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diff docs/scripts/txt/SimilarityMatricesFingerprints.txt @ 0:4816e4a8ae95 draft default tip
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| author | deepakjadmin |
|---|---|
| date | Wed, 20 Jan 2016 09:23:18 -0500 |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/docs/scripts/txt/SimilarityMatricesFingerprints.txt Wed Jan 20 09:23:18 2016 -0500 @@ -0,0 +1,1363 @@ +NAME + SimilarityMatricesFingerprints.pl - Calculate similarity matrices using + fingerprints strings data in SD, FP and CSV/TSV text file(s) + +SYNOPSIS + SimilarityMatricesFingerprints.pl SDFile(s) FPFile(s) TextFile(s)... + + SimilarityMatricesFingerprints.pl [--alpha *number*] [--beta *number*] + [-b, --BitVectorComparisonMode *All | "TanimotoSimilarity,[ + TverskySimilarity, ... ]"*] [-c, --ColMode *ColNum | ColLabel*] + [--CompoundIDCol *col number | col name*] [--CompoundIDPrefix *text*] + [--CompoundIDField *DataFieldName*] [--CompoundIDMode *DataField | + MolName | LabelPrefix | MolNameOrLabelPrefix*] [-d, --detail + *InfoLevel*] [-f, --fast] [--FingerprintsCol *col number | col name*] + [--FingerprintsField *FieldLabel*] [-h, --help] [--InDelim *comma | + semicolon*] [--InputDataMode *LoadInMemory | ScanFile*] [-m, --mode + *AutoDetect | FingerprintsBitVectorString | FingerprintsVectorString*] + [--OutDelim *comma | tab | semicolon*] [--OutMatrixFormat + *RowsAndColumns | IDPairsAndValue*] [--OutMatrixType *FullMatrix | + UpperTriangularMatrix | LowerTriangularMatrix*] [-o, --overwrite] [-p, + --precision *number*] [-q, --quote *Yes | No*] [-r, --root *RootName*] + [-v, --VectorComparisonMode *All | "TanimotoSimilairy, [ + ManhattanDistance, ...]"*] [--VectorComparisonFormulism *All | + "AlgebraicForm, [BinaryForm, SetTheoreticForm]"*] [-w, --WorkingDir + dirname] SDFile(s) FPFile(s) TextFile(s)... + +DESCRIPTION + Calculate similarity matrices using fingerprint bit-vector or vector + strings data in *SD, FP and CSV/TSV* text file(s) and generate CSV/TSV + text file(s) containing values for specified similarity and distance + coefficients. + + The scripts SimilarityMatrixSDFiles.pl and SimilarityMatrixTextFiles.pl + have been removed from the current release of MayaChemTools and their + functionality merged with this script. + + The valid *SDFile* extensions are *.sdf* and *.sd*. All SD files in a + current directory can be specified either by **.sdf* or the current + directory name. + + The valid *FPFile* extensions are *.fpf* and *.fp*. All FP files in a + current directory can be specified either by **.fpf* or the current + directory name. + + The valid *TextFile* extensions are *.csv* and *.tsv* for + comma/semicolon and tab delimited text files respectively. All other + file names are ignored. All text files in a current directory can be + specified by **.csv*, **.tsv*, or the current directory name. The + --indelim option determines the format of *TextFile(s)*. 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 *Text* file 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 *All | + "TanimotoSimilarity,[TverskySimilarity,...]"* + Specify what similarity coefficients to use for calculating + similarity matrices for fingerprints bit-vector strings data values + in *TextFile(s)*: calculate similarity matrices for all supported + similarity coefficients or specify a comma delimited list of + similarity coefficients. Possible values: *All | + "TanimotoSimilarity,[TverskySimilarity,...]*. Default: + *TanimotoSimilarity* + + *All* uses complete list of supported 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' + + -c, --ColMode *ColNum | ColLabel* + Specify how columns are identified in *TextFile(s)*: using column + number or column label. Possible values: *ColNum or ColLabel*. + Default value: *ColNum*. + + --CompoundIDCol *col number | col name* + This value is -c, --ColMode mode specific. It specifies input + *TextFile(s)* column to use for generating compound ID for + similarity matrices in output *TextFile(s)*. Possible values: *col + number or col label*. Default value: *first column containing the + word compoundID in its column label or sequentially generated IDs*. + + --CompoundIDPrefix *text* + Specify compound ID prefix to use during sequential generation of + compound IDs for input *SDFile(s)* and *TextFile(s)*. Default value: + *Cmpd*. The default value generates compound IDs which look like + Cmpd<Number>. + + For input *SDFile(s)*, this value is only used during *LabelPrefix | + MolNameOrLabelPrefix* values of --CompoundIDMode option; otherwise, + it's ignored. + + Examples for *LabelPrefix* or *MolNameOrLabelPrefix* value of + --CompoundIDMode: + + Compound + + The values specified above generates compound IDs which correspond + to Compound<Number> instead of default value of Cmpd<Number>. + + --CompoundIDField *DataFieldName* + Specify input *SDFile(s)* datafield label for generating compound + IDs. This value is only used during *DataField* value of + --CompoundIDMode option. + + Examples for *DataField* value of --CompoundIDMode: + + MolID + ExtReg + + --CompoundIDMode *DataField | MolName | LabelPrefix | + MolNameOrLabelPrefix* + Specify how to generate compound IDs from input *SDFile(s)* for + similarity matrix CSV/TSV text file(s): use a *SDFile(s)* datafield + value; use molname line from *SDFile(s)*; generate a sequential ID + with specific prefix; use combination of both MolName and + LabelPrefix with usage of LabelPrefix values for empty molname + lines. + + Possible values: *DataField | MolName | LabelPrefix | + MolNameOrLabelPrefix*. Default: *LabelPrefix*. + + For *MolNameAndLabelPrefix* value of --CompoundIDMode, molname line + in *SDFile(s)* takes precedence over sequential compound IDs + generated using *LabelPrefix* and only empty molname values are + replaced with sequential compound IDs. + + -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 *TextFile(s)* and --FingerprintsField for *SDFile(s)* are + assumed to contain valid fingerprints data and no checking is + performed before calculating similarity matrices. By default, + fingerprints data is validated before computing pairwise similarity + and distance coefficients. + + --FingerprintsCol *col number | col name* + This value is -c, --colmode specific. It specifies fingerprints + column to use during calculation similarity matrices for + *TextFile(s)*. Possible values: *col number or col label*. Default + value: *first column containing the word Fingerprints in its column + label*. + + --FingerprintsField *FieldLabel* + Fingerprints field label to use during calculation similarity + matrices for *SDFile(s)*. Default value: *first data field label + containing the word Fingerprints in its label* + + -h, --help + Print this help message. + + --InDelim *comma | semicolon* + Input delimiter for 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. + + --InputDataMode *LoadInMemory | ScanFile* + Specify how fingerprints bit-vector or vector strings data from *SD, + FP and CSV/TSV* fingerprint file(s) is processed: Retrieve, process + and load all available fingerprints data in memory; Retrieve and + process data for fingerprints one at a time. Possible values : + *LoadInMemory | ScanFile*. Default: *LoadInMemory*. + + During *LoadInMemory* value of --InputDataMode, fingerprints + bit-vector or vector strings data from input file is retrieved, + processed, and loaded into memory all at once as fingerprints + objects for generation for similarity matrices. + + During *ScanFile* value of --InputDataMode, multiple passes over the + input fingerprints file are performed to retrieve and process + fingerprints bit-vector or vector strings data one at a time to + generate fingerprints objects used during generation of similarity + matrices. A temporary copy of the input fingerprints file is made at + the start and deleted after generating the matrices. + + *ScanFile* value of --InputDataMode allows processing of arbitrary + large fingerprints files without any additional memory requirement. + + -m, --mode *AutoDetect | FingerprintsBitVectorString | + FingerprintsVectorString* + Format of fingerprint strings data in *TextFile(s)*: 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*. + + --OutDelim *comma | tab | semicolon* + Delimiter for output CSV/TSV text file(s). Possible values: *comma, + tab, or semicolon* Default value: *comma*. + + --OutMatrixFormat *RowsAndColumns | IDPairsAndValue* + Specify how similarity or distance values calculated for + fingerprints vector and bit-vector strings are written to the output + CSV/TSV text file(s): Generate text files containing rows and + columns with their labels corresponding to compound IDs and each + matrix element value corresponding to similarity or distance between + corresponding compounds; Generate text files containing rows + containing compoundIDs for two compounds followed by similarity or + distance value between these compounds. + + Possible values: *RowsAndColumns, or IDPairsAndValue*. Default + value: *RowsAndColumns*. + + The value of --OutMatrixFormat in conjunction with --OutMatrixType + determines type of data written to output files and allows + generation of up to 6 different output data formats: + + OutMatrixFormat OutMatrixType + + RowsAndColumns FullMatrix [ DEFAULT ] + RowsAndColumns UpperTriangularMatrix + RowsAndColumns LowerTriangularMatrix + + IDPairsAndValue FullMatrix + IDPairsAndValue UpperTriangularMatrix + IDPairsAndValue LowerTriangularMatrix + + Example of data in output file for *RowsAndColumns* + --OutMatrixFormat value for *FullMatrix* valueof --OutMatrixType: + + "","Cmpd1","Cmpd2","Cmpd3","Cmpd4","Cmpd5","Cmpd6",... ... + "Cmpd1","1","0.04","0.25","0.13","0.11","0.2",... ... + "Cmpd2","0.04","1","0.06","0.05","0.19","0.07",... ... + "Cmpd3","0.25","0.06","1","0.12","0.22","0.25",... ... + "Cmpd4","0.13","0.05","0.12","1","0.11","0.13",... ... + "Cmpd5","0.11","0.19","0.22","0.11","1","0.17",... ... + "Cmpd6","0.2","0.07","0.25","0.13","0.17","1",... ... + ... ... .. + ... ... .. + ... ... .. + + Example of data in output file for *RowsAndColumns* + --OutMatrixFormat value for *UpperTriangularMatrix* value of + --OutMatrixType: + + "","Cmpd1","Cmpd2","Cmpd3","Cmpd4","Cmpd5","Cmpd6",... ... + "Cmpd1","1","0.04","0.25","0.13","0.11","0.2",... ... + "Cmpd2","1","0.06","0.05","0.19","0.07",... ... + "Cmpd3","1","0.12","0.22","0.25",... ... + "Cmpd4","1","0.11","0.13",... ... + "Cmpd5","1","0.17",... ... + "Cmpd6","1",... ... + ... ... .. + ... ... .. + ... ... .. + + Example of data in output file for *RowsAndColumns* + --OutMatrixFormat value for *LowerTriangularMatrix* value of + --OutMatrixType: + + "","Cmpd1","Cmpd2","Cmpd3","Cmpd4","Cmpd5","Cmpd6",... ... + "Cmpd1","1" + "Cmpd2","0.04","1" + "Cmpd3","0.25","0.06","1" + "Cmpd4","0.13","0.05","0.12","1" + "Cmpd5","0.11","0.19","0.22","0.11","1" + "Cmpd6","0.2","0.07","0.25","0.13","0.17","1" + ... ... .. + ... ... .. + ... ... .. + + Example of data in output file for *IDPairsAndValue* + --OutMatrixFormat value for <FullMatrix> value of OutMatrixType: + + "CmpdID1","CmpdID2","Coefficient Value" + "Cmpd1","Cmpd1","1" + "Cmpd1","Cmpd2","0.04" + "Cmpd1","Cmpd3","0.25" + "Cmpd1","Cmpd4","0.13" + ... ... ... + ... ... ... + ... ... ... + "Cmpd2","Cmpd1","0.04" + "Cmpd2","Cmpd2","1" + "Cmpd2","Cmpd3","0.06" + "Cmpd2","Cmpd4","0.05" + ... ... ... + ... ... ... + ... ... ... + "Cmpd3","Cmpd1","0.25" + "Cmpd3","Cmpd2","0.06" + "Cmpd3","Cmpd3","1" + "Cmpd3","Cmpd4","0.12" + ... ... ... + ... ... ... + ... ... ... + + Example of data in output file for *IDPairsAndValue* + --OutMatrixFormat value for <UpperTriangularMatrix> value of + --OutMatrixType: + + "CmpdID1","CmpdID2","Coefficient Value" + "Cmpd1","Cmpd1","1" + "Cmpd1","Cmpd2","0.04" + "Cmpd1","Cmpd3","0.25" + "Cmpd1","Cmpd4","0.13" + ... ... ... + ... ... ... + ... ... ... + "Cmpd2","Cmpd2","1" + "Cmpd2","Cmpd3","0.06" + "Cmpd2","Cmpd4","0.05" + ... ... ... + ... ... ... + ... ... ... + "Cmpd3","Cmpd3","1" + "Cmpd3","Cmpd4","0.12" + ... ... ... + ... ... ... + ... ... ... + + Example of data in output file for *IDPairsAndValue* + --OutMatrixFormat value for <LowerTriangularMatrix> value of + --OutMatrixType: + + "CmpdID1","CmpdID2","Coefficient Value" + "Cmpd1","Cmpd1","1" + "Cmpd2","Cmpd1","0.04" + "Cmpd2","Cmpd2","1" + "Cmpd3","Cmpd1","0.25" + "Cmpd3","Cmpd2","0.06" + "Cmpd3","Cmpd3","1" + "Cmpd4","Cmpd1","0.13" + "Cmpd4","Cmpd2","0.05" + "Cmpd4","Cmpd3","0.12" + "Cmpd4","Cmpd4","1" + ... ... ... + ... ... ... + ... ... ... + + --OutMatrixType *FullMatrix | UpperTriangularMatrix | + LowerTriangularMatrix* + Type of similarity or distance matrix to calculate for fingerprints + vector and bit-vector strings: Calculate full matrix; Calculate + lower triangular matrix including diagonal; Calculate upper + triangular matrix including diagonal. + + Possible values: *FullMatrix, UpperTriangularMatrix, or + LowerTriangularMatrix*. Default value: *FullMatrix*. + + The value of --OutMatrixType in conjunction with --OutMatrixFormat + determines type of data written to output files. + + -o, --overwrite + Overwrite existing files + + -p, --precision *number* + Precision of calculated values in the output file. 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(s). + Possible values: *Yes or No*. Default value: *Yes*. + + -r, --root *RootName* + New file name is generated using the root: + <Root><BitVectorComparisonMode>.<Ext> or + <Root><VectorComparisonMode><VectorComparisonFormulism>.<Ext>. The + csv, and tsv <Ext> values are used for comma/semicolon, and tab + delimited text files respectively. This option is ignored for + multiple input files. + + -v, --VectorComparisonMode *All | + "TanimotoSimilarity,[ManhattanDistance,...]"* + Specify what similarity or distance coefficients to use for + calculating similarity matrices for fingerprint vector strings data + values in *TextFile(s)*: calculate similarity matrices for all + supported similarity and distance coefficients or specify a comma + delimited list of similarity and distance coefficients. Possible + values: *All | "TanimotoSimilairy,[ManhattanDistance,..]"*. Default: + *TanimotoSimilarity*. + + The value of -v, --VectorComparisonMode, in conjunction with + --VectorComparisonFormulism, decides which type of similarity and + distance coefficient formulism gets used. + + *All* uses complete list of supported 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 *All | + "AlgebraicForm,[BinaryForm,SetTheoreticForm]"* + Specify fingerprints vector comparison formulism to use for + calculation similarity and distance coefficients during -v, + --VectorComparisonMode: use all supported comparison formulisms or + specify a comma delimited. Possible values: *All | + "AlgebraicForm,[BinaryForm,SetTheoreticForm]"*. Default value: + *AlgebraicForm*. + + *All* uses all three forms of supported vector comparison formulism + for values of -v, --VectorComparisonMode option. + + 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 generate a similarity matrix corresponding to Tanimoto similarity + coefficient for fingerprints bit-vector strings data corresponding to + supported fingerprints in text file present in a column name containing + Fingerprint substring by loading all fingerprints data into memory and + create a SampleFPHexTanimotoSimilarity.csv file containing compound IDs + retrieved from column name containing CompoundID substring, type: + + % SimilarityMatricesFingerprints.pl -o SampleFPHex.csv + + To generate a similarity matrix corresponding to Tanimoto similarity + coefficient for fingerprints bit-vector strings data corresponding to + supported fingerprints in SD File present in a data field with + Fingerprint substring in its label by loading all fingerprints data into + memory and create a SampleFPHexTanimotoSimilarity.csv file containing + sequentially generated compound IDs with Cmpd prefix, type: + + % SimilarityMatricesFingerprints.pl -o SampleFPHex.sdf + + To generate a similarity matrix corresponding to Tanimoto similarity + coefficient for fingerprints bit-vector strings data corresponding to + supported fingerprints in FP file by loading all fingerprints data into + memory and create a SampleFPHexTanimotoSimilarity.csv file along with + compound IDs retrieved from FP file, type: + + % SimilarityMatricesFingerprints.pl -o SampleFPHex.fpf + + To generate a lower triangular similarity matrix corresponding to + Tanimoto similarity coefficient for fingerprints bit-vector strings data + corresponding to supported fingerprints in text file present in a column + name containing Fingerprint substring by loading all fingerprints data + into memory and create a SampleFPHexTanimotoSimilarity.csv file + containing compound IDs retrieved from column name containing CompoundID + substring, type: + + % SimilarityMatricesFingerprints.pl -o --InputDataMode LoadInMemory + --OutMatrixFormat RowsAndColumns --OutMatrixType LowerTriangularMatrix + SampleFPHex.csv + + To generate a upper triangular similarity matrix corresponding to + Tanimoto similarity coefficient for fingerprints bit-vector strings data + corresponding to supported fingerprints in text file present in a column + name containing Fingerprint substring by loading all fingerprints data + into memory and create a SampleFPHexTanimotoSimilarity.csv file in + IDPairsAndValue format containing compound IDs retrieved from column + name containing CompoundID substring, type: + + % SimilarityMatricesFingerprints.pl -o --InputDataMode LoadInMemory + --OutMatrixFormat IDPairsAndValue --OutMatrixType UpperTriangularMatrix + SampleFPHex.csv + + To generate a full similarity matrix corresponding to Tanimoto + similarity coefficient for fingerprints bit-vector strings data + corresponding to supported fingerprints in text file present in a column + name containing Fingerprint substring by scanning file without loading + all fingerprints data into memory and create a + SampleFPHexTanimotoSimilarity.csv file containing compound IDs retrieved + from column name containing CompoundID substring, type: + + % SimilarityMatricesFingerprints.pl -o --InputDataMode ScanFile + --OutMatrixFormat RowsAndColumns --OutMatrixType FullMatrix + SampleFPHex.csv + + To generate a lower triangular similarity matrix corresponding to + Tanimoto similarity coefficient for fingerprints bit-vector strings data + corresponding to supported fingerprints in text file present in a column + name containing Fingerprint substring by scanning file without loading + all fingerprints data into memory and create a + SampleFPHexTanimotoSimilarity.csv file in IDPairsAndValue format + containing compound IDs retrieved from column name containing CompoundID + substring, type: + + % SimilarityMatricesFingerprints.pl -o --InputDataMode ScanFile + --OutMatrixFormat IDPairsAndValue --OutMatrixType LowerTriangularMatrix + SampleFPHex.csv + + To generate a similarity matrix corresponding to Tanimoto similarity + coefficient using algebraic formulism for fingerprints vector strings + data corresponding to supported fingerprints in text file present in a + column name containing Fingerprint substring and create a + SampleFPCountTanimotoSimilarityAlgebraicForm.csv file containing + compound IDs retrieved from column name containing CompoundID substring, + type: + + % SimilarityMatricesFingerprints.pl -o SampleFPCount.csv + + To generate a similarity matrix corresponding to Tanimoto similarity + coefficient using algebraic formulism for fingerprints vector strings + data corresponding to supported fingerprints in SD file present in a + data field with Fingerprint substring in its label and create a + SampleFPCountTanimotoSimilarityAlgebraicForm.csv file containing + sequentially generated compound IDs with Cmpd prefix, type: + + % SimilarityMatricesFingerprints.pl -o SampleFPCount.sdf + + To generate a similarity matrix corresponding to Tanimoto similarity + coefficient using algebraic formulism vector strings data corresponding + to supported fingerprints in FP file and create a + SampleFPCountTanimotoSimilarityAlgebraicForm.csv file along with + compound IDs retrieved from FP file, type: + + % SimilarityMatricesFingerprints.pl -o SampleFPCount.fpf + + To generate a similarity matrix corresponding to Tanimoto similarity + coefficient for fingerprints bit-vector strings data corresponding to + supported fingerprints in text file present in a column name containing + Fingerprint substring and create a SampleFPHexTanimotoSimilarity.csv + file in IDPairsAndValue format containing compound IDs retrieved from + column name containing CompoundID substring, type: + + % SimilarityMatricesFingerprints.pl --OutMatrixFormat IDPairsAndValue -o + SampleFPHex.csv + + To generate a similarity matrix corresponding to Tanimoto similarity + coefficient for fingerprints bit-vector strings data corresponding to + supported fingerprints in SD file present in a data field with + Fingerprint substring in its label and create a + SampleFPHexTanimotoSimilarity.csv file in IDPairsAndValue format + containing sequentially generated compound IDs with Cmpd prefix, type: + + % SimilarityMatricesFingerprints.pl --OutMatrixFormat IDPairsAndValue -o + SampleFPHex.sdf + + To generate a similarity matrix corresponding to Tanimoto similarity + coefficient for fingerprints bit-vector strings data corresponding to + supported fingerprints in FP file and create a + SampleFPHexTanimotoSimilarity.csv file in IDPairsAndValue format along + with compound IDs retrieved from FP file, type: + + % SimilarityMatricesFingerprints.pl --OutMatrixFormat IDPairsAndValue -o + SampleFPHex.fpf + + To generate a similarity matrix corresponding to Tanimoto similarity + coefficient for fingerprints bit-vector strings data corresponding to + supported fingerprints in SD file present in a data field with + Fingerprint substring in its label and create a + SampleFPHexTanimotoSimilarity.csv file containing compound IDs from mol + name line, type: + + % SimilarityMatricesFingerprints.pl --CompoundIDMode MolName -o + SampleFPHex.sdf + + To generate a similarity matrix corresponding to Tanimoto similarity + coefficient for fingerprints bit-vector strings data corresponding to + supported fingerprints present in a data field with Fingerprint + substring in its label and create a SampleFPHexTanimotoSimilarity.csv + file containing compound IDs from data field name Mol_ID, type: + + % SimilarityMatricesFingerprints.pl --CompoundIDMode DataField + --CompoundIDField Mol_ID -o SampleFPBin.sdf + + To generate similarity matrices corresponding to Buser, Dice and + Tanimoto similarity coefficient for fingerprints bit-vector strings data + corresponding to supported fingerprints present in a column name + containing Fingerprint substring and create + SampleFPBin[CoefficientName]Similarity.csv files containing compound IDs + retrieved from column name containing CompoundID substring, type: + + % SimilarityMatricesFingerprints.pl -b "BuserSimilarity,DiceSimilarity, + TanimotoSimilarity" -o SampleFPBin.csv + + To generate similarity matrices corresponding to Buser, Dice and + Tanimoto similarity coefficient for fingerprints bit-vector strings data + corresponding to supported fingerprints present in a data field with + Fingerprint substring in its label and create + SampleFPBin[CoefficientName]Similarity.csv files containing sequentially + generated compound IDs with Cmpd prefix, type: + + % SimilarityMatricesFingerprints.pl -b "BuserSimilarity,DiceSimilarity, + TanimotoSimilarity" -o SampleFPBin.sdf + + To generate similarity matrices corresponding to CityBlock distance and + Tanimoto similarity coefficients using algebraic formulism for + fingerprints vector strings data corresponding to supported fingerprints + present in a column name containing Fingerprint substring and create + SampleFPCount[CoefficientName]AlgebraicForm.csv files containing + compound IDs retrieved from column name containing CompoundID substring, + type: + + % SimilarityMatricesFingerprints.pl -v "CityBlockDistance, + TanimotoSimilarity" -o SampleFPCount.csv + + To generate similarity matrices corresponding to CityBlock distance and + Tanimoto similarity coefficients using algebraic formulism for + fingerprints vector strings data corresponding to supported fingerprints + present in a data field with Fingerprint substring in its label and + create SampleFPCount[CoefficientName]AlgebraicForm.csv files containing + sequentially generated compound IDs with Cmpd prefix, type: + + % SimilarityMatricesFingerprints.pl -v "CityBlockDistance, + TanimotoSimilarity" -o SampleFPCount.sdf + + To generate similarity matrices corresponding to CityBlock distance + Tanimoto similarity coefficients using binary formulism for fingerprints + vector strings data corresponding to supported fingerprints present in a + column name containing Fingerprint substring and create + SampleFPCount[CoefficientName]Binary.csv files containing compound IDs + retrieved from column name containing CompoundID substring, type: + + % SimilarityMatricesFingerprints.pl -v "CityBlockDistance, + TanimotoSimilarity" --VectorComparisonFormulism BinaryForm -o + SampleFPCount.csv + + To generate similarity matrices corresponding to CityBlock distance + Tanimoto similarity coefficients using binary formulism for fingerprints + vector strings data corresponding to supported fingerprints present in a + data field with Fingerprint substring in its label and create + SampleFPCount[CoefficientName]Binary.csv files containing sequentially + generated compound IDs with Cmpd prefix, type: + + % SimilarityMatricesFingerprints.pl -v "CityBlockDistance, + TanimotoSimilarity" --VectorComparisonFormulism BinaryForm -o + SampleFPCount.sdf + + To generate similarity matrices corresponding to CityBlock distance + Tanimoto similarity coefficients using all supported comparison + formulisms for fingerprints vector strings data corresponding to + supported fingerprints present in a column name containing Fingerprint + substring and create SampleFPCount[CoefficientName][FormulismName].csv + files containing compound IDs retrieved from column name containing + CompoundID substring, type: + + % SimilarityMatricesFingerprints.pl -v "CityBlockDistance, + TanimotoSimilarity" --VectorComparisonFormulism All -o SampleFPCount.csv + + To generate similarity matrices corresponding to CityBlock distance + Tanimoto similarity coefficients using all supported comparison + formulisms for fingerprints vector strings data corresponding to + supported fingerprints present in a data field with Fingerprint + substring in its label and create + SampleFPCount[CoefficientName][FormulismName].csv files containing + sequentially generated compound IDs with Cmpd prefix, type: + + % SimilarityMatricesFingerprints.pl -v "CityBlockDistance,TanimotoSimilarity" + --VectorComparisonFormulism All -o SampleFPCount.sdf + + To generate similarity matrices corresponding to all available + similarity coefficient for fingerprints bit-vector strings data + corresponding to supported fingerprints present in a column name + containing Fingerprint substring and create + SampleFPHex[CoefficientName].csv files containing compound IDs retrieved + from column name containing CompoundID substring, type: + + % SimilarityMatricesFingerprints.pl -m AutoDetect --BitVectorComparisonMode + All --alpha 0.5 -beta 0.5 -o SampleFPHex.csv + + To generate similarity matrices corresponding to all available + similarity coefficient for fingerprints bit-vector strings data + corresponding to supported fingerprints present in a data field with + Fingerprint substring in its label and create + SampleFPHex[CoefficientName].csv files containing sequentially generated + compound IDs with Cmpd prefix, type + + % SimilarityMatricesFingerprints.pl -m AutoDetect --BitVectorComparisonMode + All --alpha 0.5 -beta 0.5 -o SampleFPHex.sdf + + To generate similarity matrices corresponding to all available + similarity and distance coefficients using all comparison formulism for + fingerprints vector strings data corresponding to supported fingerprints + present in a column name containing Fingerprint substring and create + SampleFPCount[CoefficientName][FormulismName].csv files containing + compound IDs retrieved from column name containing CompoundID substring, + type: + + % SimilarityMatricesFingerprints.pl -m AutoDetect --VectorComparisonMode + All --VectorComparisonFormulism All -o SampleFPCount.csv + + To generate similarity matrices corresponding to all available + similarity and distance coefficients using all comparison formulism for + fingerprints vector strings data corresponding to supported fingerprints + present in a data field with Fingerprint substring in its label and + create SampleFPCount[CoefficientName][FormulismName].csv files + containing sequentially generated compound IDs with Cmpd prefix, type: + + % SimilarityMatricesFingerprints.pl -m AutoDetect --VectorComparisonMode + All --VectorComparisonFormulism All -o SampleFPCount.sdf + + To generate a similarity matrix corresponding to Tanimoto similarity + coefficient for fingerprints bit-vector strings data corresponding to + supported fingerprints present in a column number 2 and create a + SampleFPHexTanimotoSimilarity.csv file containing compound IDs retrieved + column number 1, type: + + % SimilarityMatricesFingerprints.pl --ColMode ColNum --CompoundIDCol 1 + --FingerprintsCol 2 -o SampleFPHex.csv + + To generate a similarity matrix corresponding to Tanimoto similarity + coefficient for fingerprints bit-vector strings data corresponding to + supported fingerprints present in a data field name Fingerprints and + create a SampleFPHexTanimotoSimilarity.csv file containing compound IDs + present in data field name Mol_ID, type: + + % SimilarityMatricesFingerprints.pl --FingerprintsField Fingerprints + --CompoundIDMode DataField --CompoundIDField Mol_ID -o SampleFPHex.sdf + + To generate a similarity matrix corresponding to Tversky similarity + coefficient for fingerprints bit-vector strings data corresponding to + supported fingerprints present in a column named Fingerprints and create + a SampleFPHexTverskySimilarity.tsv file containing compound IDs + retrieved column named CompoundID, type: + + % SimilarityMatricesFingerprints.pl --BitVectorComparisonMode + TverskySimilarity --alpha 0.5 --ColMode ColLabel --CompoundIDCol + CompoundID --FingerprintsCol Fingerprints --OutDelim Tab --quote No + -o SampleFPHex.csv + + To generate a similarity matrix corresponding to Tanimoto similarity + coefficient for fingerprints bit-vector strings data corresponding to + supported fingerprints present in a data field with Fingerprint + substring in its label and create a SampleFPHexTanimotoSimilarity.csv + file containing compound IDs from molname line or sequentially generated + compound IDs with Mol prefix, type: + + % SimilarityMatricesFingerprints.pl --CompoundIDMode MolnameOrLabelPrefix + --CompoundIDPrefix Mol -o SampleFPHex.sdf + + To generate a similarity matrix corresponding to Tanimoto similarity + coefficient for fingerprints bit-vector strings data corresponding to + supported fingerprints present in a data field with Fingerprint + substring in its label and create a SampleFPHexTanimotoSimilarity.tsv + file containing sequentially generated compound IDs with Cmpd prefix, + type: + + % SimilarityMatricesFingerprints.pl -OutDelim Tab --quote No -o SampleFPHex.sdf + +AUTHOR + Manish Sud <msud@san.rr.com> + +SEE ALSO + InfoFingerprintsFiles.pl, SimilaritySearchingFingerprints.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. +