NAME
    TopologicalAtomPairsFingerprints

SYNOPSIS
    use Fingerprints::TopologicalAtomPairsFingerprints;

    use Fingerprints::TopologicalAtomPairsFingerprints qw(:all);

DESCRIPTION
    TopologicalAtomPairsFingerprints [ Ref 57, Ref 59, Ref 72 ] class
    provides the following methods:

    new, GenerateFingerprints, GetAtomPairIDs, GetDescription,
    SetAtomIdentifierType, SetAtomicInvariantsToUse,
    SetFunctionalClassesToUse, SetMaxDistance, SetMinDistance,
    StringifyTopologicalAtomPairsFingerprints

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

    The current release of MayaChemTools supports generation of
    AtomTypesFingerpritns corresponding to following AtomtomIdentifierTypes:

        AtomicInvariantsAtomTypes, DREIDINGAtomTypes, EStateAtomTypes,
        FunctionalClassAtomTypes, MMFF94AtomTypes, SLogPAtomTypes,
        SYBYLAtomTypes, TPSAAtomTypes, UFFAtomTypes

    Based on the values specified for AtomIdentifierType along with other
    specified parameters such as AtomicInvariantsToUse and
    FunctionalClassesToUse, initial atom types are assigned to all
    non-hydrogen atoms in a molecule. Using the distance matrix for the
    molecule and initial atom types assigned to non-hydrogen atoms, all
    unique atom pairs within MinDistance and MaxDistance are identified and
    counted. An atom pair identifier is generated for each unique atom pair;
    the format of atom pair identifier is:

        <AtomType1>-D<n>-<AtomType2>

        AtomType1, AtomType2: Atom types assigned to atom1 and atom2
        D: Distance between atom1 and atom2

        where AtomType1 <= AtomType2

    The atom pair identifiers for all unique atom pairs corresponding to
    non-hydrogen atoms constitute topological atom pairs fingerprints of the
    molecule.

    The current release of MayaChemTools generates the following types of
    topological atom pairs fingerprints vector strings:

        FingerprintsVector;TopologicalAtomPairs:AtomicInvariantsAtomTypes:MinD
        istance1:MaxDistance10;223;NumericalValues;IDsAndValuesString;C.X1.BO1
        .H3-D1-C.X3.BO3.H1 C.X2.BO2.H2-D1-C.X2.BO2.H2 C.X2.BO2.H2-D1-C.X3.BO3.
        H1 C.X2.BO2.H2-D1-C.X3.BO4 C.X2.BO2.H2-D1-N.X3.BO3 C.X2.BO3.H1-D1-...;
        2 1 4 1 1 10 8 1 2 6 1 2 2 1 2 1 2 2 1 2 1 5 1 10 12 2 2 1 2 1 9 1 3 1
        1 1 2 2 1 3 6 1 6 14 2 2 2 3 1 3 1 8 2 2 1 3 2 6 1 2 2 5 1 3 1 23 1...

        FingerprintsVector;TopologicalAtomPairs:AtomicInvariantsAtomTypes:MinD
        istance1:MaxDistance10;223;NumericalValues;IDsAndValuesPairsString;C.X
        1.BO1.H3-D1-C.X3.BO3.H1 2 C.X2.BO2.H2-D1-C.X2.BO2.H2 1 C.X2.BO2.H2-D1-
        C.X3.BO3.H1 4 C.X2.BO2.H2-D1-C.X3.BO4 1 C.X2.BO2.H2-D1-N.X3.BO3 1 C.X2
        .BO3.H1-D1-C.X2.BO3.H1 10 C.X2.BO3.H1-D1-C.X3.BO4 8 C.X3.BO3.H1-D1-C.X
        3.BO4 1 C.X3.BO3.H1-D1-O.X1.BO1.H1 2 C.X3.BO4-D1-C.X3.BO4 6 C.X3.BO...

        FingerprintsVector;TopologicalAtomPairs:DREIDINGAtomTypes:MinDistance1
        :MaxDistance10;157;NumericalValues;IDsAndValuesString;C_2-D1-C_3 C_2-D
        1-C_R C_2-D1-N_3 C_2-D1-O_2 C_2-D1-O_3 C_3-D1-C_3 C_3-D1-C_R C_3-D1-N_
        R C_3-D1-O_3 C_R-D1-C_R C_R-D1-F_ C_R-D1-N_3 C_R-D1-N_R C_2-D2-C_3 C_2
        1 1 1 2 1 7 1 1 2 23 1 1 2 1 3 5 5 2 1 5 28 2 3 3 1 1 1 2 4 1 1 4 9 3
        1 4 24 2 4 3 3 4 5 5 14 1 1 2 3 22 1 3 4 4 1 1 1 1 2 2 5 1 4 21 3 1...

        FingerprintsVector;TopologicalAtomPairs:EStateAtomTypes:MinDistance1:M
        axDistance10;251;NumericalValues;IDsAndValuesString;aaCH-D1-aaCH aaCH-
        D1-aasC aasC-D1-aasC aasC-D1-aasN aasC-D1-dssC aasC-D1-sF aasC-D1-ssNH
        aasC-D1-sssCH aasN-D1-ssCH2 dO-D1-dssC dssC-D1-sOH dssC-D1-ssCH2 d...;
        10 8 5 2 1 1 1 1 1 2 1 1 1 2 2 1 4 10 12 2 2 6 3 1 3 2 2 1 1 1 1 1 1 1
        1 1 5 2 1 1 6 12 2 2 2 2 6 1 3 2 2 5 2 2 1 2 1 1 1 1 1 1 3 1 3 19 2...

        FingerprintsVector;TopologicalAtomPairs:FunctionalClassAtomTypes:MinDi
        stance1:MaxDistance10;144;NumericalValues;IDsAndValuesString;Ar-D1-Ar
        Ar-D1-Ar.HBA Ar-D1-HBD Ar-D1-Hal Ar-D1-None Ar.HBA-D1-None HBA-D1-NI H
        BA-D1-None HBA.HBD-D1-NI HBA.HBD-D1-None HBD-D1-None NI-D1-None No...;
        23 2 1 1 2 1 1 1 1 2 1 1 7 28 3 1 3 2 8 2 1 1 1 5 1 5 24 3 3 4 2 13 4
        1 1 4 1 5 22 4 4 3 1 19 1 1 1 1 1 2 2 3 1 1 8 25 4 5 2 3 1 26 1 4 1 ...

        FingerprintsVector;TopologicalAtomPairs:MMFF94AtomTypes:MinDistance1:M
        axDistance10;227;NumericalValues;IDsAndValuesPairsString;C5A-D1-C5B 2 
        C5A-D1-CB 1 C5A-D1-CR 1 C5A-D1-N5 2 C5B-D1-C5B 1 C5B-D1-C=ON 1 C5B-D1-
        CB 1 C=ON-D1-NC=O 1 C=ON-D1-O=CN 1 CB-D1-CB 18 CB-D1-F 1 CB-D1-NC=O 1
        COO-D1-CR 1 COO-D1-O=CO 1 COO-D1-OC=O 1 CR-D1-CR 7 CR-D1-N5 1 CR-D1-OR
        2 C5A-D2-C5A 1 C5A-D2-C5B 2 C5A-D2-C=ON 1 C5A-D2-CB 3 C5A-D2-CR 4 ...

        FingerprintsVector;TopologicalAtomPairs:SLogPAtomTypes:MinDistance1:Ma
        xDistance10;329;NumericalValues;IDsAndValuesPairsString;C1-D1-C10 1 C1
        -D1-C11 2 C1-D1-C5 1 C1-D1-CS 4 C10-D1-N11 1 C11-D1-C21 1 C14-D1-C18 2
        C14-D1-F 1 C18-D1-C18 10 C18-D1-C20 4 C18-D1-C22 2 C20-D1-C20 3 C20-D
        1-C21 1 C20-D1-N11 1 C21-D1-C21 1 C21-D1-C5 1 C21-D1-N11 1 C22-D1-N4 1
        C5-D1-N4 1 C5-D1-O10 1 C5-D1-O2 1 C5-D1-O9 1 CS-D1-O2 2 C1-D2-C1 3...

        FingerprintsVector;TopologicalAtomPairs:SYBYLAtomTypes:MinDistance1:Ma
        xDistance10;159;NumericalValues;IDsAndValuesPairsString;C.2-D1-C.3 1 C
        .2-D1-C.ar 1 C.2-D1-N.am 1 C.2-D1-O.2 1 C.2-D1-O.co2 2 C.3-D1-C.3 7 C.
        3-D1-C.ar 1 C.3-D1-N.ar 1 C.3-D1-O.3 2 C.ar-D1-C.ar 23 C.ar-D1-F 1 C.a
        r-D1-N.am 1 C.ar-D1-N.ar 2 C.2-D2-C.3 1 C.2-D2-C.ar 3 C.3-D2-C.3 5 C.3
        -D2-C.ar 5 C.3-D2-N.ar 2 C.3-D2-O.3 4 C.3-D2-O.co2 2 C.ar-D2-C.ar 2...

        FingerprintsVector;TopologicalAtomPairs:TPSAAtomTypes:MinDistance1:Max
        Distance10;64;NumericalValues;IDsAndValuesPairsString;N21-D1-None 3 N7
        -D1-None 2 None-D1-None 34 None-D1-O3 2 None-D1-O4 3 N21-D2-None 5 N7-
        D2-None 3 N7-D2-O3 1 None-D2-None 44 None-D2-O3 2 None-D2-O4 5 O3-D2-O
        4 1 N21-D3-None 7 N7-D3-None 4 None-D3-None 45 None-D3-O3 4 None-D3-O4
        5 N21-D4-N7 1 N21-D4-None 5 N21-D4-O3 1 N21-D4-O4 1 N7-D4-None 4 N...

        FingerprintsVector;TopologicalAtomPairs:UFFAtomTypes:MinDistance1:MaxD
        istance10;157;NumericalValues;IDsAndValuesPairsString;C_2-D1-C_3 1 C_2
        -D1-C_R 1 C_2-D1-N_3 1 C_2-D1-O_2 2 C_2-D1-O_3 1 C_3-D1-C_3 7 C_3-D1-C
        _R 1 C_3-D1-N_R 1 C_3-D1-O_3 2 C_R-D1-C_R 23 C_R-D1-F_ 1 C_R-D1-N_3 1 
        C_R-D1-N_R 2 C_2-D2-C_3 1 C_2-D2-C_R 3 C_3-D2-C_3 5 C_3-D2-C_R 5 C_3-D
        2-N_R 2 C_3-D2-O_2 1 C_3-D2-O_3 5 C_R-D2-C_R 28 C_R-D2-F_ 2 C_R-D2-...

  METHODS
    new
            $NewTopologicalAtomPairsFingerprints = new TopologicalAtomPairsFingerprints(
                                                           %NamesAndValues);

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

            Molecule = ''
            Type = 'TopologicalAtomPairs'
            MinDistance = 1
            MaxDistance = 10
            AtomIdentifierType = ''
            AtomicInvariantsToUse = ['AS', 'X', 'BO', 'H', 'FC']
            FunctionalClassesToUse = ['HBD', 'HBA', 'PI', 'NI', 'Ar', 'Hal']

        Examples:

            $TopologicalAtomPairsFingerprints = new TopologicalAtomPairsFingerprints(
                                      'Molecule' => $Molecule,
                                      'AtomIdentifierType' =>
                                                      'AtomicInvariantsAtomTypes');

            $TopologicalAtomPairsFingerprints = new TopologicalAtomPairsFingerprints(
                                      'Molecule' => $Molecule,
                                      'MinDistance' => 1,
                                      'MaxDistance' => 10,
                                      'AtomIdentifierType' =>
                                                      'AtomicInvariantsAtomTypes',
                                      'AtomicInvariantsToUse' =>
                                                      ['AS', 'X', 'BO', 'H', 'FC'] );

            $TopologicalAtomPairsFingerprints = new TopologicalAtomPairsFingerprints(
                                      'Molecule' => $Molecule,
                                      'AtomIdentifierType' =>
                                                      'EStateAtomTypes');

            $TopologicalAtomPairsFingerprints = new TopologicalAtomPairsFingerprints(
                                      'Molecule' => $Molecule,
                                      'AtomIdentifierType' =>
                                                      'SLogPAtomTypes');

            $TopologicalAtomPairsFingerprints = new TopologicalAtomPairsFingerprints(
                                      'Molecule' => $Molecule,
                                      'MinDistance' => 1,
                                      'MaxDistance' => 10,
                                      'AtomIdentifierType' =>
                                                      'FunctionalClassAtomTypes',
                                      'FunctionalClassesToUse' =>
                                                      ['HBD', 'HBA', 'PI', 'NI', 'Ar', 'Hal']);


            $TopologicalAtomPairsFingerprints->GenerateFingerprints();
            print "$TopologicalAtomPairsFingerprints\n";

    GetDescription
            $Description = $TopologicalAtomPairsFingerprints->GetDescription();

        Returns a string containing description of topological atom pairs
        fingerprints fingerprints.

    GenerateFingerprints
            $TopologicalAtomPairsFingerprints->GenerateFingerprints();

        Generates topological atom pairs fingerprints and returns
        *TopologicalAtomPairsFingerprints*.

    GetAtomPairIDs
            $AtomPairIDsRef = $TopologicalAtomPairsFingerprints->GetAtomPairIDs();
            @AtomPairIDs = $TopologicalAtomPairsFingerprints->GetAtomPairIDs();

        Returns atom pair IDs corresponding to atom pairs count values in
        topological atom pairs fingerprints vector as an array or reference
        to an array.

    SetAtomIdentifierType
            $TopologicalAtomPairsFingerprints->SetAtomIdentifierType($IdentifierType);

        Sets atom *IdentifierType* to use during atom pairs fingerprints
        generation and returns *TopologicalAtomPairsFingerprints*.

        Possible values: *AtomicInvariantsAtomTypes, DREIDINGAtomTypes,
        EStateAtomTypes, FunctionalClassAtomTypes, MMFF94AtomTypes,
        SLogPAtomTypes, SYBYLAtomTypes, TPSAAtomTypes, UFFAtomTypes*.

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

        Sets atomic invariants to use during *AtomicInvariantsAtomTypes*
        value of *AtomIdentifierType* for topological atom pairs
        fingerprints generation and returns
        *TopologicalAtomPairsFingerprints*.

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

        *AtomTypes::AtomicInvariantsAtomTypes* module is used to assign
        atomic invariant atom types.

    SetFunctionalClassesToUse
            $TopologicalAtomPairsFingerprints->SetFunctionalClassesToUse($ValuesRef);
            $TopologicalAtomPairsFingerprints->SetFunctionalClassesToUse(@Values);

        Sets functional classes invariants to use during
        *FunctionalClassAtomTypes* value of *AtomIdentifierType* for
        topological atom pairs fingerprints generation and returns
        *TopologicalAtomPairsFingerprints*.

        Possible values for atom functional classes are: *Ar, CA, H, HBA,
        HBD, Hal, NI, PI, RA*. Default value [ Ref 24 ]:
        *HBD,HBA,PI,NI,Ar,Hal*.

        The functional class abbreviations correspond to:

            HBD: HydrogenBondDonor
            HBA: HydrogenBondAcceptor
            PI :  PositivelyIonizable
            NI : NegativelyIonizable
            Ar : Aromatic
            Hal : Halogen
            H : Hydrophobic
            RA : RingAtom
            CA : ChainAtom

         Functional class atom type specification for an atom corresponds to:

            Ar.CA.H.HBA.HBD.Hal.NI.PI.RA or None

        *AtomTypes::FunctionalClassAtomTypes* module is used to assign
        functional class atom types. It uses following definitions [ Ref
        60-61, Ref 65-66 ]:

            HydrogenBondDonor: NH, NH2, OH
            HydrogenBondAcceptor: N[!H], O
            PositivelyIonizable: +, NH2
            NegativelyIonizable: -, C(=O)OH, S(=O)OH, P(=O)OH

    SetMaxDistance
            $TopologicalAtomPairsFingerprints->SetMaxDistance($Distance);

        Sets maximum distance to use during topological atom pairs
        fingerprints generation and returns
        *TopologicalAtomPairsFingerprints*.

    SetMinDistance
            $TopologicalAtomPairsFingerprints->SetMinDistance($Distance);

        Sets minimum distance to use during topological atom pairs
        fingerprints generation and returns
        *TopologicalAtomPairsFingerprints*.

    StringifyTopologicalAtomPairsFingerprints
            $String = $TopologicalAtomPairsFingerprints->
                          StringifyTopologicalAtomPairsFingerprints();

        Returns a string containing information about
        *TopologicalAtomPairsFingerprints* object.

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

SEE ALSO
    Fingerprints.pm, FingerprintsStringUtil.pm,
    AtomNeighborhoodsFingerprints.pm, AtomTypesFingerprints.pm,
    EStateIndiciesFingerprints.pm, ExtendedConnectivityFingerprints.pm,
    MACCSKeys.pm, PathLengthFingerprints.pm,
    TopologicalAtomTripletsFingerprints.pm,
    TopologicalAtomTorsionsFingerprints.pm,
    TopologicalPharmacophoreAtomPairsFingerprints.pm,
    TopologicalPharmacophoreAtomTripletsFingerprints.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.

