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<a href="Bio-module.html">Package Bio</a> ::
Package Pathway
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<h1 class="epydoc">Source Code for <a href="Bio.Pathway-module.html">Package Bio.Pathway</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 Tarjei Mikkelsen. All rights reserved.</tt> </tt>
<a name="L2"></a><tt class="py-lineno"> 2</tt> <tt class="py-line"><tt class="py-comment"></tt><tt class="py-comment"># This code is part of the Biopython distribution and governed by its</tt> </tt>
<a name="L3"></a><tt class="py-lineno"> 3</tt> <tt class="py-line"><tt class="py-comment"></tt><tt class="py-comment"># license. Please see the LICENSE file that should have been included</tt> </tt>
<a name="L4"></a><tt class="py-lineno"> 4</tt> <tt class="py-line"><tt class="py-comment"></tt><tt class="py-comment"># as part of this package.</tt> </tt>
<a name="L5"></a><tt class="py-lineno"> 5</tt> <tt class="py-line"><tt class="py-comment"></tt> </tt>
<a name="L6"></a><tt class="py-lineno"> 6</tt> <tt class="py-line"><tt class="py-docstring">"""BioPython Pathway module.</tt> </tt>
<a name="L7"></a><tt class="py-lineno"> 7</tt> <tt class="py-line"><tt class="py-docstring"></tt> </tt>
<a name="L8"></a><tt class="py-lineno"> 8</tt> <tt class="py-line"><tt class="py-docstring">Bio.Pathway is a lightweight class library designed to support the following tasks:</tt> </tt>
<a name="L9"></a><tt class="py-lineno"> 9</tt> <tt class="py-line"><tt class="py-docstring"></tt> </tt>
<a name="L10"></a><tt class="py-lineno"> 10</tt> <tt class="py-line"><tt class="py-docstring"> - Data interchange and preprocessing between pathway databases and analysis software. </tt> </tt>
<a name="L11"></a><tt class="py-lineno"> 11</tt> <tt class="py-line"><tt class="py-docstring"> - Quick prototyping of pathway analysis algorithms</tt> </tt>
<a name="L12"></a><tt class="py-lineno"> 12</tt> <tt class="py-line"><tt class="py-docstring"></tt> </tt>
<a name="L13"></a><tt class="py-lineno"> 13</tt> <tt class="py-line"><tt class="py-docstring">The basic object in the Bio.Pathway model is Interaction, which represents an arbitrary</tt> </tt>
<a name="L14"></a><tt class="py-lineno"> 14</tt> <tt class="py-line"><tt class="py-docstring">interaction between any number of biochemical species.</tt> </tt>
<a name="L15"></a><tt class="py-lineno"> 15</tt> <tt class="py-line"><tt class="py-docstring"></tt> </tt>
<a name="L16"></a><tt class="py-lineno"> 16</tt> <tt class="py-line"><tt class="py-docstring">Network objects are used to represent the connectivity between species in pathways</tt> </tt>
<a name="L17"></a><tt class="py-lineno"> 17</tt> <tt class="py-line"><tt class="py-docstring">and reaction networks.</tt> </tt>
<a name="L18"></a><tt class="py-lineno"> 18</tt> <tt class="py-line"><tt class="py-docstring"></tt> </tt>
<a name="L19"></a><tt class="py-lineno"> 19</tt> <tt class="py-line"><tt class="py-docstring">For applications where it is not neccessary to explicitly represent network connectivity,</tt> </tt>
<a name="L20"></a><tt class="py-lineno"> 20</tt> <tt class="py-line"><tt class="py-docstring">the specialized classes Reaction and System should be used in place of Interacton and</tt> </tt>
<a name="L21"></a><tt class="py-lineno"> 21</tt> <tt class="py-line"><tt class="py-docstring">Network.</tt> </tt>
<a name="L22"></a><tt class="py-lineno"> 22</tt> <tt class="py-line"><tt class="py-docstring"></tt> </tt>
<a name="L23"></a><tt class="py-lineno"> 23</tt> <tt class="py-line"><tt class="py-docstring">The Bio.Pathway classes, especially Interaction, are intentionally</tt> </tt>
<a name="L24"></a><tt class="py-lineno"> 24</tt> <tt class="py-line"><tt class="py-docstring">desgined to be very flexible. Their intended use are as wrappers around database</tt> </tt>
<a name="L25"></a><tt class="py-lineno"> 25</tt> <tt class="py-line"><tt class="py-docstring">specific records, such as BIND objects. The value-added in this module is a</tt> </tt>
<a name="L26"></a><tt class="py-lineno"> 26</tt> <tt class="py-line"><tt class="py-docstring">framework for representing collections of reactions in a way that supports</tt> </tt>
<a name="L27"></a><tt class="py-lineno"> 27</tt> <tt class="py-line"><tt class="py-docstring">graph theoretic and numeric analysis.</tt> </tt>
<a name="L28"></a><tt class="py-lineno"> 28</tt> <tt class="py-line"><tt class="py-docstring"></tt> </tt>
<a name="L29"></a><tt class="py-lineno"> 29</tt> <tt class="py-line"><tt class="py-docstring">Note: This module should be regarded as a prototype only. API changes are likely.</tt> </tt>
<a name="L30"></a><tt class="py-lineno"> 30</tt> <tt class="py-line"><tt class="py-docstring"> Comments and feature requests are most welcome.</tt> </tt>
<a name="L31"></a><tt class="py-lineno"> 31</tt> <tt class="py-line"><tt class="py-docstring">"""</tt> </tt>
<a name="L32"></a><tt class="py-lineno"> 32</tt> <tt class="py-line"> </tt>
<a name="L33"></a><tt class="py-lineno"> 33</tt> <tt class="py-line"> </tt>
<a name="L34"></a><tt class="py-lineno"> 34</tt> <tt class="py-line"><tt class="py-keyword">from</tt> <tt id="link-0" class="py-name" targets="Package Bio=Bio-module.html"><a title="Bio" class="py-name" href="#" onclick="return doclink('link-0', 'Bio', 'link-0');">Bio</a></tt><tt class="py-op">.</tt><tt id="link-1" class="py-name" targets="Package Bio.Pathway=Bio.Pathway-module.html"><a title="Bio.Pathway" class="py-name" href="#" onclick="return doclink('link-1', 'Pathway', 'link-1');">Pathway</a></tt><tt class="py-op">.</tt><tt id="link-2" class="py-name" targets="Package Bio.Pathway.Rep=Bio.Pathway.Rep-module.html,Function Martel.Rep()=Martel-module.html#Rep"><a title="Bio.Pathway.Rep
Martel.Rep" class="py-name" href="#" onclick="return doclink('link-2', 'Rep', 'link-2');">Rep</a></tt><tt class="py-op">.</tt><tt id="link-3" class="py-name" targets="Module Bio.Pathway.Rep.HashSet=Bio.Pathway.Rep.HashSet-module.html,Class Bio.Pathway.Rep.HashSet.HashSet=Bio.Pathway.Rep.HashSet.HashSet-class.html"><a title="Bio.Pathway.Rep.HashSet
Bio.Pathway.Rep.HashSet.HashSet" class="py-name" href="#" onclick="return doclink('link-3', 'HashSet', 'link-3');">HashSet</a></tt> <tt class="py-keyword">import</tt> <tt class="py-op">*</tt> </tt>
<a name="L35"></a><tt class="py-lineno"> 35</tt> <tt class="py-line"><tt class="py-keyword">from</tt> <tt id="link-4" class="py-name"><a title="Bio" class="py-name" href="#" onclick="return doclink('link-4', 'Bio', 'link-0');">Bio</a></tt><tt class="py-op">.</tt><tt id="link-5" class="py-name"><a title="Bio.Pathway" class="py-name" href="#" onclick="return doclink('link-5', 'Pathway', 'link-1');">Pathway</a></tt><tt class="py-op">.</tt><tt id="link-6" class="py-name"><a title="Bio.Pathway.Rep
Martel.Rep" class="py-name" href="#" onclick="return doclink('link-6', 'Rep', 'link-2');">Rep</a></tt><tt class="py-op">.</tt><tt id="link-7" class="py-name" targets="Module Bio.Pathway.Rep.MultiGraph=Bio.Pathway.Rep.MultiGraph-module.html,Class Bio.Pathway.Rep.MultiGraph.MultiGraph=Bio.Pathway.Rep.MultiGraph.MultiGraph-class.html"><a title="Bio.Pathway.Rep.MultiGraph
Bio.Pathway.Rep.MultiGraph.MultiGraph" class="py-name" href="#" onclick="return doclink('link-7', 'MultiGraph', 'link-7');">MultiGraph</a></tt> <tt class="py-keyword">import</tt> <tt class="py-op">*</tt> </tt>
<a name="L36"></a><tt class="py-lineno"> 36</tt> <tt class="py-line"> </tt>
<a name="L37"></a><tt class="py-lineno"> 37</tt> <tt class="py-line"> </tt>
<a name="Reaction"></a><div id="Reaction-def"><a name="L38"></a><tt class="py-lineno"> 38</tt> <a class="py-toggle" href="#" id="Reaction-toggle" onclick="return toggle('Reaction');">-</a><tt class="py-line"><tt class="py-keyword">class</tt> <a class="py-def-name" href="Bio.Pathway.Reaction-class.html">Reaction</a><tt class="py-op">:</tt> </tt>
</div><div id="Reaction-collapsed" style="display:none;" pad="+++" indent="++++"></div><div id="Reaction-expanded"><a name="L39"></a><tt class="py-lineno"> 39</tt> <tt class="py-line"> <tt class="py-docstring">"""Abstraction for a biochemical transformation.</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 class represents a (potentially reversible) biochemical</tt> </tt>
<a name="L42"></a><tt class="py-lineno"> 42</tt> <tt class="py-line"><tt class="py-docstring"> transformation of the type:</tt> </tt>
<a name="L43"></a><tt class="py-lineno"> 43</tt> <tt class="py-line"><tt class="py-docstring"></tt> </tt>
<a name="L44"></a><tt class="py-lineno"> 44</tt> <tt class="py-line"><tt class="py-docstring"> a S1 + b S2 + ... --> c P1 + d P2 + ...</tt> </tt>
<a name="L45"></a><tt class="py-lineno"> 45</tt> <tt class="py-line"><tt class="py-docstring"></tt> </tt>
<a name="L46"></a><tt class="py-lineno"> 46</tt> <tt class="py-line"><tt class="py-docstring"> where</tt> </tt>
<a name="L47"></a><tt class="py-lineno"> 47</tt> <tt class="py-line"><tt class="py-docstring"> - a, b, c, d ... are positive numeric stochiometric coefficients,</tt> </tt>
<a name="L48"></a><tt class="py-lineno"> 48</tt> <tt class="py-line"><tt class="py-docstring"> - S1, S2, ... are substrates</tt> </tt>
<a name="L49"></a><tt class="py-lineno"> 49</tt> <tt class="py-line"><tt class="py-docstring"> - P1, P2, ... are products</tt> </tt>
<a name="L50"></a><tt class="py-lineno"> 50</tt> <tt class="py-line"><tt class="py-docstring"></tt> </tt>
<a name="L51"></a><tt class="py-lineno"> 51</tt> <tt class="py-line"><tt class="py-docstring"> A Reaction should be viewed as the net result of one or more individual</tt> </tt>
<a name="L52"></a><tt class="py-lineno"> 52</tt> <tt class="py-line"><tt class="py-docstring"> reaction steps, where each step is potentially facilitated by a different</tt> </tt>
<a name="L53"></a><tt class="py-lineno"> 53</tt> <tt class="py-line"><tt class="py-docstring"> catalyst. Support for 'Reaction algebra' will be added at some point in</tt> </tt>
<a name="L54"></a><tt class="py-lineno"> 54</tt> <tt class="py-line"><tt class="py-docstring"> the future.</tt> </tt>
<a name="L55"></a><tt class="py-lineno"> 55</tt> <tt class="py-line"><tt class="py-docstring"></tt> </tt>
<a name="L56"></a><tt class="py-lineno"> 56</tt> <tt class="py-line"><tt class="py-docstring"> Attributes:</tt> </tt>
<a name="L57"></a><tt class="py-lineno"> 57</tt> <tt class="py-line"><tt class="py-docstring"></tt> </tt>
<a name="L58"></a><tt class="py-lineno"> 58</tt> <tt class="py-line"><tt class="py-docstring"> reactants -- map of involved species to their stochiometric coefficients:</tt> </tt>
<a name="L59"></a><tt class="py-lineno"> 59</tt> <tt class="py-line"><tt class="py-docstring"> reactants[S] = stochiometric constant for S</tt> </tt>
<a name="L60"></a><tt class="py-lineno"> 60</tt> <tt class="py-line"><tt class="py-docstring"> catalysts -- list of tuples of catalysts required for this reaction</tt> </tt>
<a name="L61"></a><tt class="py-lineno"> 61</tt> <tt class="py-line"><tt class="py-docstring"> reversible -- true iff reaction is reversible</tt> </tt>
<a name="L62"></a><tt class="py-lineno"> 62</tt> <tt class="py-line"><tt class="py-docstring"> data -- reference to arbitrary additional data</tt> </tt>
<a name="L63"></a><tt class="py-lineno"> 63</tt> <tt class="py-line"><tt class="py-docstring"></tt> </tt>
<a name="L64"></a><tt class="py-lineno"> 64</tt> <tt class="py-line"><tt class="py-docstring"> Invariants:</tt> </tt>
<a name="L65"></a><tt class="py-lineno"> 65</tt> <tt class="py-line"><tt class="py-docstring"></tt> </tt>
<a name="L66"></a><tt class="py-lineno"> 66</tt> <tt class="py-line"><tt class="py-docstring"> for all S in reactants.keys(): reactants[S] != 0</tt> </tt>
<a name="L67"></a><tt class="py-lineno"> 67</tt> <tt class="py-line"><tt class="py-docstring"> for all C in catalysts.keys(): catalysts[C] != 0</tt> </tt>
<a name="L68"></a><tt class="py-lineno"> 68</tt> <tt class="py-line"><tt class="py-docstring"></tt> </tt>
<a name="L69"></a><tt class="py-lineno"> 69</tt> <tt class="py-line"><tt class="py-docstring"> """</tt> </tt>
<a name="L70"></a><tt class="py-lineno"> 70</tt> <tt class="py-line"> </tt>
<a name="Reaction.__init__"></a><div id="Reaction.__init__-def"><a name="L71"></a><tt class="py-lineno"> 71</tt> <a class="py-toggle" href="#" id="Reaction.__init__-toggle" onclick="return toggle('Reaction.__init__');">-</a><tt class="py-line"> <tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.Pathway.Reaction-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">reactants</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">catalysts</tt> <tt class="py-op">=</tt> <tt class="py-op">[</tt><tt class="py-op">]</tt><tt class="py-op">,</tt> </tt>
<a name="L72"></a><tt class="py-lineno"> 72</tt> <tt class="py-line"> <tt class="py-param">reversible</tt> <tt class="py-op">=</tt> <tt class="py-number">0</tt><tt class="py-op">,</tt> <tt class="py-param">data</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="Reaction.__init__-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="Reaction.__init__-expanded"><a name="L73"></a><tt class="py-lineno"> 73</tt> <tt class="py-line"> <tt class="py-docstring">"""Initializes a new Reaction object."""</tt> </tt>
<a name="L74"></a><tt class="py-lineno"> 74</tt> <tt class="py-line"> <tt class="py-comment"># enforce invariants on reactants:</tt> </tt>
<a name="L75"></a><tt class="py-lineno"> 75</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">reactants</tt> <tt class="py-op">=</tt> <tt class="py-name">reactants</tt><tt class="py-op">.</tt><tt id="link-8" class="py-name" targets="Method Bio.Crystal.Crystal.copy()=Bio.Crystal.Crystal-class.html#copy,Method Bio.GA.Organism.Organism.copy()=Bio.GA.Organism.Organism-class.html#copy,Method Bio.GenBank.NCBIDictionary.copy()=Bio.GenBank.NCBIDictionary-class.html#copy,Method Bio.PDB.Vector'.Vector.copy()=Bio.PDB.Vector%27.Vector-class.html#copy,Method Bio.Prosite.ExPASyDictionary.copy()=Bio.Prosite.ExPASyDictionary-class.html#copy,Method Bio.Prosite.Pattern.PrositeTerm.copy()=Bio.Prosite.Pattern.PrositeTerm-class.html#copy,Method Bio.Prosite.Prodoc.ExPASyDictionary.copy()=Bio.Prosite.Prodoc.ExPASyDictionary-class.html#copy,Method Bio.PubMed.Dictionary.copy()=Bio.PubMed.Dictionary-class.html#copy,Method Bio.SwissProt.SProt.ExPASyDictionary.copy()=Bio.SwissProt.SProt.ExPASyDictionary-class.html#copy,Method Martel.Expression.Any.copy()=Martel.Expression.Any-class.html#copy,Method Martel.Expression.AnyEol.copy()=Martel.Expression.AnyEol-class.html#copy,Method Martel.Expression.Assert.copy()=Martel.Expression.Assert-class.html#copy,Method Martel.Expression.AtBeginning.copy()=Martel.Expression.AtBeginning-class.html#copy,Method Martel.Expression.AtEnd.copy()=Martel.Expression.AtEnd-class.html#copy,Method Martel.Expression.Debug.copy()=Martel.Expression.Debug-class.html#copy,Method Martel.Expression.Dot.copy()=Martel.Expression.Dot-class.html#copy,Method Martel.Expression.Expression.copy()=Martel.Expression.Expression-class.html#copy,Method Martel.Expression.ExpressionList.copy()=Martel.Expression.ExpressionList-class.html#copy,Method Martel.Expression.FastFeature.copy()=Martel.Expression.FastFeature-class.html#copy,Method Martel.Expression.Group.copy()=Martel.Expression.Group-class.html#copy,Method Martel.Expression.GroupRef.copy()=Martel.Expression.GroupRef-class.html#copy,Method Martel.Expression.HeaderFooter.copy()=Martel.Expression.HeaderFooter-class.html#copy,Method Martel.Expression.Literal.copy()=Martel.Expression.Literal-class.html#copy,Method Martel.Expression.MaxRepeat.copy()=Martel.Expression.MaxRepeat-class.html#copy,Method Martel.Expression.NullOp.copy()=Martel.Expression.NullOp-class.html#copy,Method Martel.Expression.ParseRecords.copy()=Martel.Expression.ParseRecords-class.html#copy,Method Martel.Expression.PassThrough.copy()=Martel.Expression.PassThrough-class.html#copy,Method Martel.Expression.Str.copy()=Martel.Expression.Str-class.html#copy,Method Martel.IterParser.IterHeaderFooter.copy()=Martel.IterParser.IterHeaderFooter-class.html#copy,Method Martel.IterParser.IterRecords.copy()=Martel.IterParser.IterRecords-class.html#copy,Method Martel.Iterator.IteratorRecords.copy()=Martel.Iterator.IteratorRecords-class.html#copy,Method Martel.Parser.HeaderFooterParser.copy()=Martel.Parser.HeaderFooterParser-class.html#copy,Method Martel.Parser.Parser.copy()=Martel.Parser.Parser-class.html#copy,Method Martel.Parser.RecordParser.copy()=Martel.Parser.RecordParser-class.html#copy"><a title="Bio.Crystal.Crystal.copy
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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-9', 'keys', 'link-9');">keys</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
<a name="L77"></a><tt class="py-lineno"> 77</tt> <tt class="py-line"> <tt class="py-keyword">if</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">reactants</tt><tt class="py-op">[</tt><tt class="py-name">r</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="L78"></a><tt class="py-lineno"> 78</tt> <tt class="py-line"> <tt class="py-keyword">del</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">reactants</tt><tt class="py-op">[</tt><tt class="py-name">r</tt><tt class="py-op">]</tt> </tt>
<a name="L79"></a><tt class="py-lineno"> 79</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">catalysts</tt> <tt class="py-op">=</tt> <tt id="link-10" class="py-name"><a title="Bio.Pathway.Rep.HashSet
Bio.Pathway.Rep.HashSet.HashSet" class="py-name" href="#" onclick="return doclink('link-10', 'HashSet', 'link-3');">HashSet</a></tt><tt class="py-op">(</tt><tt class="py-name">catalysts</tt><tt class="py-op">)</tt><tt class="py-op">.</tt><tt id="link-11" class="py-name" targets="Method Bio.Pathway.Rep.HashSet.HashSet.list()=Bio.Pathway.Rep.HashSet.HashSet-class.html#list"><a title="Bio.Pathway.Rep.HashSet.HashSet.list" class="py-name" href="#" onclick="return doclink('link-11', 'list', 'link-11');">list</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
<a name="L80"></a><tt class="py-lineno"> 80</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-12" 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-12', 'data', 'link-12');">data</a></tt> <tt class="py-op">=</tt> <tt id="link-13" class="py-name"><a title="BioSQL.BioSeq.DBSeq.data" class="py-name" href="#" onclick="return doclink('link-13', 'data', 'link-12');">data</a></tt> </tt>
<a name="L81"></a><tt class="py-lineno"> 81</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">reversible</tt> <tt class="py-op">=</tt> <tt class="py-name">reversible</tt> </tt>
</div><a name="L82"></a><tt class="py-lineno"> 82</tt> <tt class="py-line"> </tt>
<a name="Reaction.__eq__"></a><div id="Reaction.__eq__-def"><a name="L83"></a><tt class="py-lineno"> 83</tt> <a class="py-toggle" href="#" id="Reaction.__eq__-toggle" onclick="return toggle('Reaction.__eq__');">-</a><tt class="py-line"> <tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.Pathway.Reaction-class.html#__eq__">__eq__</a><tt class="py-op">(</tt><tt class="py-param">self</tt><tt class="py-op">,</tt> <tt class="py-param">r</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="Reaction.__eq__-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="Reaction.__eq__-expanded"><a name="L84"></a><tt class="py-lineno"> 84</tt> <tt class="py-line"> <tt class="py-docstring">"""Returns true iff self is equal to r."""</tt> </tt>
<a name="L85"></a><tt class="py-lineno"> 85</tt> <tt class="py-line"> <tt class="py-keyword">return</tt> <tt class="py-name">isinstance</tt><tt class="py-op">(</tt><tt class="py-name">r</tt><tt class="py-op">,</tt> <tt id="link-14" class="py-name" targets="Class Bio.Pathway.Reaction=Bio.Pathway.Reaction-class.html"><a title="Bio.Pathway.Reaction" class="py-name" href="#" onclick="return doclink('link-14', 'Reaction', 'link-14');">Reaction</a></tt><tt class="py-op">)</tt> <tt class="py-keyword">and</tt> \ </tt>
<a name="L86"></a><tt class="py-lineno"> 86</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">reactants</tt> <tt class="py-op">==</tt> <tt class="py-name">r</tt><tt class="py-op">.</tt><tt class="py-name">reactants</tt> <tt class="py-keyword">and</tt> \ </tt>
<a name="L87"></a><tt class="py-lineno"> 87</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">catalysts</tt> <tt class="py-op">==</tt> <tt class="py-name">r</tt><tt class="py-op">.</tt><tt class="py-name">catalysts</tt> <tt class="py-keyword">and</tt> \ </tt>
<a name="L88"></a><tt class="py-lineno"> 88</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-15" class="py-name"><a title="BioSQL.BioSeq.DBSeq.data" class="py-name" href="#" onclick="return doclink('link-15', 'data', 'link-12');">data</a></tt> <tt class="py-op">==</tt> <tt class="py-name">r</tt><tt class="py-op">.</tt><tt id="link-16" class="py-name"><a title="BioSQL.BioSeq.DBSeq.data" class="py-name" href="#" onclick="return doclink('link-16', 'data', 'link-12');">data</a></tt> <tt class="py-keyword">and</tt> \ </tt>
<a name="L89"></a><tt class="py-lineno"> 89</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">reversible</tt> <tt class="py-op">==</tt> <tt class="py-name">r</tt><tt class="py-op">.</tt><tt class="py-name">reversible</tt> </tt>
</div><a name="L90"></a><tt class="py-lineno"> 90</tt> <tt class="py-line"> </tt>
<a name="Reaction.__ne__"></a><div id="Reaction.__ne__-def"><a name="L91"></a><tt class="py-lineno"> 91</tt> <a class="py-toggle" href="#" id="Reaction.__ne__-toggle" onclick="return toggle('Reaction.__ne__');">-</a><tt class="py-line"> <tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.Pathway.Reaction-class.html#__ne__">__ne__</a><tt class="py-op">(</tt><tt class="py-param">self</tt><tt class="py-op">,</tt> <tt class="py-param">r</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="Reaction.__ne__-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="Reaction.__ne__-expanded"><a name="L92"></a><tt class="py-lineno"> 92</tt> <tt class="py-line"> <tt class="py-docstring">"""Returns true iff self is not equal to r."""</tt> </tt>
<a name="L93"></a><tt class="py-lineno"> 93</tt> <tt class="py-line"> <tt class="py-keyword">return</tt> <tt class="py-keyword">not</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-17" class="py-name" targets="Method Bio.Crystal.Chain.__eq__()=Bio.Crystal.Chain-class.html#__eq__,Method Bio.Crystal.Hetero.__eq__()=Bio.Crystal.Hetero-class.html#__eq__,Method Bio.EUtils.Datatypes.CheckLinkSet.__eq__()=Bio.EUtils.Datatypes.CheckLinkSet-class.html#__eq__,Method Bio.EUtils.Datatypes.DBIds.__eq__()=Bio.EUtils.Datatypes.DBIds-class.html#__eq__,Method Bio.EUtils.Datatypes.Date.__eq__()=Bio.EUtils.Datatypes.Date-class.html#__eq__,Method Bio.EUtils.Datatypes.IdCheck.__eq__()=Bio.EUtils.Datatypes.IdCheck-class.html#__eq__,Method Bio.EUtils.Datatypes.IdUrlSet.__eq__()=Bio.EUtils.Datatypes.IdUrlSet-class.html#__eq__,Method Bio.EUtils.Datatypes.Link.__eq__()=Bio.EUtils.Datatypes.Link-class.html#__eq__,Method Bio.EUtils.Datatypes.LinkSetDb.__eq__()=Bio.EUtils.Datatypes.LinkSetDb-class.html#__eq__,Method Bio.EUtils.Datatypes.LinksLinkSet.__eq__()=Bio.EUtils.Datatypes.LinksLinkSet-class.html#__eq__,Method Bio.EUtils.Datatypes.NeighborLinkSet.__eq__()=Bio.EUtils.Datatypes.NeighborLinkSet-class.html#__eq__,Method Bio.EUtils.Datatypes.ObjUrl.__eq__()=Bio.EUtils.Datatypes.ObjUrl-class.html#__eq__,Method Bio.EUtils.Datatypes.Problem.__eq__()=Bio.EUtils.Datatypes.Problem-class.html#__eq__,Method Bio.EUtils.Datatypes.Provider.__eq__()=Bio.EUtils.Datatypes.Provider-class.html#__eq__,Method Bio.EUtils.MultiDict.OrderedMultiDict.__eq__()=Bio.EUtils.MultiDict.OrderedMultiDict-class.html#__eq__,Method Bio.EUtils.MultiDict.UnorderedMultiDict.__eq__()=Bio.EUtils.MultiDict.UnorderedMultiDict-class.html#__eq__,Method Bio.LocusLink.web_parse.Token.__eq__()=Bio.LocusLink.web_parse.Token-class.html#__eq__,Method Bio.Pathway.Reaction.__eq__()=Bio.Pathway.Reaction-class.html#__eq__,Method Bio.Pathway.Rep.Graph.Graph.__eq__()=Bio.Pathway.Rep.Graph.Graph-class.html#__eq__,Method Bio.Pathway.Rep.HashSet.HashSet.__eq__()=Bio.Pathway.Rep.HashSet.HashSet-class.html#__eq__,Method Bio.Pathway.Rep.MultiGraph.MultiGraph.__eq__()=Bio.Pathway.Rep.MultiGraph.MultiGraph-class.html#__eq__,Method Bio.Restriction.Restriction.FormattedSeq.__eq__()=Bio.Restriction.Restriction.FormattedSeq-class.html#__eq__,Method Bio.Restriction.Restriction.RestrictionType.__eq__()=Bio.Restriction.Restriction.RestrictionType-class.html#__eq__"><a title="Bio.Crystal.Chain.__eq__
Bio.Crystal.Hetero.__eq__
Bio.EUtils.Datatypes.CheckLinkSet.__eq__
Bio.EUtils.Datatypes.DBIds.__eq__
Bio.EUtils.Datatypes.Date.__eq__
Bio.EUtils.Datatypes.IdCheck.__eq__
Bio.EUtils.Datatypes.IdUrlSet.__eq__
Bio.EUtils.Datatypes.Link.__eq__
Bio.EUtils.Datatypes.LinkSetDb.__eq__
Bio.EUtils.Datatypes.LinksLinkSet.__eq__
Bio.EUtils.Datatypes.NeighborLinkSet.__eq__
Bio.EUtils.Datatypes.ObjUrl.__eq__
Bio.EUtils.Datatypes.Problem.__eq__
Bio.EUtils.Datatypes.Provider.__eq__
Bio.EUtils.MultiDict.OrderedMultiDict.__eq__
Bio.EUtils.MultiDict.UnorderedMultiDict.__eq__
Bio.LocusLink.web_parse.Token.__eq__
Bio.Pathway.Reaction.__eq__
Bio.Pathway.Rep.Graph.Graph.__eq__
Bio.Pathway.Rep.HashSet.HashSet.__eq__
Bio.Pathway.Rep.MultiGraph.MultiGraph.__eq__
Bio.Restriction.Restriction.FormattedSeq.__eq__
Bio.Restriction.Restriction.RestrictionType.__eq__" class="py-name" href="#" onclick="return doclink('link-17', '__eq__', 'link-17');">__eq__</a></tt><tt class="py-op">(</tt><tt class="py-name">r</tt><tt class="py-op">)</tt> </tt>
</div><a name="L94"></a><tt class="py-lineno"> 94</tt> <tt class="py-line"> </tt>
<a name="Reaction.__hash__"></a><div id="Reaction.__hash__-def"><a name="L95"></a><tt class="py-lineno"> 95</tt> <a class="py-toggle" href="#" id="Reaction.__hash__-toggle" onclick="return toggle('Reaction.__hash__');">-</a><tt class="py-line"> <tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.Pathway.Reaction-class.html#__hash__">__hash__</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="Reaction.__hash__-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="Reaction.__hash__-expanded"><a name="L96"></a><tt class="py-lineno"> 96</tt> <tt class="py-line"> <tt class="py-docstring">"""Returns a hashcode for self."""</tt> </tt>
<a name="L97"></a><tt class="py-lineno"> 97</tt> <tt class="py-line"> <tt class="py-name">t</tt> <tt class="py-op">=</tt> <tt class="py-name">tuple</tt><tt class="py-op">(</tt><tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-18" class="py-name" targets="Method Bio.Pathway.Network.species()=Bio.Pathway.Network-class.html#species,Method Bio.Pathway.Reaction.species()=Bio.Pathway.Reaction-class.html#species,Method Bio.Pathway.System.species()=Bio.Pathway.System-class.html#species"><a title="Bio.Pathway.Network.species
Bio.Pathway.Reaction.species
Bio.Pathway.System.species" class="py-name" href="#" onclick="return doclink('link-18', 'species', 'link-18');">species</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt><tt class="py-op">)</tt> </tt>
<a name="L98"></a><tt class="py-lineno"> 98</tt> <tt class="py-line"> <tt class="py-keyword">return</tt> <tt class="py-name">hash</tt><tt class="py-op">(</tt><tt class="py-name">t</tt><tt class="py-op">)</tt> </tt>
</div><a name="L99"></a><tt class="py-lineno"> 99</tt> <tt class="py-line"> </tt>
<a name="Reaction.__repr__"></a><div id="Reaction.__repr__-def"><a name="L100"></a><tt class="py-lineno">100</tt> <a class="py-toggle" href="#" id="Reaction.__repr__-toggle" onclick="return toggle('Reaction.__repr__');">-</a><tt class="py-line"> <tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.Pathway.Reaction-class.html#__repr__">__repr__</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="Reaction.__repr__-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="Reaction.__repr__-expanded"><a name="L101"></a><tt class="py-lineno">101</tt> <tt class="py-line"> <tt class="py-docstring">"""Returns a debugging string representation of self."""</tt> </tt>
<a name="L102"></a><tt class="py-lineno">102</tt> <tt class="py-line"> <tt class="py-keyword">return</tt> <tt class="py-string">"Reaction("</tt> <tt class="py-op">+</tt> \ </tt>
<a name="L103"></a><tt class="py-lineno">103</tt> <tt class="py-line"> <tt class="py-string">","</tt><tt class="py-op">.</tt><tt class="py-name">join</tt><tt class="py-op">(</tt><tt id="link-19" 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-19', 'map', 'link-19');">map</a></tt><tt class="py-op">(</tt><tt class="py-name">repr</tt><tt class="py-op">,</tt><tt class="py-op">[</tt><tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">reactants</tt><tt class="py-op">,</tt> </tt>
<a name="L104"></a><tt class="py-lineno">104</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">catalysts</tt><tt class="py-op">,</tt> </tt>
<a name="L105"></a><tt class="py-lineno">105</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-20" class="py-name"><a title="BioSQL.BioSeq.DBSeq.data" class="py-name" href="#" onclick="return doclink('link-20', 'data', 'link-12');">data</a></tt><tt class="py-op">,</tt> </tt>
<a name="L106"></a><tt class="py-lineno">106</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">reversible</tt><tt class="py-op">]</tt><tt class="py-op">)</tt><tt class="py-op">)</tt> <tt class="py-op">+</tt> <tt class="py-string">")"</tt> </tt>
</div><a name="L107"></a><tt class="py-lineno">107</tt> <tt class="py-line"> </tt>
<a name="Reaction.__str__"></a><div id="Reaction.__str__-def"><a name="L108"></a><tt class="py-lineno">108</tt> <a class="py-toggle" href="#" id="Reaction.__str__-toggle" onclick="return toggle('Reaction.__str__');">-</a><tt class="py-line"> <tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.Pathway.Reaction-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="Reaction.__str__-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="Reaction.__str__-expanded"><a name="L109"></a><tt class="py-lineno">109</tt> <tt class="py-line"> <tt class="py-docstring">"""Returns a string representation of self."""</tt> </tt>
<a name="L110"></a><tt class="py-lineno">110</tt> <tt class="py-line"> <tt class="py-name">substrates</tt> <tt class="py-op">=</tt> <tt class="py-string">""</tt> </tt>
<a name="L111"></a><tt class="py-lineno">111</tt> <tt class="py-line"> <tt class="py-name">products</tt> <tt class="py-op">=</tt> <tt class="py-string">""</tt> </tt>
<a name="L112"></a><tt class="py-lineno">112</tt> <tt class="py-line"> <tt class="py-name">all_species</tt> <tt class="py-op">=</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">reactants</tt><tt class="py-op">.</tt><tt id="link-21" 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-21', 'keys', 'link-9');">keys</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
<a name="L113"></a><tt class="py-lineno">113</tt> <tt class="py-line"> <tt class="py-name">all_species</tt><tt class="py-op">.</tt><tt id="link-22" 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-22', 'sort', 'link-22');">sort</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
<a name="L114"></a><tt class="py-lineno">114</tt> <tt class="py-line"> <tt class="py-keyword">for</tt> <tt id="link-23" class="py-name"><a title="Bio.Pathway.Network.species
Bio.Pathway.Reaction.species
Bio.Pathway.System.species" class="py-name" href="#" onclick="return doclink('link-23', 'species', 'link-18');">species</a></tt> <tt class="py-keyword">in</tt> <tt class="py-name">all_species</tt><tt class="py-op">:</tt> </tt>
<a name="L115"></a><tt class="py-lineno">115</tt> <tt class="py-line"> <tt class="py-name">stoch</tt> <tt class="py-op">=</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">reactants</tt><tt class="py-op">[</tt><tt id="link-24" class="py-name"><a title="Bio.Pathway.Network.species
Bio.Pathway.Reaction.species
Bio.Pathway.System.species" class="py-name" href="#" onclick="return doclink('link-24', 'species', 'link-18');">species</a></tt><tt class="py-op">]</tt> </tt>
<a name="L116"></a><tt class="py-lineno">116</tt> <tt class="py-line"> <tt class="py-keyword">if</tt> <tt class="py-name">stoch</tt> <tt class="py-op"><</tt> <tt class="py-number">0</tt><tt class="py-op">:</tt> </tt>
<a name="L117"></a><tt class="py-lineno">117</tt> <tt class="py-line"> <tt class="py-comment"># species is a substrate:</tt> </tt>
<a name="L118"></a><tt class="py-lineno">118</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-keyword">if</tt> <tt class="py-name">substrates</tt> <tt class="py-op">!=</tt> <tt class="py-string">""</tt><tt class="py-op">:</tt> </tt>
<a name="L119"></a><tt class="py-lineno">119</tt> <tt class="py-line"> <tt class="py-name">substrates</tt> <tt class="py-op">=</tt> <tt class="py-name">substrates</tt> <tt class="py-op">+</tt> <tt class="py-string">" + "</tt> </tt>
<a name="L120"></a><tt class="py-lineno">120</tt> <tt class="py-line"> <tt class="py-keyword">if</tt> <tt class="py-name">stoch</tt> <tt class="py-op">!=</tt> <tt class="py-op">-</tt><tt class="py-number">1</tt><tt class="py-op">:</tt> </tt>
<a name="L121"></a><tt class="py-lineno">121</tt> <tt class="py-line"> <tt class="py-name">substrates</tt> <tt class="py-op">=</tt> <tt class="py-name">substrates</tt> <tt class="py-op">+</tt> <tt class="py-name">str</tt><tt class="py-op">(</tt><tt id="link-25" class="py-name" targets="Method Bio.FSSP.FSSPAlignDict.abs()=Bio.FSSP.FSSPAlignDict-class.html#abs"><a title="Bio.FSSP.FSSPAlignDict.abs" class="py-name" href="#" onclick="return doclink('link-25', 'abs', 'link-25');">abs</a></tt><tt class="py-op">(</tt><tt class="py-name">stoch</tt><tt class="py-op">)</tt><tt class="py-op">)</tt> <tt class="py-op">+</tt> <tt class="py-string">" "</tt> </tt>
<a name="L122"></a><tt class="py-lineno">122</tt> <tt class="py-line"> <tt class="py-name">substrates</tt> <tt class="py-op">=</tt> <tt class="py-name">substrates</tt> <tt class="py-op">+</tt> <tt class="py-name">str</tt><tt class="py-op">(</tt><tt id="link-26" class="py-name"><a title="Bio.Pathway.Network.species
Bio.Pathway.Reaction.species
Bio.Pathway.System.species" class="py-name" href="#" onclick="return doclink('link-26', 'species', 'link-18');">species</a></tt><tt class="py-op">)</tt> </tt>
<a name="L123"></a><tt class="py-lineno">123</tt> <tt class="py-line"> <tt class="py-keyword">elif</tt> <tt class="py-name">stoch</tt> <tt class="py-op">></tt> <tt class="py-number">0</tt><tt class="py-op">:</tt> </tt>
<a name="L124"></a><tt class="py-lineno">124</tt> <tt class="py-line"> <tt class="py-comment"># species is a product:</tt> </tt>
<a name="L125"></a><tt class="py-lineno">125</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-keyword">if</tt> <tt class="py-name">products</tt> <tt class="py-op">!=</tt> <tt class="py-string">""</tt><tt class="py-op">:</tt> </tt>
<a name="L126"></a><tt class="py-lineno">126</tt> <tt class="py-line"> <tt class="py-name">products</tt> <tt class="py-op">=</tt> <tt class="py-name">products</tt> <tt class="py-op">+</tt> <tt class="py-string">" + "</tt> </tt>
<a name="L127"></a><tt class="py-lineno">127</tt> <tt class="py-line"> <tt class="py-keyword">if</tt> <tt class="py-name">stoch</tt> <tt class="py-op">!=</tt> <tt class="py-number">1</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">products</tt> <tt class="py-op">=</tt> <tt class="py-name">products</tt> <tt class="py-op">+</tt> <tt class="py-name">str</tt><tt class="py-op">(</tt><tt class="py-name">stoch</tt><tt class="py-op">)</tt> <tt class="py-op">+</tt> <tt class="py-string">" "</tt> </tt>
<a name="L129"></a><tt class="py-lineno">129</tt> <tt class="py-line"> <tt class="py-name">products</tt> <tt class="py-op">=</tt> <tt class="py-name">products</tt> <tt class="py-op">+</tt> <tt class="py-name">str</tt><tt class="py-op">(</tt><tt id="link-27" class="py-name"><a title="Bio.Pathway.Network.species
Bio.Pathway.Reaction.species
Bio.Pathway.System.species" class="py-name" href="#" onclick="return doclink('link-27', 'species', 'link-18');">species</a></tt><tt class="py-op">)</tt> </tt>
<a name="L130"></a><tt class="py-lineno">130</tt> <tt class="py-line"> <tt class="py-keyword">else</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">raise</tt> <tt class="py-name">AttributeError</tt><tt class="py-op">,</tt> <tt class="py-string">"Invalid 0 coefficient in Reaction.reactants"</tt> </tt>
<a name="L132"></a><tt class="py-lineno">132</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">reversible</tt><tt class="py-op">:</tt> </tt>
<a name="L133"></a><tt class="py-lineno">133</tt> <tt class="py-line"> <tt class="py-keyword">return</tt> <tt class="py-name">substrates</tt> <tt class="py-op">+</tt> <tt class="py-string">" <=> "</tt> <tt class="py-op">+</tt> <tt class="py-name">products</tt> </tt>
<a name="L134"></a><tt class="py-lineno">134</tt> <tt class="py-line"> <tt class="py-keyword">else</tt><tt class="py-op">:</tt> </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">substrates</tt> <tt class="py-op">+</tt> <tt class="py-string">" --> "</tt> <tt class="py-op">+</tt> <tt class="py-name">products</tt> </tt>
</div><a name="L136"></a><tt class="py-lineno">136</tt> <tt class="py-line"> </tt>
<a name="Reaction.reverse"></a><div id="Reaction.reverse-def"><a name="L137"></a><tt class="py-lineno">137</tt> <a class="py-toggle" href="#" id="Reaction.reverse-toggle" onclick="return toggle('Reaction.reverse');">-</a><tt class="py-line"> <tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.Pathway.Reaction-class.html#reverse">reverse</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="Reaction.reverse-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="Reaction.reverse-expanded"><a name="L138"></a><tt class="py-lineno">138</tt> <tt class="py-line"> <tt class="py-docstring">"""Returns a new Reaction that is the reverse of self."""</tt> </tt>
<a name="L139"></a><tt class="py-lineno">139</tt> <tt class="py-line"> <tt class="py-name">reactants</tt> <tt class="py-op">=</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">for</tt> <tt class="py-name">r</tt> <tt class="py-keyword">in</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">reactants</tt><tt class="py-op">.</tt><tt id="link-28" 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-28', 'keys', 'link-9');">keys</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
<a name="L141"></a><tt class="py-lineno">141</tt> <tt class="py-line"> <tt class="py-name">reactants</tt><tt class="py-op">[</tt><tt class="py-name">r</tt><tt class="py-op">]</tt> <tt class="py-op">=</tt> <tt class="py-op">-</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">reactants</tt><tt class="py-op">[</tt><tt class="py-name">r</tt><tt class="py-op">]</tt> </tt>
<a name="L142"></a><tt class="py-lineno">142</tt> <tt class="py-line"> <tt class="py-keyword">return</tt> <tt id="link-29" class="py-name"><a title="Bio.Pathway.Reaction" class="py-name" href="#" onclick="return doclink('link-29', 'Reaction', 'link-14');">Reaction</a></tt><tt class="py-op">(</tt><tt class="py-name">reactants</tt><tt class="py-op">,</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">catalysts</tt><tt class="py-op">,</tt> </tt>
<a name="L143"></a><tt class="py-lineno">143</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">reversible</tt><tt class="py-op">,</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-30" class="py-name"><a title="BioSQL.BioSeq.DBSeq.data" class="py-name" href="#" onclick="return doclink('link-30', 'data', 'link-12');">data</a></tt><tt class="py-op">)</tt> </tt>
</div><a name="L144"></a><tt class="py-lineno">144</tt> <tt class="py-line"> </tt>
<a name="Reaction.species"></a><div id="Reaction.species-def"><a name="L145"></a><tt class="py-lineno">145</tt> <a class="py-toggle" href="#" id="Reaction.species-toggle" onclick="return toggle('Reaction.species');">-</a><tt class="py-line"> <tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.Pathway.Reaction-class.html#species">species</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="Reaction.species-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="Reaction.species-expanded"><a name="L146"></a><tt class="py-lineno">146</tt> <tt class="py-line"> <tt class="py-docstring">"""Returns a list of all Species involved in self."""</tt> </tt>
<a name="L147"></a><tt class="py-lineno">147</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">reactants</tt><tt class="py-op">.</tt><tt id="link-31" 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-31', 'keys', 'link-9');">keys</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
</div></div><a name="L148"></a><tt class="py-lineno">148</tt> <tt class="py-line"> </tt>
<a name="L149"></a><tt class="py-lineno">149</tt> <tt class="py-line"> </tt>
<a name="System"></a><div id="System-def"><a name="L150"></a><tt class="py-lineno">150</tt> <a class="py-toggle" href="#" id="System-toggle" onclick="return toggle('System');">-</a><tt class="py-line"><tt class="py-keyword">class</tt> <a class="py-def-name" href="Bio.Pathway.System-class.html">System</a><tt class="py-op">:</tt> </tt>
</div><div id="System-collapsed" style="display:none;" pad="+++" indent="++++"></div><div id="System-expanded"><a name="L151"></a><tt class="py-lineno">151</tt> <tt class="py-line"> <tt class="py-docstring">"""Abstraction for a collection of reactions.</tt> </tt>
<a name="L152"></a><tt class="py-lineno">152</tt> <tt class="py-line"><tt class="py-docstring"></tt> </tt>
<a name="L153"></a><tt class="py-lineno">153</tt> <tt class="py-line"><tt class="py-docstring"> This class is used in the Bio.Pathway framework to represent an arbitrary</tt> </tt>
<a name="L154"></a><tt class="py-lineno">154</tt> <tt class="py-line"><tt class="py-docstring"> collection of reactions without explicitly defined links.</tt> </tt>
<a name="L155"></a><tt class="py-lineno">155</tt> <tt class="py-line"><tt class="py-docstring"></tt> </tt>
<a name="L156"></a><tt class="py-lineno">156</tt> <tt class="py-line"><tt class="py-docstring"> Attributes:</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"> None </tt> </tt>
<a name="L159"></a><tt class="py-lineno">159</tt> <tt class="py-line"><tt class="py-docstring"> """</tt> </tt>
<a name="L160"></a><tt class="py-lineno">160</tt> <tt class="py-line"> </tt>
<a name="System.__init__"></a><div id="System.__init__-def"><a name="L161"></a><tt class="py-lineno">161</tt> <a class="py-toggle" href="#" id="System.__init__-toggle" onclick="return toggle('System.__init__');">-</a><tt class="py-line"> <tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.Pathway.System-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">reactions</tt> <tt class="py-op">=</tt> <tt class="py-op">[</tt><tt class="py-op">]</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="System.__init__-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="System.__init__-expanded"><a name="L162"></a><tt class="py-lineno">162</tt> <tt class="py-line"> <tt class="py-docstring">"""Initializes a new System object."""</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">__reactions</tt> <tt class="py-op">=</tt> <tt id="link-32" class="py-name"><a title="Bio.Pathway.Rep.HashSet
Bio.Pathway.Rep.HashSet.HashSet" class="py-name" href="#" onclick="return doclink('link-32', 'HashSet', 'link-3');">HashSet</a></tt><tt class="py-op">(</tt><tt id="link-33" class="py-name" targets="Method Bio.Pathway.System.reactions()=Bio.Pathway.System-class.html#reactions"><a title="Bio.Pathway.System.reactions" class="py-name" href="#" onclick="return doclink('link-33', 'reactions', 'link-33');">reactions</a></tt><tt class="py-op">)</tt> </tt>
</div><a name="L164"></a><tt class="py-lineno">164</tt> <tt class="py-line"> </tt>
<a name="System.__repr__"></a><div id="System.__repr__-def"><a name="L165"></a><tt class="py-lineno">165</tt> <a class="py-toggle" href="#" id="System.__repr__-toggle" onclick="return toggle('System.__repr__');">-</a><tt class="py-line"> <tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.Pathway.System-class.html#__repr__">__repr__</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="System.__repr__-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="System.__repr__-expanded"><a name="L166"></a><tt class="py-lineno">166</tt> <tt class="py-line"> <tt class="py-docstring">"""Returns a debugging string representation of self."""</tt> </tt>
<a name="L167"></a><tt class="py-lineno">167</tt> <tt class="py-line"> <tt class="py-keyword">return</tt> <tt class="py-string">"System("</tt> <tt class="py-op">+</tt> <tt class="py-string">","</tt><tt class="py-op">.</tt><tt class="py-name">join</tt><tt class="py-op">(</tt><tt id="link-34" class="py-name"><a title="Bio.GFF.FeatureAggregate.map" class="py-name" href="#" onclick="return doclink('link-34', 'map', 'link-19');">map</a></tt><tt class="py-op">(</tt><tt class="py-name">repr</tt><tt class="py-op">,</tt><tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">__reactions</tt><tt class="py-op">.</tt><tt id="link-35" class="py-name"><a title="Bio.Pathway.Rep.HashSet.HashSet.list" class="py-name" href="#" onclick="return doclink('link-35', 'list', 'link-11');">list</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt><tt class="py-op">)</tt><tt class="py-op">)</tt> <tt class="py-op">+</tt> <tt class="py-string">")"</tt> </tt>
</div><a name="L168"></a><tt class="py-lineno">168</tt> <tt class="py-line"> </tt>
<a name="System.__str__"></a><div id="System.__str__-def"><a name="L169"></a><tt class="py-lineno">169</tt> <a class="py-toggle" href="#" id="System.__str__-toggle" onclick="return toggle('System.__str__');">-</a><tt class="py-line"> <tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.Pathway.System-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="System.__str__-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="System.__str__-expanded"><a name="L170"></a><tt class="py-lineno">170</tt> <tt class="py-line"> <tt class="py-docstring">"""Returns a string representation of self."""</tt> </tt>
<a name="L171"></a><tt class="py-lineno">171</tt> <tt class="py-line"> <tt class="py-keyword">return</tt> <tt class="py-string">"System of "</tt> <tt class="py-op">+</tt> <tt class="py-name">str</tt><tt class="py-op">(</tt><tt class="py-name">len</tt><tt class="py-op">(</tt><tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">__reactions</tt><tt class="py-op">)</tt><tt class="py-op">)</tt> <tt class="py-op">+</tt> \ </tt>
<a name="L172"></a><tt class="py-lineno">172</tt> <tt class="py-line"> <tt class="py-string">" reactions involving "</tt> <tt class="py-op">+</tt> <tt class="py-name">str</tt><tt class="py-op">(</tt><tt class="py-name">len</tt><tt class="py-op">(</tt><tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-36" class="py-name"><a title="Bio.Pathway.Network.species
Bio.Pathway.Reaction.species
Bio.Pathway.System.species" class="py-name" href="#" onclick="return doclink('link-36', 'species', 'link-18');">species</a></tt><tt class="py-op">(</tt><tt class="py-op">)</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 class="py-string">" species"</tt> </tt>
</div><a name="L174"></a><tt class="py-lineno">174</tt> <tt class="py-line"> </tt>
<a name="System.add_reaction"></a><div id="System.add_reaction-def"><a name="L175"></a><tt class="py-lineno">175</tt> <a class="py-toggle" href="#" id="System.add_reaction-toggle" onclick="return toggle('System.add_reaction');">-</a><tt class="py-line"> <tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.Pathway.System-class.html#add_reaction">add_reaction</a><tt class="py-op">(</tt><tt class="py-param">self</tt><tt class="py-op">,</tt> <tt class="py-param">reaction</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="System.add_reaction-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="System.add_reaction-expanded"><a name="L176"></a><tt class="py-lineno">176</tt> <tt class="py-line"> <tt class="py-docstring">"""Adds reaction to self."""</tt> </tt>
<a name="L177"></a><tt class="py-lineno">177</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">__reactions</tt><tt class="py-op">.</tt><tt id="link-37" class="py-name" targets="Variable Bio.Affy.CelFile.add=Bio.Affy.CelFile-module.html#add,Method Bio.EUtils.POM.ElementNode.add()=Bio.EUtils.POM.ElementNode-class.html#add,Method Bio.GFF.easy.Location.add()=Bio.GFF.easy.Location-class.html#add,Method Bio.Graphics.BasicChromosome._ChromosomeComponent.add()=Bio.Graphics.BasicChromosome._ChromosomeComponent-class.html#add,Variable Bio.LogisticRegression.add=Bio.LogisticRegression-module.html#add,Variable Bio.MarkovModel.add=Bio.MarkovModel-module.html#add,Variable Bio.MaxEntropy.add=Bio.MaxEntropy-module.html#add,Variable Bio.NaiveBayes.add=Bio.NaiveBayes-module.html#add,Method Bio.Nexus.Nexus.StepMatrix.add()=Bio.Nexus.Nexus.StepMatrix-class.html#add,Method Bio.Nexus.Nodes.Chain.add()=Bio.Nexus.Nodes.Chain-class.html#add,Method Bio.PDB.Entity.Entity.add()=Bio.PDB.Entity.Entity-class.html#add,Method Bio.PDB.Residue.DisorderedResidue.add()=Bio.PDB.Residue.DisorderedResidue-class.html#add,Method Bio.PDB.Residue.Residue.add()=Bio.PDB.Residue.Residue-class.html#add,Method Bio.Pathway.Rep.HashSet.HashSet.add()=Bio.Pathway.Rep.HashSet.HashSet-class.html#add,Method Bio.Restriction.Restriction.RestrictionBatch.add()=Bio.Restriction.Restriction.RestrictionBatch-class.html#add,Variable Bio.Statistics.lowess.add=Bio.Statistics.lowess-module.html#add,Method Bio.config.FormatRegistry.FormatGroup.add()=Bio.config.FormatRegistry.FormatGroup-class.html#add,Method Bio.config.Registry.RegisterableGroup.add()=Bio.config.Registry.RegisterableGroup-class.html#add,Variable Bio.distance.add=Bio.distance-module.html#add,Variable Bio.kNN.add=Bio.kNN-module.html#add,Method Martel.Dispatch.MulticallEnd.add()=Martel.Dispatch.MulticallEnd-class.html#add,Method Martel.Dispatch.MulticallStart.add()=Martel.Dispatch.MulticallStart-class.html#add"><a title="Bio.Affy.CelFile.add
Bio.EUtils.POM.ElementNode.add
Bio.GFF.easy.Location.add
Bio.Graphics.BasicChromosome._ChromosomeComponent.add
Bio.LogisticRegression.add
Bio.MarkovModel.add
Bio.MaxEntropy.add
Bio.NaiveBayes.add
Bio.Nexus.Nexus.StepMatrix.add
Bio.Nexus.Nodes.Chain.add
Bio.PDB.Entity.Entity.add
Bio.PDB.Residue.DisorderedResidue.add
Bio.PDB.Residue.Residue.add
Bio.Pathway.Rep.HashSet.HashSet.add
Bio.Restriction.Restriction.RestrictionBatch.add
Bio.Statistics.lowess.add
Bio.config.FormatRegistry.FormatGroup.add
Bio.config.Registry.RegisterableGroup.add
Bio.distance.add
Bio.kNN.add
Martel.Dispatch.MulticallEnd.add
Martel.Dispatch.MulticallStart.add" class="py-name" href="#" onclick="return doclink('link-37', 'add', 'link-37');">add</a></tt><tt class="py-op">(</tt><tt id="link-38" class="py-name" targets="Method Bio.MetaTool._RecordConsumer.reaction()=Bio.MetaTool._RecordConsumer-class.html#reaction,Variable Bio.MetaTool.metatool_format.reaction=Bio.MetaTool.metatool_format-module.html#reaction"><a title="Bio.MetaTool._RecordConsumer.reaction
Bio.MetaTool.metatool_format.reaction" class="py-name" href="#" onclick="return doclink('link-38', 'reaction', 'link-38');">reaction</a></tt><tt class="py-op">)</tt> </tt>
</div><a name="L178"></a><tt class="py-lineno">178</tt> <tt class="py-line"> </tt>
<a name="System.remove_reaction"></a><div id="System.remove_reaction-def"><a name="L179"></a><tt class="py-lineno">179</tt> <a class="py-toggle" href="#" id="System.remove_reaction-toggle" onclick="return toggle('System.remove_reaction');">-</a><tt class="py-line"> <tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.Pathway.System-class.html#remove_reaction">remove_reaction</a><tt class="py-op">(</tt><tt class="py-param">self</tt><tt class="py-op">,</tt> <tt class="py-param">reaction</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="System.remove_reaction-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="System.remove_reaction-expanded"><a name="L180"></a><tt class="py-lineno">180</tt> <tt class="py-line"> <tt class="py-docstring">"""Removes reaction from self."""</tt> </tt>
<a name="L181"></a><tt class="py-lineno">181</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">__reactions</tt><tt class="py-op">.</tt><tt id="link-39" class="py-name" targets="Method Bio.Crystal.Chain.remove()=Bio.Crystal.Chain-class.html#remove,Method Bio.GFF.GenericTools.TempFile.remove()=Bio.GFF.GenericTools.TempFile-class.html#remove,Method Bio.Graphics.BasicChromosome._ChromosomeComponent.remove()=Bio.Graphics.BasicChromosome._ChromosomeComponent-class.html#remove,Method Bio.Pathway.Rep.HashSet.HashSet.remove()=Bio.Pathway.Rep.HashSet.HashSet-class.html#remove,Method Bio.Restriction.Restriction.RestrictionBatch.remove()=Bio.Restriction.Restriction.RestrictionBatch-class.html#remove,Method Bio.Seq.MutableSeq.remove()=Bio.Seq.MutableSeq-class.html#remove,Method BioSQL.Loader.DatabaseRemover.remove()=BioSQL.Loader.DatabaseRemover-class.html#remove"><a title="Bio.Crystal.Chain.remove
Bio.GFF.GenericTools.TempFile.remove
Bio.Graphics.BasicChromosome._ChromosomeComponent.remove
Bio.Pathway.Rep.HashSet.HashSet.remove
Bio.Restriction.Restriction.RestrictionBatch.remove
Bio.Seq.MutableSeq.remove
BioSQL.Loader.DatabaseRemover.remove" class="py-name" href="#" onclick="return doclink('link-39', 'remove', 'link-39');">remove</a></tt><tt class="py-op">(</tt><tt id="link-40" class="py-name"><a title="Bio.MetaTool._RecordConsumer.reaction
Bio.MetaTool.metatool_format.reaction" class="py-name" href="#" onclick="return doclink('link-40', 'reaction', 'link-38');">reaction</a></tt><tt class="py-op">)</tt> </tt>
</div><a name="L182"></a><tt class="py-lineno">182</tt> <tt class="py-line"> </tt>
<a name="System.reactions"></a><div id="System.reactions-def"><a name="L183"></a><tt class="py-lineno">183</tt> <a class="py-toggle" href="#" id="System.reactions-toggle" onclick="return toggle('System.reactions');">-</a><tt class="py-line"> <tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.Pathway.System-class.html#reactions">reactions</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="System.reactions-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="System.reactions-expanded"><a name="L184"></a><tt class="py-lineno">184</tt> <tt class="py-line"> <tt class="py-docstring">"""Returns a list of the reactions in this system."""</tt> </tt>
<a name="L185"></a><tt class="py-lineno">185</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">__reactions</tt><tt class="py-op">.</tt><tt id="link-41" class="py-name"><a title="Bio.Pathway.Rep.HashSet.HashSet.list" class="py-name" href="#" onclick="return doclink('link-41', 'list', 'link-11');">list</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
</div><a name="L186"></a><tt class="py-lineno">186</tt> <tt class="py-line"> </tt>
<a name="System.species"></a><div id="System.species-def"><a name="L187"></a><tt class="py-lineno">187</tt> <a class="py-toggle" href="#" id="System.species-toggle" onclick="return toggle('System.species');">-</a><tt class="py-line"> <tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.Pathway.System-class.html#species">species</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="System.species-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="System.species-expanded"><a name="L188"></a><tt class="py-lineno">188</tt> <tt class="py-line"> <tt class="py-docstring">"""Returns a list of the species in this system."""</tt> </tt>
<a name="L189"></a><tt class="py-lineno">189</tt> <tt class="py-line"> <tt id="link-42" 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-42', 's', 'link-42');">s</a></tt> <tt class="py-op">=</tt> <tt id="link-43" class="py-name"><a title="Bio.Pathway.Rep.HashSet
Bio.Pathway.Rep.HashSet.HashSet" class="py-name" href="#" onclick="return doclink('link-43', 'HashSet', 'link-3');">HashSet</a></tt><tt class="py-op">(</tt><tt class="py-name">reduce</tt><tt class="py-op">(</tt><tt class="py-keyword">lambda</tt> <tt id="link-44" class="py-name"><a title="Martel.test.test_swissprot38.s" class="py-name" href="#" onclick="return doclink('link-44', 's', 'link-42');">s</a></tt><tt class="py-op">,</tt><tt id="link-45" 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-45', 'x', 'link-45');">x</a></tt><tt class="py-op">:</tt> <tt id="link-46" class="py-name"><a title="Martel.test.test_swissprot38.s" class="py-name" href="#" onclick="return doclink('link-46', 's', 'link-42');">s</a></tt> <tt class="py-op">+</tt> <tt id="link-47" class="py-name"><a title="Bio.MarkovModel.x
Bio.Statistics.lowess.x" class="py-name" href="#" onclick="return doclink('link-47', 'x', 'link-45');">x</a></tt><tt class="py-op">,</tt> </tt>
<a name="L190"></a><tt class="py-lineno">190</tt> <tt class="py-line"> <tt class="py-op">[</tt><tt id="link-48" class="py-name"><a title="Bio.MarkovModel.x
Bio.Statistics.lowess.x" class="py-name" href="#" onclick="return doclink('link-48', 'x', 'link-45');">x</a></tt><tt class="py-op">.</tt><tt id="link-49" class="py-name"><a title="Bio.Pathway.Network.species
Bio.Pathway.Reaction.species
Bio.Pathway.System.species" class="py-name" href="#" onclick="return doclink('link-49', 'species', 'link-18');">species</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt> <tt class="py-keyword">for</tt> <tt id="link-50" class="py-name"><a title="Bio.MarkovModel.x
Bio.Statistics.lowess.x" class="py-name" href="#" onclick="return doclink('link-50', 'x', 'link-45');">x</a></tt> <tt class="py-keyword">in</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-51" class="py-name"><a title="Bio.Pathway.System.reactions" class="py-name" href="#" onclick="return doclink('link-51', 'reactions', 'link-33');">reactions</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt><tt class="py-op">]</tt><tt class="py-op">,</tt> <tt class="py-op">[</tt><tt class="py-op">]</tt><tt class="py-op">)</tt><tt class="py-op">)</tt> </tt>
<a name="L191"></a><tt class="py-lineno">191</tt> <tt class="py-line"> <tt class="py-keyword">return</tt> <tt id="link-52" class="py-name"><a title="Martel.test.test_swissprot38.s" class="py-name" href="#" onclick="return doclink('link-52', 's', 'link-42');">s</a></tt><tt class="py-op">.</tt><tt id="link-53" class="py-name"><a title="Bio.Pathway.Rep.HashSet.HashSet.list" class="py-name" href="#" onclick="return doclink('link-53', 'list', 'link-11');">list</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
</div><a name="L192"></a><tt class="py-lineno">192</tt> <tt class="py-line"> </tt>
<a name="System.stochiometry"></a><div id="System.stochiometry-def"><a name="L193"></a><tt class="py-lineno">193</tt> <a class="py-toggle" href="#" id="System.stochiometry-toggle" onclick="return toggle('System.stochiometry');">-</a><tt class="py-line"> <tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.Pathway.System-class.html#stochiometry">stochiometry</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="System.stochiometry-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="System.stochiometry-expanded"><a name="L194"></a><tt class="py-lineno">194</tt> <tt class="py-line"> <tt class="py-docstring">"""Computes the stoichiometry matrix for self.</tt> </tt>
<a name="L195"></a><tt class="py-lineno">195</tt> <tt class="py-line"><tt class="py-docstring"></tt> </tt>
<a name="L196"></a><tt class="py-lineno">196</tt> <tt class="py-line"><tt class="py-docstring"> Returns (species, reactions, stoch) where</tt> </tt>
<a name="L197"></a><tt class="py-lineno">197</tt> <tt class="py-line"><tt class="py-docstring"></tt> </tt>
<a name="L198"></a><tt class="py-lineno">198</tt> <tt class="py-line"><tt class="py-docstring"> species = ordered list of species in this system</tt> </tt>
<a name="L199"></a><tt class="py-lineno">199</tt> <tt class="py-line"><tt class="py-docstring"> reactions = ordered list of reactions in this system</tt> </tt>
<a name="L200"></a><tt class="py-lineno">200</tt> <tt class="py-line"><tt class="py-docstring"> stoch = 2D array where stoch[i][j] is coef of the</tt> </tt>
<a name="L201"></a><tt class="py-lineno">201</tt> <tt class="py-line"><tt class="py-docstring"> jth species in the ith reaction, as defined</tt> </tt>
<a name="L202"></a><tt class="py-lineno">202</tt> <tt class="py-line"><tt class="py-docstring"> by species and reactions above</tt> </tt>
<a name="L203"></a><tt class="py-lineno">203</tt> <tt class="py-line"><tt class="py-docstring"> """</tt> </tt>
<a name="L204"></a><tt class="py-lineno">204</tt> <tt class="py-line"> <tt class="py-comment"># Note: This an inefficient and ugly temporary implementation.</tt> </tt>
<a name="L205"></a><tt class="py-lineno">205</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-comment"># To be practical, stochiometric matrices should probably</tt> </tt>
<a name="L206"></a><tt class="py-lineno">206</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-comment"># be implemented by sparse matrices, which would require</tt> </tt>
<a name="L207"></a><tt class="py-lineno">207</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-comment"># NumPy dependencies.</tt> </tt>
<a name="L208"></a><tt class="py-lineno">208</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-comment">#</tt> </tt>
<a name="L209"></a><tt class="py-lineno">209</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-comment"># PS: We should implement automatic checking for NumPy here.</tt> </tt>
<a name="L210"></a><tt class="py-lineno">210</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt id="link-54" class="py-name"><a title="Bio.Pathway.Network.species
Bio.Pathway.Reaction.species
Bio.Pathway.System.species" class="py-name" href="#" onclick="return doclink('link-54', 'species', 'link-18');">species</a></tt> <tt class="py-op">=</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-55" class="py-name"><a title="Bio.Pathway.Network.species
Bio.Pathway.Reaction.species
Bio.Pathway.System.species" class="py-name" href="#" onclick="return doclink('link-55', 'species', 'link-18');">species</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
<a name="L211"></a><tt class="py-lineno">211</tt> <tt class="py-line"> <tt id="link-56" class="py-name"><a title="Bio.Pathway.System.reactions" class="py-name" href="#" onclick="return doclink('link-56', 'reactions', 'link-33');">reactions</a></tt> <tt class="py-op">=</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-57" class="py-name"><a title="Bio.Pathway.System.reactions" class="py-name" href="#" onclick="return doclink('link-57', 'reactions', 'link-33');">reactions</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
<a name="L212"></a><tt class="py-lineno">212</tt> <tt class="py-line"> <tt class="py-name">stoch</tt> <tt class="py-op">=</tt> <tt class="py-op">[</tt><tt class="py-op">]</tt> <tt class="py-op">*</tt> <tt class="py-name">len</tt><tt class="py-op">(</tt><tt id="link-58" class="py-name"><a title="Bio.Pathway.System.reactions" class="py-name" href="#" onclick="return doclink('link-58', 'reactions', 'link-33');">reactions</a></tt><tt class="py-op">)</tt> </tt>
<a name="L213"></a><tt class="py-lineno">213</tt> <tt class="py-line"> <tt class="py-keyword">for</tt> <tt id="link-59" 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-59', 'i', 'link-59');">i</a></tt> <tt class="py-keyword">in</tt> <tt class="py-name">range</tt><tt class="py-op">(</tt><tt class="py-name">len</tt><tt class="py-op">(</tt><tt id="link-60" class="py-name"><a title="Bio.Pathway.System.reactions" class="py-name" href="#" onclick="return doclink('link-60', 'reactions', 'link-33');">reactions</a></tt><tt class="py-op">)</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
<a name="L214"></a><tt class="py-lineno">214</tt> <tt class="py-line"> <tt class="py-name">stoch</tt><tt class="py-op">[</tt><tt id="link-61" class="py-name"><a title="Bio.PDB.Polypeptide.i" class="py-name" href="#" onclick="return doclink('link-61', 'i', 'link-59');">i</a></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-name">len</tt><tt class="py-op">(</tt><tt id="link-62" class="py-name"><a title="Bio.Pathway.Network.species
Bio.Pathway.Reaction.species
Bio.Pathway.System.species" class="py-name" href="#" onclick="return doclink('link-62', 'species', 'link-18');">species</a></tt><tt class="py-op">)</tt> </tt>
<a name="L215"></a><tt class="py-lineno">215</tt> <tt class="py-line"> <tt class="py-keyword">for</tt> <tt id="link-63" class="py-name"><a title="Martel.test.test_swissprot38.s" class="py-name" href="#" onclick="return doclink('link-63', 's', 'link-42');">s</a></tt> <tt class="py-keyword">in</tt> <tt id="link-64" class="py-name"><a title="Bio.Pathway.System.reactions" class="py-name" href="#" onclick="return doclink('link-64', 'reactions', 'link-33');">reactions</a></tt><tt class="py-op">[</tt><tt id="link-65" class="py-name"><a title="Bio.PDB.Polypeptide.i" class="py-name" href="#" onclick="return doclink('link-65', 'i', 'link-59');">i</a></tt><tt class="py-op">]</tt><tt class="py-op">.</tt><tt id="link-66" class="py-name"><a title="Bio.Pathway.Network.species
Bio.Pathway.Reaction.species
Bio.Pathway.System.species" class="py-name" href="#" onclick="return doclink('link-66', 'species', 'link-18');">species</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
<a name="L216"></a><tt class="py-lineno">216</tt> <tt class="py-line"> <tt class="py-name">stoch</tt><tt class="py-op">[</tt><tt id="link-67" class="py-name"><a title="Bio.Pathway.Network.species
Bio.Pathway.Reaction.species
Bio.Pathway.System.species" class="py-name" href="#" onclick="return doclink('link-67', 'species', 'link-18');">species</a></tt><tt class="py-op">.</tt><tt id="link-68" 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-68', 'index', 'link-68');">index</a></tt><tt class="py-op">(</tt><tt id="link-69" class="py-name"><a title="Martel.test.test_swissprot38.s" class="py-name" href="#" onclick="return doclink('link-69', 's', 'link-42');">s</a></tt><tt class="py-op">)</tt><tt class="py-op">]</tt> <tt class="py-op">=</tt> <tt id="link-70" class="py-name"><a title="Bio.Pathway.System.reactions" class="py-name" href="#" onclick="return doclink('link-70', 'reactions', 'link-33');">reactions</a></tt><tt class="py-op">[</tt><tt id="link-71" class="py-name"><a title="Bio.PDB.Polypeptide.i" class="py-name" href="#" onclick="return doclink('link-71', 'i', 'link-59');">i</a></tt><tt class="py-op">]</tt><tt class="py-op">.</tt><tt class="py-name">reactants</tt><tt class="py-op">[</tt><tt id="link-72" class="py-name"><a title="Martel.test.test_swissprot38.s" class="py-name" href="#" onclick="return doclink('link-72', 's', 'link-42');">s</a></tt><tt class="py-op">]</tt> </tt>
<a name="L217"></a><tt class="py-lineno">217</tt> <tt class="py-line"> <tt class="py-keyword">return</tt> <tt class="py-op">(</tt><tt id="link-73" class="py-name"><a title="Bio.Pathway.Network.species
Bio.Pathway.Reaction.species
Bio.Pathway.System.species" class="py-name" href="#" onclick="return doclink('link-73', 'species', 'link-18');">species</a></tt><tt class="py-op">,</tt> <tt id="link-74" class="py-name"><a title="Bio.Pathway.System.reactions" class="py-name" href="#" onclick="return doclink('link-74', 'reactions', 'link-33');">reactions</a></tt><tt class="py-op">,</tt> <tt class="py-name">stoch</tt><tt class="py-op">)</tt> </tt>
</div></div><a name="L218"></a><tt class="py-lineno">218</tt> <tt class="py-line"> </tt>
<a name="L219"></a><tt class="py-lineno">219</tt> <tt class="py-line"> </tt>
<a name="Interaction"></a><div id="Interaction-def"><a name="L220"></a><tt class="py-lineno">220</tt> <a class="py-toggle" href="#" id="Interaction-toggle" onclick="return toggle('Interaction');">-</a><tt class="py-line"><tt class="py-keyword">class</tt> <a class="py-def-name" href="Bio.Pathway.Interaction-class.html">Interaction</a><tt class="py-op">:</tt> </tt>
</div><div id="Interaction-collapsed" style="display:none;" pad="+++" indent="++++"></div><div id="Interaction-expanded"><a name="L221"></a><tt class="py-lineno">221</tt> <tt class="py-line"> <tt class="py-docstring">"""An arbitrary interaction between any number of species.</tt> </tt>
<a name="L222"></a><tt class="py-lineno">222</tt> <tt class="py-line"><tt class="py-docstring"></tt> </tt>
<a name="L223"></a><tt class="py-lineno">223</tt> <tt class="py-line"><tt class="py-docstring"> This class definition is inteded solely as a minimal wrapper interface that should</tt> </tt>
<a name="L224"></a><tt class="py-lineno">224</tt> <tt class="py-line"><tt class="py-docstring"> be implemented and extended by more specific abstractions.</tt> </tt>
<a name="L225"></a><tt class="py-lineno">225</tt> <tt class="py-line"><tt class="py-docstring"></tt> </tt>
<a name="L226"></a><tt class="py-lineno">226</tt> <tt class="py-line"><tt class="py-docstring"> Attributes:</tt> </tt>
<a name="L227"></a><tt class="py-lineno">227</tt> <tt class="py-line"><tt class="py-docstring"></tt> </tt>
<a name="L228"></a><tt class="py-lineno">228</tt> <tt class="py-line"><tt class="py-docstring"> data -- reference to arbitrary additional data</tt> </tt>
<a name="L229"></a><tt class="py-lineno">229</tt> <tt class="py-line"><tt class="py-docstring"> """</tt> </tt>
<a name="L230"></a><tt class="py-lineno">230</tt> <tt class="py-line"> </tt>
<a name="Interaction.__init_"></a><div id="Interaction.__init_-def"><a name="L231"></a><tt class="py-lineno">231</tt> <a class="py-toggle" href="#" id="Interaction.__init_-toggle" onclick="return toggle('Interaction.__init_');">-</a><tt class="py-line"> <tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.Pathway.Interaction-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">data</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="Interaction.__init_-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="Interaction.__init_-expanded"><a name="L232"></a><tt class="py-lineno">232</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-75" class="py-name"><a title="BioSQL.BioSeq.DBSeq.data" class="py-name" href="#" onclick="return doclink('link-75', 'data', 'link-12');">data</a></tt> <tt class="py-op">=</tt> <tt id="link-76" class="py-name"><a title="BioSQL.BioSeq.DBSeq.data" class="py-name" href="#" onclick="return doclink('link-76', 'data', 'link-12');">data</a></tt> </tt>
</div><a name="L233"></a><tt class="py-lineno">233</tt> <tt class="py-line"> </tt>
<a name="Interaction.__hash__"></a><div id="Interaction.__hash__-def"><a name="L234"></a><tt class="py-lineno">234</tt> <a class="py-toggle" href="#" id="Interaction.__hash__-toggle" onclick="return toggle('Interaction.__hash__');">-</a><tt class="py-line"> <tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.Pathway.Interaction-class.html#__hash__">__hash__</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="Interaction.__hash__-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="Interaction.__hash__-expanded"><a name="L235"></a><tt class="py-lineno">235</tt> <tt class="py-line"> <tt class="py-docstring">"""Returns a hashcode for self."""</tt> </tt>
<a name="L236"></a><tt class="py-lineno">236</tt> <tt class="py-line"> <tt class="py-keyword">return</tt> <tt class="py-name">hash</tt><tt class="py-op">(</tt><tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-77" class="py-name"><a title="BioSQL.BioSeq.DBSeq.data" class="py-name" href="#" onclick="return doclink('link-77', 'data', 'link-12');">data</a></tt><tt class="py-op">)</tt> </tt>
</div><a name="L237"></a><tt class="py-lineno">237</tt> <tt class="py-line"> </tt>
<a name="Interaction.__repr__"></a><div id="Interaction.__repr__-def"><a name="L238"></a><tt class="py-lineno">238</tt> <a class="py-toggle" href="#" id="Interaction.__repr__-toggle" onclick="return toggle('Interaction.__repr__');">-</a><tt class="py-line"> <tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.Pathway.Interaction-class.html#__repr__">__repr__</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="Interaction.__repr__-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="Interaction.__repr__-expanded"><a name="L239"></a><tt class="py-lineno">239</tt> <tt class="py-line"> <tt class="py-docstring">"""Returns a debugging string representation of self."""</tt> </tt>
<a name="L240"></a><tt class="py-lineno">240</tt> <tt class="py-line"> <tt class="py-keyword">return</tt> <tt class="py-string">"Interaction("</tt> <tt class="py-op">+</tt> <tt class="py-name">repr</tt><tt class="py-op">(</tt><tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-78" class="py-name"><a title="BioSQL.BioSeq.DBSeq.data" class="py-name" href="#" onclick="return doclink('link-78', 'data', 'link-12');">data</a></tt><tt class="py-op">)</tt> <tt class="py-op">+</tt> <tt class="py-string">")"</tt> </tt>
</div><a name="L241"></a><tt class="py-lineno">241</tt> <tt class="py-line"> </tt>
<a name="Interaction.__str__"></a><div id="Interaction.__str__-def"><a name="L242"></a><tt class="py-lineno">242</tt> <a class="py-toggle" href="#" id="Interaction.__str__-toggle" onclick="return toggle('Interaction.__str__');">-</a><tt class="py-line"> <tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.Pathway.Interaction-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="Interaction.__str__-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="Interaction.__str__-expanded"><a name="L243"></a><tt class="py-lineno">243</tt> <tt class="py-line"> <tt class="py-docstring">"""Returns a string representation of self."""</tt> </tt>
<a name="L244"></a><tt class="py-lineno">244</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">str</tt><tt class="py-op">(</tt><tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-79" class="py-name"><a title="BioSQL.BioSeq.DBSeq.data" class="py-name" href="#" onclick="return doclink('link-79', 'data', 'link-12');">data</a></tt><tt class="py-op">)</tt> <tt class="py-op">+</tt> <tt class="py-string">">"</tt> </tt>
</div></div><a name="L245"></a><tt class="py-lineno">245</tt> <tt class="py-line"> </tt>
<a name="L246"></a><tt class="py-lineno">246</tt> <tt class="py-line"> </tt>
<a name="Network"></a><div id="Network-def"><a name="L247"></a><tt class="py-lineno">247</tt> <a class="py-toggle" href="#" id="Network-toggle" onclick="return toggle('Network');">-</a><tt class="py-line"><tt class="py-keyword">class</tt> <a class="py-def-name" href="Bio.Pathway.Network-class.html">Network</a><tt class="py-op">:</tt> </tt>
</div><div id="Network-collapsed" style="display:none;" pad="+++" indent="++++"></div><div id="Network-expanded"><a name="L248"></a><tt class="py-lineno">248</tt> <tt class="py-line"> <tt class="py-docstring">"""A set of species that are explicitly linked by interactions.</tt> </tt>
<a name="L249"></a><tt class="py-lineno">249</tt> <tt class="py-line"><tt class="py-docstring"></tt> </tt>
<a name="L250"></a><tt class="py-lineno">250</tt> <tt class="py-line"><tt class="py-docstring"> The network is a directed multigraph with labeled edges. The nodes in the graph</tt> </tt>
<a name="L251"></a><tt class="py-lineno">251</tt> <tt class="py-line"><tt class="py-docstring"> are the biochemical species involved. The edges represent an interaction between</tt> </tt>
<a name="L252"></a><tt class="py-lineno">252</tt> <tt class="py-line"><tt class="py-docstring"> two species, and the edge label is a reference to the associated Interaction</tt> </tt>
<a name="L253"></a><tt class="py-lineno">253</tt> <tt class="py-line"><tt class="py-docstring"> object.</tt> </tt>
<a name="L254"></a><tt class="py-lineno">254</tt> <tt class="py-line"><tt class="py-docstring"></tt> </tt>
<a name="L255"></a><tt class="py-lineno">255</tt> <tt class="py-line"><tt class="py-docstring"> Attributes:</tt> </tt>
<a name="L256"></a><tt class="py-lineno">256</tt> <tt class="py-line"><tt class="py-docstring"></tt> </tt>
<a name="L257"></a><tt class="py-lineno">257</tt> <tt class="py-line"><tt class="py-docstring"> None</tt> </tt>
<a name="L258"></a><tt class="py-lineno">258</tt> <tt class="py-line"><tt class="py-docstring"> </tt> </tt>
<a name="L259"></a><tt class="py-lineno">259</tt> <tt class="py-line"><tt class="py-docstring"> """</tt> </tt>
<a name="L260"></a><tt class="py-lineno">260</tt> <tt class="py-line"> </tt>
<a name="Network.__init__"></a><div id="Network.__init__-def"><a name="L261"></a><tt class="py-lineno">261</tt> <a class="py-toggle" href="#" id="Network.__init__-toggle" onclick="return toggle('Network.__init__');">-</a><tt class="py-line"> <tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.Pathway.Network-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">species</tt> <tt class="py-op">=</tt> <tt class="py-op">[</tt><tt class="py-op">]</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="Network.__init__-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="Network.__init__-expanded"><a name="L262"></a><tt class="py-lineno">262</tt> <tt class="py-line"> <tt class="py-docstring">"""Initializes a new Network object."""</tt> </tt>
<a name="L263"></a><tt class="py-lineno">263</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">__graph</tt> <tt class="py-op">=</tt> <tt id="link-80" class="py-name"><a title="Bio.Pathway.Rep.MultiGraph
Bio.Pathway.Rep.MultiGraph.MultiGraph" class="py-name" href="#" onclick="return doclink('link-80', 'MultiGraph', 'link-7');">MultiGraph</a></tt><tt class="py-op">(</tt><tt id="link-81" class="py-name"><a title="Bio.Pathway.Network.species
Bio.Pathway.Reaction.species
Bio.Pathway.System.species" class="py-name" href="#" onclick="return doclink('link-81', 'species', 'link-18');">species</a></tt><tt class="py-op">)</tt> </tt>
</div><a name="L264"></a><tt class="py-lineno">264</tt> <tt class="py-line"> </tt>
<a name="Network.__repr__"></a><div id="Network.__repr__-def"><a name="L265"></a><tt class="py-lineno">265</tt> <a class="py-toggle" href="#" id="Network.__repr__-toggle" onclick="return toggle('Network.__repr__');">-</a><tt class="py-line"> <tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.Pathway.Network-class.html#__repr__">__repr__</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="Network.__repr__-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="Network.__repr__-expanded"><a name="L266"></a><tt class="py-lineno">266</tt> <tt class="py-line"> <tt class="py-docstring">"""Returns a debugging string representation of this network."""</tt> </tt>
<a name="L267"></a><tt class="py-lineno">267</tt> <tt class="py-line"> <tt class="py-keyword">return</tt> <tt class="py-string">"<Network: __graph: "</tt> <tt class="py-op">+</tt> <tt class="py-name">repr</tt><tt class="py-op">(</tt><tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">__graph</tt><tt class="py-op">)</tt> <tt class="py-op">+</tt> <tt class="py-string">">"</tt> </tt>
</div><a name="L268"></a><tt class="py-lineno">268</tt> <tt class="py-line"> </tt>
<a name="Network.__str__"></a><div id="Network.__str__-def"><a name="L269"></a><tt class="py-lineno">269</tt> <a class="py-toggle" href="#" id="Network.__str__-toggle" onclick="return toggle('Network.__str__');">-</a><tt class="py-line"> <tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.Pathway.Network-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="Network.__str__-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="Network.__str__-expanded"><a name="L270"></a><tt class="py-lineno">270</tt> <tt class="py-line"> <tt class="py-docstring">"""Returns a string representation of this network."""</tt> </tt>
<a name="L271"></a><tt class="py-lineno">271</tt> <tt class="py-line"> <tt class="py-keyword">return</tt> <tt class="py-string">"Network of "</tt> <tt class="py-op">+</tt> <tt class="py-name">str</tt><tt class="py-op">(</tt><tt class="py-name">len</tt><tt class="py-op">(</tt><tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-82" class="py-name"><a title="Bio.Pathway.Network.species
Bio.Pathway.Reaction.species
Bio.Pathway.System.species" class="py-name" href="#" onclick="return doclink('link-82', 'species', 'link-18');">species</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt><tt class="py-op">)</tt><tt class="py-op">)</tt> <tt class="py-op">+</tt> <tt class="py-string">" species and "</tt> <tt class="py-op">+</tt> \ </tt>
<a name="L272"></a><tt class="py-lineno">272</tt> <tt class="py-line"> <tt class="py-name">str</tt><tt class="py-op">(</tt><tt class="py-name">len</tt><tt class="py-op">(</tt><tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-83" class="py-name" targets="Method Bio.Pathway.Network.interactions()=Bio.Pathway.Network-class.html#interactions"><a title="Bio.Pathway.Network.interactions" class="py-name" href="#" onclick="return doclink('link-83', 'interactions', 'link-83');">interactions</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt><tt class="py-op">)</tt><tt class="py-op">)</tt> <tt class="py-op">+</tt> <tt class="py-string">" interactions."</tt> </tt>
</div><a name="L273"></a><tt class="py-lineno">273</tt> <tt class="py-line"> </tt>
<a name="Network.add_species"></a><div id="Network.add_species-def"><a name="L274"></a><tt class="py-lineno">274</tt> <a class="py-toggle" href="#" id="Network.add_species-toggle" onclick="return toggle('Network.add_species');">-</a><tt class="py-line"> <tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.Pathway.Network-class.html#add_species">add_species</a><tt class="py-op">(</tt><tt class="py-param">self</tt><tt class="py-op">,</tt> <tt class="py-param">species</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="Network.add_species-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="Network.add_species-expanded"><a name="L275"></a><tt class="py-lineno">275</tt> <tt class="py-line"> <tt class="py-docstring">"""Adds species to this network."""</tt> </tt>
<a name="L276"></a><tt class="py-lineno">276</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">__graph</tt><tt class="py-op">.</tt><tt id="link-84" class="py-name" targets="Method Bio.Pathway.Rep.Graph.Graph.add_node()=Bio.Pathway.Rep.Graph.Graph-class.html#add_node,Method Bio.Pathway.Rep.MultiGraph.MultiGraph.add_node()=Bio.Pathway.Rep.MultiGraph.MultiGraph-class.html#add_node"><a title="Bio.Pathway.Rep.Graph.Graph.add_node
Bio.Pathway.Rep.MultiGraph.MultiGraph.add_node" class="py-name" href="#" onclick="return doclink('link-84', 'add_node', 'link-84');">add_node</a></tt><tt class="py-op">(</tt><tt id="link-85" class="py-name"><a title="Bio.Pathway.Network.species
Bio.Pathway.Reaction.species
Bio.Pathway.System.species" class="py-name" href="#" onclick="return doclink('link-85', 'species', 'link-18');">species</a></tt><tt class="py-op">)</tt> </tt>
</div><a name="L277"></a><tt class="py-lineno">277</tt> <tt class="py-line"> </tt>
<a name="Network.add_interaction"></a><div id="Network.add_interaction-def"><a name="L278"></a><tt class="py-lineno">278</tt> <a class="py-toggle" href="#" id="Network.add_interaction-toggle" onclick="return toggle('Network.add_interaction');">-</a><tt class="py-line"> <tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.Pathway.Network-class.html#add_interaction">add_interaction</a><tt class="py-op">(</tt><tt class="py-param">self</tt><tt class="py-op">,</tt> <tt class="py-param">source</tt><tt class="py-op">,</tt> <tt class="py-param">sink</tt><tt class="py-op">,</tt> <tt class="py-param">interaction</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="Network.add_interaction-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="Network.add_interaction-expanded"><a name="L279"></a><tt class="py-lineno">279</tt> <tt class="py-line"> <tt class="py-docstring">"""Adds interaction to this network."""</tt> </tt>
<a name="L280"></a><tt class="py-lineno">280</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">__graph</tt><tt class="py-op">.</tt><tt id="link-86" class="py-name" targets="Method Bio.Pathway.Rep.Graph.Graph.add_edge()=Bio.Pathway.Rep.Graph.Graph-class.html#add_edge,Method Bio.Pathway.Rep.MultiGraph.MultiGraph.add_edge()=Bio.Pathway.Rep.MultiGraph.MultiGraph-class.html#add_edge"><a title="Bio.Pathway.Rep.Graph.Graph.add_edge
Bio.Pathway.Rep.MultiGraph.MultiGraph.add_edge" class="py-name" href="#" onclick="return doclink('link-86', 'add_edge', 'link-86');">add_edge</a></tt><tt class="py-op">(</tt><tt id="link-87" class="py-name" targets="Method Bio.GenBank._FeatureConsumer.source()=Bio.GenBank._FeatureConsumer-class.html#source,Method Bio.GenBank._RecordConsumer.source()=Bio.GenBank._RecordConsumer-class.html#source,Method Bio.Medline._RecordConsumer.source()=Bio.Medline._RecordConsumer-class.html#source,Method Bio.Pathway.Network.source()=Bio.Pathway.Network-class.html#source,Method Bio.Rebase._RecordConsumer.source()=Bio.Rebase._RecordConsumer-class.html#source"><a title="Bio.GenBank._FeatureConsumer.source
Bio.GenBank._RecordConsumer.source
Bio.Medline._RecordConsumer.source
Bio.Pathway.Network.source
Bio.Rebase._RecordConsumer.source" class="py-name" href="#" onclick="return doclink('link-87', 'source', 'link-87');">source</a></tt><tt class="py-op">,</tt> <tt id="link-88" class="py-name" targets="Method Bio.Pathway.Network.sink()=Bio.Pathway.Network-class.html#sink"><a title="Bio.Pathway.Network.sink" class="py-name" href="#" onclick="return doclink('link-88', 'sink', 'link-88');">sink</a></tt><tt class="py-op">,</tt> <tt class="py-name">interaction</tt><tt class="py-op">)</tt> </tt>
</div><a name="L281"></a><tt class="py-lineno">281</tt> <tt class="py-line"> </tt>
<a name="Network.source"></a><div id="Network.source-def"><a name="L282"></a><tt class="py-lineno">282</tt> <a class="py-toggle" href="#" id="Network.source-toggle" onclick="return toggle('Network.source');">-</a><tt class="py-line"> <tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.Pathway.Network-class.html#source">source</a><tt class="py-op">(</tt><tt class="py-param">self</tt><tt class="py-op">,</tt> <tt class="py-param">species</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="Network.source-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="Network.source-expanded"><a name="L283"></a><tt class="py-lineno">283</tt> <tt class="py-line"> <tt class="py-docstring">"""Returns list of unique sources for species."""</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">__graph</tt><tt class="py-op">.</tt><tt id="link-89" class="py-name" targets="Method Bio.Pathway.Rep.Graph.Graph.parents()=Bio.Pathway.Rep.Graph.Graph-class.html#parents,Method Bio.Pathway.Rep.MultiGraph.MultiGraph.parents()=Bio.Pathway.Rep.MultiGraph.MultiGraph-class.html#parents"><a title="Bio.Pathway.Rep.Graph.Graph.parents
Bio.Pathway.Rep.MultiGraph.MultiGraph.parents" class="py-name" href="#" onclick="return doclink('link-89', 'parents', 'link-89');">parents</a></tt><tt class="py-op">(</tt><tt id="link-90" class="py-name"><a title="Bio.Pathway.Network.species
Bio.Pathway.Reaction.species
Bio.Pathway.System.species" class="py-name" href="#" onclick="return doclink('link-90', 'species', 'link-18');">species</a></tt><tt class="py-op">)</tt> </tt>
</div><a name="L285"></a><tt class="py-lineno">285</tt> <tt class="py-line"> </tt>
<a name="Network.source_interactions"></a><div id="Network.source_interactions-def"><a name="L286"></a><tt class="py-lineno">286</tt> <a class="py-toggle" href="#" id="Network.source_interactions-toggle" onclick="return toggle('Network.source_interactions');">-</a><tt class="py-line"> <tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.Pathway.Network-class.html#source_interactions">source_interactions</a><tt class="py-op">(</tt><tt class="py-param">self</tt><tt class="py-op">,</tt> <tt class="py-param">species</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="Network.source_interactions-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="Network.source_interactions-expanded"><a name="L287"></a><tt class="py-lineno">287</tt> <tt class="py-line"> <tt class="py-docstring">"""Returns list of (source, interaction) pairs for species."""</tt> </tt>
<a name="L288"></a><tt class="py-lineno">288</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">__graph</tt><tt class="py-op">.</tt><tt id="link-91" class="py-name" targets="Method Bio.Pathway.Rep.Graph.Graph.parent_edges()=Bio.Pathway.Rep.Graph.Graph-class.html#parent_edges,Method Bio.Pathway.Rep.MultiGraph.MultiGraph.parent_edges()=Bio.Pathway.Rep.MultiGraph.MultiGraph-class.html#parent_edges"><a title="Bio.Pathway.Rep.Graph.Graph.parent_edges
Bio.Pathway.Rep.MultiGraph.MultiGraph.parent_edges" class="py-name" href="#" onclick="return doclink('link-91', 'parent_edges', 'link-91');">parent_edges</a></tt><tt class="py-op">(</tt><tt id="link-92" class="py-name"><a title="Bio.Pathway.Network.species
Bio.Pathway.Reaction.species
Bio.Pathway.System.species" class="py-name" href="#" onclick="return doclink('link-92', 'species', 'link-18');">species</a></tt><tt class="py-op">)</tt> </tt>
</div><a name="L289"></a><tt class="py-lineno">289</tt> <tt class="py-line"> </tt>
<a name="Network.sink"></a><div id="Network.sink-def"><a name="L290"></a><tt class="py-lineno">290</tt> <a class="py-toggle" href="#" id="Network.sink-toggle" onclick="return toggle('Network.sink');">-</a><tt class="py-line"> <tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.Pathway.Network-class.html#sink">sink</a><tt class="py-op">(</tt><tt class="py-param">self</tt><tt class="py-op">,</tt> <tt class="py-param">species</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="Network.sink-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="Network.sink-expanded"><a name="L291"></a><tt class="py-lineno">291</tt> <tt class="py-line"> <tt class="py-docstring">"""Returns list of unique sinks for species."""</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 class="py-name">__graph</tt><tt class="py-op">.</tt><tt id="link-93" 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-93', 'children', 'link-93');">children</a></tt><tt class="py-op">(</tt><tt id="link-94" class="py-name"><a title="Bio.Pathway.Network.species
Bio.Pathway.Reaction.species
Bio.Pathway.System.species" class="py-name" href="#" onclick="return doclink('link-94', 'species', 'link-18');">species</a></tt><tt class="py-op">)</tt> </tt>
</div><a name="L293"></a><tt class="py-lineno">293</tt> <tt class="py-line"> </tt>
<a name="Network.sink_interactions"></a><div id="Network.sink_interactions-def"><a name="L294"></a><tt class="py-lineno">294</tt> <a class="py-toggle" href="#" id="Network.sink_interactions-toggle" onclick="return toggle('Network.sink_interactions');">-</a><tt class="py-line"> <tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.Pathway.Network-class.html#sink_interactions">sink_interactions</a><tt class="py-op">(</tt><tt class="py-param">self</tt><tt class="py-op">,</tt> <tt class="py-param">species</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="Network.sink_interactions-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="Network.sink_interactions-expanded"><a name="L295"></a><tt class="py-lineno">295</tt> <tt class="py-line"> <tt class="py-docstring">"""Returns list of (sink, interaction) pairs for species."""</tt> </tt>
<a name="L296"></a><tt class="py-lineno">296</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">__graph</tt><tt class="py-op">.</tt><tt id="link-95" class="py-name" targets="Method Bio.Pathway.Rep.Graph.Graph.child_edges()=Bio.Pathway.Rep.Graph.Graph-class.html#child_edges,Method Bio.Pathway.Rep.MultiGraph.MultiGraph.child_edges()=Bio.Pathway.Rep.MultiGraph.MultiGraph-class.html#child_edges"><a title="Bio.Pathway.Rep.Graph.Graph.child_edges
Bio.Pathway.Rep.MultiGraph.MultiGraph.child_edges" class="py-name" href="#" onclick="return doclink('link-95', 'child_edges', 'link-95');">child_edges</a></tt><tt class="py-op">(</tt><tt id="link-96" class="py-name"><a title="Bio.Pathway.Network.species
Bio.Pathway.Reaction.species
Bio.Pathway.System.species" class="py-name" href="#" onclick="return doclink('link-96', 'species', 'link-18');">species</a></tt><tt class="py-op">)</tt> </tt>
</div><a name="L297"></a><tt class="py-lineno">297</tt> <tt class="py-line"> </tt>
<a name="Network.species"></a><div id="Network.species-def"><a name="L298"></a><tt class="py-lineno">298</tt> <a class="py-toggle" href="#" id="Network.species-toggle" onclick="return toggle('Network.species');">-</a><tt class="py-line"> <tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.Pathway.Network-class.html#species">species</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="Network.species-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="Network.species-expanded"><a name="L299"></a><tt class="py-lineno">299</tt> <tt class="py-line"> <tt class="py-docstring">"""Returns list of the species in this network."""</tt> </tt>
<a name="L300"></a><tt class="py-lineno">300</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">__graph</tt><tt class="py-op">.</tt><tt id="link-97" 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-97', 'nodes', 'link-97');">nodes</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
</div><a name="L301"></a><tt class="py-lineno">301</tt> <tt class="py-line"> </tt>
<a name="Network.interactions"></a><div id="Network.interactions-def"><a name="L302"></a><tt class="py-lineno">302</tt> <a class="py-toggle" href="#" id="Network.interactions-toggle" onclick="return toggle('Network.interactions');">-</a><tt class="py-line"> <tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.Pathway.Network-class.html#interactions">interactions</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="Network.interactions-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="Network.interactions-expanded"><a name="L303"></a><tt class="py-lineno">303</tt> <tt class="py-line"> <tt class="py-docstring">"""Returns list of the unique interactions in this network."""</tt> </tt>
<a name="L304"></a><tt class="py-lineno">304</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">__graph</tt><tt class="py-op">.</tt><tt id="link-98" class="py-name" targets="Method Bio.Pathway.Rep.Graph.Graph.labels()=Bio.Pathway.Rep.Graph.Graph-class.html#labels,Method Bio.Pathway.Rep.MultiGraph.MultiGraph.labels()=Bio.Pathway.Rep.MultiGraph.MultiGraph-class.html#labels"><a title="Bio.Pathway.Rep.Graph.Graph.labels
Bio.Pathway.Rep.MultiGraph.MultiGraph.labels" class="py-name" href="#" onclick="return doclink('link-98', 'labels', 'link-98');">labels</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
</div></div><a name="L305"></a><tt class="py-lineno">305</tt> <tt class="py-line"> </tt><script type="text/javascript">
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