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3 <title>MayaChemTools:Documentation:MolecularDescriptors::RingsCountDescriptors.pm</title>
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13 <div class="DocNav">
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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="./MolecularVolumeDescriptors.html" title="MolecularVolumeDescriptors.html">Previous</a> <a href="./index.html" title="Table of Contents">TOC</a> <a href="./RotatableBondsDescriptors.html" title="RotatableBondsDescriptors.html">Next</a></td><td width="34%" align="middle"><strong>MolecularDescriptors::RingsCountDescriptors.pm</strong></td><td width="33%" align="right"><a href="././code/RingsCountDescriptors.html" title="View source code">Code</a> | <a href="./../pdf/RingsCountDescriptors.pdf" title="PDF US Letter Size">PDF</a> | <a href="./../pdfgreen/RingsCountDescriptors.pdf" title="PDF US Letter Size with narrow margins: www.changethemargins.com">PDFGreen</a> | <a href="./../pdfa4/RingsCountDescriptors.pdf" title="PDF A4 Size">PDFA4</a> | <a href="./../pdfa4green/RingsCountDescriptors.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>RingsCountDescriptors</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 MolecularDescriptors::RingsCountDescriptors;</p>
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26 <p>use MolecularDescriptors::RingsCountDescriptors 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>RingsCountDescriptors</strong> class provides the following methods:</p>
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31 <p> <a href="#new">new</a>, <a href="#generatedescriptors">GenerateDescriptors</a>, <a href="#getdescriptornames">GetDescriptorNames</a>, <a href="#stringifyringscountdescriptors">StringifyRingsCountDescriptors</a>
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32 </p><p><strong>RingsCountDescriptors</strong> is derived from <strong>MolecularDescriptors</strong> class which in turn
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33 is derived from <strong>ObjectProperty</strong> base class that provides methods not explicitly defined
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34 in <strong>RingsCountDescriptors</strong>, <strong>MolecularDescriptors</strong> or <strong>ObjectProperty</strong> classes using Perl's
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35 AUTOLOAD functionality. These methods are generated on-the-fly for a specified object property:</p>
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36 <div class="OptionsBox">
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37 Set<PropertyName>(<PropertyValue>);
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38 <br/> $PropertyValue = Get<PropertyName>();
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39 <br/> Delete<PropertyName>();</div>
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40 <p><strong>RingsCountDescriptors</strong> class doesn't perform any ring or aromaticity detection before
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41 counting their number in a molecule. Instead, it assumes ring and aromaticity detection have
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42 been performed by caller using <strong>DetectRings</strong> [Ref 31] and <strong>DetectAromaticity</strong> methods
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43 available in <strong>Molecule</strong>.</p>
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44 <p><strong>DetectAromaticity</strong> method available in <strong>Molecule</strong> class assigns aromaticity to rings
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45 using Huckel rule as explained below:</p>
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46 <p>o Ring aromaticity is determined using Huckel's rule: a ring containing 4n + 2 pi electrons is
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47 considered aromatic.</p>
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48 <p>o Hetrocyclic rings containing N, O and S atoms fall into two classes: Basic aromatic and
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49 Non-basic aromatic. In Basic aromatic hetrocyclic rings, heteroatom itself is involved in a
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50 double bond. (e.g. Pyridine) However, in non-basic hetrocyclic rings, heteroatom might have
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51 an attached hydrogen atom and the remaining lone pair contribute to electron delocalization
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52 and contributes to 4n + 2 electrons. (e.g. Pyrrole, Furan)</p>
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53 <p>o For molecules containing fused rings, each fused ring set is considered as one aromatic
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54 system for counting pi electrons to satisfy Huckel's rule; In case of a failure, rings in
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55 fused set are treated individually for aromaticity detection. Additionally, non-fused
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56 rings are handled on their own during aromaticity detection.</p>
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57 <p>
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58 </p>
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59 <h2>METHODS</h2>
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60 <dl>
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61 <dt><strong><a name="new" class="item"><strong>new</strong></a></strong></dt>
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62 <dd>
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63 <div class="OptionsBox">
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64 $NewRingsCountDescriptors = new MolecularDescriptors::
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65 RingsCountDescriptors(
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66 %NamesAndValues);</div>
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67 <p>Using specified <em>RingsCountDescriptors</em> property names and values hash, <strong>new</strong>
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68 method creates a new object and returns a reference to newly created <strong>RingsCountDescriptors</strong>
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69 object. By default, the following properties are initialized:</p>
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70 <div class="OptionsBox">
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71 Molecule = ''
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72 <br/> Type = 'RingsCount'</div>
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73 <div class="OptionsBox">
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74 @DescriptorNames = ('Rings', 'AromaticRings')
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75 <br/> @DescriptorValues = ('None', 'None')</div>
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76 <p>Examples:</p>
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77 <div class="OptionsBox">
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78 $RingsCountDescriptors = new MolecularDescriptors::RingsCountDescriptors(
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79 'Molecule' => $Molecule);</div>
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80 <div class="OptionsBox">
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81 $RingsCountDescriptors = new MolecularDescriptors::RingsCountDescriptors();</div>
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82 <div class="OptionsBox">
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83 $RingsCountDescriptors->SetMolecule($Molecule);
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84 <br/> $RingsCountDescriptors->GenerateDescriptors();
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85 <br/> print "RingsCountDescriptors: $RingsCountDescriptors\n";</div>
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86 </dd>
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87 <dt><strong><a name="generatedescriptors" class="item"><strong>GenerateDescriptors</strong></a></strong></dt>
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88 <dd>
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89 <div class="OptionsBox">
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90 $RingsCountDescriptors->GenerateDescriptors();</div>
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91 <p>Calculate number of rings and aromatic rings in a molecule and returns
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92 <em>RingsCountDescriptors</em>.</p>
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93 </dd>
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94 <dt><strong><a name="getdescriptornames" class="item"><strong>GetDescriptorNames</strong></a></strong></dt>
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95 <dd>
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96 <div class="OptionsBox">
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97 @DescriptorNames = $RingsCountDescriptors->GetDescriptorNames();
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98 <br/> @DescriptorNames = MolecularDescriptors::RingsCountDescriptors::
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99 GetDescriptorNames();</div>
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100 <p>Returns all available descriptor names as an array.</p>
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101 </dd>
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102 <dt><strong><a name="stringifyringscountdescriptors" class="item"><strong>StringifyRingsCountDescriptors</strong></a></strong></dt>
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103 <dd>
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104 <div class="OptionsBox">
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105 $String = $RingsCountDescriptors->
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106 StringifyRingsCountDescriptors();</div>
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107 <p>Returns a string containing information about <em>RingsCountDescriptors</em> object.</p>
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108 </dd>
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109 </dl>
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110 <p>
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111 </p>
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112 <h2>AUTHOR</h2>
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113 <p><a href="mailto:msud@san.rr.com">Manish Sud</a></p>
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114 <p>
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115 </p>
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116 <h2>SEE ALSO</h2>
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117 <p><a href="./MolecularDescriptors.html">MolecularDescriptors.pm</a>, <a href="./MolecularDescriptorsGenerator.html">MolecularDescriptorsGenerator.pm</a>
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118 </p>
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119 <p>
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120 </p>
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121 <h2>COPYRIGHT</h2>
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122 <p>Copyright (C) 2015 Manish Sud. All rights reserved.</p>
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123 <p>This file is part of MayaChemTools.</p>
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124 <p>MayaChemTools is free software; you can redistribute it and/or modify it under
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125 the terms of the GNU Lesser General Public License as published by the Free
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126 Software Foundation; either version 3 of the License, or (at your option)
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127 any later version.</p>
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128 <p> </p><p> </p><div class="DocNav">
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129 <table width="100%" border=0 cellpadding=0 cellspacing=2>
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130 <tr align="left" valign="top"><td width="33%" align="left"><a href="./MolecularVolumeDescriptors.html" title="MolecularVolumeDescriptors.html">Previous</a> <a href="./index.html" title="Table of Contents">TOC</a> <a href="./RotatableBondsDescriptors.html" title="RotatableBondsDescriptors.html">Next</a></td><td width="34%" align="middle"><strong>March 29, 2015</strong></td><td width="33%" align="right"><strong>MolecularDescriptors::RingsCountDescriptors.pm</strong></td></tr>
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131 </table>
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