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diff mayachemtools/docs/modules/man3/MolecularVolumeDescriptors.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/MolecularVolumeDescriptors.3 Wed Jan 20 11:55:01 2016 -0500 @@ -0,0 +1,267 @@ +.\" 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" +MolecularVolumeDescriptors +.SH "SYNOPSIS" +.IX Header "SYNOPSIS" +use MolecularDescriptors::MolecularVolumeDescriptors; +.PP +use MolecularDescriptors::MolecularVolumeDescriptors qw(:all); +.SH "DESCRIPTION" +.IX Header "DESCRIPTION" +\&\fBMolecularVolumeDescriptors\fR class provides the following methods: +.PP +new, GenerateDescriptors, GetDescriptorNames, +GetVDWAtomRadiiAndVolumesData, StringifyMolecularVolumeDescriptors +.PP +\&\fBMolecularVolumeDescriptors\fR is derived from \fBMolecularDescriptors\fR class which in turn +is derived from \fBObjectProperty\fR base class that provides methods not explicitly defined +in \fBMolecularVolumeDescriptors\fR, \fBMolecularDescriptors\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 +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: +.PP +.Vb 4 +\& vdwMolecularVolume = SumOfAtomicVDWVolumeContributions +\& \- 5.92 * NumOfBonds +\& \- 14.7 * NumOfAromaticRings +\& \- 3.8 * NumOfNonAromaticRings +.Ve +.PP +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 * \s-1PI\s0 * (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. +.SS "\s-1METHODS\s0" +.IX Subsection "METHODS" +.IP "\fBnew\fR" 4 +.IX Item "new" +.Vb 3 +\& $NewMolecularVolumeDescriptors = new MolecularDescriptors:: +\& MolecularVolumeDescriptors( +\& %NamesAndValues); +.Ve +.Sp +Using specified \fIMolecularVolumeDescriptors\fR property names and values hash, \fBnew\fR +method creates a new object and returns a reference to newly created \fBMolecularVolumeDescriptors\fR +object. By default, the following properties are initialized: +.Sp +.Vb 4 +\& Molecule = \*(Aq\*(Aq +\& Type = \*(AqMolecularVolume\*(Aq +\& @DescriptorNames = (\*(AqMolecularVolume\*(Aq) +\& @DescriptorValues = (\*(AqNone\*(Aq) +.Ve +.Sp +Examples: +.Sp +.Vb 2 +\& $MolecularVolumeDescriptors = new MolecularDescriptors:: +\& MolecularVolumeDescriptors(); +\& +\& $MolecularVolumeDescriptors\->SetMolecule($Molecule); +\& $MolecularVolumeDescriptors\->GenerateDescriptors(); +\& print "MolecularVolumeDescriptors: $MolecularVolumeDescriptors\en"; +.Ve +.IP "\fBGenerateDescriptors\fR" 4 +.IX Item "GenerateDescriptors" +.Vb 1 +\& $MolecularVolumeDescriptors\->GenerateDescriptors(); +.Ve +.Sp +Calculate van der Waals molecular volume descriptor for a molecule and returns +\&\fIMolecularVolumeDescriptors\fR. +.IP "\fBGetDescriptorNames\fR" 4 +.IX Item "GetDescriptorNames" +.Vb 3 +\& @DescriptorNames = $MolecularVolumeDescriptors\->GetDescriptorNames(); +\& @DescriptorNames = MolecularDescriptors::MolecularVolumeDescriptors:: +\& GetDescriptorNames(); +.Ve +.Sp +Returns all available descriptor names as an array. +.IP "\fBGetVDWAtomRadiiAndVolumesData\fR" 4 +.IX Item "GetVDWAtomRadiiAndVolumesData" +.Vb 4 +\& $VDWVolumeDataMapRef = $MolecularVolumeDescriptors\-> +\& GetVDWAtomRadiiAndVolumesData(); +\& $VDWVolumeDataMapRef = MolecularDescriptors::MolecularVolumeDescriptors:: +\& GetVDWAtomRadiiAndVolumesData(); +.Ve +.Sp +Returns a hash reference to van der Waals atom symbols corresponding to atom types +and associated data loaded from VDWAtomRadiiAndVolumes.csv data file as a reference +to hash with the following hash data format: +.Sp +.Vb 5 +\& @{$VDWVolumeDataMap{AtomTypes}} \- Array of all possible atom +\& types for all atom symbols +\& @{$VDWVolumeDataMap\->{ColLabels}} \- Array of column labels +\& %{$VDWVolumeDataMap\->{DataCol<Num>}} \- Hash keys pair: +\& DataCol<Num>, AtomType +.Ve +.IP "\fBStringifyMolecularVolumeDescriptors\fR" 4 +.IX Item "StringifyMolecularVolumeDescriptors" +.Vb 2 +\& $String = $MolecularVolumeDescriptors\-> +\& StringifyMolecularVolumeDescriptors(); +.Ve +.Sp +Returns a string containing information about \fIMolecularVolumeDescriptors\fR object. +.SH "AUTHOR" +.IX Header "AUTHOR" +Manish Sud <msud@san.rr.com> +.SH "SEE ALSO" +.IX Header "SEE ALSO" +MolecularDescriptors.pm, MolecularDescriptorsGenerator.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.