt class="py-op">)</tt> </tt>
</div><a name="L474"></a><tt class="py-lineno">474</tt> <tt class="py-line"> </tt>
<a name="L475"></a><tt class="py-lineno">475</tt> <tt class="py-line"> </tt>
<a name="Scop.write_cla_sql"></a><div id="Scop.write_cla_sql-def"><a name="L476"></a><tt class="py-lineno">476</tt> <a class="py-toggle" href="#" id="Scop.write_cla_sql-toggle" onclick="return toggle('Scop.write_cla_sql');">-</a><tt class="py-line"> <tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.SCOP.Scop-class.html#write_cla_sql">write_cla_sql</a><tt class="py-op">(</tt><tt class="py-param">self</tt><tt class="py-op">,</tt> <tt class="py-param">handle</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="Scop.write_cla_sql-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="Scop.write_cla_sql-expanded"><a name="L477"></a><tt class="py-lineno">477</tt> <tt class="py-line"> <tt class="py-docstring">"""Write CLA data to SQL database"""</tt> </tt>
<a name="L478"></a><tt class="py-lineno">478</tt> <tt class="py-line"> <tt class="py-name">cur</tt> <tt class="py-op">=</tt> <tt id="link-241" class="py-name"><a title="Bio.LocusLink.web_parse.handle
Bio.Ndb.handle" class="py-name" href="#" onclick="return doclink('link-241', 'handle', 'link-48');">handle</a></tt><tt class="py-op">.</tt><tt id="link-242" class="py-name"><a title="Bio.DocSQL.Query.cursor
Bio.DocSQL.QuerySingle.cursor" class="py-name" href="#" onclick="return doclink('link-242', 'cursor', 'link-142');">cursor</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
<a name="L479"></a><tt class="py-lineno">479</tt> <tt class="py-line"> </tt>
<a name="L480"></a><tt class="py-lineno">480</tt> <tt class="py-line"> <tt class="py-name">cur</tt><tt class="py-op">.</tt><tt id="link-243" class="py-name"><a title="BioSQL.BioSeqDatabase.Adaptor.execute" class="py-name" href="#" onclick="return doclink('link-243', 'execute', 'link-143');">execute</a></tt><tt class="py-op">(</tt><tt class="py-string">"DROP TABLE IF EXISTS cla"</tt><tt class="py-op">)</tt> </tt>
<a name="L481"></a><tt class="py-lineno">481</tt> <tt class="py-line"> <tt class="py-name">cur</tt><tt class="py-op">.</tt><tt id="link-244" class="py-name"><a title="BioSQL.BioSeqDatabase.Adaptor.execute" class="py-name" href="#" onclick="return doclink('link-244', 'execute', 'link-143');">execute</a></tt><tt class="py-op">(</tt><tt class="py-string">"CREATE TABLE cla (sunid INT, sid CHAR(8), pdbid CHAR(4),\</tt> </tt>
<a name="L482"></a><tt class="py-lineno">482</tt> <tt class="py-line"><tt class="py-string"> residues VARCHAR(50), sccs CHAR(10), cl INT, cf INT, sf INT, fa INT,\</tt> </tt>
<a name="L483"></a><tt class="py-lineno">483</tt> <tt class="py-line"><tt class="py-string"> dm INT, sp INT, px INT, PRIMARY KEY (sunid), INDEX (SID) )"</tt><tt class="py-op">)</tt> </tt>
<a name="L484"></a><tt class="py-lineno">484</tt> <tt class="py-line"> </tt>
<a name="L485"></a><tt class="py-lineno">485</tt> <tt class="py-line"> <tt class="py-keyword">for</tt> <tt class="py-name">n</tt> <tt class="py-keyword">in</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">_sidDict</tt><tt class="py-op">.</tt><tt id="link-245" class="py-name"><a title="Bio.Crystal.Crystal.values
Bio.EUtils.MultiDict._BaseMultiDict.values
Bio.GenBank.NCBIDictionary.values
Bio.Mindy.BaseDB.DictLookup.values
Bio.Prosite.ExPASyDictionary.values
Bio.Prosite.Prodoc.ExPASyDictionary.values
Bio.PubMed.Dictionary.values
Bio.SwissProt.SProt.ExPASyDictionary.values
Bio.config.Registry.Registry.values
BioSQL.BioSeqDatabase.BioSeqDatabase.values
BioSQL.BioSeqDatabase.DBServer.values
Martel.Parser.MartelAttributeList.values" class="py-name" href="#" onclick="return doclink('link-245', 'values', 'link-113');">values</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
<a name="L486"></a><tt class="py-lineno">486</tt> <tt class="py-line"> <tt class="py-name">c</tt> <tt class="py-op">=</tt> <tt class="py-name">n</tt><tt class="py-op">.</tt><tt id="link-246" class="py-name"><a title="Bio.SCOP.Domain.toClaRecord" class="py-name" href="#" onclick="return doclink('link-246', 'toClaRecord', 'link-141');">toClaRecord</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
<a name="L487"></a><tt class="py-lineno">487</tt> <tt class="py-line"> <tt class="py-name">cur</tt><tt class="py-op">.</tt><tt id="link-247" class="py-name"><a title="BioSQL.BioSeqDatabase.Adaptor.execute" class="py-name" href="#" onclick="return doclink('link-247', 'execute', 'link-143');">execute</a></tt><tt class="py-op">(</tt> <tt class="py-string">"INSERT INTO cla VALUES (%s,%s,%s,%s,%s,%s,%s,%s,%s,%s,%s,%s)"</tt><tt class="py-op">,</tt> </tt>
<a name="L488"></a><tt class="py-lineno">488</tt> <tt class="py-line"> <tt class="py-op">(</tt><tt class="py-name">n</tt><tt class="py-op">.</tt><tt class="py-name">sunid</tt><tt class="py-op">,</tt> <tt class="py-name">n</tt><tt class="py-op">.</tt><tt class="py-name">sid</tt><tt class="py-op">,</tt> <tt class="py-name">c</tt><tt class="py-op">.</tt><tt class="py-name">residues</tt><tt class="py-op">.</tt><tt class="py-name">pdbid</tt><tt class="py-op">,</tt> <tt class="py-name">c</tt><tt class="py-op">.</tt><tt class="py-name">residues</tt><tt class="py-op">,</tt> <tt class="py-name">n</tt><tt class="py-op">.</tt><tt class="py-name">sccs</tt><tt class="py-op">,</tt> </tt>
<a name="L489"></a><tt class="py-lineno">489</tt> <tt class="py-line"> <tt class="py-name">n</tt><tt class="py-op">.</tt><tt id="link-248" class="py-name" targets="Method Bio.SCOP.Node.getAscendent()=Bio.SCOP.Node-class.html#getAscendent"><a title="Bio.SCOP.Node.getAscendent" class="py-name" href="#" onclick="return doclink('link-248', 'getAscendent', 'link-248');">getAscendent</a></tt><tt class="py-op">(</tt><tt class="py-string">'cl'</tt><tt class="py-op">)</tt><tt class="py-op">.</tt><tt class="py-name">sunid</tt><tt class="py-op">,</tt> <tt class="py-name">n</tt><tt class="py-op">.</tt><tt id="link-249" class="py-name"><a title="Bio.SCOP.Node.getAscendent" class="py-name" href="#" onclick="return doclink('link-249', 'getAscendent', 'link-248');">getAscendent</a></tt><tt class="py-op">(</tt><tt class="py-string">'cf'</tt><tt class="py-op">)</tt><tt class="py-op">.</tt><tt class="py-name">sunid</tt><tt class="py-op">,</tt> </tt>
<a name="L490"></a><tt class="py-lineno">490</tt> <tt class="py-line"> <tt class="py-name">n</tt><tt class="py-op">.</tt><tt id="link-250" class="py-name"><a title="Bio.SCOP.Node.getAscendent" class="py-name" href="#" onclick="return doclink('link-250', 'getAscendent', 'link-248');">getAscendent</a></tt><tt class="py-op">(</tt><tt class="py-string">'sf'</tt><tt class="py-op">)</tt><tt class="py-op">.</tt><tt class="py-name">sunid</tt><tt class="py-op">,</tt> <tt class="py-name">n</tt><tt class="py-op">.</tt><tt id="link-251" class="py-name"><a title="Bio.SCOP.Node.getAscendent" class="py-name" href="#" onclick="return doclink('link-251', 'getAscendent', 'link-248');">getAscendent</a></tt><tt class="py-op">(</tt><tt class="py-string">'fa'</tt><tt class="py-op">)</tt><tt class="py-op">.</tt><tt class="py-name">sunid</tt><tt class="py-op">,</tt> </tt>
<a name="L491"></a><tt class="py-lineno">491</tt> <tt class="py-line"> <tt class="py-name">n</tt><tt class="py-op">.</tt><tt id="link-252" class="py-name"><a title="Bio.SCOP.Node.getAscendent" class="py-name" href="#" onclick="return doclink('link-252', 'getAscendent', 'link-248');">getAscendent</a></tt><tt class="py-op">(</tt><tt class="py-string">'dm'</tt><tt class="py-op">)</tt><tt class="py-op">.</tt><tt class="py-name">sunid</tt><tt class="py-op">,</tt> <tt class="py-name">n</tt><tt class="py-op">.</tt><tt id="link-253" class="py-name"><a title="Bio.SCOP.Node.getAscendent" class="py-name" href="#" onclick="return doclink('link-253', 'getAscendent', 'link-248');">getAscendent</a></tt><tt class="py-op">(</tt><tt class="py-string">'sp'</tt><tt class="py-op">)</tt><tt class="py-op">.</tt><tt class="py-name">sunid</tt><tt class="py-op">,</tt> </tt>
<a name="L492"></a><tt class="py-lineno">492</tt> <tt class="py-line"> <tt class="py-name">n</tt><tt class="py-op">.</tt><tt class="py-name">sunid</tt> <tt class="py-op">)</tt><tt class="py-op">)</tt> </tt>
</div><a name="L493"></a><tt class="py-lineno">493</tt> <tt class="py-line"> </tt>
<a name="L494"></a><tt class="py-lineno">494</tt> <tt class="py-line"> </tt>
<a name="Scop.write_des_sql"></a><div id="Scop.write_des_sql-def"><a name="L495"></a><tt class="py-lineno">495</tt> <a class="py-toggle" href="#" id="Scop.write_des_sql-toggle" onclick="return toggle('Scop.write_des_sql');">-</a><tt class="py-line"> <tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.SCOP.Scop-class.html#write_des_sql">write_des_sql</a><tt class="py-op">(</tt><tt class="py-param">self</tt><tt class="py-op">,</tt> <tt class="py-param">handle</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="Scop.write_des_sql-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="Scop.write_des_sql-expanded"><a name="L496"></a><tt class="py-lineno">496</tt> <tt class="py-line"> <tt class="py-docstring">"""Write DES data to SQL database"""</tt> </tt>
<a name="L497"></a><tt class="py-lineno">497</tt> <tt class="py-line"> <tt class="py-name">cur</tt> <tt class="py-op">=</tt> <tt id="link-254" class="py-name"><a title="Bio.LocusLink.web_parse.handle
Bio.Ndb.handle" class="py-name" href="#" onclick="return doclink('link-254', 'handle', 'link-48');">handle</a></tt><tt class="py-op">.</tt><tt id="link-255" class="py-name"><a title="Bio.DocSQL.Query.cursor
Bio.DocSQL.QuerySingle.cursor" class="py-name" href="#" onclick="return doclink('link-255', 'cursor', 'link-142');">cursor</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
<a name="L498"></a><tt class="py-lineno">498</tt> <tt class="py-line"> </tt>
<a name="L499"></a><tt class="py-lineno">499</tt> <tt class="py-line"> <tt class="py-name">cur</tt><tt class="py-op">.</tt><tt id="link-256" class="py-name"><a title="BioSQL.BioSeqDatabase.Adaptor.execute" class="py-name" href="#" onclick="return doclink('link-256', 'execute', 'link-143');">execute</a></tt><tt class="py-op">(</tt><tt class="py-string">"DROP TABLE IF EXISTS des"</tt><tt class="py-op">)</tt> </tt>
<a name="L500"></a><tt class="py-lineno">500</tt> <tt class="py-line"> <tt class="py-name">cur</tt><tt class="py-op">.</tt><tt id="link-257" class="py-name"><a title="BioSQL.BioSeqDatabase.Adaptor.execute" class="py-name" href="#" onclick="return doclink('link-257', 'execute', 'link-143');">execute</a></tt><tt class="py-op">(</tt><tt class="py-string">"CREATE TABLE des (sunid INT, type CHAR(2), sccs CHAR(10),\</tt> </tt>
<a name="L501"></a><tt class="py-lineno">501</tt> <tt class="py-line"><tt class="py-string"> description VARCHAR(255),\</tt> </tt>
<a name="L502"></a><tt class="py-lineno">502</tt> <tt class="py-line"><tt class="py-string"> PRIMARY KEY (sunid) )"</tt><tt class="py-op">)</tt> </tt>
<a name="L503"></a><tt class="py-lineno">503</tt> <tt class="py-line"> </tt>
<a name="L504"></a><tt class="py-lineno">504</tt> <tt class="py-line"> <tt class="py-keyword">for</tt> <tt class="py-name">n</tt> <tt class="py-keyword">in</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">_sunidDict</tt><tt class="py-op">.</tt><tt id="link-258" class="py-name"><a title="Bio.Crystal.Crystal.values
Bio.EUtils.MultiDict._BaseMultiDict.values
Bio.GenBank.NCBIDictionary.values
Bio.Mindy.BaseDB.DictLookup.values
Bio.Prosite.ExPASyDictionary.values
Bio.Prosite.Prodoc.ExPASyDictionary.values
Bio.PubMed.Dictionary.values
Bio.SwissProt.SProt.ExPASyDictionary.values
Bio.config.Registry.Registry.values
BioSQL.BioSeqDatabase.BioSeqDatabase.values
BioSQL.BioSeqDatabase.DBServer.values
Martel.Parser.MartelAttributeList.values" class="py-name" href="#" onclick="return doclink('link-258', 'values', 'link-113');">values</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
<a name="L505"></a><tt class="py-lineno">505</tt> <tt class="py-line"> <tt class="py-name">cur</tt><tt class="py-op">.</tt><tt id="link-259" class="py-name"><a title="BioSQL.BioSeqDatabase.Adaptor.execute" class="py-name" href="#" onclick="return doclink('link-259', 'execute', 'link-143');">execute</a></tt><tt class="py-op">(</tt> <tt class="py-string">"INSERT INTO des VALUES (%s,%s,%s,%s)"</tt><tt class="py-op">,</tt> </tt>
<a name="L506"></a><tt class="py-lineno">506</tt> <tt class="py-line"> <tt class="py-op">(</tt> <tt class="py-name">n</tt><tt class="py-op">.</tt><tt class="py-name">sunid</tt><tt class="py-op">,</tt> <tt class="py-name">n</tt><tt class="py-op">.</tt><tt id="link-260" class="py-name"><a title="Bio.GenBank.LocationParser.Integer.type
Bio.GenBank.LocationParser.Symbol.type
Bio.GenBank.LocationParser.UnsignedInteger.type" class="py-name" href="#" onclick="return doclink('link-260', 'type', 'link-59');">type</a></tt><tt class="py-op">,</tt> <tt class="py-name">n</tt><tt class="py-op">.</tt><tt class="py-name">sccs</tt><tt class="py-op">,</tt> <tt class="py-name">n</tt><tt class="py-op">.</tt><tt id="link-261" class="py-name"><a title="Bio.Blast.NCBIStandalone._DescriptionConsumer.description
Bio.Enzyme._RecordConsumer.description
Bio.Prosite._RecordConsumer.description
Bio.Std.description
Bio.SwissProt.SProt._RecordConsumer.description
Bio.SwissProt.SProt._SequenceConsumer.description
Martel.setup.run_local_tests.description" class="py-name" href="#" onclick="return doclink('link-261', 'description', 'link-44');">description</a></tt> <tt class="py-op">)</tt> <tt class="py-op">)</tt> </tt>
</div></div><a name="L507"></a><tt class="py-lineno">507</tt> <tt class="py-line"> </tt>
<a name="L508"></a><tt class="py-lineno">508</tt> <tt class="py-line"> </tt>
<a name="L509"></a><tt class="py-lineno">509</tt> <tt class="py-line"> </tt>
<a name="Node"></a><div id="Node-def"><a name="L510"></a><tt class="py-lineno">510</tt> <a class="py-toggle" href="#" id="Node-toggle" onclick="return toggle('Node');">-</a><tt class="py-line"><tt class="py-keyword">class</tt> <a class="py-def-name" href="Bio.SCOP.Node-class.html">Node</a> <tt class="py-op">:</tt> </tt>
</div><div id="Node-collapsed" style="display:none;" pad="+++" indent="++++"></div><div id="Node-expanded"><a name="L511"></a><tt class="py-lineno">511</tt> <tt class="py-line"> <tt class="py-docstring">""" A node in the Scop hierarchy</tt> </tt>
<a name="L512"></a><tt class="py-lineno">512</tt> <tt class="py-line"><tt class="py-docstring"></tt> </tt>
<a name="L513"></a><tt class="py-lineno">513</tt> <tt class="py-line"><tt class="py-docstring"> sunid -- SCOP unique identifiers. e.g. '14986'</tt> </tt>
<a name="L514"></a><tt class="py-lineno">514</tt> <tt class="py-line"><tt class="py-docstring"></tt> </tt>
<a name="L515"></a><tt class="py-lineno">515</tt> <tt class="py-line"><tt class="py-docstring"> parent -- The parent node</tt> </tt>
<a name="L516"></a><tt class="py-lineno">516</tt> <tt class="py-line"><tt class="py-docstring"></tt> </tt>
<a name="L517"></a><tt class="py-lineno">517</tt> <tt class="py-line"><tt class="py-docstring"> children -- A list of child nodes</tt> </tt>
<a name="L518"></a><tt class="py-lineno">518</tt> <tt class="py-line"><tt class="py-docstring"></tt> </tt>
<a name="L519"></a><tt class="py-lineno">519</tt> <tt class="py-line"><tt class="py-docstring"> sccs -- SCOP concise classification string. e.g. 'a.1.1.2'</tt> </tt>
<a name="L520"></a><tt class="py-lineno">520</tt> <tt class="py-line"><tt class="py-docstring"></tt> </tt>
<a name="L521"></a><tt class="py-lineno">521</tt> <tt class="py-line"><tt class="py-docstring"> type -- A 2 letter node type code. e.g. 'px' for domains</tt> </tt>
<a name="L522"></a><tt class="py-lineno">522</tt> <tt class="py-line"><tt class="py-docstring"></tt> </tt>
<a name="L523"></a><tt class="py-lineno">523</tt> <tt class="py-line"><tt class="py-docstring"> description -- </tt> </tt>
<a name="L524"></a><tt class="py-lineno">524</tt> <tt class="py-line"><tt class="py-docstring"> </tt> </tt>
<a name="L525"></a><tt class="py-lineno">525</tt> <tt class="py-line"><tt class="py-docstring"> """</tt> </tt>
<a name="Node.__init__"></a><div id="Node.__init__-def"><a name="L526"></a><tt class="py-lineno">526</tt> <a class="py-toggle" href="#" id="Node.__init__-toggle" onclick="return toggle('Node.__init__');">-</a><tt class="py-line"> <tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.SCOP.Node-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">scop</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="Node.__init__-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="Node.__init__-expanded"><a name="L527"></a><tt class="py-lineno">527</tt> <tt class="py-line"> <tt class="py-docstring">"""Create a Node in the scop hierarchy. If a Scop instance is provided to the</tt> </tt>
<a name="L528"></a><tt class="py-lineno">528</tt> <tt class="py-line"><tt class="py-docstring"> constructor, this will be used to lookup related references using the SQL</tt> </tt>
<a name="L529"></a><tt class="py-lineno">529</tt> <tt class="py-line"><tt class="py-docstring"> methods. If no instance is provided, it is assumed the whole tree exists</tt> </tt>
<a name="L530"></a><tt class="py-lineno">530</tt> <tt class="py-line"><tt class="py-docstring"> and is connected."""</tt> </tt>
<a name="L531"></a><tt class="py-lineno">531</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">sunid</tt><tt class="py-op">=</tt><tt class="py-string">''</tt> </tt>
<a name="L532"></a><tt class="py-lineno">532</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">parent</tt> <tt class="py-op">=</tt> <tt class="py-name">None</tt> </tt>
<a name="L533"></a><tt class="py-lineno">533</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-262" class="py-name"><a title="Bio.Pathway.Rep.Graph.Graph.children
Bio.Pathway.Rep.MultiGraph.MultiGraph.children" class="py-name" href="#" onclick="return doclink('link-262', 'children', 'link-89');">children</a></tt><tt class="py-op">=</tt><tt class="py-op">[</tt><tt class="py-op">]</tt> </tt>
<a name="L534"></a><tt class="py-lineno">534</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">sccs</tt> <tt class="py-op">=</tt> <tt class="py-string">''</tt> </tt>
<a name="L535"></a><tt class="py-lineno">535</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-263" class="py-name"><a title="Bio.GenBank.LocationParser.Integer.type
Bio.GenBank.LocationParser.Symbol.type
Bio.GenBank.LocationParser.UnsignedInteger.type" class="py-name" href="#" onclick="return doclink('link-263', 'type', 'link-59');">type</a></tt> <tt class="py-op">=</tt><tt class="py-string">''</tt> </tt>
<a name="L536"></a><tt class="py-lineno">536</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-264" class="py-name"><a title="Bio.Blast.NCBIStandalone._DescriptionConsumer.description
Bio.Enzyme._RecordConsumer.description
Bio.Prosite._RecordConsumer.description
Bio.Std.description
Bio.SwissProt.SProt._RecordConsumer.description
Bio.SwissProt.SProt._SequenceConsumer.description
Martel.setup.run_local_tests.description" class="py-name" href="#" onclick="return doclink('link-264', 'description', 'link-44');">description</a></tt> <tt class="py-op">=</tt><tt class="py-string">''</tt> </tt>
<a name="L537"></a><tt class="py-lineno">537</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">scop</tt><tt class="py-op">=</tt><tt class="py-name">scop</tt> </tt>
</div><a name="L538"></a><tt class="py-lineno">538</tt> <tt class="py-line"> </tt>
<a name="Node.__str__"></a><div id="Node.__str__-def"><a name="L539"></a><tt class="py-lineno">539</tt> <a class="py-toggle" href="#" id="Node.__str__-toggle" onclick="return toggle('Node.__str__');">-</a><tt class="py-line"> <tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.SCOP.Node-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="Node.__str__-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="Node.__str__-expanded"><a name="L540"></a><tt class="py-lineno">540</tt> <tt class="py-line"> <tt id="link-265" 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-265', 's', 'link-265');">s</a></tt> <tt class="py-op">=</tt> <tt class="py-op">[</tt><tt class="py-op">]</tt> </tt>
<a name="L541"></a><tt class="py-lineno">541</tt> <tt class="py-line"> <tt id="link-266" class="py-name"><a title="Martel.test.test_swissprot38.s" class="py-name" href="#" onclick="return doclink('link-266', 's', 'link-265');">s</a></tt><tt class="py-op">.</tt><tt id="link-267" 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-267', 'append', 'link-68');">append</a></tt><tt class="py-op">(</tt><tt class="py-name">str</tt><tt class="py-op">(</tt><tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">sunid</tt><tt class="py-op">)</tt><tt class="py-op">)</tt> </tt>
<a name="L542"></a><tt class="py-lineno">542</tt> <tt class="py-line"> <tt id="link-268" class="py-name"><a title="Martel.test.test_swissprot38.s" class="py-name" href="#" onclick="return doclink('link-268', 's', 'link-265');">s</a></tt><tt class="py-op">.</tt><tt id="link-269" 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-269', 'append', 'link-68');">append</a></tt><tt class="py-op">(</tt><tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">sccs</tt><tt class="py-op">)</tt> </tt>
<a name="L543"></a><tt class="py-lineno">543</tt> <tt class="py-line"> <tt id="link-270" class="py-name"><a title="Martel.test.test_swissprot38.s" class="py-name" href="#" onclick="return doclink('link-270', 's', 'link-265');">s</a></tt><tt class="py-op">.</tt><tt id="link-271" 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-271', 'append', 'link-68');">append</a></tt><tt class="py-op">(</tt><tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-272" class="py-name"><a title="Bio.GenBank.LocationParser.Integer.type
Bio.GenBank.LocationParser.Symbol.type
Bio.GenBank.LocationParser.UnsignedInteger.type" class="py-name" href="#" onclick="return doclink('link-272', 'type', 'link-59');">type</a></tt><tt class="py-op">)</tt> </tt>
<a name="L544"></a><tt class="py-lineno">544</tt> <tt class="py-line"> <tt id="link-273" class="py-name"><a title="Martel.test.test_swissprot38.s" class="py-name" href="#" onclick="return doclink('link-273', 's', 'link-265');">s</a></tt><tt class="py-op">.</tt><tt id="link-274" 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-274', 'append', 'link-68');">append</a></tt><tt class="py-op">(</tt><tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-275" class="py-name"><a title="Bio.Blast.NCBIStandalone._DescriptionConsumer.description
Bio.Enzyme._RecordConsumer.description
Bio.Prosite._RecordConsumer.description
Bio.Std.description
Bio.SwissProt.SProt._RecordConsumer.description
Bio.SwissProt.SProt._SequenceConsumer.description
Martel.setup.run_local_tests.description" class="py-name" href="#" onclick="return doclink('link-275', 'description', 'link-44');">description</a></tt><tt class="py-op">)</tt> </tt>
<a name="L545"></a><tt class="py-lineno">545</tt> <tt class="py-line"> </tt>
<a name="L546"></a><tt class="py-lineno">546</tt> <tt class="py-line"> <tt class="py-keyword">return</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-276" class="py-name"><a title="Martel.test.test_swissprot38.s" class="py-name" href="#" onclick="return doclink('link-276', 's', 'link-265');">s</a></tt><tt class="py-op">)</tt> </tt>
</div><a name="L547"></a><tt class="py-lineno">547</tt> <tt class="py-line"> </tt>
<a name="Node.toHieRecord"></a><div id="Node.toHieRecord-def"><a name="L548"></a><tt class="py-lineno">548</tt> <a class="py-toggle" href="#" id="Node.toHieRecord-toggle" onclick="return toggle('Node.toHieRecord');">-</a><tt class="py-line"> <tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.SCOP.Node-class.html#toHieRecord">toHieRecord</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="Node.toHieRecord-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="Node.toHieRecord-expanded"><a name="L549"></a><tt class="py-lineno">549</tt> <tt class="py-line"> <tt class="py-docstring">"""Return an Hie.Record"""</tt> </tt>
<a name="L550"></a><tt class="py-lineno">550</tt> <tt class="py-line"> <tt class="py-name">rec</tt> <tt class="py-op">=</tt> <tt id="link-277" class="py-name"><a title="Bio.SCOP.Hie" class="py-name" href="#" onclick="return doclink('link-277', 'Hie', 'link-2');">Hie</a></tt><tt class="py-op">.</tt><tt id="link-278" class="py-name" targets="Module Bio.Blast.Record=Bio.Blast.Record-module.html,Module Bio.CDD.Record=Bio.CDD.Record-module.html,Class Bio.CDD.Record.Record=Bio.CDD.Record.Record-class.html,Class Bio.Cluster.Record=Bio.Cluster.Record-class.html,Class Bio.Compass.Record=Bio.Compass.Record-class.html,Module Bio.ECell.Record=Bio.ECell.Record-module.html,Class Bio.ECell.Record.Record=Bio.ECell.Record.Record-class.html,Class Bio.Fasta.Record=Bio.Fasta.Record-class.html,Module Bio.GenBank.Record=Bio.GenBank.Record-module.html,Class Bio.GenBank.Record.Record=Bio.GenBank.Record.Record-class.html,Module Bio.Geo.Record=Bio.Geo.Record-module.html,Class Bio.Geo.Record.Record=Bio.Geo.Record.Record-class.html,Class Bio.Gobase.Record=Bio.Gobase.Record-class.html,Module Bio.IntelliGenetics.Record=Bio.IntelliGenetics.Record-module.html,Class Bio.IntelliGenetics.Record.Record=Bio.IntelliGenetics.Record.Record-class.html,Class Bio.InterPro.Record=Bio.InterPro.Record-class.html,Class Bio.KEGG.Compound.Record=Bio.KEGG.Compound.Record-class.html,Class Bio.KEGG.Enzyme.Record=Bio.KEGG.Enzyme.Record-class.html,Class Bio.LocusLink.Record=Bio.LocusLink.Record-class.html,Class Bio.LocusLink.web_parse.Record=Bio.LocusLink.web_parse.Record-class.html,Class Bio.Medline.Record=Bio.Medline.Record-class.html,Module Bio.MetaTool.Record=Bio.MetaTool.Record-module.html,Class Bio.MetaTool.Record.Record=Bio.MetaTool.Record.Record-class.html,Module Bio.NBRF.Record=Bio.NBRF.Record-module.html,Class Bio.NBRF.Record.Record=Bio.NBRF.Record.Record-class.html,Class Bio.Ndb.Record=Bio.Ndb.Record-class.html,Class Bio.PopGen.FDist.Record=Bio.PopGen.FDist.Record-class.html,Class Bio.PopGen.GenePop.Record=Bio.PopGen.GenePop.Record-class.html,Class Bio.Prosite.Prodoc.Record=Bio.Prosite.Prodoc.Record-class.html,Class Bio.Prosite.Record=Bio.Prosite.Record-class.html,Class Bio.Rebase.Record=Bio.Rebase.Record-class.html,Class Bio.SCOP.Cla.Record=Bio.SCOP.Cla.Record-class.html,Class Bio.SCOP.Des.Record=Bio.SCOP.Des.Record-class.html,Class Bio.SCOP.Dom.Record=Bio.SCOP.Dom.Record-class.html,Class Bio.SCOP.Hie.Record=Bio.SCOP.Hie.Record-class.html,Module Bio.Saf.Record=Bio.Saf.Record-module.html,Class Bio.Saf.Record.Record=Bio.Saf.Record.Record-class.html,Class Bio.Sequencing.Phd.Record=Bio.Sequencing.Phd.Record-class.html,Class Bio.SwissProt.KeyWList.Record=Bio.SwissProt.KeyWList.Record-class.html,Class Bio.SwissProt.SProt.Record=Bio.SwissProt.SProt.Record-class.html"><a title="Bio.Blast.Record
Bio.CDD.Record
Bio.CDD.Record.Record
Bio.Cluster.Record
Bio.Compass.Record
Bio.ECell.Record
Bio.ECell.Record.Record
Bio.Fasta.Record
Bio.GenBank.Record
Bio.GenBank.Record.Record
Bio.Geo.Record
Bio.Geo.Record.Record
Bio.Gobase.Record
Bio.IntelliGenetics.Record
Bio.IntelliGenetics.Record.Record
Bio.InterPro.Record
Bio.KEGG.Compound.Record
Bio.KEGG.Enzyme.Record
Bio.LocusLink.Record
Bio.LocusLink.web_parse.Record
Bio.Medline.Record
Bio.MetaTool.Record
Bio.MetaTool.Record.Record
Bio.NBRF.Record
Bio.NBRF.Record.Record
Bio.Ndb.Record
Bio.PopGen.FDist.Record
Bio.PopGen.GenePop.Record
Bio.Prosite.Prodoc.Record
Bio.Prosite.Record
Bio.Rebase.Record
Bio.SCOP.Cla.Record
Bio.SCOP.Des.Record
Bio.SCOP.Dom.Record
Bio.SCOP.Hie.Record
Bio.Saf.Record
Bio.Saf.Record.Record
Bio.Sequencing.Phd.Record
Bio.SwissProt.KeyWList.Record
Bio.SwissProt.SProt.Record" class="py-name" href="#" onclick="return doclink('link-278', 'Record', 'link-278');">Record</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
<a name="L551"></a><tt class="py-lineno">551</tt> <tt class="py-line"> <tt class="py-name">rec</tt><tt class="py-op">.</tt><tt class="py-name">sunid</tt> <tt class="py-op">=</tt> <tt class="py-name">str</tt><tt class="py-op">(</tt><tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">sunid</tt><tt class="py-op">)</tt> </tt>
<a name="L552"></a><tt class="py-lineno">552</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-279" class="py-name" targets="Method Bio.SCOP.Node.getParent()=Bio.SCOP.Node-class.html#getParent"><a title="Bio.SCOP.Node.getParent" class="py-name" href="#" onclick="return doclink('link-279', 'getParent', 'link-279');">getParent</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt> <tt class="py-op">:</tt> <tt class="py-comment">#Not root node</tt> </tt>
<a name="L553"></a><tt class="py-lineno">553</tt> <tt class="py-line"> <tt class="py-name">rec</tt><tt class="py-op">.</tt><tt class="py-name">parent</tt> <tt class="py-op">=</tt> <tt class="py-name">str</tt><tt class="py-op">(</tt><tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-280" class="py-name"><a title="Bio.SCOP.Node.getParent" class="py-name" href="#" onclick="return doclink('link-280', 'getParent', 'link-279');">getParent</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt><tt class="py-op">.</tt><tt class="py-name">sunid</tt><tt class="py-op">)</tt> </tt>
<a name="L554"></a><tt class="py-lineno">554</tt> <tt class="py-line"> <tt class="py-keyword">else</tt><tt class="py-op">:</tt> </tt>
<a name="L555"></a><tt class="py-lineno">555</tt> <tt class="py-line"> <tt class="py-name">rec</tt><tt class="py-op">.</tt><tt class="py-name">parent</tt> <tt class="py-op">=</tt> <tt class="py-string">'-'</tt> </tt>
<a name="L556"></a><tt class="py-lineno">556</tt> <tt class="py-line"> <tt class="py-keyword">for</tt> <tt class="py-name">c</tt> <tt class="py-keyword">in</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-281" class="py-name"><a title="Bio.SCOP.Node.getChildren" class="py-name" href="#" onclick="return doclink('link-281', 'getChildren', 'link-187');">getChildren</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt> <tt class="py-op">:</tt> </tt>
<a name="L557"></a><tt class="py-lineno">557</tt> <tt class="py-line"> <tt class="py-name">rec</tt><tt class="py-op">.</tt><tt id="link-282" class="py-name"><a title="Bio.Pathway.Rep.Graph.Graph.children
Bio.Pathway.Rep.MultiGraph.MultiGraph.children" class="py-name" href="#" onclick="return doclink('link-282', 'children', 'link-89');">children</a></tt><tt class="py-op">.</tt><tt id="link-283" 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-283', 'append', 'link-68');">append</a></tt><tt class="py-op">(</tt><tt class="py-name">str</tt><tt class="py-op">(</tt><tt class="py-name">c</tt><tt class="py-op">.</tt><tt class="py-name">sunid</tt><tt class="py-op">)</tt><tt class="py-op">)</tt> </tt>
<a name="L558"></a><tt class="py-lineno">558</tt> <tt class="py-line"> <tt class="py-keyword">return</tt> <tt class="py-name">rec</tt> </tt>
</div><a name="L559"></a><tt class="py-lineno">559</tt> <tt class="py-line"> </tt>
<a name="Node.toDesRecord"></a><div id="Node.toDesRecord-def"><a name="L560"></a><tt class="py-lineno">560</tt> <a class="py-toggle" href="#" id="Node.toDesRecord-toggle" onclick="return toggle('Node.toDesRecord');">-</a><tt class="py-line"> <tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.SCOP.Node-class.html#toDesRecord">toDesRecord</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="Node.toDesRecord-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="Node.toDesRecord-expanded"><a name="L561"></a><tt class="py-lineno">561</tt> <tt class="py-line"> <tt class="py-docstring">"""Return a Des.Record"""</tt> </tt>
<a name="L562"></a><tt class="py-lineno">562</tt> <tt class="py-line"> <tt class="py-name">rec</tt> <tt class="py-op">=</tt> <tt id="link-284" class="py-name"><a title="Bio.SCOP.Des" class="py-name" href="#" onclick="return doclink('link-284', 'Des', 'link-0');">Des</a></tt><tt class="py-op">.</tt><tt id="link-285" class="py-name"><a title="Bio.Blast.Record
Bio.CDD.Record
Bio.CDD.Record.Record
Bio.Cluster.Record
Bio.Compass.Record
Bio.ECell.Record
Bio.ECell.Record.Record
Bio.Fasta.Record
Bio.GenBank.Record
Bio.GenBank.Record.Record
Bio.Geo.Record
Bio.Geo.Record.Record
Bio.Gobase.Record
Bio.IntelliGenetics.Record
Bio.IntelliGenetics.Record.Record
Bio.InterPro.Record
Bio.KEGG.Compound.Record
Bio.KEGG.Enzyme.Record
Bio.LocusLink.Record
Bio.LocusLink.web_parse.Record
Bio.Medline.Record
Bio.MetaTool.Record
Bio.MetaTool.Record.Record
Bio.NBRF.Record
Bio.NBRF.Record.Record
Bio.Ndb.Record
Bio.PopGen.FDist.Record
Bio.PopGen.GenePop.Record
Bio.Prosite.Prodoc.Record
Bio.Prosite.Record
Bio.Rebase.Record
Bio.SCOP.Cla.Record
Bio.SCOP.Des.Record
Bio.SCOP.Dom.Record
Bio.SCOP.Hie.Record
Bio.Saf.Record
Bio.Saf.Record.Record
Bio.Sequencing.Phd.Record
Bio.SwissProt.KeyWList.Record
Bio.SwissProt.SProt.Record" class="py-name" href="#" onclick="return doclink('link-285', 'Record', 'link-278');">Record</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
<a name="L563"></a><tt class="py-lineno">563</tt> <tt class="py-line"> <tt class="py-name">rec</tt><tt class="py-op">.</tt><tt class="py-name">sunid</tt> <tt class="py-op">=</tt> <tt class="py-name">str</tt><tt class="py-op">(</tt><tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">sunid</tt><tt class="py-op">)</tt> </tt>
<a name="L564"></a><tt class="py-lineno">564</tt> <tt class="py-line"> <tt class="py-name">rec</tt><tt class="py-op">.</tt><tt class="py-name">nodetype</tt> <tt class="py-op">=</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-286" class="py-name"><a title="Bio.GenBank.LocationParser.Integer.type
Bio.GenBank.LocationParser.Symbol.type
Bio.GenBank.LocationParser.UnsignedInteger.type" class="py-name" href="#" onclick="return doclink('link-286', 'type', 'link-59');">type</a></tt> </tt>
<a name="L565"></a><tt class="py-lineno">565</tt> <tt class="py-line"> <tt class="py-name">rec</tt><tt class="py-op">.</tt><tt class="py-name">sccs</tt> <tt class="py-op">=</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">sccs</tt> </tt>
<a name="L566"></a><tt class="py-lineno">566</tt> <tt class="py-line"> <tt class="py-name">rec</tt><tt class="py-op">.</tt><tt id="link-287" class="py-name"><a title="Bio.Blast.NCBIStandalone._DescriptionConsumer.description
Bio.Enzyme._RecordConsumer.description
Bio.Prosite._RecordConsumer.description
Bio.Std.description
Bio.SwissProt.SProt._RecordConsumer.description
Bio.SwissProt.SProt._SequenceConsumer.description
Martel.setup.run_local_tests.description" class="py-name" href="#" onclick="return doclink('link-287', 'description', 'link-44');">description</a></tt> <tt class="py-op">=</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-288" class="py-name"><a title="Bio.Blast.NCBIStandalone._DescriptionConsumer.description
Bio.Enzyme._RecordConsumer.description
Bio.Prosite._RecordConsumer.description
Bio.Std.description
Bio.SwissProt.SProt._RecordConsumer.description
Bio.SwissProt.SProt._SequenceConsumer.description
Martel.setup.run_local_tests.description" class="py-name" href="#" onclick="return doclink('link-288', 'description', 'link-44');">description</a></tt> </tt>
<a name="L567"></a><tt class="py-lineno">567</tt> <tt class="py-line"> <tt class="py-keyword">return</tt> <tt class="py-name">rec</tt> </tt>
</div><a name="L568"></a><tt class="py-lineno">568</tt> <tt class="py-line"> </tt>
<a name="Node.getChildren"></a><div id="Node.getChildren-def"><a name="L569"></a><tt class="py-lineno">569</tt> <a class="py-toggle" href="#" id="Node.getChildren-toggle" onclick="return toggle('Node.getChildren');">-</a><tt class="py-line"> <tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.SCOP.Node-class.html#getChildren">getChildren</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="Node.getChildren-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="Node.getChildren-expanded"><a name="L570"></a><tt class="py-lineno">570</tt> <tt class="py-line"> <tt class="py-docstring">"""Return a list of children of this Node"""</tt> </tt>
<a name="L571"></a><tt class="py-lineno">571</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">scop</tt> <tt class="py-keyword">is</tt> <tt class="py-name">None</tt><tt class="py-op">:</tt> </tt>
<a name="L572"></a><tt class="py-lineno">572</tt> <tt class="py-line"> <tt class="py-keyword">return</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-289" class="py-name"><a title="Bio.Pathway.Rep.Graph.Graph.children
Bio.Pathway.Rep.MultiGraph.MultiGraph.children" class="py-name" href="#" onclick="return doclink('link-289', 'children', 'link-89');">children</a></tt> </tt>
<a name="L573"></a><tt class="py-lineno">573</tt> <tt class="py-line"> <tt class="py-keyword">else</tt><tt class="py-op">:</tt> </tt>
<a name="L574"></a><tt class="py-lineno">574</tt> <tt class="py-line"> <tt class="py-keyword">return</tt> <tt id="link-290" class="py-name"><a title="Bio.GFF.FeatureAggregate.map" class="py-name" href="#" onclick="return doclink('link-290', 'map', 'link-28');">map</a></tt> <tt class="py-op">(</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">scop</tt><tt class="py-op">.</tt><tt id="link-291" class="py-name"><a title="Bio.SCOP.Scop.getNodeBySunid" class="py-name" href="#" onclick="return doclink('link-291', 'getNodeBySunid', 'link-103');">getNodeBySunid</a></tt><tt class="py-op">,</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-292" class="py-name"><a title="Bio.Pathway.Rep.Graph.Graph.children
Bio.Pathway.Rep.MultiGraph.MultiGraph.children" class="py-name" href="#" onclick="return doclink('link-292', 'children', 'link-89');">children</a></tt> <tt class="py-op">)</tt> </tt>
</div><a name="L575"></a><tt class="py-lineno">575</tt> <tt class="py-line"> </tt>
<a name="Node.getParent"></a><div id="Node.getParent-def"><a name="L576"></a><tt class="py-lineno">576</tt> <a class="py-toggle" href="#" id="Node.getParent-toggle" onclick="return toggle('Node.getParent');">-</a><tt class="py-line"> <tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.SCOP.Node-class.html#getParent">getParent</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="Node.getParent-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="Node.getParent-expanded"><a name="L577"></a><tt class="py-lineno">577</tt> <tt class="py-line"> <tt class="py-docstring">"""Return the parent of this Node"""</tt> </tt>
<a name="L578"></a><tt class="py-lineno">578</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">scop</tt> <tt class="py-keyword">is</tt> <tt class="py-name">None</tt><tt class="py-op">:</tt> </tt>
<a name="L579"></a><tt class="py-lineno">579</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">parent</tt> </tt>
<a name="L580"></a><tt class="py-lineno">580</tt> <tt class="py-line"> <tt class="py-keyword">else</tt><tt class="py-op">:</tt> </tt>
<a name="L581"></a><tt class="py-lineno">581</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">scop</tt><tt class="py-op">.</tt><tt id="link-293" class="py-name"><a title="Bio.SCOP.Scop.getNodeBySunid" class="py-name" href="#" onclick="return doclink('link-293', 'getNodeBySunid', 'link-103');">getNodeBySunid</a></tt><tt class="py-op">(</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">parent</tt> <tt class="py-op">)</tt> </tt>
</div><a name="L582"></a><tt class="py-lineno">582</tt> <tt class="py-line"> </tt>
<a name="Node.getDescendents"></a><div id="Node.getDescendents-def"><a name="L583"></a><tt class="py-lineno">583</tt> <a class="py-toggle" href="#" id="Node.getDescendents-toggle" onclick="return toggle('Node.getDescendents');">-</a><tt class="py-line"> <tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.SCOP.Node-class.html#getDescendents">getDescendents</a><tt class="py-op">(</tt> <tt class="py-param">self</tt><tt class="py-op">,</tt> <tt class="py-param">node_type</tt><tt class="py-op">)</tt> <tt class="py-op">:</tt> </tt>
</div><div id="Node.getDescendents-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="Node.getDescendents-expanded"><a name="L584"></a><tt class="py-lineno">584</tt> <tt class="py-line"> <tt class="py-docstring">""" Return a list of all decendent nodes of the given type. Node type can a</tt> </tt>
<a name="L585"></a><tt class="py-lineno">585</tt> <tt class="py-line"><tt class="py-docstring"> two letter code or longer description. e.g. 'fa' or 'family'</tt> </tt>
<a name="L586"></a><tt class="py-lineno">586</tt> <tt class="py-line"><tt class="py-docstring"> """</tt> </tt>
<a name="L587"></a><tt class="py-lineno">587</tt> <tt class="py-line"> <tt class="py-keyword">if</tt> <tt id="link-294" class="py-name"><a title="Bio.SCOP._nodetype_to_code" class="py-name" href="#" onclick="return doclink('link-294', '_nodetype_to_code', 'link-13');">_nodetype_to_code</a></tt><tt class="py-op">.</tt><tt id="link-295" class="py-name"><a title="Bio.Crystal.Crystal.has_key
Bio.EUtils.POM.ElementNode.has_key
Bio.GenBank.NCBIDictionary.has_key
Bio.PDB.AbstractPropertyMap.AbstractPropertyMap.has_key
Bio.PDB.FragmentMapper'.FragmentMapper.has_key
Bio.Prosite.ExPASyDictionary.has_key
Bio.Prosite.Prodoc.ExPASyDictionary.has_key
Bio.PubMed.Dictionary.has_key
Bio.SwissProt.SProt.ExPASyDictionary.has_key
Martel.Parser.MartelAttributeList.has_key" class="py-name" href="#" onclick="return doclink('link-295', 'has_key', 'link-80');">has_key</a></tt><tt class="py-op">(</tt><tt class="py-name">node_type</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
<a name="L588"></a><tt class="py-lineno">588</tt> <tt class="py-line"> <tt class="py-name">node_type</tt> <tt class="py-op">=</tt> <tt id="link-296" class="py-name"><a title="Bio.SCOP._nodetype_to_code" class="py-name" href="#" onclick="return doclink('link-296', '_nodetype_to_code', 'link-13');">_nodetype_to_code</a></tt><tt class="py-op">[</tt><tt class="py-name">node_type</tt><tt class="py-op">]</tt> </tt>
<a name="L589"></a><tt class="py-lineno">589</tt> <tt class="py-line"> </tt>
<a name="L590"></a><tt class="py-lineno">590</tt> <tt class="py-line"> <tt id="link-297" class="py-name"><a title="Bio.Pathway.Rep.Graph.Graph.nodes
Bio.Pathway.Rep.MultiGraph.MultiGraph.nodes" class="py-name" href="#" onclick="return doclink('link-297', 'nodes', 'link-112');">nodes</a></tt> <tt class="py-op">=</tt> <tt class="py-op">[</tt><tt class="py-name">self</tt><tt class="py-op">]</tt> </tt>
<a name="L591"></a><tt class="py-lineno">591</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">scop</tt><tt class="py-op">:</tt> </tt>
<a name="L592"></a><tt class="py-lineno">592</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">scop</tt><tt class="py-op">.</tt><tt id="link-298" class="py-name"><a title="Bio.SCOP.Scop.getDescendentsFromSQL" class="py-name" href="#" onclick="return doclink('link-298', 'getDescendentsFromSQL', 'link-189');">getDescendentsFromSQL</a></tt><tt class="py-op">(</tt><tt class="py-name">self</tt><tt class="py-op">,</tt><tt class="py-name">node_type</tt><tt class="py-op">)</tt> </tt>
<a name="L593"></a><tt class="py-lineno">593</tt> <tt class="py-line"> <tt class="py-keyword">while</tt> <tt id="link-299" class="py-name"><a title="Bio.Pathway.Rep.Graph.Graph.nodes
Bio.Pathway.Rep.MultiGraph.MultiGraph.nodes" class="py-name" href="#" onclick="return doclink('link-299', 'nodes', 'link-112');">nodes</a></tt><tt class="py-op">[</tt><tt class="py-number">0</tt><tt class="py-op">]</tt><tt class="py-op">.</tt><tt id="link-300" class="py-name"><a title="Bio.GenBank.LocationParser.Integer.type
Bio.GenBank.LocationParser.Symbol.type
Bio.GenBank.LocationParser.UnsignedInteger.type" class="py-name" href="#" onclick="return doclink('link-300', 'type', 'link-59');">type</a></tt> <tt class="py-op">!=</tt> <tt class="py-name">node_type</tt><tt class="py-op">:</tt> </tt>
<a name="L594"></a><tt class="py-lineno">594</tt> <tt class="py-line"> <tt class="py-keyword">if</tt> <tt id="link-301" class="py-name"><a title="Bio.Pathway.Rep.Graph.Graph.nodes
Bio.Pathway.Rep.MultiGraph.MultiGraph.nodes" class="py-name" href="#" onclick="return doclink('link-301', 'nodes', 'link-112');">nodes</a></tt><tt class="py-op">[</tt><tt class="py-number">0</tt><tt class="py-op">]</tt><tt class="py-op">.</tt><tt id="link-302" class="py-name"><a title="Bio.GenBank.LocationParser.Integer.type
Bio.GenBank.LocationParser.Symbol.type
Bio.GenBank.LocationParser.UnsignedInteger.type" class="py-name" href="#" onclick="return doclink('link-302', 'type', 'link-59');">type</a></tt> <tt class="py-op">==</tt> <tt class="py-string">'px'</tt> <tt class="py-op">:</tt> <tt class="py-keyword">return</tt> <tt class="py-op">[</tt><tt class="py-op">]</tt> <tt class="py-comment"># Fell of the bottom of the hierarchy</tt> </tt>
<a name="L595"></a><tt class="py-lineno">595</tt> <tt class="py-line"> <tt class="py-name">child_list</tt> <tt class="py-op">=</tt> <tt class="py-op">[</tt><tt class="py-op">]</tt> </tt>
<a name="L596"></a><tt class="py-lineno">596</tt> <tt class="py-line"> <tt class="py-keyword">for</tt> <tt class="py-name">n</tt> <tt class="py-keyword">in</tt> <tt id="link-303" class="py-name"><a title="Bio.Pathway.Rep.Graph.Graph.nodes
Bio.Pathway.Rep.MultiGraph.MultiGraph.nodes" class="py-name" href="#" onclick="return doclink('link-303', 'nodes', 'link-112');">nodes</a></tt><tt class="py-op">:</tt> </tt>
<a name="L597"></a><tt class="py-lineno">597</tt> <tt class="py-line"> <tt class="py-keyword">for</tt> <tt class="py-name">child</tt> <tt class="py-keyword">in</tt> <tt class="py-name">n</tt><tt class="py-op">.</tt><tt id="link-304" class="py-name"><a title="Bio.SCOP.Node.getChildren" class="py-name" href="#" onclick="return doclink('link-304', 'getChildren', 'link-187');">getChildren</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
<a name="L598"></a><tt class="py-lineno">598</tt> <tt class="py-line"> <tt class="py-name">child_list</tt><tt class="py-op">.</tt><tt id="link-305" 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-305', 'append', 'link-68');">append</a></tt><tt class="py-op">(</tt> <tt class="py-name">child</tt> <tt class="py-op">)</tt> </tt>
<a name="L599"></a><tt class="py-lineno">599</tt> <tt class="py-line"> <tt id="link-306" class="py-name"><a title="Bio.Pathway.Rep.Graph.Graph.nodes
Bio.Pathway.Rep.MultiGraph.MultiGraph.nodes" class="py-name" href="#" onclick="return doclink('link-306', 'nodes', 'link-112');">nodes</a></tt> <tt class="py-op">=</tt> <tt class="py-name">child_list</tt> </tt>
<a name="L600"></a><tt class="py-lineno">600</tt> <tt class="py-line"> </tt>
<a name="L601"></a><tt class="py-lineno">601</tt> <tt class="py-line"> <tt class="py-keyword">return</tt> <tt id="link-307" class="py-name"><a title="Bio.Pathway.Rep.Graph.Graph.nodes
Bio.Pathway.Rep.MultiGraph.MultiGraph.nodes" class="py-name" href="#" onclick="return doclink('link-307', 'nodes', 'link-112');">nodes</a></tt> </tt>
</div><a name="L602"></a><tt class="py-lineno">602</tt> <tt class="py-line"> </tt>
<a name="L603"></a><tt class="py-lineno">603</tt> <tt class="py-line"> </tt>
<a name="Node.getAscendent"></a><div id="Node.getAscendent-def"><a name="L604"></a><tt class="py-lineno">604</tt> <a class="py-toggle" href="#" id="Node.getAscendent-toggle" onclick="return toggle('Node.getAscendent');">-</a><tt class="py-line"> <tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.SCOP.Node-class.html#getAscendent">getAscendent</a><tt class="py-op">(</tt> <tt class="py-param">self</tt><tt class="py-op">,</tt> <tt class="py-param">node_type</tt><tt class="py-op">)</tt> <tt class="py-op">:</tt> </tt>
</div><div id="Node.getAscendent-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="Node.getAscendent-expanded"><a name="L605"></a><tt class="py-lineno">605</tt> <tt class="py-line"> <tt class="py-docstring">""" Return the ancenstor node of the given type, or None.Node type can a</tt> </tt>
<a name="L606"></a><tt class="py-lineno">606</tt> <tt class="py-line"><tt class="py-docstring"> two letter code or longer description. e.g. 'fa' or 'family'"""</tt> </tt>
<a name="L607"></a><tt class="py-lineno">607</tt> <tt class="py-line"> <tt class="py-keyword">if</tt> <tt id="link-308" class="py-name"><a title="Bio.SCOP._nodetype_to_code" class="py-name" href="#" onclick="return doclink('link-308', '_nodetype_to_code', 'link-13');">_nodetype_to_code</a></tt><tt class="py-op">.</tt><tt id="link-309" class="py-name"><a title="Bio.Crystal.Crystal.has_key
Bio.EUtils.POM.ElementNode.has_key
Bio.GenBank.NCBIDictionary.has_key
Bio.PDB.AbstractPropertyMap.AbstractPropertyMap.has_key
Bio.PDB.FragmentMapper'.FragmentMapper.has_key
Bio.Prosite.ExPASyDictionary.has_key
Bio.Prosite.Prodoc.ExPASyDictionary.has_key
Bio.PubMed.Dictionary.has_key
Bio.SwissProt.SProt.ExPASyDictionary.has_key
Martel.Parser.MartelAttributeList.has_key" class="py-name" href="#" onclick="return doclink('link-309', 'has_key', 'link-80');">has_key</a></tt><tt class="py-op">(</tt><tt class="py-name">node_type</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
<a name="L608"></a><tt class="py-lineno">608</tt> <tt class="py-line"> <tt class="py-name">node_type</tt> <tt class="py-op">=</tt> <tt id="link-310" class="py-name"><a title="Bio.SCOP._nodetype_to_code" class="py-name" href="#" onclick="return doclink('link-310', '_nodetype_to_code', 'link-13');">_nodetype_to_code</a></tt><tt class="py-op">[</tt><tt class="py-name">node_type</tt><tt class="py-op">]</tt> </tt>
<a name="L609"></a><tt class="py-lineno">609</tt> <tt class="py-line"> </tt>
<a name="L610"></a><tt class="py-lineno">610</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">scop</tt><tt class="py-op">:</tt> </tt>
<a name="L611"></a><tt class="py-lineno">611</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">scop</tt><tt class="py-op">.</tt><tt id="link-311" class="py-name" targets="Method Bio.SCOP.Scop.getAscendentFromSQL()=Bio.SCOP.Scop-class.html#getAscendentFromSQL"><a title="Bio.SCOP.Scop.getAscendentFromSQL" class="py-name" href="#" onclick="return doclink('link-311', 'getAscendentFromSQL', 'link-311');">getAscendentFromSQL</a></tt><tt class="py-op">(</tt><tt class="py-name">self</tt><tt class="py-op">,</tt><tt class="py-name">node_type</tt><tt class="py-op">)</tt> </tt>
<a name="L612"></a><tt class="py-lineno">612</tt> <tt class="py-line"> <tt class="py-keyword">else</tt><tt class="py-op">:</tt> </tt>
<a name="L613"></a><tt class="py-lineno">613</tt> <tt class="py-line"> <tt class="py-name">n</tt> <tt class="py-op">=</tt> <tt class="py-name">self</tt> </tt>
<a name="L614"></a><tt class="py-lineno">614</tt> <tt class="py-line"> <tt class="py-keyword">if</tt> <tt class="py-name">n</tt><tt class="py-op">.</tt><tt id="link-312" class="py-name"><a title="Bio.GenBank.LocationParser.Integer.type
Bio.GenBank.LocationParser.Symbol.type
Bio.GenBank.LocationParser.UnsignedInteger.type" class="py-name" href="#" onclick="return doclink('link-312', 'type', 'link-59');">type</a></tt> <tt class="py-op">==</tt> <tt class="py-name">node_type</tt><tt class="py-op">:</tt> <tt class="py-keyword">return</tt> <tt class="py-name">None</tt> </tt>
<a name="L615"></a><tt class="py-lineno">615</tt> <tt class="py-line"> <tt class="py-keyword">while</tt> <tt class="py-name">n</tt><tt class="py-op">.</tt><tt id="link-313" class="py-name"><a title="Bio.GenBank.LocationParser.Integer.type
Bio.GenBank.LocationParser.Symbol.type
Bio.GenBank.LocationParser.UnsignedInteger.type" class="py-name" href="#" onclick="return doclink('link-313', 'type', 'link-59');">type</a></tt> <tt class="py-op">!=</tt> <tt class="py-name">node_type</tt><tt class="py-op">:</tt> </tt>
<a name="L616"></a><tt class="py-lineno">616</tt> <tt class="py-line"> <tt class="py-keyword">if</tt> <tt class="py-name">n</tt><tt class="py-op">.</tt><tt id="link-314" class="py-name"><a title="Bio.GenBank.LocationParser.Integer.type
Bio.GenBank.LocationParser.Symbol.type
Bio.GenBank.LocationParser.UnsignedInteger.type" class="py-name" href="#" onclick="return doclink('link-314', 'type', 'link-59');">type</a></tt> <tt class="py-op">==</tt> <tt class="py-string">'ro'</tt><tt class="py-op">:</tt> <tt class="py-keyword">return</tt> <tt class="py-name">None</tt> <tt class="py-comment"># Fell of the top of the hierarchy</tt> </tt>
<a name="L617"></a><tt class="py-lineno">617</tt> <tt class="py-line"> <tt class="py-name">n</tt> <tt class="py-op">=</tt> <tt class="py-name">n</tt><tt class="py-op">.</tt><tt id="link-315" class="py-name"><a title="Bio.SCOP.Node.getParent" class="py-name" href="#" onclick="return doclink('link-315', 'getParent', 'link-279');">getParent</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
<a name="L618"></a><tt class="py-lineno">618</tt> <tt class="py-line"> </tt>
<a name="L619"></a><tt class="py-lineno">619</tt> <tt class="py-line"> <tt class="py-keyword">return</tt> <tt class="py-name">n</tt> </tt>
</div></div><a name="L620"></a><tt class="py-lineno">620</tt> <tt class="py-line"> </tt>
<a name="L621"></a><tt class="py-lineno">621</tt> <tt class="py-line"> </tt>
<a name="L622"></a><tt class="py-lineno">622</tt> <tt class="py-line"> </tt>
<a name="Domain"></a><div id="Domain-def"><a name="L623"></a><tt class="py-lineno">623</tt> <a class="py-toggle" href="#" id="Domain-toggle" onclick="return toggle('Domain');">-</a><tt class="py-line"><tt class="py-keyword">class</tt> <a class="py-def-name" href="Bio.SCOP.Domain-class.html">Domain</a><tt class="py-op">(</tt><tt class="py-base-class">Node</tt><tt class="py-op">)</tt> <tt class="py-op">:</tt> </tt>
</div><div id="Domain-collapsed" style="display:none;" pad="+++" indent="++++"></div><div id="Domain-expanded"><a name="L624"></a><tt class="py-lineno">624</tt> <tt class="py-line"> <tt class="py-docstring">""" A SCOP domain. A leaf node in the Scop hierarchy.</tt> </tt>
<a name="L625"></a><tt class="py-lineno">625</tt> <tt class="py-line"><tt class="py-docstring"></tt> </tt>
<a name="L626"></a><tt class="py-lineno">626</tt> <tt class="py-line"><tt class="py-docstring"> sid -- The SCOP domain identifier. e.g. 'd5hbib_'</tt> </tt>
<a name="L627"></a><tt class="py-lineno">627</tt> <tt class="py-line"><tt class="py-docstring"></tt> </tt>
<a name="L628"></a><tt class="py-lineno">628</tt> <tt class="py-line"><tt class="py-docstring"> residues -- A Residue object. It defines the collection</tt> </tt>
<a name="L629"></a><tt class="py-lineno">629</tt> <tt class="py-line"><tt class="py-docstring"> of PDB atoms that make up this domain.</tt> </tt>
<a name="L630"></a><tt class="py-lineno">630</tt> <tt class="py-line"><tt class="py-docstring"> """</tt> </tt>
<a name="Domain.__init__"></a><div id="Domain.__init__-def"><a name="L631"></a><tt class="py-lineno">631</tt> <a class="py-toggle" href="#" id="Domain.__init__-toggle" onclick="return toggle('Domain.__init__');">-</a><tt class="py-line"> <tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.SCOP.Domain-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">scop</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="Domain.__init__-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="Domain.__init__-expanded"><a name="L632"></a><tt class="py-lineno">632</tt> <tt class="py-line"> <tt id="link-316" class="py-name"><a title="Bio.Nexus.Nodes.Node
Bio.SCOP.Node" class="py-name" href="#" onclick="return doclink('link-316', 'Node', 'link-58');">Node</a></tt><tt class="py-op">.</tt><tt id="link-317" class="py-name" targets="Method Bio.Affy.CelFile.CelConsumer.__init__()=Bio.Affy.CelFile.CelConsumer-class.html#__init__,Method Bio.Affy.CelFile.CelParser.__init__()=Bio.Affy.CelFile.CelParser-class.html#__init__,Method Bio.Affy.CelFile.CelRecord.__init__()=Bio.Affy.CelFile.CelRecord-class.html#__init__,Method Bio.Ais.Immune.__init__()=Bio.Ais.Immune-class.html#__init__,Method Bio.Ais.Lymphocyte.__init__()=Bio.Ais.Lymphocyte-class.html#__init__,Method Bio.Align.AlignInfo.PSSM.__init__()=Bio.Align.AlignInfo.PSSM-class.html#__init__,Method Bio.Align.AlignInfo.SummaryInfo.__init__()=Bio.Align.AlignInfo.SummaryInfo-class.html#__init__,Method Bio.Align.FormatConvert.FormatConverter.__init__()=Bio.Align.FormatConvert.FormatConverter-class.html#__init__,Method Bio.Align.Generic.Alignment.__init__()=Bio.Align.Generic.Alignment-class.html#__init__,Method Bio.AlignAce.Applications.AlignAceCommandline.__init__()=Bio.AlignAce.Applications.AlignAceCommandline-class.html#__init__,Method Bio.AlignAce.Applications.CompareAceCommandline.__init__()=Bio.AlignAce.Applications.CompareAceCommandline-class.html#__init__,Method Bio.AlignAce.Motif.Motif.__init__()=Bio.AlignAce.Motif.Motif-class.html#__init__,Method Bio.AlignAce.Parser.AlignAceConsumer.__init__()=Bio.AlignAce.Parser.AlignAceConsumer-class.html#__init__,Method Bio.AlignAce.Parser.AlignAceParser.__init__()=Bio.AlignAce.Parser.AlignAceParser-class.html#__init__,Method Bio.AlignAce.Parser.CompareAceConsumer.__init__()=Bio.AlignAce.Parser.CompareAceConsumer-class.html#__init__,Method Bio.AlignAce.Parser.CompareAceParser.__init__()=Bio.AlignAce.Parser.CompareAceParser-class.html#__init__,Method Bio.AlignIO.Interfaces.AlignmentIterator.__init__()=Bio.AlignIO.Interfaces.AlignmentIterator-class.html#__init__,Method Bio.AlignIO.Interfaces.AlignmentWriter.__init__()=Bio.AlignIO.Interfaces.AlignmentWriter-class.html#__init__,Method Bio.AlignIO.Interfaces.SequentialAlignmentWriter.__init__()=Bio.AlignIO.Interfaces.SequentialAlignmentWriter-class.html#__init__,Method Bio.Alphabet.AlphabetEncoder.__init__()=Bio.Alphabet.AlphabetEncoder-class.html#__init__,Method Bio.Alphabet.Gapped.__init__()=Bio.Alphabet.Gapped-class.html#__init__,Method Bio.Alphabet.HasStopCodon.__init__()=Bio.Alphabet.HasStopCodon-class.html#__init__,Method Bio.Application.AbstractCommandline.__init__()=Bio.Application.AbstractCommandline-class.html#__init__,Method Bio.Application.ApplicationResult.__init__()=Bio.Application.ApplicationResult-class.html#__init__,Method Bio.Application._AbstractParameter.__init__()=Bio.Application._AbstractParameter-class.html#__init__,Method 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Bio.PDB.StructureAlignment'.StructureAlignment.__init__
Bio.PDB.StructureBuilder.StructureBuilder.__init__
Bio.PDB.Superimposer'.Superimposer.__init__
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Bio.PopGen.SimCoal.Async.SimCoalCache.__init__
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Bio.PopGen.SimCoal.Controller.SimCoalController.__init__
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Bio.Prosite.ExPASyDictionary.__init__
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Bio.Prosite.Prodoc.Reference.__init__
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Bio.Restriction._Update.RestrictionCompiler.newenzyme.__init__
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Bio.Restriction._Update.Update.FtpNameError.__init__
Bio.Restriction._Update.Update.FtpPasswordError.__init__
Bio.Restriction._Update.Update.RebaseUpdate.__init__
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Bio.SCOP.Cla.Index.__init__
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Bio.SCOP.Hie.Record.__init__
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Bio.Saf.Iterator.__init__
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Bio.Saf._RecordConsumer.__init__
Bio.Saf._Scanner.__init__
Bio.Search.Algorithm.__init__
Bio.Search.Database.__init__
Bio.Search.HSP.__init__
Bio.Search.HSPSeq.__init__
Bio.Search.Hit.__init__
Bio.Search.HomologySeq.__init__
Bio.Search.Query.__init__
Bio.Search.Search.__init__
Bio.Search.TableInfo.__init__
Bio.Search._SeqLength.__init__
Bio.Seq.MutableSeq.__init__
Bio.Seq.Seq.__init__
Bio.SeqFeature.AbstractPosition.__init__
Bio.SeqFeature.AfterPosition.__init__
Bio.SeqFeature.BeforePosition.__init__
Bio.SeqFeature.BetweenPosition.__init__
Bio.SeqFeature.ExactPosition.__init__
Bio.SeqFeature.FeatureLocation.__init__
Bio.SeqFeature.OneOfPosition.__init__
Bio.SeqFeature.PositionGap.__init__
Bio.SeqFeature.Reference.__init__
Bio.SeqFeature.SeqFeature.__init__
Bio.SeqFeature.WithinPosition.__init__
Bio.SeqIO.ClustalIO.ClustalWriter.__init__
Bio.SeqIO.FastaIO.FastaWriter.__init__
Bio.SeqIO.Interfaces.InterlacedSequenceIterator.__init__
Bio.SeqIO.Interfaces.SequenceIterator.__init__
Bio.SeqIO.Interfaces.SequenceWriter.__init__
Bio.SeqIO.Interfaces.SequentialSequenceWriter.__init__
Bio.SeqIO.PhylipIO.PhylipWriter.__init__
Bio.SeqIO.StockholmIO.StockholmIterator.__init__
Bio.SeqIO.StockholmIO.StockholmWriter.__init__
Bio.SeqRecord.SeqRecord.__init__
Bio.SeqUtils.CodonUsage.CodonAdaptationIndex.__init__
Bio.SeqUtils.IsoelectricPoint.IsoelectricPoint.__init__
Bio.SeqUtils.MissingTable.__init__
Bio.SeqUtils.ProtParam.ProteinAnalysis.__init__
Bio.Sequencing.Ace.ACEFileRecord.__init__
Bio.Sequencing.Ace.ACEParser.__init__
Bio.Sequencing.Ace.Contig.__init__
Bio.Sequencing.Ace.Iterator.__init__
Bio.Sequencing.Ace.Reads.__init__
Bio.Sequencing.Ace.RecordParser.__init__
Bio.Sequencing.Ace._RecordConsumer.__init__
Bio.Sequencing.Ace.af.__init__
Bio.Sequencing.Ace.bs.__init__
Bio.Sequencing.Ace.ct.__init__
Bio.Sequencing.Ace.ds.__init__
Bio.Sequencing.Ace.qa.__init__
Bio.Sequencing.Ace.rd.__init__
Bio.Sequencing.Ace.rt.__init__
Bio.Sequencing.Ace.wa.__init__
Bio.Sequencing.Ace.wr.__init__
Bio.Sequencing.Phd.Iterator.__init__
Bio.Sequencing.Phd.Record.__init__
Bio.Sequencing.Phd.RecordParser.__init__
Bio.Sequencing.Phd._RecordConsumer.__init__
Bio.Std.StdTerm.__init__
Bio.StdHandler.ConvertDispatchHandler.__init__
Bio.StdHandler.ConvertHandler.__init__
Bio.StdHandler.Feature.__init__
Bio.StdHandler.Handle_dbxref.__init__
Bio.StdHandler.Handle_feature_location.__init__
Bio.StdHandler.Handle_feature_qualifier.__init__
Bio.StdHandler.Handle_features.__init__
Bio.StdHandler.Handle_hsp.__init__
Bio.StdHandler.RecognizeHandler.__init__
Bio.SubsMat.FreqTable.FreqTable.__init__
Bio.SubsMat.SeqMat.__init__
Bio.SwissProt.KeyWList.ListParser.__init__
Bio.SwissProt.KeyWList.Record.__init__
Bio.SwissProt.KeyWList._ListConsumer.__init__
Bio.SwissProt.KeyWList._Scanner.__init__
Bio.SwissProt.SProt.Dictionary.__init__
Bio.SwissProt.SProt.ExPASyDictionary.__init__
Bio.SwissProt.SProt.Iterator.__init__
Bio.SwissProt.SProt.Record.__init__
Bio.SwissProt.SProt.RecordParser.__init__
Bio.SwissProt.SProt.Reference.__init__
Bio.SwissProt.SProt.SequenceParser.__init__
Bio.SwissProt.SProt._RecordConsumer.__init__
Bio.SwissProt.SProt._SequenceConsumer.__init__
Bio.Transcribe.Transcribe.__init__
Bio.Translate.Translator.__init__
Bio.UniGene.Iterator.__init__
Bio.UniGene.RecordParser.__init__
Bio.UniGene.UnigeneProtsimRecord.__init__
Bio.UniGene.UnigeneRecord.__init__
Bio.UniGene.UnigeneSTSRecord.__init__
Bio.UniGene.UnigeneSequenceRecord.__init__
Bio.UniGene._RecordConsumer.__init__
Bio.WWW.RequestLimiter.__init__
Bio.Wise.dnal.Statistics.__init__
Bio.Wise.psw.AlignmentColumn.__init__
Bio.Wise.psw.ColumnUnit.__init__
Bio.Writer.Writer.__init__
Bio.biblio.Biblio.__init__
Bio.biblio.BiblioCollection.__init__
Bio.builders.Search.search.BuildSearch.__init__
Bio.builders.SeqRecord.sequence.BuildSeqRecord.__init__
Bio.config.DBRegistry.BioCorbaDB.__init__
Bio.config.DBRegistry.BioSQLDB.__init__
Bio.config.DBRegistry.CGIDB.__init__
Bio.config.DBRegistry.DBGroup.__init__
Bio.config.DBRegistry.DBObject.__init__
Bio.config.DBRegistry.DBRegistry.__init__
Bio.config.DBRegistry.EUtilsDB.__init__
Bio.config.DBRegistry.IndexedFileDB.__init__
Bio.config.FormatRegistry.FormatGroup.__init__
Bio.config.FormatRegistry.FormatObject.__init__
Bio.config.FormatRegistry.FormatRegistry.__init__
Bio.config.Registry.RegisterableGroup.__init__
Bio.config.Registry.RegisterableObject.__init__
Bio.config.Registry.Registry.__init__
Bio.config.SeqDBRegistry.SeqDBRegistry.__init__
Bio.config._stanzaformat.Stanza.__init__
Bio.config._stanzaformat.StanzaFormat.__init__
Bio.config._support.make_cached_expression.__init__
Bio.config._support.make_rate_limited_function.__init__
Bio.kNN.kNN.__init__
Bio.pairwise2.affine_penalty.__init__
Bio.pairwise2.dictionary_match.__init__
Bio.pairwise2.identity_match.__init__
Bio.writers.SeqRecord.embl.WriteEmbl.__init__
Bio.writers.SeqRecord.fasta.WriteFasta.__init__
BioSQL.BioSeq.DBSeq.__init__
BioSQL.BioSeq.DBSeqRecord.__init__
BioSQL.BioSeqDatabase.Adaptor.__init__
BioSQL.BioSeqDatabase.BioSeqDatabase.__init__
BioSQL.BioSeqDatabase.DBServer.__init__
BioSQL.DBUtils.Generic_dbutils.__init__
BioSQL.Loader.DatabaseLoader.__init__
BioSQL.Loader.DatabaseRemover.__init__
Martel.Dispatch.Callback.__init__
Martel.Dispatch.DispatchHandler.__init__
Martel.Dispatch.Dispatcher.__init__
Martel.Dispatch.Multicall.__init__
Martel.Dispatch.RemapEnd.__init__
Martel.Dispatch.RemapStart.__init__
Martel.Expression.Alt.__init__
Martel.Expression.Any.__init__
Martel.Expression.Assert.__init__
Martel.Expression.Debug.__init__
Martel.Expression.FastFeature.__init__
Martel.Expression.Group.__init__
Martel.Expression.GroupRef.__init__
Martel.Expression.HeaderFooter.__init__
Martel.Expression.Literal.__init__
Martel.Expression.MaxRepeat.__init__
Martel.Expression.NullOp.__init__
Martel.Expression.ParseRecords.__init__
Martel.Expression.PassThrough.__init__
Martel.Expression.Seq.__init__
Martel.Expression.Str.__init__
Martel.Generate.CheckAssert.__init__
Martel.Generate.CheckAssertNot.__init__
Martel.Generate.CheckGroupRef.__init__
Martel.Generate.GeneratorState.__init__
Martel.Generate.HandleRepeatCount.__init__
Martel.Generate.SetGroupValue.__init__
Martel.Generate._call_call.__init__
Martel.Generate._call_calltag.__init__
Martel.Generate.print_debug.__init__
Martel.Generate.print_info.__init__
Martel.IterParser.IterHeaderFooter.__init__
Martel.IterParser.IterRecords.__init__
Martel.Iterator.EventStream.__init__
Martel.Iterator.HeaderFooterEventStream.__init__
Martel.Iterator.Iterate.__init__
Martel.Iterator.Iterator.__init__
Martel.Iterator.IteratorHeaderFooter.__init__
Martel.Iterator.IteratorRecords.__init__
Martel.Iterator.RecordEventStream.__init__
Martel.Iterator.StoreEvents.__init__
Martel.LAX.ElementInfo.__init__
Martel.LAX.LAX.__init__
Martel.Parser.HeaderFooterParser.__init__
Martel.Parser.Parser.__init__
Martel.Parser.ParserIncompleteException.__init__
Martel.Parser.ParserPositionException.__init__
Martel.Parser.RecordParser.__init__
Martel.RecordReader.CountLines.__init__
Martel.RecordReader.EndsWith.__init__
Martel.RecordReader.Everything.__init__
Martel.RecordReader.Nothing.__init__
Martel.RecordReader.RecordReader.__init__
Martel.RecordReader.StartsWith.__init__
Martel.RecordReader.Until.__init__
Martel.convert_re.GroupNames.__init__
Martel.msre_parse.Pattern.__init__
Martel.msre_parse.SubPattern.__init__
Martel.msre_parse.Tokenizer.__init__
Martel.test.support.CheckGood.__init__
Martel.test.support.Dump.__init__
Martel.test.support.Storage.__init__
Martel.test.test_Parser.CountErrors.__init__
Martel.test.test_Parser.CountRecords.__init__
Martel.test.test_delimiter.CatchFields.__init__
Martel.test.test_optimize.GetErrorPos.__init__" class="py-name" href="#" onclick="return doclink('link-317', '__init__', 'link-317');">__init__</a></tt><tt class="py-op">(</tt><tt class="py-name">self</tt><tt class="py-op">,</tt><tt class="py-name">scop</tt><tt class="py-op">=</tt><tt class="py-name">scop</tt><tt class="py-op">)</tt> </tt>
<a name="L633"></a><tt class="py-lineno">633</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">sid</tt> <tt class="py-op">=</tt> <tt class="py-string">''</tt> </tt>
<a name="L634"></a><tt class="py-lineno">634</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">residues</tt> <tt class="py-op">=</tt> <tt class="py-name">None</tt> </tt>
</div><a name="L635"></a><tt class="py-lineno">635</tt> <tt class="py-line"> </tt>
<a name="Domain.__str__"></a><div id="Domain.__str__-def"><a name="L636"></a><tt class="py-lineno">636</tt> <a class="py-toggle" href="#" id="Domain.__str__-toggle" onclick="return toggle('Domain.__str__');">-</a><tt class="py-line"> <tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.SCOP.Domain-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="Domain.__str__-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="Domain.__str__-expanded"><a name="L637"></a><tt class="py-lineno">637</tt> <tt class="py-line"> <tt id="link-318" class="py-name"><a title="Martel.test.test_swissprot38.s" class="py-name" href="#" onclick="return doclink('link-318', 's', 'link-265');">s</a></tt> <tt class="py-op">=</tt> <tt class="py-op">[</tt><tt class="py-op">]</tt> </tt>
<a name="L638"></a><tt class="py-lineno">638</tt> <tt class="py-line"> <tt id="link-319" class="py-name"><a title="Martel.test.test_swissprot38.s" class="py-name" href="#" onclick="return doclink('link-319', 's', 'link-265');">s</a></tt><tt class="py-op">.</tt><tt id="link-320" 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-320', 'append', 'link-68');">append</a></tt><tt class="py-op">(</tt><tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">sid</tt><tt class="py-op">)</tt> </tt>
<a name="L639"></a><tt class="py-lineno">639</tt> <tt class="py-line"> <tt id="link-321" class="py-name"><a title="Martel.test.test_swissprot38.s" class="py-name" href="#" onclick="return doclink('link-321', 's', 'link-265');">s</a></tt><tt class="py-op">.</tt><tt id="link-322" 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-322', 'append', 'link-68');">append</a></tt><tt class="py-op">(</tt><tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">sccs</tt><tt class="py-op">)</tt> </tt>
<a name="L640"></a><tt class="py-lineno">640</tt> <tt class="py-line"> <tt id="link-323" class="py-name"><a title="Martel.test.test_swissprot38.s" class="py-name" href="#" onclick="return doclink('link-323', 's', 'link-265');">s</a></tt><tt class="py-op">.</tt><tt id="link-324" 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-324', 'append', 'link-68');">append</a></tt><tt class="py-op">(</tt><tt class="py-string">"("</tt><tt class="py-op">+</tt><tt class="py-name">str</tt><tt class="py-op">(</tt><tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">residues</tt><tt class="py-op">)</tt><tt class="py-op">+</tt><tt class="py-string">")"</tt><tt class="py-op">)</tt> </tt>
<a name="L641"></a><tt class="py-lineno">641</tt> <tt class="py-line"> </tt>
<a name="L642"></a><tt class="py-lineno">642</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 id="link-325" class="py-name"><a title="Bio.SCOP.Node.getParent" class="py-name" href="#" onclick="return doclink('link-325', 'getParent', 'link-279');">getParent</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt> <tt class="py-op">:</tt> </tt>
<a name="L643"></a><tt class="py-lineno">643</tt> <tt class="py-line"> <tt id="link-326" class="py-name"><a title="Martel.test.test_swissprot38.s" class="py-name" href="#" onclick="return doclink('link-326', 's', 'link-265');">s</a></tt><tt class="py-op">.</tt><tt id="link-327" 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-327', 'append', 'link-68');">append</a></tt><tt class="py-op">(</tt><tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-328" class="py-name"><a title="Bio.Blast.NCBIStandalone._DescriptionConsumer.description
Bio.Enzyme._RecordConsumer.description
Bio.Prosite._RecordConsumer.description
Bio.Std.description
Bio.SwissProt.SProt._RecordConsumer.description
Bio.SwissProt.SProt._SequenceConsumer.description
Martel.setup.run_local_tests.description" class="py-name" href="#" onclick="return doclink('link-328', 'description', 'link-44');">description</a></tt><tt class="py-op">)</tt> </tt>
<a name="L644"></a><tt class="py-lineno">644</tt> <tt class="py-line"> <tt class="py-keyword">else</tt> <tt class="py-op">:</tt> </tt>
<a name="L645"></a><tt class="py-lineno">645</tt> <tt class="py-line"> <tt class="py-name">sp</tt> <tt class="py-op">=</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-329" class="py-name"><a title="Bio.SCOP.Node.getParent" class="py-name" href="#" onclick="return doclink('link-329', 'getParent', 'link-279');">getParent</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
<a name="L646"></a><tt class="py-lineno">646</tt> <tt class="py-line"> <tt class="py-name">dm</tt> <tt class="py-op">=</tt> <tt class="py-name">sp</tt><tt class="py-op">.</tt><tt id="link-330" class="py-name"><a title="Bio.SCOP.Node.getParent" class="py-name" href="#" onclick="return doclink('link-330', 'getParent', 'link-279');">getParent</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
<a name="L647"></a><tt class="py-lineno">647</tt> <tt class="py-line"> <tt id="link-331" class="py-name"><a title="Martel.test.test_swissprot38.s" class="py-name" href="#" onclick="return doclink('link-331', 's', 'link-265');">s</a></tt><tt class="py-op">.</tt><tt id="link-332" 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-332', 'append', 'link-68');">append</a></tt><tt class="py-op">(</tt><tt class="py-name">dm</tt><tt class="py-op">.</tt><tt id="link-333" class="py-name"><a title="Bio.Blast.NCBIStandalone._DescriptionConsumer.description
Bio.Enzyme._RecordConsumer.description
Bio.Prosite._RecordConsumer.description
Bio.Std.description
Bio.SwissProt.SProt._RecordConsumer.description
Bio.SwissProt.SProt._SequenceConsumer.description
Martel.setup.run_local_tests.description" class="py-name" href="#" onclick="return doclink('link-333', 'description', 'link-44');">description</a></tt><tt class="py-op">)</tt> </tt>
<a name="L648"></a><tt class="py-lineno">648</tt> <tt class="py-line"> <tt id="link-334" class="py-name"><a title="Martel.test.test_swissprot38.s" class="py-name" href="#" onclick="return doclink('link-334', 's', 'link-265');">s</a></tt><tt class="py-op">.</tt><tt id="link-335" 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-335', 'append', 'link-68');">append</a></tt><tt class="py-op">(</tt><tt class="py-string">"{"</tt><tt class="py-op">+</tt><tt class="py-name">sp</tt><tt class="py-op">.</tt><tt id="link-336" class="py-name"><a title="Bio.Blast.NCBIStandalone._DescriptionConsumer.description
Bio.Enzyme._RecordConsumer.description
Bio.Prosite._RecordConsumer.description
Bio.Std.description
Bio.SwissProt.SProt._RecordConsumer.description
Bio.SwissProt.SProt._SequenceConsumer.description
Martel.setup.run_local_tests.description" class="py-name" href="#" onclick="return doclink('link-336', 'description', 'link-44');">description</a></tt><tt class="py-op">+</tt><tt class="py-string">"}"</tt><tt class="py-op">)</tt> </tt>
<a name="L649"></a><tt class="py-lineno">649</tt> <tt class="py-line"> </tt>
<a name="L650"></a><tt class="py-lineno">650</tt> <tt class="py-line"> <tt class="py-keyword">return</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-337" class="py-name"><a title="Martel.test.test_swissprot38.s" class="py-name" href="#" onclick="return doclink('link-337', 's', 'link-265');">s</a></tt><tt class="py-op">)</tt> </tt>
</div><a name="L651"></a><tt class="py-lineno">651</tt> <tt class="py-line"> </tt>
<a name="Domain.toDesRecord"></a><div id="Domain.toDesRecord-def"><a name="L652"></a><tt class="py-lineno">652</tt> <a class="py-toggle" href="#" id="Domain.toDesRecord-toggle" onclick="return toggle('Domain.toDesRecord');">-</a><tt class="py-line"> <tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.SCOP.Domain-class.html#toDesRecord">toDesRecord</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="Domain.toDesRecord-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="Domain.toDesRecord-expanded"><a name="L653"></a><tt class="py-lineno">653</tt> <tt class="py-line"> <tt class="py-docstring">"""Return a Des.Record"""</tt> </tt>
<a name="L654"></a><tt class="py-lineno">654</tt> <tt class="py-line"> <tt class="py-name">rec</tt> <tt class="py-op">=</tt> <tt id="link-338" class="py-name"><a title="Bio.Nexus.Nodes.Node
Bio.SCOP.Node" class="py-name" href="#" onclick="return doclink('link-338', 'Node', 'link-58');">Node</a></tt><tt class="py-op">.</tt><tt id="link-339" class="py-name"><a title="Bio.SCOP.Domain.toDesRecord
Bio.SCOP.Node.toDesRecord" class="py-name" href="#" onclick="return doclink('link-339', 'toDesRecord', 'link-131');">toDesRecord</a></tt><tt class="py-op">(</tt><tt class="py-name">self</tt><tt class="py-op">)</tt> </tt>
<a name="L655"></a><tt class="py-lineno">655</tt> <tt class="py-line"> <tt class="py-name">rec</tt><tt class="py-op">.</tt><tt id="link-340" class="py-name"><a title="Bio.Encodings.IUPACEncoding.name" class="py-name" href="#" onclick="return doclink('link-340', 'name', 'link-67');">name</a></tt> <tt class="py-op">=</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">sid</tt> </tt>
<a name="L656"></a><tt class="py-lineno">656</tt> <tt class="py-line"> <tt class="py-keyword">return</tt> <tt class="py-name">rec</tt> </tt>
</div><a name="L657"></a><tt class="py-lineno">657</tt> <tt class="py-line"> </tt>
<a name="Domain.toClaRecord"></a><div id="Domain.toClaRecord-def"><a name="L658"></a><tt class="py-lineno">658</tt> <a class="py-toggle" href="#" id="Domain.toClaRecord-toggle" onclick="return toggle('Domain.toClaRecord');">-</a><tt class="py-line"> <tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.SCOP.Domain-class.html#toClaRecord">toClaRecord</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="Domain.toClaRecord-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="Domain.toClaRecord-expanded"><a name="L659"></a><tt class="py-lineno">659</tt> <tt class="py-line"> <tt class="py-docstring">"""Return a Cla.Record"""</tt> </tt>
<a name="L660"></a><tt class="py-lineno">660</tt> <tt class="py-line"> <tt class="py-name">rec</tt> <tt class="py-op">=</tt> <tt id="link-341" class="py-name"><a title="Bio.SCOP.Cla" class="py-name" href="#" onclick="return doclink('link-341', 'Cla', 'link-1');">Cla</a></tt><tt class="py-op">.</tt><tt id="link-342" class="py-name"><a title="Bio.Blast.Record
Bio.CDD.Record
Bio.CDD.Record.Record
Bio.Cluster.Record
Bio.Compass.Record
Bio.ECell.Record
Bio.ECell.Record.Record
Bio.Fasta.Record
Bio.GenBank.Record
Bio.GenBank.Record.Record
Bio.Geo.Record
Bio.Geo.Record.Record
Bio.Gobase.Record
Bio.IntelliGenetics.Record
Bio.IntelliGenetics.Record.Record
Bio.InterPro.Record
Bio.KEGG.Compound.Record
Bio.KEGG.Enzyme.Record
Bio.LocusLink.Record
Bio.LocusLink.web_parse.Record
Bio.Medline.Record
Bio.MetaTool.Record
Bio.MetaTool.Record.Record
Bio.NBRF.Record
Bio.NBRF.Record.Record
Bio.Ndb.Record
Bio.PopGen.FDist.Record
Bio.PopGen.GenePop.Record
Bio.Prosite.Prodoc.Record
Bio.Prosite.Record
Bio.Rebase.Record
Bio.SCOP.Cla.Record
Bio.SCOP.Des.Record
Bio.SCOP.Dom.Record
Bio.SCOP.Hie.Record
Bio.Saf.Record
Bio.Saf.Record.Record
Bio.Sequencing.Phd.Record
Bio.SwissProt.KeyWList.Record
Bio.SwissProt.SProt.Record" class="py-name" href="#" onclick="return doclink('link-342', 'Record', 'link-278');">Record</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
<a name="L661"></a><tt class="py-lineno">661</tt> <tt class="py-line"> <tt class="py-name">rec</tt><tt class="py-op">.</tt><tt class="py-name">sid</tt> <tt class="py-op">=</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">sid</tt> </tt>
<a name="L662"></a><tt class="py-lineno">662</tt> <tt class="py-line"> <tt class="py-name">rec</tt><tt class="py-op">.</tt><tt class="py-name">residues</tt> <tt class="py-op">=</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">residues</tt> </tt>
<a name="L663"></a><tt class="py-lineno">663</tt> <tt class="py-line"> <tt class="py-name">rec</tt><tt class="py-op">.</tt><tt class="py-name">sccs</tt> <tt class="py-op">=</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">sccs</tt> </tt>
<a name="L664"></a><tt class="py-lineno">664</tt> <tt class="py-line"> <tt class="py-name">rec</tt><tt class="py-op">.</tt><tt class="py-name">sunid</tt> <tt class="py-op">=</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">sunid</tt> </tt>
<a name="L665"></a><tt class="py-lineno">665</tt> <tt class="py-line"> </tt>
<a name="L666"></a><tt class="py-lineno">666</tt> <tt class="py-line"> <tt class="py-name">n</tt> <tt class="py-op">=</tt> <tt class="py-name">self</tt> </tt>
<a name="L667"></a><tt class="py-lineno">667</tt> <tt class="py-line"> <tt class="py-keyword">while</tt> <tt class="py-name">n</tt><tt class="py-op">.</tt><tt class="py-name">sunid</tt> <tt class="py-op">!=</tt> <tt class="py-number">0</tt><tt class="py-op">:</tt> <tt class="py-comment">#Not root node</tt> </tt>
<a name="L668"></a><tt class="py-lineno">668</tt> <tt class="py-line"> <tt class="py-name">rec</tt><tt class="py-op">.</tt><tt class="py-name">hierarchy</tt><tt class="py-op">.</tt><tt id="link-343" 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-343', 'append', 'link-68');">append</a></tt><tt class="py-op">(</tt> <tt class="py-op">(</tt><tt class="py-name">n</tt><tt class="py-op">.</tt><tt id="link-344" class="py-name"><a title="Bio.GenBank.LocationParser.Integer.type
Bio.GenBank.LocationParser.Symbol.type
Bio.GenBank.LocationParser.UnsignedInteger.type" class="py-name" href="#" onclick="return doclink('link-344', 'type', 'link-59');">type</a></tt><tt class="py-op">,</tt> <tt class="py-name">str</tt><tt class="py-op">(</tt><tt class="py-name">n</tt><tt class="py-op">.</tt><tt class="py-name">sunid</tt><tt class="py-op">)</tt><tt class="py-op">)</tt> <tt class="py-op">)</tt> </tt>
<a name="L669"></a><tt class="py-lineno">669</tt> <tt class="py-line"> <tt class="py-name">n</tt> <tt class="py-op">=</tt> <tt class="py-name">n</tt><tt class="py-op">.</tt><tt id="link-345" class="py-name"><a title="Bio.SCOP.Node.getParent" class="py-name" href="#" onclick="return doclink('link-345', 'getParent', 'link-279');">getParent</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
<a name="L670"></a><tt class="py-lineno">670</tt> <tt class="py-line"> </tt>
<a name="L671"></a><tt class="py-lineno">671</tt> <tt class="py-line"> <tt class="py-name">rec</tt><tt class="py-op">.</tt><tt class="py-name">hierarchy</tt><tt class="py-op">.</tt><tt id="link-346" class="py-name" targets="Method Bio.GFF.easy.Location.reverse()=Bio.GFF.easy.Location-class.html#reverse,Method Bio.Pathway.Reaction.reverse()=Bio.Pathway.Reaction-class.html#reverse,Method Bio.Seq.MutableSeq.reverse()=Bio.Seq.MutableSeq-class.html#reverse,Function Bio.SeqUtils.reverse()=Bio.SeqUtils-module.html#reverse"><a title="Bio.GFF.easy.Location.reverse
Bio.Pathway.Reaction.reverse
Bio.Seq.MutableSeq.reverse
Bio.SeqUtils.reverse" class="py-name" href="#" onclick="return doclink('link-346', 'reverse', 'link-346');">reverse</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
<a name="L672"></a><tt class="py-lineno">672</tt> <tt class="py-line"> </tt>
<a name="L673"></a><tt class="py-lineno">673</tt> <tt class="py-line"> <tt class="py-keyword">return</tt> <tt class="py-name">rec</tt> </tt>
</div></div><a name="L674"></a><tt class="py-lineno">674</tt> <tt class="py-line"> </tt>
<a name="Astral"></a><div id="Astral-def"><a name="L675"></a><tt class="py-lineno">675</tt> <a class="py-toggle" href="#" id="Astral-toggle" onclick="return toggle('Astral');">-</a><tt class="py-line"><tt class="py-keyword">class</tt> <a class="py-def-name" href="Bio.SCOP.Astral-class.html">Astral</a><tt class="py-op">:</tt> </tt>
</div><div id="Astral-collapsed" style="display:none;" pad="+++" indent="++++"></div><div id="Astral-expanded"><a name="L676"></a><tt class="py-lineno">676</tt> <tt class="py-line"> <tt class="py-docstring">"""Abstraction of the ASTRAL database, which has sequences for all the SCOP domains,</tt> </tt>
<a name="L677"></a><tt class="py-lineno">677</tt> <tt class="py-line"><tt class="py-docstring"> as well as clusterings by percent id or evalue.</tt> </tt>
<a name="L678"></a><tt class="py-lineno">678</tt> <tt class="py-line"><tt class="py-docstring"> """</tt> </tt>
<a name="L679"></a><tt class="py-lineno">679</tt> <tt class="py-line"> </tt>
<a name="Astral.__init__"></a><div id="Astral.__init__-def"><a name="L680"></a><tt class="py-lineno">680</tt> <a class="py-toggle" href="#" id="Astral.__init__-toggle" onclick="return toggle('Astral.__init__');">-</a><tt class="py-line"> <tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.SCOP.Astral-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">dir_path</tt><tt class="py-op">=</tt><tt class="py-name">None</tt><tt class="py-op">,</tt> <tt class="py-param">version</tt><tt class="py-op">=</tt><tt class="py-name">None</tt><tt class="py-op">,</tt> <tt class="py-param">scop</tt><tt class="py-op">=</tt><tt class="py-name">None</tt><tt class="py-op">,</tt> <tt class="py-param">ind_file</tt><tt class="py-op">=</tt><tt class="py-name">None</tt><tt class="py-op">,</tt> </tt>
<a name="L681"></a><tt class="py-lineno">681</tt> <tt class="py-line"> <tt class="py-param">astral_file</tt><tt class="py-op">=</tt><tt class="py-name">None</tt><tt class="py-op">,</tt> <tt class="py-param">db_handle</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="Astral.__init__-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="Astral.__init__-expanded"><a name="L682"></a><tt class="py-lineno">682</tt> <tt class="py-line"> <tt class="py-docstring">"""</tt> </tt>
<a name="L683"></a><tt class="py-lineno">683</tt> <tt class="py-line"><tt class="py-docstring"> Initialise the astral database.</tt> </tt>
<a name="L684"></a><tt class="py-lineno">684</tt> <tt class="py-line"><tt class="py-docstring"> </tt> </tt>
<a name="L685"></a><tt class="py-lineno">685</tt> <tt class="py-line"><tt class="py-docstring"> You must provide either a directory of SCOP files:</tt> </tt>
<a name="L686"></a><tt class="py-lineno">686</tt> <tt class="py-line"><tt class="py-docstring"> </tt> </tt>
<a name="L687"></a><tt class="py-lineno">687</tt> <tt class="py-line"><tt class="py-docstring"> dir_path - string, the path to location of the scopseq-x.xx directory</tt> </tt>
<a name="L688"></a><tt class="py-lineno">688</tt> <tt class="py-line"><tt class="py-docstring"> (not the directory itself), and</tt> </tt>
<a name="L689"></a><tt class="py-lineno">689</tt> <tt class="py-line"><tt class="py-docstring"> version -a version number.</tt> </tt>
<a name="L690"></a><tt class="py-lineno">690</tt> <tt class="py-line"><tt class="py-docstring"> </tt> </tt>
<a name="L691"></a><tt class="py-lineno">691</tt> <tt class="py-line"><tt class="py-docstring"> or, a FASTA file:</tt> </tt>
<a name="L692"></a><tt class="py-lineno">692</tt> <tt class="py-line"><tt class="py-docstring"> </tt> </tt>
<a name="L693"></a><tt class="py-lineno">693</tt> <tt class="py-line"><tt class="py-docstring"> astral_file - string, a path to a fasta file (which will be loaded in memory)</tt> </tt>
<a name="L694"></a><tt class="py-lineno">694</tt> <tt class="py-line"><tt class="py-docstring"> </tt> </tt>
<a name="L695"></a><tt class="py-lineno">695</tt> <tt class="py-line"><tt class="py-docstring"> or, a MYSQL database:</tt> </tt>
<a name="L696"></a><tt class="py-lineno">696</tt> <tt class="py-line"><tt class="py-docstring"> </tt> </tt>
<a name="L697"></a><tt class="py-lineno">697</tt> <tt class="py-line"><tt class="py-docstring"> db_handle - a database handle for a MYSQL database containing a table</tt> </tt>
<a name="L698"></a><tt class="py-lineno">698</tt> <tt class="py-line"><tt class="py-docstring"> 'astral' with the astral data in it. This can be created</tt> </tt>
<a name="L699"></a><tt class="py-lineno">699</tt> <tt class="py-line"><tt class="py-docstring"> using writeToSQL.</tt> </tt>
<a name="L700"></a><tt class="py-lineno">700</tt> <tt class="py-line"><tt class="py-docstring"> </tt> </tt>
<a name="L701"></a><tt class="py-lineno">701</tt> <tt class="py-line"><tt class="py-docstring"> Note that the ind_file argument is deprecated.</tt> </tt>
<a name="L702"></a><tt class="py-lineno">702</tt> <tt class="py-line"><tt class="py-docstring"> """</tt> </tt>
<a name="L703"></a><tt class="py-lineno">703</tt> <tt class="py-line"> <tt class="py-keyword">if</tt> <tt class="py-name">ind_file</tt> <tt class="py-op">:</tt> </tt>
<a name="L704"></a><tt class="py-lineno">704</tt> <tt class="py-line"> <tt class="py-keyword">raise</tt> <tt class="py-name">RuntimeError</tt><tt class="py-op">,</tt> <tt class="py-string">"The ind_file (index file) argument is deprecated"</tt> </tt>
<a name="L705"></a><tt class="py-lineno">705</tt> <tt class="py-line"> </tt>
<a name="L706"></a><tt class="py-lineno">706</tt> <tt class="py-line"> <tt class="py-keyword">if</tt> <tt class="py-name">astral_file</tt><tt class="py-op">==</tt><tt class="py-name">dir_path</tt><tt class="py-op">==</tt><tt class="py-name">db_handle</tt><tt class="py-op">==</tt><tt class="py-name">None</tt><tt class="py-op">:</tt> </tt>
<a name="L707"></a><tt class="py-lineno">707</tt> <tt class="py-line"> <tt class="py-keyword">raise</tt> <tt class="py-name">RunTimeError</tt><tt class="py-op">,</tt><tt class="py-string">"Need either file handle, or (dir_path + version)\</tt> </tt>
<a name="L708"></a><tt class="py-lineno">708</tt> <tt class="py-line"><tt class="py-string"> or database handle to construct Astral"</tt> </tt>
<a name="L709"></a><tt class="py-lineno">709</tt> <tt class="py-line"> <tt class="py-keyword">if</tt> <tt class="py-keyword">not</tt> <tt class="py-name">scop</tt><tt class="py-op">:</tt> </tt>
<a name="L710"></a><tt class="py-lineno">710</tt> <tt class="py-line"> <tt class="py-keyword">raise</tt> <tt class="py-name">RuntimeError</tt><tt class="py-op">,</tt> <tt class="py-string">"Must provide a Scop instance to construct"</tt> </tt>
<a name="L711"></a><tt class="py-lineno">711</tt> <tt class="py-line"> </tt>
<a name="L712"></a><tt class="py-lineno">712</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">scop</tt> <tt class="py-op">=</tt> <tt class="py-name">scop</tt> </tt>
<a name="L713"></a><tt class="py-lineno">713</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">db_handle</tt> <tt class="py-op">=</tt> <tt class="py-name">db_handle</tt> </tt>
<a name="L714"></a><tt class="py-lineno">714</tt> <tt class="py-line"> </tt>
<a name="L715"></a><tt class="py-lineno">715</tt> <tt class="py-line"> </tt>
<a name="L716"></a><tt class="py-lineno">716</tt> <tt class="py-line"> <tt class="py-keyword">if</tt> <tt class="py-keyword">not</tt> <tt class="py-name">astral_file</tt> <tt class="py-keyword">and</tt> <tt class="py-keyword">not</tt> <tt class="py-name">db_handle</tt><tt class="py-op">:</tt> </tt>
<a name="L717"></a><tt class="py-lineno">717</tt> <tt class="py-line"> <tt class="py-keyword">if</tt> <tt class="py-name">dir_path</tt> <tt class="py-op">==</tt> <tt class="py-name">None</tt> <tt class="py-keyword">or</tt> <tt id="link-347" class="py-name"><a title="Bio.AlignAce.Parser.AlignAceConsumer.version
Bio.Blast.NCBIStandalone._HeaderConsumer.version
Bio.GenBank._FeatureConsumer.version
Bio.GenBank._RecordConsumer.version
Bio.MetaTool.metatool_format.version
Bio.expressions.genbank.version" class="py-name" href="#" onclick="return doclink('link-347', 'version', 'link-47');">version</a></tt> <tt class="py-op">==</tt> <tt class="py-name">None</tt><tt class="py-op">:</tt> </tt>
<a name="L718"></a><tt class="py-lineno">718</tt> <tt class="py-line"> <tt class="py-keyword">raise</tt> <tt class="py-name">RuntimeError</tt><tt class="py-op">,</tt> <tt class="py-string">"must provide dir_path and version"</tt> </tt>
<a name="L719"></a><tt class="py-lineno">719</tt> <tt class="py-line"> </tt>
<a name="L720"></a><tt class="py-lineno">720</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-348" class="py-name"><a title="Bio.AlignAce.Parser.AlignAceConsumer.version
Bio.Blast.NCBIStandalone._HeaderConsumer.version
Bio.GenBank._FeatureConsumer.version
Bio.GenBank._RecordConsumer.version
Bio.MetaTool.metatool_format.version
Bio.expressions.genbank.version" class="py-name" href="#" onclick="return doclink('link-348', 'version', 'link-47');">version</a></tt> <tt class="py-op">=</tt> <tt id="link-349" class="py-name"><a title="Bio.AlignAce.Parser.AlignAceConsumer.version
Bio.Blast.NCBIStandalone._HeaderConsumer.version
Bio.GenBank._FeatureConsumer.version
Bio.GenBank._RecordConsumer.version
Bio.MetaTool.metatool_format.version
Bio.expressions.genbank.version" class="py-name" href="#" onclick="return doclink('link-349', 'version', 'link-47');">version</a></tt> </tt>
<a name="L721"></a><tt class="py-lineno">721</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">path</tt> <tt class="py-op">=</tt> <tt class="py-name">os</tt><tt class="py-op">.</tt><tt class="py-name">path</tt><tt class="py-op">.</tt><tt class="py-name">join</tt><tt class="py-op">(</tt> <tt class="py-name">dir_path</tt><tt class="py-op">,</tt> <tt class="py-string">"scopseq-%s"</tt> <tt class="py-op">%</tt> <tt id="link-350" class="py-name"><a title="Bio.AlignAce.Parser.AlignAceConsumer.version
Bio.Blast.NCBIStandalone._HeaderConsumer.version
Bio.GenBank._FeatureConsumer.version
Bio.GenBank._RecordConsumer.version
Bio.MetaTool.metatool_format.version
Bio.expressions.genbank.version" class="py-name" href="#" onclick="return doclink('link-350', 'version', 'link-47');">version</a></tt><tt class="py-op">)</tt> </tt>
<a name="L722"></a><tt class="py-lineno">722</tt> <tt class="py-line"> <tt class="py-name">astral_file</tt> <tt class="py-op">=</tt> <tt class="py-string">"astral-scopdom-seqres-all-%s.fa"</tt> <tt class="py-op">%</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-351" class="py-name"><a title="Bio.AlignAce.Parser.AlignAceConsumer.version
Bio.Blast.NCBIStandalone._HeaderConsumer.version
Bio.GenBank._FeatureConsumer.version
Bio.GenBank._RecordConsumer.version
Bio.MetaTool.metatool_format.version
Bio.expressions.genbank.version" class="py-name" href="#" onclick="return doclink('link-351', 'version', 'link-47');">version</a></tt> </tt>
<a name="L723"></a><tt class="py-lineno">723</tt> <tt class="py-line"> <tt class="py-name">astral_file</tt> <tt class="py-op">=</tt> <tt class="py-name">os</tt><tt class="py-op">.</tt><tt class="py-name">path</tt><tt class="py-op">.</tt><tt class="py-name">join</tt> <tt class="py-op">(</tt><tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">path</tt><tt class="py-op">,</tt> <tt class="py-name">astral_file</tt><tt class="py-op">)</tt> </tt>
<a name="L724"></a><tt class="py-lineno">724</tt> <tt class="py-line"> </tt>
<a name="L725"></a><tt class="py-lineno">725</tt> <tt class="py-line"> <tt class="py-keyword">if</tt> <tt class="py-name">astral_file</tt><tt class="py-op">:</tt> </tt>
<a name="L726"></a><tt class="py-lineno">726</tt> <tt class="py-line"> <tt class="py-comment">#Build a dictionary of SeqRecord objects in the FASTA file, IN MEMORY</tt> </tt>
<a name="L727"></a><tt class="py-lineno">727</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">fasta_dict</tt> <tt class="py-op">=</tt> <tt id="link-352" class="py-name"><a title="Bio.SeqIO" class="py-name" href="#" onclick="return doclink('link-352', 'SeqIO', 'link-5');">SeqIO</a></tt><tt class="py-op">.</tt><tt id="link-353" class="py-name" targets="Function Bio.SeqIO.to_dict()=Bio.SeqIO-module.html#to_dict"><a title="Bio.SeqIO.to_dict" class="py-name" href="#" onclick="return doclink('link-353', 'to_dict', 'link-353');">to_dict</a></tt><tt class="py-op">(</tt><tt id="link-354" class="py-name"><a title="Bio.SeqIO" class="py-name" href="#" onclick="return doclink('link-354', 'SeqIO', 'link-5');">SeqIO</a></tt><tt class="py-op">.</tt><tt id="link-355" class="py-name"><a title="Bio.Affy.CelFile.CelParser.parse
Bio.AlignAce.Parser.AlignAceParser.parse
Bio.AlignAce.Parser.CompareAceParser.parse
Bio.AlignIO.parse
Bio.Blast.NCBIStandalone.BlastErrorParser.parse
Bio.Blast.NCBIStandalone.BlastParser.parse
Bio.Blast.NCBIStandalone.PSIBlastParser.parse
Bio.Blast.NCBIWWW.BlastParser.parse
Bio.Blast.NCBIXML.BlastParser.parse
Bio.Blast.NCBIXML.parse
Bio.CDD.RecordParser.parse
Bio.Compass.RecordParser.parse
Bio.Decode.parse
Bio.ECell.RecordParser.parse
Bio.EUtils.POM.POMDocument.parse
Bio.EUtils.parse
Bio.Emboss.Primer.Primer3Parser.parse
Bio.Emboss.Primer.PrimerSearchParser.parse
Bio.Enzyme.RecordParser.parse
Bio.Fasta.RecordParser.parse
Bio.Fasta.SequenceParser.parse
Bio.GenBank.FeatureParser.parse
Bio.GenBank.LocationParser.parse
Bio.GenBank.RecordParser.parse
Bio.GenBank.Scanner.InsdcScanner.parse
Bio.Geo.parse
Bio.Gobase.RecordParser.parse
Bio.IntelliGenetics.RecordParser.parse
Bio.InterPro.InterProParser.parse
Bio.KEGG.Compound.parse
Bio.KEGG.Enzyme.parse
Bio.KEGG.Map.parse
Bio.LocusLink.RecordParser.parse
Bio.LocusLink.web_parse.LocusLinkParser.parse
Bio.MEME.Parser.MASTParser.parse
Bio.MEME.Parser.MEMEParser.parse
Bio.Medline.RecordParser.parse
Bio.MetaTool.RecordParser.parse
Bio.NBRF.RecordParser.parse
Bio.Ndb.NdbParser.parse
Bio.ParserSupport.AbstractParser.parse
Bio.Parsers.spark.GenericParser.parse
Bio.PopGen.FDist.RecordParser.parse
Bio.PopGen.GenePop.RecordParser.parse
Bio.PopGen.GenePop.parse
Bio.Prosite.Prodoc.RecordParser.parse
Bio.Prosite.Prodoc.parse
Bio.Prosite.RecordParser.parse
Bio.Prosite.parse
Bio.Rebase.RecordParser.parse
Bio.SCOP.Cla.Parser.parse
Bio.SCOP.Cla.parse
Bio.SCOP.Des.Parser.parse
Bio.SCOP.Des.parse
Bio.SCOP.Dom.Parser.parse
Bio.SCOP.Dom.parse
Bio.SCOP.Hie.Parser.parse
Bio.SCOP.Hie.parse
Bio.SCOP.Raf.Parser.parse
Bio.SCOP.Raf.parse
Bio.Saf.RecordParser.parse
Bio.SeqIO.parse
Bio.Sequencing.Ace.ACEParser.parse
Bio.Sequencing.Ace.RecordParser.parse
Bio.Sequencing.Phd.RecordParser.parse
Bio.SwissProt.KeyWList.ListParser.parse
Bio.SwissProt.KeyWList.parse
Bio.SwissProt.SProt.RecordParser.parse
Bio.SwissProt.SProt.SequenceParser.parse
Bio.SwissProt.parse
Bio.UniGene.RecordParser.parse
Bio.Wise.psw.parse
Martel.Parser.HeaderFooterParser.parse
Martel.Parser.Parser.parse
Martel.Parser.RecordParser.parse
Martel.msre_parse.parse" class="py-name" href="#" onclick="return doclink('link-355', 'parse', 'link-62');">parse</a></tt><tt class="py-op">(</tt><tt id="link-356" class="py-name"><a title="Bio.Mindy.FlatDB.open
Bio.Mindy.open" class="py-name" href="#" onclick="return doclink('link-356', 'open', 'link-49');">open</a></tt><tt class="py-op">(</tt><tt class="py-name">astral_file</tt><tt class="py-op">)</tt><tt class="py-op">,</tt> <tt class="py-string">"fasta"</tt><tt class="py-op">)</tt><tt class="py-op">)</tt> </tt>
<a name="L728"></a><tt class="py-lineno">728</tt> <tt class="py-line"> </tt>
<a name="L729"></a><tt class="py-lineno">729</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">astral_file</tt> <tt class="py-op">=</tt> <tt class="py-name">astral_file</tt> </tt>
<a name="L730"></a><tt class="py-lineno">730</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">EvDatasets</tt> <tt class="py-op">=</tt> <tt class="py-op">{</tt><tt class="py-op">}</tt> </tt>
<a name="L731"></a><tt class="py-lineno">731</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">EvDatahash</tt> <tt class="py-op">=</tt> <tt class="py-op">{</tt><tt class="py-op">}</tt> </tt>
<a name="L732"></a><tt class="py-lineno">732</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">IdDatasets</tt> <tt class="py-op">=</tt> <tt class="py-op">{</tt><tt class="py-op">}</tt> </tt>
<a name="L733"></a><tt class="py-lineno">733</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">IdDatahash</tt> <tt class="py-op">=</tt> <tt class="py-op">{</tt><tt class="py-op">}</tt> </tt>
</div><a name="L734"></a><tt class="py-lineno">734</tt> <tt class="py-line"> </tt>
<a name="L735"></a><tt class="py-lineno">735</tt> <tt class="py-line"> </tt>
<a name="Astral.domainsClusteredByEv"></a><div id="Astral.domainsClusteredByEv-def"><a name="L736"></a><tt class="py-lineno">736</tt> <a class="py-toggle" href="#" id="Astral.domainsClusteredByEv-toggle" onclick="return toggle('Astral.domainsClusteredByEv');">-</a><tt class="py-line"> <tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.SCOP.Astral-class.html#domainsClusteredByEv">domainsClusteredByEv</a><tt class="py-op">(</tt><tt class="py-param">self</tt><tt class="py-op">,</tt><tt class="py-param">id</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="Astral.domainsClusteredByEv-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="Astral.domainsClusteredByEv-expanded"><a name="L737"></a><tt class="py-lineno">737</tt> <tt class="py-line"> <tt class="py-docstring">"""get domains clustered by evalue"""</tt> </tt>
<a name="L738"></a><tt class="py-lineno">738</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">EvDatasets</tt><tt class="py-op">.</tt><tt id="link-357" class="py-name"><a title="Bio.Crystal.Crystal.has_key
Bio.EUtils.POM.ElementNode.has_key
Bio.GenBank.NCBIDictionary.has_key
Bio.PDB.AbstractPropertyMap.AbstractPropertyMap.has_key
Bio.PDB.FragmentMapper'.FragmentMapper.has_key
Bio.Prosite.ExPASyDictionary.has_key
Bio.Prosite.Prodoc.ExPASyDictionary.has_key
Bio.PubMed.Dictionary.has_key
Bio.SwissProt.SProt.ExPASyDictionary.has_key
Martel.Parser.MartelAttributeList.has_key" class="py-name" href="#" onclick="return doclink('link-357', 'has_key', 'link-80');">has_key</a></tt><tt class="py-op">(</tt><tt id="link-358" class="py-name" targets="Variable Bio.Data.CodonTable.id=Bio.Data.CodonTable-module.html#id,Variable Bio.Encodings.IUPACEncoding.id=Bio.Encodings.IUPACEncoding-module.html#id,Method Bio.GFF.Feature.id()=Bio.GFF.Feature-class.html#id"><a title="Bio.Data.CodonTable.id
Bio.Encodings.IUPACEncoding.id
Bio.GFF.Feature.id" class="py-name" href="#" onclick="return doclink('link-358', 'id', 'link-358');">id</a></tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
<a name="L739"></a><tt class="py-lineno">739</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">db_handle</tt><tt class="py-op">:</tt> </tt>
<a name="L740"></a><tt class="py-lineno">740</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">EvDatasets</tt><tt class="py-op">[</tt><tt id="link-359" class="py-name"><a title="Bio.Data.CodonTable.id
Bio.Encodings.IUPACEncoding.id
Bio.GFF.Feature.id" class="py-name" href="#" onclick="return doclink('link-359', 'id', 'link-358');">id</a></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-360" class="py-name" targets="Method Bio.SCOP.Astral.getAstralDomainsFromSQL()=Bio.SCOP.Astral-class.html#getAstralDomainsFromSQL"><a title="Bio.SCOP.Astral.getAstralDomainsFromSQL" class="py-name" href="#" onclick="return doclink('link-360', 'getAstralDomainsFromSQL', 'link-360');">getAstralDomainsFromSQL</a></tt><tt class="py-op">(</tt><tt id="link-361" class="py-name"><a title="Bio.SCOP.astralEv_to_sql" class="py-name" href="#" onclick="return doclink('link-361', 'astralEv_to_sql', 'link-18');">astralEv_to_sql</a></tt><tt class="py-op">[</tt><tt id="link-362" class="py-name"><a title="Bio.Data.CodonTable.id
Bio.Encodings.IUPACEncoding.id
Bio.GFF.Feature.id" class="py-name" href="#" onclick="return doclink('link-362', 'id', 'link-358');">id</a></tt><tt class="py-op">]</tt><tt class="py-op">)</tt> </tt>
<a name="L741"></a><tt class="py-lineno">741</tt> <tt class="py-line"> </tt>
<a name="L742"></a><tt class="py-lineno">742</tt> <tt class="py-line"> <tt class="py-keyword">else</tt><tt class="py-op">:</tt> </tt>
<a name="L743"></a><tt class="py-lineno">743</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">path</tt><tt class="py-op">:</tt> </tt>
<a name="L744"></a><tt class="py-lineno">744</tt> <tt class="py-line"> <tt class="py-keyword">raise</tt> <tt class="py-name">RuntimeError</tt><tt class="py-op">,</tt> <tt class="py-string">"No scopseq directory specified"</tt> </tt>
<a name="L745"></a><tt class="py-lineno">745</tt> <tt class="py-line"> </tt>
<a name="L746"></a><tt class="py-lineno">746</tt> <tt class="py-line"> <tt class="py-name">file_prefix</tt> <tt class="py-op">=</tt> <tt class="py-string">"astral-scopdom-seqres-sel-gs"</tt> </tt>
<a name="L747"></a><tt class="py-lineno">747</tt> <tt class="py-line"> <tt class="py-name">filename</tt> <tt class="py-op">=</tt> <tt class="py-string">"%s-e100m-%s-%s.id"</tt> <tt class="py-op">%</tt> <tt class="py-op">(</tt><tt class="py-name">file_prefix</tt><tt class="py-op">,</tt> <tt id="link-363" class="py-name"><a title="Bio.SCOP.astralEv_to_file" class="py-name" href="#" onclick="return doclink('link-363', 'astralEv_to_file', 'link-17');">astralEv_to_file</a></tt><tt class="py-op">[</tt><tt id="link-364" class="py-name"><a title="Bio.Data.CodonTable.id
Bio.Encodings.IUPACEncoding.id
Bio.GFF.Feature.id" class="py-name" href="#" onclick="return doclink('link-364', 'id', 'link-358');">id</a></tt><tt class="py-op">]</tt> <tt class="py-op">,</tt> </tt>
<a name="L748"></a><tt class="py-lineno">748</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-365" class="py-name"><a title="Bio.AlignAce.Parser.AlignAceConsumer.version
Bio.Blast.NCBIStandalone._HeaderConsumer.version
Bio.GenBank._FeatureConsumer.version
Bio.GenBank._RecordConsumer.version
Bio.MetaTool.metatool_format.version
Bio.expressions.genbank.version" class="py-name" href="#" onclick="return doclink('link-365', 'version', 'link-47');">version</a></tt><tt class="py-op">)</tt> </tt>
<a name="L749"></a><tt class="py-lineno">749</tt> <tt class="py-line"> <tt class="py-name">filename</tt> <tt class="py-op">=</tt> <tt class="py-name">os</tt><tt class="py-op">.</tt><tt class="py-name">path</tt><tt class="py-op">.</tt><tt class="py-name">join</tt><tt class="py-op">(</tt><tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">path</tt><tt class="py-op">,</tt><tt class="py-name">filename</tt><tt class="py-op">)</tt> </tt>
<a name="L750"></a><tt class="py-lineno">750</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">EvDatasets</tt><tt class="py-op">[</tt><tt id="link-366" class="py-name"><a title="Bio.Data.CodonTable.id
Bio.Encodings.IUPACEncoding.id
Bio.GFF.Feature.id" class="py-name" href="#" onclick="return doclink('link-366', 'id', 'link-358');">id</a></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-367" class="py-name" targets="Method Bio.SCOP.Astral.getAstralDomainsFromFile()=Bio.SCOP.Astral-class.html#getAstralDomainsFromFile"><a title="Bio.SCOP.Astral.getAstralDomainsFromFile" class="py-name" href="#" onclick="return doclink('link-367', 'getAstralDomainsFromFile', 'link-367');">getAstralDomainsFromFile</a></tt><tt class="py-op">(</tt><tt class="py-name">filename</tt><tt class="py-op">)</tt> </tt>
<a name="L751"></a><tt class="py-lineno">751</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">EvDatasets</tt><tt class="py-op">[</tt><tt id="link-368" class="py-name"><a title="Bio.Data.CodonTable.id
Bio.Encodings.IUPACEncoding.id
Bio.GFF.Feature.id" class="py-name" href="#" onclick="return doclink('link-368', 'id', 'link-358');">id</a></tt><tt class="py-op">]</tt> </tt>
</div><a name="L752"></a><tt class="py-lineno">752</tt> <tt class="py-line"> </tt>
<a name="L753"></a><tt class="py-lineno">753</tt> <tt class="py-line"> </tt>
<a name="Astral.domainsClusteredById"></a><div id="Astral.domainsClusteredById-def"><a name="L754"></a><tt class="py-lineno">754</tt> <a class="py-toggle" href="#" id="Astral.domainsClusteredById-toggle" onclick="return toggle('Astral.domainsClusteredById');">-</a><tt class="py-line"> <tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.SCOP.Astral-class.html#domainsClusteredById">domainsClusteredById</a><tt class="py-op">(</tt><tt class="py-param">self</tt><tt class="py-op">,</tt><tt class="py-param">id</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="Astral.domainsClusteredById-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="Astral.domainsClusteredById-expanded"><a name="L755"></a><tt class="py-lineno">755</tt> <tt class="py-line"> <tt class="py-docstring">"""get domains clustered by percent id"""</tt> </tt>
<a name="L756"></a><tt class="py-lineno">756</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">IdDatasets</tt><tt class="py-op">.</tt><tt id="link-369" class="py-name"><a title="Bio.Crystal.Crystal.has_key
Bio.EUtils.POM.ElementNode.has_key
Bio.GenBank.NCBIDictionary.has_key
Bio.PDB.AbstractPropertyMap.AbstractPropertyMap.has_key
Bio.PDB.FragmentMapper'.FragmentMapper.has_key
Bio.Prosite.ExPASyDictionary.has_key
Bio.Prosite.Prodoc.ExPASyDictionary.has_key
Bio.PubMed.Dictionary.has_key
Bio.SwissProt.SProt.ExPASyDictionary.has_key
Martel.Parser.MartelAttributeList.has_key" class="py-name" href="#" onclick="return doclink('link-369', 'has_key', 'link-80');">has_key</a></tt><tt class="py-op">(</tt><tt id="link-370" class="py-name"><a title="Bio.Data.CodonTable.id
Bio.Encodings.IUPACEncoding.id
Bio.GFF.Feature.id" class="py-name" href="#" onclick="return doclink('link-370', 'id', 'link-358');">id</a></tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
<a name="L757"></a><tt class="py-lineno">757</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">db_handle</tt><tt class="py-op">:</tt> </tt>
<a name="L758"></a><tt class="py-lineno">758</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">IdDatasets</tt><tt class="py-op">[</tt><tt id="link-371" class="py-name"><a title="Bio.Data.CodonTable.id
Bio.Encodings.IUPACEncoding.id
Bio.GFF.Feature.id" class="py-name" href="#" onclick="return doclink('link-371', 'id', 'link-358');">id</a></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-372" class="py-name"><a title="Bio.SCOP.Astral.getAstralDomainsFromSQL" class="py-name" href="#" onclick="return doclink('link-372', 'getAstralDomainsFromSQL', 'link-360');">getAstralDomainsFromSQL</a></tt><tt class="py-op">(</tt><tt class="py-string">"id"</tt><tt class="py-op">+</tt><tt class="py-name">str</tt><tt class="py-op">(</tt><tt id="link-373" class="py-name"><a title="Bio.Data.CodonTable.id
Bio.Encodings.IUPACEncoding.id
Bio.GFF.Feature.id" class="py-name" href="#" onclick="return doclink('link-373', 'id', 'link-358');">id</a></tt><tt class="py-op">)</tt><tt class="py-op">)</tt> </tt>
<a name="L759"></a><tt class="py-lineno">759</tt> <tt class="py-line"> </tt>
<a name="L760"></a><tt class="py-lineno">760</tt> <tt class="py-line"> <tt class="py-keyword">else</tt><tt class="py-op">:</tt> </tt>
<a name="L761"></a><tt class="py-lineno">761</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">path</tt><tt class="py-op">:</tt> </tt>
<a name="L762"></a><tt class="py-lineno">762</tt> <tt class="py-line"> <tt class="py-keyword">raise</tt> <tt class="py-name">RuntimeError</tt><tt class="py-op">,</tt> <tt class="py-string">"No scopseq directory specified"</tt> </tt>
<a name="L763"></a><tt class="py-lineno">763</tt> <tt class="py-line"> </tt>
<a name="L764"></a><tt class="py-lineno">764</tt> <tt class="py-line"> <tt class="py-name">file_prefix</tt> <tt class="py-op">=</tt> <tt class="py-string">"astral-scopdom-seqres-sel-gs"</tt> </tt>
<a name="L765"></a><tt class="py-lineno">765</tt> <tt class="py-line"> <tt class="py-name">filename</tt> <tt class="py-op">=</tt> <tt class="py-string">"%s-bib-%s-%s.id"</tt> <tt class="py-op">%</tt> <tt class="py-op">(</tt><tt class="py-name">file_prefix</tt><tt class="py-op">,</tt> <tt id="link-374" class="py-name"><a title="Bio.Data.CodonTable.id
Bio.Encodings.IUPACEncoding.id
Bio.GFF.Feature.id" class="py-name" href="#" onclick="return doclink('link-374', 'id', 'link-358');">id</a></tt><tt class="py-op">,</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-375" class="py-name"><a title="Bio.AlignAce.Parser.AlignAceConsumer.version
Bio.Blast.NCBIStandalone._HeaderConsumer.version
Bio.GenBank._FeatureConsumer.version
Bio.GenBank._RecordConsumer.version
Bio.MetaTool.metatool_format.version
Bio.expressions.genbank.version" class="py-name" href="#" onclick="return doclink('link-375', 'version', 'link-47');">version</a></tt><tt class="py-op">)</tt> </tt>
<a name="L766"></a><tt class="py-lineno">766</tt> <tt class="py-line"> <tt class="py-name">filename</tt> <tt class="py-op">=</tt> <tt class="py-name">os</tt><tt class="py-op">.</tt><tt class="py-name">path</tt><tt class="py-op">.</tt><tt class="py-name">join</tt><tt class="py-op">(</tt><tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">path</tt><tt class="py-op">,</tt><tt class="py-name">filename</tt><tt class="py-op">)</tt> </tt>
<a name="L767"></a><tt class="py-lineno">767</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">IdDatasets</tt><tt class="py-op">[</tt><tt id="link-376" class="py-name"><a title="Bio.Data.CodonTable.id
Bio.Encodings.IUPACEncoding.id
Bio.GFF.Feature.id" class="py-name" href="#" onclick="return doclink('link-376', 'id', 'link-358');">id</a></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-377" class="py-name"><a title="Bio.SCOP.Astral.getAstralDomainsFromFile" class="py-name" href="#" onclick="return doclink('link-377', 'getAstralDomainsFromFile', 'link-367');">getAstralDomainsFromFile</a></tt><tt class="py-op">(</tt><tt class="py-name">filename</tt><tt class="py-op">)</tt> </tt>
<a name="L768"></a><tt class="py-lineno">768</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">IdDatasets</tt><tt class="py-op">[</tt><tt id="link-378" class="py-name"><a title="Bio.Data.CodonTable.id
Bio.Encodings.IUPACEncoding.id
Bio.GFF.Feature.id" class="py-name" href="#" onclick="return doclink('link-378', 'id', 'link-358');">id</a></tt><tt class="py-op">]</tt> </tt>
</div><a name="L769"></a><tt class="py-lineno">769</tt> <tt class="py-line"> </tt>
<a name="L770"></a><tt class="py-lineno">770</tt> <tt class="py-line"> </tt>
<a name="Astral.getAstralDomainsFromFile"></a><div id="Astral.getAstralDomainsFromFile-def"><a name="L771"></a><tt class="py-lineno">771</tt> <a class="py-toggle" href="#" id="Astral.getAstralDomainsFromFile-toggle" onclick="return toggle('Astral.getAstralDomainsFromFile');">-</a><tt class="py-line"> <tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.SCOP.Astral-class.html#getAstralDomainsFromFile">getAstralDomainsFromFile</a><tt class="py-op">(</tt><tt class="py-param">self</tt><tt class="py-op">,</tt><tt class="py-param">filename</tt><tt class="py-op">=</tt><tt class="py-name">None</tt><tt class="py-op">,</tt><tt class="py-param">file_handle</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="Astral.getAstralDomainsFromFile-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="Astral.getAstralDomainsFromFile-expanded"><a name="L772"></a><tt class="py-lineno">772</tt> <tt class="py-line"> <tt class="py-docstring">"""Get the scop domains from a file containing a list of sids"""</tt> </tt>
<a name="L773"></a><tt class="py-lineno">773</tt> <tt class="py-line"> <tt class="py-keyword">if</tt> <tt class="py-name">file_handle</tt> <tt class="py-op">==</tt> <tt class="py-name">filename</tt> <tt class="py-op">==</tt> <tt class="py-name">none</tt><tt class="py-op">:</tt> </tt>
<a name="L774"></a><tt class="py-lineno">774</tt> <tt class="py-line"> <tt class="py-keyword">raise</tt> <tt class="py-name">RuntimeError</tt><tt class="py-op">,</tt> <tt class="py-string">"You must provide a filename or handle"</tt> </tt>
<a name="L775"></a><tt class="py-lineno">775</tt> <tt class="py-line"> <tt class="py-keyword">if</tt> <tt class="py-keyword">not</tt> <tt class="py-name">file_handle</tt><tt class="py-op">:</tt> </tt>
<a name="L776"></a><tt class="py-lineno">776</tt> <tt class="py-line"> <tt class="py-name">file_handle</tt> <tt class="py-op">=</tt> <tt id="link-379" class="py-name"><a title="Bio.Mindy.FlatDB.open
Bio.Mindy.open" class="py-name" href="#" onclick="return doclink('link-379', 'open', 'link-49');">open</a></tt><tt class="py-op">(</tt><tt class="py-name">filename</tt><tt class="py-op">)</tt> </tt>
<a name="L777"></a><tt class="py-lineno">777</tt> <tt class="py-line"> <tt class="py-name">doms</tt> <tt class="py-op">=</tt> <tt class="py-op">[</tt><tt class="py-op">]</tt> </tt>
<a name="L778"></a><tt class="py-lineno">778</tt> <tt class="py-line"> <tt class="py-keyword">while</tt> <tt class="py-number">1</tt><tt class="py-op">:</tt> </tt>
<a name="L779"></a><tt class="py-lineno">779</tt> <tt class="py-line"> <tt class="py-name">line</tt> <tt class="py-op">=</tt> <tt class="py-name">file_handle</tt><tt class="py-op">.</tt><tt id="link-380" class="py-name" targets="Method Bio.EUtils.ReseekFile.ReseekFile.readline()=Bio.EUtils.ReseekFile.ReseekFile-class.html#readline,Method Bio.File.SGMLHandle.readline()=Bio.File.SGMLHandle-class.html#readline,Method Bio.File.UndoHandle.readline()=Bio.File.UndoHandle-class.html#readline,Method Bio.SGMLExtractor.SGMLExtractorHandle.readline()=Bio.SGMLExtractor.SGMLExtractorHandle-class.html#readline"><a title="Bio.EUtils.ReseekFile.ReseekFile.readline
Bio.File.SGMLHandle.readline
Bio.File.UndoHandle.readline
Bio.SGMLExtractor.SGMLExtractorHandle.readline" class="py-name" href="#" onclick="return doclink('link-380', 'readline', 'link-380');">readline</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
<a name="L780"></a><tt class="py-lineno">780</tt> <tt class="py-line"> <tt class="py-keyword">if</tt> <tt class="py-keyword">not</tt> <tt class="py-name">line</tt><tt class="py-op">:</tt> </tt>
<a name="L781"></a><tt class="py-lineno">781</tt> <tt class="py-line"> <tt class="py-keyword">break</tt> </tt>
<a name="L782"></a><tt class="py-lineno">782</tt> <tt class="py-line"> <tt class="py-name">line</tt> <tt class="py-op">=</tt> <tt class="py-name">line</tt><tt class="py-op">.</tt><tt class="py-name">rstrip</tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
<a name="L783"></a><tt class="py-lineno">783</tt> <tt class="py-line"> <tt class="py-name">doms</tt><tt class="py-op">.</tt><tt id="link-381" 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-381', 'append', 'link-68');">append</a></tt><tt class="py-op">(</tt><tt class="py-name">line</tt><tt class="py-op">)</tt> </tt>
<a name="L784"></a><tt class="py-lineno">784</tt> <tt class="py-line"> <tt class="py-keyword">if</tt> <tt class="py-name">filename</tt><tt class="py-op">:</tt> </tt>
<a name="L785"></a><tt class="py-lineno">785</tt> <tt class="py-line"> <tt class="py-name">file_handle</tt><tt class="py-op">.</tt><tt id="link-382" class="py-name"><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-382', 'close', 'link-100');">close</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
<a name="L786"></a><tt class="py-lineno">786</tt> <tt class="py-line"> </tt>
<a name="L787"></a><tt class="py-lineno">787</tt> <tt class="py-line"> <tt class="py-name">doms</tt> <tt class="py-op">=</tt> <tt id="link-383" class="py-name" targets="Function Bio.FSSP.FSSPTools.filter()=Bio.FSSP.FSSPTools-module.html#filter,Method Bio.FilteredReader.FilteredReader.filter()=Bio.FilteredReader.FilteredReader-class.html#filter,Variable Bio.expressions.swissprot.filter=Bio.expressions.swissprot-module.html#filter"><a title="Bio.FSSP.FSSPTools.filter
Bio.FilteredReader.FilteredReader.filter
Bio.expressions.swissprot.filter" class="py-name" href="#" onclick="return doclink('link-383', 'filter', 'link-383');">filter</a></tt><tt class="py-op">(</tt> <tt class="py-keyword">lambda</tt> <tt class="py-name">a</tt><tt class="py-op">:</tt> <tt class="py-name">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-string">'d'</tt><tt class="py-op">,</tt> <tt class="py-name">doms</tt> <tt class="py-op">)</tt> </tt>
<a name="L788"></a><tt class="py-lineno">788</tt> <tt class="py-line"> <tt class="py-name">doms</tt> <tt class="py-op">=</tt> <tt id="link-384" class="py-name"><a title="Bio.GFF.FeatureAggregate.map" class="py-name" href="#" onclick="return doclink('link-384', 'map', 'link-28');">map</a></tt><tt class="py-op">(</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">scop</tt><tt class="py-op">.</tt><tt id="link-385" class="py-name" targets="Method Bio.SCOP.Scop.getDomainBySid()=Bio.SCOP.Scop-class.html#getDomainBySid"><a title="Bio.SCOP.Scop.getDomainBySid" class="py-name" href="#" onclick="return doclink('link-385', 'getDomainBySid', 'link-385');">getDomainBySid</a></tt><tt class="py-op">,</tt> <tt class="py-name">doms</tt> <tt class="py-op">)</tt> </tt>
<a name="L789"></a><tt class="py-lineno">789</tt> <tt class="py-line"> <tt class="py-keyword">return</tt> <tt class="py-name">doms</tt> </tt>
</div><a name="L790"></a><tt class="py-lineno">790</tt> <tt class="py-line"> </tt>
<a name="Astral.getAstralDomainsFromSQL"></a><div id="Astral.getAstralDomainsFromSQL-def"><a name="L791"></a><tt class="py-lineno">791</tt> <a class="py-toggle" href="#" id="Astral.getAstralDomainsFromSQL-toggle" onclick="return toggle('Astral.getAstralDomainsFromSQL');">-</a><tt class="py-line"> <tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.SCOP.Astral-class.html#getAstralDomainsFromSQL">getAstralDomainsFromSQL</a><tt class="py-op">(</tt><tt class="py-param">self</tt><tt class="py-op">,</tt> <tt class="py-param">column</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="Astral.getAstralDomainsFromSQL-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="Astral.getAstralDomainsFromSQL-expanded"><a name="L792"></a><tt class="py-lineno">792</tt> <tt class="py-line"> <tt class="py-docstring">"""Load a set of astral domains from a column in the astral table of a MYSQL</tt> </tt>
<a name="L793"></a><tt class="py-lineno">793</tt> <tt class="py-line"><tt class="py-docstring"> database (which can be created with writeToSQL(...)"""</tt> </tt>
<a name="L794"></a><tt class="py-lineno">794</tt> <tt class="py-line"> <tt class="py-name">cur</tt> <tt class="py-op">=</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">db_handle</tt><tt class="py-op">.</tt><tt id="link-386" class="py-name"><a title="Bio.DocSQL.Query.cursor
Bio.DocSQL.QuerySingle.cursor" class="py-name" href="#" onclick="return doclink('link-386', 'cursor', 'link-142');">cursor</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
<a name="L795"></a><tt class="py-lineno">795</tt> <tt class="py-line"> <tt class="py-name">cur</tt><tt class="py-op">.</tt><tt id="link-387" class="py-name"><a title="BioSQL.BioSeqDatabase.Adaptor.execute" class="py-name" href="#" onclick="return doclink('link-387', 'execute', 'link-143');">execute</a></tt><tt class="py-op">(</tt><tt class="py-string">"SELECT sid FROM astral WHERE "</tt><tt class="py-op">+</tt><tt class="py-name">column</tt><tt class="py-op">+</tt><tt class="py-string">"=1"</tt><tt class="py-op">)</tt> </tt>
<a name="L796"></a><tt class="py-lineno">796</tt> <tt class="py-line"> <tt id="link-388" class="py-name"><a title="BioSQL.BioSeq.DBSeq.data" class="py-name" href="#" onclick="return doclink('link-388', 'data', 'link-145');">data</a></tt> <tt class="py-op">=</tt> <tt class="py-name">cur</tt><tt class="py-op">.</tt><tt class="py-name">fetchall</tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
<a name="L797"></a><tt class="py-lineno">797</tt> <tt class="py-line"> <tt id="link-389" class="py-name"><a title="BioSQL.BioSeq.DBSeq.data" class="py-name" href="#" onclick="return doclink('link-389', 'data', 'link-145');">data</a></tt> <tt class="py-op">=</tt> <tt id="link-390" class="py-name"><a title="Bio.GFF.FeatureAggregate.map" class="py-name" href="#" onclick="return doclink('link-390', 'map', 'link-28');">map</a></tt><tt class="py-op">(</tt> <tt class="py-keyword">lambda</tt> <tt id="link-391" class="py-name" targets="Variable Bio.MarkovModel.x=Bio.MarkovModel-module.html#x,Variable Bio.Statistics.lowess.x=Bio.Statistics.lowess-module.html#x"><a title="Bio.MarkovModel.x
Bio.Statistics.lowess.x" class="py-name" href="#" onclick="return doclink('link-391', 'x', 'link-391');">x</a></tt><tt class="py-op">:</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">scop</tt><tt class="py-op">.</tt><tt id="link-392" class="py-name"><a title="Bio.SCOP.Scop.getDomainBySid" class="py-name" href="#" onclick="return doclink('link-392', 'getDomainBySid', 'link-385');">getDomainBySid</a></tt><tt class="py-op">(</tt><tt id="link-393" class="py-name"><a title="Bio.MarkovModel.x
Bio.Statistics.lowess.x" class="py-name" href="#" onclick="return doclink('link-393', 'x', 'link-391');">x</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-op">,</tt> <tt id="link-394" class="py-name"><a title="BioSQL.BioSeq.DBSeq.data" class="py-name" href="#" onclick="return doclink('link-394', 'data', 'link-145');">data</a></tt><tt class="py-op">)</tt> </tt>
<a name="L798"></a><tt class="py-lineno">798</tt> <tt class="py-line"> </tt>
<a name="L799"></a><tt class="py-lineno">799</tt> <tt class="py-line"> <tt class="py-keyword">return</tt> <tt id="link-395" class="py-name"><a title="BioSQL.BioSeq.DBSeq.data" class="py-name" href="#" onclick="return doclink('link-395', 'data', 'link-145');">data</a></tt> </tt>
</div><a name="L800"></a><tt class="py-lineno">800</tt> <tt class="py-line"> </tt>
<a name="L801"></a><tt class="py-lineno">801</tt> <tt class="py-line"> </tt>
<a name="Astral.getSeqBySid"></a><div id="Astral.getSeqBySid-def"><a name="L802"></a><tt class="py-lineno">802</tt> <a class="py-toggle" href="#" id="Astral.getSeqBySid-toggle" onclick="return toggle('Astral.getSeqBySid');">-</a><tt class="py-line"> <tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.SCOP.Astral-class.html#getSeqBySid">getSeqBySid</a><tt class="py-op">(</tt><tt class="py-param">self</tt><tt class="py-op">,</tt><tt class="py-param">domain</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="Astral.getSeqBySid-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="Astral.getSeqBySid-expanded"><a name="L803"></a><tt class="py-lineno">803</tt> <tt class="py-line"> <tt class="py-docstring">"""get the seq record of a given domain from its sid"""</tt> </tt>
<a name="L804"></a><tt class="py-lineno">804</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">db_handle</tt> <tt class="py-keyword">is</tt> <tt class="py-name">None</tt><tt class="py-op">:</tt> </tt>
<a name="L805"></a><tt class="py-lineno">805</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">fasta_dict</tt><tt class="py-op">[</tt><tt class="py-name">domain</tt><tt class="py-op">]</tt><tt class="py-op">.</tt><tt id="link-396" 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-396', 'seq', 'link-396');">seq</a></tt> </tt>
<a name="L806"></a><tt class="py-lineno">806</tt> <tt class="py-line"> </tt>
<a name="L807"></a><tt class="py-lineno">807</tt> <tt class="py-line"> <tt class="py-keyword">else</tt><tt class="py-op">:</tt> </tt>
<a name="L808"></a><tt class="py-lineno">808</tt> <tt class="py-line"> <tt class="py-name">cur</tt> <tt class="py-op">=</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">db_handle</tt><tt class="py-op">.</tt><tt id="link-397" class="py-name"><a title="Bio.DocSQL.Query.cursor
Bio.DocSQL.QuerySingle.cursor" class="py-name" href="#" onclick="return doclink('link-397', 'cursor', 'link-142');">cursor</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
<a name="L809"></a><tt class="py-lineno">809</tt> <tt class="py-line"> <tt class="py-name">cur</tt><tt class="py-op">.</tt><tt id="link-398" class="py-name"><a title="BioSQL.BioSeqDatabase.Adaptor.execute" class="py-name" href="#" onclick="return doclink('link-398', 'execute', 'link-143');">execute</a></tt><tt class="py-op">(</tt><tt class="py-string">"SELECT seq FROM astral WHERE sid=%s"</tt><tt class="py-op">,</tt> <tt class="py-name">domain</tt><tt class="py-op">)</tt> </tt>
<a name="L810"></a><tt class="py-lineno">810</tt> <tt class="py-line"> <tt class="py-keyword">return</tt> <tt id="link-399" class="py-name"><a title="Bio.Seq
Bio.Seq.Seq
Martel.Expression.Seq
Martel.Seq" class="py-name" href="#" onclick="return doclink('link-399', 'Seq', 'link-10');">Seq</a></tt><tt class="py-op">(</tt><tt class="py-name">cur</tt><tt class="py-op">.</tt><tt class="py-name">fetchone</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 class="py-op">)</tt> </tt>
</div><a name="L811"></a><tt class="py-lineno">811</tt> <tt class="py-line"> </tt>
<a name="Astral.getSeq"></a><div id="Astral.getSeq-def"><a name="L812"></a><tt class="py-lineno">812</tt> <a class="py-toggle" href="#" id="Astral.getSeq-toggle" onclick="return toggle('Astral.getSeq');">-</a><tt class="py-line"> <tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.SCOP.Astral-class.html#getSeq">getSeq</a><tt class="py-op">(</tt><tt class="py-param">self</tt><tt class="py-op">,</tt><tt class="py-param">domain</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="Astral.getSeq-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="Astral.getSeq-expanded"><a name="L813"></a><tt class="py-lineno">813</tt> <tt class="py-line"> <tt class="py-docstring">"""Return seq associated with domain"""</tt> </tt>
<a name="L814"></a><tt class="py-lineno">814</tt> <tt class="py-line"> <tt class="py-keyword">return</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-400" class="py-name" targets="Method Bio.SCOP.Astral.getSeqBySid()=Bio.SCOP.Astral-class.html#getSeqBySid"><a title="Bio.SCOP.Astral.getSeqBySid" class="py-name" href="#" onclick="return doclink('link-400', 'getSeqBySid', 'link-400');">getSeqBySid</a></tt><tt class="py-op">(</tt><tt class="py-name">domain</tt><tt class="py-op">.</tt><tt class="py-name">sid</tt><tt class="py-op">)</tt> </tt>
</div><a name="L815"></a><tt class="py-lineno">815</tt> <tt class="py-line"> </tt>
<a name="L816"></a><tt class="py-lineno">816</tt> <tt class="py-line"> </tt>
<a name="Astral.hashedDomainsById"></a><div id="Astral.hashedDomainsById-def"><a name="L817"></a><tt class="py-lineno">817</tt> <a class="py-toggle" href="#" id="Astral.hashedDomainsById-toggle" onclick="return toggle('Astral.hashedDomainsById');">-</a><tt class="py-line"> <tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.SCOP.Astral-class.html#hashedDomainsById">hashedDomainsById</a><tt class="py-op">(</tt><tt class="py-param">self</tt><tt class="py-op">,</tt><tt class="py-param">id</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="Astral.hashedDomainsById-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="Astral.hashedDomainsById-expanded"><a name="L818"></a><tt class="py-lineno">818</tt> <tt class="py-line"> <tt class="py-docstring">"""Get domains clustered by sequence identity in a dict"""</tt> </tt>
<a name="L819"></a><tt class="py-lineno">819</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">IdDatahash</tt><tt class="py-op">.</tt><tt id="link-401" class="py-name"><a title="Bio.Crystal.Crystal.has_key
Bio.EUtils.POM.ElementNode.has_key
Bio.GenBank.NCBIDictionary.has_key
Bio.PDB.AbstractPropertyMap.AbstractPropertyMap.has_key
Bio.PDB.FragmentMapper'.FragmentMapper.has_key
Bio.Prosite.ExPASyDictionary.has_key
Bio.Prosite.Prodoc.ExPASyDictionary.has_key
Bio.PubMed.Dictionary.has_key
Bio.SwissProt.SProt.ExPASyDictionary.has_key
Martel.Parser.MartelAttributeList.has_key" class="py-name" href="#" onclick="return doclink('link-401', 'has_key', 'link-80');">has_key</a></tt><tt class="py-op">(</tt><tt id="link-402" class="py-name"><a title="Bio.Data.CodonTable.id
Bio.Encodings.IUPACEncoding.id
Bio.GFF.Feature.id" class="py-name" href="#" onclick="return doclink('link-402', 'id', 'link-358');">id</a></tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
<a name="L820"></a><tt class="py-lineno">820</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">IdDatahash</tt><tt class="py-op">[</tt><tt id="link-403" class="py-name"><a title="Bio.Data.CodonTable.id
Bio.Encodings.IUPACEncoding.id
Bio.GFF.Feature.id" class="py-name" href="#" onclick="return doclink('link-403', 'id', 'link-358');">id</a></tt><tt class="py-op">]</tt> <tt class="py-op">=</tt> <tt class="py-op">{</tt><tt class="py-op">}</tt> </tt>
<a name="L821"></a><tt class="py-lineno">821</tt> <tt class="py-line"> <tt class="py-keyword">for</tt> <tt id="link-404" class="py-name"><a title="Bio.EUtils.setup.d" class="py-name" href="#" onclick="return doclink('link-404', 'd', 'link-188');">d</a></tt> <tt class="py-keyword">in</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-405" class="py-name" targets="Method Bio.SCOP.Astral.domainsClusteredById()=Bio.SCOP.Astral-class.html#domainsClusteredById"><a title="Bio.SCOP.Astral.domainsClusteredById" class="py-name" href="#" onclick="return doclink('link-405', 'domainsClusteredById', 'link-405');">domainsClusteredById</a></tt><tt class="py-op">(</tt><tt id="link-406" class="py-name"><a title="Bio.Data.CodonTable.id
Bio.Encodings.IUPACEncoding.id
Bio.GFF.Feature.id" class="py-name" href="#" onclick="return doclink('link-406', 'id', 'link-358');">id</a></tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
<a name="L822"></a><tt class="py-lineno">822</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">IdDatahash</tt><tt class="py-op">[</tt><tt id="link-407" class="py-name"><a title="Bio.Data.CodonTable.id
Bio.Encodings.IUPACEncoding.id
Bio.GFF.Feature.id" class="py-name" href="#" onclick="return doclink('link-407', 'id', 'link-358');">id</a></tt><tt class="py-op">]</tt><tt class="py-op">[</tt><tt id="link-408" class="py-name"><a title="Bio.EUtils.setup.d" class="py-name" href="#" onclick="return doclink('link-408', 'd', 'link-188');">d</a></tt><tt class="py-op">]</tt> <tt class="py-op">=</tt> <tt class="py-number">1</tt> </tt>
<a name="L823"></a><tt class="py-lineno">823</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">IdDatahash</tt><tt class="py-op">[</tt><tt id="link-409" class="py-name"><a title="Bio.Data.CodonTable.id
Bio.Encodings.IUPACEncoding.id
Bio.GFF.Feature.id" class="py-name" href="#" onclick="return doclink('link-409', 'id', 'link-358');">id</a></tt><tt class="py-op">]</tt> </tt>
</div><a name="L824"></a><tt class="py-lineno">824</tt> <tt class="py-line"> </tt>
<a name="Astral.hashedDomainsByEv"></a><div id="Astral.hashedDomainsByEv-def"><a name="L825"></a><tt class="py-lineno">825</tt> <a class="py-toggle" href="#" id="Astral.hashedDomainsByEv-toggle" onclick="return toggle('Astral.hashedDomainsByEv');">-</a><tt class="py-line"> <tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.SCOP.Astral-class.html#hashedDomainsByEv">hashedDomainsByEv</a><tt class="py-op">(</tt><tt class="py-param">self</tt><tt class="py-op">,</tt><tt class="py-param">id</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="Astral.hashedDomainsByEv-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="Astral.hashedDomainsByEv-expanded"><a name="L826"></a><tt class="py-lineno">826</tt> <tt class="py-line"> <tt class="py-docstring">"""Get domains clustered by evalue in a dict"""</tt> </tt>
<a name="L827"></a><tt class="py-lineno">827</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">EvDatahash</tt><tt class="py-op">.</tt><tt id="link-410" class="py-name"><a title="Bio.Crystal.Crystal.has_key
Bio.EUtils.POM.ElementNode.has_key
Bio.GenBank.NCBIDictionary.has_key
Bio.PDB.AbstractPropertyMap.AbstractPropertyMap.has_key
Bio.PDB.FragmentMapper'.FragmentMapper.has_key
Bio.Prosite.ExPASyDictionary.has_key
Bio.Prosite.Prodoc.ExPASyDictionary.has_key
Bio.PubMed.Dictionary.has_key
Bio.SwissProt.SProt.ExPASyDictionary.has_key
Martel.Parser.MartelAttributeList.has_key" class="py-name" href="#" onclick="return doclink('link-410', 'has_key', 'link-80');">has_key</a></tt><tt class="py-op">(</tt><tt id="link-411" class="py-name"><a title="Bio.Data.CodonTable.id
Bio.Encodings.IUPACEncoding.id
Bio.GFF.Feature.id" class="py-name" href="#" onclick="return doclink('link-411', 'id', 'link-358');">id</a></tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
<a name="L828"></a><tt class="py-lineno">828</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">EvDatahash</tt><tt class="py-op">[</tt><tt id="link-412" class="py-name"><a title="Bio.Data.CodonTable.id
Bio.Encodings.IUPACEncoding.id
Bio.GFF.Feature.id" class="py-name" href="#" onclick="return doclink('link-412', 'id', 'link-358');">id</a></tt><tt class="py-op">]</tt> <tt class="py-op">=</tt> <tt class="py-op">{</tt><tt class="py-op">}</tt> </tt>
<a name="L829"></a><tt class="py-lineno">829</tt> <tt class="py-line"> <tt class="py-keyword">for</tt> <tt id="link-413" class="py-name"><a title="Bio.EUtils.setup.d" class="py-name" href="#" onclick="return doclink('link-413', 'd', 'link-188');">d</a></tt> <tt class="py-keyword">in</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-414" class="py-name" targets="Method Bio.SCOP.Astral.domainsClusteredByEv()=Bio.SCOP.Astral-class.html#domainsClusteredByEv"><a title="Bio.SCOP.Astral.domainsClusteredByEv" class="py-name" href="#" onclick="return doclink('link-414', 'domainsClusteredByEv', 'link-414');">domainsClusteredByEv</a></tt><tt class="py-op">(</tt><tt id="link-415" class="py-name"><a title="Bio.Data.CodonTable.id
Bio.Encodings.IUPACEncoding.id
Bio.GFF.Feature.id" class="py-name" href="#" onclick="return doclink('link-415', 'id', 'link-358');">id</a></tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
<a name="L830"></a><tt class="py-lineno">830</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">EvDatahash</tt><tt class="py-op">[</tt><tt id="link-416" class="py-name"><a title="Bio.Data.CodonTable.id
Bio.Encodings.IUPACEncoding.id
Bio.GFF.Feature.id" class="py-name" href="#" onclick="return doclink('link-416', 'id', 'link-358');">id</a></tt><tt class="py-op">]</tt><tt class="py-op">[</tt><tt id="link-417" class="py-name"><a title="Bio.EUtils.setup.d" class="py-name" href="#" onclick="return doclink('link-417', 'd', 'link-188');">d</a></tt><tt class="py-op">]</tt> <tt class="py-op">=</tt> <tt class="py-number">1</tt> </tt>
<a name="L831"></a><tt class="py-lineno">831</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">EvDatahash</tt><tt class="py-op">[</tt><tt id="link-418" class="py-name"><a title="Bio.Data.CodonTable.id
Bio.Encodings.IUPACEncoding.id
Bio.GFF.Feature.id" class="py-name" href="#" onclick="return doclink('link-418', 'id', 'link-358');">id</a></tt><tt class="py-op">]</tt> </tt>
</div><a name="L832"></a><tt class="py-lineno">832</tt> <tt class="py-line"> </tt>
<a name="L833"></a><tt class="py-lineno">833</tt> <tt class="py-line"> </tt>
<a name="Astral.isDomainInId"></a><div id="Astral.isDomainInId-def"><a name="L834"></a><tt class="py-lineno">834</tt> <a class="py-toggle" href="#" id="Astral.isDomainInId-toggle" onclick="return toggle('Astral.isDomainInId');">-</a><tt class="py-line"> <tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.SCOP.Astral-class.html#isDomainInId">isDomainInId</a><tt class="py-op">(</tt><tt class="py-param">self</tt><tt class="py-op">,</tt><tt class="py-param">dom</tt><tt class="py-op">,</tt><tt class="py-param">id</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="Astral.isDomainInId-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="Astral.isDomainInId-expanded"><a name="L835"></a><tt class="py-lineno">835</tt> <tt class="py-line"> <tt class="py-docstring">"""Returns true if the domain is in the astral clusters for percent ID"""</tt> </tt>
<a name="L836"></a><tt class="py-lineno">836</tt> <tt class="py-line"> <tt class="py-keyword">return</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-419" class="py-name" targets="Method Bio.SCOP.Astral.hashedDomainsById()=Bio.SCOP.Astral-class.html#hashedDomainsById"><a title="Bio.SCOP.Astral.hashedDomainsById" class="py-name" href="#" onclick="return doclink('link-419', 'hashedDomainsById', 'link-419');">hashedDomainsById</a></tt><tt class="py-op">(</tt><tt id="link-420" class="py-name"><a title="Bio.Data.CodonTable.id
Bio.Encodings.IUPACEncoding.id
Bio.GFF.Feature.id" class="py-name" href="#" onclick="return doclink('link-420', 'id', 'link-358');">id</a></tt><tt class="py-op">)</tt><tt class="py-op">.</tt><tt id="link-421" class="py-name"><a title="Bio.Crystal.Crystal.has_key
Bio.EUtils.POM.ElementNode.has_key
Bio.GenBank.NCBIDictionary.has_key
Bio.PDB.AbstractPropertyMap.AbstractPropertyMap.has_key
Bio.PDB.FragmentMapper'.FragmentMapper.has_key
Bio.Prosite.ExPASyDictionary.has_key
Bio.Prosite.Prodoc.ExPASyDictionary.has_key
Bio.PubMed.Dictionary.has_key
Bio.SwissProt.SProt.ExPASyDictionary.has_key
Martel.Parser.MartelAttributeList.has_key" class="py-name" href="#" onclick="return doclink('link-421', 'has_key', 'link-80');">has_key</a></tt><tt class="py-op">(</tt><tt class="py-name">dom</tt><tt class="py-op">)</tt> </tt>
</div><a name="L837"></a><tt class="py-lineno">837</tt> <tt class="py-line"> </tt>
<a name="Astral.isDomainInEv"></a><div id="Astral.isDomainInEv-def"><a name="L838"></a><tt class="py-lineno">838</tt> <a class="py-toggle" href="#" id="Astral.isDomainInEv-toggle" onclick="return toggle('Astral.isDomainInEv');">-</a><tt class="py-line"> <tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.SCOP.Astral-class.html#isDomainInEv">isDomainInEv</a><tt class="py-op">(</tt><tt class="py-param">self</tt><tt class="py-op">,</tt><tt class="py-param">dom</tt><tt class="py-op">,</tt><tt class="py-param">id</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="Astral.isDomainInEv-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="Astral.isDomainInEv-expanded"><a name="L839"></a><tt class="py-lineno">839</tt> <tt class="py-line"> <tt class="py-docstring">"""Returns true if the domain is in the ASTRAL clusters for evalues"""</tt> </tt>
<a name="L840"></a><tt class="py-lineno">840</tt> <tt class="py-line"> <tt class="py-keyword">return</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-422" class="py-name" targets="Method Bio.SCOP.Astral.hashedDomainsByEv()=Bio.SCOP.Astral-class.html#hashedDomainsByEv"><a title="Bio.SCOP.Astral.hashedDomainsByEv" class="py-name" href="#" onclick="return doclink('link-422', 'hashedDomainsByEv', 'link-422');">hashedDomainsByEv</a></tt><tt class="py-op">(</tt><tt id="link-423" class="py-name"><a title="Bio.Data.CodonTable.id
Bio.Encodings.IUPACEncoding.id
Bio.GFF.Feature.id" class="py-name" href="#" onclick="return doclink('link-423', 'id', 'link-358');">id</a></tt><tt class="py-op">)</tt><tt class="py-op">.</tt><tt id="link-424" class="py-name"><a title="Bio.Crystal.Crystal.has_key
Bio.EUtils.POM.ElementNode.has_key
Bio.GenBank.NCBIDictionary.has_key
Bio.PDB.AbstractPropertyMap.AbstractPropertyMap.has_key
Bio.PDB.FragmentMapper'.FragmentMapper.has_key
Bio.Prosite.ExPASyDictionary.has_key
Bio.Prosite.Prodoc.ExPASyDictionary.has_key
Bio.PubMed.Dictionary.has_key
Bio.SwissProt.SProt.ExPASyDictionary.has_key
Martel.Parser.MartelAttributeList.has_key" class="py-name" href="#" onclick="return doclink('link-424', 'has_key', 'link-80');">has_key</a></tt><tt class="py-op">(</tt><tt class="py-name">dom</tt><tt class="py-op">)</tt> </tt>
</div><a name="L841"></a><tt class="py-lineno">841</tt> <tt class="py-line"> </tt>
<a name="L842"></a><tt class="py-lineno">842</tt> <tt class="py-line"> </tt>
<a name="Astral.writeToSQL"></a><div id="Astral.writeToSQL-def"><a name="L843"></a><tt class="py-lineno">843</tt> <a class="py-toggle" href="#" id="Astral.writeToSQL-toggle" onclick="return toggle('Astral.writeToSQL');">-</a><tt class="py-line"> <tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.SCOP.Astral-class.html#writeToSQL">writeToSQL</a><tt class="py-op">(</tt><tt class="py-param">self</tt><tt class="py-op">,</tt> <tt class="py-param">db_handle</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="Astral.writeToSQL-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="Astral.writeToSQL-expanded"><a name="L844"></a><tt class="py-lineno">844</tt> <tt class="py-line"> <tt class="py-docstring">"""Write the ASTRAL database to a MYSQL database"""</tt> </tt>
<a name="L845"></a><tt class="py-lineno">845</tt> <tt class="py-line"> <tt class="py-name">cur</tt> <tt class="py-op">=</tt> <tt class="py-name">db_handle</tt><tt class="py-op">.</tt><tt id="link-425" class="py-name"><a title="Bio.DocSQL.Query.cursor
Bio.DocSQL.QuerySingle.cursor" class="py-name" href="#" onclick="return doclink('link-425', 'cursor', 'link-142');">cursor</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
<a name="L846"></a><tt class="py-lineno">846</tt> <tt class="py-line"> </tt>
<a name="L847"></a><tt class="py-lineno">847</tt> <tt class="py-line"> <tt class="py-name">cur</tt><tt class="py-op">.</tt><tt id="link-426" class="py-name"><a title="BioSQL.BioSeqDatabase.Adaptor.execute" class="py-name" href="#" onclick="return doclink('link-426', 'execute', 'link-143');">execute</a></tt><tt class="py-op">(</tt><tt class="py-string">"DROP TABLE IF EXISTS astral"</tt><tt class="py-op">)</tt> </tt>
<a name="L848"></a><tt class="py-lineno">848</tt> <tt class="py-line"> <tt class="py-name">cur</tt><tt class="py-op">.</tt><tt id="link-427" class="py-name"><a title="BioSQL.BioSeqDatabase.Adaptor.execute" class="py-name" href="#" onclick="return doclink('link-427', 'execute', 'link-143');">execute</a></tt><tt class="py-op">(</tt><tt class="py-string">"CREATE TABLE astral (sid CHAR(8), seq TEXT, PRIMARY KEY (sid))"</tt><tt class="py-op">)</tt> </tt>
<a name="L849"></a><tt class="py-lineno">849</tt> <tt class="py-line"> </tt>
<a name="L850"></a><tt class="py-lineno">850</tt> <tt class="py-line"> <tt class="py-keyword">for</tt> <tt class="py-name">dom</tt> <tt class="py-keyword">in</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">fasta_dict</tt><tt class="py-op">.</tt><tt id="link-428" class="py-name" targets="Method Bio.Crystal.Crystal.keys()=Bio.Crystal.Crystal-class.html#keys,Method Bio.EUtils.MultiDict._BaseMultiDict.keys()=Bio.EUtils.MultiDict._BaseMultiDict-class.html#keys,Method Bio.GenBank.NCBIDictionary.keys()=Bio.GenBank.NCBIDictionary-class.html#keys,Method Bio.Mindy.BaseDB.DictLookup.keys()=Bio.Mindy.BaseDB.DictLookup-class.html#keys,Method Bio.Mindy.BaseDB.OpenDB.keys()=Bio.Mindy.BaseDB.OpenDB-class.html#keys,Method Bio.Mindy.BerkeleyDB.PrimaryNamespace.keys()=Bio.Mindy.BerkeleyDB.PrimaryNamespace-class.html#keys,Method Bio.Mindy.BerkeleyDB.SecondaryNamespace.keys()=Bio.Mindy.BerkeleyDB.SecondaryNamespace-class.html#keys,Method Bio.Mindy.FlatDB.PrimaryNamespace.keys()=Bio.Mindy.FlatDB.PrimaryNamespace-class.html#keys,Method Bio.Mindy.FlatDB.PrimaryTable.keys()=Bio.Mindy.FlatDB.PrimaryTable-class.html#keys,Method Bio.Mindy.FlatDB.SecondaryNamespace.keys()=Bio.Mindy.FlatDB.SecondaryNamespace-class.html#keys,Method Bio.Mindy.FlatDB.SecondaryTable.keys()=Bio.Mindy.FlatDB.SecondaryTable-class.html#keys,Method Bio.PDB.AbstractPropertyMap.AbstractPropertyMap.keys()=Bio.PDB.AbstractPropertyMap.AbstractPropertyMap-class.html#keys,Method Bio.Prosite.ExPASyDictionary.keys()=Bio.Prosite.ExPASyDictionary-class.html#keys,Method Bio.Prosite.Prodoc.ExPASyDictionary.keys()=Bio.Prosite.Prodoc.ExPASyDictionary-class.html#keys,Method Bio.PubMed.Dictionary.keys()=Bio.PubMed.Dictionary-class.html#keys,Method Bio.SwissProt.SProt.Dictionary.keys()=Bio.SwissProt.SProt.Dictionary-class.html#keys,Method Bio.SwissProt.SProt.ExPASyDictionary.keys()=Bio.SwissProt.SProt.ExPASyDictionary-class.html#keys,Method Bio.config.Registry.Registry.keys()=Bio.config.Registry.Registry-class.html#keys,Method BioSQL.BioSeqDatabase.BioSeqDatabase.keys()=BioSQL.BioSeqDatabase.BioSeqDatabase-class.html#keys,Method BioSQL.BioSeqDatabase.DBServer.keys()=BioSQL.BioSeqDatabase.DBServer-class.html#keys,Method Martel.Parser.MartelAttributeList.keys()=Martel.Parser.MartelAttributeList-class.html#keys"><a title="Bio.Crystal.Crystal.keys
Bio.EUtils.MultiDict._BaseMultiDict.keys
Bio.GenBank.NCBIDictionary.keys
Bio.Mindy.BaseDB.DictLookup.keys
Bio.Mindy.BaseDB.OpenDB.keys
Bio.Mindy.BerkeleyDB.PrimaryNamespace.keys
Bio.Mindy.BerkeleyDB.SecondaryNamespace.keys
Bio.Mindy.FlatDB.PrimaryNamespace.keys
Bio.Mindy.FlatDB.PrimaryTable.keys
Bio.Mindy.FlatDB.SecondaryNamespace.keys
Bio.Mindy.FlatDB.SecondaryTable.keys
Bio.PDB.AbstractPropertyMap.AbstractPropertyMap.keys
Bio.Prosite.ExPASyDictionary.keys
Bio.Prosite.Prodoc.ExPASyDictionary.keys
Bio.PubMed.Dictionary.keys
Bio.SwissProt.SProt.Dictionary.keys
Bio.SwissProt.SProt.ExPASyDictionary.keys
Bio.config.Registry.Registry.keys
BioSQL.BioSeqDatabase.BioSeqDatabase.keys
BioSQL.BioSeqDatabase.DBServer.keys
Martel.Parser.MartelAttributeList.keys" class="py-name" href="#" onclick="return doclink('link-428', 'keys', 'link-428');">keys</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
<a name="L851"></a><tt class="py-lineno">851</tt> <tt class="py-line"> <tt class="py-name">cur</tt><tt class="py-op">.</tt><tt id="link-429" class="py-name"><a title="BioSQL.BioSeqDatabase.Adaptor.execute" class="py-name" href="#" onclick="return doclink('link-429', 'execute', 'link-143');">execute</a></tt><tt class="py-op">(</tt> <tt class="py-string">"INSERT INTO astral (sid,seq) values (%s,%s)"</tt><tt class="py-op">,</tt> </tt>
<a name="L852"></a><tt class="py-lineno">852</tt> <tt class="py-line"> <tt class="py-op">(</tt><tt class="py-name">dom</tt><tt class="py-op">,</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">fasta_dict</tt><tt class="py-op">[</tt><tt class="py-name">dom</tt><tt class="py-op">]</tt><tt class="py-op">.</tt><tt id="link-430" 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-430', 'seq', 'link-396');">seq</a></tt><tt class="py-op">.</tt><tt id="link-431" class="py-name"><a title="BioSQL.BioSeq.DBSeq.data" class="py-name" href="#" onclick="return doclink('link-431', 'data', 'link-145');">data</a></tt><tt class="py-op">)</tt><tt class="py-op">)</tt> </tt>
<a name="L853"></a><tt class="py-lineno">853</tt> <tt class="py-line"> </tt>
<a name="L854"></a><tt class="py-lineno">854</tt> <tt class="py-line"> </tt>
<a name="L855"></a><tt class="py-lineno">855</tt> <tt class="py-line"> <tt class="py-keyword">for</tt> <tt id="link-432" 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-432', 'i', 'link-432');">i</a></tt> <tt class="py-keyword">in</tt> <tt id="link-433" class="py-name"><a title="Bio.SCOP.astralBibIds" class="py-name" href="#" onclick="return doclink('link-433', 'astralBibIds', 'link-15');">astralBibIds</a></tt><tt class="py-op">:</tt> </tt>
<a name="L856"></a><tt class="py-lineno">856</tt> <tt class="py-line"> <tt class="py-name">cur</tt><tt class="py-op">.</tt><tt id="link-434" class="py-name"><a title="BioSQL.BioSeqDatabase.Adaptor.execute" class="py-name" href="#" onclick="return doclink('link-434', 'execute', 'link-143');">execute</a></tt><tt class="py-op">(</tt><tt class="py-string">"ALTER TABLE astral ADD (id"</tt><tt class="py-op">+</tt><tt class="py-name">str</tt><tt class="py-op">(</tt><tt id="link-435" class="py-name"><a title="Bio.PDB.Polypeptide.i" class="py-name" href="#" onclick="return doclink('link-435', 'i', 'link-432');">i</a></tt><tt class="py-op">)</tt><tt class="py-op">+</tt><tt class="py-string">" TINYINT)"</tt><tt class="py-op">)</tt> </tt>
<a name="L857"></a><tt class="py-lineno">857</tt> <tt class="py-line"> </tt>
<a name="L858"></a><tt class="py-lineno">858</tt> <tt class="py-line"> <tt class="py-keyword">for</tt> <tt id="link-436" class="py-name"><a title="Bio.EUtils.setup.d" class="py-name" href="#" onclick="return doclink('link-436', 'd', 'link-188');">d</a></tt> <tt class="py-keyword">in</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-437" class="py-name"><a title="Bio.SCOP.Astral.domainsClusteredById" class="py-name" href="#" onclick="return doclink('link-437', 'domainsClusteredById', 'link-405');">domainsClusteredById</a></tt><tt class="py-op">(</tt><tt id="link-438" class="py-name"><a title="Bio.PDB.Polypeptide.i" class="py-name" href="#" onclick="return doclink('link-438', 'i', 'link-432');">i</a></tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
<a name="L859"></a><tt class="py-lineno">859</tt> <tt class="py-line"> <tt class="py-name">cur</tt><tt class="py-op">.</tt><tt id="link-439" class="py-name"><a title="BioSQL.BioSeqDatabase.Adaptor.execute" class="py-name" href="#" onclick="return doclink('link-439', 'execute', 'link-143');">execute</a></tt><tt class="py-op">(</tt><tt class="py-string">"UPDATE astral SET id"</tt><tt class="py-op">+</tt><tt class="py-name">str</tt><tt class="py-op">(</tt><tt id="link-440" class="py-name"><a title="Bio.PDB.Polypeptide.i" class="py-name" href="#" onclick="return doclink('link-440', 'i', 'link-432');">i</a></tt><tt class="py-op">)</tt><tt class="py-op">+</tt><tt class="py-string">"=1 WHERE sid=%s"</tt><tt class="py-op">,</tt> </tt>
<a name="L860"></a><tt class="py-lineno">860</tt> <tt class="py-line"> <tt id="link-441" class="py-name"><a title="Bio.EUtils.setup.d" class="py-name" href="#" onclick="return doclink('link-441', 'd', 'link-188');">d</a></tt><tt class="py-op">.</tt><tt class="py-name">sid</tt><tt class="py-op">)</tt> </tt>
<a name="L861"></a><tt class="py-lineno">861</tt> <tt class="py-line"> </tt>
<a name="L862"></a><tt class="py-lineno">862</tt> <tt class="py-line"> <tt class="py-keyword">for</tt> <tt class="py-name">ev</tt> <tt class="py-keyword">in</tt> <tt id="link-442" class="py-name"><a title="Bio.SCOP.astralEvs" class="py-name" href="#" onclick="return doclink('link-442', 'astralEvs', 'link-16');">astralEvs</a></tt><tt class="py-op">:</tt> </tt>
<a name="L863"></a><tt class="py-lineno">863</tt> <tt class="py-line"> <tt class="py-name">cur</tt><tt class="py-op">.</tt><tt id="link-443" class="py-name"><a title="BioSQL.BioSeqDatabase.Adaptor.execute" class="py-name" href="#" onclick="return doclink('link-443', 'execute', 'link-143');">execute</a></tt><tt class="py-op">(</tt><tt class="py-string">"ALTER TABLE astral ADD ("</tt><tt class="py-op">+</tt><tt id="link-444" class="py-name"><a title="Bio.SCOP.astralEv_to_sql" class="py-name" href="#" onclick="return doclink('link-444', 'astralEv_to_sql', 'link-18');">astralEv_to_sql</a></tt><tt class="py-op">[</tt><tt class="py-name">ev</tt><tt class="py-op">]</tt><tt class="py-op">+</tt><tt class="py-string">" TINYINT)"</tt><tt class="py-op">)</tt> </tt>
<a name="L864"></a><tt class="py-lineno">864</tt> <tt class="py-line"> </tt>
<a name="L865"></a><tt class="py-lineno">865</tt> <tt class="py-line"> <tt class="py-keyword">for</tt> <tt id="link-445" class="py-name"><a title="Bio.EUtils.setup.d" class="py-name" href="#" onclick="return doclink('link-445', 'd', 'link-188');">d</a></tt> <tt class="py-keyword">in</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-446" class="py-name"><a title="Bio.SCOP.Astral.domainsClusteredByEv" class="py-name" href="#" onclick="return doclink('link-446', 'domainsClusteredByEv', 'link-414');">domainsClusteredByEv</a></tt><tt class="py-op">(</tt><tt class="py-name">ev</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
<a name="L866"></a><tt class="py-lineno">866</tt> <tt class="py-line"> </tt>
<a name="L867"></a><tt class="py-lineno">867</tt> <tt class="py-line"> <tt class="py-name">cur</tt><tt class="py-op">.</tt><tt id="link-447" class="py-name"><a title="BioSQL.BioSeqDatabase.Adaptor.execute" class="py-name" href="#" onclick="return doclink('link-447', 'execute', 'link-143');">execute</a></tt><tt class="py-op">(</tt><tt class="py-string">"UPDATE astral SET "</tt><tt class="py-op">+</tt><tt id="link-448" class="py-name"><a title="Bio.SCOP.astralEv_to_sql" class="py-name" href="#" onclick="return doclink('link-448', 'astralEv_to_sql', 'link-18');">astralEv_to_sql</a></tt><tt class="py-op">[</tt><tt class="py-name">ev</tt><tt class="py-op">]</tt><tt class="py-op">+</tt><tt class="py-string">"=1 WHERE sid=%s"</tt><tt class="py-op">,</tt> </tt>
<a name="L868"></a><tt class="py-lineno">868</tt> <tt class="py-line"> <tt id="link-449" class="py-name"><a title="Bio.EUtils.setup.d" class="py-name" href="#" onclick="return doclink('link-449', 'd', 'link-188');">d</a></tt><tt class="py-op">.</tt><tt class="py-name">sid</tt><tt class="py-op">)</tt> </tt>
</div></div><a name="L869"></a><tt class="py-lineno">869</tt> <tt class="py-line"> </tt>
<a name="search"></a><div id="search-def"><a name="L870"></a><tt class="py-lineno">870</tt> <a class="py-toggle" href="#" id="search-toggle" onclick="return toggle('search');">-</a><tt class="py-line"><tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.SCOP-module.html#search">search</a><tt class="py-op">(</tt><tt class="py-param">pdb</tt><tt class="py-op">=</tt><tt class="py-name">None</tt><tt class="py-op">,</tt> <tt class="py-param">key</tt><tt class="py-op">=</tt><tt class="py-name">None</tt><tt class="py-op">,</tt> <tt class="py-param">sid</tt><tt class="py-op">=</tt><tt class="py-name">None</tt><tt class="py-op">,</tt> <tt class="py-param">disp</tt><tt class="py-op">=</tt><tt class="py-name">None</tt><tt class="py-op">,</tt> <tt class="py-param">dir</tt><tt class="py-op">=</tt><tt class="py-name">None</tt><tt class="py-op">,</tt> <tt class="py-param">loc</tt><tt class="py-op">=</tt><tt class="py-name">None</tt><tt class="py-op">,</tt> </tt>
<a name="L871"></a><tt class="py-lineno">871</tt> <tt class="py-line"> <tt class="py-param">cgi</tt><tt class="py-op">=</tt><tt class="py-string">'http://scop.mrc-lmb.cam.ac.uk/scop/search.cgi'</tt><tt class="py-op">,</tt> <tt class="py-op">**</tt><tt class="py-param">keywds</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="search-collapsed" style="display:none;" pad="+++" indent="++++"></div><div id="search-expanded"><a name="L872"></a><tt class="py-lineno">872</tt> <tt class="py-line"> <tt class="py-docstring">"""search(pdb=None, key=None, sid=None, disp=None, dir=None, loc=None,</tt> </tt>
<a name="L873"></a><tt class="py-lineno">873</tt> <tt class="py-line"><tt class="py-docstring"> cgi='http://scop.mrc-lmb.cam.ac.uk/scop/search.cgi', **keywds)</tt> </tt>
<a name="L874"></a><tt class="py-lineno">874</tt> <tt class="py-line"><tt class="py-docstring"></tt> </tt>
<a name="L875"></a><tt class="py-lineno">875</tt> <tt class="py-line"><tt class="py-docstring"> Access search.cgi and return a handle to the results. See the</tt> </tt>
<a name="L876"></a><tt class="py-lineno">876</tt> <tt class="py-line"><tt class="py-docstring"> online help file for an explanation of the parameters:</tt> </tt>
<a name="L877"></a><tt class="py-lineno">877</tt> <tt class="py-line"><tt class="py-docstring"> http://scop.mrc-lmb.cam.ac.uk/scop/help.html</tt> </tt>
<a name="L878"></a><tt class="py-lineno">878</tt> <tt class="py-line"><tt class="py-docstring"></tt> </tt>
<a name="L879"></a><tt class="py-lineno">879</tt> <tt class="py-line"><tt class="py-docstring"> Raises an IOError if there's a network error.</tt> </tt>
<a name="L880"></a><tt class="py-lineno">880</tt> <tt class="py-line"><tt class="py-docstring"></tt> </tt>
<a name="L881"></a><tt class="py-lineno">881</tt> <tt class="py-line"><tt class="py-docstring"> """</tt> </tt>
<a name="L882"></a><tt class="py-lineno">882</tt> <tt class="py-line"> <tt class="py-name">params</tt> <tt class="py-op">=</tt> <tt class="py-op">{</tt><tt class="py-string">'pdb'</tt> <tt class="py-op">:</tt> <tt id="link-450" 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-450', 'pdb', 'link-450');">pdb</a></tt><tt class="py-op">,</tt> <tt class="py-string">'key'</tt> <tt class="py-op">:</tt> <tt id="link-451" 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-451', 'key', 'link-451');">key</a></tt><tt class="py-op">,</tt> <tt class="py-string">'sid'</tt> <tt class="py-op">:</tt> <tt class="py-name">sid</tt><tt class="py-op">,</tt> <tt class="py-string">'disp'</tt> <tt class="py-op">:</tt> <tt class="py-name">disp</tt><tt class="py-op">,</tt> </tt>
<a name="L883"></a><tt class="py-lineno">883</tt> <tt class="py-line"> <tt class="py-string">'dir'</tt> <tt class="py-op">:</tt> <tt class="py-name">dir</tt><tt class="py-op">,</tt> <tt class="py-string">'loc'</tt> <tt class="py-op">:</tt> <tt class="py-name">loc</tt><tt class="py-op">}</tt> </tt>
<a name="L884"></a><tt class="py-lineno">884</tt> <tt class="py-line"> <tt class="py-name">variables</tt> <tt class="py-op">=</tt> <tt class="py-op">{</tt><tt class="py-op">}</tt> </tt>
<a name="L885"></a><tt class="py-lineno">885</tt> <tt class="py-line"> <tt class="py-keyword">for</tt> <tt class="py-name">k</tt> <tt class="py-keyword">in</tt> <tt class="py-name">params</tt><tt class="py-op">.</tt><tt id="link-452" class="py-name"><a title="Bio.Crystal.Crystal.keys
Bio.EUtils.MultiDict._BaseMultiDict.keys
Bio.GenBank.NCBIDictionary.keys
Bio.Mindy.BaseDB.DictLookup.keys
Bio.Mindy.BaseDB.OpenDB.keys
Bio.Mindy.BerkeleyDB.PrimaryNamespace.keys
Bio.Mindy.BerkeleyDB.SecondaryNamespace.keys
Bio.Mindy.FlatDB.PrimaryNamespace.keys
Bio.Mindy.FlatDB.PrimaryTable.keys
Bio.Mindy.FlatDB.SecondaryNamespace.keys
Bio.Mindy.FlatDB.SecondaryTable.keys
Bio.PDB.AbstractPropertyMap.AbstractPropertyMap.keys
Bio.Prosite.ExPASyDictionary.keys
Bio.Prosite.Prodoc.ExPASyDictionary.keys
Bio.PubMed.Dictionary.keys
Bio.SwissProt.SProt.Dictionary.keys
Bio.SwissProt.SProt.ExPASyDictionary.keys
Bio.config.Registry.Registry.keys
BioSQL.BioSeqDatabase.BioSeqDatabase.keys
BioSQL.BioSeqDatabase.DBServer.keys
Martel.Parser.MartelAttributeList.keys" class="py-name" href="#" onclick="return doclink('link-452', 'keys', 'link-428');">keys</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
<a name="L886"></a><tt class="py-lineno">886</tt> <tt class="py-line"> <tt class="py-keyword">if</tt> <tt class="py-name">params</tt><tt class="py-op">[</tt><tt class="py-name">k</tt><tt class="py-op">]</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="L887"></a><tt class="py-lineno">887</tt> <tt class="py-line"> <tt class="py-name">variables</tt><tt class="py-op">[</tt><tt class="py-name">k</tt><tt class="py-op">]</tt> <tt class="py-op">=</tt> <tt class="py-name">params</tt><tt class="py-op">[</tt><tt class="py-name">k</tt><tt class="py-op">]</tt> </tt>
<a name="L888"></a><tt class="py-lineno">888</tt> <tt class="py-line"> <tt class="py-name">variables</tt><tt class="py-op">.</tt><tt id="link-453" class="py-name" targets="Method Bio.GenBank.NCBIDictionary.update()=Bio.GenBank.NCBIDictionary-class.html#update,Method Bio.Index._InMemoryIndex.update()=Bio.Index._InMemoryIndex-class.html#update,Method Bio.NeuralNetwork.BackPropagation.Layer.HiddenLayer.update()=Bio.NeuralNetwork.BackPropagation.Layer.HiddenLayer-class.html#update,Method Bio.NeuralNetwork.BackPropagation.Layer.InputLayer.update()=Bio.NeuralNetwork.BackPropagation.Layer.InputLayer-class.html#update,Method Bio.NeuralNetwork.BackPropagation.Layer.OutputLayer.update()=Bio.NeuralNetwork.BackPropagation.Layer.OutputLayer-class.html#update,Method Bio.Prosite.ExPASyDictionary.update()=Bio.Prosite.ExPASyDictionary-class.html#update,Method Bio.Prosite.Prodoc.ExPASyDictionary.update()=Bio.Prosite.Prodoc.ExPASyDictionary-class.html#update,Method Bio.PubMed.Dictionary.update()=Bio.PubMed.Dictionary-class.html#update,Method Bio.Restriction._Update.Update.RebaseUpdate.update()=Bio.Restriction._Update.Update.RebaseUpdate-class.html#update,Method Bio.SwissProt.SProt.ExPASyDictionary.update()=Bio.SwissProt.SProt.ExPASyDictionary-class.html#update"><a title="Bio.GenBank.NCBIDictionary.update
Bio.Index._InMemoryIndex.update
Bio.NeuralNetwork.BackPropagation.Layer.HiddenLayer.update
Bio.NeuralNetwork.BackPropagation.Layer.InputLayer.update
Bio.NeuralNetwork.BackPropagation.Layer.OutputLayer.update
Bio.Prosite.ExPASyDictionary.update
Bio.Prosite.Prodoc.ExPASyDictionary.update
Bio.PubMed.Dictionary.update
Bio.Restriction._Update.Update.RebaseUpdate.update
Bio.SwissProt.SProt.ExPASyDictionary.update" class="py-name" href="#" onclick="return doclink('link-453', 'update', 'link-453');">update</a></tt><tt class="py-op">(</tt><tt class="py-name">keywds</tt><tt class="py-op">)</tt> </tt>
<a name="L889"></a><tt class="py-lineno">889</tt> <tt class="py-line"> <tt class="py-keyword">return</tt> <tt id="link-454" class="py-name" targets="Function Bio.Entrez._open()=Bio.Entrez-module.html#_open,Function Bio.Mindy.BerkeleyDB._open()=Bio.Mindy.BerkeleyDB-module.html#_open,Function Bio.SCOP._open()=Bio.SCOP-module.html#_open,Function Bio.WWW.ExPASy._open()=Bio.WWW.ExPASy-module.html#_open,Function Bio.WWW.NCBI._open()=Bio.WWW.NCBI-module.html#_open"><a title="Bio.Entrez._open
Bio.Mindy.BerkeleyDB._open
Bio.SCOP._open
Bio.WWW.ExPASy._open
Bio.WWW.NCBI._open" class="py-name" href="#" onclick="return doclink('link-454', '_open', 'link-454');">_open</a></tt><tt class="py-op">(</tt><tt class="py-name">cgi</tt><tt class="py-op">,</tt> <tt class="py-name">variables</tt><tt class="py-op">)</tt> </tt>
</div><a name="L890"></a><tt class="py-lineno">890</tt> <tt class="py-line"> </tt>
<a name="_open"></a><div id="_open-def"><a name="L891"></a><tt class="py-lineno">891</tt> <a class="py-toggle" href="#" id="_open-toggle" onclick="return toggle('_open');">-</a><tt class="py-line"><tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.SCOP-module.html#_open">_open</a><tt class="py-op">(</tt><tt class="py-param">cgi</tt><tt class="py-op">,</tt> <tt class="py-param">params</tt><tt class="py-op">=</tt><tt class="py-op">{</tt><tt class="py-op">}</tt><tt class="py-op">,</tt> <tt class="py-param">get</tt><tt class="py-op">=</tt><tt class="py-number">1</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="_open-collapsed" style="display:none;" pad="+++" indent="++++"></div><div id="_open-expanded"><a name="L892"></a><tt class="py-lineno">892</tt> <tt class="py-line"> <tt class="py-docstring">"""_open(cgi, params={}, get=1) -> UndoHandle</tt> </tt>
<a name="L893"></a><tt class="py-lineno">893</tt> <tt class="py-line"><tt class="py-docstring"></tt> </tt>
<a name="L894"></a><tt class="py-lineno">894</tt> <tt class="py-line"><tt class="py-docstring"> Open a handle to SCOP. cgi is the URL for the cgi script to access.</tt> </tt>
<a name="L895"></a><tt class="py-lineno">895</tt> <tt class="py-line"><tt class="py-docstring"> params is a dictionary with the options to pass to it. get is a boolean</tt> </tt>
<a name="L896"></a><tt class="py-lineno">896</tt> <tt class="py-line"><tt class="py-docstring"> that describes whether a GET should be used. Does some</tt> </tt>
<a name="L897"></a><tt class="py-lineno">897</tt> <tt class="py-line"><tt class="py-docstring"> simple error checking, and will raise an IOError if it encounters one.</tt> </tt>
<a name="L898"></a><tt class="py-lineno">898</tt> <tt class="py-line"><tt class="py-docstring"></tt> </tt>
<a name="L899"></a><tt class="py-lineno">899</tt> <tt class="py-line"><tt class="py-docstring"> """</tt> </tt>
<a name="L900"></a><tt class="py-lineno">900</tt> <tt class="py-line"> <tt class="py-keyword">import</tt> <tt class="py-name">urllib</tt> </tt>
<a name="L901"></a><tt class="py-lineno">901</tt> <tt class="py-line"> <tt class="py-keyword">from</tt> <tt id="link-455" class="py-name"><a title="Bio" class="py-name" href="#" onclick="return doclink('link-455', 'Bio', 'link-4');">Bio</a></tt> <tt class="py-keyword">import</tt> <tt id="link-456" class="py-name" targets="Module Bio.File=Bio.File-module.html"><a title="Bio.File" class="py-name" href="#" onclick="return doclink('link-456', 'File', 'link-456');">File</a></tt> </tt>
<a name="L902"></a><tt class="py-lineno">902</tt> <tt class="py-line"> <tt class="py-comment"># Open a handle to SCOP.</tt> </tt>
<a name="L903"></a><tt class="py-lineno">903</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-name">options</tt> <tt class="py-op">=</tt> <tt class="py-name">urllib</tt><tt class="py-op">.</tt><tt class="py-name">urlencode</tt><tt class="py-op">(</tt><tt class="py-name">params</tt><tt class="py-op">)</tt> </tt>
<a name="L904"></a><tt class="py-lineno">904</tt> <tt class="py-line"> <tt class="py-keyword">if</tt> <tt id="link-457" class="py-name" targets="Method Bio.Crystal.Crystal.get()=Bio.Crystal.Crystal-class.html#get,Method Bio.Data.CodonTable.AmbiguousForwardTable.get()=Bio.Data.CodonTable.AmbiguousForwardTable-class.html#get,Method Bio.EUtils.MultiDict._BaseMultiDict.get()=Bio.EUtils.MultiDict._BaseMultiDict-class.html#get,Method Bio.EUtils.POM.ElementNode.get()=Bio.EUtils.POM.ElementNode-class.html#get,Method Bio.GenBank.NCBIDictionary.get()=Bio.GenBank.NCBIDictionary-class.html#get,Method Bio.Mindy.BaseDB.DictLookup.get()=Bio.Mindy.BaseDB.DictLookup-class.html#get,Method Bio.Prosite.ExPASyDictionary.get()=Bio.Prosite.ExPASyDictionary-class.html#get,Method Bio.Prosite.Prodoc.ExPASyDictionary.get()=Bio.Prosite.Prodoc.ExPASyDictionary-class.html#get,Method Bio.PubMed.Dictionary.get()=Bio.PubMed.Dictionary-class.html#get,Method Bio.Restriction.Restriction.RestrictionBatch.get()=Bio.Restriction.Restriction.RestrictionBatch-class.html#get,Method Bio.Restriction._Update.RestrictionCompiler.DictionaryBuilder.get()=Bio.Restriction._Update.RestrictionCompiler.DictionaryBuilder-class.html#get,Method Bio.SeqUtils.MissingTable.get()=Bio.SeqUtils.MissingTable-class.html#get,Method Bio.SwissProt.SProt.ExPASyDictionary.get()=Bio.SwissProt.SProt.ExPASyDictionary-class.html#get,Method Bio.config.DBRegistry.DBGroup.get()=Bio.config.DBRegistry.DBGroup-class.html#get,Method Bio.config.DBRegistry.DBObject.get()=Bio.config.DBRegistry.DBObject-class.html#get,Method Bio.config.Registry.Registry.get()=Bio.config.Registry.Registry-class.html#get,Method Martel.Parser.MartelAttributeList.get()=Martel.Parser.MartelAttributeList-class.html#get,Method Martel.msre_parse.Tokenizer.get()=Martel.msre_parse.Tokenizer-class.html#get"><a title="Bio.Crystal.Crystal.get
Bio.Data.CodonTable.AmbiguousForwardTable.get
Bio.EUtils.MultiDict._BaseMultiDict.get
Bio.EUtils.POM.ElementNode.get
Bio.GenBank.NCBIDictionary.get
Bio.Mindy.BaseDB.DictLookup.get
Bio.Prosite.ExPASyDictionary.get
Bio.Prosite.Prodoc.ExPASyDictionary.get
Bio.PubMed.Dictionary.get
Bio.Restriction.Restriction.RestrictionBatch.get
Bio.Restriction._Update.RestrictionCompiler.DictionaryBuilder.get
Bio.SeqUtils.MissingTable.get
Bio.SwissProt.SProt.ExPASyDictionary.get
Bio.config.DBRegistry.DBGroup.get
Bio.config.DBRegistry.DBObject.get
Bio.config.Registry.Registry.get
Martel.Parser.MartelAttributeList.get
Martel.msre_parse.Tokenizer.get" class="py-name" href="#" onclick="return doclink('link-457', 'get', 'link-457');">get</a></tt><tt class="py-op">:</tt> <tt class="py-comment"># do a GET</tt> </tt>
<a name="L905"></a><tt class="py-lineno">905</tt> <tt class="py-line"> <tt class="py-name">fullcgi</tt> <tt class="py-op">=</tt> <tt class="py-name">cgi</tt> </tt>
<a name="L906"></a><tt class="py-lineno">906</tt> <tt class="py-line"> <tt class="py-keyword">if</tt> <tt class="py-name">options</tt><tt class="py-op">:</tt> </tt>
<a name="L907"></a><tt class="py-lineno">907</tt> <tt class="py-line"> <tt class="py-name">fullcgi</tt> <tt class="py-op">=</tt> <tt class="py-string">"%s?%s"</tt> <tt class="py-op">%</tt> <tt class="py-op">(</tt><tt class="py-name">cgi</tt><tt class="py-op">,</tt> <tt class="py-name">options</tt><tt class="py-op">)</tt> </tt>
<a name="L908"></a><tt class="py-lineno">908</tt> <tt class="py-line"> <tt id="link-458" class="py-name"><a title="Bio.LocusLink.web_parse.handle
Bio.Ndb.handle" class="py-name" href="#" onclick="return doclink('link-458', 'handle', 'link-48');">handle</a></tt> <tt class="py-op">=</tt> <tt class="py-name">urllib</tt><tt class="py-op">.</tt><tt class="py-name">urlopen</tt><tt class="py-op">(</tt><tt class="py-name">fullcgi</tt><tt class="py-op">)</tt> </tt>
<a name="L909"></a><tt class="py-lineno">909</tt> <tt class="py-line"> <tt class="py-keyword">else</tt><tt class="py-op">:</tt> <tt class="py-comment"># do a POST</tt> </tt>
<a name="L910"></a><tt class="py-lineno">910</tt> <tt class="py-line"> <tt id="link-459" class="py-name"><a title="Bio.LocusLink.web_parse.handle
Bio.Ndb.handle" class="py-name" href="#" onclick="return doclink('link-459', 'handle', 'link-48');">handle</a></tt> <tt class="py-op">=</tt> <tt class="py-name">urllib</tt><tt class="py-op">.</tt><tt class="py-name">urlopen</tt><tt class="py-op">(</tt><tt class="py-name">cgi</tt><tt class="py-op">,</tt> <tt class="py-name">options</tt><tt class="py-op">)</tt> </tt>
<a name="L911"></a><tt class="py-lineno">911</tt> <tt class="py-line"> </tt>
<a name="L912"></a><tt class="py-lineno">912</tt> <tt class="py-line"> <tt class="py-comment"># Wrap the handle inside an UndoHandle.</tt> </tt>
<a name="L913"></a><tt class="py-lineno">913</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-name">uhandle</tt> <tt class="py-op">=</tt> <tt id="link-460" class="py-name"><a title="Bio.File" class="py-name" href="#" onclick="return doclink('link-460', 'File', 'link-456');">File</a></tt><tt class="py-op">.</tt><tt id="link-461" class="py-name" targets="Class Bio.File.UndoHandle=Bio.File.UndoHandle-class.html"><a title="Bio.File.UndoHandle" class="py-name" href="#" onclick="return doclink('link-461', 'UndoHandle', 'link-461');">UndoHandle</a></tt><tt class="py-op">(</tt><tt id="link-462" class="py-name"><a title="Bio.LocusLink.web_parse.handle
Bio.Ndb.handle" class="py-name" href="#" onclick="return doclink('link-462', 'handle', 'link-48');">handle</a></tt><tt class="py-op">)</tt> </tt>
<a name="L914"></a><tt class="py-lineno">914</tt> <tt class="py-line"> <tt class="py-comment"># Should I check for 404? timeout? etc?</tt> </tt>
<a name="L915"></a><tt class="py-lineno">915</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-keyword">return</tt> <tt class="py-name">uhandle</tt> </tt>
</div><a name="L916"></a><tt class="py-lineno">916</tt> <tt class="py-line"> </tt><script type="text/javascript">
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