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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/EStateValuesDescriptors.html Wed Jan 20 11:55:01 2016 -0500 @@ -0,0 +1,156 @@ +<html> +<head> +<title>MayaChemTools:Documentation:AtomicDescriptors::EStateValuesDescriptors.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="./AtomicDescriptors.html" title="AtomicDescriptors.html">Previous</a> <a href="./index.html" title="Table of Contents">TOC</a> <a href="./AtomicInvariantsAtomTypes.html" title="AtomicInvariantsAtomTypes.html">Next</a></td><td width="34%" align="middle"><strong>AtomicDescriptors::EStateValuesDescriptors.pm</strong></td><td width="33%" align="right"><a href="././code/EStateValuesDescriptors.html" title="View source code">Code</a> | <a href="./../pdf/EStateValuesDescriptors.pdf" title="PDF US Letter Size">PDF</a> | <a href="./../pdfgreen/EStateValuesDescriptors.pdf" title="PDF US Letter Size with narrow margins: www.changethemargins.com">PDFGreen</a> | <a href="./../pdfa4/EStateValuesDescriptors.pdf" title="PDF A4 Size">PDFA4</a> | <a href="./../pdfa4green/EStateValuesDescriptors.pdf" title="PDF A4 Size with narrow margins: www.changethemargins.com">PDFA4Green</a></td></tr> +</table> +</div> +<p> +</p> +<h2>NAME</h2> +<p>EStateValuesDescriptors</p> +<p> +</p> +<h2>SYNOPSIS</h2> +<p>use AtomicDescriptors::EStateValuesDescriptors;</p> +<p>use AtomicDescriptors::EStateValuesDescriptors qw(:all);</p> +<p> +</p> +<h2>DESCRIPTION</h2> +<p><strong>EStateValuesDescriptors</strong> class provides the following methods:</p> +<p> <a href="#new">new</a>, <a href="#generatedescriptors">GenerateDescriptors</a>, <a href="#stringifyestatevaluesdescriptors">StringifyEStateValuesDescriptors</a> +</p><p><strong>EStateValuesDescriptors</strong> is derived from <strong>AtomicValues</strong> class which in turn +is derived from <strong>ObjectProperty</strong> base class that provides methods not explicitly defined +in <strong>EStateValuesDescriptors</strong>, <strong>AtomicValues</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>For calculation of electrotopological state (E-state) values for non-hydrogen atoms:</p> +<p>Let:</p> +<div class="OptionsBox"> + N = Principal quantum number or period number corresponding to +<br/> element symbol</div> +<div class="OptionsBox"> + Sigma = Number of sigma electrons involves in bonds to hydrogen and + non-hydrogen atoms attached to atom + = Number of sigma bonds to hydrogen and non-hydrogen atoms + attached to atom +<br/> PI = Number of PI electrons involved in bonds to non-hydrogen atoms + attached to atom + = Number of PI bonds to non-hydrogen atoms attached to atom</div> +<div class="OptionsBox"> + LP = Number of lone pair electrons on atom</div> +<div class="OptionsBox"> + Zv = Number of electrons in valence shell of atom</div> +<div class="OptionsBox"> + X = Number of non-hydrogen atom neighbors or heavy atoms attached +<br/> to atom +<br/> H = Number of implicit and explicit hydrogens for atom</div> +<div class="OptionsBox"> + Delta = Number of sigma electrons involved to bonds to non-hydrogen + atoms +<br/> DeltaV = ValenceDelta = Number of valence shell electrons not involved + in bonding to hydrogen atoms</div> +<div class="OptionsBox"> + Ii = Intrinsic state value for atom i</div> +<div class="OptionsBox"> + DeltaIi = Sum of perturbations to intrinsic state value Ii of atom i + by all other atoms besides atom i</div> +<div class="OptionsBox"> + DeltaIij = Perturbation to intrinsic state value Ii of atom i by atom j</div> +<div class="OptionsBox"> + Dij = Graph/bond distance between atom i and j +<br/> Rij = Dij + 1</div> +<div class="OptionsBox"> + Si = E-state value for atom i</div> +<p>Then:</p> +<div class="OptionsBox"> + Delta = Sigma - H = X</div> +<div class="OptionsBox"> + DeltaV = Zv - H + = Sigma + PI + LP - H</div> +<div class="OptionsBox"> + Ii = ( ( ( 2 / N ) ** 2 ) * DeltaV + 1 ) / Delta</div> +<div class="OptionsBox"> + DeltaIi = SUM ( (Ii - Ij) / (Rij ** 2) ) for j = 1 to num of atoms skipping atom i</div> +<div class="OptionsBox"> + Si = Ii + DeltaIi</div> +<p>The current release of MayaChemTools doesn't support calculation of E-state +values [ Ref 75-78 ] for hydrogens.</p> +<p> +</p> +<h2>METHODS</h2> +<dl> +<dt><strong><a name="new" class="item"><strong>new</strong></a></strong></dt> +<dd> +<div class="OptionsBox"> + $NewEStateValuesDescriptors = new AtomicDescriptors:: + EStateValuesDescriptors(%NamesAndValues);</div> +<p>Using specified <em>EStateValuesDescriptors</em> property names and values hash, <strong>new</strong> +method creates a new object and returns a reference to newly created <strong>EStateValuesDescriptors</strong> +object. By default, the following properties are initialized:</p> +<div class="OptionsBox"> + Molecule = '' +<br/> Type = 'EState' +<br/> IgnoreHydrogens = 1</div> +<p>Examples:</p> +<div class="OptionsBox"> + $EStateValuesDescriptors = new AtomicDescriptors::EStateValuesDescriptors( + 'Molecule' => $Molecule, + 'IgnoreHydrogens' => 1);</div> +</dd> +<dt><strong><a name="generatedescriptors" class="item"><strong>GenerateDescriptors</strong></a></strong></dt> +<dd> +<div class="OptionsBox"> + $EStateValuesDescriptors->GenerateDescriptors();</div> +<p>Calculates E-state atomic descriptors for all the atoms in a molecule and returns +<em>EStateValuesDescriptors</em>.</p> +</dd> +<dt><strong><a name="stringifyestatevaluesdescriptors" class="item"><strong>StringifyEStateValuesDescriptors</strong></a></strong></dt> +<dd> +<div class="OptionsBox"> + $String = $EStateValuesDescriptors->StringifyEStateValuesDescriptors();</div> +<p>Returns a string containing information about <em>EStateValuesDescriptors</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="./AtomicDescriptors.html">AtomicDescriptors.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="./AtomicDescriptors.html" title="AtomicDescriptors.html">Previous</a> <a href="./index.html" title="Table of Contents">TOC</a> <a href="./AtomicInvariantsAtomTypes.html" title="AtomicInvariantsAtomTypes.html">Next</a></td><td width="34%" align="middle"><strong>March 29, 2015</strong></td><td width="33%" align="right"><strong>AtomicDescriptors::EStateValuesDescriptors.pm</strong></td></tr> +</table> +</div> +<br /> +<center> +<img src="../../images/h2o2.png"> +</center> +</body> +</html>