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| author | deepakjadmin |
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| date | Wed, 20 Jan 2016 11:55:01 -0500 |
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| 1 <html> | |
| 2 <head> | |
| 3 <title>MayaChemTools:Documentation:MolecularDescriptors::RingsCountDescriptors.pm</title> | |
| 4 <meta http-equiv="content-type" content="text/html;charset=utf-8"> | |
| 5 <link rel="stylesheet" type="text/css" href="../../css/MayaChemTools.css"> | |
| 6 </head> | |
| 7 <body leftmargin="20" rightmargin="20" topmargin="10" bottommargin="10"> | |
| 8 <br/> | |
| 9 <center> | |
| 10 <a href="http://www.mayachemtools.org" title="MayaChemTools Home"><img src="../../images/MayaChemToolsLogo.gif" border="0" alt="MayaChemTools"></a> | |
| 11 </center> | |
| 12 <br/> | |
| 13 <div class="DocNav"> | |
| 14 <table width="100%" border=0 cellpadding=0 cellspacing=2> | |
| 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> | |
| 16 </table> | |
| 17 </div> | |
| 18 <p> | |
| 19 </p> | |
| 20 <h2>NAME</h2> | |
| 21 <p>RingsCountDescriptors</p> | |
| 22 <p> | |
| 23 </p> | |
| 24 <h2>SYNOPSIS</h2> | |
| 25 <p>use MolecularDescriptors::RingsCountDescriptors;</p> | |
| 26 <p>use MolecularDescriptors::RingsCountDescriptors qw(:all);</p> | |
| 27 <p> | |
| 28 </p> | |
| 29 <h2>DESCRIPTION</h2> | |
| 30 <p><strong>RingsCountDescriptors</strong> class provides the following methods:</p> | |
| 31 <p> <a href="#new">new</a>, <a href="#generatedescriptors">GenerateDescriptors</a>, <a href="#getdescriptornames">GetDescriptorNames</a>, <a href="#stringifyringscountdescriptors">StringifyRingsCountDescriptors</a> | |
| 32 </p><p><strong>RingsCountDescriptors</strong> is derived from <strong>MolecularDescriptors</strong> class which in turn | |
| 33 is derived from <strong>ObjectProperty</strong> base class that provides methods not explicitly defined | |
| 34 in <strong>RingsCountDescriptors</strong>, <strong>MolecularDescriptors</strong> or <strong>ObjectProperty</strong> classes using Perl's | |
| 35 AUTOLOAD functionality. These methods are generated on-the-fly for a specified object property:</p> | |
| 36 <div class="OptionsBox"> | |
| 37 Set<PropertyName>(<PropertyValue>); | |
| 38 <br/> $PropertyValue = Get<PropertyName>(); | |
| 39 <br/> Delete<PropertyName>();</div> | |
| 40 <p><strong>RingsCountDescriptors</strong> class doesn't perform any ring or aromaticity detection before | |
| 41 counting their number in a molecule. Instead, it assumes ring and aromaticity detection have | |
| 42 been performed by caller using <strong>DetectRings</strong> [Ref 31] and <strong>DetectAromaticity</strong> methods | |
| 43 available in <strong>Molecule</strong>.</p> | |
| 44 <p><strong>DetectAromaticity</strong> method available in <strong>Molecule</strong> class assigns aromaticity to rings | |
| 45 using Huckel rule as explained below:</p> | |
| 46 <p>o Ring aromaticity is determined using Huckel's rule: a ring containing 4n + 2 pi electrons is | |
| 47 considered aromatic.</p> | |
| 48 <p>o Hetrocyclic rings containing N, O and S atoms fall into two classes: Basic aromatic and | |
| 49 Non-basic aromatic. In Basic aromatic hetrocyclic rings, heteroatom itself is involved in a | |
| 50 double bond. (e.g. Pyridine) However, in non-basic hetrocyclic rings, heteroatom might have | |
| 51 an attached hydrogen atom and the remaining lone pair contribute to electron delocalization | |
| 52 and contributes to 4n + 2 electrons. (e.g. Pyrrole, Furan)</p> | |
| 53 <p>o For molecules containing fused rings, each fused ring set is considered as one aromatic | |
| 54 system for counting pi electrons to satisfy Huckel's rule; In case of a failure, rings in | |
| 55 fused set are treated individually for aromaticity detection. Additionally, non-fused | |
| 56 rings are handled on their own during aromaticity detection.</p> | |
| 57 <p> | |
| 58 </p> | |
| 59 <h2>METHODS</h2> | |
| 60 <dl> | |
| 61 <dt><strong><a name="new" class="item"><strong>new</strong></a></strong></dt> | |
| 62 <dd> | |
| 63 <div class="OptionsBox"> | |
| 64 $NewRingsCountDescriptors = new MolecularDescriptors:: | |
| 65 RingsCountDescriptors( | |
| 66 %NamesAndValues);</div> | |
| 67 <p>Using specified <em>RingsCountDescriptors</em> property names and values hash, <strong>new</strong> | |
| 68 method creates a new object and returns a reference to newly created <strong>RingsCountDescriptors</strong> | |
| 69 object. By default, the following properties are initialized:</p> | |
| 70 <div class="OptionsBox"> | |
| 71 Molecule = '' | |
| 72 <br/> Type = 'RingsCount'</div> | |
| 73 <div class="OptionsBox"> | |
| 74 @DescriptorNames = ('Rings', 'AromaticRings') | |
| 75 <br/> @DescriptorValues = ('None', 'None')</div> | |
| 76 <p>Examples:</p> | |
| 77 <div class="OptionsBox"> | |
| 78 $RingsCountDescriptors = new MolecularDescriptors::RingsCountDescriptors( | |
| 79 'Molecule' => $Molecule);</div> | |
| 80 <div class="OptionsBox"> | |
| 81 $RingsCountDescriptors = new MolecularDescriptors::RingsCountDescriptors();</div> | |
| 82 <div class="OptionsBox"> | |
| 83 $RingsCountDescriptors->SetMolecule($Molecule); | |
| 84 <br/> $RingsCountDescriptors->GenerateDescriptors(); | |
| 85 <br/> print "RingsCountDescriptors: $RingsCountDescriptors\n";</div> | |
| 86 </dd> | |
| 87 <dt><strong><a name="generatedescriptors" class="item"><strong>GenerateDescriptors</strong></a></strong></dt> | |
| 88 <dd> | |
| 89 <div class="OptionsBox"> | |
| 90 $RingsCountDescriptors->GenerateDescriptors();</div> | |
| 91 <p>Calculate number of rings and aromatic rings in a molecule and returns | |
| 92 <em>RingsCountDescriptors</em>.</p> | |
| 93 </dd> | |
| 94 <dt><strong><a name="getdescriptornames" class="item"><strong>GetDescriptorNames</strong></a></strong></dt> | |
| 95 <dd> | |
| 96 <div class="OptionsBox"> | |
| 97 @DescriptorNames = $RingsCountDescriptors->GetDescriptorNames(); | |
| 98 <br/> @DescriptorNames = MolecularDescriptors::RingsCountDescriptors:: | |
| 99 GetDescriptorNames();</div> | |
| 100 <p>Returns all available descriptor names as an array.</p> | |
| 101 </dd> | |
| 102 <dt><strong><a name="stringifyringscountdescriptors" class="item"><strong>StringifyRingsCountDescriptors</strong></a></strong></dt> | |
| 103 <dd> | |
| 104 <div class="OptionsBox"> | |
| 105 $String = $RingsCountDescriptors-> | |
| 106 StringifyRingsCountDescriptors();</div> | |
| 107 <p>Returns a string containing information about <em>RingsCountDescriptors</em> object.</p> | |
| 108 </dd> | |
| 109 </dl> | |
| 110 <p> | |
| 111 </p> | |
| 112 <h2>AUTHOR</h2> | |
| 113 <p><a href="mailto:msud@san.rr.com">Manish Sud</a></p> | |
| 114 <p> | |
| 115 </p> | |
| 116 <h2>SEE ALSO</h2> | |
| 117 <p><a href="./MolecularDescriptors.html">MolecularDescriptors.pm</a>, <a href="./MolecularDescriptorsGenerator.html">MolecularDescriptorsGenerator.pm</a> | |
| 118 </p> | |
| 119 <p> | |
| 120 </p> | |
| 121 <h2>COPYRIGHT</h2> | |
| 122 <p>Copyright (C) 2015 Manish Sud. All rights reserved.</p> | |
| 123 <p>This file is part of MayaChemTools.</p> | |
| 124 <p>MayaChemTools is free software; you can redistribute it and/or modify it under | |
| 125 the terms of the GNU Lesser General Public License as published by the Free | |
| 126 Software Foundation; either version 3 of the License, or (at your option) | |
| 127 any later version.</p> | |
| 128 <p> </p><p> </p><div class="DocNav"> | |
| 129 <table width="100%" border=0 cellpadding=0 cellspacing=2> | |
| 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> | |
| 131 </table> | |
| 132 </div> | |
| 133 <br /> | |
| 134 <center> | |
| 135 <img src="../../images/h2o2.png"> | |
| 136 </center> | |
| 137 </body> | |
| 138 </html> |