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| author | deepakjadmin |
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| date | Wed, 20 Jan 2016 11:55:01 -0500 |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/mayachemtools/docs/modules/html/HydrogenBondsDescriptors.html Wed Jan 20 11:55:01 2016 -0500 @@ -0,0 +1,151 @@ +<html> +<head> +<title>MayaChemTools:Documentation:MolecularDescriptors::HydrogenBondsDescriptors.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="./Fsp3CarbonsDescriptors.html" title="Fsp3CarbonsDescriptors.html">Previous</a> <a href="./index.html" title="Table of Contents">TOC</a> <a href="./MolecularComplexityDescriptors.html" title="MolecularComplexityDescriptors.html">Next</a></td><td width="34%" align="middle"><strong>MolecularDescriptors::HydrogenBondsDescriptors.pm</strong></td><td width="33%" align="right"><a href="././code/HydrogenBondsDescriptors.html" title="View source code">Code</a> | <a href="./../pdf/HydrogenBondsDescriptors.pdf" title="PDF US Letter Size">PDF</a> | <a href="./../pdfgreen/HydrogenBondsDescriptors.pdf" title="PDF US Letter Size with narrow margins: www.changethemargins.com">PDFGreen</a> | <a href="./../pdfa4/HydrogenBondsDescriptors.pdf" title="PDF A4 Size">PDFA4</a> | <a href="./../pdfa4green/HydrogenBondsDescriptors.pdf" title="PDF A4 Size with narrow margins: www.changethemargins.com">PDFA4Green</a></td></tr> +</table> +</div> +<p> +</p> +<h2>NAME</h2> +<p>HydrogenBondsDescriptors</p> +<p> +</p> +<h2>SYNOPSIS</h2> +<p>use MolecularDescriptors::HydrogenBondsDescriptors;</p> +<p>use MolecularDescriptors::HydrogenBondsDescriptors qw(:all);</p> +<p> +</p> +<h2>DESCRIPTION</h2> +<p><strong>HydrogenBondsDescriptors</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="#sethydrogenbondstype">SetHydrogenBondsType</a> +, <a href="#stringifyhydrogenbondsdescriptors">StringifyHydrogenBondsDescriptors</a> +</p><p><strong>HydrogenBondsDescriptors</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>HydrogenBondsDescriptors</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>The current release of MayaChemTools supports identification of two types of hydrogen bond +donor and acceptor atoms with these names:</p> +<div class="OptionsBox"> + HBondsType1 or HydrogenBondsType1 +<br/> HBondsType2 or HydrogenBondsType2</div> +<p>The names of these hydrogen bond types are rather arbitrary. However, their definitions have +specific meaning and are as follows:</p> +<div class="OptionsBox"> + HydrogenBondsType1 [ Ref 60-61, Ref 65-66 ]:</div> +<div class="OptionsBox"> + Donor: NH, NH2, OH - Any N and O with available H + Acceptor: N[!H], O - Any N without available H and any O</div> +<div class="OptionsBox"> + HydrogenBondsType2 [ Ref 91 ]:</div> +<div class="OptionsBox"> + Donor: NH, NH2, OH - N and O with available H + Acceptor: N, O - And N and O</div> +<p>By default, <em>HydrogenBondsType2</em> is used to calculate number hydrogen bond donor +and acceptor atoms. This corresponds to <strong>RuleOf5</strong> definition of hydrogen bond donors +and acceptors.</p> +<p> +</p> +<h2>METHODS</h2> +<dl> +<dt><strong><a name="new" class="item"><strong>new</strong></a></strong></dt> +<dd> +<div class="OptionsBox"> + $HydrogenBondsDescriptors = new MolecularDescriptors:: + HydrogenBondsDescriptors(%NamesAndValues);</div> +<p>Using specified <em>HydrogenBondsDescriptors</em> property names and values hash, <strong>new</strong> +method creates a new object and returns a reference to newly created <strong>HydrogenBondsDescriptors</strong> +object. By default, the following properties are initialized:</p> +<div class="OptionsBox"> + Molecule = '' +<br/> Type = 'HydrogenBonds' +<br/> HydrogenBondsType = 'HBondsType2' +<br/> @DescriptorNames = ('HydrogenBondDonors', 'HydrogenBondAcceptors') +<br/> @DescriptorValues = ('None', 'None')</div> +<p>Examples:</p> +<div class="OptionsBox"> + $HydrogenBondsDescriptors = new MolecularDescriptors:: + HydrogenBondsDescriptors();</div> +<div class="OptionsBox"> + $HydrogenBondsDescriptors = new MolecularDescriptors:: + HydrogenBondsDescriptors( + 'HydrogenBondsType' => 'HBondsType2');</div> +<div class="OptionsBox"> + $HydrogenBondsDescriptors->SetMolecule($Molecule); +<br/> $HydrogenBondsDescriptors->GenerateDescriptors(); +<br/> print "HydrogenBondsDescriptors: $HydrogenBondsDescriptors\n";</div> +</dd> +<dt><strong><a name="generatedescriptors" class="item"><strong>GenerateDescriptors</strong></a></strong></dt> +<dd> +<div class="OptionsBox"> + $HydrogenBondsDescriptors->GenerateDescriptors();</div> +<p>Calculates number of hydrogen bond donors and acceptors a molecule and returns +<em>HydrogenBondsDescriptors</em>.</p> +</dd> +<dt><strong><a name="getdescriptornames" class="item"><strong>GetDescriptorNames</strong></a></strong></dt> +<dd> +<div class="OptionsBox"> + @DescriptorNames = $HydrogenBondsDescriptors->GetDescriptorNames(); +<br/> @DescriptorNames = MolecularDescriptors::HydrogenBondsDescriptors:: + GetDescriptorNames();</div> +<p>Returns all available descriptor names as an array.</p> +</dd> +<dt><strong><a name="sethydrogenbondstype" class="item"><strong>SetHydrogenBondsType</strong></a></strong></dt> +<dd> +<div class="OptionsBox"> + $HydrogenBondsDescriptors->SetHydrogenBondsType($HBondsType);</div> +<p>Sets value of hydrogen bonds type to use during calculation of descriptors and returns +<em>HydrogenBondsDescriptors</em>. Possible values: <em>HBondsType1, HydrogenBondsType1, +HBondsType2, HydrogenBondsType2</em>.</p> +</dd> +<dt><strong><a name="stringifyhydrogenbondsdescriptors" class="item"><strong>StringifyHydrogenBondsDescriptors</strong></a></strong></dt> +<dd> +<div class="OptionsBox"> + $String = $HydrogenBondsDescriptors-> + StringifyHydrogenBondsDescriptors();</div> +<p>Returns a string containing information about <em>HydrogenBondsDescriptors</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="./Fsp3CarbonsDescriptors.html" title="Fsp3CarbonsDescriptors.html">Previous</a> <a href="./index.html" title="Table of Contents">TOC</a> <a href="./MolecularComplexityDescriptors.html" title="MolecularComplexityDescriptors.html">Next</a></td><td width="34%" align="middle"><strong>March 29, 2015</strong></td><td width="33%" align="right"><strong>MolecularDescriptors::HydrogenBondsDescriptors.pm</strong></td></tr> +</table> +</div> +<br /> +<center> +<img src="../../images/h2o2.png"> +</center> +</body> +</html>