NAME
    TPSAAtomTypes

SYNOPSIS
    use AtomTypes::TPSAAtomTypes;

    use AtomTypes::TPSAAtomTypes qw(:all);

DESCRIPTION
    TPSAAtomTypes class provides the following methods:

    new, AssignAtomTypes, GetAllPossibleTPSAAtomTypes, GetTPSAAtomTypesData,
    StringifyTPSAAtomTypes

    The following functions are available:

    GetAllPossibleTPSAAtomTypes, GetTPSAAtomTypesData

    TPSAAtomTypes is derived from AtomTypes class which in turn is derived
    from ObjectProperty base class that provides methods not explicitly
    defined in TPSAAtomTypes, 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 TPSAAomTypes.csv distributed with MayaChemTools release
    contains all possible topological surface area (TPSA) [ Ref 90-91 ] atom
    types.

    The atom type symbols assigned by MayaChemTools are not used in the
    original publication and the numbers in atom symbols for element types
    simply correspond to their order of appearance in Table 1 [ Ref 90 ].

    Examples of TPSA atom types:

        N1, N2, N3, O1, O2, O3, S1, S2, P1, P2 and so on

  METHODS
    new
            $NewTPSAAtomTypes = new AtomTypes::TPSAAtomTypes(%NamesAndValues);

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

            Molecule = ''
            Type = 'TPSA'
            IgnorePhosphorus = 0
            IgnoreSulfur = 0

        Examples:

            $TPSAAtomTypes = new AtomTypes::TPSAAtomTypes(
                                      'Molecule' => $Molecule,
                                      'IgnorePhosphorus' => 0,
                                      'IgnoreSulfur' => 0);

    AssignAtomTypes
            $TPSAAtomTypes->AssignAtomTypes();

        Assigns TPSA atom types to all the atoms in a molecule and returns
        *TPSAAtomTypes*.

    GetAllPossibleTPSAAtomTypes
            $AllAtomTypesDataRef = $TPSAAtomTypes->
                                   GetAllPossibleTPSAAtomTypes();
            $AllAtomTypesDataRef = AtomTypes::TPSAAtomTypes::
                                   GetAllPossibleTPSAAtomTypes();

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

    GetTPSAAtomTypesData
            $AtomTypesDataMapRef = $TPSAAtomTypes->GetTPSAAtomTypesData();
            $AtomTypesDataMapRef = AtomTypes::TPSAAtomTypes::GetTPSAAtomTypesData();

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

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

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

        Returns 1 or 0 based on whether atom types assignment was
        successfully performed. This method overrides the same method
        available in the base class AtomTypes.pm used to derived this class.
        It checks for successful atom type assignments for nitrogen and
        oxygen atoms with an optional check for phosphorous and sulfur
        atoms.

    StringifyTPSAAtomTypes
            $String = $TPSAAtomTypes->StringifyTPSAAtomTypes();

        Returns a string containing information about *TPSAAtomTypes*
        object.

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

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

