NAME
    TopologicalPharmacophoreAtomTripletsFingerprints.pl - Generate
    topological pharmacophore atom triplets fingerprints for SD files

SYNOPSIS
    TopologicalPharmacophoreAtomTripletsFingerprints.pl SDFile(s)...

    TopologicalPharmacophoreAtomTripletsFingerprints.pl [--AromaticityModel
    *AromaticityModelType*] [--AtomTripletsSetSizeToUse *ArbitrarySize |
    FixedSize*] [-a, --AtomTypesToUse *"AtomType1, AtomType2..."*]
    [--AtomTypesWeight *"AtomType1, Weight1, AtomType2, Weight2..."*]
    [--CompoundID *DataFieldName or LabelPrefixString*] [--CompoundIDLabel
    *text*] [--CompoundIDMode] [--DataFields *"FieldLabel1,
    FieldLabel2,..."*] [-d, --DataFieldsMode *All | Common | Specify |
    CompoundID*] [--DistanceBinSize *number*] [-f, --Filter *Yes | No*]
    [--FingerprintsLabelMode *FingerprintsLabelOnly |
    FingerprintsLabelWithIDs*] [--FingerprintsLabel *text*] [-h, --help]
    [-k, --KeepLargestComponent *Yes | No*] [--MinDistance *number*]
    [--MaxDistance *number*] [--OutDelim *comma | tab | semicolon*]
    [--output *SD | FP | text | all*] [-o, --overwrite] [-q, --quote *Yes |
    No*] [-r, --root *RootName*] [-u, --UseTriangleInequality *Yes | No*]
    [-v, --VectorStringFormat *ValuesString, IDsAndValuesString |
    IDsAndValuesPairsString | ValuesAndIDsString | ValuesAndIDsPairsString*]
    [-w, --WorkingDir dirname] SDFile(s)...

DESCRIPTION
    Generate topological pharmacophore atom triplets fingerprints [ Ref 66,
    Ref 68-71 ] 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.

    Based on the values specified for --AtomTypesToUse, pharmacophore atom
    types are assigned to all non-hydrogen atoms in a molecule and a
    distance matrix is generated. Using --MinDistance, --MaxDistance, and
    --DistanceBinSize values, a binned distance matrix is generated with
    lower bound on the distance bin as the distance in distance matrix; the
    lower bound on the distance bin is also used as the distance between
    atom pairs for generation of atom triplet identifiers.

    A pharmacophore atom triplets basis set is generated for all unique atom
    triplets constituting atom pairs binned distances between --MinDistance
    and --MaxDistance. The value of --UseTriangleInequality determines
    whether the triangle inequality test is applied during generation of
    atom triplets basis set. The lower distance bound, along with specified
    pharmacophore types, is used during generation of atom triplet IDs.

        Let:

        P = Valid pharmacophore atom type

        Px = Pharmacophore atom x
        Py = Pharmacophore atom y
        Pz = Pharmacophore atom z

        Dmin = Minimum distance corresponding to number of bonds between two atoms
        Dmax = Maximum distance corresponding to number of bonds between two atoms
        D = Distance corresponding to number of bonds between two atom

        Bsize  = Distance bin size
        Nbins = Number of distance bins

        Dxy = Distance or lower bound of binned distance between Px and Py
        Dxz = Distance or lower bound of binned distance between Px and Pz
        Dyz = Distance or lower bound of binned distance between Py and Pz

        Then:

        PxDyz-PyDxz-PzDxy = Pharmacophore atom triplet IDs for atom types Px,
                            Py, and Pz

        For example: H1-H1-H1, H2-HBA-H2 and so on

        For default values of Dmin = 1 , Dmax = 10 and Bsize = 2:

        the number of distance bins, Nbins = 5, are:

        [1, 2] [3, 4] [5, 6] [7, 8] [9 10]

        and atom triplet basis set size is 2692.

        Atom triplet basis set size for various values of Dmin, Dmax and Bsize in
        conjunction with usage of triangle inequality is:

        Dmin    Dmax   Bsize   UseTriangleInequality   TripletBasisSetSize
        1       10     2       No                      4960
        1       10     2       Yes                     2692 [ Default ]
        2       12     2       No                      8436
        2       12     2       Yes                     4494

    Using binned distance matrix and pharmacohore atom types, occurrence of
    unique pharmacohore atom triplets is counted.

    The final pharmacophore atom triples count along with atom pair
    identifiers involving all non-hydrogen atoms constitute pharmacophore
    topological atom triplets fingerprints of the molecule.

    For *ArbitrarySize* value of --AtomTripletsSetSizeToUse option, the
    fingerprint vector correspond to only those topological pharmacophore
    atom triplets which are present and have non-zero count. However, for
    *FixedSize* value of --AtomTripletsSetSizeToUse option, the fingerprint
    vector contains all possible valid topological pharmacophore atom
    triplets with both zero and non-zero count values.

    Example of *SD* file containing topological pharmacophore atom triplets
    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

        >  <TopologicalPharmacophoreAtomTripletsFingerprints>
        FingerprintsVector;TopologicalPharmacophoreAtomTriplets:ArbitrarySize:
        MinDistance1:MaxDistance10;696;NumericalValues;IDsAndValuesString;Ar1-
        Ar1-Ar1 Ar1-Ar1-H1 Ar1-Ar1-HBA1 Ar1-Ar1-HBD1 Ar1-H1-H1 Ar1-H1-HBA1 Ar1
        -H1-HBD1 Ar1-HBA1-HBD1 H1-H1-H1 H1-H1-HBA1 H1-H1-HBD1 H1-HBA1-HBA1 H1-
        HBA1-HBD1 H1-HBA1-NI1 H1-HBD1-NI1 HBA1-HBA1-NI1 HBA1-HBD1-NI1 Ar1-...;
        46 106 8 3 83 11 4 1 21 5 3 1 2 2 1 1 1 100 101 18 11 145 132 26 14 23
        28 3 3 5 4 61 45 10 4 16 20 7 5 1 3 4 5 3 1 1 1 1 5 4 2 1 2 2 2 1 1 1
        119 123 24 15 185 202 41 25 22 17 3 5 85 95 18 11 23 17 3 1 1 6 4 ...

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

    Example of *FP* file containing topological pharmacophore atom triplets
    fingerprints string data:

        #
        # Package = MayaChemTools 7.4
        # Release Date = Oct 21, 2010
        #
        # TimeStamp = Fri Mar 11 15:38:58 2011
        #
        # FingerprintsStringType = FingerprintsVector
        #
        # Description = TopologicalPharmacophoreAtomTriplets:ArbitrarySize:M...
        # VectorStringFormat = IDsAndValuesString
        # VectorValuesType = NumericalValues
        #
        Cmpd1 696;Ar1-Ar1-Ar1 Ar1-Ar1-H1 Ar1-Ar1-HBA1 Ar1-Ar1-HBD1...;;46 106...
        Cmpd2 251;H1-H1-H1 H1-H1-HBA1 H1-H1-HBD1 H1-H1-NI1...;4 1 3 1 1 2 2...
        ... ...
        ... ..

    Example of CSV *Text* file containing topological pharmacophore atom
    triplets fingerprints string data:

        "CompoundID","TopologicalPharmacophoreAtomTripletsFingerprints"
        "Cmpd1","FingerprintsVector;TopologicalPharmacophoreAtomTriplets:Arbitr
        arySize:MinDistance1:MaxDistance10;696;NumericalValues;IDsAndValuesStri
        ng;Ar1-Ar1-Ar1 Ar1-Ar1-H1 Ar1-Ar1-HBA1 Ar1-Ar1-HBD1 Ar1-H1-H1 Ar1-H1-HB
        A1 Ar1-H1-HBD1 Ar1-HBA1-HBD1 H1-H1-H1 H1-H1-HBA1 H1-H1-HBD1 H1-HBA1-HBA
        1 H1-HBA1-HBD1 H1-HBA1-NI1 H1-HBD1-NI1 HBA1-HBA1-NI1 HBA1-HBD1-NI1 A...;
        46 106 8 3 83 11 4 1 21 5 3 1 2 2 1 1 1 100 101 18 11 145 132 26 14 23
        28 3 3 5 4 61 45 10 4 16 20 7 5 1 3 4 5 3 1 1 1 1 5 4 2 1 2 2 2 1 1 1
        119 123 24 15 185 202 41 25 22 17 3 5 85 95 18 11 23 17 3 1 1 6 4 ...
        ... ...
        ... ...

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

        FingerprintsVector;TopologicalPharmacophoreAtomTriplets:ArbitrarySize:
        MinDistance1:MaxDistance10;696;NumericalValues;IDsAndValuesString;Ar1-
        Ar1-Ar1 Ar1-Ar1-H1 Ar1-Ar1-HBA1 Ar1-Ar1-HBD1 Ar1-H1-H1 Ar1-H1-HBA1 Ar1
        -H1-HBD1 Ar1-HBA1-HBD1 H1-H1-H1 H1-H1-HBA1 H1-H1-HBD1 H1-HBA1-HBA1 H1-
        HBA1-HBD1 H1-HBA1-NI1 H1-HBD1-NI1 HBA1-HBA1-NI1 HBA1-HBD1-NI1 Ar1-...;
        46 106 8 3 83 11 4 1 21 5 3 1 2 2 1 1 1 100 101 18 11 145 132 26 14 23
        28 3 3 5 4 61 45 10 4 16 20 7 5 1 3 4 5 3 1 1 1 1 5 4 2 1 2 2 2 1 1 1
        119 123 24 15 185 202 41 25 22 17 3 5 85 95 18 11 23 17 3 1 1 6 4 ...

        FingerprintsVector;TopologicalPharmacophoreAtomTriplets:FixedSize:MinD
        istance1:MaxDistance10;2692;OrderedNumericalValues;ValuesString;46 106
        8 3 0 0 83 11 4 0 0 0 1 0 0 0 0 0 0 0 0 21 5 3 0 0 1 2 2 0 0 1 0 0 0
        0 0 0 1 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 100 101 18 11 0 0 145 132 26
        14 0 0 23 28 3 3 0 0 5 4 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 61 45 10 4 0
        0 16 20 7 5 1 0 3 4 5 3 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 0 5 ...

        FingerprintsVector;TopologicalPharmacophoreAtomTriplets:FixedSize:MinD
        istance1:MaxDistance10;2692;OrderedNumericalValues;IDsAndValuesString;
        Ar1-Ar1-Ar1 Ar1-Ar1-H1 Ar1-Ar1-HBA1 Ar1-Ar1-HBD1 Ar1-Ar1-NI1 Ar1-Ar1-P
        I1 Ar1-H1-H1 Ar1-H1-HBA1 Ar1-H1-HBD1 Ar1-H1-NI1 Ar1-H1-PI1 Ar1-HBA1-HB
        A1 Ar1-HBA1-HBD1 Ar1-HBA1-NI1 Ar1-HBA1-PI1 Ar1-HBD1-HBD1 Ar1-HBD1-...;
        46 106 8 3 0 0 83 11 4 0 0 0 1 0 0 0 0 0 0 0 0 21 5 3 0 0 1 2 2 0 0 1
        0 0 0 0 0 0 1 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 100 101 18 11 0 0 145
        132 26 14 0 0 23 28 3 3 0 0 5 4 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 61 ...

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.

    --AtomTripletsSetSizeToUse *ArbitrarySize | FixedSize*
        Atom triplets set size to use during generation of topological
        pharmacophore atom triplets fingerprints.

        Possible values: *ArbitrarySize | FixedSize*; Default value:
        *ArbitrarySize*.

        For *ArbitrarySize* value of --AtomTripletsSetSizeToUse option, the
        fingerprint vector correspond to only those topological
        pharmacophore atom triplets which are present and have non-zero
        count. However, for *FixedSize* value of --AtomTripletsSetSizeToUse
        option, the fingerprint vector contains all possible valid
        topological pharmacophore atom triplets with both zero and non-zero
        count values.

    -a, --AtomTypesToUse *"AtomType1,AtomType2,..."*
        Pharmacophore atom types to use during generation of topological
        phramacophore atom triplets. It's a list of comma separated valid
        pharmacophore atom types.

        Possible values for pharmacophore atom types are: *Ar, CA, H, HBA,
        HBD, Hal, NI, PI, RA*. Default value [ Ref 71 ] :
        *HBD,HBA,PI,NI,H,Ar*.

        The pharmacophore atom types abbreviations correspond to:

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

        *AtomTypes::FunctionalClassAtomTypes* module is used to assign
        pharmacophore 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 CSV/TSV text file(s) used
        during *CompoundID* value of --DataFieldsMode option. Default value:
        *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 value: *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*.

    --DistanceBinSize *number*
        Distance bin size used to bin distances between atom pairs in atom
        triplets. Default value: *2*. Valid values: positive integers.

        For default --MinDistance and --MaxDistance values of 1 and 10 with
        --DistanceBinSize of 2 [ Ref 70 ], the following 5 distance bins are
        generated:

            [1, 2] [3, 4] [5, 6] [7, 8] [9 10]

        The lower distance bound on the distance bin is uses to bin the
        distance between atom pairs in atom triplets. So in the previous
        example, atom pairs with distances 1 and 2 fall in first distance
        bin, atom pairs with distances 3 and 4 fall in second distance bin
        and so on.

        In order to distribute distance bins of equal size, the last bin is
        allowed to go past --MaxDistance by up to distance bin size. For
        example, --MinDistance and --MaxDistance values of 2 and 10 with
        --DistanceBinSize of 2 generates the following 6 distance bins:

            [2, 3] [4, 5] [6, 7] [8, 9] [10 11]

    -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 topological atom
        pair count value IDs to --FingerprintsLabel option value.

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

        Topological atom pairs IDs appended to --FingerprintsLabel value
        during *FingerprintsLabelWithIDs* values of --FingerprintsLabelMode
        correspond to atom pair count values in fingerprint vector string.

        *FingerprintsLabelWithIDs* value of --FingerprintsLabelMode is
        ignored during *ArbitrarySize* value of --AtomTripletsSetSizeToUse
        option and topological atom triplets IDs not appended to the label.

    --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: *TopologicalPharmacophoreAtomTripletsFingerprints*.

    -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.

    --MinDistance *number*
        Minimum bond distance between atom pairs corresponding to atom
        triplets for generating topological pharmacophore atom triplets.
        Default value: *1*. Valid values: positive integers and less than
        --MaxDistance.

    --MaxDistance *number*
        Maximum bond distance between atom pairs corresponding to atom
        triplets for generating topological pharmacophore atom triplets.
        Default value: *10*. Valid values: positive integers and greater
        than --MinDistance.

    --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><TopologicalPharmacophoreAtomTripletsFP>.<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.

    -u, --UseTriangleInequality *Yes | No*
        Specify whether to imply triangle distance inequality test to
        distances between atom pairs in atom triplets during generation of
        atom triplets basis set generation. Possible values: *Yes or No*.
        Default value: *Yes*.

        Triangle distance inequality test implies that distance or binned
        distance between any two atom pairs in an atom triplet must be less
        than the sum of distances or binned distances between other two
        atoms pairs and greater than the difference of their distances.

            For atom triplet PxDyz-PyDxz-PzDxy to satisfy triangle inequality:

            Dyz > |Dxz - Dxy| and Dyz < Dxz + Dxy
            Dxz > |Dyz - Dxy| and Dyz < Dyz + Dxy
            Dxy > |Dyz - Dxz| and Dxy < Dyz + Dxz

    -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 option. Possible values:
        *ValuesString, IDsAndValuesString | IDsAndValuesPairsString |
        ValuesAndIDsString | ValuesAndIDsPairsString*. Defaultvalue:
        *ValuesString*.

        Default value during *FixedSize* value of --AtomTripletsSetSizeToUse
        option: *ValuesString*. Default value during *ArbitrarySize* value
        of --AtomTripletsSetSizeToUse option: *IDsAndValuesString*.

        *ValuesString* option value is not allowed for *ArbitrarySize* value
        of --AtomTripletsSetSizeToUse option.

        Examples:

            FingerprintsVector;TopologicalPharmacophoreAtomTriplets:ArbitrarySize:
            MinDistance1:MaxDistance10;696;NumericalValues;IDsAndValuesString;Ar1-
            Ar1-Ar1 Ar1-Ar1-H1 Ar1-Ar1-HBA1 Ar1-Ar1-HBD1 Ar1-H1-H1 Ar1-H1-HBA1 Ar1
            -H1-HBD1 Ar1-HBA1-HBD1 H1-H1-H1 H1-H1-HBA1 H1-H1-HBD1 H1-HBA1-HBA1 H1-
            HBA1-HBD1 H1-HBA1-NI1 H1-HBD1-NI1 HBA1-HBA1-NI1 HBA1-HBD1-NI1 Ar1-...;
            46 106 8 3 83 11 4 1 21 5 3 1 2 2 1 1 1 100 101 18 11 145 132 26 14 23
            28 3 3 5 4 61 45 10 4 16 20 7 5 1 3 4 5 3 1 1 1 1 5 4 2 1 2 2 2 1 1 1
            119 123 24 15 185 202 41 25 22 17 3 5 85 95 18 11 23 17 3 1 1 6 4 ...

            FingerprintsVector;TopologicalPharmacophoreAtomTriplets:FixedSize:MinD
            istance1:MaxDistance10;2692;OrderedNumericalValues;ValuesString;46 106
            8 3 0 0 83 11 4 0 0 0 1 0 0 0 0 0 0 0 0 21 5 3 0 0 1 2 2 0 0 1 0 0 0
            0 0 0 1 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 100 101 18 11 0 0 145 132 26
            14 0 0 23 28 3 3 0 0 5 4 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 61 45 10 4 0
            0 16 20 7 5 1 0 3 4 5 3 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 0 5 ...

            FingerprintsVector;TopologicalPharmacophoreAtomTriplets:FixedSize:MinD
            istance1:MaxDistance10;2692;OrderedNumericalValues;ValuesAndIDsPairsSt
            ring;46 Ar1-Ar1-Ar1 106 Ar1-Ar1-H1 8 Ar1-Ar1-HBA1 3 Ar1-Ar1-HBD1 0 Ar1
            -Ar1-NI1 0 Ar1-Ar1-PI1 83 Ar1-H1-H1 11 Ar1-H1-HBA1 4 Ar1-H1-HBD1 0 Ar1
            -H1-NI1 0 Ar1-H1-PI1 0 Ar1-HBA1-HBA1 1 Ar1-HBA1-HBD1 0 Ar1-HBA1-NI1 0
            Ar1-HBA1-PI1 0 Ar1-HBD1-HBD1 0 Ar1-HBD1-NI1 0 Ar1-HBD1-PI1 0 Ar1-NI...

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

EXAMPLES
    To generate topological pharmacophore atom triplets fingerprints of
    arbitrary size corresponding to 5 distance bins spanning distances from
    1 through 10 using default atoms with distances satisfying triangle
    inequality and create a SampleTPATFP.csv file containing sequential
    compound IDs along with fingerprints vector strings data in ValuesString
    format, type:

        % TopologicalPharmacophoreAtomTripletsFingerprints.pl -r SampleTPATFP
          -o Sample.sdf

    To generate topological pharmacophore atom triplets fingerprints of
    fixed size corresponding to 5 distance bins spanning distances from 1
    through 10 using default atoms with distances satisfying triangle
    inequality and create a SampleTPATFP.csv file containing sequential
    compound IDs along with fingerprints vector strings data in ValuesString
    format, type:

        % TopologicalPharmacophoreAtomTripletsFingerprints.pl
          --AtomTripletsSetSizeToUse FixedSize -r SampleTPATFP -o Sample.sdf

    To generate topological pharmacophore atom triplets fingerprints of
    arbitrary size corresponding to 5 distance bins spanning distances from
    1 through 10 using default atoms with distances satisfying triangle
    inequality and create SampleTPATFP.sdf, SampleTPATFP.fpf and
    SampleTPATFP.csv files with CSV file containing sequential compound IDs
    along with fingerprints vector strings data in ValuesString format,
    type:

        % TopologicalPharmacophoreAtomTripletsFingerprints.pl --output all
          -r SampleTPATFP -o Sample.sdf

    To generate topological pharmacophore atom triplets fingerprints of
    arbitrary size corresponding to 5 distance bins spanning distances from
    1 through 10 using default atoms with distances satisfying triangle
    inequality and create a SampleTPATFP.csv file containing sequential
    compound IDs along with fingerprints vector strings data in ValuesString
    format and atom triplets IDs in the fingerprint data column label
    starting with Fingerprints, type:

        % TopologicalPharmacophoreAtomTripletsFingerprints.pl
          --FingerprintsLabelMode FingerprintsLabelWithIDs --FingerprintsLabel
          Fingerprints -r SampleTPATFP -o Sample.sdf

    To generate topological pharmacophore atom triplets fingerprints of
    arbitrary size corresponding to 5 distance bins spanning distances from
    1 through 10 using default atoms with distances not satisfying triangle
    inequality and create a SampleTPATFP.csv file containing sequential
    compound IDs along with fingerprints vector strings data in ValuesString
    format, type:

        % TopologicalPharmacophoreAtomTripletsFingerprints.pl
          --UseTriangleInequality No -r SampleTPATFP -o Sample.sdf

    To generate topological pharmacophore atom triplets fingerprints of
    arbitrary size corresponding to 6 distance bins spanning distances from
    1 through 12 using default atoms with distances satisfying triangle
    inequality and create a SampleTPATFP.csv file containing sequential
    compound IDs along with fingerprints vector strings data in ValuesString
    format, type:

        % TopologicalPharmacophoreAtomTripletsFingerprints.pl
          --UseTriangleInequality Yes --MinDistance 1 --MaxDistance 12
          --DistanceBinSIze 2 -r SampleTPATFP -o Sample.sdf

    To generate topological pharmacophore atom triplets fingerprints of
    arbitrary size corresponding to 6 distance bins spanning distances from
    1 through 12 using "HBD,HBA,PI, NI, H, Ar" atoms with distances
    satisfying triangle inequality and create a SampleTPATFP.csv file
    containing sequential compound IDs along with fingerprints vector
    strings data in ValuesString format, type:

        % TopologicalPharmacophoreAtomTripletsFingerprints.pl
          --AtomTypesToUse "HBD,HBA,PI,NI,H,Ar" --UseTriangleInequality Yes
          --MinDistance 1 --MaxDistance 12 --DistanceBinSIze 2
          --VectorStringFormat ValuesString -r SampleTPATFP -o Sample.sdf

    To generate topological pharmacophore atom triplets fingerprints of
    arbitrary size corresponding to 5 distance bins spanning distances from
    1 through 10 using default atoms with distances satisfying triangle
    inequality and create a SampleTPATFP.csv file containing sequential
    compound IDs from molecule name line along with fingerprints vector
    strings data in ValuesString format, type:

        % TopologicalPharmacophoreAtomTripletsFingerprints.pl --DataFieldsMode
          CompoundID -CompoundIDMode MolName  -r SampleTPATFP -o Sample.sdf

    To generate topological pharmacophore atom triplets fingerprints of
    arbitrary size corresponding to 5 distance bins spanning distances from
    1 through 10 using default atoms with distances satisfying triangle
    inequality and create a SampleTPATFP.csv file containing sequential
    compound IDs using specified data field along with fingerprints vector
    strings data in ValuesString format, type:

        % TopologicalPharmacophoreAtomTripletsFingerprints.pl --DataFieldsMode
          CompoundID -CompoundIDMode DataField --CompoundID Mol_ID
          -r SampleTPATFP -o Sample.sdf

    To generate topological pharmacophore atom triplets fingerprints of
    arbitrary size corresponding to 5 distance bins spanning distances from
    1 through 10 using default atoms with distances satisfying triangle
    inequality and create a SampleTPATFP.csv file containing sequential
    compound IDs using combination of molecule name line and an explicit
    compound prefix along with fingerprints vector strings data, type:

        % TopologicalPharmacophoreAtomTripletsFingerprints.pl --DataFieldsMode
          CompoundID -CompoundIDMode MolnameOrLabelPrefix
          --CompoundID Cmpd --CompoundIDLabel MolID -r SampleSampleTPATFP
          -o Sample.sdf

    To generate topological pharmacophore atom triplets fingerprints of
    arbitrary size corresponding to 5 distance bins spanning distances from
    1 through 10 using default atoms with distances satisfying triangle
    inequality and create a SampleTPATFP.csv file containing specific data
    fields columns along with fingerprints vector strings data, type:

        % TopologicalPharmacophoreAtomTripletsFingerprints.pl --DataFieldsMode
          Specify --DataFields Mol_ID -r SampleTPATFP -o Sample.sdf

    To generate topological pharmacophore atom triplets fingerprints of
    arbitrary size corresponding to 5 distance bins spanning distances from
    1 through 10 using default atoms with distances satisfying triangle
    inequality and create a SampleTPATFP.csv file containing common data
    fields columns along with fingerprints vector strings data, type:

        % TopologicalPharmacophoreAtomTripletsFingerprints.pl --DataFieldsMode
          Common -r SampleTPATFP -o Sample.sdf

    To generate topological pharmacophore atom triplets fingerprints of
    arbitrary size corresponding to 5 distance bins spanning distances from
    1 through 10 using default atoms with distances satisfying triangle
    inequality and create SampleTPATFP.sdf, SampleTPATFP.fpf and
    SampleTPATFP.csv files containing all data fields columns in CSV file
    along with fingerprints data, type:

        % TopologicalPharmacophoreAtomTripletsFingerprints.pl --DataFieldsMode
          All  --output all -r SampleTPATFP -o Sample.sdf

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

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

