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.\" ========================================================================
.\"
.IX Title "TPSADESCRIPTORS 1"
.TH TPSADESCRIPTORS 1 "2015-03-29" "perl v5.14.2" "MayaChemTools"
.\" For nroff, turn off justification.  Always turn off hyphenation; it makes
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.SH "NAME"
TPSADescriptors
.SH "SYNOPSIS"
.IX Header "SYNOPSIS"
use MolecularDescriptors::TPSADescriptors;
.PP
use MolecularDescriptors::TPSADescriptors qw(:all);
.SH "DESCRIPTION"
.IX Header "DESCRIPTION"
\&\fBTPSADescriptors\fR class provides the following methods:
.PP
new, GenerateDescriptors, GetDescriptorNames, StringifyTPSADescriptors
.PP
\&\fBTPSADescriptors\fR is derived from \fBMolecularDescriptors\fR class which in turn
is  derived from \fBObjectProperty\fR base class that provides methods not explicitly defined
in \fBTPSADescriptors\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
After Topological Polar Surface Area (\s-1TPSA\s0) atom types [ Ref 90\-91 ] has been assigned
to appropriate atoms in a molecule using AtomTypes::TPSAAtomTypes.pm module,  \s-1TPSA\s0 value
is calculated by adding up contributions of each appropriate atom type.
.PP
By default, MayaChemTools only uses nitrogen and oxygen atoms during calculation
of \s-1TPSA\s0 and ignores phosphorous and sulfur atoms. [ Ref 90 \- 91 ]
.SS "\s-1METHODS\s0"
.IX Subsection "METHODS"
.IP "\fBnew\fR" 4
.IX Item "new"
.Vb 2
\&    $NewTPSADescriptors = new MolecularDescriptors::TPSADescriptors(
\&                                                   %NamesAndValues);
.Ve
.Sp
Using specified \fITPSADescriptors\fR property names and values hash, \fBnew\fR
method creates a new object and returns a reference to newly created \fBTPSADescriptors\fR
object. By default, the following properties are initialized:
.Sp
.Vb 6
\&    Molecule = \*(Aq\*(Aq
\&    Type = \*(AqTPSA\*(Aq
\&    IgnorePhosphorus = 1
\&    IgnoreSulfur = 1
\&    @DescriptorNames = (\*(AqTPSA\*(Aq)
\&    @DescriptorValues = (\*(AqNone\*(Aq)
.Ve
.Sp
Examples:
.Sp
.Vb 2
\&    $TPSADescriptors = new MolecularDescriptors::TPSADescriptors(
\&                              \*(AqMolecule\*(Aq => $Molecule);
\&
\&    $TPSADescriptors = new MolecularDescriptors::TPSADescriptors();
\&
\&    $TPSADescriptors = new MolecularDescriptors::TPSADescriptors(
\&                              \*(AqIgnorePhosphorus\*(Aq => 0,
\&                              \*(AqIgnoreSulfur\*(Aq => 0);
\&
\&    $TPSADescriptors\->SetMolecule($Molecule);
\&    $TPSADescriptors\->GenerateDescriptors();
\&    print "TPSADescriptors: $TPSADescriptors\en";
.Ve
.IP "\fBGenerateDescriptors\fR" 4
.IX Item "GenerateDescriptors"
.Vb 1
\&    $TPSADescriptors\->GenerateDescriptors();
.Ve
.Sp
Calculate \s-1TPSA\s0 value for a molecule and returns \fITPSADescriptors\fR.
.IP "\fBGetDescriptorNames\fR" 4
.IX Item "GetDescriptorNames"
.Vb 3
\&    @DescriptorNames = $TPSADescriptors\->GetDescriptorNames();
\&    @DescriptorNames = MolecularDescriptors::TPSADescriptors::
\&                       GetDescriptorNames();
.Ve
.Sp
Returns all available descriptor names as an array.
.IP "\fBStringifyTPSADescriptors\fR" 4
.IX Item "StringifyTPSADescriptors"
.Vb 1
\&    $String = $TPSADescriptors\->StringifyTPSADescriptors();
.Ve
.Sp
Returns a string containing information about \fITPSADescriptors\fR object.
.SH "AUTHOR"
.IX Header "AUTHOR"
Manish Sud <[e-mail]>
.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.