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<html> <head> <title>MayaChemTools:Documentation:MolecularDescriptors::RingsCountDescriptors.pm</title> <meta http-equiv="content-type" content="text/html;charset=utf-8"> <link rel="stylesheet" type="text/css" href="../../css/MayaChemTools.css"> </head> <body leftmargin="20" rightmargin="20" topmargin="10" bottommargin="10"> <br/> <center> <a href="http://www.mayachemtools.org" title="MayaChemTools Home"><img src="../../images/MayaChemToolsLogo.gif" border="0" alt="MayaChemTools"></a> </center> <br/> <div class="DocNav"> <table width="100%" border=0 cellpadding=0 cellspacing=2> <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> </table> </div> <p> </p> <h2>NAME</h2> <p>RingsCountDescriptors</p> <p> </p> <h2>SYNOPSIS</h2> <p>use MolecularDescriptors::RingsCountDescriptors;</p> <p>use MolecularDescriptors::RingsCountDescriptors qw(:all);</p> <p> </p> <h2>DESCRIPTION</h2> <p><strong>RingsCountDescriptors</strong> class provides the following methods:</p> <p> <a href="#new">new</a>, <a href="#generatedescriptors">GenerateDescriptors</a>, <a href="#getdescriptornames">GetDescriptorNames</a>, <a href="#stringifyringscountdescriptors">StringifyRingsCountDescriptors</a> </p><p><strong>RingsCountDescriptors</strong> is derived from <strong>MolecularDescriptors</strong> class which in turn is derived from <strong>ObjectProperty</strong> base class that provides methods not explicitly defined in <strong>RingsCountDescriptors</strong>, <strong>MolecularDescriptors</strong> or <strong>ObjectProperty</strong> classes using Perl's AUTOLOAD functionality. These methods are generated on-the-fly for a specified object property:</p> <div class="OptionsBox"> Set<PropertyName>(<PropertyValue>); <br/> $PropertyValue = Get<PropertyName>(); <br/> Delete<PropertyName>();</div> <p><strong>RingsCountDescriptors</strong> class doesn't perform any ring or aromaticity detection before counting their number in a molecule. Instead, it assumes ring and aromaticity detection have been performed by caller using <strong>DetectRings</strong> [Ref 31] and <strong>DetectAromaticity</strong> methods available in <strong>Molecule</strong>.</p> <p><strong>DetectAromaticity</strong> method available in <strong>Molecule</strong> class assigns aromaticity to rings using Huckel rule as explained below:</p> <p>o Ring aromaticity is determined using Huckel's rule: a ring containing 4n + 2 pi electrons is considered aromatic.</p> <p>o Hetrocyclic rings containing N, O and S atoms fall into two classes: Basic aromatic and Non-basic aromatic. In Basic aromatic hetrocyclic rings, heteroatom itself is involved in a double bond. (e.g. Pyridine) However, in non-basic hetrocyclic rings, heteroatom might have an attached hydrogen atom and the remaining lone pair contribute to electron delocalization and contributes to 4n + 2 electrons. (e.g. Pyrrole, Furan)</p> <p>o For molecules containing fused rings, each fused ring set is considered as one aromatic system for counting pi electrons to satisfy Huckel's rule; In case of a failure, rings in fused set are treated individually for aromaticity detection. Additionally, non-fused rings are handled on their own during aromaticity detection.</p> <p> </p> <h2>METHODS</h2> <dl> <dt><strong><a name="new" class="item"><strong>new</strong></a></strong></dt> <dd> <div class="OptionsBox"> $NewRingsCountDescriptors = new MolecularDescriptors:: RingsCountDescriptors( %NamesAndValues);</div> <p>Using specified <em>RingsCountDescriptors</em> property names and values hash, <strong>new</strong> method creates a new object and returns a reference to newly created <strong>RingsCountDescriptors</strong> object. By default, the following properties are initialized:</p> <div class="OptionsBox"> Molecule = '' <br/> Type = 'RingsCount'</div> <div class="OptionsBox"> @DescriptorNames = ('Rings', 'AromaticRings') <br/> @DescriptorValues = ('None', 'None')</div> <p>Examples:</p> <div class="OptionsBox"> $RingsCountDescriptors = new MolecularDescriptors::RingsCountDescriptors( 'Molecule' => $Molecule);</div> <div class="OptionsBox"> $RingsCountDescriptors = new MolecularDescriptors::RingsCountDescriptors();</div> <div class="OptionsBox"> $RingsCountDescriptors->SetMolecule($Molecule); <br/> $RingsCountDescriptors->GenerateDescriptors(); <br/> print "RingsCountDescriptors: $RingsCountDescriptors\n";</div> </dd> <dt><strong><a name="generatedescriptors" class="item"><strong>GenerateDescriptors</strong></a></strong></dt> <dd> <div class="OptionsBox"> $RingsCountDescriptors->GenerateDescriptors();</div> <p>Calculate number of rings and aromatic rings in a molecule and returns <em>RingsCountDescriptors</em>.</p> </dd> <dt><strong><a name="getdescriptornames" class="item"><strong>GetDescriptorNames</strong></a></strong></dt> <dd> <div class="OptionsBox"> @DescriptorNames = $RingsCountDescriptors->GetDescriptorNames(); <br/> @DescriptorNames = MolecularDescriptors::RingsCountDescriptors:: GetDescriptorNames();</div> <p>Returns all available descriptor names as an array.</p> </dd> <dt><strong><a name="stringifyringscountdescriptors" class="item"><strong>StringifyRingsCountDescriptors</strong></a></strong></dt> <dd> <div class="OptionsBox"> $String = $RingsCountDescriptors-> StringifyRingsCountDescriptors();</div> <p>Returns a string containing information about <em>RingsCountDescriptors</em> object.</p> </dd> </dl> <p> </p> <h2>AUTHOR</h2> <p><a href="mailto:msud@san.rr.com">Manish Sud</a></p> <p> </p> <h2>SEE ALSO</h2> <p><a href="./MolecularDescriptors.html">MolecularDescriptors.pm</a>, <a href="./MolecularDescriptorsGenerator.html">MolecularDescriptorsGenerator.pm</a> </p> <p> </p> <h2>COPYRIGHT</h2> <p>Copyright (C) 2015 Manish Sud. All rights reserved.</p> <p>This file is part of MayaChemTools.</p> <p>MayaChemTools is free software; you can redistribute it and/or modify it under the terms of the GNU Lesser General Public License as published by the Free Software Foundation; either version 3 of the License, or (at your option) any later version.</p> <p> </p><p> </p><div class="DocNav"> <table width="100%" border=0 cellpadding=0 cellspacing=2> <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> </table> </div> <br /> <center> <img src="../../images/h2o2.png"> </center> </body> </html>