NAME
    AtomTypes - AtomTypes class

SYNOPSIS
    use AtomTypes::AtomTypes;

    use AtomTypes::AtomTypes qw(:all);

DESCRIPTION
    AtomTypes base class used to derive all other atom types classes
    provides the following methods:

    new, GetAtomType, GetAtomTypes, IsAtomTypesAssignmentSuccessful,
    LoadAtomTypesData, SetAtomType, SetMolecule, SetType

    AtomTypes class is derived from ObjectProperty base class which provides
    methods not explicitly defined in Fingerprints 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>();

  METHODS
    new
            $NewAtomTypes = new AtomTypes::AtomTypes(%NamesAndValues);

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

            Molecule = '';
            Type = '';
            IgnoreHydrogens = 0;

    GetAtomType
            $AtomType = $AtomTypes->GetAtomType($Atom);

        Returns AtomType value string assigned to *Atom* by *AtomTypes*
        object.

    GetAtomTypes
            %AtomTypes = $AtomTypes->GetAtomTypes();

        Returns atom types assigned to atoms by *AtomTypes* object as a hash
        with atom ID and atom types as key and value pairs.

    IsAtomTypesAssignmentSuccessful
            $Status = $AtomTypes->IsAtomTypesAssignmentSuccessful();

        Returns 1 or 0 based on whether atom types assignment was
        successfully performed. For a successful atom types assignment, all
        atoms must have an atom type other than a string *None*.

    LoadAtomTypesData
            $AtomTypes->LoadAtomTypesData($AtomTypesDataMapRef);
            AtomTypes::AtomTypes::LoadAtomTypesData($AtomTypesDataMapRef);

        Loads atom types data from the specified CSV atom type file into the
        specified hash reference.

        The lines starting with # are treated as comments and ignored. First
        line not starting with # must contain column labels and the number
        of columns in all other data rows must match the number of column
        labels.

        The first column is assumed to contain atom types; all other columns
        contain data as indicated in their column labels.

        In order to avoid dependence of data access on the specified column
        labels, the column data is loaded into hash with *DataColNum* and
        *AtomType* as hash keys; however, the data for the first column
        which is treated as AtomTypes is also loaded into an array with
        AtomTypes as hash key. The format of the data structure loaded into
        a specified hash reference is:

            @{$AtomTypesDataMapRef->{AtomTypes}} - Array of all possible atom
                                                   types for all atoms
            @{$AtomTypesDataMapRef->{NonHydrogenAtomTypes}} - Array of all possible
                                                   atom types for non-hydrogen atoms
            @{$AtomTypesDataMapRef->{ColLabels}} - Array of column labels
            %{$AtomTypesDataMapRef->{DataCol<ColNum>}} - Hash keys pair:
                                                   <DataCol<ColNum>, AtomType>

        *ColNum* starts from 1. Column data for first column is not loaded
        into *DataColNum*, *AtomType* hash keys pairs.

    SetAtomType
            $AtomTypes->SetAtomType($Atom, $AtomType);

        Assigns specific *AtomType* to *Atom* and returns *AtomTypes*.

    SetMolecule
            $AtomTypes->SetMolecule($Molecule);

        Sets *Molecule* object for *AtomTypes* and retuens *AtomTypes*.

    SetType
            $AtomTypes->SetType($Type);

        Sets *Type* for *AtomTypes* object and retuens *AtomTypes*.

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

SEE ALSO
    AtomicInvariantsAtomTypes.pm, DREIDINGAtomTypes.pm, EStateAtomTypes.pm,
    FunctionalClassAtomTypes.pm, MMFF94AtomTypes.pm, SLogPAtomTypes.pm,
    SYBYLAtomTypes.pm, TPSAAtomTypes.pm, UFFAtomTypes.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.

