NAME
    HydrogenBondsDescriptors

SYNOPSIS
    use MolecularDescriptors::HydrogenBondsDescriptors;

    use MolecularDescriptors::HydrogenBondsDescriptors qw(:all);

DESCRIPTION
    HydrogenBondsDescriptors class provides the following methods:

    new, GenerateDescriptors, GetDescriptorNames, SetHydrogenBondsType,
    StringifyHydrogenBondsDescriptors

    HydrogenBondsDescriptors is derived from MolecularDescriptors class
    which in turn is derived from ObjectProperty base class that provides
    methods not explicitly defined in HydrogenBondsDescriptors,
    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>();

    The current release of MayaChemTools supports identification of two
    types of hydrogen bond donor and acceptor atoms with these names:

        HBondsType1 or HydrogenBondsType1
        HBondsType2 or HydrogenBondsType2

    The names of these hydrogen bond types are rather arbitrary. However,
    their definitions have specific meaning and are as follows:

        HydrogenBondsType1 [ Ref 60-61, Ref 65-66 ]:

            Donor: NH, NH2, OH - Any N and O with available H
            Acceptor: N[!H], O - Any N without available H and any O

        HydrogenBondsType2 [ Ref 91 ]:

            Donor: NH, NH2, OH - N and O with available H
            Acceptor: N, O - And N and O

    By default, *HydrogenBondsType2* is used to calculate number hydrogen
    bond donor and acceptor atoms. This corresponds to RuleOf5 definition of
    hydrogen bond donors and acceptors.

  METHODS
    new
            $HydrogenBondsDescriptors = new MolecularDescriptors::
                                        HydrogenBondsDescriptors(%NamesAndValues);

        Using specified *HydrogenBondsDescriptors* property names and values
        hash, new method creates a new object and returns a reference to
        newly created HydrogenBondsDescriptors object. By default, the
        following properties are initialized:

            Molecule = ''
            Type = 'HydrogenBonds'
            HydrogenBondsType = 'HBondsType2'
            @DescriptorNames = ('HydrogenBondDonors', 'HydrogenBondAcceptors')
            @DescriptorValues = ('None', 'None')

        Examples:

            $HydrogenBondsDescriptors = new MolecularDescriptors::
                                        HydrogenBondsDescriptors();

            $HydrogenBondsDescriptors = new MolecularDescriptors::
                                        HydrogenBondsDescriptors(
                                        'HydrogenBondsType' => 'HBondsType2');

            $HydrogenBondsDescriptors->SetMolecule($Molecule);
            $HydrogenBondsDescriptors->GenerateDescriptors();
            print "HydrogenBondsDescriptors: $HydrogenBondsDescriptors\n";

    GenerateDescriptors
            $HydrogenBondsDescriptors->GenerateDescriptors();

        Calculates number of hydrogen bond donors and acceptors a molecule
        and returns *HydrogenBondsDescriptors*.

    GetDescriptorNames
            @DescriptorNames = $HydrogenBondsDescriptors->GetDescriptorNames();
            @DescriptorNames = MolecularDescriptors::HydrogenBondsDescriptors::
                               GetDescriptorNames();

        Returns all available descriptor names as an array.

    SetHydrogenBondsType
            $HydrogenBondsDescriptors->SetHydrogenBondsType($HBondsType);

        Sets value of hydrogen bonds type to use during calculation of
        descriptors and returns *HydrogenBondsDescriptors*. Possible values:
        *HBondsType1, HydrogenBondsType1, HBondsType2, HydrogenBondsType2*.

    StringifyHydrogenBondsDescriptors
            $String = $HydrogenBondsDescriptors->
                                      StringifyHydrogenBondsDescriptors();

        Returns a string containing information about
        *HydrogenBondsDescriptors* object.

AUTHOR
    Manish Sud <msud@san.rr.com>

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.

