NAME
    AtomTypesFingerprints.pl - Generate atom types fingerprints for SD files

SYNOPSIS
    AtomTypesFingerprints.pl SDFile(s)...

    AtomTypesFingerprints.pl [--AromaticityModel *AromaticityModelType*]
    [-a, --AtomIdentifierType *AtomicInvariantsAtomTypes | DREIDINGAtomTypes
    | EStateAtomTypes | MMFF94AtomTypes | SLogPAtomTypes | SYBYLAtomTypes |
    TPSAAtomTypes | UFFAtomTypes*] [--AtomicInvariantsToUse
    *"AtomicInvariant, AtomicInvariant..."*] [--FunctionalClassesToUse
    *"FunctionalClass1,FunctionalClass2..."*] [--AtomTypesSetToUse
    *ArbitrarySize | FixedSize*] [--BitsOrder *Ascending | Descending*] [-b,
    --BitStringFormat *BinaryString | HexadecimalString*] [--CompoundID
    *DataFieldName or LabelPrefixString*] [--CompoundIDLabel *text*]
    [--CompoundIDMode *DataField | MolName | LabelPrefix |
    MolNameOrLabelPrefix*] [--DataFields *"FieldLabel1,FieldLabel2,..."*]
    [-d, --DataFieldsMode *All | Common | Specify | CompoundID*] [-f,
    --Filter *Yes | No*] [--FingerprintsLabelMode *FingerprintsLabelOnly |
    FingerprintsLabelWithIDs*] [--FingerprintsLabel *text*] [-h, --help]
    [-k, --KeepLargestComponent *Yes | No*] [-m, --mode *AtomTypesCount |
    AtomTypesBits*] [-i, --IgnoreHydrogens *Yes | No*] [--OutDelim *comma |
    tab | semicolon*] [--output *SD |FP | text | all*] [-o, --overwrite]
    [-q, --quote *Yes | No*] [-r, --root *RootName*] [-s, --size *number*]
    [--ValuesPrecision *number*] [-v, --VectorStringFormat
    *IDsAndValuesString | IDsAndValuesPairsString | ValuesAndIDsString |
    ValuesAndIDsPairsString*] [-w, --WorkingDir *DirName*]

DESCRIPTION
    Generate atom types fingerprints for *SDFile(s)* and create appropriate
    SD, FP or CSV/TSV text file(s) containing fingerprints bit-vector or
    vector strings corresponding to molecular fingerprints.

    Multiple SDFile names are separated by spaces. The valid file extensions
    are *.sdf* and *.sd*. All other file names are ignored. All the SD files
    in a current directory can be specified either by **.sdf* or the current
    directory name.

    The current release of MayaChemTools supports generation of atom types
    fingerpritns corresponding to following -a, --AtomIdentifierTypes:

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

    Based on the values specified for -a, --AtomIdentifierType along with
    other specified parameters such as --AtomicInvariantsToUse and
    --FunctionalClassesToUse, initial atom types are assigned to all
    non-hydrogen atoms or all atoms in a molecule

    Using the assigned atom types and specified -m, --Mode, one of the
    following types of fingerprints are generated:

        AtomTypesCount - A vector containing count of atom types
        AtomTypesBits - A bit vector indicating presence/absence of atom types

    For *AtomTypesCount* fingerprints, two types of atom types set size are
    allowed as value of --AtomTypesSetToUse option:

        ArbitrarySize - Corresponds to only atom types detected in molecule
        FixedSize - Corresponds to fixed number of atom types previously defined

    For *AtomTypesBits* fingerprints, only *FixedSize* atom type set is
    allowed.

    *ArbitrarySize* corresponds to atom types detected in a molecule where
    as *FixedSize* implies a fix number of all possible atom types
    previously defined for a specific -a, --AtomIdentifierType.

    Fix number of all possible atom types for supported
    *AtomIdentifierTypes* in current release of MayaChemTools are:

        AtomIdentifier       Total    TotalWithoutHydrogens

        DREIDINGAtomTypes    37       34
        EStateAtomTypes      109      87
        MMFF94AtomTypes      212      171
        SLogPAtomTypes       72       67
        SYBYLAtomTypes       45       44
        TPSAAtomTypes        47       47
        UFFAtomTypes         126      124

    The current release of MayaChemTools generates the following atom types
    fingerprints bit-vector and vector strings:

        FingerprintsVector;AtomTypesCount:AtomicInvariantsAtomTypes:ArbitraryS
        ize;10;NumericalValues;IDsAndValuesString;C.X1.BO1.H3 C.X2.BO2.H2 C.X2
        .BO3.H1 C.X3.BO3.H1 C.X3.BO4 F.X1.BO1 N.X2.BO2.H1 N.X3.BO3 O.X1.BO1.H1
        O.X1.BO2;2 4 14 3 10 1 1 1 3 2

        FingerprintsVector;AtomTypesCount:DREIDINGAtomTypes:ArbitrarySize;8;Nu
        mericalValues;IDsAndValuesString;C_2 C_3 C_R F_ N_3 N_R O_2 O_3;2 9 22
        1 1 1 2 3

        FingerprintsVector;AtomTypesCount:DREIDINGAtomTypes:FixedSize;34;Order
        edNumericalValues;IDsAndValuesString;B_3 B_2 C_3 C_R C_2 C_1 N_3 N_R N
        _2 N_1 O_3 O_R O_2 O_1 F_ Al3 Si3 P_3 S_3 Cl Ga3 Ge3 As3 Se3 Br In3 Sn
        3 Sb3 Te3 I_ Na Ca Fe Zn;0 0 9 22 2 0 1 1 0 0 3 0 2 0 1 0 0 0 0 0 0 0 
        0 0 0 0 0 0 0 0 0 0 0 0

        FingerprintsBitVector;AtomTypesBits:DREIDINGAtomTypes:FixedSize;34;Bin
        aryString;Ascending;0011101100101010000000000000000000000000

        FingerprintsVector;AtomTypesCount:EStateAtomTypes:ArbitrarySize;11;Num
        ericalValues;IDsAndValuesString;aaCH aasC aasN dO dssC sCH3 sF sOH ssC
        H2 ssNH sssCH;14 8 1 2 2 2 1 3 4 1 3

        FingerprintsVector;AtomTypesCount:EStateAtomTypes:FixedSize;87;Ordered
        NumericalValues;IDsAndValuesString;sLi ssBe ssssBem sBH2 ssBH sssB sss
        sBm sCH3 dCH2 ssCH2 tCH dsCH aaCH sssCH ddC tsC dssC aasC aaaC ssssC s
        NH3p sNH2 ssNH2p dNH ssNH aaNH tN sssNHp dsN aaN sssN ddsN aasN ss...;
        0 0 0 0 0 0 0 2 0 4 0 0 14 3 0 0 2 8 0 0 0 0 0 0 1 0 0 0 0 0 0 0 1 0 3 2 0 0
        0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0...

        FingerprintsBitVector;AtomTypesBits:EStateAtomTypes:FixedSize;87;Binar
        yString;Ascending;0000000101001100110000001000000010110000100000000000
        000000000000000000000000000000000000

        FingerprintsVector;AtomTypesCount:FunctionalClassAtomTypes:ArbitrarySi
        ze;8;NumericalValues;IDsAndValuesString;Ar Ar.HBA HBA HBA.HBD HBD Hal 
        NI None;22 1 2 3 1 1 1 10

        FingerprintsVector;AtomTypesCount:MMFF94AtomTypes:ArbitrarySize;13;Num
        ericalValues;IDsAndValuesString;C5A C5B C=ON CB COO CR F N5 NC=O O=CN
        O=CO OC=O OR;2 2 1 18 1 9 1 1 1 1 1 1 2

        FingerprintsVector;AtomTypesCount:MMFF94AtomTypes:FixedSize;171;Ordere
        dNumericalValues;IDsAndValuesString;CR C=C CSP2 C=O C=N CGD C=OR C=ON
        CONN COO COON COOO C=OS C=S C=SN CSO2 CS=O CSS C=P CSP =C= OR OC=O OC=
        C OC=N OC=S ONO2 ON=O OSO3 OSO2 OSO OS=O -OS OPO3 OPO2 OPO -OP -O-...;
        9 0 0 0 0 0 0 1 0 1 0 0 0 0 0 0 0 0 0 0 0 2 1 0 0 0 0 0 0 0 0 0 0 0 0
        0 0 0 0 1 0 1 0 0 0 0 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
        0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 18 0 0 0 0 0 0 0 0 ...

        FingerprintsBitVector;AtomTypesBits:MMFF94AtomTypes:FixedSize;171;Bina
        ryString;Ascending;100000010100000000000110000000000000000101000000100
        0100000000000000000000000000000000000000000100000000000000000000000000
        0000000011000000000000000001000000000000000000000000000

        FingerprintsVector;AtomTypesCount:SLogPAtomTypes:ArbitrarySize;16;Nume
        ricalValues;IDsAndValuesString;C1 C10 C11 C14 C18 C20 C21 C22 C5 CS F
        N11 N4 O10 O2 O9;5 1 1 1 14 4 2 1 2 2 1 1 1 1 3 1

        FingerprintsVector;AtomTypesCount:SLogPAtomTypes:FixedSize;67;OrderedN
        umericalValues;IDsAndValuesString;C1 C2 C3 C4 C5 C6 C7 C8 C9 C10 C11 C
        12 C13 C14 C15 C16 C17 C18 C19 C20 C21 C22 C23 C24 C25 C26 C27 CS N1 N
        2 N3 N4 N5 N6 N7 N8 N9 N10 N11 N12 N13 N14 NS O1 O2 O3 O4 O5 O6 O7 O8
        O9 O10 O11 O12 OS F Cl Br I Hal P S1 S2 S3 Me1 Me2;5 0 0 0 2 0 0 0 0 1
        1 0 0 1 0 0 0 14 0 4 2 1 0 0 0 0 0 2 0 0 0 1 0 0 0 0 0 0 1 0 0 0 0...

        FingerprintsBitVector;AtomTypesBits:SLogPAtomTypes:FixedSize;67;Binary
        String;Ascending;10001000011001000101110000010001000000100000100000011
        0001000000000000000

        FingerprintsVector;AtomTypesCount:SYBYLAtomTypes:ArbitrarySize;9;Numer
        icalValues;IDsAndValuesString;C.2 C.3 C.ar F N.am N.ar O.2 O.3 O.co2;2
        9 22 1 1 1 1 2 2

        FingerprintsVector;AtomTypesCount:SYBYLAtomTypes:FixedSize;44;OrderedN
        umericalValues;IDsAndValuesString;C.3 C.2 C.1 C.ar C.cat N.3 N.2 N.1 N
        .ar N.am N.pl3 N.4 O.3 O.2 O.co2 S.3 S.2 S.o S.o2 P.3 F Cl Br I ANY HA
        L HET Li Na Mg Al Si K Ca Cr.th Cr.oh Mn Fe Co.oh Cu Zn Se Mo Sn;9 2 0
        22 0 0 0 0 1 1 0 0 2 1 2 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
        0 0 0 0 0 0 0

        FingerprintsBitVector;AtomTypesBits:SYBYLAtomTypes:FixedSize;44;Binary
        String;Ascending;110100001100111000001000000000000000000000000000

        FingerprintsVector;AtomTypesCount:TPSAAtomTypes:FixedSize;47;OrderedNu
        mericalValues;IDsAndValuesString;N1 N2 N3 N4 N5 N6 N7 N8 N9 N10 N11 N1
        2 N13 N14 N15 N16 N17 N18 N19 N20 N21 N22 N23 N24 N25 N26 N O1 O2 O3 O
        4 O5 O6 O S1 S2 S3 S4 S5 S6 S7 S P1 P2 P3 P4 P;0 0 0 0 0 0 1 0 0 0 0 0
        0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 2 3 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0

        FingerprintsBitVector;AtomTypesBits:TPSAAtomTypes:FixedSize;47;BinaryS
        tring;Ascending;000000100000000000001000000001100000000000000000

        FingerprintsVector;AtomTypesCount:UFFAtomTypes:ArbitrarySize;8;Numeric
        alValues;IDsAndValuesString;C_2 C_3 C_R F_ N_3 N_R O_2 O_3;2 9 22 1 1
        1 2 3

        FingerprintsVector;AtomTypesCount:UFFAtomTypes;124;OrderedNumerical
        Values;IDsAndValuesString;He4+4 Li Be3+2 B_3 B_2 C_3 C_R C_2 C_1 N_3 N_
        R N_2 N_1 O_3 O_3_z O_R O_2 O_1 F_ Ne4+4 Na Mg3+2 Al3 Si3 P_3+3 P_3+5 P
        _3+q S_3+2 S_3+4 S_3+6 S_R S_2 Cl Ar4+4 K_ Ca6+2 Sc3+3 Ti3+4 Ti6+4 V_3+
        ;0 0 0 0 0 12 0 3 0 3 0 1 0 2 0 0 2 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
        0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 ...

        FingerprintsVector;AtomTypesCount:UFFAtomTypes:FixedSize;124;OrderedNu
        mericalValues;IDsAndValuesString;He4+4 Li Be3+2 B_3 B_2 C_3 C_R C_2 C_
        1 N_3 N_R N_2 N_1 O_3 O_3_z O_R O_2 O_1 F_ Ne4+4 Na Mg3+2 Al3 Si3 P_3+
        3 P_3+5 P_3+q S_3+2 S_3+4 S_3+6 S_R S_2 Cl Ar4+4 K_ Ca6+2 Sc3+3 Ti...;
        0 0 0 0 0 9 22 2 0 1 1 0 0 3 0 0 2 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
        0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
        0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0...

        FingerprintsBitVector;AtomTypesBits:UFFAtomTypes:FixedSize;124;BinaryS
        tring;Ascending;000001110110010010100000000000000000000000000000000000
        0000000000000000000000000000000000000000000000000000000000000000000000

OPTIONS
    --AromaticityModel *MDLAromaticityModel | TriposAromaticityModel |
    MMFFAromaticityModel | ChemAxonBasicAromaticityModel |
    ChemAxonGeneralAromaticityModel | DaylightAromaticityModel |
    MayaChemToolsAromaticityModel*
        Specify aromaticity model to use during detection of aromaticity.
        Possible values in the current release are: *MDLAromaticityModel,
        TriposAromaticityModel, MMFFAromaticityModel,
        ChemAxonBasicAromaticityModel, ChemAxonGeneralAromaticityModel,
        DaylightAromaticityModel or MayaChemToolsAromaticityModel*. Default
        value: *MayaChemToolsAromaticityModel*.

        The supported aromaticity model names along with model specific
        control parameters are defined in AromaticityModelsData.csv, which
        is distributed with the current release and is available under
        lib/data directory. Molecule.pm module retrieves data from this file
        during class instantiation and makes it available to method
        DetectAromaticity for detecting aromaticity corresponding to a
        specific model.

    -a, --AtomIdentifierType *AtomicInvariantsAtomTypes | DREIDINGAtomTypes
    | EStateAtomTypes | FunctionalClassAtomTypes | MMFF94AtomTypes |
    SLogPAtomTypes | SYBYLAtomTypes | TPSAAtomTypes | UFFAtomTypes*
        Specify atom identifier type to use for assignment of atom types to
        hydrogen and/or non-hydrogen atoms during calculation of atom types
        fingerprints. Possible values in the current release are:
        *AtomicInvariantsAtomTypes, DREIDINGAtomTypes, EStateAtomTypes,
        FunctionalClassAtomTypes, MMFF94AtomTypes, SLogPAtomTypes,
        SYBYLAtomTypes, TPSAAtomTypes, UFFAtomTypes*. Default value:
        *AtomicInvariantsAtomTypes*.

    --AtomicInvariantsToUse *"AtomicInvariant,AtomicInvariant..."*
        This value is used during *AtomicInvariantsAtomTypes* value of a,
        --AtomIdentifierType option. It's a list of comma separated valid
        atomic invariant atom types.

        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.

    --FunctionalClassesToUse *"FunctionalClass1,FunctionalClass2..."*
        This value is used during *FunctionalClassAtomTypes* value of a,
        --AtomIdentifierType option. It's a list of comma separated valid
        functional classes.

        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

        *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

    --AtomTypesSetToUse *ArbitrarySize | FixedSize*
        Atom types set size to use during generation of atom types
        fingerprints.

        Possible values for *AtomTypesCount* values of -m, --mode option:
        *ArbitrarySize | FixedSize*; Default value: *ArbitrarySize*.

        Possible values for *AtomTypesBits* value of -m, --mode option:
        *FixedSize*; Default value: *FixedSize*.

        *FixedSize* value is not supported for *AtomicInvariantsAtomTypes*
        value of -a, --AtomIdentifierType option.

        *ArbitrarySize* corresponds to only atom types detected in molecule;
        *FixedSize* corresponds to fixed number of previously defined atom
        types for specified -a, --AtomIdentifierType.

    --BitsOrder *Ascending | Descending*
        Bits order to use during generation of fingerprints bit-vector
        string for *AtomTypesBits* value of =item --BitsOrder *Ascending |
        Descending*

        Bits order to use during generation of fingerprints bit-vector
        string for *AtomTypesBits* value of -m, --mode option. Possible
        values: *Ascending, Descending*. Default: *Ascending*.

        *Ascending* bit order which corresponds to first bit in each byte as
        the lowest bit as opposed to the highest bit.

        Internally, bits are stored in *Ascending* order using Perl vec
        function. Regardless of machine order, big-endian or little-endian,
        vec function always considers first string byte as the lowest byte
        and first bit within each byte as the lowest bit.

    -b, --BitStringFormat *BinaryString | HexadecimalString*
        Format of fingerprints bit-vector string data in output SD, FP or
        CSV/TSV text file(s) specified by --output used during
        *AtomTypesBits* value of -m, --mode option. Possible values:
        *BinaryString, HexadecimalString*. Default value: *BinaryString*.

        *BinaryString* corresponds to an ASCII string containing 1s and 0s.
        *HexadecimalString* contains bit values in ASCII hexadecimal format.

        Examples:

            FingerprintsBitVector;AtomTypesBits:DREIDINGAtomTypes;34;BinaryString;
            Ascending;0010101010101000000000000000000000000000

            FingerprintsBitVector;AtomTypesBits:MMFF94AtomTypes;171;BinaryString;
            Ascending;1000010101000000000001100000000000000001010000101000000000000
            00000000000000000000000000000000000001000000000000000000000000000000000
            0000000000000000000000000000000000000000000

    --CompoundID *DataFieldName or LabelPrefixString*
        This value is --CompoundIDMode specific and indicates how compound
        ID is generated.

        For *DataField* value of --CompoundIDMode option, it corresponds to
        datafield label name whose value is used as compound ID; otherwise,
        it's a prefix string used for generating compound IDs like
        LabelPrefixString<Number>. Default value, *Cmpd*, generates compound
        IDs which look like Cmpd<Number>.

        Examples for *DataField* value of --CompoundIDMode:

            MolID
            ExtReg

        Examples for *LabelPrefix* or *MolNameOrLabelPrefix* value of
        --CompoundIDMode:

            Compound

        The value specified above generates compound IDs which correspond to
        Compound<Number> instead of default value of Cmpd<Number>.

    --CompoundIDLabel *text*
        Specify compound ID column label for FP or CSV/TSV text file(s) used
        during *CompoundID* value of --DataFieldsMode option. Default:
        *CompoundID*.

    --CompoundIDMode *DataField | MolName | LabelPrefix |
    MolNameOrLabelPrefix*
        Specify how to generate compound IDs and write to FP or CSV/TSV text
        file(s) along with generated fingerprints for *FP | text | all*
        values of --output option: use a *SDFile(s)* datafield value; use
        molname line from *SDFile(s)*; generate a sequential ID with
        specific prefix; use combination of both MolName and LabelPrefix
        with usage of LabelPrefix values for empty molname lines.

        Possible values: *DataField | MolName | LabelPrefix |
        MolNameOrLabelPrefix*. Default: *LabelPrefix*.

        For *MolNameAndLabelPrefix* value of --CompoundIDMode, molname line
        in *SDFile(s)* takes precedence over sequential compound IDs
        generated using *LabelPrefix* and only empty molname values are
        replaced with sequential compound IDs.

        This is only used for *CompoundID* value of --DataFieldsMode option.

    --DataFields *"FieldLabel1,FieldLabel2,..."*
        Comma delimited list of *SDFiles(s)* data fields to extract and
        write to CSV/TSV text file(s) along with generated fingerprints for
        *text | all* values of --output option.

        This is only used for *Specify* value of --DataFieldsMode option.

        Examples:

            Extreg
            MolID,CompoundName

    -d, --DataFieldsMode *All | Common | Specify | CompoundID*
        Specify how data fields in *SDFile(s)* are transferred to output
        CSV/TSV text file(s) along with generated fingerprints for *text |
        all* values of --output option: transfer all SD data field; transfer
        SD data files common to all compounds; extract specified data
        fields; generate a compound ID using molname line, a compound
        prefix, or a combination of both. Possible values: *All | Common |
        specify | CompoundID*. Default value: *CompoundID*.

    -f, --Filter *Yes | No*
        Specify whether to check and filter compound data in SDFile(s).
        Possible values: *Yes or No*. Default value: *Yes*.

        By default, compound data is checked before calculating fingerprints
        and compounds containing atom data corresponding to non-element
        symbols or no atom data are ignored.

    --FingerprintsLabelMode *FingerprintsLabelOnly |
    FingerprintsLabelWithIDs*
        Specify how fingerprints label is generated in conjunction with
        --FingerprintsLabel option value: use fingerprints label generated
        only by --FingerprintsLabel option value or append atom type value
        IDs to --FingerprintsLabel option value.

        Possible values: *FingerprintsLabelOnly | FingerprintsLabelWithIDs*.
        Default value: *FingerprintsLabelOnly*.

        This option is only used for *FixedSize* value of -e,
        --AtomTypesSetToUse option during generation of *AtomTypesCount*
        fingerprints and ignored for *AtomTypesBits*.

        Atom type IDs appended to --FingerprintsLabel value during
        *FingerprintsLabelWithIDs* values of --FingerprintsLabelMode
        correspond to fixed number of previously defined atom types.

    --FingerprintsLabel *text*
        SD data label or text file column label to use for fingerprints
        string in output SD or CSV/TSV text file(s) specified by --output.
        Default value: *AtomTypesFingerprints*.

    -h, --help
        Print this help message.

    -i, --IgnoreHydrogens *Yes | No*
        Ignore hydrogens during fingerprints generation. Possible values:
        *Yes or No*. Default value: *Yes*.

        For *yes* value of -i, --IgnoreHydrogens, any explicit hydrogens are
        also used for generation of atom type fingerprints; implicit
        hydrogens are still ignored.

    -k, --KeepLargestComponent *Yes | No*
        Generate fingerprints for only the largest component in molecule.
        Possible values: *Yes or No*. Default value: *Yes*.

        For molecules containing multiple connected components, fingerprints
        can be generated in two different ways: use all connected components
        or just the largest connected component. By default, all atoms
        except for the largest connected component are deleted before
        generation of fingerprints.

    -m, --mode *AtomTypesCount | AtomTypesBits*
        Specify type of atom types fingerprints to generate for molecules in
        *SDFile(s)*. Possible values: *AtomTypesCount or AtomTypesBits*.
        Default value: *AtomTypesCount*.

        For *AtomTypesCount* values of -m, --mode option, a fingerprint
        vector string is generated. The vector string corresponding to
        *AtomTypesCount* contains count of atom types.

        For *AtomTypesBits* value of -m, --mode option, a fingerprint
        bit-vector string containing zeros and ones indicating presence or
        absence of atom types is generated.

        For *AtomTypesCount* atom types fingerprints, two types of atom
        types set size can be specified using -a, --AtomTypesSetToUse
        option: *ArbitrarySize or FixedSize*. *ArbitrarySize* corrresponds
        to only atom types detected in molecule; *FixedSize* corresponds to
        fixed number of atom types previously defined.

        For *AtomTypesBits* atom types fingeprints, only *FixedSize* is
        allowed.

        Combination of -m, --Mode and --AtomTypesSetToUse along with -a,
        --AtomtomIdentifierType allows generation of following different
        atom types fingerprints:

            Mode                  AtomIdentifierType           AtomTypesSetToUse

            AtomTypesCount        AtomicInvariantsAtomTypes    ArbitrarySize [ Default ]

            AtomTypesCount        DREIDINGAtomTypes            ArbitrarySize
            AtomTypesCount        DREIDINGAtomTypes            FixedSize
            AtomTypesBits         DREIDINGAtomTypes            FixedSize

            AtomTypesCount        EStateAtomTypes              ArbitrarySize
            AtomTypesCount        EStateAtomTypes              FixedSize
            AtomTypesBits         EStateAtomTypes              FixedSize

            AtomTypesCount        FunctionalClassAtomTypes    ArbitrarySize

            AtomTypesCount        MMFF94AtomTypes              ArbitrarySize
            AtomTypesCount        MMFF94AtomTypes              FixedSize
            AtomTypesBits         MMFF94AtomTypes              FixedSize

            AtomTypesCount        SLogPAtomTypes               ArbitrarySize
            AtomTypesCount        SLogPAtomTypes               FixedSize
            AtomTypesBits         SLogPAtomTypes               FixedSize

            AtomTypesCount        SYBYLAtomTypes               ArbitrarySize
            AtomTypesCount        SYBYLAtomTypes               FixedSize
            AtomTypesBits         SYBYLAtomTypes               FixedSize

            AtomTypesCount        TPSAAtomTypes                 FixedSize
            AtomTypesBits         TPSAAtomTypes                 FixedSize

            AtomTypesCount        UFFAtomTypes                 ArbitrarySize
            AtomTypesCount        UFFAtomTypes                 FixedSize
            AtomTypesBits         UFFAtomTypes                 FixedSize

        The default is to generate *AtomicInvariantAtomTypes* fingeprints
        corresponding to *ArbitrarySize* as value of --AtomTypesSetToUse
        option.

    --OutDelim *comma | tab | semicolon*
        Delimiter for output CSV/TSV text file(s). Possible values: *comma,
        tab, or semicolon* Default value: *comma*.

    --output *SD | FP | text | all*
        Type of output files to generate. Possible values: *SD, FP, text, or
        all*. Default value: *text*.

    -o, --overwrite
        Overwrite existing files.

    -q, --quote *Yes | No*
        Put quote around column values in output CSV/TSV text file(s).
        Possible values: *Yes or No*. Default value: *Yes*.

    -r, --root *RootName*
        New file name is generated using the root: <Root>.<Ext>. Default for
        new file names: <SDFileName><AtomTypesFP>.<Ext>. The file type
        determines <Ext> value. The sdf, fpf, csv, and tsv <Ext> values are
        used for SD, FP, comma/semicolon, and tab delimited text files,
        respectively.This option is ignored for multiple input files.

    -v, --VectorStringFormat *ValuesString | IDsAndValuesString |
    IDsAndValuesPairsString | ValuesAndIDsString | ValuesAndIDsPairsString*
        Format of fingerprints vector string data in output SD, FP or
        CSV/TSV text file(s) specified by --output used during
        <AtomTypesCount> value of -m, --mode option. Possible values:
        *ValuesString, IDsAndValuesString | IDsAndValuesPairsString |
        ValuesAndIDsString | ValuesAndIDsPairsString*.

        Default value during *ArbitrarySize* value of -e,
        --AtomTypesSetToUse option: *IDsAndValuesString*. Default value
        during *FixedSize* value of -e, --AtomTypesSetToUse option:
        *ValuesString*.

        Example of *SD* file containing atom types fingerprints string data:

            ... ...
            ... ...
            $$$$
            ... ...
            ... ...
            ... ...
            41 44  0  0  0  0  0  0  0  0999 V2000
             -3.3652    1.4499    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
            ... ...
            2  3  1  0  0  0  0
            ... ...
            M  END
            >  <CmpdID>
            Cmpd1

            >  <AtomTypesFingerprints>
            FingerprintsVector;AtomTypesCount:AtomicInvariantsAtomTypes:ArbitrarySi
            ze;10;NumericalValues;IDsAndValuesString;C.X1.BO1.H3 C.X2.BO2.H2 C.X2.B
            O3.H1 C.X3.BO3.H1 C.X3.BO4 F.X1.BO1 N.X2.BO2.H1 N.X3.BO3 O.X1.BO1.H1 O.
            X1.BO2;2 4 14 3 10 1 1 1 3 2

            $$$$
            ... ...
            ... ...

        Example of *FP* file containing atom types fingerprints string data:

            #
            # Package = MayaChemTools 7.4
            # Release Date = Oct 21, 2010
            #
            # TimeStamp = Fri Mar 11 14:28:07 2011
            #
            # FingerprintsStringType = FingerprintsVector
            #
            # Description = AtomTypesCount:AtomicInvariantsAtomTypes:ArbitrarySize
            # VectorStringFormat = IDsAndValuesString
            # VectorValuesType = NumericalValues
            #
            Cmpd1 10;C.X1.BO1.H3 C.X2.BO2.H2 C.X2.BO3.H1 C.X3.BO3.H1 C.X3.BO4 F...
            Cmpd2 9;C.X1.BO1.H3 C.X2.BO2.H2 C.X3.BO3.H1 C.X3.BO4 N.X1.BO1.H2 N....
            ... ...
            ... ..

        Example of CSV *Text* file atom types containing fingerprints string
        data:

            "CompoundID","AtomTypesFingerprints"
            "Cmpd1","FingerprintsVector;AtomTypesCount:AtomicInvariantsAtomTypes:Ar
            bitrarySize;10;NumericalValues;IDsAndValuesString;C.X1.BO1.H3 C.X2.BO2.
            H2 C.X2.BO3.H1 C.X3.BO3.H1 C.X3.BO4 F.X1.BO1 N.X2.BO2.H1 N.X3.BO3 O.X1.
            BO1.H1 O.X1.BO2;2 4 14 3 10 1 1 1 3 2"
            O.X1.BO2;3 3 6 3 1 1 2 2 2"
            ... ...
            ... ...

        Examples:

            FingerprintsVector;AtomTypesCount:EStateAtomTypes:ArbitrarySize;11;Num
            ericalValues;IDsAndValuesString;aaCH aasC aasN dO dssC sCH3 sF sOH ssC
            H2 ssNH sssCH;14 8 1 2 2 2 1 3 4 1 3

            FingerprintsVector;AtomTypesCount:SYBYLAtomTypes:ArbitrarySize;9;Numer
            icalValues;IDsAndValuesString;C.2 C.3 C.ar F N.am N.ar O.2 O.3 O.co2;2
            9 22 1 1 1 1 2 2

            FingerprintsVector;AtomTypesCount:SYBYLAtomTypes:FixedSize;44;OrderedN
            umericalValues;IDsAndValuesString;C.3 C.2 C.1 C.ar C.cat N.3 N.2 N.1 N
            .ar N.am N.pl3 N.4 O.3 O.2 O.co2 S.3 S.2 S.o S.o2 P.3 F Cl Br I ANY HA
            L HET Li Na Mg Al Si K Ca Cr.th Cr.oh Mn Fe Co.oh Cu Zn Se Mo Sn;9 2 0
            22 0 0 0 0 1 1 0 0 2 1 2 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
            0 0 0 0 0 0 0

    -w, --WorkingDir *DirName*
        Location of working directory. Default: current directory.

EXAMPLES
    To generate atomic invariants atom types count fingerprints of arbitrary
    size in vector string format and create a SampleATFP.csv file containing
    sequential compound IDs along with fingerprints vector strings data,
    type:

        % AtomTypesFingerprints.pl -r SampleATFP -o Sample.sdf

    To generate functional class atom types count fingerprints of arbitrary
    size in vector string format and create a SampleATFP.csv file containing
    sequential compound IDs along with fingerprints vector strings data,
    type:

        % AtomTypesFingerprints.pl -m AtomTypesCount -a FunctionalClassAtomTypes
          -r SampleATFP -o Sample.sdf

    To generate E-state atom types count fingerprints of arbitrary size in
    vector string format and create a SampleATFP.csv file containing
    sequential compound IDs along with fingerprints vector strings data,
    type:

        % AtomTypesFingerprints.pl -m AtomTypesCount -a EStateAtomTypes
          --AtomTypesSetToUse ArbitrarySize -r SampleATFP -o Sample.sdf

    To generate E-state atom types count fingerprints of fixed size in
    vector string with IDsAndValues format and create a SampleATFP.csv file
    containing sequential compound IDs along with fingerprints vector
    strings data, type:

        % AtomTypesFingerprints.pl -m AtomTypesCount -a EStateAtomTypes
          --AtomTypesSetToUse FixedSize -v IDsAndValuesString
          -r SampleATFP -o Sample.sdf

    To generate E-state atom types bits fingerprints of fixed size in
    bit-vector string format and create a SampleATFP.csv file containing
    sequential compound IDs along with fingerprints vector strings data,
    type:

        % AtomTypesFingerprints.pl -m AtomTypesBits -a EStateAtomTypes
          --AtomTypesSetToUse FixedSize -r SampleATFP -o Sample.sdf

    To generate MMFF94 atom types count fingerprints of arbitrary size in
    vector string format and create a SampleATFP.csv file containing
    sequential compound IDs along with fingerprints vector strings data,
    type:

        % AtomTypesFingerprints.pl -m AtomTypesCount -a MMFF94AtomTypes
          --AtomTypesSetToUse ArbitrarySize -r SampleATFP -o Sample.sdf

    To generate MMFF94 atom types count fingerprints of fixed size in vector
    string format and create a SampleATFP.csv file containing sequential
    compound IDs along with fingerprints vector strings data, type:

        % AtomTypesFingerprints.pl -m AtomTypesCount -a MMFF94AtomTypes
          --AtomTypesSetToUse FixedSize -r SampleATFP -o Sample.sdf

    To generate MMFF94 atom types count fingerprints of fixed size in vector
    string with IDsAndValues format and create a SampleATFP.csv file
    containing sequential compound IDs along with fingerprints vector
    strings data, type:

        % AtomTypesFingerprints.pl -m AtomTypesCount -a MMFF94AtomTypes
          --AtomTypesSetToUse FixedSize -v IDsAndValuesString
          -r SampleATFP -o Sample.sdf

    To generate MMFF94 atom types bits fingerprints of fixed size in
    bit-vector string format and create a SampleATFP.csv file containing
    sequential compound IDs along with fingerprints vector strings data,
    type:

        % AtomTypesFingerprints.pl -m AtomTypesBits -a MMFF94AtomTypes
          --AtomTypesSetToUse FixedSize -r SampleATFP -o Sample.sdf

    To generate MMFF94 atom types count fingerprints of arbitrary size in
    vector string format and create a SampleATFP.csv file containing
    compound ID from molecule name line along with fingerprints vector
    strings data, type

        % AtomTypesFingerprints.pl -m AtomTypesCount -a MMFF94AtomTypes
          --DataFieldsMode CompoundID --CompoundIDMode MolName
          -r SampleATFP -o Sample.sdf

    To generate MMFF94 atom types count fingerprints of arbitrary size in
    vector string format and create a SampleATFP.csv file containing
    compound IDs using specified data field along with fingerprints vector
    strings data, type:

        % AtomTypesFingerprints.pl -m AtomTypesCount -a MMFF94AtomTypes
          --DataFieldsMode CompoundID --CompoundIDMode DataField --CompoundID
          Mol_ID -r SampleATFP -o Sample.sdf

    To generate MMFF94 atom types count fingerprints of arbitrary size in
    vector string format and create a SampleATFP.csv file containing
    compound ID using combination of molecule name line and an explicit
    compound prefix along with fingerprints vector strings data, type:

        % AtomTypesFingerprints.pl -m AtomTypesCount -a MMFF94AtomTypes
          --DataFieldsMode CompoundID --CompoundIDMode MolnameOrLabelPrefix
          --CompoundID Cmpd --CompoundIDLabel MolID -r SampleATFP -o Sample.sdf

    To generate MMFF94 atom types count fingerprints of arbitrary size in
    vector string format and create a SampleATFP.csv file containing
    specific data fields columns along with fingerprints vector strings
    data, type:

        % AtomTypesFingerprints.pl -m AtomTypesCount -a MMFF94AtomTypes
          --DataFieldsMode Specify --DataFields Mol_ID -r SampleATFP
          -o Sample.sdf

    To generate MMFF94 atom types count fingerprints of arbitrary size in
    vector string format and create a SampleATFP.csv file containing common
    data fields columns along with fingerprints vector strings data, type:

        % AtomTypesFingerprints.pl -m AtomTypesCount -a MMFF94AtomTypes
         --DataFieldsMode Common -r SampleATFP -o Sample.sdf

    To generate MMFF94 atom types count fingerprints of arbitrary size in
    vector string format and create SampleATFP.sdf, SampleATFP.fpf and
    SampleATFP.csv files containing all data fields columns in CSV file
    along with fingerprints vector strings data, type:

        % AtomTypesFingerprints.pl -m AtomTypesCount -a MMFF94AtomTypes
         --DataFieldsMode All --output all -r SampleATFP -o Sample.sdf

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

SEE ALSO
    InfoFingerprintsFiles.pl, SimilarityMatricesFingerprints.pl,
    AtomNeighborhoodsFingerprints.pl, ExtendedConnectivityFingerprints.pl,
    MACCSKeysFingeprints.pl, PathLengthFingerprints.pl,
    TopologicalAtomPairsFingerprints.pl,
    TopologicalAtomTorsionsFingerprints.pl,
    TopologicalPharmacophoreAtomPairsFingerprints.pl,
    TopologicalPharmacophoreAtomTripletsFingerprints.pl

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.

