NAME
    TopologicalPharmacophoreAtomPairsFingerprints.pl - Generate topological
    pharmacophore atom pairs fingerprints for SD files

SYNOPSIS
    TopologicalPharmacophoreAtomPairsFingerprints.pl SDFile(s)...

    TopologicalPharmacophoreAtomPairsFingerprints.pl [--AromaticityModel
    *AromaticityModelType*] [--AtomPairsSetSizeToUse *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*] [-f, --Filter *Yes | No*] [--FingerprintsLabelMode
    *FingerprintsLabelOnly | FingerprintsLabelWithIDs*] [--FingerprintsLabel
    *text*] [--FuzzifyAtomPairsCount *Yes | No*] [--FuzzificationMode
    *FuzzyBinning | FuzzyBinSmoothing*] [--FuzzificationMethodology
    *FuzzyBinning | FuzzyBinSmoothing*] [--FuzzFactor *number*] [-h, --help]
    [-k, --KeepLargestComponent *Yes | No*] [--MinDistance *number*]
    [--MaxDistance *number*] [-n, --NormalizationMethodology *None |
    ByHeavyAtomsCount | ByAtomTypesCount*] [--OutDelim *comma | tab |
    semicolon*] [--output *SD | FP | text | all*] [-o, --overwrite] [-q,
    --quote *Yes | No*] [-r, --root *RootName*] [--ValuesPrecision *number*]
    [-v, --VectorStringFormat *ValuesString, IDsAndValuesString |
    IDsAndValuesPairsString | ValuesAndIDsString | ValuesAndIDsPairsString*]
    [-w, --WorkingDir dirname] SDFile(s)...

DESCRIPTION
    Generate topological pharmacophore atom pairs fingerprints [ Ref 60-62,
    Ref 65, Ref 68 ] 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. A pharmacophore atom pairs basis set is
    initialized for all unique possible pairs within --MinDistance and
    --MaxDistance range.

        Let:

        P = Valid pharmacophore atom type

        Px = Pharmacophore atom type x
        Py = Pharmacophore atom type y

        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 atoms

        Px-Dn-Py = Pharmacophore atom pair ID for atom types Px and Py at
                   distance Dn

        P = Number of pharmacophore atom types to consider
        PPDn = Number of possible unique pharmacophore atom pairs at a distance Dn

        PPT = Total number of possible pharmacophore atom pairs at all distances
              between Dmin and Dmax

        Then:

        PPD =  (P * (P - 1))/2 + P

        PPT = ((Dmax - Dmin) + 1) * ((P * (P - 1))/2 + P)
            = ((Dmax - Dmin) + 1) * PPD

        So for default values of Dmin = 1, Dmax = 10 and P = 5,

        PPD =  (5 * (5 - 1))/2 + 5 = 15
        PPT = ((10 - 1) + 1) * 15 = 150

        The pharmacophore atom pairs bais set includes 150 values.

        The atom pair IDs correspond to:

        Px-Dn-Py = Pharmacophore atom pair ID for atom types Px and Py at
                   distance Dn

        For example: H-D1-H, H-D2-HBA, PI-D5-PI and so on

    Using distance matrix and pharmacohore atom types, occurrence of unique
    pharmacohore atom pairs is counted. The contribution of each atom type
    to atom pair interaction is optionally weighted by specified
    --AtomTypesWeight before assigning its count to appropriate distance
    bin. Based on --NormalizationMethodology option, pharmacophore atom
    pairs count is optionally normalized. Additionally, pharmacohore atom
    pairs count is optionally fuzzified before or after the normalization
    controlled by values of --FuzzifyAtomPairsCount, --FuzzificationMode,
    --FuzzificationMethodology and --FuzzFactor options.

    The final pharmacophore atom pairs count along with atom pair
    identifiers involving all non-hydrogen atoms, with optional
    normalization and fuzzification, constitute pharmacophore topological
    atom pairs fingerprints of the molecule.

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

    Example of *SD* file containing topological pharmacophore atom pairs
    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

        >  <TopologicalPharmacophoreAtomPairsFingerprints>
        FingerprintsVector;TopologicalPharmacophoreAtomPairs:ArbitrarySize:Min
        Distance1:MaxDistance10;54;NumericalValues;IDsAndValuesString;H-D1-H H
        -D1-NI HBA-D1-NI HBD-D1-NI H-D2-H H-D2-HBA H-D2-HBD HBA-D2-HBA HBA-D2-
        HBD H-D3-H H-D3-HBA H-D3-HBD H-D3-NI HBA-D3-NI HBD-D3-NI H-D4-H H-D...;
        18 1 2 1 22 12 8 1 2 18 6 3 1 1 1 22 13 6 5 7 2 28 9 5 1 1 1 36 16 10 3
        4 1 37 10 8 1 35 10 9 3 3 1 28 7 7 4 18 16 12 5 1 2 1

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

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

        #
        # Package = MayaChemTools 7.4
        # Release Date = Oct 21, 2010
        #
        # TimeStamp = Fri Mar 11 15:32:48 2011
        #
        # FingerprintsStringType = FingerprintsVector
        #
        # Description = TopologicalPharmacophoreAtomPairs:ArbitrarySize:MinDistance1:MaxDistance10
        # VectorStringFormat = IDsAndValuesString
        # VectorValuesType = NumericalValues
        #
        Cmpd1 54;H-D1-H H-D1-NI HBA-D1-NI HBD-D1-NI H-D2-H H-D2-HBA...;18 1 2...
        Cmpd2 61;H-D1-H H-D1-NI HBA-D1-NI HBD-D1-NI H-D2-H H-D2-HBA...;5 1 2 ...
        ... ...
        ... ..

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

        "CompoundID","TopologicalPharmacophoreAtomPairsFingerprints"
        "Cmpd1","FingerprintsVector;TopologicalPharmacophoreAtomPairs:Arbitrary
        Size:MinDistance1:MaxDistance10;54;NumericalValues;IDsAndValuesString;H
        -D1-H H-D1-NI HBA-D1-NI HBD-D1-NI H-D2-H H-D2-HBA H-D2-HBD HBA-D2-HBA H
        BA-D2-HBD H-D3-H H-D3-HBA H-D3-HBD H-D3-NI HBA-D3-NI HBD-D3-NI H-D4...;
        18 1 2 1 22 12 8 1 2 18 6 3 1 1 1 22 13 6 5 7 2 28 9 5 1 1 1 36 16 10 3
        4 1 37 10 8 1 35 10 9 3 3 1 28 7 7 4 18 16 12 5 1 2 1"
        ... ...
        ... ...

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

        FingerprintsVector;TopologicalPharmacophoreAtomPairs:ArbitrarySize:Min
        Distance1:MaxDistance10;54;NumericalValues;IDsAndValuesString;H-D1-H H
        -D1-NI HBA-D1-NI HBD-D1-NI H-D2-H H-D2-HBA H-D2-HBD HBA-D2-HBA HBA-D2-
        HBD H-D3-H H-D3-HBA H-D3-HBD H-D3-NI HBA-D3-NI HBD-D3-NI H-D4-H H-D4-H
        BA H-D4-HBD HBA-D4-HBA HBA-D4-HBD HBD-D4-HBD H-D5-H H-D5-HBA H-D5-...;
        18 1 2 1 22 12 8 1 2 18 6 3 1 1 1 22 13 6 5 7 2 28 9 5 1 1 1 36 16 10
        3 4 1 37 10 8 1 35 10 9 3 3 1 28 7 7 4 18 16 12 5 1 2 1

        FingerprintsVector;TopologicalPharmacophoreAtomPairs:FixedSize:MinDist
        ance1:MaxDistance10;150;OrderedNumericalValues;ValuesString;18 0 0 1 0
        0 0 2 0 0 1 0 0 0 0 22 12 8 0 0 1 2 0 0 0 0 0 0 0 0 18 6 3 1 0 0 0 1
        0 0 1 0 0 0 0 22 13 6 0 0 5 7 0 0 2 0 0 0 0 0 28 9 5 1 0 0 0 1 0 0 1 0
        0 0 0 36 16 10 0 0 3 4 0 0 1 0 0 0 0 0 37 10 8 0 0 0 0 1 0 0 0 0 0 0
        0 35 10 9 0 0 3 3 0 0 1 0 0 0 0 0 28 7 7 4 0 0 0 0 0 0 0 0 0 0 0 18...

        FingerprintsVector;TopologicalPharmacophoreAtomPairs:FixedSize:MinDist
        ance1:MaxDistance10;150;OrderedNumericalValues;IDsAndValuesString;H-D1
        -H H-D1-HBA H-D1-HBD H-D1-NI H-D1-PI HBA-D1-HBA HBA-D1-HBD HBA-D1-NI H
        BA-D1-PI HBD-D1-HBD HBD-D1-NI HBD-D1-PI NI-D1-NI NI-D1-PI PI-D1-PI H-D
        2-H H-D2-HBA H-D2-HBD H-D2-NI H-D2-PI HBA-D2-HBA HBA-D2-HBD HBA-D2...;
        18 0 0 1 0 0 0 2 0 0 1 0 0 0 0 22 12 8 0 0 1 2 0 0 0 0 0 0 0 0 18 6 3
        1 0 0 0 1 0 0 1 0 0 0 0 22 13 6 0 0 5 7 0 0 2 0 0 0 0 0 28 9 5 1 0 0 0
        1 0 0 1 0 0 0 0 36 16 10 0 0 3 4 0 0 1 0 0 0 0

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.

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

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

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

    -a, --AtomTypesToUse *"AtomType1,AtomType2,..."*
        Pharmacophore atom types to use during generation of topological
        phramacophore atom pairs. 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 60-62 ] :
        *HBD,HBA,PI,NI,H*.

        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

    --AtomTypesWeight *"AtomType1,Weight1,AtomType2,Weight2..."*
        Weights of specified pharmacophore atom types to use during
        calculation of their contribution to atom pair count. Default value:
        *None*. Valid values: real numbers greater than 0. In general it's
        comma delimited list of valid atom type and its weight.

        The weight values allow to increase the importance of specific
        pharmacophore atom type in the generated fingerprints. A weight
        value of 0 for an atom type eliminates its contribution to atom pair
        count where as weight value of 2 doubles its contribution.

    --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*.

    -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 --AtomPairsSetSizeToUse
        option and topological atom pairs 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: *TopologicalPharmacophoreAtomPairsFingerprints*.

    --FuzzifyAtomPairsCount *Yes | No*
        To fuzzify or not to fuzzify atom pairs count. Possible values: *Yes
        or No*. Default value: *No*.

    --FuzzificationMode *BeforeNormalization | AfterNormalization*
        When to fuzzify atom pairs count. Possible values:
        *BeforeNormalization | AfterNormalizationYes*. Default value:
        *AfterNormalization*.

    --FuzzificationMethodology *FuzzyBinning | FuzzyBinSmoothing*
        How to fuzzify atom pairs count. Possible values: *FuzzyBinning |
        FuzzyBinSmoothing*. Default value: *FuzzyBinning*.

        In conjunction with values for options --FuzzifyAtomPairsCount,
        --FuzzificationMode and --FuzzFactor, --FuzzificationMethodology
        option is used to fuzzify pharmacophore atom pairs count.

        Let:

            Px = Pharmacophore atom type x
            Py = Pharmacophore atom type y
            PPxy = Pharmacophore atom pair between atom type Px and Py

            PPxyDn = Pharmacophore atom pairs count between atom type Px and Py
                     at distance Dn
            PPxyDn-1 = Pharmacophore atom pairs count between atom type Px and Py
                       at distance Dn - 1
            PPxyDn+1 = Pharmacophore atom pairs count between atom type Px and Py
                       at distance Dn + 1

            FF = FuzzFactor for FuzzyBinning and FuzzyBinSmoothing

        Then:

        For *FuzzyBinning*:

            PPxyDn = PPxyDn (Unchanged)

            PPxyDn-1 = PPxyDn-1 + PPxyDn * FF
            PPxyDn+1 = PPxyDn+1 + PPxyDn * FF

        For *FuzzyBinSmoothing*:

            PPxyDn = PPxyDn - PPxyDn * 2FF for Dmin < Dn < Dmax
            PPxyDn = PPxyDn - PPxyDn * FF for Dn = Dmin or Dmax

            PPxyDn-1 = PPxyDn-1 + PPxyDn * FF
            PPxyDn+1 = PPxyDn+1 + PPxyDn * FF

        In both fuzzification schemes, a value of 0 for FF implies no
        fuzzification of occurrence counts. A value of 1 during
        *FuzzyBinning* corresponds to maximum fuzzification of occurrence
        counts; however, a value of 1 during *FuzzyBinSmoothing* ends up
        completely distributing the value over the previous and next
        distance bins.

        So for default value of --FuzzFactor (FF) 0.15, the occurrence count
        of pharmacohore atom pairs at distance Dn during FuzzyBinning is
        left unchanged and the counts at distances Dn -1 and Dn + 1 are
        incremented by PPxyDn * 0.15.

        And during *FuzzyBinSmoothing* the occurrence counts at Distance Dn
        is scaled back using multiplicative factor of (1 - 2*0.15) and the
        occurrence counts at distances Dn -1 and Dn + 1 are incremented by
        PPxyDn * 0.15. In otherwords, occurrence bin count is smoothed out
        by distributing it over the previous and next distance value.

    --FuzzFactor *number*
        Specify by how much to fuzzify atom pairs count. Default value:
        *0.15*. Valid values: For *FuzzyBinning* value of
        --FuzzificationMethodology option: *between 0 and 1.0*; For
        *FuzzyBinSmoothing* value of --FuzzificationMethodology option:
        *between 0 and 0.5*.

    -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 for generating topological
        pharmacophore atom pairs. Default value: *1*. Valid values: positive
        integers including 0 and less than --MaxDistance.

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

    -n, --NormalizationMethodology *None | ByHeavyAtomsCount |
    ByAtomTypesCount*
        Normalization methodology to use for scaling the occurrence count of
        pharmacophore atom pairs within specified distance range. Possible
        values: *None, ByHeavyAtomsCount or ByAtomTypesCount*. Default
        value: *None*.

    --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><TopologicalPharmacophoreAtomPairsFP>.<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.

    --ValuesPrecision *number*
        Precision of atom pairs count real values which might be generated
        after normalization or fuzzification. Default value: up to *2*
        decimal places. Valid values: positive integers.

    -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*.

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

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

        Examples:

            FingerprintsVector;TopologicalPharmacophoreAtomPairs:ArbitrarySize:Min
            Distance1:MaxDistance10;54;NumericalValues;IDsAndValuesString;H-D1-H H
            -D1-NI HBA-D1-NI HBD-D1-NI H-D2-H H-D2-HBA H-D2-HBD HBA-D2-HBA HBA-D2-
            HBD H-D3-H H-D3-HBA H-D3-HBD H-D3-NI HBA-D3-NI HBD-D3-NI H-D4-H H-D4-H
            BA H-D4-HBD HBA-D4-HBA HBA-D4-HBD HBD-D4-HBD H-D5-H H-D5-HBA H-D5-...;
            18 1 2 1 22 12 8 1 2 18 6 3 1 1 1 22 13 6 5 7 2 28 9 5 1 1 1 36 16 10
            3 4 1 37 10 8 1 35 10 9 3 3 1 28 7 7 4 18 16 12 5 1 2 1

            FingerprintsVector;TopologicalPharmacophoreAtomPairs:FixedSize:MinDist
            ance1:MaxDistance10;150;OrderedNumericalValues;ValuesString;18 0 0 1 0
            0 0 2 0 0 1 0 0 0 0 22 12 8 0 0 1 2 0 0 0 0 0 0 0 0 18 6 3 1 0 0 0 1
            0 0 1 0 0 0 0 22 13 6 0 0 5 7 0 0 2 0 0 0 0 0 28 9 5 1 0 0 0 1 0 0 1 0
            0 0 0 36 16 10 0 0 3 4 0 0 1 0 0 0 0 0 37 10 8 0 0 0 0 1 0 0 0 0 0 0
            0 35 10 9 0 0 3 3 0 0 1 0 0 0 0 0 28 7 7 4 0 0 0 0 0 0 0 0 0 0 0 18...

            FingerprintsVector;TopologicalPharmacophoreAtomPairs:FixedSize:MinDist
            ance1:MaxDistance10;150;OrderedNumericalValues;IDsAndValuesString;H-D1
            -H H-D1-HBA H-D1-HBD H-D1-NI H-D1-PI HBA-D1-HBA HBA-D1-HBD HBA-D1-NI H
            BA-D1-PI HBD-D1-HBD HBD-D1-NI HBD-D1-PI NI-D1-NI NI-D1-PI PI-D1-PI H-D
            2-H H-D2-HBA H-D2-HBD H-D2-NI H-D2-PI HBA-D2-HBA HBA-D2-HBD HBA-D2...;
            18 0 0 1 0 0 0 2 0 0 1 0 0 0 0 22 12 8 0 0 1 2 0 0 0 0 0 0 0 0 18 6 3
            1 0 0 0 1 0 0 1 0 0 0 0 22 13 6 0 0 5 7 0 0 2 0 0 0 0 0 28 9 5 1 0 0 0
            1 0 0 1 0 0 0 0 36 16 10 0 0 3 4 0 0 1 0 0 0 0

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

EXAMPLES
    To generate topological pharmacophore atom pairs fingerprints of
    arbitrary size corresponding to distances from 1 through 10 using
    default atom types with no weighting, normalization, and fuzzification
    of atom pairs count and create a SampleTPAPFP.csv file containing
    sequential compound IDs along with fingerprints vector strings data in
    ValuesString format, type:

        % TopologicalPharmacophoreAtomPairsFingerprints.pl -r SampleTPAPFP
          -o Sample.sdf

    To generate topological pharmacophore atom pairs fingerprints of fixed
    size corresponding to distances from 1 through 10 using default atom
    types with no weighting, normalization, and fuzzification of atom pairs
    count and create a SampleTPAPFP.csv file containing sequential compound
    IDs along with fingerprints vector strings data in ValuesString format,
    type:

        % TopologicalPharmacophoreAtomPairsFingerprints.pl
           --AtomPairsSetSizeToUse FixedSize -r SampleTPAPFP-o Sample.sdf

    To generate topological pharmacophore atom pairs fingerprints of
    arbitrary size corresponding to distances from 1 through 10 using
    default atom types with no weighting, normalization, and fuzzification
    of atom pairs count and create SampleTPAPFP.sdf, SampleTPAPFP.fpf and
    SampleTPAPFP.csv files containing sequential compound IDs in CSV file
    along with fingerprints vector strings data in ValuesString format,
    type:

        % TopologicalPharmacophoreAtomPairsFingerprints.pl --output all
          -r SampleTPAPFP -o Sample.sdf

    To generate topological pharmacophore atom pairs fingerprints of
    arbitrary size corresponding to distances from 1 through 10 using
    default atom types with no weighting, normalization, and fuzzification
    of atom pairs count and create a SampleTPAPFP.csv file containing
    sequential compound IDs along with fingerprints vector strings data in
    IDsAndValuesPairsString format, type:

        % TopologicalPharmacophoreAtomPairsFingerprints.pl --VectorStringFormat
          IDsAndValuesPairsString -r SampleTPAPFP -o Sample.sdf

    To generate topological pharmacophore atom pairs fingerprints of
    arbitrary size corresponding to distances from 1 through 6 using default
    atom types with no weighting, normalization, and fuzzification of atom
    pairs count and create a SampleTPAPFP.csv file containing sequential
    compound IDs along with fingerprints vector strings data in ValuesString
    format, type:

        % TopologicalPharmacophoreAtomPairsFingerprints.pl --MinDistance 1
          -MaxDistance 6 -r SampleTPAPFP -o Sample.sdf

    To generate topological pharmacophore atom pairs fingerprints of
    arbitrary size corresponding to distances from 1 through 10 using
    "HBD,HBA,PI,NI" atom types with double the weighting for "HBD,HBA" and
    normalization by HeavyAtomCount but no fuzzification of atom pairs count
    and create a SampleTPAPFP.csv file containing sequential compound IDs
    along with fingerprints vector strings data in ValuesString format,
    type:

        % TopologicalPharmacophoreAtomPairsFingerprints.pl --MinDistance 1
          -MaxDistance 10  --AtomTypesToUse "HBD,HBA,PI, NI"  --AtomTypesWeight
          "HBD,2,HBA,2,PI,1,NI,1" --NormalizationMethodology ByHeavyAtomsCount
          --FuzzifyAtomPairsCount No -r SampleTPAPFP -o Sample.sdf

    To generate topological pharmacophore atom pairs fingerprints of
    arbitrary size corresponding to distances from 1 through 10 using
    "HBD,HBA,PI,NI,H" atom types with no weighting of atom types and
    normalization but with fuzzification of atom pairs count using
    FuzzyBinning methodology with FuzzFactor value 0.15 and create a
    SampleTPAPFP.csv file containing sequential compound IDs along with
    fingerprints vector strings data in ValuesString format, type:

        % TopologicalPharmacophoreAtomPairsFingerprints.pl --MinDistance 1
          --MaxDistance 10  --AtomTypesToUse "HBD,HBA,PI, NI,H"  --AtomTypesWeight
          "HBD,1,HBA,1,PI,1,NI,1,H,1" --NormalizationMethodology None
          --FuzzifyAtomPairsCount Yes --FuzzificationMethodology FuzzyBinning
          --FuzzFactor  0.5 -r SampleTPAPFP -o Sample.sdf

    To generate topological pharmacophore atom pairs fingerprints of
    arbitrary size corresponding to distances distances from 1 through 10
    using default atom types with no weighting, normalization, and
    fuzzification of atom pairs count and create a SampleTPAPFP.csv file
    containing compound ID from molecule name line along with fingerprints
    vector strings data, type:

        % TopologicalPharmacophoreAtomPairsFingerprints.pl --DataFieldsMode
          CompoundID -CompoundIDMode MolName -r SampleTPAPFP -o Sample.sdf

    To generate topological pharmacophore atom pairs fingerprints of
    arbitrary size corresponding to distances from 1 through 10 using
    default atom types with no weighting, normalization, and fuzzification
    of atom pairs count and create a SampleTPAPFP.csv file containing
    compound IDs using specified data field along with fingerprints vector
    strings data, type:

        % TopologicalPharmacophoreAtomPairsFingerprints.pl --DataFieldsMode
          CompoundID -CompoundIDMode DataField --CompoundID Mol_ID
          -r SampleTPAPFP -o Sample.sdf

    To generate topological pharmacophore atom pairs fingerprints of
    arbitrary size corresponding to distances from 1 through 10 using
    default atom types with no weighting, normalization, and fuzzification
    of atom pairs count and create a SampleTPAPFP.csv file containing
    compound ID using combination of molecule name line and an explicit
    compound prefix along with fingerprints vector strings data, type:

        % TopologicalPharmacophoreAtomPairsFingerprints.pl --DataFieldsMode
          CompoundID -CompoundIDMode MolnameOrLabelPrefix
          --CompoundID Cmpd --CompoundIDLabel MolID -r SampleTPAPFP -o Sample.sdf

    To generate topological pharmacophore atom pairs fingerprints of
    arbitrary size corresponding to distances from 1 through 10 using
    default atom types with no weighting, normalization, and fuzzification
    of atom pairs count and create a SampleTPAPFP.csv file containing
    specific data fields columns along with fingerprints vector strings
    data, type:

        % TopologicalPharmacophoreAtomPairsFingerprints.pl --DataFieldsMode
          Specify --DataFields Mol_ID -r SampleTPAPFP -o Sample.sdf

    To generate topological pharmacophore atom pairs fingerprints of
    arbitrary size corresponding to distances from 1 through 10 using
    default atom types with no weighting, normalization, and fuzzification
    of atom pairs count and create a SampleTPAPFP.csv file containing common
    data fields columns along with fingerprints vector strings data, type:

        % TopologicalPharmacophoreAtomPairsFingerprints.pl --DataFieldsMode
          Common -r SampleTPAPFP -o Sample.sdf

    To generate topological pharmacophore atom pairs fingerprints of
    arbitrary size corresponding to distances from 1 through 10 using
    default atom types with no weighting, normalization, and fuzzification
    of atom pairs count and create SampleTPAPFP.sdf, SampleTPAPFP.fpf, and
    SampleTPAPFP.csv files containing all data fields columns in CSV file
    along with fingerprints data, type:

        % TopologicalPharmacophoreAtomPairsFingerprints.pl --DataFieldsMode
          All  --output all -r SampleTPAPFP -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,
    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.

