NAME
    MMFF94AtomTypes

SYNOPSIS
    use AtomTypes::MMFF94AtomTypes;

    use AtomTypes::MMFF94AtomTypes qw(:all);

DESCRIPTION
    MMFF94AtomTypes class provides the following methods:

    new, AssignAtomTypes, GetAllPossibleMMFF94AtomTypes,
    GetAllPossibleMMFF94NonHydrogenAtomTypes, GetMMFF94AtomTypesData,
    StringifyMMFF94AtomTypes

    The following functions are available:

    GetAllPossibleMMFF94AtomTypes, GetAllPossibleMMFF94NonHydrogenAtomTypes,
    GetMMFF94AtomTypesData

    MMFF94AtomTypes is derived from AtomTypes class which in turn is derived
    from ObjectProperty base class that provides methods not explicitly
    defined in MMFF94AtomTypes, AtomTypes 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 data file MMFF94AtomTypes.csv distributed with MayaChemTools release
    contains all possible MMFF94 [ Ref 83-87 ] atom types.

    Examples of MMFF94 atom types:

        CR, C=C, C=N, C=S, NR, N=C, OR, OC=O and so on

  METHODS
    new
            $NewMMFF94AtomTypes = new AtomTypes::MMFF94AtomTypes(%NamesAndValues);

        Using specified *MMFF94AtomTypes* property names and values hash,
        new method creates a new object and returns a reference to newly
        created MMFF94AtomTypes object. By default, the following properties
        are initialized:

            Molecule = ''
            Type = 'MMFF94'
            IgnoreHydrogens = 0

        Examples:

            $MMFF94AtomTypes = new AtomTypes::MMFF94AtomTypes(
                                      'Molecule' => $Molecule,
                                      'IgnoreHydrogens' => 0);

    AssignAtomTypes
            $MMFF94AtomTypes->AssignAtomTypes();

        Assigns MMFF94 atom types to all the atoms in a molecule and returns
        *MMFF94AtomTypes*.

    GetAllPossibleMMFF94AtomTypes
            $AllAtomTypesDataRef = $MMFF94AtomTypes->
                                   GetAllPossibleMMFF94AtomTypes();
            $AllAtomTypesDataRef = AtomTypes::MMFF94AtomTypes::
                                   GetAllPossibleMMFF94AtomTypes();

        Returns all possible MMFF94 atom types corresponding to hydrogen and
        non-hydrogen atoms as an array reference.

    GetAllPossibleMMFF94NonHydrogenAtomTypes
            $AtomTypesDataRef = $MMFF94AtomTypes->
                                GetAllPossibleMMFF94NonHydrogenAtomTypes();
            $AtomTypesDataRef = AtomTypes::MMFF94AtomTypes::
                                GetAllPossibleMMFF94NonHydrogenAtomTypes();

        Returns all possible MMFF94 atom types corresponding to non-hydrogen
        atoms as an array reference.

    GetMMFF94AtomTypesData
            $AtomTypesDataMapRef = $MMFF94AtomTypes->GetMMFF94AtomTypesData();
            $AtomTypesDataMapRef = AtomTypes::MMFF94AtomTypes::
                                   GetMMFF94AtomTypesData();

        Returns MMFF94 atom types and associated data loaded from MMFF94
        data file as a reference to hash with the following hash data
        format:

            @{$MMFF94AtomTypesDataMap{AtomTypes}} - Array of all possible atom
                                      types for all atoms
            @{$MMFF94AtomTypesDataMap{NonHydrogenAtomTypes}} - Array of all
                                      possible atom types for non-hydrogen atoms
            @{$MMFF94AtomTypesDataMap->{ColLabels}} - Array of column labels
            %{$MMFF94AtomTypesDataMap->{DataCol<Num>}} - Hash keys pair:
                                                         DataCol<Num>, AtomType

    StringifyMMFF94AtomTypes
            $String = $MMFF94AtomTypes->StringifyMMFF94AtomTypes();

        Returns a string containing information about *MMFF94AtomTypes*
        object.

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

SEE ALSO
    AtomTypes.pm, AtomicInvariantsAtomTypes.pm, DREIDINGAtomTypes.pm,
    EStateAtomTypes.pm, FunctionalClassAtomTypes.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.

