NAME
    AtomNeighborhoodsFingerprints

SYNOPSIS
    use Fingerprints::AtomNeighborhoodsFingerprints;

    use Fingerprints::AtomNeighborhoodsFingerprints qw(:all);

DESCRIPTION
    AtomNeighborhoodsFingerprints [ Ref 53-56, Ref 73 ] class provides the
    following methods:

    new, GenerateFingerprints, GetDescription, SetAtomIdentifierType,
    SetAtomicInvariantsToUse, SetFunctionalClassesToUse,
    SetMaxNeighborhoodRadius, SetMinNeighborhoodRadius,
    StringifyAtomNeighborhoodsFingerprints

    AtomNeighborhoodsFingerprints is derived from Fingerprints class which
    in turn is derived from ObjectProperty base class that provides methods
    not explicitly defined in AtomNeighborhoodsFingerprints, 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
    AtomNeighborhoodsFingerprints corresponding to following
    AtomIdentifierTypes:

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

    Based on the values specified for AtomIdentifierType along with other
    specified sucb as AtomicInvariantsToUse and FunctionalClassesToUse,
    initial atom types are assigned to all non-hydrogen atoms in a molecule.
    Using atom neighborhoods around each non-hydrogen central atom
    corresponding to radii between specified values MinNeighborhoodRadius
    and MaxNeighborhoodRadius, unique atom types at each radii level are
    counted and an atom neighborhood identifier is generated.

    The format of an atom neighborhood identifier around a central
    non-hydrogen atom at a specific radius is:

        NR<n>-<AtomType>-ATC<n>

        NR: Neighborhood radius
        AtomType: Assigned atom type
        ATC: Atom type count

    The atom neighborhood identifier for non-hydrogen central atom
    corresponding to all specified radii is generated by concatenating
    neighborhood identifiers at each radii by colon as a delimiter:

        NR<n>-<AtomType>-ATC<n>:NR<n>-<AtomType>-ATC<n>:...

    The atom neighborhood identifiers for all non-hydrogen central atoms at
    all specified radii are concatenated using space as a delimiter and
    constitute atom neighborhood fingerprint of the molecule.

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

        FingerprintsVector;AtomNeighborhoods:AtomicInvariantsAtomTypes:MinRadi
        us0:MaxRadius2;41;AlphaNumericalValues;ValuesString;NR0-C.X1.BO1.H3-AT
        C1:NR1-C.X3.BO3.H1-ATC1:NR2-C.X1.BO1.H3-ATC1:NR2-C.X3.BO4-ATC1 NR0-C.X
        1.BO1.H3-ATC1:NR1-C.X3.BO3.H1-ATC1:NR2-C.X1.BO1.H3-ATC1:NR2-C.X3.BO4-A
        TC1 NR0-C.X2.BO2.H2-ATC1:NR1-C.X2.BO2.H2-ATC1:NR1-C.X3.BO3.H1-ATC1:NR2
        -C.X2.BO2.H2-ATC1:NR2-N.X3.BO3-ATC1:NR2-O.X1.BO1.H1-ATC1 NR0-C.X2.B...

        FingerprintsVector;AtomNeighborhoods:DREIDINGAtomTypes:MinRadius0:MaxR
        adius2;41;AlphaNumericalValues;ValuesString;NR0-C_2-ATC1:NR1-C_3-ATC1:
        NR1-O_2-ATC1:NR1-O_3-ATC1:NR2-C_3-ATC1 NR0-C_2-ATC1:NR1-C_R-ATC1:NR1-N
        _3-ATC1:NR1-O_2-ATC1:NR2-C_R-ATC3 NR0-C_3-ATC1:NR1-C_2-ATC1:NR1-C_3-AT
        C1:NR2-C_3-ATC1:NR2-O_2-ATC1:NR2-O_3-ATC2 NR0-C_3-ATC1:NR1-C_3-ATC1:NR
        1-N_R-ATC1:NR2-C_3-ATC1:NR2-C_R-ATC2 NR0-C_3-ATC1:NR1-C_3-ATC1:NR2-...

        FingerprintsVector;AtomNeighborhoods:EStateAtomTypes:MinRadius0:MaxRad
        ius2;41;AlphaNumericalValues;ValuesString;NR0-aaCH-ATC1:NR1-aaCH-ATC1:
        NR1-aasC-ATC1:NR2-aaCH-ATC1:NR2-aasC-ATC1:NR2-sF-ATC1 NR0-aaCH-ATC1:NR
        1-aaCH-ATC1:NR1-aasC-ATC1:NR2-aaCH-ATC1:NR2-aasC-ATC1:NR2-sF-ATC1 NR0-
        aaCH-ATC1:NR1-aaCH-ATC1:NR1-aasC-ATC1:NR2-aaCH-ATC1:NR2-aasC-ATC2 NR0-
        aaCH-ATC1:NR1-aaCH-ATC1:NR1-aasC-ATC1:NR2-aaCH-ATC1:NR2-aasC-ATC2 N...

        FingerprintsVector;AtomNeighborhoods:FunctionalClassAtomTypes:MinRadiu
        s0:MaxRadius2;41;AlphaNumericalValues;ValuesString;NR0-Ar-ATC1:NR1-Ar-
        ATC1:NR1-Ar.HBA-ATC1:NR1-None-ATC1:NR2-Ar-ATC2:NR2-None-ATC4 NR0-Ar-AT
        C1:NR1-Ar-ATC2:NR1-Ar.HBA-ATC1:NR2-Ar-ATC5:NR2-None-ATC1 NR0-Ar-ATC1:N
        R1-Ar-ATC2:NR1-HBD-ATC1:NR2-Ar-ATC2:NR2-None-ATC1 NR0-Ar-ATC1:NR1-Ar-A
        TC2:NR1-Hal-ATC1:NR2-Ar-ATC2 NR0-Ar-ATC1:NR1-Ar-ATC2:NR1-None-ATC1:...

        FingerprintsVector;AtomNeighborhoods:MMFF94AtomTypes:MinRadius0:MaxRad
        ius2;41;AlphaNumericalValues;ValuesString;NR0-C5A-ATC1:NR1-C5B-ATC1:NR
        1-CB-ATC1:NR1-N5-ATC1:NR2-C5A-ATC1:NR2-C5B-ATC1:NR2-CB-ATC3:NR2-CR-ATC
        1 NR0-C5A-ATC1:NR1-C5B-ATC1:NR1-CR-ATC1:NR1-N5-ATC1:NR2-C5A-ATC1:NR2-C
        5B-ATC1:NR2-C=ON-ATC1:NR2-CR-ATC3 NR0-C5B-ATC1:NR1-C5A-ATC1:NR1-C5B-AT
        C1:NR1-C=ON-ATC1:NR2-C5A-ATC1:NR2-CB-ATC1:NR2-CR-ATC1:NR2-N5-ATC1:N...

        FingerprintsVector;AtomNeighborhoods:SLogPAtomTypes:MinRadius0:MaxRadi
        us2;41;AlphaNumericalValues;ValuesString;NR0-C1-ATC1:NR1-C10-ATC1:NR1-
        CS-ATC1:NR2-C1-ATC1:NR2-N11-ATC1:NR2-O2-ATC1 NR0-C1-ATC1:NR1-C11-ATC1:
        NR2-C1-ATC1:NR2-C21-ATC1 NR0-C1-ATC1:NR1-C11-ATC1:NR2-C1-ATC1:NR2-C21-
        ATC1 NR0-C1-ATC1:NR1-C5-ATC1:NR1-CS-ATC1:NR2-C1-ATC1:NR2-O2-ATC2:NR2-O
        9-ATC1 NR0-C1-ATC1:NR1-CS-ATC2:NR2-C1-ATC2:NR2-O2-ATC2 NR0-C10-ATC1...

        FingerprintsVector;AtomNeighborhoods:SYBYLAtomTypes:MinRadius0:MaxRadi
        us2;41;AlphaNumericalValues;ValuesString;NR0-C.2-ATC1:NR1-C.3-ATC1:NR1
        -O.co2-ATC2:NR2-C.3-ATC1 NR0-C.2-ATC1:NR1-C.ar-ATC1:NR1-N.am-ATC1:NR1-
        O.2-ATC1:NR2-C.ar-ATC3 NR0-C.3-ATC1:NR1-C.2-ATC1:NR1-C.3-ATC1:NR2-C.3-
        ATC1:NR2-O.3-ATC1:NR2-O.co2-ATC2 NR0-C.3-ATC1:NR1-C.3-ATC1:NR1-N.ar-AT
        C1:NR2-C.3-ATC1:NR2-C.ar-ATC2 NR0-C.3-ATC1:NR1-C.3-ATC1:NR2-C.3-ATC...

        FingerprintsVector;AtomNeighborhoods:TPSAAtomTypes:MinRadius0:MaxRadiu
        s2;41;AlphaNumericalValues;ValuesString;NR0-N21-ATC1:NR1-None-ATC3:NR2
        -None-ATC5 NR0-N7-ATC1:NR1-None-ATC2:NR2-None-ATC3:NR2-O3-ATC1 NR0-Non
        e-ATC1:NR1-N21-ATC1:NR1-None-ATC1:NR2-None-ATC3 NR0-None-ATC1:NR1-N21-
        ATC1:NR1-None-ATC2:NR2-None-ATC6 NR0-None-ATC1:NR1-N21-ATC1:NR1-None-A
        TC2:NR2-None-ATC6 NR0-None-ATC1:NR1-N7-ATC1:NR1-None-ATC1:NR1-O3-AT...

        FingerprintsVector;AtomNeighborhoods:UFFAtomTypes:MinRadius0:MaxRadius
        2;41;AlphaNumericalValues;ValuesString;NR0-C_2-ATC1:NR1-C_3-ATC1:NR1-O
        _2-ATC1:NR1-O_3-ATC1:NR2-C_3-ATC1 NR0-C_2-ATC1:NR1-C_R-ATC1:NR1-N_3-AT
        C1:NR1-O_2-ATC1:NR2-C_R-ATC3 NR0-C_3-ATC1:NR1-C_2-ATC1:NR1-C_3-ATC1:NR
        2-C_3-ATC1:NR2-O_2-ATC1:NR2-O_3-ATC2 NR0-C_3-ATC1:NR1-C_3-ATC1:NR1-N_R
        -ATC1:NR2-C_3-ATC1:NR2-C_R-ATC2 NR0-C_3-ATC1:NR1-C_3-ATC1:NR2-C_3-A...

  METHODS
    new
            $NewAtomNeighborhoodsFingerprints = new AtomNeighborhoodsFingerprints(
                                                           %NamesAndValues);

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

            Molecule = ''
            Type = 'AtomNeighborhoods'
            MinNeighborhoodRadius = 0
            MaxNeighborhoodRadius = 2
            AtomIdentifierType = ''
            AtomicInvariantsToUse = ['AS', 'X', 'BO', 'H', 'FC', 'MN']
            FunctionalClassesToUse = ['HBD', 'HBA', 'PI', 'NI', 'Ar', 'Hal']

        Examples:

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

            $AtomNeighborhoodsFingerprints = new AtomNeighborhoodsFingerprints(
                                      'Molecule' => $Molecule,
                                      'MinNeighborhoodRadius' => 0,
                                      'MaxNeighborhoodRadius' => 2,
                                      'AtomIdentifierType' =>
                                                      'AtomicInvariantsAtomTypes',
                                      'AtomicInvariantsToUse' =>
                                                      ['AS', 'X', 'BO', 'H', 'FC'] );

            $AtomNeighborhoodsFingerprints = new AtomNeighborhoodsFingerprints(
                                      'Molecule' => $Molecule,
                                      'AtomIdentifierType' =>
                                                      'SYBYLAtomTypes');

            $AtomNeighborhoodsFingerprints = new AtomNeighborhoodsFingerprints(
                                      'Molecule' => $Molecule,
                                      'AtomIdentifierType' =>
                                                      'MMFF94AtomTypes');

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

            $AtomNeighborhoodsFingerprints = new AtomNeighborhoodsFingerprints(
                                      'Molecule' => $Molecule,
                                      'MinNeighborhoodRadius' => 0,
                                      'MaxNeighborhoodRadius' => 2,
                                      'AtomIdentifierType' =>
                                                      'FunctionalClassAtomTypes',
                                      'FunctionalClassesToUse' =>
                                                  ['HBD', 'HBA', 'PI', 'NI', 'Ar', 'Hal'] );

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

    GenerateFingerprints
            $AtomNeighborhoodsFingerprints->GenerateFingerprints();

        Generates atom neighborhood fingerprints and returns
        *AtomNeighborhoodsFingerprints*.

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

        Returns a string containing description of atom neighborhood
        fingerprints.

    SetAtomIdentifierType
            $AtomNeighborhoodsFingerprints->SetAtomIdentifierType($IdentifierType);

        Sets atom *IdentifierType* to use during atom neighborhood
        fingerprints generation and returns *AtomNeighborhoodsFingerprints*.

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

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

        Sets atomic invariants to use during *AtomicInvariantsAtomTypes*
        value of *AtomIdentifierType* for atom neighborhood fingerprints
        generation and returns *AtomNeighborhoodsFingerprints*.

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

        Sets functional classes invariants to use during
        *FunctionalClassAtomTypes* value of *AtomIdentifierType* for atom
        neighborhoods fingerprints generation and returns
        *AtomNeighborhoodsFingerprints*.

        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

    SetMaxNeighborhoodRadius
            $AtomNeighborhoodsFingerprints->SetMaxNeighborhoodRadius($Radius);

        Sets maximum neighborhood radius to use during atom neighborhood
        fingerprints generation and returns *AtomNeighborhoodsFingerprints*.

    SetMinNeighborhoodRadius
            $AtomNeighborhoodsFingerprints->SetMinNeighborhoodRadius($Radius);

        Sets minimum neighborhood radius to use during atom neighborhood
        fingerprints generation and returns *AtomNeighborhoodsFingerprints*.

    StringifyAtomNeighborhoodsFingerprints
            $String = $Fingerprints->StringifyAtomNeighborhoodsFingerprints();

        Returns a string containing information about
        *AtomNeighborhoodsFingerprints* object.

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

SEE ALSO
    Fingerprints.pm, FingerprintsStringUtil.pm, AtomTypesFingerprints.pm,
    EStateIndiciesFingerprints.pm, ExtendedConnectivityFingerprints.pm,
    MACCSKeys.pm, PathLengthFingerprints.pm,
    TopologicalAtomPairsFingerprints.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.

