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3 <title>MayaChemTools:Documentation:Graph::CyclesDetection.pm</title>
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14 <table width="100%" border=0 cellpadding=0 cellspacing=2>
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15 <tr align="left" valign="top"><td width="33%" align="left"><a href="./TopologicalPharmacophoreAtomTripletsFingerprints.html" title="TopologicalPharmacophoreAtomTripletsFingerprints.html">Previous</a> <a href="./index.html" title="Table of Contents">TOC</a> <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> | <a href="./../pdf/CyclesDetection.pdf" title="PDF US Letter Size">PDF</a> | <a href="./../pdfgreen/CyclesDetection.pdf" title="PDF US Letter Size with narrow margins: www.changethemargins.com">PDFGreen</a> | <a href="./../pdfa4/CyclesDetection.pdf" title="PDF A4 Size">PDFA4</a> | <a href="./../pdfa4green/CyclesDetection.pdf" title="PDF A4 Size with narrow margins: www.changethemargins.com">PDFA4Green</a></td></tr>
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16 </table>
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17 </div>
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18 <p>
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19 </p>
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20 <h2>NAME</h2>
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21 <p>CyclesDetection</p>
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22 <p>
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23 </p>
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24 <h2>SYNOPSIS</h2>
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25 <p>use Graph::CyclesDetection;</p>
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26 <p>use Graph::CyclesDetection qw(:all);</p>
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27 <p>
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28 </p>
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29 <h2>DESCRIPTION</h2>
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30 <p><strong>CyclesDetection</strong> class provides the following methods:</p>
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31 <p> <a href="#new">new</a>, <a href="#copy">Copy</a>, <a href="#detectcycles">DetectCycles</a>, <a href="#detectcyclesusingcollapsingpathgraphmethodology">DetectCyclesUsingCollapsingPathGraphMethodology</a>
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32 , <a href="#getallcyclicpaths">GetAllCyclicPaths</a>, <a href="#getindependentcyclicpaths">GetIndependentCyclicPaths</a>, <a href="#stringifycyclesdetection">StringifyCyclesDetection</a>
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33 </p><p>Cycles in a <strong>Graph</strong> are detected using collapsing path graph [Ref 31]
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34 methodology.</p>
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35 <p>
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36 </p>
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37 <h2>METHODS</h2>
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38 <dl>
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39 <dt><strong><a name="new" class="item"><strong>new</strong></a></strong></dt>
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40 <dd>
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41 <div class="OptionsBox">
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42 $NewCyclesDetection = new Graph::CyclesDetection($Graph);</div>
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43 <p>Using specified <em>Graph</em>, <strong>new</strong> method creates a new <strong>CyclesDetection</strong> object and returns
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44 newly created <strong>CyclesDetection</strong> object.</p>
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45 </dd>
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46 <dt><strong><a name="copy" class="item"><strong>Copy</strong></a></strong></dt>
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47 <dd>
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48 <div class="OptionsBox">
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49 $NewCyclesDetection = $CyclesDetection->Copy();</div>
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50 <p>Copies <em>CyclesDetection</em> and its associated data using <strong>Storable::dclone</strong> and returns a new
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51 <strong>CyclesDetection</strong> object.</p>
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52 </dd>
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53 <dt><strong><a name="detectcycles" class="item"><strong>DetectCycles</strong></a></strong></dt>
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54 <dd>
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55 <div class="OptionsBox">
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56 $CyclesDetection->DetectCycles();</div>
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57 <p>Detects all cycles in a graph and returns <em>CyclesDetection</em>.</p>
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58 </dd>
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59 <dt><strong><a name="detectcyclesusingcollapsingpathgraphmethodology" class="item"><strong>DetectCyclesUsingCollapsingPathGraphMethodology</strong></a></strong></dt>
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60 <dd>
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61 <div class="OptionsBox">
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62 $CyclesDetection->DetectCyclesUsingCollapsingPathGraphMethodology();</div>
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63 <p>Detects all cycles in a graph using collapsing path graph [Ref 31] methodology
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64 and returns <em>CyclesDetection</em>.</p>
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65 </dd>
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66 <dt><strong><a name="getallcyclicpaths" class="item"><strong>GetAllCyclicPaths</strong></a></strong></dt>
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67 <dd>
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68 <div class="OptionsBox">
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69 @AllCyclicPaths = $CyclesDetection->GetAllCyclicPaths();
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70 <br/> $NumOfAllCyclicPaths = $CyclesDetection->GetAllCyclicPaths();</div>
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71 <p>Returns an array containing references to all cyclic paths identified during cycles
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72 detection. In scalar text, number of cycles is returned.</p>
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73 </dd>
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74 <dt><strong><a name="getindependentcyclicpaths" class="item"><strong>GetIndependentCyclicPaths</strong></a></strong></dt>
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75 <dd>
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76 <div class="OptionsBox">
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77 @IndependentCyclicPaths = $CyclesDetection->GetAllCyclicPaths();
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78 <br/> $NumOfIndependentCyclicPaths = $CyclesDetection->GetAllCyclicPaths();</div>
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79 <p>Returns an array containing references to independent cyclic paths identified during cycles
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80 detection. In scalar text, number of cycles is returned.</p>
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81 <p>A set of independent cycles identified during cycles detection doesn't correspond to the basis set of
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82 rings or smallest set of smallest rings (SSSR) [ Refs 29-30 ]; instead, set of cycles indentified
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83 as independent cycles simply correpond to cycles which contain no other cycle as their
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84 subcycles and can't be described as a linear combination of smaller cycles. And it also happens
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85 to contain all the rings in basis set of rings and SSSR. In other words, it's a superset of a basis set
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86 of cycles and SSSR. For example, six four membered cycles are indentified for cubane, which is one
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87 more than the basis set of cycles.</p>
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88 </dd>
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89 <dt><strong><a name="stringifycyclesdetection" class="item"><strong>StringifyCyclesDetection</strong></a></strong></dt>
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90 <dd>
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91 <div class="OptionsBox">
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92 $String = $CyclesDetection->StringifyCyclesDetection();</div>
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93 <p>Returns a string containing information about <em>CyclesDetection</em> object.</p>
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94 </dd>
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95 </dl>
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96 <p>
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97 </p>
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98 <h2>AUTHOR</h2>
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99 <p><a href="mailto:msud@san.rr.com">Manish Sud</a></p>
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100 <p>
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101 </p>
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102 <h2>SEE ALSO</h2>
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103 <p><a href="./Graph.html">Graph.pm</a>, <a href="./Path.html">Path.pm</a>, <a href="./PathGraph.html">PathGraph.pm</a>
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104 </p>
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105 <p>
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106 </p>
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107 <h2>COPYRIGHT</h2>
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108 <p>Copyright (C) 2015 Manish Sud. All rights reserved.</p>
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109 <p>This file is part of MayaChemTools.</p>
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110 <p>MayaChemTools is free software; you can redistribute it and/or modify it under
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111 the terms of the GNU Lesser General Public License as published by the Free
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112 Software Foundation; either version 3 of the License, or (at your option)
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113 any later version.</p>
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114 <p> </p><p> </p><div class="DocNav">
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115 <table width="100%" border=0 cellpadding=0 cellspacing=2>
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116 <tr align="left" valign="top"><td width="33%" align="left"><a href="./TopologicalPharmacophoreAtomTripletsFingerprints.html" title="TopologicalPharmacophoreAtomTripletsFingerprints.html">Previous</a> <a href="./index.html" title="Table of Contents">TOC</a> <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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117 </table>
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118 </div>
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