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.\" ========================================================================
.\"
.IX Title "RINGSCOUNTDESCRIPTORS 1"
.TH RINGSCOUNTDESCRIPTORS 1 "2015-03-29" "perl v5.14.2" "MayaChemTools"
.\" For nroff, turn off justification.  Always turn off hyphenation; it makes
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.nh
.SH "NAME"
RingsCountDescriptors
.SH "SYNOPSIS"
.IX Header "SYNOPSIS"
use MolecularDescriptors::RingsCountDescriptors;
.PP
use MolecularDescriptors::RingsCountDescriptors qw(:all);
.SH "DESCRIPTION"
.IX Header "DESCRIPTION"
\&\fBRingsCountDescriptors\fR class provides the following methods:
.PP
new, GenerateDescriptors, GetDescriptorNames, StringifyRingsCountDescriptors
.PP
\&\fBRingsCountDescriptors\fR is derived from \fBMolecularDescriptors\fR class which in turn
is  derived from \fBObjectProperty\fR base class that provides methods not explicitly defined
in \fBRingsCountDescriptors\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
\&\fBRingsCountDescriptors\fR class doesn't perform any ring or aromaticity detection before
counting their number in a molecule. Instead, it assumes ring and aromaticity detection have
been performed by caller using \fBDetectRings\fR [Ref 31] and \fBDetectAromaticity\fR methods
available in \fBMolecule\fR.
.PP
\&\fBDetectAromaticity\fR method available in \fBMolecule\fR class assigns aromaticity to rings
using Huckel rule as explained below:
.PP
o Ring aromaticity is determined using Huckel's rule: a ring containing 4n + 2 pi electrons is
considered aromatic.
.PP
o Hetrocyclic rings containing N, O and S atoms fall into two classes: Basic aromatic and
Non-basic aromatic. In Basic aromatic hetrocyclic rings, heteroatom itself is involved in a
double bond. (e.g. Pyridine) However, in non-basic hetrocyclic rings, heteroatom might have
an attached hydrogen atom and the remaining lone pair contribute to electron delocalization
and contributes to 4n + 2 electrons. (e.g. Pyrrole, Furan)
.PP
o For molecules containing fused rings, each fused ring set is considered as one aromatic
system for counting pi electrons to satisfy Huckel's rule; In case of a failure, rings in
fused set are treated individually for aromaticity detection. Additionally, non-fused
rings are handled on their own during aromaticity detection.
.SS "\s-1METHODS\s0"
.IX Subsection "METHODS"
.IP "\fBnew\fR" 4
.IX Item "new"
.Vb 3
\&    $NewRingsCountDescriptors = new MolecularDescriptors::
\&                                RingsCountDescriptors(
\&                                %NamesAndValues);
.Ve
.Sp
Using specified \fIRingsCountDescriptors\fR property names and values hash, \fBnew\fR
method creates a new object and returns a reference to newly created \fBRingsCountDescriptors\fR
object. By default, the following properties are initialized:
.Sp
.Vb 2
\&    Molecule = \*(Aq\*(Aq
\&    Type = \*(AqRingsCount\*(Aq
\&
\&    @DescriptorNames = (\*(AqRings\*(Aq, \*(AqAromaticRings\*(Aq)
\&    @DescriptorValues = (\*(AqNone\*(Aq, \*(AqNone\*(Aq)
.Ve
.Sp
Examples:
.Sp
.Vb 2
\&    $RingsCountDescriptors = new MolecularDescriptors::RingsCountDescriptors(
\&                              \*(AqMolecule\*(Aq => $Molecule);
\&
\&    $RingsCountDescriptors = new MolecularDescriptors::RingsCountDescriptors();
\&
\&    $RingsCountDescriptors\->SetMolecule($Molecule);
\&    $RingsCountDescriptors\->GenerateDescriptors();
\&    print "RingsCountDescriptors: $RingsCountDescriptors\en";
.Ve
.IP "\fBGenerateDescriptors\fR" 4
.IX Item "GenerateDescriptors"
.Vb 1
\&    $RingsCountDescriptors\->GenerateDescriptors();
.Ve
.Sp
Calculate number of rings and aromatic rings in a molecule and returns
\&\fIRingsCountDescriptors\fR.
.IP "\fBGetDescriptorNames\fR" 4
.IX Item "GetDescriptorNames"
.Vb 3
\&    @DescriptorNames = $RingsCountDescriptors\->GetDescriptorNames();
\&    @DescriptorNames = MolecularDescriptors::RingsCountDescriptors::
\&                       GetDescriptorNames();
.Ve
.Sp
Returns all available descriptor names as an array.
.IP "\fBStringifyRingsCountDescriptors\fR" 4
.IX Item "StringifyRingsCountDescriptors"
.Vb 2
\&    $String = $RingsCountDescriptors\->
\&                              StringifyRingsCountDescriptors();
.Ve
.Sp
Returns a string containing information about \fIRingsCountDescriptors\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.