NAME
    SYBYLAtomTypes

SYNOPSIS
    use AtomTypes::SYBYLAtomTypes;

    use AtomTypes::SYBYLAtomTypes qw(:all);

DESCRIPTION
    SYBYLAtomTypes class provides the following methods:

    new, AssignAtomTypes, GetAllPossibleSYBYLAtomTypes,
    GetAllPossibleSYBYLNonHydrogenAtomTypes, GetSYBYLAtomTypesData,
    StringifySYBYLAtomTypes

    The following functions are available:

    GetAllPossibleSYBYLAtomTypes, GetAllPossibleSYBYLNonHydrogenAtomTypes,
    GetSYBYLAtomTypesData

    SYBYLAtomTypes is derived from AtomTypes class which in turn is derived
    from ObjectProperty base class that provides methods not explicitly
    defined in SYBYLAtomTypes, 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 SYBYLAomTypes.csv distributed with MayaChemTools release
    contains all possible Triops SYBYL [ Ref 79-80 ] atom types.

    Examples of SYBYL atom types:

        C.3,C.2, C.ar, N.3, N.2, N.ar and so on

  METHODS
    new
            $NewSYBYLAtomTypes = new AtomTypes::SYBYLAtomTypes(%NamesAndValues);

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

            Molecule = ''
            Type = 'SYBYL'
            IgnoreHydrogens = 0

        Examples:

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

    AssignAtomTypes
            $SYBYLAtomTypes->AssignAtomTypes();

        Assigns SYBYL atom types to all the atoms in a molecule and returns
        *SYBYLAtomTypes*.

    GetAllPossibleSYBYLAtomTypes
            $AllAtomTypesDataRef = $SYBYLAtomTypes->
                                   GetAllPossibleSYBYLAtomTypes();
            $AllAtomTypesDataRef = AtomTypes::SYBYLAtomTypes::
                                   GetAllPossibleSYBYLAtomTypes();

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

    GetAllPossibleSYBYLNonHydrogenAtomTypes
            $AtomTypesDataRef = $SYBYLAtomTypes->
                                GetAllPossibleSYBYLNonHydrogenAtomTypes();
            $AtomTypesDataRef = AtomTypes::SYBYLAtomTypes::
                                GetAllPossibleSYBYLNonHydrogenAtomTypes();

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

    GetSYBYLAtomTypesData
            $AtomTypesDataMapRef = $SYBYLAtomTypes->GetSYBYLAtomTypesData();
            $AtomTypesDataMapRef = AtomTypes::SYBYLAtomTypes::GetSYBYLAtomTypesData();

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

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

    StringifySYBYLAtomTypes
            $String = $SYBYLAtomTypes->StringifySYBYLAtomTypes();

        Returns a string containing information about *SYBYLAtomTypes*
        object.

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

SEE ALSO
    AtomTypes.pm, AtomicInvariantsAtomTypes.pm, DREIDINGAtomTypes.pm,
    EStateAtomTypes.pm, FunctionalClassAtomTypes.pm, MMFF94AtomTypes.pm,
    SLogPAtomTypes.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.

