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| author | deepakjadmin |
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| date | Wed, 20 Jan 2016 09:23:18 -0500 |
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| 1 <html> | |
| 2 <head> | |
| 3 <title>MayaChemTools:Documentation:MolecularDescriptors::MolecularVolumeDescriptors.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="./MolecularDescriptorsGenerator.html" title="MolecularDescriptorsGenerator.html">Previous</a> <a href="./index.html" title="Table of Contents">TOC</a> <a href="./RingsCountDescriptors.html" title="RingsCountDescriptors.html">Next</a></td><td width="34%" align="middle"><strong>MolecularDescriptors::MolecularVolumeDescriptors.pm</strong></td><td width="33%" align="right"><a href="././code/MolecularVolumeDescriptors.html" title="View source code">Code</a> | <a href="./../pdf/MolecularVolumeDescriptors.pdf" title="PDF US Letter Size">PDF</a> | <a href="./../pdfgreen/MolecularVolumeDescriptors.pdf" title="PDF US Letter Size with narrow margins: www.changethemargins.com">PDFGreen</a> | <a href="./../pdfa4/MolecularVolumeDescriptors.pdf" title="PDF A4 Size">PDFA4</a> | <a href="./../pdfa4green/MolecularVolumeDescriptors.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>MolecularVolumeDescriptors</p> | |
| 22 <p> | |
| 23 </p> | |
| 24 <h2>SYNOPSIS</h2> | |
| 25 <p>use MolecularDescriptors::MolecularVolumeDescriptors;</p> | |
| 26 <p>use MolecularDescriptors::MolecularVolumeDescriptors qw(:all);</p> | |
| 27 <p> | |
| 28 </p> | |
| 29 <h2>DESCRIPTION</h2> | |
| 30 <p><strong>MolecularVolumeDescriptors</strong> class provides the following methods:</p> | |
| 31 <p> <a href="#new">new</a>, <a href="#generatedescriptors">GenerateDescriptors</a>, <a href="#getdescriptornames">GetDescriptorNames</a> | |
| 32 , <a href="#getvdwatomradiiandvolumesdata">GetVDWAtomRadiiAndVolumesData</a>, <a href="#stringifymolecularvolumedescriptors">StringifyMolecularVolumeDescriptors</a> | |
| 33 </p><p><strong>MolecularVolumeDescriptors</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>MolecularVolumeDescriptors</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>van der Waals molecular volume [ Ref 93 ] (A**3/molecule) of a molecule is | |
| 42 calculated using atomic and bonds contributions along with adjustments for | |
| 43 aromatic and non-aromatic rings using the following equation:</p> | |
| 44 <div class="OptionsBox"> | |
| 45 vdwMolecularVolume = SumOfAtomicVDWVolumeContributions | |
| 46 - 5.92 * NumOfBonds | |
| 47 - 14.7 * NumOfAromaticRings | |
| 48 - 3.8 * NumOfNonAromaticRings</div> | |
| 49 <p>van der Waals atomic volume for atoms is taken from data file VDWAtomRadiiAndVolumes.csv | |
| 50 distributed with MayaChemTools. It contains van der Waals atom radii and atom and volumes | |
| 51 data for 38 elements; Table 2 [ Ref 93 ] contains data for only 15 elements. After converting | |
| 52 valid van der Waals atom radius data from pm (picometer) to A (Angstrom) available under column | |
| 53 name VanderWaalsRadius in PeriodicTableElementsData.csv data file, van der Waals atom volume | |
| 54 is calculated using: 4/3 * PI * (Radius ** 3). For elements specified in Table 2 [ Ref 93 ] - | |
| 55 H, B, C, N, O, F, Si, P, S, Cl, As, Se, Br, Te, I - the van der Waals atom radii and calculated | |
| 56 atom volumes match the values in the table.</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 $NewMolecularVolumeDescriptors = new MolecularDescriptors:: | |
| 65 MolecularVolumeDescriptors( | |
| 66 %NamesAndValues);</div> | |
| 67 <p>Using specified <em>MolecularVolumeDescriptors</em> property names and values hash, <strong>new</strong> | |
| 68 method creates a new object and returns a reference to newly created <strong>MolecularVolumeDescriptors</strong> | |
| 69 object. By default, the following properties are initialized:</p> | |
| 70 <div class="OptionsBox"> | |
| 71 Molecule = '' | |
| 72 <br/> Type = 'MolecularVolume' | |
| 73 <br/> @DescriptorNames = ('MolecularVolume') | |
| 74 <br/> @DescriptorValues = ('None')</div> | |
| 75 <p>Examples:</p> | |
| 76 <div class="OptionsBox"> | |
| 77 $MolecularVolumeDescriptors = new MolecularDescriptors:: | |
| 78 MolecularVolumeDescriptors();</div> | |
| 79 <div class="OptionsBox"> | |
| 80 $MolecularVolumeDescriptors->SetMolecule($Molecule); | |
| 81 <br/> $MolecularVolumeDescriptors->GenerateDescriptors(); | |
| 82 <br/> print "MolecularVolumeDescriptors: $MolecularVolumeDescriptors\n";</div> | |
| 83 </dd> | |
| 84 <dt><strong><a name="generatedescriptors" class="item"><strong>GenerateDescriptors</strong></a></strong></dt> | |
| 85 <dd> | |
| 86 <div class="OptionsBox"> | |
| 87 $MolecularVolumeDescriptors->GenerateDescriptors();</div> | |
| 88 <p>Calculate van der Waals molecular volume descriptor for a molecule and returns | |
| 89 <em>MolecularVolumeDescriptors</em>.</p> | |
| 90 </dd> | |
| 91 <dt><strong><a name="getdescriptornames" class="item"><strong>GetDescriptorNames</strong></a></strong></dt> | |
| 92 <dd> | |
| 93 <div class="OptionsBox"> | |
| 94 @DescriptorNames = $MolecularVolumeDescriptors->GetDescriptorNames(); | |
| 95 <br/> @DescriptorNames = MolecularDescriptors::MolecularVolumeDescriptors:: | |
| 96 GetDescriptorNames();</div> | |
| 97 <p>Returns all available descriptor names as an array.</p> | |
| 98 </dd> | |
| 99 <dt><strong><a name="getvdwatomradiiandvolumesdata" class="item"><strong>GetVDWAtomRadiiAndVolumesData</strong></a></strong></dt> | |
| 100 <dd> | |
| 101 <div class="OptionsBox"> | |
| 102 $VDWVolumeDataMapRef = $MolecularVolumeDescriptors-> | |
| 103 GetVDWAtomRadiiAndVolumesData(); | |
| 104 <br/> $VDWVolumeDataMapRef = MolecularDescriptors::MolecularVolumeDescriptors:: | |
| 105 GetVDWAtomRadiiAndVolumesData();</div> | |
| 106 <p>Returns a hash reference to van der Waals atom symbols corresponding to atom types | |
| 107 and associated data loaded from VDWAtomRadiiAndVolumes.csv data file as a reference | |
| 108 to hash with the following hash data format:</p> | |
| 109 <div class="OptionsBox"> | |
| 110 @{$VDWVolumeDataMap{AtomTypes}} - Array of all possible atom | |
| 111 types for all atom symbols | |
| 112 <br/> @{$VDWVolumeDataMap->{ColLabels}} - Array of column labels | |
| 113 <br/> %{$VDWVolumeDataMap->{DataCol<Num>}} - Hash keys pair: | |
| 114 DataCol<Num>, AtomType</div> | |
| 115 </dd> | |
| 116 <dt><strong><a name="stringifymolecularvolumedescriptors" class="item"><strong>StringifyMolecularVolumeDescriptors</strong></a></strong></dt> | |
| 117 <dd> | |
| 118 <div class="OptionsBox"> | |
| 119 $String = $MolecularVolumeDescriptors-> | |
| 120 StringifyMolecularVolumeDescriptors();</div> | |
| 121 <p>Returns a string containing information about <em>MolecularVolumeDescriptors</em> object.</p> | |
| 122 </dd> | |
| 123 </dl> | |
| 124 <p> | |
| 125 </p> | |
| 126 <h2>AUTHOR</h2> | |
| 127 <p><a href="mailto:msud@san.rr.com">Manish Sud</a></p> | |
| 128 <p> | |
| 129 </p> | |
| 130 <h2>SEE ALSO</h2> | |
| 131 <p><a href="./MolecularDescriptors.html">MolecularDescriptors.pm</a>, <a href="./MolecularDescriptorsGenerator.html">MolecularDescriptorsGenerator.pm</a> | |
| 132 </p> | |
| 133 <p> | |
| 134 </p> | |
| 135 <h2>COPYRIGHT</h2> | |
| 136 <p>Copyright (C) 2015 Manish Sud. All rights reserved.</p> | |
| 137 <p>This file is part of MayaChemTools.</p> | |
| 138 <p>MayaChemTools is free software; you can redistribute it and/or modify it under | |
| 139 the terms of the GNU Lesser General Public License as published by the Free | |
| 140 Software Foundation; either version 3 of the License, or (at your option) | |
| 141 any later version.</p> | |
| 142 <p> </p><p> </p><div class="DocNav"> | |
| 143 <table width="100%" border=0 cellpadding=0 cellspacing=2> | |
| 144 <tr align="left" valign="top"><td width="33%" align="left"><a href="./MolecularDescriptorsGenerator.html" title="MolecularDescriptorsGenerator.html">Previous</a> <a href="./index.html" title="Table of Contents">TOC</a> <a href="./RingsCountDescriptors.html" title="RingsCountDescriptors.html">Next</a></td><td width="34%" align="middle"><strong>March 29, 2015</strong></td><td width="33%" align="right"><strong>MolecularDescriptors::MolecularVolumeDescriptors.pm</strong></td></tr> | |
| 145 </table> | |
| 146 </div> | |
| 147 <br /> | |
| 148 <center> | |
| 149 <img src="../../images/h2o2.png"> | |
| 150 </center> | |
| 151 </body> | |
| 152 </html> |