NAME
    ExtendedConnectivityFingerprints.pl - Generate extended connectivity
    fingerprints for SD files

SYNOPSIS
    ExtendedConnectivityFingerprints.pl SDFile(s)...

    ExtendedConnectivityFingerprints.pl [--AromaticityModel
    *AromaticityModelType*] [-a, --AtomIdentifierType
    *AtomicInvariantsAtomTypes*] [--AtomicInvariantsToUse
    *"AtomicInvariant,AtomicInvariant..."*] [--FunctionalClassesToUse
    *"FunctionalClass1,FunctionalClass2..."*] [--BitsOrder *Ascending |
    Descending*] [-b, --BitStringFormat *BinaryString | HexadecimalString*]
    [--CompoundID *DataFieldName or LabelPrefixString*] [--CompoundIDLabel
    *text*] [--CompoundIDMode] [--DataFields
    *"FieldLabel1,FieldLabel2,..."*] [-d, --DataFieldsMode *All | Common |
    Specify | CompoundID*] [-f, --Filter *Yes | No*] [--FingerprintsLabel
    *text*] [-h, --help] [-k, --KeepLargestComponent *Yes | No*] [-m, --mode
    *ExtendedConnectivity | ExtendedConnecticityCount |
    ExtendedConnecticityBits*] [-n, --NeighborhoodRadius *number*]
    [--OutDelim *comma | tab | semicolon*] [--output *SD | FP | text | all*]
    [-o, --overwrite] [-q, --quote *Yes | No*] [-r, --root *RootName*] [-s,
    --size *number*] [--UsePerlCoreRandom *Yes | No*] [-v,
    --VectorStringFormat *IDsAndValuesString | IDsAndValuesPairsString |
    ValuesAndIDsString | ValuesAndIDsPairsString*] [-w, --WorkingDir
    dirname] SDFile(s)...

DESCRIPTION
    Generate extended connectivity fingerprints [ Ref 48, Ref 52 ] for
    *SDFile(s)* and create appropriate SD, FP or CSV/TSV text file(s)
    containing fingerprints 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 extended
    connectivity fingerprints corresponding to following -a,
    --AtomIdentifierTypes:

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

    Based on values specified for -a, --AtomIdentifierType,
    --AtomicInvariantsToUse and --FunctionalClassesToUse, initial atom types
    are assigned to all non-hydrogen atoms in a molecule and these atom
    types strings are converted into initial atom identifier integers using
    TextUtil::HashCode function. The duplicate atom identifiers are removed.

    For -n, --NeighborhoodRadius value of *0*, the initial set of unique
    atom identifiers comprises the molecule fingerprints. Otherwise, atom
    neighborhoods are generated for each non-hydrogen atom up to specified
    -n, --NeighborhoodRadius value. For each non-hydrogen central atom at a
    specific radius, its neighbors at next radius level along with their
    bond orders and previously calculated atom identifiers are collected
    which in turn are used to generate a new integer atom identifier; the
    bond orders and atom identifier pairs list is first sorted by bond order
    followed by atom identifiers to make these values graph invariant.

    After integer atom identifiers have been generated for all non-hydrogen
    atoms at all specified neighborhood radii, the duplicate integer atom
    identifiers corresponding to same hash code value generated using
    TextUtil::HashCode are tracked by keeping the atom identifiers at lower
    radius. Additionally, all structurally duplicate integer atom
    identifiers at each specified radius are also tracked by identifying
    equivalent atoms and bonds corresponding to substructures used for
    generating atom identifier and keeping integer atom identifier with
    lowest value.

    For *ExtendedConnnectivity* value of fingerprints -m, --mode, the
    duplicate identifiers are removed from the list and the unique atom
    identifiers constitute the extended connectivity fingerprints of a
    molecule.

    For *ExtendedConnnectivityCount* value of fingerprints -m, --mode, the
    occurrence of each unique atom identifiers appears is counted and the
    unique atom identifiers along with their count constitute the extended
    connectivity fingerprints of a molecule.

    For *ExtendedConnectivityBits* value of fingerprints -m, --mode, the
    unique atom identifiers are used as a random number seed to generate a
    random integer value between 0 and --Size which in turn is used to set
    corresponding bits in the fingerprint bit-vector string.

    Example of *SD* file containing extended connectivity 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

        >  <ExtendedConnectivityFingerprints>
        FingerprintsVector;ExtendedConnectivity:AtomicInvariantsAtomTypes:Radiu
        s2;60;AlphaNumericalValues;ValuesString;73555770 333564680 352413391 66
        6191900 1001270906 1371674323 1481469939 1977749791 2006158649 21414087
        99 49532520 64643108 79385615 96062769 273726379 564565671 855141035 90
        6706094 988546669 1018231313 1032696425 1197507444 1331250018 133853...

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

    Example of *FP* file containing extended connectivity fingerprints
    string data:

        #
        # Package = MayaChemTools 7.4
        # Release Date = Oct 21, 2010
        #
        # TimeStamp = Fri Mar 11 14:43:57 2011
        #
        # FingerprintsStringType = FingerprintsVector
        #
        # Description = ExtendedConnectivity:AtomicInvariantsAtomTypes:Radius2
        # VectorStringFormat = ValuesString
        # VectorValuesType = AlphaNumericalValues
        #
        Cmpd1 60;73555770 333564680 352413391 666191900 1001270906 137167432...
        Cmpd2 41;73555770 333564680 666191900 1142173602 1363635752 14814699...
        ... ...
        ... ..

    Example of CSV *Text* file containing extended connectivity fingerprints
    string data:

        "CompoundID","ExtendedConnectivityFingerprints"
        "Cmpd1","FingerprintsVector;ExtendedConnectivity:AtomicInvariantsAtomTy
        pes:Radius2;60;AlphaNumericalValues;ValuesString;73555770 333564680 352
        413391 666191900 1001270906 1371674323 1481469939 1977749791 2006158649
        2141408799 49532520 64643108 79385615 96062769 273726379 564565671 8551
        41035 906706094 988546669 1018231313 1032696425 1197507444 13312500..."
        ... ...
        ... ...

    The current release of MayaChemTools generates the following types of
    extended connectivity fingerprints vector strings:

        FingerprintsVector;ExtendedConnectivity:AtomicInvariantsAtomTypes:Radi
        us2;60;AlphaNumericalValues;ValuesString;73555770 333564680 352413391
        666191900 1001270906 1371674323 1481469939 1977749791 2006158649 21414
        08799 49532520 64643108 79385615 96062769 273726379 564565671 85514103
        5 906706094 988546669 1018231313 1032696425 1197507444 1331250018 1338
        532734 1455473691 1607485225 1609687129 1631614296 1670251330 17303...

        FingerprintsVector;ExtendedConnectivityCount:AtomicInvariantsAtomTypes
        :Radius2;60;NumericalValues;IDsAndValuesString;73555770 333564680 3524
        13391 666191900 1001270906 1371674323 1481469939 1977749791 2006158649
        2141408799 49532520 64643108 79385615 96062769 273726379 564565671...;
        3 2 1 1 14 1 2 10 4 3 1 1 1 1 2 1 2 1 1 1 2 3 1 1 2 1 3 3 8 2 2 2 6 2
        1 2 1 1 2 1 1 1 2 1 1 2 1 2 1 1 1 1 1 1 1 1 1 2 1 1

        FingerprintsBitVector;ExtendedConnectivityBits:AtomicInvariantsAtomTyp
        es:Radius2;1024;BinaryString;Ascending;0000000000000000000000000000100
        0000000001010000000110000011000000000000100000000000000000000000100001
        1000000110000000000000000000000000010011000000000000000000000000010000
        0000000000000000000000000010000000000000000001000000000000000000000000
        0000000000010000100001000000000000101000000000000000100000000000000...

        FingerprintsBitVector;ExtendedConnectivityBits:AtomicInvariantsAtomTyp
        es:Radius2;1024;HexadecimalString;Ascending;000000010050c0600800000803
        0300000091000004000000020000100000000124008200020000000040020000000000
        2080000000820040010020000000008040000000000080001000000000400000000000
        4040000090000061010000000800200000000000001400000000020080000000000020
        00008020200000408000

        FingerprintsVector;ExtendedConnectivity:FunctionalClassAtomTypes:Radiu
        s2;57;AlphaNumericalValues;ValuesString;24769214 508787397 850393286 8
        62102353 981185303 1231636850 1649386610 1941540674 263599683 32920567
        1 571109041 639579325 683993318 723853089 810600886 885767127 90326012
        7 958841485 981022393 1126908698 1152248391 1317567065 1421489994 1455
        632544 1557272891 1826413669 1983319256 2015750777 2029559552 20404...

        FingerprintsVector;ExtendedConnectivityCount:FunctionalClassAtomTypes:
        Radius2;57;NumericalValues;IDsAndValuesString;24769214 508787397 85039
        3286 862102353 981185303 1231636850 1649386610 1941540674 263599683 32
        9205671 571109041 639579325 683993318 723853089 810600886 885767127...;
        1 1 1 10 2 22 3 1 3 3 1 1 1 3 2 2 1 2 2 2 3 1 1 1 1 1 14 1 1 1 1 1 1 2
        1 2 1 1 2 2 1 1 2 1 1 1 2 1 1 2 1 1 1 1 1 1 1

        FingerprintsBitVector;ExtendedConnectivityBits:FunctionalClassAtomType
        s:Radius2;1024;BinaryString;Ascending;00000000000000000000100000000000
        0000000001000100000000001000000000000000000000000000000000101000000010
        0000001000000000010000000000000000000000000000000000000000000000000100
        0000000000001000000000000001000000000001001000000000000000000000000000
        0000000000000000100000000000001000000000000000000000000000000000000...

        FingerprintsVector;ExtendedConnectivity:DREIDINGAtomTypes:Radius2;56;A
        lphaNumericalValues;ValuesString;280305427 357928343 721790579 1151822
        898 1207111054 1380963747 1568213839 1603445250 4559268 55012922 18094
        0813 335715751 534801009 684609658 829361048 972945982 999881534 10076
        55741 1213692591 1222032501 1224517934 1235687794 1244268533 152812070
        0 1629595024 1856308891 1978806036 2001865095 2096549435 172675415 ...

        FingerprintsVector;ExtendedConnectivity:EStateAtomTypes:Radius2;62;Alp
        haNumericalValues;ValuesString;25189973 528584866 662581668 671034184
        926543080 1347067490 1738510057 1759600920 2034425745 2097234755 21450
        44754 96779665 180364292 341712110 345278822 386540408 387387308 50430
        1706 617094135 771528807 957666640 997798220 1158349170 1291258082 134
        1138533 1395329837 1420277211 1479584608 1486476397 1487556246 1566...

        FingerprintsVector;ExtendedConnectivity:MMFF94AtomTypes:Radius2;64;Alp
        haNumericalValues;ValuesString;224051550 746527773 998750766 103704190
        2 1239701709 1248384926 1259447756 1521678386 1631549126 1909437580 20
        37095052 2104274756 2117729376 8770364 31445800 81450228 314289324 344
        041929 581773587 638555787 692022098 811840536 929651561 936421792 988
        636432 1048624296 1054288509 1369487579 1454058929 1519352190 17271...

        FingerprintsVector;ExtendedConnectivity:SLogPAtomTypes:Radius2;71;Alph
        aNumericalValues;ValuesString;78989290 116507218 489454042 888737940 1
        162561799 1241797255 1251494264 1263717127 1471206899 1538061784 17654
        07295 1795036542 1809833874 2020454493 2055310842 2117729376 11868981
        56731842 149505242 184525155 196984339 288181334 481409282 556716568 6
        41915747 679881756 721736571 794256218 908276640 992898760 10987549...

        FingerprintsVector;ExtendedConnectivity:SYBYLAtomTypes:Radius2;58;Alph
        aNumericalValues;ValuesString;199957044 313356892 455463968 465982819
        1225318176 1678585943 1883366064 1963811677 2117729376 113784599 19153
        8837 196629033 263865277 416380653 477036669 681527491 730724924 90906
        5537 1021959189 1133014972 1174311016 1359441203 1573452838 1661585138
        1668649038 1684198062 1812312554 1859266290 1891651106 2072549404 ...

        FingerprintsVector;ExtendedConnectivity:TPSAAtomTypes:Radius2;47;Alpha
        NumericalValues;ValuesString;20818206 259344053 862102353 1331904542 1
        700688206 265614156 363161397 681332588 810600886 885767127 950172500
        951454814 1059668746 1247054493 1382302230 1399502637 1805025917 19189
        39561 2114677228 2126402271 8130483 17645742 32278373 149975755 160327
        654 256360355 279492740 291251259 317592700 333763396 972105960 101...

        FingerprintsVector;ExtendedConnectivity:UFFAtomTypes:Radius2;56;AlphaN
        umericalValues;ValuesString;280305427 357928343 721790579 1151822898 1
        207111054 1380963747 1568213839 1603445250 4559268 55012922 180940813
        335715751 534801009 684609658 829361048 972945982 999881534 1007655741
        1213692591 1222032501 1224517934 1235687794 1244268533 1528120700 162
        9595024 1856308891 1978806036 2001865095 2096549435 172675415 18344...

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 |
    FunctionalClassAtomTypes | DREIDINGAtomTypes | EStateAtomTypes |
    MMFF94AtomTypes | SLogPAtomTypes | SYBYLAtomTypes | TPSAAtomTypes |
    UFFAtomTypes*
        Specify atom identifier type to use for assignment of initial atom
        identifier to non-hydrogen atoms during calculation of extended
        connectivity fingerprints [ Ref 48, Ref 52]. Possible values in the
        current release are: *AtomicInvariantsAtomTypes,
        FunctionalClassAtomTypes, DREIDINGAtomTypes, EStateAtomTypes,
        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 invarians are: *AS, X, BO, LBO, SB, DB,
        TB, H, Ar, RA, FC, MN, SM*. Default value [ Ref 24 ]:
        *AS,X,BO,H,FC,MN*.

        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.

    --BitsOrder *Ascending | Descending*
        Bits order to use during generation of fingerprints bit-vector
        string for *ExtendedConnectivityBits* 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
        *ExtendedConnectivityBits* 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;ExtendedConnectivityBits:AtomicInvariantsAtomTyp
            es:Radius2;1024;BinaryString;Ascending;0000000000000000000000000000100
            0000000001010000000110000011000000000000100000000000000000000000100001
            1000000110000000000000000000000000010011000000000000000000000000010000
            0000000000000000000000000010000000000000000001000000000000000000000000
            0000000000010000100001000000000000101000000000000000100000000000000...

            FingerprintsBitVector;ExtendedConnectivityBits:FunctionalClassAtomType
            s:Radius2;1024;BinaryString;Ascending;00000000000000000000100000000000
            0000000001000100000000001000000000000000000000000000000000101000000010
            0000001000000000010000000000000000000000000000000000000000000000000100
            0000000000001000000000000001000000000001001000000000000000000000000000
            0000000000000000100000000000001000000000000000000000000000000000000...

    --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

    --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.

    --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: *ExtendedConnectivityFingerprints*.

    -h, --help
        Print this help message.

    -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 *ExtendedConnectivity | ExtendedConnectivityCount |
    ExtendedConnectivityBits*
        Specify type of extended connectivity fingerprints to generate for
        molecules in *SDFile(s)*. Possible values: *ExtendedConnectivity,
        ExtendedConnecticityCount or ExtendedConnectivityBits*. Default
        value: *ExtendedConnectivity*.

        For *ExtendedConnnectivity* value of fingerprints -m, --mode, a
        fingerprint vector containing unique atom identifiers constitute the
        extended connectivity fingerprints of a molecule.

        For *ExtendedConnnectivityCount* value of fingerprints -m, --mode, a
        fingerprint vector containing unique atom identifiers along with
        their count constitute the extended connectivity fingerprints of a
        molecule.

        For *ExtendedConnnectivityBits* value of fingerprints -m, --mode, a
        fingerprint bit vector indicating presence/absence of structurally
        unique atom identifiers constitute the extended connectivity
        fingerprints of a molecule.

    -n, --NeighborhoodRadius *number*
        Atomic neighborhood radius for generating extended connectivity
        neighborhoods. Default value: *2*. Valid values: >= 0. Neighborhood
        radius of zero correspond to just the list of non-hydrogen atoms.

        Default value of *2* for atomic neighborhood radius generates
        extended connectivity fingerprints corresponding to path length or
        diameter value of *4* [ Ref 52b ].

    --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><ExtendedConnectivityFP>.<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.

    -s, --size *number*
        Size of bit-vector to use during generation of fingerprints
        bit-vector string for *ExtendedConnectivityBits* value of -m,
        --mode. Default value: *1024*. Valid values correspond to any
        positive integer which satisfies the following criteria: power of 2,
        >= 32 and <= 2 ** 32.

        Examples:

           512
           1024
           2048

    --UsePerlCoreRandom *Yes | No*
        Specify whether to use Perl CORE::rand or MayaChemTools
        MathUtil::random function during random number generation for
        setting bits in fingerprints bit-vector strings. Possible values:
        *Yes or No*. Default value: *Yes*.

        *No* value option for --UsePerlCoreRandom allows the generation of
        fingerprints bit-vector strings which are same across different
        platforms.

        The random number generator implemented in MayaChemTools is a
        variant of linear congruential generator (LCG) as described by
        Miller et al. [ Ref 120 ]. It is also referred to as Lehmer random
        number generator or Park-Miller random number generator.

        Unlike Perl's core random number generator function rand, the random
        number generator implemented in MayaChemTools, MathUtil::random,
        generates consistent random values across different platforms for a
        specific random seed and leads to generation of portable
        fingerprints bit-vector strings.

    -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
        <ExtendedConnectivityCount> value of -m, --mode option. Possible
        values: *ValuesString, IDsAndValuesString | IDsAndValuesPairsString
        | ValuesAndIDsString | ValuesAndIDsPairsString*.

        Default value during <ExtendedConnectivityCount> value of -m, --mode
        option: *IDsAndValuesString*.

        Default value during <ExtendedConnectivity> value of -m, --mode
        option: *ValuesString*.

        Examples:

            FingerprintsVector;ExtendedConnectivity:AtomicInvariantsAtomTypes:Radi
            us2;60;AlphaNumericalValues;ValuesString;73555770 333564680 352413391
            666191900 1001270906 1371674323 1481469939 1977749791 2006158649 21414
            08799 49532520 64643108 79385615 96062769 273726379 564565671 85514103
            5 906706094 988546669 1018231313 1032696425 1197507444 1331250018 1338
            532734 1455473691 1607485225 1609687129 1631614296 1670251330 17303...

            FingerprintsVector;ExtendedConnectivityCount:AtomicInvariantsAtomTypes
            :Radius2;60;NumericalValues;IDsAndValuesString;73555770 333564680 3524
            13391 666191900 1001270906 1371674323 1481469939 1977749791 2006158649
            2141408799 49532520 64643108 79385615 96062769 273726379 564565671...;
            3 2 1 1 14 1 2 10 4 3 1 1 1 1 2 1 2 1 1 1 2 3 1 1 2 1 3 3 8 2 2 2 6 2
            1 2 1 1 2 1 1 1 2 1 1 2 1 2 1 1 1 1 1 1 1 1 1 2 1 1

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

EXAMPLES
    To generate extended connectivity fingerprints corresponding to
    neighborhood radius up to 2 using atomic invariants atom types in vector
    string format and create a SampleECAIFP.csv file containing sequential
    compound IDs along with fingerprints vector strings data, type:

        % ExtendedConnectivityFingerprints.pl -r SampleECAIFP -o Sample.sdf

    To generate extended connectivity count fingerprints corresponding to
    neighborhood radius up to 2 using atomic invariants atom types in vector
    string format and create a SampleECAIFP.csv file containing sequential
    compound IDs along with fingerprints vector strings data, type:

        % ExtendedConnectivityFingerprints.pl -m ExtendedConnectivityCount
          -r SampleECAIFP -o Sample.sdf

    To generate extended connectivity bits fingerprints as hexadecimal
    bit-string corresponding to neighborhood radius up to 2 using atomic
    invariants atom types in vector string format and create a
    SampleECAIFP.csv file containing sequential compound IDs along with
    fingerprints vector strings data, type:

        % ExtendedConnectivityFingerprints.pl -m ExtendedConnectivityBits
          -r SampleECAIFP -o Sample.sdf

    To generate extended connectivity bits fingerprints as binary bit-string
    corresponding to neighborhood radius up to 2 using atomic invariants
    atom types in vector string format and create a SampleECAIFP.csv file
    containing sequential compound IDs along with fingerprints vector
    strings data, type:

        % ExtendedConnectivityFingerprints.pl -m ExtendedConnectivityBits
          --BitStringFormat BinaryString -r SampleECAIFP -o Sample.sdf

    To generate extended connectivity fingerprints corresponding to
    neighborhood radius up to 2 using atomic invariants atom types in vector
    string format and create SampleECAIFP.sdf, SampleECAIFP.fpf and
    SampleECAIFP.csv files containing sequential compound IDs in CSV file
    along with fingerprints vector strings data, type:

        % ExtendedConnectivityFingerprints.pl --output all -r SampleECAIFP
          -o Sample.sdf

    To generate extended connectivity count fingerprints corresponding to
    neighborhood radius up to 2 using atomic invariants atom types in vector
    string format and create SampleECAIFP.sdf, SampleECAIFP.fpf and
    SampleECAIFP.csv files containing sequential compound IDs in CSV file
    along with fingerprints vector strings data, type:

        % ExtendedConnectivityFingerprints.pl -m ExtendedConnectivityCount
          --output all -r SampleECAIFP -o Sample.sdf

    To generate extended connectivity fingerprints corresponding to
    neighborhood radius up to 2 using functional class atom types in vector
    string format and create a SampleECFCFP.csv file containing sequential
    compound IDs along with fingerprints vector strings data, type:

        % ExtendedConnectivityFingerprints.pl -a FunctionalClassAtomTypes
          -r SampleECFCFP -o Sample.sdf

    To generate extended connectivity fingerprints corresponding to
    neighborhood radius up to 2 using DREIDING atom types in vector string
    format and create a SampleECFP.csv file containing sequential compound
    IDs along with fingerprints vector strings data, type:

        % ExtendedConnectivityFingerprints.pl -a DREIDINGAtomTypes
          -r SampleECFP -o Sample.sdf

    To generate extended connectivity fingerprints corresponding to
    neighborhood radius up to 2 using E-state atom types in vector string
    format and create a SampleECFP.csv file containing sequential compound
    IDs along with fingerprints vector strings data, type:

        % ExtendedConnectivityFingerprints.pl -a EStateAtomTypes
          -r SampleECFP -o Sample.sdf

    To generate extended connectivity fingerprints corresponding to
    neighborhood radius up to 2 using MMFF94 atom types in vector string
    format and create a SampleECFP.csv file containing sequential compound
    IDs along with fingerprints vector strings data, type:

        % ExtendedConnectivityFingerprints.pl -a MMFF94AtomTypes
          -r SampleECFP -o Sample.sdf

    To generate extended connectivity fingerprints corresponding to
    neighborhood radius up to 2 using SLogP atom types in vector string
    format and create a SampleECFP.csv file containing sequential compound
    IDs along with fingerprints vector strings data, type:

        % ExtendedConnectivityFingerprints.pl -a SLogPAtomTypes
          -r SampleECFP -o Sample.sdf

    To generate extended connectivity fingerprints corresponding to
    neighborhood radius up to 2 using SYBYL atom types in vector string
    format and create a SampleECFP.csv file containing sequential compound
    IDs along with fingerprints vector strings data, type:

        % ExtendedConnectivityFingerprints.pl -a SYBYLAtomTypes
          -r SampleECFP -o Sample.sdf

    To generate extended connectivity fingerprints corresponding to
    neighborhood radius up to 2 using TPSA atom types in vector string
    format and create a SampleECFP.csv file containing sequential compound
    IDs along with fingerprints vector strings data, type:

        % ExtendedConnectivityFingerprints.pl -a TPSAAtomTypes
          -r SampleECFP -o Sample.sdf

    To generate extended connectivity fingerprints corresponding to
    neighborhood radius up to 2 using UFF atom types in vector string format
    and create a SampleECFP.csv file containing sequential compound IDs
    along with fingerprints vector strings data, type:

        % ExtendedConnectivityFingerprints.pl -a UFFAtomTypes
          -r SampleECFP -o Sample.sdf

    To generate extended connectivity fingerprints corresponding to
    neighborhood radius up to 3 using atomic invariants atom types in vector
    string format and create a SampleECAIFP.csv file containing sequential
    compound IDs along with fingerprints vector strings data, type:

        % ExtendedConnectivityFingerprints.pl -a AtomicInvariantsAtomTypes -n 3
          -r SampleECAIFP -o Sample.sdf

    To generate extended connectivity fingerprints corresponding to
    neighborhood radius up to 3 using functional class atom types in vector
    string format and create a SampleECFCFP.csv file containing sequential
    compound IDs along with fingerprints vector strings data, type:

        % ExtendedConnectivityFingerprints.pl -a FunctionalClassAtomTypes -n 3
          -r SampleECFCFP -o Sample.sdf

    To generate extended connectivity fingerprints corresponding to
    neighborhood radius up to 2 using only AS,X atomic invariants atom types
    in vector string format and create a SampleECAIFP.csv file containing
    sequential compound IDs along with fingerprints vector strings data,
    type:

        % ExtendedConnectivityFingerprints.pl -a AtomicInvariantsAtomTypes
          --AtomicInvariantsToUse "AS,X" -r SampleECAIFP -o Sample.sdf

    To generate extended connectivity fingerprints corresponding to
    neighborhood radius up to 2 using only HBD,HBA functional class atom
    types in vector string format and create a SampleECFCFP.csv file
    containing sequential compound IDs along with fingerprints vector
    strings data, type:

        % ExtendedConnectivityFingerprints.pl -a FunctionalClassAtomTypes
          --FunctionalClassesToUse "HBD,HBA" -r SampleECFCFP -o Sample.sdf

    To generate extended connectivity fingerprints corresponding to
    neighborhood radius up to 2 using atomic invariants atom types in vector
    string format and create a SampleECAIFP.csv file containing compound ID
    from molecule name line along with fingerprints vector strings data,
    type:

        % ExtendedConnectivityFingerprints.pl -a AtomicInvariantsAtomTypes
          --DataFieldsMode CompoundID -CompoundIDMode MolName
          -r SampleECAIFP -o Sample.sdf

    To generate extended connectivity fingerprints corresponding to
    neighborhood radius up to 2 using functional class atom types in vector
    string format and create a SampleECFCFP.csv file containing compound IDs
    using specified data field along with fingerprints vector strings data,
    type:

        % ExtendedConnectivityFingerprints.pl -a FunctionalClassAtomTypes
          --DataFieldsMode CompoundID -CompoundIDMode DataField --CompoundID Mol_ID
          -r SampleECFCFP -o Sample.sdf

    To generate extended connectivity fingerprints corresponding to
    neighborhood radius up to 2 using atomic invariants atom types in vector
    string format and create a SampleECAIFP.tsv file containing compound ID
    using combination of molecule name line and an explicit compound prefix
    along with fingerprints vector strings data, type:

        % ExtendedConnectivityFingerprints.pl -a AtomicInvariantsAtomTypes
          --DataFieldsMode CompoundID -CompoundIDMode MolnameOrLabelPrefix
          --CompoundID Cmpd --CompoundIDLabel MolID -r SampleECAIFP -o Sample.sdf

    To generate extended connectivity fingerprints corresponding to
    neighborhood radius up to 2 using functional class atom types in vector
    string format and create a SampleECFCFP.csv file containing specific
    data fields columns along with fingerprints vector strings data, type:

        % ExtendedConnectivityFingerprints.pl -a FunctionalClassAtomTypes
          --DataFieldsMode  Specify --DataFields Mol_ID -r SampleECFCFP
          -o Sample.sdf

    To generate extended connectivity fingerprints corresponding to
    neighborhood radius up to 2 using atomic invariants atom types in vector
    string format and create a SampleECAIFP.tsv file containing common data
    fields columns along with fingerprints vector strings data, type:

        % ExtendedConnectivityFingerprints.pl -a AtomicInvariantsAtomTypes
          --DataFieldsMode Common -r SampleECAIFP -o Sample.sdf

    To generate extended connectivity fingerprints corresponding to
    neighborhood radius up to 2 using functional class atom types in vector
    string format and create SampleECFCFP.sdf, SampleECFCFP.fpf and
    SampleECFCFP.csv files containing all data fields columns in CSV file
    along with fingerprints vector strings data, type:

        % ExtendedConnectivityFingerprints.pl -a FunctionalClassAtomTypes
          --DataFieldsMode All  --output all -r SampleECFCFP
          -o Sample.sdf

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

SEE ALSO
    InfoFingerprintsFiles.pl, SimilarityMatricesFingerprints.pl,
    AtomNeighborhoodsFingerprints.pl, MACCSKeysFingerprints.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.

