NAME
    AtomicInvariantsAtomTypes

SYNOPSIS
    use AtomTypes::AtomicInvariantsAtomTypes;

    use AtomTypes::AtomicInvariantsAtomTypes qw(:all);

DESCRIPTION
    AtomicInvariantsAtomTypes class provides the following methods:

    new, AssignAtomTypes, GetAtomicInvariantsOrder,
    GetAvailableAtomicInvariants, IsAtomicInvariantAvailable,
    SetAtomicInvariantsToUse, StringifyAtomicInvariantsAtomTypes

    The following functions are available:

    GetAvailableAtomicInvariants, IsAtomicInvariantAvailable

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

    Possible values for atomic invariants are: *AS, X, BO, LBO, SB, DB, TB,
    H, Ar, RA, FC, MN, SM*. Default atom invariants values: *AS,X,BO,H,FC*.

    The atomic invariants abbreviations correspond to:

        AS = Atom symbol corresponding to element symbol

        X<n>   = Number of non-hydrogen atom neighbors or heavy atoms
        BO<n> = Sum of bond orders to non-hydrogen atom neighbors or heavy atoms
        LBO<n> = Largest bond order of non-hydrogen atom neighbors or heavy atoms
        SB<n> = Number of single bonds to non-hydrogen atom neighbors or heavy atoms
        DB<n> = Number of double bonds to non-hydrogen atom neighbors or heavy atoms
        TB<n> = Number of triple bonds to non-hydrogen atom neighbors or heavy atoms
        H<n>   = Number of implicit and explicit hydrogens for atom
        Ar     = Aromatic annotation indicating whether atom is aromatic
        RA     = Ring atom annotation indicating whether atom is a ring
        FC<+n/-n> = Formal charge assigned to atom
        MN<n> = Mass number indicating isotope other than most abundant isotope
        SM<n> = Spin multiplicity of atom. Possible values: 1 (singlet), 2 (doublet) or
                3 (triplet)

    Atom type generated by AtomTypes::AtomTypes::AtomicInvariantsAtomTypes
    class corresponds to:

        AS.X<n>.BO<n>.LBO<n>.<SB><n>.<DB><n>.<TB><n>.H<n>.Ar.RA.FC<+n/-n>.MN<n>.SM<n>

    Except for AS which is a required atomic invariant in atom types, all
    other atomic invariants are optional. Atom type specification doesn't
    include atomic invariants with zero or undefined values.

    In addition to usage of abbreviations for specifying atomic invariants,
    the following descriptive words are also allowed:

        X : NumOfNonHydrogenAtomNeighbors or NumOfHeavyAtomNeighbors
        BO : SumOfBondOrdersToNonHydrogenAtoms or SumOfBondOrdersToHeavyAtoms
        LBO : LargestBondOrderToNonHydrogenAtoms or LargestBondOrderToHeavyAtoms
        SB :  NumOfSingleBondsToNonHydrogenAtoms or NumOfSingleBondsToHeavyAtoms
        DB : NumOfDoubleBondsToNonHydrogenAtoms or NumOfDoubleBondsToHeavyAtoms
        TB : NumOfTripleBondsToNonHydrogenAtoms or NumOfTripleBondsToHeavyAtoms
        H :  NumOfImplicitAndExplicitHydrogens
        Ar : Aromatic
        RA : RingAtom
        FC : FormalCharge
        MN : MassNumber
        SM : SpinMultiplicity

     Notes:

        . AtomicInvariants with zero or undefined values are not shown.
        . LBO with value of 1 is not shown. And absence of LBO in AtomTypes
          implies the largest bond order value is one.
        . SB, DB and TB with values of zero are not shown.
        . The difference in BO and X values corresponds to numbed of pi electrons [ Ref 57 ].

    Examples of atomic invariant atom types:

        . O.X1.BO1.H1 - Hydroxyl oxygen in carboxylate with attached hydrogen
          and no explicit charge
        . O.X1.BO1.FC-1 - Hydroxyl ozygen in carboxylate with explicit negative
          charge
        . O.X1.BO2 - Carbonyl oxygen in carboxylate with double bond to carbon
        . O.X2.BO2 - Hydroxyl ozygen in carboxylate attached to carbonyl carbon
          and another heavy atom
        . C.X2.BO3.H1.Ar - Aromatic carbon

  METHODS
    new
            $NewAtomicInvariantsAtomTypes = new AtomTypes::AtomicInvariantsAtomTypes(
                                                           %NamesAndValues);

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

            Molecule = ''
            Type = 'AtomicInvariants'
            IgnoreHydrogens = 0
            AtomicInvariantsToUse = AS,X,BO,H,FC

        Examples:

            $AtomicInvariantsAtomTypes = new AtomTypes::AtomicInvariantsAtomTypes(
                                      'Molecule' => $Molecule,
                                      'IgnoreHydrogens' => 0,
                                      'AtomicInvariantsToUse' =>
                                                 ['AS', 'X', 'BO', 'H', 'FC']);

    AssignAtomTypes
            $AtomicInvariantsAtomTypes->AssignAtomTypes();

        Assigns atomic invariant atom types to all the atoms in a molecule
        and returns *AtomicInvariantsAtomTypes*.

    GetAtomicInvariantsOrder
            @AtomicInvariantsOrder = $AtomicInvariantsAtomTypes->
                                     GetAtomicInvariantsOrder();

        Returns an array obtaining order of atomic invariants used to
        generate atom types.

    GetAvailableAtomicInvariants
            %AvailableAtomicInvariants = $AtomicInvariantsAtomTypes->
                                         GetAvailableAtomicInvariants();

        Returns available atomic invariants as a hash containing available
        atomic invariants and their description as key/value pairs.

    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.

    IsAtomicInvariantAvailable
            $Status = $AtomicInvariantsAtomTypes->
                      IsAtomicInvariantAvailable($AtomicInvariant);
            $Status = AtomTypes::AtomicInvariantsAtomTypes::
                      IsAtomicInvariantAvailable($AtomicInvariant);

        Returns 1 or 0 based on whether *AtomicInvariant* is valid.

    SetAtomicInvariantsToUse
            $AtomicInvariantsAtomTypes->SetAtomicInvariantsToUse($ValuesRef);
            $AtomicInvariantsAtomTypes->SetAtomicInvariantsToUse(@Values);

        Sets atomic invariants to use for generating and assigning atom
        types and returns *AtomicInvariantsAtomTypes*.

    StringifyAtomicInvariantsAtomTypes
            $String = $AtomicInvariantsAtomTypes->StringifyAtomicInvariantsAtomTypes();

        Returns a string containing information about
        *AtomicInvariantsAtomTypes* object.

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

SEE ALSO
    AtomTypes.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.

