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<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>