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| author | deepakjadmin |
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| 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/man1/SimilarityMatricesFingerprints.1 Wed Jan 20 09:23:18 2016 -0500 @@ -0,0 +1,1424 @@ +.\" Automatically generated by Pod::Man 2.25 (Pod::Simple 3.22) +.\" +.\" Standard preamble: +.\" ======================================================================== +.de Sp \" Vertical space (when we can't use .PP) +.if t .sp .5v +.if n .sp +.. +.de Vb \" Begin verbatim text +.ft CW +.nf +.ne \\$1 +.. +.de Ve \" End verbatim text +.ft R +.fi +.. +.\" Set up some character translations and predefined strings. \*(-- will +.\" give an unbreakable dash, \*(PI will give pi, \*(L" will give a left +.\" double quote, and \*(R" will give a right double quote. \*(C+ will +.\" give a nicer C++. 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Always turn off hyphenation; it makes +.\" way too many mistakes in technical documents. +.if n .ad l +.nh +.SH "NAME" +SimilarityMatricesFingerprints.pl \- Calculate similarity matrices using fingerprints strings data in SD, FP and CSV/TSV text file(s) +.SH "SYNOPSIS" +.IX Header "SYNOPSIS" +SimilarityMatricesFingerprints.pl SDFile(s) FPFile(s) TextFile(s)... +.PP +SimilarityMatricesFingerprints.pl [\fB\-\-alpha\fR \fInumber\fR] [\fB\-\-beta\fR \fInumber\fR] +[\fB\-b, \-\-BitVectorComparisonMode\fR \fIAll | \*(L"TanimotoSimilarity,[ TverskySimilarity, ... ]\*(R"\fR] +[\fB\-c, \-\-ColMode\fR \fIColNum | ColLabel\fR] [\fB\-\-CompoundIDCol\fR \fIcol number | col name\fR] +[\fB\-\-CompoundIDPrefix\fR \fItext\fR] [\fB\-\-CompoundIDField\fR \fIDataFieldName\fR] +[\fB\-\-CompoundIDMode\fR \fIDataField | MolName | LabelPrefix | MolNameOrLabelPrefix\fR] +[\fB\-d, \-\-detail\fR \fIInfoLevel\fR] [\fB\-f, \-\-fast\fR] [\fB\-\-FingerprintsCol\fR \fIcol number | col name\fR] +[\fB\-\-FingerprintsField\fR \fIFieldLabel\fR] [\fB\-h, \-\-help\fR] [\fB\-\-InDelim\fR \fIcomma | semicolon\fR] +[\fB\-\-InputDataMode\fR \fILoadInMemory | ScanFile\fR] +[\fB\-m, \-\-mode\fR \fIAutoDetect | FingerprintsBitVectorString | FingerprintsVectorString\fR] +[\fB\-\-OutDelim\fR \fIcomma | tab | semicolon\fR] [\fB\-\-OutMatrixFormat\fR \fIRowsAndColumns | IDPairsAndValue\fR] +[\fB\-\-OutMatrixType\fR \fIFullMatrix | UpperTriangularMatrix | LowerTriangularMatrix\fR] +[\fB\-o, \-\-overwrite\fR] [\fB\-p, \-\-precision\fR \fInumber\fR] +[\fB\-q, \-\-quote\fR \fIYes | No\fR] [\fB\-r, \-\-root\fR \fIRootName\fR] +[\fB\-v, \-\-VectorComparisonMode\fR \fIAll | \*(L"TanimotoSimilairy, [ ManhattanDistance, ...]\*(R"\fR] +[\fB\-\-VectorComparisonFormulism\fR \fIAll | \*(L"AlgebraicForm, [BinaryForm, SetTheoreticForm]\*(R"\fR] +[\fB\-w, \-\-WorkingDir\fR dirname] SDFile(s) FPFile(s) TextFile(s)... +.SH "DESCRIPTION" +.IX Header "DESCRIPTION" +Calculate similarity matrices using fingerprint bit-vector or vector strings data in \fI\s-1SD\s0, \s-1FP\s0 +and \s-1CSV/TSV\s0\fR text file(s) and generate \s-1CSV/TSV\s0 text file(s) containing values for specified +similarity and distance coefficients. +.PP +The scripts SimilarityMatrixSDFiles.pl and SimilarityMatrixTextFiles.pl have been removed from the +current release of MayaChemTools and their functionality merged with this script. +.PP +The valid \fISDFile\fR extensions are \fI.sdf\fR and \fI.sd\fR. All \s-1SD\s0 files in a current directory +can be specified either by \fI*.sdf\fR or the current directory name. +.PP +The valid \fIFPFile\fR extensions are \fI.fpf\fR and \fI.fp\fR. All \s-1FP\s0 files in a current directory +can be specified either by \fI*.fpf\fR or the current directory name. +.PP +The valid \fITextFile\fR extensions are \fI.csv\fR and \fI.tsv\fR 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 \fI*.csv\fR, \fI*.tsv\fR, or the current directory +name. The \fB\-\-indelim\fR option determines the format of \fITextFile(s)\fR. Any file +which doesn't correspond to the format indicated by \fB\-\-indelim\fR option is ignored. +.PP +Example of \fI\s-1FP\s0\fR file containing fingerprints bit-vector string data: +.PP +.Vb 10 +\& # +\& # 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... +\& ... ... +\& ... .. +.Ve +.PP +Example of \fI\s-1FP\s0\fR file containing fingerprints vector string data: +.PP +.Vb 10 +\& # +\& # 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 ... +\& ... ... +\& ... ... +.Ve +.PP +Example of \fI\s-1SD\s0\fR file containing fingerprints bit-vector string data: +.PP +.Vb 10 +\& ... ... +\& ... ... +\& $$$$ +\& ... ... +\& ... ... +\& ... ... +\& 41 44 0 0 0 0 0 0 0 0999 V2000 +\& \-3.3652 1.4499 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 +\& ... ... +\& 2 3 1 0 0 0 0 +\& ... ... +\& M END +\& > <CmpdID> +\& Cmpd1 +\& +\& > <PathLengthFingerprints> +\& FingerprintsBitVector;PathLengthBits:AtomicInvariantsAtomTypes:MinLengt +\& h1:MaxLength8;1024;HexadecimalString;Ascending;9c8460989ec8a49913991a66 +\& 03130b0a19e8051c89184414953800cc2151082844a201042800130860308e8204d4028 +\& 00831048940e44281c00060449a5000ac80c894114e006321264401600846c050164462 +\& 08190410805000304a10205b0100e04c0038ba0fad0209c0ca8b1200012268b61c0026a +\& aa0660a11014a011d46 +\& +\& $$$$ +\& ... ... +\& ... ... +.Ve +.PP +Example of \s-1CSV\s0 \fIText\fR file containing fingerprints bit-vector string data: +.PP +.Vb 7 +\& "CompoundID","PathLengthFingerprints" +\& "Cmpd1","FingerprintsBitVector;PathLengthBits:AtomicInvariantsAtomTypes +\& :MinLength1:MaxLength8;1024;HexadecimalString;Ascending;9c8460989ec8a4 +\& 9913991a6603130b0a19e8051c89184414953800cc2151082844a20104280013086030 +\& 8e8204d402800831048940e44281c00060449a5000ac80c894114e006321264401..." +\& ... ... +\& ... ... +.Ve +.PP +The current release of MayaChemTools supports the following types of fingerprint +bit-vector and vector strings: +.PP +.Vb 6 +\& 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 ... +.Ve +.SH "OPTIONS" +.IX Header "OPTIONS" +.IP "\fB\-\-alpha\fR \fInumber\fR" 4 +.IX Item "--alpha number" +Value of alpha parameter for calculating \fITversky\fR similarity coefficient specified for +\&\fB\-b, \-\-BitVectorComparisonMode\fR option. It corresponds to weights assigned for bits set +to \*(L"1\*(R" in a pair of fingerprint bit-vectors during the calculation of similarity coefficient. Possible +values: \fI0 to 1\fR. Default value: <0.5>. +.IP "\fB\-\-beta\fR \fInumber\fR" 4 +.IX Item "--beta number" +Value of beta parameter for calculating \fIWeightedTanimoto\fR and \fIWeightedTversky\fR +similarity coefficients specified for \fB\-b, \-\-BitVectorComparisonMode\fR option. It is used to +weight the contributions of bits set to \*(L"0\*(R" during the calculation of similarity coefficients. Possible +values: \fI0 to 1\fR. Default value of <1> makes \fIWeightedTanimoto\fR and \fIWeightedTversky\fR +equivalent to \fITanimoto\fR and \fITversky\fR. +.ie n .IP "\fB\-b, \-\-BitVectorComparisonMode\fR \fIAll | ""TanimotoSimilarity,[TverskySimilarity,...]""\fR" 4 +.el .IP "\fB\-b, \-\-BitVectorComparisonMode\fR \fIAll | ``TanimotoSimilarity,[TverskySimilarity,...]''\fR" 4 +.IX Item "-b, --BitVectorComparisonMode All | TanimotoSimilarity,[TverskySimilarity,...]" +Specify what similarity coefficients to use for calculating similarity matrices for fingerprints bit-vector +strings data values in \fITextFile(s)\fR: calculate similarity matrices for all supported similarity +coefficients or specify a comma delimited list of similarity coefficients. Possible values: +\&\fIAll | "TanimotoSimilarity,[TverskySimilarity,...]\fR. Default: \fITanimotoSimilarity\fR +.Sp +\&\fIAll\fR uses complete list of supported similarity coefficients: \fIBaroniUrbaniSimilarity, 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\fR. These similarity coefficients are described below. +.Sp +For two fingerprint bit-vectors A and B of same size, let: +.Sp +.Vb 4 +\& 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 +.Ve +.Sp +Then, various similarity coefficients [ Ref. 40 \- 42 ] for a pair of bit-vectors A and B are +defined as follows: +.Sp +\&\fIBaroniUrbaniSimilarity\fR: ( \s-1SQRT\s0( Nc * Nd ) + Nc ) / ( \s-1SQRT\s0 ( Nc * Nd ) + Nc + ( Na \- Nc ) + ( Nb \- Nc ) ) ( same as Buser ) +.Sp +\&\fIBuserSimilarity\fR: ( \s-1SQRT\s0 ( Nc * Nd ) + Nc ) / ( \s-1SQRT\s0 ( Nc * Nd ) + Nc + ( Na \- Nc ) + ( Nb \- Nc ) ) ( same as BaroniUrbani ) +.Sp +\&\fICosineSimilarity\fR: Nc / \s-1SQRT\s0 ( Na * Nb ) (same as Ochiai) +.Sp +\&\fIDiceSimilarity\fR: (2 * Nc) / ( Na + Nb ) +.Sp +\&\fIDennisSimilarity\fR: ( Nc * Nd \- ( ( Na \- Nc ) * ( Nb \- Nc ) ) ) / \s-1SQRT\s0 ( Nt * Na * Nb) +.Sp +\&\fIForbesSimilarity\fR: ( Nt * Nc ) / ( Na * Nb ) +.Sp +\&\fIFossumSimilarity\fR: ( Nt * ( ( Nc \- 1/2 ) ** 2 ) / ( Na * Nb ) +.Sp +\&\fIHamannSimilarity\fR: ( ( Nc + Nd ) \- ( Na \- Nc ) \- ( Nb \- Nc ) ) / Nt +.Sp +\&\fIJaccardSimilarity\fR: Nc / ( ( Na \- Nc) + ( Nb \- Nc ) + Nc ) = Nc / ( Na + Nb \- Nc ) (same as Tanimoto) +.Sp +\&\fIKulczynski1Similarity\fR: Nc / ( ( Na \- Nc ) + ( Nb \- Nc) ) = Nc / ( Na + Nb \- 2Nc ) +.Sp +\&\fIKulczynski2Similarity\fR: ( ( Nc / 2 ) * ( 2 * Nc + ( Na \- Nc ) + ( Nb \- Nc) ) ) / ( ( Nc + ( Na \- Nc ) ) * ( Nc + ( Nb \- Nc ) ) ) = 0.5 * ( Nc / Na + Nc / Nb ) +.Sp +\&\fIMatchingSimilarity\fR: ( Nc + Nd ) / Nt +.Sp +\&\fIMcConnaugheySimilarity\fR: ( Nc ** 2 \- ( Na \- Nc ) * ( Nb \- Nc) ) / ( Na * Nb ) +.Sp +\&\fIOchiaiSimilarity\fR: Nc / \s-1SQRT\s0 ( Na * Nb ) (same as Cosine) +.Sp +\&\fIPearsonSimilarity\fR: ( ( Nc * Nd ) \- ( ( Na \- Nc ) * ( Nb \- Nc ) ) / \s-1SQRT\s0 ( Na * Nb * ( Na \- Nc + Nd ) * ( Nb \- Nc + Nd ) ) +.Sp +\&\fIRogersTanimotoSimilarity\fR: ( Nc + Nd ) / ( ( Na \- Nc) + ( Nb \- Nc) + Nt) = ( Nc + Nd ) / ( Na + Nb \- 2Nc + Nt) +.Sp +\&\fIRussellRaoSimilarity\fR: Nc / Nt +.Sp +\&\fISimpsonSimilarity\fR: Nc / \s-1MIN\s0 ( Na, Nb) +.Sp +\&\fISkoalSneath1Similarity\fR: Nc / ( Nc + 2 * ( Na \- Nc) + 2 * ( Nb \- Nc) ) = Nc / ( 2 * Na + 2 * Nb \- 3 * Nc ) +.Sp +\&\fISkoalSneath2Similarity\fR: ( 2 * Nc + 2 * Nd ) / ( Nc + Nd + Nt ) +.Sp +\&\fISkoalSneath3Similarity\fR: ( Nc + Nd ) / ( ( Na \- Nc ) + ( Nb \- Nc ) ) = ( Nc + Nd ) / ( Na + Nb \- 2 * Nc ) +.Sp +\&\fITanimotoSimilarity\fR: Nc / ( ( Na \- Nc) + ( Nb \- Nc ) + Nc ) = Nc / ( Na + Nb \- Nc ) (same as Jaccard) +.Sp +\&\fITverskySimilarity\fR: Nc / ( alpha * ( Na \- Nc ) + ( 1 \- alpha) * ( Nb \- Nc) + Nc ) = Nc / ( alpha * ( Na \- Nb ) + Nb) +.Sp +\&\fIYuleSimilarity\fR: ( ( Nc * Nd ) \- ( ( Na \- Nc ) * ( Nb \- Nc ) ) ) / ( ( Nc * Nd ) + ( ( Na \- Nc ) * ( Nb \- Nc ) ) ) +.Sp +Values of Tanimoto/Jaccard and Tversky coefficients are dependent on only those bit which +are set to \*(L"1\*(R" 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. +.Sp +Let: +.Sp +.Vb 3 +\& Na\*(Aq = Number of bits set to "0" in A +\& Nb\*(Aq = Number of bits set to "0" in B +\& Nc\*(Aq = Number of bits set to "0" in both A and B +.Ve +.Sp +Tanimoto': Nc' / ( ( Na' \- Nc') + ( Nb' \- Nc' ) + Nc' ) = Nc' / ( Na' + Nb' \- Nc' ) +.Sp +Tversky': Nc' / ( alpha * ( Na' \- Nc' ) + ( 1 \- alpha) * ( Nb' \- Nc' ) + Nc' ) = Nc' / ( alpha * ( Na' \- Nb' ) + Nb') +.Sp +Then: +.Sp +\&\fIWeightedTanimotoSimilarity\fR = beta * Tanimoto + (1 \- beta) * Tanimoto' +.Sp +\&\fIWeightedTverskySimilarity\fR = beta * Tversky + (1 \- beta) * Tversky' +.IP "\fB\-c, \-\-ColMode\fR \fIColNum | ColLabel\fR" 4 +.IX Item "-c, --ColMode ColNum | ColLabel" +Specify how columns are identified in \fITextFile(s)\fR: using column number or column +label. Possible values: \fIColNum or ColLabel\fR. Default value: \fIColNum\fR. +.IP "\fB\-\-CompoundIDCol\fR \fIcol number | col name\fR" 4 +.IX Item "--CompoundIDCol col number | col name" +This value is \fB\-c, \-\-ColMode\fR mode specific. It specifies input \fITextFile(s)\fR column to use for +generating compound \s-1ID\s0 for similarity matrices in output \fITextFile(s)\fR. Possible values: \fIcol number +or col label\fR. Default value: \fIfirst column containing the word compoundID in its column label or sequentially +generated IDs\fR. +.IP "\fB\-\-CompoundIDPrefix\fR \fItext\fR" 4 +.IX Item "--CompoundIDPrefix text" +Specify compound \s-1ID\s0 prefix to use during sequential generation of compound IDs for input \fISDFile(s)\fR +and \fITextFile(s)\fR. Default value: \fICmpd\fR. The default value generates compound IDs which look +like Cmpd<Number>. +.Sp +For input \fISDFile(s)\fR, this value is only used during \fILabelPrefix | MolNameOrLabelPrefix\fR values +of \fB\-\-CompoundIDMode\fR option; otherwise, it's ignored. +.Sp +Examples for \fILabelPrefix\fR or \fIMolNameOrLabelPrefix\fR value of \fB\-\-CompoundIDMode\fR: +.Sp +.Vb 1 +\& Compound +.Ve +.Sp +The values specified above generates compound IDs which correspond to Compound<Number> +instead of default value of Cmpd<Number>. +.IP "\fB\-\-CompoundIDField\fR \fIDataFieldName\fR" 4 +.IX Item "--CompoundIDField DataFieldName" +Specify input \fISDFile(s)\fR datafield label for generating compound IDs. This value is only used +during \fIDataField\fR value of \fB\-\-CompoundIDMode\fR option. +.Sp +Examples for \fIDataField\fR value of \fB\-\-CompoundIDMode\fR: +.Sp +.Vb 2 +\& MolID +\& ExtReg +.Ve +.IP "\fB\-\-CompoundIDMode\fR \fIDataField | MolName | LabelPrefix | MolNameOrLabelPrefix\fR" 4 +.IX Item "--CompoundIDMode DataField | MolName | LabelPrefix | MolNameOrLabelPrefix" +Specify how to generate compound IDs from input \fISDFile(s)\fR for similarity matrix \s-1CSV/TSV\s0 text +file(s): use a \fISDFile(s)\fR datafield value; use molname line from \fISDFile(s)\fR; generate a sequential \s-1ID\s0 +with specific prefix; use combination of both MolName and LabelPrefix with usage of LabelPrefix values +for empty molname lines. +.Sp +Possible values: \fIDataField | MolName | LabelPrefix | MolNameOrLabelPrefix\fR. +Default: \fILabelPrefix\fR. +.Sp +For \fIMolNameAndLabelPrefix\fR value of \fB\-\-CompoundIDMode\fR, molname line in \fISDFile(s)\fR takes +precedence over sequential compound IDs generated using \fILabelPrefix\fR and only empty molname +values are replaced with sequential compound IDs. +.IP "\fB\-d, \-\-detail\fR \fIInfoLevel\fR" 4 +.IX Item "-d, --detail InfoLevel" +Level of information to print about lines being ignored. Default: \fI1\fR. Possible values: +\&\fI1, 2 or 3\fR. +.IP "\fB\-f, \-\-fast\fR" 4 +.IX Item "-f, --fast" +In this mode, fingerprints columns specified using \fB\-\-FingerprintsCol\fR for \fITextFile(s)\fR and +\&\fB\-\-FingerprintsField\fR for \fISDFile(s)\fR 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. +.IP "\fB\-\-FingerprintsCol\fR \fIcol number | col name\fR" 4 +.IX Item "--FingerprintsCol col number | col name" +This value is \fB\-c, \-\-colmode\fR specific. It specifies fingerprints column to use during +calculation similarity matrices for \fITextFile(s)\fR. Possible values: \fIcol number or col label\fR. +Default value: \fIfirst column containing the word Fingerprints in its column label\fR. +.IP "\fB\-\-FingerprintsField\fR \fIFieldLabel\fR" 4 +.IX Item "--FingerprintsField FieldLabel" +Fingerprints field label to use during calculation similarity matrices for \fISDFile(s)\fR. +Default value: \fIfirst data field label containing the word Fingerprints in its label\fR +.IP "\fB\-h, \-\-help\fR" 4 +.IX Item "-h, --help" +Print this help message. +.IP "\fB\-\-InDelim\fR \fIcomma | semicolon\fR" 4 +.IX Item "--InDelim comma | semicolon" +Input delimiter for \s-1CSV\s0 \fITextFile(s)\fR. Possible values: \fIcomma or semicolon\fR. +Default value: \fIcomma\fR. For \s-1TSV\s0 files, this option is ignored and \fItab\fR is used as a +delimiter. +.IP "\fB\-\-InputDataMode\fR \fILoadInMemory | ScanFile\fR" 4 +.IX Item "--InputDataMode LoadInMemory | ScanFile" +Specify how fingerprints bit-vector or vector strings data from \fI\s-1SD\s0, \s-1FP\s0 and \s-1CSV/TSV\s0\fR +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 +: \fILoadInMemory | ScanFile\fR. Default: \fILoadInMemory\fR. +.Sp +During \fILoadInMemory\fR value of \fB\-\-InputDataMode\fR, 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. +.Sp +During \fIScanFile\fR value of \fB\-\-InputDataMode\fR, 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. +.Sp +\&\fIScanFile\fR value of \fB\-\-InputDataMode\fR allows processing of arbitrary large fingerprints files +without any additional memory requirement. +.IP "\fB\-m, \-\-mode\fR \fIAutoDetect | FingerprintsBitVectorString | FingerprintsVectorString\fR" 4 +.IX Item "-m, --mode AutoDetect | FingerprintsBitVectorString | FingerprintsVectorString" +Format of fingerprint strings data in \fITextFile(s)\fR: automatically detect format of fingerprints +string created by MayaChemTools fingerprints generation scripts or explicitly specify its format. +Possible values: \fIAutoDetect | FingerprintsBitVectorString | FingerprintsVectorString\fR. Default +value: \fIAutoDetect\fR. +.IP "\fB\-\-OutDelim\fR \fIcomma | tab | semicolon\fR" 4 +.IX Item "--OutDelim comma | tab | semicolon" +Delimiter for output \s-1CSV/TSV\s0 text file(s). Possible values: \fIcomma, tab, or semicolon\fR +Default value: \fIcomma\fR. +.IP "\fB\-\-OutMatrixFormat\fR \fIRowsAndColumns | IDPairsAndValue\fR" 4 +.IX Item "--OutMatrixFormat RowsAndColumns | IDPairsAndValue" +Specify how similarity or distance values calculated for fingerprints vector and bit-vector strings +are written to the output \s-1CSV/TSV\s0 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. +.Sp +Possible values: \fIRowsAndColumns, or IDPairsAndValue\fR. Default value: \fIRowsAndColumns\fR. +.Sp +The value of \fB\-\-OutMatrixFormat\fR in conjunction with \fB\-\-OutMatrixType\fR determines type +of data written to output files and allows generation of up to 6 different output data formats: +.Sp +.Vb 1 +\& OutMatrixFormat OutMatrixType +\& +\& RowsAndColumns FullMatrix [ DEFAULT ] +\& RowsAndColumns UpperTriangularMatrix +\& RowsAndColumns LowerTriangularMatrix +\& +\& IDPairsAndValue FullMatrix +\& IDPairsAndValue UpperTriangularMatrix +\& IDPairsAndValue LowerTriangularMatrix +.Ve +.Sp +Example of data in output file for \fIRowsAndColumns\fR \fB\-\-OutMatrixFormat\fR value for +\&\fIFullMatrix\fR valueof \fB\-\-OutMatrixType\fR: +.Sp +.Vb 10 +\& "","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",... ... +\& ... ... .. +\& ... ... .. +\& ... ... .. +.Ve +.Sp +Example of data in output file for \fIRowsAndColumns\fR \fB\-\-OutMatrixFormat\fR value for +\&\fIUpperTriangularMatrix\fR value of \fB\-\-OutMatrixType\fR: +.Sp +.Vb 10 +\& "","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",... ... +\& ... ... .. +\& ... ... .. +\& ... ... .. +.Ve +.Sp +Example of data in output file for \fIRowsAndColumns\fR \fB\-\-OutMatrixFormat\fR value for +\&\fILowerTriangularMatrix\fR value of \fB\-\-OutMatrixType\fR: +.Sp +.Vb 10 +\& "","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" +\& ... ... .. +\& ... ... .. +\& ... ... .. +.Ve +.Sp +Example of data in output file for \fIIDPairsAndValue\fR \fB\-\-OutMatrixFormat\fR value for +<FullMatrix> value of \fBOutMatrixType\fR: +.Sp +.Vb 10 +\& "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" +\& ... ... ... +\& ... ... ... +\& ... ... ... +.Ve +.Sp +Example of data in output file for \fIIDPairsAndValue\fR \fB\-\-OutMatrixFormat\fR value for +<UpperTriangularMatrix> value of \fB\-\-OutMatrixType\fR: +.Sp +.Vb 10 +\& "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" +\& ... ... ... +\& ... ... ... +\& ... ... ... +.Ve +.Sp +Example of data in output file for \fIIDPairsAndValue\fR \fB\-\-OutMatrixFormat\fR value for +<LowerTriangularMatrix> value of \fB\-\-OutMatrixType\fR: +.Sp +.Vb 10 +\& "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" +\& ... ... ... +\& ... ... ... +\& ... ... ... +.Ve +.IP "\fB\-\-OutMatrixType\fR \fIFullMatrix | UpperTriangularMatrix | LowerTriangularMatrix\fR" 4 +.IX Item "--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. +.Sp +Possible values: \fIFullMatrix, UpperTriangularMatrix, or LowerTriangularMatrix\fR. Default value: +\&\fIFullMatrix\fR. +.Sp +The value of \fB\-\-OutMatrixType\fR in conjunction with \fB\-\-OutMatrixFormat\fR determines type +of data written to output files. +.IP "\fB\-o, \-\-overwrite\fR" 4 +.IX Item "-o, --overwrite" +Overwrite existing files +.IP "\fB\-p, \-\-precision\fR \fInumber\fR" 4 +.IX Item "-p, --precision number" +Precision of calculated values in the output file. Default: up to \fI2\fR decimal places. +Valid values: positive integers. +.IP "\fB\-q, \-\-quote\fR \fIYes | No\fR" 4 +.IX Item "-q, --quote Yes | No" +Put quote around column values in output \s-1CSV/TSV\s0 text file(s). Possible values: +\&\fIYes or No\fR. Default value: \fIYes\fR. +.IP "\fB\-r, \-\-root\fR \fIRootName\fR" 4 +.IX Item "-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. +.ie n .IP "\fB\-v, \-\-VectorComparisonMode\fR \fIAll | ""TanimotoSimilarity,[ManhattanDistance,...]""\fR" 4 +.el .IP "\fB\-v, \-\-VectorComparisonMode\fR \fIAll | ``TanimotoSimilarity,[ManhattanDistance,...]''\fR" 4 +.IX Item "-v, --VectorComparisonMode All | TanimotoSimilarity,[ManhattanDistance,...]" +Specify what similarity or distance coefficients to use for calculating similarity matrices for +fingerprint vector strings data values in \fITextFile(s)\fR: calculate similarity matrices for all +supported similarity and distance coefficients or specify a comma delimited list of similarity +and distance coefficients. Possible values: \fIAll | \*(L"TanimotoSimilairy,[ManhattanDistance,..]\*(R"\fR. +Default: \fITanimotoSimilarity\fR. +.Sp +The value of \fB\-v, \-\-VectorComparisonMode\fR, in conjunction with \fB\-\-VectorComparisonFormulism\fR, +decides which type of similarity and distance coefficient formulism gets used. +.Sp +\&\fIAll\fR uses complete list of supported similarity and distance coefficients: \fICosineSimilarity, +CzekanowskiSimilarity, DiceSimilarity, OchiaiSimilarity, JaccardSimilarity, SorensonSimilarity, TanimotoSimilarity, +CityBlockDistance, EuclideanDistance, HammingDistance, ManhattanDistance, SoergelDistance\fR. These +similarity and distance coefficients are described below. +.Sp +\&\fBFingerprintsVector.pm\fR module, used to calculate similarity and distance coefficients, +provides support to perform comparison between vectors containing three different types of +values: +.Sp +Type I: OrderedNumericalValues +.Sp +.Vb 3 +\& . 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. +.Ve +.Sp +Type \s-1II:\s0 UnorderedNumericalValues +.Sp +.Vb 3 +\& . 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 +.Ve +.Sp +Type \s-1III:\s0 AlphaNumericalValues +.Sp +.Vb 3 +\& . Size of two vectors might not be same +\& . Vectors contain unordered alphanumerical values. For example: Extended +\& connectivity fingerprints, atom neighborhood fingerprints. +.Ve +.Sp +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. +.Sp +Three forms of similarity and distance calculation between two vectors, specified using \fB\-\-VectorComparisonFormulism\fR +option, are supported: \fIAlgebraicForm, BinaryForm or SetTheoreticForm\fR. +.Sp +For \fIBinaryForm\fR, 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. +.Sp +For two fingerprint vectors A and B of same size containing OrderedNumericalValues, let: +.Sp +.Vb 1 +\& 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 +.Ve +.Sp +For SetTheoreticForm of calculation between two vectors, let: +.Sp +.Vb 2 +\& SetIntersectionXaXb = SUM ( MIN ( Xai, Xbi ) ) +\& SetDifferenceXaXb = SUM ( Xai ) + SUM ( Xbi ) \- SUM ( MIN ( Xai, Xbi ) ) +.Ve +.Sp +For BinaryForm of calculation between two vectors, let: +.Sp +.Vb 5 +\& 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 +.Ve +.Sp +Additionally, for BinaryForm various values also correspond to: +.Sp +.Vb 4 +\& Na = | Xa | +\& Nb = | Xb | +\& Nc = | SetIntersectionXaXb | +\& Nd = N \- | SetDifferenceXaXb | +\& +\& | SetDifferenceXaXb | = N \- Nd = Na + Nb \- Nc + Nd \- Nd = Na + Nb \- Nc +\& = | Xa | + | Xb | \- | SetIntersectionXaXb | +.Ve +.Sp +Various similarity and distance coefficients [ Ref 40, Ref 62, Ref 64 ] for a pair of vectors A and B +in \fIAlgebraicForm, BinaryForm and SetTheoreticForm\fR are defined as follows: +.Sp +\&\fBCityBlockDistance\fR: ( same as HammingDistance and ManhattanDistance) +.Sp +\&\fIAlgebraicForm\fR: \s-1SUM\s0 ( \s-1ABS\s0 ( Xai \- Xbi ) ) +.Sp +\&\fIBinaryForm\fR: ( Na \- Nc ) + ( Nb \- Nc ) = Na + Nb \- 2 * Nc +.Sp +\&\fISetTheoreticForm\fR: | SetDifferenceXaXb | \- | SetIntersectionXaXb | = \s-1SUM\s0 ( Xai ) + \s-1SUM\s0 ( Xbi ) \- 2 * ( \s-1SUM\s0 ( \s-1MIN\s0 ( Xai, Xbi ) ) ) +.Sp +\&\fBCosineSimilarity\fR: ( same as OchiaiSimilarityCoefficient) +.Sp +\&\fIAlgebraicForm\fR: \s-1SUM\s0 ( Xai * Xbi ) / \s-1SQRT\s0 ( \s-1SUM\s0 ( Xai ** 2) * \s-1SUM\s0 ( Xbi ** 2) ) +.Sp +\&\fIBinaryForm\fR: Nc / \s-1SQRT\s0 ( Na * Nb) +.Sp +\&\fISetTheoreticForm\fR: | SetIntersectionXaXb | / \s-1SQRT\s0 ( |Xa| * |Xb| ) = \s-1SUM\s0 ( \s-1MIN\s0 ( Xai, Xbi ) ) / \s-1SQRT\s0 ( \s-1SUM\s0 ( Xai ) * \s-1SUM\s0 ( Xbi ) ) +.Sp +\&\fBCzekanowskiSimilarity\fR: ( same as DiceSimilarity and SorensonSimilarity) +.Sp +\&\fIAlgebraicForm\fR: ( 2 * ( \s-1SUM\s0 ( Xai * Xbi ) ) ) / ( \s-1SUM\s0 ( Xai ** 2) + \s-1SUM\s0 ( Xbi **2 ) ) +.Sp +\&\fIBinaryForm\fR: 2 * Nc / ( Na + Nb ) +.Sp +\&\fISetTheoreticForm\fR: 2 * | SetIntersectionXaXb | / ( |Xa| + |Xb| ) = 2 * ( \s-1SUM\s0 ( \s-1MIN\s0 ( Xai, Xbi ) ) ) / ( \s-1SUM\s0 ( Xai ) + \s-1SUM\s0 ( Xbi ) ) +.Sp +\&\fBDiceSimilarity\fR: ( same as CzekanowskiSimilarity and SorensonSimilarity) +.Sp +\&\fIAlgebraicForm\fR: ( 2 * ( \s-1SUM\s0 ( Xai * Xbi ) ) ) / ( \s-1SUM\s0 ( Xai ** 2) + \s-1SUM\s0 ( Xbi **2 ) ) +.Sp +\&\fIBinaryForm\fR: 2 * Nc / ( Na + Nb ) +.Sp +\&\fISetTheoreticForm\fR: 2 * | SetIntersectionXaXb | / ( |Xa| + |Xb| ) = 2 * ( \s-1SUM\s0 ( \s-1MIN\s0 ( Xai, Xbi ) ) ) / ( \s-1SUM\s0 ( Xai ) + \s-1SUM\s0 ( Xbi ) ) +.Sp +\&\fBEuclideanDistance\fR: +.Sp +\&\fIAlgebraicForm\fR: \s-1SQRT\s0 ( \s-1SUM\s0 ( ( ( Xai \- Xbi ) ** 2 ) ) ) +.Sp +\&\fIBinaryForm\fR: \s-1SQRT\s0 ( ( Na \- Nc ) + ( Nb \- Nc ) ) = \s-1SQRT\s0 ( Na + Nb \- 2 * Nc ) +.Sp +\&\fISetTheoreticForm\fR: \s-1SQRT\s0 ( | SetDifferenceXaXb | \- | SetIntersectionXaXb | ) = \s-1SQRT\s0 ( \s-1SUM\s0 ( Xai ) + \s-1SUM\s0 ( Xbi ) \- 2 * ( \s-1SUM\s0 ( \s-1MIN\s0 ( Xai, Xbi ) ) ) ) +.Sp +\&\fBHammingDistance\fR: ( same as CityBlockDistance and ManhattanDistance) +.Sp +\&\fIAlgebraicForm\fR: \s-1SUM\s0 ( \s-1ABS\s0 ( Xai \- Xbi ) ) +.Sp +\&\fIBinaryForm\fR: ( Na \- Nc ) + ( Nb \- Nc ) = Na + Nb \- 2 * Nc +.Sp +\&\fISetTheoreticForm\fR: | SetDifferenceXaXb | \- | SetIntersectionXaXb | = \s-1SUM\s0 ( Xai ) + \s-1SUM\s0 ( Xbi ) \- 2 * ( \s-1SUM\s0 ( \s-1MIN\s0 ( Xai, Xbi ) ) ) +.Sp +\&\fBJaccardSimilarity\fR: ( same as TanimotoSimilarity) +.Sp +\&\fIAlgebraicForm\fR: \s-1SUM\s0 ( Xai * Xbi ) / ( \s-1SUM\s0 ( Xai ** 2 ) + \s-1SUM\s0 ( Xbi ** 2 ) \- \s-1SUM\s0 ( Xai * Xbi ) ) +.Sp +\&\fIBinaryForm\fR: Nc / ( ( Na \- Nc ) + ( Nb \- Nc ) + Nc ) = Nc / ( Na + Nb \- Nc ) +.Sp +\&\fISetTheoreticForm\fR: | SetIntersectionXaXb | / | SetDifferenceXaXb | = \s-1SUM\s0 ( \s-1MIN\s0 ( Xai, Xbi ) ) / ( \s-1SUM\s0 ( Xai ) + \s-1SUM\s0 ( Xbi ) \- \s-1SUM\s0 ( \s-1MIN\s0 ( Xai, Xbi ) ) ) +.Sp +\&\fBManhattanDistance\fR: ( same as CityBlockDistance and HammingDistance) +.Sp +\&\fIAlgebraicForm\fR: \s-1SUM\s0 ( \s-1ABS\s0 ( Xai \- Xbi ) ) +.Sp +\&\fIBinaryForm\fR: ( Na \- Nc ) + ( Nb \- Nc ) = Na + Nb \- 2 * Nc +.Sp +\&\fISetTheoreticForm\fR: | SetDifferenceXaXb | \- | SetIntersectionXaXb | = \s-1SUM\s0 ( Xai ) + \s-1SUM\s0 ( Xbi ) \- 2 * ( \s-1SUM\s0 ( \s-1MIN\s0 ( Xai, Xbi ) ) ) +.Sp +\&\fBOchiaiSimilarity\fR: ( same as CosineSimilarity) +.Sp +\&\fIAlgebraicForm\fR: \s-1SUM\s0 ( Xai * Xbi ) / \s-1SQRT\s0 ( \s-1SUM\s0 ( Xai ** 2) * \s-1SUM\s0 ( Xbi ** 2) ) +.Sp +\&\fIBinaryForm\fR: Nc / \s-1SQRT\s0 ( Na * Nb) +.Sp +\&\fISetTheoreticForm\fR: | SetIntersectionXaXb | / \s-1SQRT\s0 ( |Xa| * |Xb| ) = \s-1SUM\s0 ( \s-1MIN\s0 ( Xai, Xbi ) ) / \s-1SQRT\s0 ( \s-1SUM\s0 ( Xai ) * \s-1SUM\s0 ( Xbi ) ) +.Sp +\&\fBSorensonSimilarity\fR: ( same as CzekanowskiSimilarity and DiceSimilarity) +.Sp +\&\fIAlgebraicForm\fR: ( 2 * ( \s-1SUM\s0 ( Xai * Xbi ) ) ) / ( \s-1SUM\s0 ( Xai ** 2) + \s-1SUM\s0 ( Xbi **2 ) ) +.Sp +\&\fIBinaryForm\fR: 2 * Nc / ( Na + Nb ) +.Sp +\&\fISetTheoreticForm\fR: 2 * | SetIntersectionXaXb | / ( |Xa| + |Xb| ) = 2 * ( \s-1SUM\s0 ( \s-1MIN\s0 ( Xai, Xbi ) ) ) / ( \s-1SUM\s0 ( Xai ) + \s-1SUM\s0 ( Xbi ) ) +.Sp +\&\fBSoergelDistance\fR: +.Sp +\&\fIAlgebraicForm\fR: \s-1SUM\s0 ( \s-1ABS\s0 ( Xai \- Xbi ) ) / \s-1SUM\s0 ( \s-1MAX\s0 ( Xai, Xbi ) ) +.Sp +\&\fIBinaryForm\fR: 1 \- Nc / ( Na + Nb \- Nc ) = ( Na + Nb \- 2 * Nc ) / ( Na + Nb \- Nc ) +.Sp +\&\fISetTheoreticForm\fR: ( | SetDifferenceXaXb | \- | SetIntersectionXaXb | ) / | SetDifferenceXaXb | = ( \s-1SUM\s0 ( Xai ) + \s-1SUM\s0 ( Xbi ) \- 2 * ( \s-1SUM\s0 ( \s-1MIN\s0 ( Xai, Xbi ) ) ) ) / ( \s-1SUM\s0 ( Xai ) + \s-1SUM\s0 ( Xbi ) \- \s-1SUM\s0 ( \s-1MIN\s0 ( Xai, Xbi ) ) ) +.Sp +\&\fBTanimotoSimilarity\fR: ( same as JaccardSimilarity) +.Sp +\&\fIAlgebraicForm\fR: \s-1SUM\s0 ( Xai * Xbi ) / ( \s-1SUM\s0 ( Xai ** 2 ) + \s-1SUM\s0 ( Xbi ** 2 ) \- \s-1SUM\s0 ( Xai * Xbi ) ) +.Sp +\&\fIBinaryForm\fR: Nc / ( ( Na \- Nc ) + ( Nb \- Nc ) + Nc ) = Nc / ( Na + Nb \- Nc ) +.Sp +\&\fISetTheoreticForm\fR: | SetIntersectionXaXb | / | SetDifferenceXaXb | = \s-1SUM\s0 ( \s-1MIN\s0 ( Xai, Xbi ) ) / ( \s-1SUM\s0 ( Xai ) + \s-1SUM\s0 ( Xbi ) \- \s-1SUM\s0 ( \s-1MIN\s0 ( Xai, Xbi ) ) ) +.ie n .IP "\fB\-\-VectorComparisonFormulism\fR \fIAll | ""AlgebraicForm,[BinaryForm,SetTheoreticForm]""\fR" 4 +.el .IP "\fB\-\-VectorComparisonFormulism\fR \fIAll | ``AlgebraicForm,[BinaryForm,SetTheoreticForm]''\fR" 4 +.IX Item "--VectorComparisonFormulism All | AlgebraicForm,[BinaryForm,SetTheoreticForm]" +Specify fingerprints vector comparison formulism to use for calculation similarity and distance +coefficients during \fB\-v, \-\-VectorComparisonMode\fR: use all supported comparison formulisms +or specify a comma delimited. Possible values: \fIAll | \*(L"AlgebraicForm,[BinaryForm,SetTheoreticForm]\*(R"\fR. +Default value: \fIAlgebraicForm\fR. +.Sp +\&\fIAll\fR uses all three forms of supported vector comparison formulism for values of \fB\-v, \-\-VectorComparisonMode\fR +option. +.Sp +For fingerprint vector strings containing \fBAlphaNumericalValues\fR data values \- \fBExtendedConnectivityFingerprints\fR, +\&\fBAtomNeighborhoodsFingerprints\fR and so on \- all three formulism result in same value during similarity and distance +calculations. +.IP "\fB\-w, \-\-WorkingDir\fR \fIDirName\fR" 4 +.IX Item "-w, --WorkingDir DirName" +Location of working directory. Default: current directory. +.SH "EXAMPLES" +.IX Header "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: +.PP +.Vb 1 +\& % SimilarityMatricesFingerprints.pl \-o SampleFPHex.csv +.Ve +.PP +To generate a similarity matrix corresponding to Tanimoto similarity coefficient for fingerprints +bit-vector strings data corresponding to supported fingerprints in \s-1SD\s0 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: +.PP +.Vb 1 +\& % SimilarityMatricesFingerprints.pl \-o SampleFPHex.sdf +.Ve +.PP +To generate a similarity matrix corresponding to Tanimoto similarity coefficient for fingerprints +bit-vector strings data corresponding to supported fingerprints in \s-1FP\s0 file by loading all fingerprints +data into memory and create a SampleFPHexTanimotoSimilarity.csv file along with compound IDs +retrieved from \s-1FP\s0 file, type: +.PP +.Vb 1 +\& % SimilarityMatricesFingerprints.pl \-o SampleFPHex.fpf +.Ve +.PP +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: +.PP +.Vb 3 +\& % SimilarityMatricesFingerprints.pl \-o \-\-InputDataMode LoadInMemory +\& \-\-OutMatrixFormat RowsAndColumns \-\-OutMatrixType LowerTriangularMatrix +\& SampleFPHex.csv +.Ve +.PP +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: +.PP +.Vb 3 +\& % SimilarityMatricesFingerprints.pl \-o \-\-InputDataMode LoadInMemory +\& \-\-OutMatrixFormat IDPairsAndValue \-\-OutMatrixType UpperTriangularMatrix +\& SampleFPHex.csv +.Ve +.PP +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: +.PP +.Vb 3 +\& % SimilarityMatricesFingerprints.pl \-o \-\-InputDataMode ScanFile +\& \-\-OutMatrixFormat RowsAndColumns \-\-OutMatrixType FullMatrix +\& SampleFPHex.csv +.Ve +.PP +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: +.PP +.Vb 3 +\& % SimilarityMatricesFingerprints.pl \-o \-\-InputDataMode ScanFile +\& \-\-OutMatrixFormat IDPairsAndValue \-\-OutMatrixType LowerTriangularMatrix +\& SampleFPHex.csv +.Ve +.PP +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: +.PP +.Vb 1 +\& % SimilarityMatricesFingerprints.pl \-o SampleFPCount.csv +.Ve +.PP +To generate a similarity matrix corresponding to Tanimoto similarity coefficient using algebraic formulism +for fingerprints vector strings data corresponding to supported fingerprints in \s-1SD\s0 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: +.PP +.Vb 1 +\& % SimilarityMatricesFingerprints.pl \-o SampleFPCount.sdf +.Ve +.PP +To generate a similarity matrix corresponding to Tanimoto similarity coefficient using algebraic formulism +vector strings data corresponding to supported fingerprints in \s-1FP\s0 file and create a +SampleFPCountTanimotoSimilarityAlgebraicForm.csv file along with compound IDs retrieved from \s-1FP\s0 file, type: +.PP +.Vb 1 +\& % SimilarityMatricesFingerprints.pl \-o SampleFPCount.fpf +.Ve +.PP +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: +.PP +.Vb 2 +\& % SimilarityMatricesFingerprints.pl \-\-OutMatrixFormat IDPairsAndValue \-o +\& SampleFPHex.csv +.Ve +.PP +To generate a similarity matrix corresponding to Tanimoto similarity coefficient for fingerprints +bit-vector strings data corresponding to supported fingerprints in \s-1SD\s0 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: +.PP +.Vb 2 +\& % SimilarityMatricesFingerprints.pl \-\-OutMatrixFormat IDPairsAndValue \-o +\& SampleFPHex.sdf +.Ve +.PP +To generate a similarity matrix corresponding to Tanimoto similarity coefficient for fingerprints +bit-vector strings data corresponding to supported fingerprints in \s-1FP\s0 file and create a +SampleFPHexTanimotoSimilarity.csv file in IDPairsAndValue format along with compound IDs retrieved +from \s-1FP\s0 file, type: +.PP +.Vb 2 +\& % SimilarityMatricesFingerprints.pl \-\-OutMatrixFormat IDPairsAndValue \-o +\& SampleFPHex.fpf +.Ve +.PP +To generate a similarity matrix corresponding to Tanimoto similarity coefficient for fingerprints +bit-vector strings data corresponding to supported fingerprints in \s-1SD\s0 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: +.PP +.Vb 2 +\& % SimilarityMatricesFingerprints.pl \-\-CompoundIDMode MolName \-o +\& SampleFPHex.sdf +.Ve +.PP +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: +.PP +.Vb 2 +\& % SimilarityMatricesFingerprints.pl \-\-CompoundIDMode DataField +\& \-\-CompoundIDField Mol_ID \-o SampleFPBin.sdf +.Ve +.PP +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: +.PP +.Vb 2 +\& % SimilarityMatricesFingerprints.pl \-b "BuserSimilarity,DiceSimilarity, +\& TanimotoSimilarity" \-o SampleFPBin.csv +.Ve +.PP +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: +.PP +.Vb 2 +\& % SimilarityMatricesFingerprints.pl \-b "BuserSimilarity,DiceSimilarity, +\& TanimotoSimilarity" \-o SampleFPBin.sdf +.Ve +.PP +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: +.PP +.Vb 2 +\& % SimilarityMatricesFingerprints.pl \-v "CityBlockDistance, +\& TanimotoSimilarity" \-o SampleFPCount.csv +.Ve +.PP +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: +.PP +.Vb 2 +\& % SimilarityMatricesFingerprints.pl \-v "CityBlockDistance, +\& TanimotoSimilarity" \-o SampleFPCount.sdf +.Ve +.PP +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: +.PP +.Vb 3 +\& % SimilarityMatricesFingerprints.pl \-v "CityBlockDistance, +\& TanimotoSimilarity" \-\-VectorComparisonFormulism BinaryForm \-o +\& SampleFPCount.csv +.Ve +.PP +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: +.PP +.Vb 3 +\& % SimilarityMatricesFingerprints.pl \-v "CityBlockDistance, +\& TanimotoSimilarity" \-\-VectorComparisonFormulism BinaryForm \-o +\& SampleFPCount.sdf +.Ve +.PP +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: +.PP +.Vb 2 +\& % SimilarityMatricesFingerprints.pl \-v "CityBlockDistance, +\& TanimotoSimilarity" \-\-VectorComparisonFormulism All \-o SampleFPCount.csv +.Ve +.PP +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: +.PP +.Vb 2 +\& % SimilarityMatricesFingerprints.pl \-v "CityBlockDistance,TanimotoSimilarity" +\& \-\-VectorComparisonFormulism All \-o SampleFPCount.sdf +.Ve +.PP +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: +.PP +.Vb 2 +\& % SimilarityMatricesFingerprints.pl \-m AutoDetect \-\-BitVectorComparisonMode +\& All \-\-alpha 0.5 \-beta 0.5 \-o SampleFPHex.csv +.Ve +.PP +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 +.PP +.Vb 2 +\& % SimilarityMatricesFingerprints.pl \-m AutoDetect \-\-BitVectorComparisonMode +\& All \-\-alpha 0.5 \-beta 0.5 \-o SampleFPHex.sdf +.Ve +.PP +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: +.PP +.Vb 2 +\& % SimilarityMatricesFingerprints.pl \-m AutoDetect \-\-VectorComparisonMode +\& All \-\-VectorComparisonFormulism All \-o SampleFPCount.csv +.Ve +.PP +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: +.PP +.Vb 2 +\& % SimilarityMatricesFingerprints.pl \-m AutoDetect \-\-VectorComparisonMode +\& All \-\-VectorComparisonFormulism All \-o SampleFPCount.sdf +.Ve +.PP +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: +.PP +.Vb 2 +\& % SimilarityMatricesFingerprints.pl \-\-ColMode ColNum \-\-CompoundIDCol 1 +\& \-\-FingerprintsCol 2 \-o SampleFPHex.csv +.Ve +.PP +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: +.PP +.Vb 2 +\& % SimilarityMatricesFingerprints.pl \-\-FingerprintsField Fingerprints +\& \-\-CompoundIDMode DataField \-\-CompoundIDField Mol_ID \-o SampleFPHex.sdf +.Ve +.PP +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: +.PP +.Vb 4 +\& % SimilarityMatricesFingerprints.pl \-\-BitVectorComparisonMode +\& TverskySimilarity \-\-alpha 0.5 \-\-ColMode ColLabel \-\-CompoundIDCol +\& CompoundID \-\-FingerprintsCol Fingerprints \-\-OutDelim Tab \-\-quote No +\& \-o SampleFPHex.csv +.Ve +.PP +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: +.PP +.Vb 2 +\& % SimilarityMatricesFingerprints.pl \-\-CompoundIDMode MolnameOrLabelPrefix +\& \-\-CompoundIDPrefix Mol \-o SampleFPHex.sdf +.Ve +.PP +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: +.PP +.Vb 1 +\& % SimilarityMatricesFingerprints.pl \-OutDelim Tab \-\-quote No \-o SampleFPHex.sdf +.Ve +.SH "AUTHOR" +.IX Header "AUTHOR" +Manish Sud <msud@san.rr.com> +.SH "SEE ALSO" +.IX Header "SEE ALSO" +InfoFingerprintsFiles.pl, SimilaritySearchingFingerprints.pl, AtomNeighborhoodsFingerprints.pl, +ExtendedConnectivityFingerprints.pl, MACCSKeysFingerprints.pl, PathLengthFingerprints.pl, +TopologicalAtomPairsFingerprints.pl, TopologicalAtomTorsionsFingerprints.pl, +TopologicalPharmacophoreAtomPairsFingerprints.pl, TopologicalPharmacophoreAtomTripletsFingerprints.pl +.SH "COPYRIGHT" +.IX Header "COPYRIGHT" +Copyright (C) 2015 Manish Sud. All rights reserved. +.PP +This file is part of MayaChemTools. +.PP +MayaChemTools is free software; you can redistribute it and/or modify it under +the terms of the \s-1GNU\s0 Lesser General Public License as published by the Free +Software Foundation; either version 3 of the License, or (at your option) +any later version.