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3 <title>MayaChemTools:Documentation:Graph::CyclesDetection.pm</title>
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15 <tr align="left" valign="top"><td width="33%" align="left"><a href="./TopologicalPharmacophoreAtomTripletsFingerprints.html" title="TopologicalPharmacophoreAtomTripletsFingerprints.html">Previous</a>&nbsp;&nbsp;<a href="./index.html" title="Table of Contents">TOC</a>&nbsp;&nbsp;<a href="./GraphMatrix.html" title="GraphMatrix.html">Next</a></td><td width="34%" align="middle"><strong>Graph::CyclesDetection.pm</strong></td><td width="33%" align="right"><a href="././code/CyclesDetection.html" title="View source code">Code</a>&nbsp;|&nbsp;<a href="./../pdf/CyclesDetection.pdf" title="PDF US Letter Size">PDF</a>&nbsp;|&nbsp;<a href="./../pdfgreen/CyclesDetection.pdf" title="PDF US Letter Size with narrow margins: www.changethemargins.com">PDFGreen</a>&nbsp;|&nbsp;<a href="./../pdfa4/CyclesDetection.pdf" title="PDF A4 Size">PDFA4</a>&nbsp;|&nbsp;<a href="./../pdfa4green/CyclesDetection.pdf" title="PDF A4 Size with narrow margins: www.changethemargins.com">PDFA4Green</a></td></tr>
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17 </div>
18 <p>
19 </p>
20 <h2>NAME</h2>
21 <p>CyclesDetection</p>
22 <p>
23 </p>
24 <h2>SYNOPSIS</h2>
25 <p>use Graph::CyclesDetection;</p>
26 <p>use Graph::CyclesDetection qw(:all);</p>
27 <p>
28 </p>
29 <h2>DESCRIPTION</h2>
30 <p><strong>CyclesDetection</strong> class provides the following methods:</p>
31 <p> <a href="#new">new</a>, <a href="#copy">Copy</a>, <a href="#detectcycles">DetectCycles</a>, <a href="#detectcyclesusingcollapsingpathgraphmethodology">DetectCyclesUsingCollapsingPathGraphMethodology</a>
32 , <a href="#getallcyclicpaths">GetAllCyclicPaths</a>, <a href="#getindependentcyclicpaths">GetIndependentCyclicPaths</a>, <a href="#stringifycyclesdetection">StringifyCyclesDetection</a>
33 </p><p>Cycles in a <strong>Graph</strong> are detected using collapsing path graph [Ref 31]
34 methodology.</p>
35 <p>
36 </p>
37 <h2>METHODS</h2>
38 <dl>
39 <dt><strong><a name="new" class="item"><strong>new</strong></a></strong></dt>
40 <dd>
41 <div class="OptionsBox">
42 $NewCyclesDetection = new Graph::CyclesDetection($Graph);</div>
43 <p>Using specified <em>Graph</em>, <strong>new</strong> method creates a new <strong>CyclesDetection</strong> object and returns
44 newly created <strong>CyclesDetection</strong> object.</p>
45 </dd>
46 <dt><strong><a name="copy" class="item"><strong>Copy</strong></a></strong></dt>
47 <dd>
48 <div class="OptionsBox">
49 $NewCyclesDetection = $CyclesDetection-&gt;Copy();</div>
50 <p>Copies <em>CyclesDetection</em> and its associated data using <strong>Storable::dclone</strong> and returns a new
51 <strong>CyclesDetection</strong> object.</p>
52 </dd>
53 <dt><strong><a name="detectcycles" class="item"><strong>DetectCycles</strong></a></strong></dt>
54 <dd>
55 <div class="OptionsBox">
56 $CyclesDetection-&gt;DetectCycles();</div>
57 <p>Detects all cycles in a graph and returns <em>CyclesDetection</em>.</p>
58 </dd>
59 <dt><strong><a name="detectcyclesusingcollapsingpathgraphmethodology" class="item"><strong>DetectCyclesUsingCollapsingPathGraphMethodology</strong></a></strong></dt>
60 <dd>
61 <div class="OptionsBox">
62 $CyclesDetection-&gt;DetectCyclesUsingCollapsingPathGraphMethodology();</div>
63 <p>Detects all cycles in a graph using collapsing path graph [Ref 31] methodology
64 and returns <em>CyclesDetection</em>.</p>
65 </dd>
66 <dt><strong><a name="getallcyclicpaths" class="item"><strong>GetAllCyclicPaths</strong></a></strong></dt>
67 <dd>
68 <div class="OptionsBox">
69 @AllCyclicPaths = $CyclesDetection-&gt;GetAllCyclicPaths();
70 <br/> $NumOfAllCyclicPaths = $CyclesDetection-&gt;GetAllCyclicPaths();</div>
71 <p>Returns an array containing references to all cyclic paths identified during cycles
72 detection. In scalar text, number of cycles is returned.</p>
73 </dd>
74 <dt><strong><a name="getindependentcyclicpaths" class="item"><strong>GetIndependentCyclicPaths</strong></a></strong></dt>
75 <dd>
76 <div class="OptionsBox">
77 @IndependentCyclicPaths = $CyclesDetection-&gt;GetAllCyclicPaths();
78 <br/> $NumOfIndependentCyclicPaths = $CyclesDetection-&gt;GetAllCyclicPaths();</div>
79 <p>Returns an array containing references to independent cyclic paths identified during cycles
80 detection. In scalar text, number of cycles is returned.</p>
81 <p>A set of independent cycles identified during cycles detection doesn't correspond to the basis set of
82 rings or smallest set of smallest rings (SSSR) [ Refs 29-30 ]; instead, set of cycles indentified
83 as independent cycles simply correpond to cycles which contain no other cycle as their
84 subcycles and can't be described as a linear combination of smaller cycles. And it also happens
85 to contain all the rings in basis set of rings and SSSR. In other words, it's a superset of a basis set
86 of cycles and SSSR. For example, six four membered cycles are indentified for cubane, which is one
87 more than the basis set of cycles.</p>
88 </dd>
89 <dt><strong><a name="stringifycyclesdetection" class="item"><strong>StringifyCyclesDetection</strong></a></strong></dt>
90 <dd>
91 <div class="OptionsBox">
92 $String = $CyclesDetection-&gt;StringifyCyclesDetection();</div>
93 <p>Returns a string containing information about <em>CyclesDetection</em> object.</p>
94 </dd>
95 </dl>
96 <p>
97 </p>
98 <h2>AUTHOR</h2>
99 <p><a href="mailto:msud@san.rr.com">Manish Sud</a></p>
100 <p>
101 </p>
102 <h2>SEE ALSO</h2>
103 <p><a href="./Graph.html">Graph.pm</a>,&nbsp<a href="./Path.html">Path.pm</a>,&nbsp<a href="./PathGraph.html">PathGraph.pm</a>
104 </p>
105 <p>
106 </p>
107 <h2>COPYRIGHT</h2>
108 <p>Copyright (C) 2015 Manish Sud. All rights reserved.</p>
109 <p>This file is part of MayaChemTools.</p>
110 <p>MayaChemTools is free software; you can redistribute it and/or modify it under
111 the terms of the GNU Lesser General Public License as published by the Free
112 Software Foundation; either version 3 of the License, or (at your option)
113 any later version.</p>
114 <p>&nbsp</p><p>&nbsp</p><div class="DocNav">
115 <table width="100%" border=0 cellpadding=0 cellspacing=2>
116 <tr align="left" valign="top"><td width="33%" align="left"><a href="./TopologicalPharmacophoreAtomTripletsFingerprints.html" title="TopologicalPharmacophoreAtomTripletsFingerprints.html">Previous</a>&nbsp;&nbsp;<a href="./index.html" title="Table of Contents">TOC</a>&nbsp;&nbsp;<a href="./GraphMatrix.html" title="GraphMatrix.html">Next</a></td><td width="34%" align="middle"><strong>March 29, 2015</strong></td><td width="33%" align="right"><strong>Graph::CyclesDetection.pm</strong></td></tr>
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