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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::HydrogenBondsDescriptors.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="./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> | |
| 16 </table> | |
| 17 </div> | |
| 18 <p> | |
| 19 </p> | |
| 20 <h2>NAME</h2> | |
| 21 <p>HydrogenBondsDescriptors</p> | |
| 22 <p> | |
| 23 </p> | |
| 24 <h2>SYNOPSIS</h2> | |
| 25 <p>use MolecularDescriptors::HydrogenBondsDescriptors;</p> | |
| 26 <p>use MolecularDescriptors::HydrogenBondsDescriptors qw(:all);</p> | |
| 27 <p> | |
| 28 </p> | |
| 29 <h2>DESCRIPTION</h2> | |
| 30 <p><strong>HydrogenBondsDescriptors</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="#sethydrogenbondstype">SetHydrogenBondsType</a> | |
| 32 , <a href="#stringifyhydrogenbondsdescriptors">StringifyHydrogenBondsDescriptors</a> | |
| 33 </p><p><strong>HydrogenBondsDescriptors</strong> is derived from <strong>MolecularDescriptors</strong> class which in turn | |
| 34 is derived from <strong>ObjectProperty</strong> base class that provides methods not explicitly defined | |
| 35 in <strong>HydrogenBondsDescriptors</strong>, <strong>MolecularDescriptors</strong> or <strong>ObjectProperty</strong> classes using Perl's | |
| 36 AUTOLOAD functionality. These methods are generated on-the-fly for a specified object property:</p> | |
| 37 <div class="OptionsBox"> | |
| 38 Set<PropertyName>(<PropertyValue>); | |
| 39 <br/> $PropertyValue = Get<PropertyName>(); | |
| 40 <br/> Delete<PropertyName>();</div> | |
| 41 <p>The current release of MayaChemTools supports identification of two types of hydrogen bond | |
| 42 donor and acceptor atoms with these names:</p> | |
| 43 <div class="OptionsBox"> | |
| 44 HBondsType1 or HydrogenBondsType1 | |
| 45 <br/> HBondsType2 or HydrogenBondsType2</div> | |
| 46 <p>The names of these hydrogen bond types are rather arbitrary. However, their definitions have | |
| 47 specific meaning and are as follows:</p> | |
| 48 <div class="OptionsBox"> | |
| 49 HydrogenBondsType1 [ Ref 60-61, Ref 65-66 ]:</div> | |
| 50 <div class="OptionsBox"> | |
| 51 Donor: NH, NH2, OH - Any N and O with available H | |
| 52 Acceptor: N[!H], O - Any N without available H and any O</div> | |
| 53 <div class="OptionsBox"> | |
| 54 HydrogenBondsType2 [ Ref 91 ]:</div> | |
| 55 <div class="OptionsBox"> | |
| 56 Donor: NH, NH2, OH - N and O with available H | |
| 57 Acceptor: N, O - And N and O</div> | |
| 58 <p>By default, <em>HydrogenBondsType2</em> is used to calculate number hydrogen bond donor | |
| 59 and acceptor atoms. This corresponds to <strong>RuleOf5</strong> definition of hydrogen bond donors | |
| 60 and acceptors.</p> | |
| 61 <p> | |
| 62 </p> | |
| 63 <h2>METHODS</h2> | |
| 64 <dl> | |
| 65 <dt><strong><a name="new" class="item"><strong>new</strong></a></strong></dt> | |
| 66 <dd> | |
| 67 <div class="OptionsBox"> | |
| 68 $HydrogenBondsDescriptors = new MolecularDescriptors:: | |
| 69 HydrogenBondsDescriptors(%NamesAndValues);</div> | |
| 70 <p>Using specified <em>HydrogenBondsDescriptors</em> property names and values hash, <strong>new</strong> | |
| 71 method creates a new object and returns a reference to newly created <strong>HydrogenBondsDescriptors</strong> | |
| 72 object. By default, the following properties are initialized:</p> | |
| 73 <div class="OptionsBox"> | |
| 74 Molecule = '' | |
| 75 <br/> Type = 'HydrogenBonds' | |
| 76 <br/> HydrogenBondsType = 'HBondsType2' | |
| 77 <br/> @DescriptorNames = ('HydrogenBondDonors', 'HydrogenBondAcceptors') | |
| 78 <br/> @DescriptorValues = ('None', 'None')</div> | |
| 79 <p>Examples:</p> | |
| 80 <div class="OptionsBox"> | |
| 81 $HydrogenBondsDescriptors = new MolecularDescriptors:: | |
| 82 HydrogenBondsDescriptors();</div> | |
| 83 <div class="OptionsBox"> | |
| 84 $HydrogenBondsDescriptors = new MolecularDescriptors:: | |
| 85 HydrogenBondsDescriptors( | |
| 86 'HydrogenBondsType' => 'HBondsType2');</div> | |
| 87 <div class="OptionsBox"> | |
| 88 $HydrogenBondsDescriptors->SetMolecule($Molecule); | |
| 89 <br/> $HydrogenBondsDescriptors->GenerateDescriptors(); | |
| 90 <br/> print "HydrogenBondsDescriptors: $HydrogenBondsDescriptors\n";</div> | |
| 91 </dd> | |
| 92 <dt><strong><a name="generatedescriptors" class="item"><strong>GenerateDescriptors</strong></a></strong></dt> | |
| 93 <dd> | |
| 94 <div class="OptionsBox"> | |
| 95 $HydrogenBondsDescriptors->GenerateDescriptors();</div> | |
| 96 <p>Calculates number of hydrogen bond donors and acceptors a molecule and returns | |
| 97 <em>HydrogenBondsDescriptors</em>.</p> | |
| 98 </dd> | |
| 99 <dt><strong><a name="getdescriptornames" class="item"><strong>GetDescriptorNames</strong></a></strong></dt> | |
| 100 <dd> | |
| 101 <div class="OptionsBox"> | |
| 102 @DescriptorNames = $HydrogenBondsDescriptors->GetDescriptorNames(); | |
| 103 <br/> @DescriptorNames = MolecularDescriptors::HydrogenBondsDescriptors:: | |
| 104 GetDescriptorNames();</div> | |
| 105 <p>Returns all available descriptor names as an array.</p> | |
| 106 </dd> | |
| 107 <dt><strong><a name="sethydrogenbondstype" class="item"><strong>SetHydrogenBondsType</strong></a></strong></dt> | |
| 108 <dd> | |
| 109 <div class="OptionsBox"> | |
| 110 $HydrogenBondsDescriptors->SetHydrogenBondsType($HBondsType);</div> | |
| 111 <p>Sets value of hydrogen bonds type to use during calculation of descriptors and returns | |
| 112 <em>HydrogenBondsDescriptors</em>. Possible values: <em>HBondsType1, HydrogenBondsType1, | |
| 113 HBondsType2, HydrogenBondsType2</em>.</p> | |
| 114 </dd> | |
| 115 <dt><strong><a name="stringifyhydrogenbondsdescriptors" class="item"><strong>StringifyHydrogenBondsDescriptors</strong></a></strong></dt> | |
| 116 <dd> | |
| 117 <div class="OptionsBox"> | |
| 118 $String = $HydrogenBondsDescriptors-> | |
| 119 StringifyHydrogenBondsDescriptors();</div> | |
| 120 <p>Returns a string containing information about <em>HydrogenBondsDescriptors</em> object.</p> | |
| 121 </dd> | |
| 122 </dl> | |
| 123 <p> | |
| 124 </p> | |
| 125 <h2>AUTHOR</h2> | |
| 126 <p><a href="mailto:msud@san.rr.com">Manish Sud</a></p> | |
| 127 <p> | |
| 128 </p> | |
| 129 <h2>SEE ALSO</h2> | |
| 130 <p><a href="./MolecularDescriptors.html">MolecularDescriptors.pm</a>, <a href="./MolecularDescriptorsGenerator.html">MolecularDescriptorsGenerator.pm</a> | |
| 131 </p> | |
| 132 <p> | |
| 133 </p> | |
| 134 <h2>COPYRIGHT</h2> | |
| 135 <p>Copyright (C) 2015 Manish Sud. All rights reserved.</p> | |
| 136 <p>This file is part of MayaChemTools.</p> | |
| 137 <p>MayaChemTools is free software; you can redistribute it and/or modify it under | |
| 138 the terms of the GNU Lesser General Public License as published by the Free | |
| 139 Software Foundation; either version 3 of the License, or (at your option) | |
| 140 any later version.</p> | |
| 141 <p> </p><p> </p><div class="DocNav"> | |
| 142 <table width="100%" border=0 cellpadding=0 cellspacing=2> | |
| 143 <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> | |
| 144 </table> | |
| 145 </div> | |
| 146 <br /> | |
| 147 <center> | |
| 148 <img src="../../images/h2o2.png"> | |
| 149 </center> | |
| 150 </body> | |
| 151 </html> |