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

Uploaded

0:4816e4a8ae95

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.