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diff mayachemtools/docs/modules/man3/EStateValuesDescriptors.3 @ 0:73ae111cf86f draft
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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/man3/EStateValuesDescriptors.3 Wed Jan 20 11:55:01 2016 -0500 @@ -0,0 +1,271 @@ +.\" Automatically generated by Pod::Man 2.25 (Pod::Simple 3.22) +.\" +.\" Standard preamble: +.\" ======================================================================== +.de Sp \" Vertical space (when we can't use .PP) +.if t .sp .5v +.if n .sp +.. +.de Vb \" Begin verbatim text +.ft CW +.nf +.ne \\$1 +.. +.de Ve \" End verbatim text +.ft R +.fi +.. +.\" Set up some character translations and predefined strings. \*(-- will +.\" give an unbreakable dash, \*(PI will give pi, \*(L" will give a left +.\" double quote, and \*(R" will give a right double quote. \*(C+ will +.\" give a nicer C++. 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Always turn off hyphenation; it makes +.\" way too many mistakes in technical documents. +.if n .ad l +.nh +.SH "NAME" +EStateValuesDescriptors +.SH "SYNOPSIS" +.IX Header "SYNOPSIS" +use AtomicDescriptors::EStateValuesDescriptors; +.PP +use AtomicDescriptors::EStateValuesDescriptors qw(:all); +.SH "DESCRIPTION" +.IX Header "DESCRIPTION" +\&\fBEStateValuesDescriptors\fR class provides the following methods: +.PP +new, GenerateDescriptors, StringifyEStateValuesDescriptors +.PP +\&\fBEStateValuesDescriptors\fR is derived from \fBAtomicValues\fR class which in turn +is derived from \fBObjectProperty\fR base class that provides methods not explicitly defined +in \fBEStateValuesDescriptors\fR, \fBAtomicValues\fR or \fBObjectProperty\fR classes using Perl's +\&\s-1AUTOLOAD\s0 functionality. These methods are generated on-the-fly for a specified object property: +.PP +.Vb 3 +\& Set<PropertyName>(<PropertyValue>); +\& $PropertyValue = Get<PropertyName>(); +\& Delete<PropertyName>(); +.Ve +.PP +For calculation of electrotopological state (E\-state) values for non-hydrogen atoms: +.PP +Let: +.PP +.Vb 2 +\& N = Principal quantum number or period number corresponding to +\& element symbol +\& +\& 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 +\& 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 +\& +\& LP = Number of lone pair electrons on atom +\& +\& Zv = Number of electrons in valence shell of atom +\& +\& X = Number of non\-hydrogen atom neighbors or heavy atoms attached +\& to atom +\& H = Number of implicit and explicit hydrogens for atom +\& +\& Delta = Number of sigma electrons involved to bonds to non\-hydrogen +\& atoms +\& DeltaV = ValenceDelta = Number of valence shell electrons not involved +\& in bonding to hydrogen atoms +\& +\& Ii = Intrinsic state value for atom i +\& +\& DeltaIi = Sum of perturbations to intrinsic state value Ii of atom i +\& by all other atoms besides atom i +\& +\& DeltaIij = Perturbation to intrinsic state value Ii of atom i by atom j +\& +\& Dij = Graph/bond distance between atom i and j +\& Rij = Dij + 1 +\& +\& Si = E\-state value for atom i +.Ve +.PP +Then: +.PP +.Vb 1 +\& Delta = Sigma \- H = X +\& +\& DeltaV = Zv \- H +\& = Sigma + PI + LP \- H +\& +\& Ii = ( ( ( 2 / N ) ** 2 ) * DeltaV + 1 ) / Delta +\& +\& DeltaIi = SUM ( (Ii \- Ij) / (Rij ** 2) ) for j = 1 to num of atoms skipping atom i +\& +\& Si = Ii + DeltaIi +.Ve +.PP +The current release of MayaChemTools doesn't support calculation of E\-state +values [ Ref 75\-78 ] for hydrogens. +.SS "\s-1METHODS\s0" +.IX Subsection "METHODS" +.IP "\fBnew\fR" 4 +.IX Item "new" +.Vb 2 +\& $NewEStateValuesDescriptors = new AtomicDescriptors:: +\& EStateValuesDescriptors(%NamesAndValues); +.Ve +.Sp +Using specified \fIEStateValuesDescriptors\fR property names and values hash, \fBnew\fR +method creates a new object and returns a reference to newly created \fBEStateValuesDescriptors\fR +object. By default, the following properties are initialized: +.Sp +.Vb 3 +\& Molecule = \*(Aq\*(Aq +\& Type = \*(AqEState\*(Aq +\& IgnoreHydrogens = 1 +.Ve +.Sp +Examples: +.Sp +.Vb 3 +\& $EStateValuesDescriptors = new AtomicDescriptors::EStateValuesDescriptors( +\& \*(AqMolecule\*(Aq => $Molecule, +\& \*(AqIgnoreHydrogens\*(Aq => 1); +.Ve +.IP "\fBGenerateDescriptors\fR" 4 +.IX Item "GenerateDescriptors" +.Vb 1 +\& $EStateValuesDescriptors\->GenerateDescriptors(); +.Ve +.Sp +Calculates E\-state atomic descriptors for all the atoms in a molecule and returns +\&\fIEStateValuesDescriptors\fR. +.IP "\fBStringifyEStateValuesDescriptors\fR" 4 +.IX Item "StringifyEStateValuesDescriptors" +.Vb 1 +\& $String = $EStateValuesDescriptors\->StringifyEStateValuesDescriptors(); +.Ve +.Sp +Returns a string containing information about \fIEStateValuesDescriptors\fR object. +.SH "AUTHOR" +.IX Header "AUTHOR" +Manish Sud <msud@san.rr.com> +.SH "SEE ALSO" +.IX Header "SEE ALSO" +AtomicDescriptors.pm +.SH "COPYRIGHT" +.IX Header "COPYRIGHT" +Copyright (C) 2015 Manish Sud. All rights reserved. +.PP +This file is part of MayaChemTools. +.PP +MayaChemTools is free software; you can redistribute it and/or modify it under +the terms of the \s-1GNU\s0 Lesser General Public License as published by the Free +Software Foundation; either version 3 of the License, or (at your option) +any later version.