NAME
    SimilaritySearchingFingerprints.pl - Perform similarity search using
    fingerprints strings data in SD, FP and CSV/TSV text file(s)

SYNOPSIS
    SimilaritySearchingFingerprints.pl ReferenceFPFile DatabaseFPFile

    SimilaritySearchingFingerprints.pl [--alpha *number*] [--beta *number*]
    [-b, --BitVectorComparisonMode *TanimotoSimilarity | TverskySimilarity |
    ...*] [--DatabaseColMode *ColNum | ColLabel*] [--DatabaseCompoundIDCol
    *col number | col name*] [--DatabaseCompoundIDPrefix *text*]
    [--DatabaseCompoundIDField *DataFieldName*] [--DatabaseCompoundIDMode
    *DataField | MolName | LabelPrefix | MolNameOrLabelPrefix*]
    [--DatabaseDataCols *"DataColNum1, DataColNum2,... " | DataColLabel1,
    DataCoLabel2,... "*] [--DatabaseDataColsMode *All | Specify |
    CompoundID*] [--DatabaseDataFields *"FieldLabel1, FieldLabel2,... "*]
    [--DatabaseDataFieldsMode *All | Common | Specify | CompoundID*]
    [--DatabaseFingerprintsCol *col number | col name*]
    [--DatabaseFingerprintsField *FieldLabel*] []--DistanceCutoff *number*]
    [-d, --detail *InfoLevel*] [-f, --fast] [--FingerprintsMode *AutoDetect
    | FingerprintsBitVectorString | FingerprintsVectorString*] [-g,
    --GroupFusionRule *Max, Mean, Median, Min, Sum, Euclidean*]
    [--GroupFusionApplyCutoff *Yes | No*] [-h, --help] [--InDelim *comma |
    semicolon*] [-k, --KNN *all | number*] [-m, --mode *IndividualReference
    | MultipleReferences*] [-n, --NumOfSimilarMolecules *number*]
    [--OutDelim *comma | tab | semicolon*] [--output *SD | text | both*]
    [-o, --overwrite] [-p, --PercentSimilarMolecules *number*] [--precision
    *number*] [-q, --quote *Yes | No*] [--ReferenceColMode *ColNum |
    ColLabel*] [--ReferenceCompoundIDCol *col number | col name*]
    [--ReferenceCompoundIDPrefix *text*] [--ReferenceCompoundIDField
    *DataFieldName*] [--ReferenceCompoundIDMode *DataField | MolName |
    LabelPrefix | MolNameOrLabelPrefix*] [--ReferenceFingerprintsCol *col
    number | col name*] [--ReferenceFingerprintsField *FieldLabel*] [-r,
    --root *RootName*] [-s, --SearchMode *SimilaritySearch |
    DissimilaritySearch*] [--SimilarCountMode *NumOfSimilar |
    PercentSimilar*] [--SimilarityCutoff *number*] [-v,
    --VectorComparisonMode *TanimotoSimilairy | ... | ManhattanDistance |
    ...*] [--VectorComparisonFormulism *AlgebraicForm | BinaryForm |
    SetTheoreticForm*] [-w, --WorkingDir dirname] ReferenceFingerprintsFile
    DatabaseFingerprintsFile

DESCRIPTION
    Perform molecular similarity search [ Ref 94-113 ] using fingerprint
    bit-vector or vector strings data in *SD, FP, or CSV/TSV text* files
    corresponding to *ReferenceFingerprintsFile* and
    *DatabaseFingerprintsFile*, and generate SD and CSV/TSV text file(s)
    containing database molecules which are similar to reference
    molecule(s). The reference molecules are also referred to as query or
    seed molecules and database molecules as target molecules in the
    literature.

    The current release of MayaChemTools supports two types of similarity
    search modes: *IndividualReference or MultipleReferences*. For default
    value of *MultipleReferences* for -m, --mode option, reference molecules
    are considered as a set and -g, --GroupFusionRule is used to calculate
    similarity of a database molecule against reference molecules set. The
    group fusion rule is also referred to as data fusion of consensus
    scoring in the literature. However, for *IndividualReference* value of
    -m, --mode option, reference molecules are treated as individual
    molecules and each reference molecule is compared against a database
    molecule by itself to identify similar molecules.

    The molecular dissimilarity search can also be performed using
    *DissimilaritySearch* value for -s, --SearchMode option. During
    dissimilarity search or usage of distance comparison coefficient in
    similarity similarity search, the meaning of fingerprints comparison
    value is automatically reversed as shown below:

        SeachMode      ComparisonCoefficient  ResultsSort   ComparisonValues

        Similarity     SimilarityCoefficient  Descending    Higher value imples
                                                            high similarity
        Similarity     DistanceCoefficient    Ascending     Lower value implies
                                                            high similarity

        Dissimilarity  SimilarityCoefficient  Ascending     Lower value implies
                                                            high dissimilarity
        Dissimilarity  DistanceCoefficient    Descending    Higher value implies
                                                            high dissimilarity

    During *IndividualReference* value of -m, --Mode option for similarity
    search, fingerprints bit-vector or vector string of each reference
    molecule is compared with database molecules using specified similarity
    or distance coefficients to identify most similar molecules for each
    reference molecule. Based on value of --SimilarCountMode, up to --n,
    --NumOfSimilarMolecules or -p, --PercentSimilarMolecules at specified
    --SimilarityCutoff or --DistanceCutoff are identified for each reference
    molecule.

    During *MultipleReferences* value -m, --mode option for similarity
    search, all reference molecules are considered as a set and -g,
    --GroupFusionRule is used to calculate similarity of a database molecule
    against reference molecules set either using all reference molecules or
    number of k-nearest neighbors (k-NN) to a database molecule specified
    using -k, --kNN. The fingerprints bit-vector or vector string of each
    reference molecule in a set is compared with a database molecule using a
    similarity or distance coefficient specified via -b,
    --BitVectorComparisonMode or -v, --VectorComparisonMode. The reference
    molecules whose comparison values with a database molecule fall outside
    specified --SimilarityCutoff or --DistanceCutoff are ignored during
    *Yes* value of --GroupFusionApplyCutoff. The specified -g,
    --GroupFusionRule is applied to -k, --kNN reference molecules to
    calculate final similarity value between a database molecule and
    reference molecules set.

    The input fingerprints *SD, FP, or Text (CSV/TSV)* files for
    *ReferenceFingerprintsFile* and *DatabaseTextFile* must contain valid
    fingerprint bit-vector or vector strings data corresponding to same type
    of fingerprints.

    The valid fingerprints *SDFile* extensions are *.sdf* and *.sd*. The
    valid fingerprints *FPFile* extensions are *.fpf* and *.fp*. The valid
    fingerprints *TextFile (CSV/TSV)* extensions are *.csv* and *.tsv* for
    comma/semicolon and tab delimited text files respectively. The --indelim
    option determines the format of *TextFile*. Any file which doesn't
    correspond to the format indicated by --indelim option is ignored.

    Example of *FP* file containing fingerprints bit-vector string data:

        #
        # Package = MayaChemTools 7.4
        # ReleaseDate = Oct 21, 2010
        #
        # TimeStamp =  Mon Mar 7 15:14:01 2011
        #
        # FingerprintsStringType = FingerprintsBitVector
        #
        # Description = PathLengthBits:AtomicInvariantsAtomTypes:MinLength1:...
        # Size = 1024
        # BitStringFormat = HexadecimalString
        # BitsOrder = Ascending
        #
        Cmpd1 9c8460989ec8a49913991a6603130b0a19e8051c89184414953800cc21510...
        Cmpd2 000000249400840040100042011001001980410c000000001010088001120...
        ... ...
        ... ..

    Example of *FP* file containing fingerprints vector string data:

        #
        # Package = MayaChemTools 7.4
        # ReleaseDate = Oct 21, 2010
        #
        # TimeStamp =  Mon Mar 7 15:14:01 2011
        #
        # FingerprintsStringType = FingerprintsVector
        #
        # Description = PathLengthBits:AtomicInvariantsAtomTypes:MinLength1:...
        # VectorStringFormat = IDsAndValuesString
        # VectorValuesType = NumericalValues
        #
        Cmpd1 338;C F N O C:C C:N C=O CC CF CN CO C:C:C C:C:N C:CC C:CF C:CN C:
        N:C C:NC CC:N CC=O CCC CCN CCO CNC NC=O O=CO C:C:C:C C:C:C:N C:C:CC...;
        33 1 2 5 21 2 2 12 1 3 3 20 2 10 2 2 1 2 2 2 8 2 5 1 1 1 19 2 8 2 2 2 2
        6 2 2 2 2 2 2 2 2 3 2 2 1 4 1 5 1 1 18 6 2 2 1 2 10 2 1 2 1 2 2 2 2 ...
        Cmpd2 103;C N O C=N C=O CC CN CO CC=O CCC CCN CCO CNC N=CN NC=O NCN O=C
        O C CC=O CCCC CCCN CCCO CCNC CNC=N CNC=O CNCN CCCC=O CCCCC CCCCN CC...;
        15 4 4 1 2 13 5 2 2 15 5 3 2 2 1 1 1 2 17 7 6 5 1 1 1 2 15 8 5 7 2 2 2 2
        1 2 1 1 3 15 7 6 8 3 4 4 3 2 2 1 2 3 14 2 4 7 4 4 4 4 1 1 1 2 1 1 1 ...
        ... ...
        ... ...

    Example of *SD* file containing fingerprints bit-vector 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

        >  <PathLengthFingerprints>
        FingerprintsBitVector;PathLengthBits:AtomicInvariantsAtomTypes:MinLengt
        h1:MaxLength8;1024;HexadecimalString;Ascending;9c8460989ec8a49913991a66
        03130b0a19e8051c89184414953800cc2151082844a201042800130860308e8204d4028
        00831048940e44281c00060449a5000ac80c894114e006321264401600846c050164462
        08190410805000304a10205b0100e04c0038ba0fad0209c0ca8b1200012268b61c0026a
        aa0660a11014a011d46

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

    Example of CSV *TextFile* containing fingerprints bit-vector string
    data:

        "CompoundID","PathLengthFingerprints"
        "Cmpd1","FingerprintsBitVector;PathLengthBits:AtomicInvariantsAtomTypes
        :MinLength1:MaxLength8;1024;HexadecimalString;Ascending;9c8460989ec8a4
        9913991a6603130b0a19e8051c89184414953800cc2151082844a20104280013086030
        8e8204d402800831048940e44281c00060449a5000ac80c894114e006321264401..."
        ... ...
        ... ...

    The current release of MayaChemTools supports the following types of
    fingerprint bit-vector and vector strings:

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

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

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

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

        FingerprintsVector;EStateIndicies:ArbitrarySize;11;NumericalValues;IDs
        AndValuesString;SaaCH SaasC SaasN SdO SdssC SsCH3 SsF SsOH SssCH2 SssN
        H SsssCH;24.778 4.387 1.993 25.023 -1.435 3.975 14.006 29.759 -0.073 3
        .024 -2.270

        FingerprintsVector;EStateIndicies:FixedSize;87;OrderedNumericalValues;
        ValuesString;0 0 0 0 0 0 0 3.975 0 -0.073 0 0 24.778 -2.270 0 0 -1.435
        4.387 0 0 0 0 0 0 3.024 0 0 0 0 0 0 0 1.993 0 29.759 25.023 0 0 0 0 1
        4.006 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
        0 0 0 0 0 0 0 0 0 0 0 0 0 0

        FingerprintsVector;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...

        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;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...

        FingerprintsBitVector;MACCSKeyBits;166;BinaryString;Ascending;00000000
        0000000000000000000000000000000001001000010010000000010010000000011100
        0100101010111100011011000100110110000011011110100110111111111111011111
        11111111111110111000

        FingerprintsBitVector;MACCSKeyBits;322;BinaryString;Ascending;11101011
        1110011111100101111111000111101100110000000000000011100010000000000000
        0000000000000000000000000000000000000000000000101000000000000000000000
        0000000000000000000000000000000000000000000000000000000000000000000000
        0000000000000000000000000000000000000011000000000000000000000000000000
        0000000000000000000000000000000000000000

        FingerprintsVector;MACCSKeyCount;166;OrderedNumericalValues;ValuesStri
        ng;0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
        0 0 0 0 0 0 0 1 0 0 3 0 0 0 0 4 0 0 2 0 0 0 0 0 0 0 0 2 0 0 2 0 0 0 0
        0 0 0 0 1 1 8 0 0 0 1 0 0 1 0 1 0 1 0 3 1 3 1 0 0 0 1 2 0 11 1 0 0 0
        5 0 0 1 2 0 1 1 0 0 0 0 0 1 1 0 1 1 1 1 0 4 0 0 1 1 0 4 6 1 1 1 2 1 1
        3 5 2 2 0 5 3 5 1 1 2 5 1 2 1 2 4 8 3 5 5 2 2 0 3 5 4 1

        FingerprintsVector;MACCSKeyCount;322;OrderedNumericalValues;ValuesStri
        ng;14 8 2 0 2 0 4 4 2 1 4 0 0 2 5 10 5 2 1 0 0 2 0 5 13 3 28 5 5 3 0 0
        0 4 2 1 1 0 1 1 0 0 2 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 22 5 3 0 0 0 1 0
        0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
        0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 11 0 2 0 0 0 0 0 0 0 0 0
        0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 ...

        FingerprintsBitVector;PathLengthBits:AtomicInvariantsAtomTypes:MinLeng
        th1:MaxLength8;1024;BinaryString;Ascending;001000010011010101011000110
        0100010101011000101001011100110001000010001001101000001001001001001000
        0010110100000111001001000001001010100100100000000011000000101001011100
        0010000001000101010100000100111100110111011011011000000010110111001101
        0101100011000000010001000011000010100011101100001000001000100000000...

        FingerprintsVector;PathLengthCount:AtomicInvariantsAtomTypes:MinLength
        1:MaxLength8;432;NumericalValues;IDsAndValuesPairsString;C.X1.BO1.H3 2
        C.X2.BO2.H2 4 C.X2.BO3.H1 14 C.X3.BO3.H1 3 C.X3.BO4 10 F.X1.BO1 1 N.X
        2.BO2.H1 1 N.X3.BO3 1 O.X1.BO1.H1 3 O.X1.BO2 2 C.X1.BO1.H3C.X3.BO3.H1
        2 C.X2.BO2.H2C.X2.BO2.H2 1 C.X2.BO2.H2C.X3.BO3.H1 4 C.X2.BO2.H2C.X3.BO
        4 1 C.X2.BO2.H2N.X3.BO3 1 C.X2.BO3.H1:C.X2.BO3.H1 10 C.X2.BO3.H1:C....

        FingerprintsVector;PathLengthCount:MMFF94AtomTypes:MinLength1:MaxLengt
        h8;463;NumericalValues;IDsAndValuesPairsString;C5A 2 C5B 2 C=ON 1 CB 1
        8 COO 1 CR 9 F 1 N5 1 NC=O 1 O=CN 1 O=CO 1 OC=O 1 OR 2 C5A:C5B 2 C5A:N
        5 2 C5ACB 1 C5ACR 1 C5B:C5B 1 C5BC=ON 1 C5BCB 1 C=ON=O=CN 1 C=ONNC=O 1
        CB:CB 18 CBF 1 CBNC=O 1 COO=O=CO 1 COOCR 1 COOOC=O 1 CRCR 7 CRN5 1 CR
        OR 2 C5A:C5B:C5B 2 C5A:C5BC=ON 1 C5A:C5BCB 1 C5A:N5:C5A 1 C5A:N5CR ...

        FingerprintsVector;TopologicalAtomPairs:AtomicInvariantsAtomTypes:MinD
        istance1:MaxDistance10;223;NumericalValues;IDsAndValuesString;C.X1.BO1
        .H3-D1-C.X3.BO3.H1 C.X2.BO2.H2-D1-C.X2.BO2.H2 C.X2.BO2.H2-D1-C.X3.BO3.
        H1 C.X2.BO2.H2-D1-C.X3.BO4 C.X2.BO2.H2-D1-N.X3.BO3 C.X2.BO3.H1-D1-...;
        2 1 4 1 1 10 8 1 2 6 1 2 2 1 2 1 2 2 1 2 1 5 1 10 12 2 2 1 2 1 9 1 3 1
        1 1 2 2 1 3 6 1 6 14 2 2 2 3 1 3 1 8 2 2 1 3 2 6 1 2 2 5 1 3 1 23 1...

        FingerprintsVector;TopologicalAtomPairs:FunctionalClassAtomTypes:MinDi
        stance1:MaxDistance10;144;NumericalValues;IDsAndValuesString;Ar-D1-Ar
        Ar-D1-Ar.HBA Ar-D1-HBD Ar-D1-Hal Ar-D1-None Ar.HBA-D1-None HBA-D1-NI H
        BA-D1-None HBA.HBD-D1-NI HBA.HBD-D1-None HBD-D1-None NI-D1-None No...;
        23 2 1 1 2 1 1 1 1 2 1 1 7 28 3 1 3 2 8 2 1 1 1 5 1 5 24 3 3 4 2 13 4
        1 1 4 1 5 22 4 4 3 1 19 1 1 1 1 1 2 2 3 1 1 8 25 4 5 2 3 1 26 1 4 1 ...

        FingerprintsVector;TopologicalAtomTorsions:AtomicInvariantsAtomTypes;3
        3;NumericalValues;IDsAndValuesString;C.X1.BO1.H3-C.X3.BO3.H1-C.X3.BO4-
        C.X3.BO4 C.X1.BO1.H3-C.X3.BO3.H1-C.X3.BO4-N.X3.BO3 C.X2.BO2.H2-C.X2.BO
        2.H2-C.X3.BO3.H1-C.X2.BO2.H2 C.X2.BO2.H2-C.X2.BO2.H2-C.X3.BO3.H1-O...;
        2 2 1 1 2 2 1 1 3 4 4 8 4 2 2 6 2 2 1 2 1 1 2 1 1 2 6 2 4 2 1 3 1

        FingerprintsVector;TopologicalAtomTorsions:EStateAtomTypes;36;Numerica
        lValues;IDsAndValuesString;aaCH-aaCH-aaCH-aaCH aaCH-aaCH-aaCH-aasC aaC
        H-aaCH-aasC-aaCH aaCH-aaCH-aasC-aasC aaCH-aaCH-aasC-sF aaCH-aaCH-aasC-
        ssNH aaCH-aasC-aasC-aasC aaCH-aasC-aasC-aasN aaCH-aasC-ssNH-dssC a...;
        4 4 8 4 2 2 6 2 2 2 4 3 2 1 3 3 2 2 2 1 2 1 1 1 2 1 1 1 1 1 1 1 2 1 1 2

        FingerprintsVector;TopologicalAtomTriplets:AtomicInvariantsAtomTypes:M
        inDistance1:MaxDistance10;3096;NumericalValues;IDsAndValuesString;C.X1
        .BO1.H3-D1-C.X1.BO1.H3-D1-C.X3.BO3.H1-D2 C.X1.BO1.H3-D1-C.X2.BO2.H2-D1
        0-C.X3.BO4-D9 C.X1.BO1.H3-D1-C.X2.BO2.H2-D3-N.X3.BO3-D4 C.X1.BO1.H3-D1
        -C.X2.BO2.H2-D4-C.X2.BO2.H2-D5 C.X1.BO1.H3-D1-C.X2.BO2.H2-D6-C.X3....;
        1 2 2 2 2 2 2 2 8 8 4 8 4 4 2 2 2 2 4 2 2 2 4 2 2 2 2 1 2 2 4 4 4 2 2
        2 4 4 4 8 4 4 2 4 4 4 2 4 4 2 2 2 2 2 2 2 2 1 2 2 2 2 2 2 2 2 2 2 8...

        FingerprintsVector;TopologicalAtomTriplets:SYBYLAtomTypes:MinDistance1
        :MaxDistance10;2332;NumericalValues;IDsAndValuesString;C.2-D1-C.2-D9-C
        .3-D10 C.2-D1-C.2-D9-C.ar-D10 C.2-D1-C.3-D1-C.3-D2 C.2-D1-C.3-D10-C.3-
        D9 C.2-D1-C.3-D2-C.3-D3 C.2-D1-C.3-D2-C.ar-D3 C.2-D1-C.3-D3-C.3-D4 C.2
        -D1-C.3-D3-N.ar-D4 C.2-D1-C.3-D3-O.3-D2 C.2-D1-C.3-D4-C.3-D5 C.2-D1-C.
        3-D5-C.3-D6 C.2-D1-C.3-D5-O.3-D4 C.2-D1-C.3-D6-C.3-D7 C.2-D1-C.3-D7...

        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;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 ...

OPTIONS
    --alpha *number*
        Value of alpha parameter for calculating *Tversky* similarity
        coefficient specified for -b, --BitVectorComparisonMode option. It
        corresponds to weights assigned for bits set to "1" in a pair of
        fingerprint bit-vectors during the calculation of similarity
        coefficient. Possible values: *0 to 1*. Default value: <0.5>.

    --beta *number*
        Value of beta parameter for calculating *WeightedTanimoto* and
        *WeightedTversky* similarity coefficients specified for -b,
        --BitVectorComparisonMode option. It is used to weight the
        contributions of bits set to "0" during the calculation of
        similarity coefficients. Possible values: *0 to 1*. Default value of
        <1> makes *WeightedTanimoto* and *WeightedTversky* equivalent to
        *Tanimoto* and *Tversky*.

    -b, --BitVectorComparisonMode *TanimotoSimilarity | TverskySimilarity |
    ...*
        Specify what similarity coefficient to use for calculating
        similarity between fingerprints bit-vector string data values in
        *ReferenceFingerprintsFile* and *DatabaseFingerprintsFile* during
        similarity search. Possible values: *TanimotoSimilarity |
        TverskySimilarity | ...*. Default: *TanimotoSimilarity*

        The current release supports the following similarity coefficients:
        *BaroniUrbaniSimilarity, BuserSimilarity, CosineSimilarity,
        DiceSimilarity, DennisSimilarity, ForbesSimilarity,
        FossumSimilarity, HamannSimilarity, JacardSimilarity,
        Kulczynski1Similarity, Kulczynski2Similarity, MatchingSimilarity,
        McConnaugheySimilarity, OchiaiSimilarity, PearsonSimilarity,
        RogersTanimotoSimilarity, RussellRaoSimilarity, SimpsonSimilarity,
        SkoalSneath1Similarity, SkoalSneath2Similarity,
        SkoalSneath3Similarity, TanimotoSimilarity, TverskySimilarity,
        YuleSimilarity, WeightedTanimotoSimilarity,
        WeightedTverskySimilarity*. These similarity coefficients are
        described below.

        For two fingerprint bit-vectors A and B of same size, let:

            Na = Number of bits set to "1" in A
            Nb = Number of bits set to "1" in B
            Nc = Number of bits set to "1" in both A and B
            Nd = Number of bits set to "0" in both A and B

            Nt = Number of bits set to "1" or "0" in A or B (Size of A or B)
            Nt = Na + Nb - Nc + Nd

            Na - Nc = Number of bits set to "1" in A but not in B
            Nb - Nc = Number of bits set to "1" in B but not in A

        Then, various similarity coefficients [ Ref. 40 - 42 ] for a pair of
        bit-vectors A and B are defined as follows:

        *BaroniUrbaniSimilarity*: ( SQRT( Nc * Nd ) + Nc ) / ( SQRT ( Nc *
        Nd ) + Nc + ( Na - Nc ) + ( Nb - Nc ) ) ( same as Buser )

        *BuserSimilarity*: ( SQRT ( Nc * Nd ) + Nc ) / ( SQRT ( Nc * Nd ) +
        Nc + ( Na - Nc ) + ( Nb - Nc ) ) ( same as BaroniUrbani )

        *CosineSimilarity*: Nc / SQRT ( Na * Nb ) (same as Ochiai)

        *DiceSimilarity*: (2 * Nc) / ( Na + Nb )

        *DennisSimilarity*: ( Nc * Nd - ( ( Na - Nc ) * ( Nb - Nc ) ) ) /
        SQRT ( Nt * Na * Nb)

        *ForbesSimilarity*: ( Nt * Nc ) / ( Na * Nb )

        *FossumSimilarity*: ( Nt * ( ( Nc - 1/2 ) ** 2 ) / ( Na * Nb )

        *HamannSimilarity*: ( ( Nc + Nd ) - ( Na - Nc ) - ( Nb - Nc ) ) / Nt

        *JaccardSimilarity*: Nc / ( ( Na - Nc) + ( Nb - Nc ) + Nc ) = Nc / (
        Na + Nb - Nc ) (same as Tanimoto)

        *Kulczynski1Similarity*: Nc / ( ( Na - Nc ) + ( Nb - Nc) ) = Nc / (
        Na + Nb - 2Nc )

        *Kulczynski2Similarity*: ( ( Nc / 2 ) * ( 2 * Nc + ( Na - Nc ) + (
        Nb - Nc) ) ) / ( ( Nc + ( Na - Nc ) ) * ( Nc + ( Nb - Nc ) ) ) = 0.5
        * ( Nc / Na + Nc / Nb )

        *MatchingSimilarity*: ( Nc + Nd ) / Nt

        *McConnaugheySimilarity*: ( Nc ** 2 - ( Na - Nc ) * ( Nb - Nc) ) / (
        Na * Nb )

        *OchiaiSimilarity*: Nc / SQRT ( Na * Nb ) (same as Cosine)

        *PearsonSimilarity*: ( ( Nc * Nd ) - ( ( Na - Nc ) * ( Nb - Nc ) ) /
        SQRT ( Na * Nb * ( Na - Nc + Nd ) * ( Nb - Nc + Nd ) )

        *RogersTanimotoSimilarity*: ( Nc + Nd ) / ( ( Na - Nc) + ( Nb - Nc)
        + Nt) = ( Nc + Nd ) / ( Na + Nb - 2Nc + Nt)

        *RussellRaoSimilarity*: Nc / Nt

        *SimpsonSimilarity*: Nc / MIN ( Na, Nb)

        *SkoalSneath1Similarity*: Nc / ( Nc + 2 * ( Na - Nc) + 2 * ( Nb -
        Nc) ) = Nc / ( 2 * Na + 2 * Nb - 3 * Nc )

        *SkoalSneath2Similarity*: ( 2 * Nc + 2 * Nd ) / ( Nc + Nd + Nt )

        *SkoalSneath3Similarity*: ( Nc + Nd ) / ( ( Na - Nc ) + ( Nb - Nc )
        ) = ( Nc + Nd ) / ( Na + Nb - 2 * Nc )

        *TanimotoSimilarity*: Nc / ( ( Na - Nc) + ( Nb - Nc ) + Nc ) = Nc /
        ( Na + Nb - Nc ) (same as Jaccard)

        *TverskySimilarity*: Nc / ( alpha * ( Na - Nc ) + ( 1 - alpha) * (
        Nb - Nc) + Nc ) = Nc / ( alpha * ( Na - Nb ) + Nb)

        *YuleSimilarity*: ( ( Nc * Nd ) - ( ( Na - Nc ) * ( Nb - Nc ) ) ) /
        ( ( Nc * Nd ) + ( ( Na - Nc ) * ( Nb - Nc ) ) )

        Values of Tanimoto/Jaccard and Tversky coefficients are dependent on
        only those bit which are set to "1" in both A and B. In order to
        take into account all bit positions, modified versions of Tanimoto [
        Ref. 42 ] and Tversky [ Ref. 43 ] have been developed.

        Let:

            Na' = Number of bits set to "0" in A
            Nb' = Number of bits set to "0" in B
            Nc' = Number of bits set to "0" in both A and B

        Tanimoto': Nc' / ( ( Na' - Nc') + ( Nb' - Nc' ) + Nc' ) = Nc' / (
        Na' + Nb' - Nc' )

        Tversky': Nc' / ( alpha * ( Na' - Nc' ) + ( 1 - alpha) * ( Nb' - Nc'
        ) + Nc' ) = Nc' / ( alpha * ( Na' - Nb' ) + Nb')

        Then:

        *WeightedTanimotoSimilarity* = beta * Tanimoto + (1 - beta) *
        Tanimoto'

        *WeightedTverskySimilarity* = beta * Tversky + (1 - beta) * Tversky'

    --DatabaseColMode *ColNum | ColLabel*
        Specify how columns are identified in database fingerprints
        *TextFile*: using column number or column label. Possible values:
        *ColNum or ColLabel*. Default value: *ColNum*.

    --DatabaseCompoundIDCol *col number | col name*
        This value is --DatabaseColMode mode specific. It specifies column
        to use for retrieving compound ID from database fingerprints
        *TextFile* during similarity and dissimilarity search for output SD
        and CSV/TSV text files. Possible values: *col number or col label*.
        Default value: *first column containing the word compoundID in its
        column label or sequentially generated IDs*.

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

    --DatabaseCompoundIDPrefix *text*
        Specify compound ID prefix to use during sequential generation of
        compound IDs for database fingerprints *SDFile* and *TextFile*.
        Default value: *Cmpd*. The default value generates compound IDs
        which look like Cmpd<Number>.

        For database fingerprints *SDFile*, this value is only used during
        *LabelPrefix | MolNameOrLabelPrefix* values of
        --DatabaseCompoundIDMode option; otherwise, it's ignored.

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

            Compound

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

    --DatabaseCompoundIDField *DataFieldName*
        Specify database fingerprints *SDFile* datafield label for
        generating compound IDs. This value is only used during *DataField*
        value of --DatabaseCompoundIDMode option.

        Examples for *DataField* value of --DatabaseCompoundIDMode:

            MolID
            ExtReg

    --DatabaseCompoundIDMode *DataField | MolName | LabelPrefix |
    MolNameOrLabelPrefix*
        Specify how to generate compound IDs from database fingerprints
        *SDFile* during similarity and dissimilarity search for output SD
        and CSV/TSV text files: use a *SDFile* datafield value; use molname
        line from *SDFile*; 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 --DatabaseCompoundIDMode,
        molname line in *SDFile* 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 --DatabaseDataFieldsMode
        option.

    --DatabaseDataCols *"DataColNum1,DataColNum2,... " |
    DataColLabel1,DataCoLabel2,... "*
        This value is --DatabaseColMode mode specific. It is a comma
        delimited list of database fingerprints *TextFile* data column
        numbers or labels to extract and write to SD and CSV/TSV text files
        along with other information for *SD | text | both* values of
        --output option.

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

        Examples:

            1,2,3
            CompoundName,MolWt

    --DatabaseDataColsMode *All | Specify | CompoundID*
        Specify how data columns from database fingerprints *TextFile* are
        transferred to output SD and CSV/TSV text files along with other
        information for *SD | text | both* values of --output option:
        transfer all data columns; extract specified data columns; generate
        a compound ID database compound prefix. Possible values: *All |
        Specify | CompoundID*. Default value: *CompoundID*.

    --DatabaseDataFields *"FieldLabel1,FieldLabel2,... "*
        Comma delimited list of database fingerprints *SDFile* data fields
        to extract and write to SD and CSV/TSV text files along with other
        information for *SD | text | both* values of --output option.

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

        Examples:

            Extreg
            MolID,CompoundName

    --DatabaseDataFieldsMode *All | Common | Specify | CompoundID*
        Specify how data fields from database fingerprints *SDFile* are
        transferred to output SD and CSV/TSV text files along with other
        information for *SD | text | both* 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*.

    --DatabaseFingerprintsCol *col number | col name*
        This value is --DatabaseColMode specific. It specifies fingerprints
        column to use during similarity and dissimilarity search for
        database fingerprints *TextFile*. Possible values: *col number or
        col label*. Default value: *first column containing the word
        Fingerprints in its column label*.

    --DatabaseFingerprintsField *FieldLabel*
        Fingerprints field label to use during similarity and dissimilarity
        search for database fingerprints *SDFile*. Default value: *first
        data field label containing the word Fingerprints in its label*

    --DistanceCutoff *number*
        Distance cutoff value to use during comparison of distance value
        between a pair of database and reference molecule calculated by
        distance comparison methods for fingerprints vector string data
        values. Possible values: *Any valid number*. Default value: *10*.

        The comparison value between a pair of database and reference
        molecule must meet the cutoff criterion as shown below:

            SeachMode      CutoffCriterion  ComparisonValues

            Similarity     <=               Lower value implies high similarity
            Dissimilarity  >=               Higher value implies high dissimilarity

        This option is only used during distance coefficients values of -v,
        --VectorComparisonMode option.

        This option is ignored during *No* value of --GroupFusionApplyCutoff
        for *MultipleReferences* -m, --mode.

    -d, --detail *InfoLevel*
        Level of information to print about lines being ignored. Default:
        *1*. Possible values: *1, 2 or 3*.

    -f, --fast
        In this mode, fingerprints columns specified using --FingerprintsCol
        for reference and database fingerprints *TextFile(s)*, and
        --FingerprintsField for reference and database fingerprints
        *SDFile(s)* are assumed to contain valid fingerprints data and no
        checking is performed before performing similarity and dissimilarity
        search. By default, fingerprints data is validated before computing
        pairwise similarity and distance coefficients.

    --FingerprintsMode *AutoDetect | FingerprintsBitVectorString |
    FingerprintsVectorString*
        Format of fingerprint strings data in reference and database
        fingerprints *SD, FP, or Text (CSV/TSV)* files: automatically detect
        format of fingerprints string created by MayaChemTools fingerprints
        generation scripts or explicitly specify its format. Possible
        values: *AutoDetect | FingerprintsBitVectorString |
        FingerprintsVectorString*. Default value: *AutoDetect*.

    -g, --GroupFusionRule *Max, Min, Mean, Median, Sum, Euclidean*
        Specify what group fusion [ Ref 94-97, Ref 100, Ref 105 ] rule to
        use for calculating similarity of a database molecule against a set
        of reference molecules during *MultipleReferences* value of
        similarity search -m, --mode. Possible values: *Max, Min, Mean,
        Median, Sum, Euclidean*. Default value: *Max*. *Mean* value
        corresponds to average or arithmetic mean. The group fusion rule is
        also referred to as data fusion of consensus scoring in the
        literature.

        For a reference molecules set and a database molecule, let:

            N = Number of reference molecules in a set

            i = ith reference reference molecule in a set
            n = Nth reference reference molecule in a set

            d = dth database molecule

            Crd = Fingerprints comparison value between rth reference and dth database
                  molecule - similarity/dissimilarity comparison using similarity or
                  distance coefficient

        Then, various group fusion rules to calculate fused similarity
        between a database molecule and reference molecules set are defined
        as follows:

        Max: MAX ( C1d, C2d, ..., Cid, ..., Cnd )

        Min: MIN ( C1d, C2d, ..., Cid, ..., Cnd )

        Mean: SUM ( C1d, C2d, ..., Cid, ..., Cnd ) / N

        Median: MEDIAN ( C1d, C2d, ..., Cid, ..., Cnd )

        Sum: SUM ( C1d, C2d, ..., Cid, ..., Cnd )

        Euclidean: SQRT( SUM( C1d ** 2, C2d ** 2, ..., Cid ** 2, ..., Cnd
        *** 2) )

        The fingerprints bit-vector or vector string of each reference
        molecule in a set is compared with a database molecule using a
        similarity or distance coefficient specified via -b,
        --BitVectorComparisonMode or -v, --VectorComparisonMode. The
        reference molecules whose comparison values with a database molecule
        fall outside specified --SimilarityCutoff or --DistanceCutoff are
        ignored during *Yes* value of --GroupFusionApplyCutoff. The
        specified -g, --GroupFusionRule is applied to -k, --kNN reference
        molecules to calculate final fused similarity value between a
        database molecule and reference molecules set.

        During dissimilarity search or usage of distance comparison
        coefficient in similarity search, the meaning of fingerprints
        comaprison value is automatically reversed as shown below:

            SeachMode      ComparisonCoefficient  ComparisonValues

            Similarity     SimilarityCoefficient  Higher value imples high similarity
            Similarity     DistanceCoefficient    Lower value implies high similarity

            Dissimilarity  SimilarityCoefficient  Lower value implies high
                                                  dissimilarity
            Dissimilarity  DistanceCoefficient    Higher value implies high
                                                  dissimilarity

        Consequently, *Max* implies highest and lowest comparison value for
        usage of similarity and distance coefficient respectively during
        similarity search. And it corresponds to lowest and highest
        comparison value for usage of similarity and distance coefficient
        respectively during dissimilarity search. During *Min* fusion rule,
        the highest and lowest comparison values are appropriately reversed.

    --GroupFusionApplyCutoff *Yes | No*
        Specify whether to apply --SimilarityCutoff or --DistanceCutoff
        values during application of -g, --GroupFusionRule to reference
        molecules set. Possible values: *Yes or No*. Default value: *Yes*.

        During *Yes* value of --GroupFusionApplyCutoff, the reference
        molecules whose comparison values with a database molecule fall
        outside specified --SimilarityCutoff or --DistanceCutoff are not
        used to calculate final fused similarity value between a database
        molecule and reference molecules set.

    -h, --help
        Print this help message.

    --InDelim *comma | semicolon*
        Input delimiter for reference and database fingerprints CSV
        *TextFile(s)*. Possible values: *comma or semicolon*. Default value:
        *comma*. For TSV files, this option is ignored and *tab* is used as
        a delimiter.

    -k, --kNN *all | number*
        Number of k-nearest neighbors (k-NN) reference molecules to use
        during -g, --GroupFusionRule for calculating similarity of a
        database molecule against a set of reference molecules. Possible
        values: *all | positive integers*. Default: *all*.

        After ranking similarity values between a database molecule and
        reference molecules during *MultipleReferences* value of similarity
        search -m, --mode option, a top -k, --KNN reference molecule are
        selected and used during -g, --GroupFusionRule.

        This option is -s, --SearchMode dependent: It corresponds to
        dissimilar molecules during *DissimilaritySearch* value of -s,
        --SearchMode option.

    -m, --mode *IndividualReference | MultipleReferences*
        Specify how to treat reference molecules in
        *ReferenceFingerprintsFile* during similarity search: Treat each
        reference molecule individually during similarity search or perform
        similarity search by treating multiple reference molecules as a set.
        Possible values: *IndividualReference | MultipleReferences*. Default
        value: *MultipleReferences*.

        During *IndividualReference* value of -m, --Mode for similarity
        search, fingerprints bit-vector or vector string of each reference
        molecule is compared with database molecules using specified
        similarity or distance coefficients to identify most similar
        molecules for each reference molecule. Based on value of
        --SimilarCountMode, upto --n, NumOfSimilarMolecules or -p,
        --PercentSimilarMolecules at specified <--SimilarityCutoff> or
        --DistanceCutoff are identified for each reference molecule.

        During *MultipleReferences* value -m, --mode for similarity search,
        all reference molecules are considered as a set and -g,
        --GroupFusionRule is used to calculate similarity of a database
        molecule against reference molecules set either using all reference
        molecules or number of k-nearest neighbors (k-NN) to a database
        molecule specified using -k, --kNN. The fingerprints bit-vector or
        vector string of each reference molecule in a set is compared with a
        database molecule using a similarity or distance coefficient
        specified via -b, --BitVectorComparisonMode or -v,
        --VectorComparisonMode. The reference molecules whose comparison
        values with a database molecule fall outside specified
        --SimilarityCutoff or --DistanceCutoff are ignored. The specified
        -g, --GroupFusionRule is applied to rest of -k, --kNN reference
        molecules to calculate final similarity value between a database
        molecule and reference molecules set.

        The meaning of similarity and distance is automatically reversed
        during *DissimilaritySearch* value of -s, --SearchMode along with
        appropriate handling of --SimilarityCutoff or --DistanceCutoff
        values.

    -n, --NumOfSimilarMolecules *number*
        Maximum number of most similar database molecules to find for each
        reference molecule or set of reference molecules based on
        *IndividualReference* or *MultipleReferences* value of similarity
        search -m, --mode option. Default: *10*. Valid values: positive
        integers.

        This option is ignored during *PercentSimilar* value of
        --SimilarCountMode option.

        This option is -s, --SearchMode dependent: It corresponds to
        dissimilar molecules during *DissimilaritySearch* value of -s,
        --SearchMode option.

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

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

    -o, --overwrite
        Overwrite existing files

    -p, --PercentSimilarMolecules *number*
        Maximum percent of mosy similar database molecules to find for each
        reference molecule or set of reference molecules based on
        *IndividualReference* or *MultipleReferences* value of similarity
        search -m, --mode option. Default: *1* percent of database
        molecules. Valid values: non-zero values in between *0 to 100*.

        This option is ignored during *NumOfSimilar* value of
        --SimilarCountMode option.

        During *PercentSimilar* value of --SimilarCountMode option, the
        number of molecules in *DatabaseFingerprintsFile* is counted and
        number of similar molecules correspond to --PercentSimilarMolecules
        of the total number of database molecules.

        This option is -s, --SearchMode dependent: It corresponds to
        dissimilar molecules during *DissimilaritySearch* value of -s,
        --SearchMode option.

    --precision *number*
        Precision of calculated similarity values for comparison and
        generating output files. Default: up to *2* decimal places. Valid
        values: positive integers.

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

    --ReferenceColMode *ColNum | ColLabel*
        Specify how columns are identified in reference fingerprints
        *TextFile*: using column number or column label. Possible values:
        *ColNum or ColLabel*. Default value: *ColNum*.

    --ReferenceCompoundIDCol *col number | col name*
        This value is --ReferenceColMode mode specific. It specifies column
        to use for retrieving compound ID from reference fingerprints
        *TextFile* during similarity and dissimilarity search for output SD
        and CSV/TSV text files. Possible values: *col number or col label*.
        Default value: *first column containing the word compoundID in its
        column label or sequentially generated IDs*.

    --ReferenceCompoundIDPrefix *text*
        Specify compound ID prefix to use during sequential generation of
        compound IDs for reference fingerprints *SDFile* and *TextFile*.
        Default value: *Cmpd*. The default value generates compound IDs
        which looks like Cmpd<Number>.

        For reference fingerprints *SDFile*, this value is only used during
        *LabelPrefix | MolNameOrLabelPrefix* values of
        --ReferenceCompoundIDMode option; otherwise, it's ignored.

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

            Compound

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

    --ReferenceCompoundIDField *DataFieldName*
        Specify reference fingerprints *SDFile* datafield label for
        generating compound IDs. This value is only used during *DataField*
        value of --ReferenceCompoundIDMode option.

        Examples for *DataField* value of --ReferenceCompoundIDMode:

            MolID
            ExtReg

    --ReferenceCompoundIDMode *DataField | MolName | LabelPrefix |
    MolNameOrLabelPrefix*
        Specify how to generate compound IDs from reference fingerprints
        *SDFile* during similarity and dissimilarity search for output SD
        and CSV/TSV text files: use a *SDFile* datafield value; use molname
        line from *SDFile*; 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 --ReferenceCompoundIDMode,
        molname line in *SDFiles* takes precedence over sequential compound
        IDs generated using *LabelPrefix* and only empty molname values are
        replaced with sequential compound IDs.

    --ReferenceFingerprintsCol *col number | col name*
        This value is --ReferenceColMode specific. It specifies fingerprints
        column to use during similarity and dissimilarity search for
        reference fingerprints *TextFile*. Possible values: *col number or
        col label*. Default value: *first column containing the word
        Fingerprints in its column label*.

    --ReferenceFingerprintsField *FieldLabel*
        Fingerprints field label to use during similarity and dissimilarity
        search for reference fingerprints *SDFile*. Default value: *first
        data field label containing the word Fingerprints in its label*

    -r, --root *RootName*
        New file name is generated using the root: <Root>.<Ext>. Default for
        new file name: <ReferenceFileName>SimilaritySearching.<Ext>. The
        output file type determines <Ext> value. The sdf, csv, and tsv <Ext>
        values are used for SD, comma/semicolon, and tab delimited text
        files respectively.

    -s, --SearchMode *SimilaritySearch | DissimilaritySearch*
        Specify how to find molecules from database molecules for individual
        reference molecules or set of reference molecules: Find similar
        molecules or dissimilar molecules from database molecules. Possible
        values: *SimilaritySearch | DissimilaritySearch*. Default value:
        *SimilaritySearch*.

        During *DissimilaritySearch* value of -s, --SearchMode option, the
        meaning of the following options is switched and they correspond to
        dissimilar molecules instead of similar molecules:
        --SimilarCountMode, -n, --NumOfSimilarMolecules,
        --PercentSimilarMolecules, -k, --kNN.

    --SimilarCountMode *NumOfSimilar | PercentSimilar*
        Specify method used to count similar molecules found from database
        molecules for individual reference molecules or set of reference
        molecules: Find number of similar molecules or percent of similar
        molecules from database molecules. Possible values: *NumOfSimilar |
        PercentSimilar*. Default value: *NumOfSimilar*.

        The values for number of similar molecules and percent similar
        molecules are specified using options -n, NumOfSimilarMolecule and
        --PercentSimilarMolecules.

        This option is -s, --SearchMode dependent: It corresponds to
        dissimilar molecules during *DissimilaritySearch* value of -s,
        --SearchMode option.

    --SimilarityCutoff *number*
        Similarity cutoff value to use during comparison of similarity value
        between a pair of database and reference molecules calculated by
        similarity comparison methods for fingerprints bit-vector vector
        strings data values. Possible values: *Any valid number*. Default
        value: *0.75*.

        The comparison value between a pair of database and reference
        molecule must meet the cutoff criterion as shown below:

            SeachMode      CutoffCriterion  ComparisonValues

            Similarity     >=               Higher value implies high similarity
            Dissimilarity  <=               Lower value implies high dissimilarity

        This option is ignored during *No* value of --GroupFusionApplyCutoff
        for *MultipleReferences* -m, --mode.

        This option is -s, --SearchMode dependent: It corresponds to
        dissimilar molecules during *DissimilaritySearch* value of -s,
        --SearchMode option.

    -v, --VectorComparisonMode *SupportedSimilarityName |
    SupportedDistanceName*
        Specify what similarity or distance coefficient to use for
        calculating similarity between fingerprint vector strings data
        values in *ReferenceFingerprintsFile* and *DatabaseFingerprintsFile*
        during similarity search. Possible values: *TanimotoSimilairy | ...
        | ManhattanDistance | ...*. Default value: *TanimotoSimilarity*.

        The value of -v, --VectorComparisonMode, in conjunction with
        --VectorComparisonFormulism, decides which type of similarity and
        distance coefficient formulism gets used.

        The current releases supports the following similarity and distance
        coefficients: *CosineSimilarity, CzekanowskiSimilarity,
        DiceSimilarity, OchiaiSimilarity, JaccardSimilarity,
        SorensonSimilarity, TanimotoSimilarity, CityBlockDistance,
        EuclideanDistance, HammingDistance, ManhattanDistance,
        SoergelDistance*. These similarity and distance coefficients are
        described below.

        FingerprintsVector.pm module, used to calculate similarity and
        distance coefficients, provides support to perform comparison
        between vectors containing three different types of values:

        Type I: OrderedNumericalValues

            . Size of two vectors are same
            . Vectors contain real values in a specific order. For example: MACCS keys
              count, Topological pharmnacophore atom pairs and so on.

        Type II: UnorderedNumericalValues

            . Size of two vectors might not be same
            . Vectors contain unordered real value identified by value IDs. For example:
              Toplogical atom pairs, Topological atom torsions and so on

        Type III: AlphaNumericalValues

            . Size of two vectors might not be same
            . Vectors contain unordered alphanumerical values. For example: Extended
              connectivity fingerprints, atom neighborhood fingerprints.

        Before performing similarity or distance calculations between
        vectors containing UnorderedNumericalValues or AlphaNumericalValues,
        the vectors are transformed into vectors containing unique
        OrderedNumericalValues using value IDs for UnorderedNumericalValues
        and values itself for AlphaNumericalValues.

        Three forms of similarity and distance calculation between two
        vectors, specified using --VectorComparisonFormulism option, are
        supported: *AlgebraicForm, BinaryForm or SetTheoreticForm*.

        For *BinaryForm*, the ordered list of processed final vector values
        containing the value or count of each unique value type is simply
        converted into a binary vector containing 1s and 0s corresponding to
        presence or absence of values before calculating similarity or
        distance between two vectors.

        For two fingerprint vectors A and B of same size containing
        OrderedNumericalValues, let:

            N = Number values in A or B

            Xa = Values of vector A
            Xb = Values of vector B

            Xai = Value of ith element in A
            Xbi = Value of ith element in B

           SUM = Sum of i over N values

        For SetTheoreticForm of calculation between two vectors, let:

            SetIntersectionXaXb = SUM ( MIN ( Xai, Xbi ) )
            SetDifferenceXaXb = SUM ( Xai ) + SUM ( Xbi ) - SUM ( MIN ( Xai, Xbi ) )

        For BinaryForm of calculation between two vectors, let:

            Na = Number of bits set to "1" in A = SUM ( Xai )
            Nb = Number of bits set to "1" in B = SUM ( Xbi )
            Nc = Number of bits set to "1" in both A and B = SUM ( Xai * Xbi )
            Nd = Number of bits set to "0" in both A and B
               = SUM ( 1 - Xai - Xbi + Xai * Xbi)

            N = Number of bits set to "1" or "0" in A or B = Size of A or B = Na + Nb - Nc + Nd

        Additionally, for BinaryForm various values also correspond to:

            Na = | Xa |
            Nb = | Xb |
            Nc = | SetIntersectionXaXb |
            Nd = N - | SetDifferenceXaXb |

            | SetDifferenceXaXb | = N - Nd = Na + Nb - Nc + Nd - Nd = Na + Nb - Nc
                                  =  | Xa | + | Xb | - | SetIntersectionXaXb |

        Various similarity and distance coefficients [ Ref 40, Ref 62, Ref
        64 ] for a pair of vectors A and B in *AlgebraicForm, BinaryForm and
        SetTheoreticForm* are defined as follows:

        CityBlockDistance: ( same as HammingDistance and ManhattanDistance)

        *AlgebraicForm*: SUM ( ABS ( Xai - Xbi ) )

        *BinaryForm*: ( Na - Nc ) + ( Nb - Nc ) = Na + Nb - 2 * Nc

        *SetTheoreticForm*: | SetDifferenceXaXb | - | SetIntersectionXaXb |
        = SUM ( Xai ) + SUM ( Xbi ) - 2 * ( SUM ( MIN ( Xai, Xbi ) ) )

        CosineSimilarity: ( same as OchiaiSimilarityCoefficient)

        *AlgebraicForm*: SUM ( Xai * Xbi ) / SQRT ( SUM ( Xai ** 2) * SUM (
        Xbi ** 2) )

        *BinaryForm*: Nc / SQRT ( Na * Nb)

        *SetTheoreticForm*: | SetIntersectionXaXb | / SQRT ( |Xa| * |Xb| ) =
        SUM ( MIN ( Xai, Xbi ) ) / SQRT ( SUM ( Xai ) * SUM ( Xbi ) )

        CzekanowskiSimilarity: ( same as DiceSimilarity and
        SorensonSimilarity)

        *AlgebraicForm*: ( 2 * ( SUM ( Xai * Xbi ) ) ) / ( SUM ( Xai ** 2) +
        SUM ( Xbi **2 ) )

        *BinaryForm*: 2 * Nc / ( Na + Nb )

        *SetTheoreticForm*: 2 * | SetIntersectionXaXb | / ( |Xa| + |Xb| ) =
        2 * ( SUM ( MIN ( Xai, Xbi ) ) ) / ( SUM ( Xai ) + SUM ( Xbi ) )

        DiceSimilarity: ( same as CzekanowskiSimilarity and
        SorensonSimilarity)

        *AlgebraicForm*: ( 2 * ( SUM ( Xai * Xbi ) ) ) / ( SUM ( Xai ** 2) +
        SUM ( Xbi **2 ) )

        *BinaryForm*: 2 * Nc / ( Na + Nb )

        *SetTheoreticForm*: 2 * | SetIntersectionXaXb | / ( |Xa| + |Xb| ) =
        2 * ( SUM ( MIN ( Xai, Xbi ) ) ) / ( SUM ( Xai ) + SUM ( Xbi ) )

        EuclideanDistance:

        *AlgebraicForm*: SQRT ( SUM ( ( ( Xai - Xbi ) ** 2 ) ) )

        *BinaryForm*: SQRT ( ( Na - Nc ) + ( Nb - Nc ) ) = SQRT ( Na + Nb -
        2 * Nc )

        *SetTheoreticForm*: SQRT ( | SetDifferenceXaXb | - |
        SetIntersectionXaXb | ) = SQRT ( SUM ( Xai ) + SUM ( Xbi ) - 2 * (
        SUM ( MIN ( Xai, Xbi ) ) ) )

        HammingDistance: ( same as CityBlockDistance and ManhattanDistance)

        *AlgebraicForm*: SUM ( ABS ( Xai - Xbi ) )

        *BinaryForm*: ( Na - Nc ) + ( Nb - Nc ) = Na + Nb - 2 * Nc

        *SetTheoreticForm*: | SetDifferenceXaXb | - | SetIntersectionXaXb |
        = SUM ( Xai ) + SUM ( Xbi ) - 2 * ( SUM ( MIN ( Xai, Xbi ) ) )

        JaccardSimilarity: ( same as TanimotoSimilarity)

        *AlgebraicForm*: SUM ( Xai * Xbi ) / ( SUM ( Xai ** 2 ) + SUM ( Xbi
        ** 2 ) - SUM ( Xai * Xbi ) )

        *BinaryForm*: Nc / ( ( Na - Nc ) + ( Nb - Nc ) + Nc ) = Nc / ( Na +
        Nb - Nc )

        *SetTheoreticForm*: | SetIntersectionXaXb | / | SetDifferenceXaXb |
        = SUM ( MIN ( Xai, Xbi ) ) / ( SUM ( Xai ) + SUM ( Xbi ) - SUM ( MIN
        ( Xai, Xbi ) ) )

        ManhattanDistance: ( same as CityBlockDistance and HammingDistance)

        *AlgebraicForm*: SUM ( ABS ( Xai - Xbi ) )

        *BinaryForm*: ( Na - Nc ) + ( Nb - Nc ) = Na + Nb - 2 * Nc

        *SetTheoreticForm*: | SetDifferenceXaXb | - | SetIntersectionXaXb |
        = SUM ( Xai ) + SUM ( Xbi ) - 2 * ( SUM ( MIN ( Xai, Xbi ) ) )

        OchiaiSimilarity: ( same as CosineSimilarity)

        *AlgebraicForm*: SUM ( Xai * Xbi ) / SQRT ( SUM ( Xai ** 2) * SUM (
        Xbi ** 2) )

        *BinaryForm*: Nc / SQRT ( Na * Nb)

        *SetTheoreticForm*: | SetIntersectionXaXb | / SQRT ( |Xa| * |Xb| ) =
        SUM ( MIN ( Xai, Xbi ) ) / SQRT ( SUM ( Xai ) * SUM ( Xbi ) )

        SorensonSimilarity: ( same as CzekanowskiSimilarity and
        DiceSimilarity)

        *AlgebraicForm*: ( 2 * ( SUM ( Xai * Xbi ) ) ) / ( SUM ( Xai ** 2) +
        SUM ( Xbi **2 ) )

        *BinaryForm*: 2 * Nc / ( Na + Nb )

        *SetTheoreticForm*: 2 * | SetIntersectionXaXb | / ( |Xa| + |Xb| ) =
        2 * ( SUM ( MIN ( Xai, Xbi ) ) ) / ( SUM ( Xai ) + SUM ( Xbi ) )

        SoergelDistance:

        *AlgebraicForm*: SUM ( ABS ( Xai - Xbi ) ) / SUM ( MAX ( Xai, Xbi )
        )

        *BinaryForm*: 1 - Nc / ( Na + Nb - Nc ) = ( Na + Nb - 2 * Nc ) / (
        Na + Nb - Nc )

        *SetTheoreticForm*: ( | SetDifferenceXaXb | - | SetIntersectionXaXb
        | ) / | SetDifferenceXaXb | = ( SUM ( Xai ) + SUM ( Xbi ) - 2 * (
        SUM ( MIN ( Xai, Xbi ) ) ) ) / ( SUM ( Xai ) + SUM ( Xbi ) - SUM (
        MIN ( Xai, Xbi ) ) )

        TanimotoSimilarity: ( same as JaccardSimilarity)

        *AlgebraicForm*: SUM ( Xai * Xbi ) / ( SUM ( Xai ** 2 ) + SUM ( Xbi
        ** 2 ) - SUM ( Xai * Xbi ) )

        *BinaryForm*: Nc / ( ( Na - Nc ) + ( Nb - Nc ) + Nc ) = Nc / ( Na +
        Nb - Nc )

        *SetTheoreticForm*: | SetIntersectionXaXb | / | SetDifferenceXaXb |
        = SUM ( MIN ( Xai, Xbi ) ) / ( SUM ( Xai ) + SUM ( Xbi ) - SUM ( MIN
        ( Xai, Xbi ) ) )

    --VectorComparisonFormulism *AlgebraicForm | BinaryForm |
    SetTheoreticForm*
        Specify fingerprints vector comparison formulism to use for
        calculation similarity and distance coefficients during -v,
        --VectorComparisonMode. Possible values: *AlgebraicForm | BinaryForm
        | SetTheoreticForm*. Default value: *AlgebraicForm*.

        For fingerprint vector strings containing AlphaNumericalValues data
        values - ExtendedConnectivityFingerprints,
        AtomNeighborhoodsFingerprints and so on - all three formulism result
        in same value during similarity and distance calculations.

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

EXAMPLES
    To perform similarity search using Tanimoto coefficient by treating all
    reference molecules as a set to find 10 most similar database molecules
    with application of Max group fusion rule and similarity cutoff to
    supported fingerprints strings data in SD fingerprints files present in
    a data fields with Fingerprint substring in their labels, and create a
    ReferenceFPHexSimilaritySearching.csv file containing sequentially
    generated database compound IDs with Cmpd prefix, type:

        % SimilaritySearchingFingerprints.pl -o ReferenceSampleFPHex.sdf
          DatabaseSampleFPHex.sdf

    To perform similarity search using Tanimoto coefficient by treating all
    reference molecules as a set to find 10 most similar database molecules
    with application of Max group fusion rule and similarity cutoff to
    supported fingerprints strings data in FP fingerprints files, and create
    a SimilaritySearchResults.csv file containing database compound IDs
    retireved from FP file, type:

        % SimilaritySearchingFingerprints.pl -r SimilaritySearchResults -o
          ReferenceSampleFPBin.fpf DatabaseSampleFPBin.fpf

    To perform similarity search using Tanimoto coefficient by treating all
    reference molecules as a set to find 10 most similar database database
    molecules with application of Max group fusion rule and similarity
    cutoff to supported fingerprints strings data in text fingerprints files
    present in a column names containing Fingerprint substring in their
    names, and create a ReferenceFPHexSimilaritySearching.csv file
    containing database compound IDs retireved column name containing
    CompoundID substring or sequentially generated compound IDs, type:

        % SimilaritySearchingFingerprints.pl -o ReferenceSampleFPCount.csv
          DatabaseSampleFPCount.csv

    To perform similarity search using Tanimoto coefficient by treating
    reference molecules as individual molecules to find 10 most similar
    database molecules for each reference molecule with application of
    similarity cutoff to supported fingerprints strings data in SD
    fingerprints files present in a data fields with Fingerprint substring
    in their labels, and create a ReferenceFPHexSimilaritySearching.csv file
    containing sequentially generated reference and database compound IDs
    with Cmpd prefix, type:

        % SimilaritySearchingFingerprints.pl -mode IndividualReference -o
          ReferenceSampleFPHex.sdf DatabaseSampleFPHex.sdf

    To perform similarity search using Tanimoto coefficient by treating
    reference molecules as individual molecules to find 10 most similar
    database molecules for each reference molecule with application of
    similarity cutoff to supported fingerprints strings data in FP
    fingerprints files, and create a ReferenceFPHexSimilaritySearching.csv
    file containing references and database compound IDs retireved from FP
    file, type:

        % SimilaritySearchingFingerprints.pl -mode IndividualReference -o
          ReferenceSampleFPHex.fpf DatabaseSampleFPHex.fpf

    To perform similarity search using Tanimoto coefficient by treating
    reference molecules as individual molecules to find 10 most similar
    database molecules for each reference molecule with application of
    similarity cutoff to supported fingerprints strings data in text
    fingerprints files present in a column names containing Fingerprint
    substring in their names, and create a
    ReferenceFPHexSimilaritySearching.csv file containing reference and
    database compound IDs retrieved column name containing CompoundID
    substring or sequentially generated compound IDs, type:

        % SimilaritySearchingFingerprints.pl -mode IndividualReference -o
          ReferenceSampleFPHex.csv DatabaseSampleFPHex.csv

    To perform dissimilarity search using Tanimoto coefficient by treating
    all reference molecules as a set to find 10 most dissimilar database
    molecules with application of Max group fusion rule and similarity
    cutoff to supported fingerprints strings data in SD fingerprints files
    present in a data fields with Fingerprint substring in their labels, and
    create a ReferenceFPHexSimilaritySearching.csv file containing
    sequentially generated database compound IDs with Cmpd prefix, type:

        % SimilaritySearchingFingerprints.pl --mode MultipleReferences --SearchMode
          DissimilaritySearch -o ReferenceSampleFPHex.sdf DatabaseSampleFPHex.sdf

    To perform similarity search using CityBlock distance by treating
    reference molecules as individual molecules to find 10 most similar
    database molecules for each reference molecule with application of
    distance cutoff to supported vector fingerprints strings data in SD
    fingerprints files present in a data fields with Fingerprint substring
    in their labels, and create a ReferenceFPHexSimilaritySearching.csv file
    containing sequentially generated reference and database compound IDs
    with Cmpd prefix, type:

        % SimilaritySearchingFingerprints.pl -mode IndividualReference
          --VectorComparisonMode CityBlockDistance --VectorComparisonFormulism
          AlgebraicForm --DistanceCutoff 10 -o
          ReferenceSampleFPCount.sdf DatabaseSampleFPCount.sdf

    To perform similarity search using Tanimoto coefficient by treating all
    reference molecules as a set to find 100 most similar database molecules
    with application of Mean group fusion rule to to top 10 reference
    molecules with in similarity cutoff of 0.75 to supported fingerprints
    strings data in FP fingerprints files, and create a
    ReferenceFPHexSimilaritySearching.csv file containing database compound
    IDs retrieved from FP file, type:

        % SimilaritySearchingFingerprints.pl --mode MultipleReferences --SearchMode
          SimilaritySearch --BitVectorComparisonMode TanimotoSimilarity
          --GroupFusionRule Mean --GroupFusionApplyCutoff Yes --kNN 10
          --SimilarityCutoff 0.75 --SimilarCountMode NumOfSimilar
          --NumOfSimilarMolecules 100 -o
          ReferenceSampleFPHex.fpf DatabaseSampleFPHex.fpf

    To perform similarity search using Tanimoto coefficient by treating
    reference molecules as individual molecules to find 2 percent of most
    similar database molecules for each reference molecule with application
    of similarity cutoff of 0.85 to supported fingerprints strings data in
    text fingerprints files present in specific columns and create a
    ReferenceFPHexSimilaritySearching.csv file containing reference and
    database compoundIDs retrieved from specific columns, type:

        % SimilaritySearchingFingerprints.pl --mode IndividualReference --SearchMode
          SimilaritySearch --BitVectorComparisonMode TanimotoSimilarity
          --ReferenceColMode ColLabel --ReferenceFingerprintsCol Fingerprints
          --ReferenceCompoundIDCol CompoundID --DatabaseColMode Collabel
          --DatabaseCompoundIDCol CompoundID --DatabaseFingerprintsCol
          Fingerprints --SimilarityCutoff 0.85 --SimilarCountMode PercentSimilar
          --PercentSimilarMolecules 2 -o
          ReferenceSampleFPHex.csv DatabaseSampleFPHex.csv

    To perform similarity search using Tanimoto coefficient by treating
    reference molecules as individual molecules to find top 50 most similar
    database molecules for each reference molecule with application of
    similarity cutoff of 0.85 to supported fingerprints strings data in SD
    fingerprints files present in specific data fields and create both
    ReferenceFPHexSimilaritySearching.csv and
    ReferenceFPHexSimilaritySearching.sdf files containing reference and
    database compoundIDs retrieved from specific data fields, type:

        % SimilaritySearchingFingerprints.pl --mode IndividualReference --SearchMode
          SimilaritySearch --BitVectorComparisonMode TanimotoSimilarity
          --ReferenceFingerprintsField Fingerprints
          --DatabaseFingerprintsField Fingerprints
          --ReferenceCompoundIDMode DataField --ReferenceCompoundIDField CmpdID
          --DatabaseCompoundIDMode DataField --DatabaseCompoundIDField CmpdID
          --SimilarityCutoff 0.85 --SimilarCountMode NumOfSimilar
          --NumOfSimilarMolecules 50 --output both -o
          ReferenceSampleFPHex.sdf DatabaseSampleFPHex.sdf

    To perform similarity search using Tanimoto coefficient by treating
    reference molecules as individual molecules to find 1 percent of most
    similar database molecules for each reference molecule with application
    of similarity cutoff to supported fingerprints strings data in SD
    fingerprints files present in specific data field labels, and create
    both ReferenceFPHexSimilaritySearching.csv
    ReferenceFPHexSimilaritySearching.sdf files containing reference and
    database compound IDs retrieved from specific data field labels along
    with other specific data for database molecules, type:

        % SimilaritySearchingFingerprints.pl --mode IndividualReference --SearchMode
          SimilaritySearch --BitVectorComparisonMode TanimotoSimilarity
          --ReferenceFingerprintsField Fingerprints
          --DatabaseFingerprintsField Fingerprints
          --ReferenceCompoundIDMode DataField --ReferenceCompoundIDField CmpdID
          --DatabaseCompoundIDMode DataField --DatabaseCompoundIDField CmpdID
          --DatabaseDataFieldsMode Specify --DatabaseDataFields "TPSA,SLogP"
          --SimilarityCutoff 0.75 --SimilarCountMode PercentSimilar
          --PercentSimilarMolecules 1 --output both --OutDelim comma --quote Yes
          --precision 3 -o ReferenceSampleFPHex.sdf DatabaseSampleFPHex.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,
    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.

