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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/MolecularVolumeDescriptors.html Wed Jan 20 11:55:01 2016 -0500 @@ -0,0 +1,152 @@ +<html> +<head> +<title>MayaChemTools:Documentation:MolecularDescriptors::MolecularVolumeDescriptors.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="./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> +</table> +</div> +<p> +</p> +<h2>NAME</h2> +<p>MolecularVolumeDescriptors</p> +<p> +</p> +<h2>SYNOPSIS</h2> +<p>use MolecularDescriptors::MolecularVolumeDescriptors;</p> +<p>use MolecularDescriptors::MolecularVolumeDescriptors qw(:all);</p> +<p> +</p> +<h2>DESCRIPTION</h2> +<p><strong>MolecularVolumeDescriptors</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="#getvdwatomradiiandvolumesdata">GetVDWAtomRadiiAndVolumesData</a>, <a href="#stringifymolecularvolumedescriptors">StringifyMolecularVolumeDescriptors</a> +</p><p><strong>MolecularVolumeDescriptors</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>MolecularVolumeDescriptors</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>van der Waals molecular volume [ Ref 93 ] (A**3/molecule) of a molecule is +calculated using atomic and bonds contributions along with adjustments for +aromatic and non-aromatic rings using the following equation:</p> +<div class="OptionsBox"> + vdwMolecularVolume = SumOfAtomicVDWVolumeContributions + - 5.92 * NumOfBonds + - 14.7 * NumOfAromaticRings + - 3.8 * NumOfNonAromaticRings</div> +<p>van der Waals atomic volume for atoms is taken from data file VDWAtomRadiiAndVolumes.csv +distributed with MayaChemTools. It contains van der Waals atom radii and atom and volumes +data for 38 elements; Table 2 [ Ref 93 ] contains data for only 15 elements. After converting +valid van der Waals atom radius data from pm (picometer) to A (Angstrom) available under column +name VanderWaalsRadius in PeriodicTableElementsData.csv data file, van der Waals atom volume +is calculated using: 4/3 * PI * (Radius ** 3). For elements specified in Table 2 [ Ref 93 ] - +H, B, C, N, O, F, Si, P, S, Cl, As, Se, Br, Te, I - the van der Waals atom radii and calculated +atom volumes match the values in the table.</p> +<p> +</p> +<h2>METHODS</h2> +<dl> +<dt><strong><a name="new" class="item"><strong>new</strong></a></strong></dt> +<dd> +<div class="OptionsBox"> + $NewMolecularVolumeDescriptors = new MolecularDescriptors:: + MolecularVolumeDescriptors( + %NamesAndValues);</div> +<p>Using specified <em>MolecularVolumeDescriptors</em> property names and values hash, <strong>new</strong> +method creates a new object and returns a reference to newly created <strong>MolecularVolumeDescriptors</strong> +object. By default, the following properties are initialized:</p> +<div class="OptionsBox"> + Molecule = '' +<br/> Type = 'MolecularVolume' +<br/> @DescriptorNames = ('MolecularVolume') +<br/> @DescriptorValues = ('None')</div> +<p>Examples:</p> +<div class="OptionsBox"> + $MolecularVolumeDescriptors = new MolecularDescriptors:: + MolecularVolumeDescriptors();</div> +<div class="OptionsBox"> + $MolecularVolumeDescriptors->SetMolecule($Molecule); +<br/> $MolecularVolumeDescriptors->GenerateDescriptors(); +<br/> print "MolecularVolumeDescriptors: $MolecularVolumeDescriptors\n";</div> +</dd> +<dt><strong><a name="generatedescriptors" class="item"><strong>GenerateDescriptors</strong></a></strong></dt> +<dd> +<div class="OptionsBox"> + $MolecularVolumeDescriptors->GenerateDescriptors();</div> +<p>Calculate van der Waals molecular volume descriptor for a molecule and returns +<em>MolecularVolumeDescriptors</em>.</p> +</dd> +<dt><strong><a name="getdescriptornames" class="item"><strong>GetDescriptorNames</strong></a></strong></dt> +<dd> +<div class="OptionsBox"> + @DescriptorNames = $MolecularVolumeDescriptors->GetDescriptorNames(); +<br/> @DescriptorNames = MolecularDescriptors::MolecularVolumeDescriptors:: + GetDescriptorNames();</div> +<p>Returns all available descriptor names as an array.</p> +</dd> +<dt><strong><a name="getvdwatomradiiandvolumesdata" class="item"><strong>GetVDWAtomRadiiAndVolumesData</strong></a></strong></dt> +<dd> +<div class="OptionsBox"> + $VDWVolumeDataMapRef = $MolecularVolumeDescriptors-> + GetVDWAtomRadiiAndVolumesData(); +<br/> $VDWVolumeDataMapRef = MolecularDescriptors::MolecularVolumeDescriptors:: + GetVDWAtomRadiiAndVolumesData();</div> +<p>Returns a hash reference to van der Waals atom symbols corresponding to atom types +and associated data loaded from VDWAtomRadiiAndVolumes.csv data file as a reference +to hash with the following hash data format:</p> +<div class="OptionsBox"> + @{$VDWVolumeDataMap{AtomTypes}} - Array of all possible atom + types for all atom symbols +<br/> @{$VDWVolumeDataMap->{ColLabels}} - Array of column labels +<br/> %{$VDWVolumeDataMap->{DataCol<Num>}} - Hash keys pair: + DataCol<Num>, AtomType</div> +</dd> +<dt><strong><a name="stringifymolecularvolumedescriptors" class="item"><strong>StringifyMolecularVolumeDescriptors</strong></a></strong></dt> +<dd> +<div class="OptionsBox"> + $String = $MolecularVolumeDescriptors-> + StringifyMolecularVolumeDescriptors();</div> +<p>Returns a string containing information about <em>MolecularVolumeDescriptors</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="./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> +</table> +</div> +<br /> +<center> +<img src="../../images/h2o2.png"> +</center> +</body> +</html>