diff docs/modules/txt/RingsCountDescriptors.txt @ 0:4816e4a8ae95 draft default tip

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+++ b/docs/modules/txt/RingsCountDescriptors.txt	Wed Jan 20 09:23:18 2016 -0500
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+NAME
+    RingsCountDescriptors
+
+SYNOPSIS
+    use MolecularDescriptors::RingsCountDescriptors;
+
+    use MolecularDescriptors::RingsCountDescriptors qw(:all);
+
+DESCRIPTION
+    RingsCountDescriptors class provides the following methods:
+
+    new, GenerateDescriptors, GetDescriptorNames,
+    StringifyRingsCountDescriptors
+
+    RingsCountDescriptors is derived from MolecularDescriptors class which
+    in turn is derived from ObjectProperty base class that provides methods
+    not explicitly defined in RingsCountDescriptors, MolecularDescriptors or
+    ObjectProperty classes using Perl's AUTOLOAD functionality. These
+    methods are generated on-the-fly for a specified object property:
+
+        Set<PropertyName>(<PropertyValue>);
+        $PropertyValue = Get<PropertyName>();
+        Delete<PropertyName>();
+
+    RingsCountDescriptors 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 DetectRings [Ref 31] and DetectAromaticity methods available in
+    Molecule.
+
+    DetectAromaticity method available in Molecule class assigns aromaticity
+    to rings using Huckel rule as explained below:
+
+    o Ring aromaticity is determined using Huckel's rule: a ring containing
+    4n + 2 pi electrons is considered aromatic.
+
+    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)
+
+    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.
+
+  METHODS
+    new
+            $NewRingsCountDescriptors = new MolecularDescriptors::
+                                        RingsCountDescriptors(
+                                        %NamesAndValues);
+
+        Using specified *RingsCountDescriptors* property names and values
+        hash, new method creates a new object and returns a reference to
+        newly created RingsCountDescriptors object. By default, the
+        following properties are initialized:
+
+            Molecule = ''
+            Type = 'RingsCount'
+
+            @DescriptorNames = ('Rings', 'AromaticRings')
+            @DescriptorValues = ('None', 'None')
+
+        Examples:
+
+            $RingsCountDescriptors = new MolecularDescriptors::RingsCountDescriptors(
+                                      'Molecule' => $Molecule);
+
+            $RingsCountDescriptors = new MolecularDescriptors::RingsCountDescriptors();
+
+            $RingsCountDescriptors->SetMolecule($Molecule);
+            $RingsCountDescriptors->GenerateDescriptors();
+            print "RingsCountDescriptors: $RingsCountDescriptors\n";
+
+    GenerateDescriptors
+            $RingsCountDescriptors->GenerateDescriptors();
+
+        Calculate number of rings and aromatic rings in a molecule and
+        returns *RingsCountDescriptors*.
+
+    GetDescriptorNames
+            @DescriptorNames = $RingsCountDescriptors->GetDescriptorNames();
+            @DescriptorNames = MolecularDescriptors::RingsCountDescriptors::
+                               GetDescriptorNames();
+
+        Returns all available descriptor names as an array.
+
+    StringifyRingsCountDescriptors
+            $String = $RingsCountDescriptors->
+                                      StringifyRingsCountDescriptors();
+
+        Returns a string containing information about
+        *RingsCountDescriptors* object.
+
+AUTHOR
+    Manish Sud <[e-mail]>
+
+SEE ALSO
+    MolecularDescriptors.pm, MolecularDescriptorsGenerator.pm
+
+COPYRIGHT
+    Copyright (C) 2015 Manish Sud. All rights reserved.
+
+    This file is part of MayaChemTools.
+
+    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.
+