Mercurial > repos > deepakjadmin > mayatool3_test2
comparison 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 |
| parents | |
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| -1:000000000000 | 0:4816e4a8ae95 |
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| 1 NAME | |
| 2 SimilarityMatricesFingerprints.pl - Calculate similarity matrices using | |
| 3 fingerprints strings data in SD, FP and CSV/TSV text file(s) | |
| 4 | |
| 5 SYNOPSIS | |
| 6 SimilarityMatricesFingerprints.pl SDFile(s) FPFile(s) TextFile(s)... | |
| 7 | |
| 8 SimilarityMatricesFingerprints.pl [--alpha *number*] [--beta *number*] | |
| 9 [-b, --BitVectorComparisonMode *All | "TanimotoSimilarity,[ | |
| 10 TverskySimilarity, ... ]"*] [-c, --ColMode *ColNum | ColLabel*] | |
| 11 [--CompoundIDCol *col number | col name*] [--CompoundIDPrefix *text*] | |
| 12 [--CompoundIDField *DataFieldName*] [--CompoundIDMode *DataField | | |
| 13 MolName | LabelPrefix | MolNameOrLabelPrefix*] [-d, --detail | |
| 14 *InfoLevel*] [-f, --fast] [--FingerprintsCol *col number | col name*] | |
| 15 [--FingerprintsField *FieldLabel*] [-h, --help] [--InDelim *comma | | |
| 16 semicolon*] [--InputDataMode *LoadInMemory | ScanFile*] [-m, --mode | |
| 17 *AutoDetect | FingerprintsBitVectorString | FingerprintsVectorString*] | |
| 18 [--OutDelim *comma | tab | semicolon*] [--OutMatrixFormat | |
| 19 *RowsAndColumns | IDPairsAndValue*] [--OutMatrixType *FullMatrix | | |
| 20 UpperTriangularMatrix | LowerTriangularMatrix*] [-o, --overwrite] [-p, | |
| 21 --precision *number*] [-q, --quote *Yes | No*] [-r, --root *RootName*] | |
| 22 [-v, --VectorComparisonMode *All | "TanimotoSimilairy, [ | |
| 23 ManhattanDistance, ...]"*] [--VectorComparisonFormulism *All | | |
| 24 "AlgebraicForm, [BinaryForm, SetTheoreticForm]"*] [-w, --WorkingDir | |
| 25 dirname] SDFile(s) FPFile(s) TextFile(s)... | |
| 26 | |
| 27 DESCRIPTION | |
| 28 Calculate similarity matrices using fingerprint bit-vector or vector | |
| 29 strings data in *SD, FP and CSV/TSV* text file(s) and generate CSV/TSV | |
| 30 text file(s) containing values for specified similarity and distance | |
| 31 coefficients. | |
| 32 | |
| 33 The scripts SimilarityMatrixSDFiles.pl and SimilarityMatrixTextFiles.pl | |
| 34 have been removed from the current release of MayaChemTools and their | |
| 35 functionality merged with this script. | |
| 36 | |
| 37 The valid *SDFile* extensions are *.sdf* and *.sd*. All SD files in a | |
| 38 current directory can be specified either by **.sdf* or the current | |
| 39 directory name. | |
| 40 | |
| 41 The valid *FPFile* extensions are *.fpf* and *.fp*. All FP files in a | |
| 42 current directory can be specified either by **.fpf* or the current | |
| 43 directory name. | |
| 44 | |
| 45 The valid *TextFile* extensions are *.csv* and *.tsv* for | |
| 46 comma/semicolon and tab delimited text files respectively. All other | |
| 47 file names are ignored. All text files in a current directory can be | |
| 48 specified by **.csv*, **.tsv*, or the current directory name. The | |
| 49 --indelim option determines the format of *TextFile(s)*. Any file which | |
| 50 doesn't correspond to the format indicated by --indelim option is | |
| 51 ignored. | |
| 52 | |
| 53 Example of *FP* file containing fingerprints bit-vector string data: | |
| 54 | |
| 55 # | |
| 56 # Package = MayaChemTools 7.4 | |
| 57 # ReleaseDate = Oct 21, 2010 | |
| 58 # | |
| 59 # TimeStamp = Mon Mar 7 15:14:01 2011 | |
| 60 # | |
| 61 # FingerprintsStringType = FingerprintsBitVector | |
| 62 # | |
| 63 # Description = PathLengthBits:AtomicInvariantsAtomTypes:MinLength1:... | |
| 64 # Size = 1024 | |
| 65 # BitStringFormat = HexadecimalString | |
| 66 # BitsOrder = Ascending | |
| 67 # | |
| 68 Cmpd1 9c8460989ec8a49913991a6603130b0a19e8051c89184414953800cc21510... | |
| 69 Cmpd2 000000249400840040100042011001001980410c000000001010088001120... | |
| 70 ... ... | |
| 71 ... .. | |
| 72 | |
| 73 Example of *FP* file containing fingerprints vector string data: | |
| 74 | |
| 75 # | |
| 76 # Package = MayaChemTools 7.4 | |
| 77 # ReleaseDate = Oct 21, 2010 | |
| 78 # | |
| 79 # TimeStamp = Mon Mar 7 15:14:01 2011 | |
| 80 # | |
| 81 # FingerprintsStringType = FingerprintsVector | |
| 82 # | |
| 83 # Description = PathLengthBits:AtomicInvariantsAtomTypes:MinLength1:... | |
| 84 # VectorStringFormat = IDsAndValuesString | |
| 85 # VectorValuesType = NumericalValues | |
| 86 # | |
| 87 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: | |
| 88 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...; | |
| 89 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 | |
| 90 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 ... | |
| 91 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 | |
| 92 O C CC=O CCCC CCCN CCCO CCNC CNC=N CNC=O CNCN CCCC=O CCCCC CCCCN CC...; | |
| 93 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 | |
| 94 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 ... | |
| 95 ... ... | |
| 96 ... ... | |
| 97 | |
| 98 Example of *SD* file containing fingerprints bit-vector string data: | |
| 99 | |
| 100 ... ... | |
| 101 ... ... | |
| 102 $$$$ | |
| 103 ... ... | |
| 104 ... ... | |
| 105 ... ... | |
| 106 41 44 0 0 0 0 0 0 0 0999 V2000 | |
| 107 -3.3652 1.4499 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 | |
| 108 ... ... | |
| 109 2 3 1 0 0 0 0 | |
| 110 ... ... | |
| 111 M END | |
| 112 > <CmpdID> | |
| 113 Cmpd1 | |
| 114 | |
| 115 > <PathLengthFingerprints> | |
| 116 FingerprintsBitVector;PathLengthBits:AtomicInvariantsAtomTypes:MinLengt | |
| 117 h1:MaxLength8;1024;HexadecimalString;Ascending;9c8460989ec8a49913991a66 | |
| 118 03130b0a19e8051c89184414953800cc2151082844a201042800130860308e8204d4028 | |
| 119 00831048940e44281c00060449a5000ac80c894114e006321264401600846c050164462 | |
| 120 08190410805000304a10205b0100e04c0038ba0fad0209c0ca8b1200012268b61c0026a | |
| 121 aa0660a11014a011d46 | |
| 122 | |
| 123 $$$$ | |
| 124 ... ... | |
| 125 ... ... | |
| 126 | |
| 127 Example of CSV *Text* file containing fingerprints bit-vector string | |
| 128 data: | |
| 129 | |
| 130 "CompoundID","PathLengthFingerprints" | |
| 131 "Cmpd1","FingerprintsBitVector;PathLengthBits:AtomicInvariantsAtomTypes | |
| 132 :MinLength1:MaxLength8;1024;HexadecimalString;Ascending;9c8460989ec8a4 | |
| 133 9913991a6603130b0a19e8051c89184414953800cc2151082844a20104280013086030 | |
| 134 8e8204d402800831048940e44281c00060449a5000ac80c894114e006321264401..." | |
| 135 ... ... | |
| 136 ... ... | |
| 137 | |
| 138 The current release of MayaChemTools supports the following types of | |
| 139 fingerprint bit-vector and vector strings: | |
| 140 | |
| 141 FingerprintsVector;AtomNeighborhoods:AtomicInvariantsAtomTypes:MinRadi | |
| 142 us0:MaxRadius2;41;AlphaNumericalValues;ValuesString;NR0-C.X1.BO1.H3-AT | |
| 143 C1:NR1-C.X3.BO3.H1-ATC1:NR2-C.X1.BO1.H3-ATC1:NR2-C.X3.BO4-ATC1 NR0-C.X | |
| 144 1.BO1.H3-ATC1:NR1-C.X3.BO3.H1-ATC1:NR2-C.X1.BO1.H3-ATC1:NR2-C.X3.BO4-A | |
| 145 TC1 NR0-C.X2.BO2.H2-ATC1:NR1-C.X2.BO2.H2-ATC1:NR1-C.X3.BO3.H1-ATC1:NR2 | |
| 146 -C.X2.BO2.H2-ATC1:NR2-N.X3.BO3-ATC1:NR2-O.X1.BO1.H1-ATC1 NR0-C.X2.B... | |
| 147 | |
| 148 FingerprintsVector;AtomTypesCount:AtomicInvariantsAtomTypes:ArbitraryS | |
| 149 ize;10;NumericalValues;IDsAndValuesString;C.X1.BO1.H3 C.X2.BO2.H2 C.X2 | |
| 150 .BO3.H1 C.X3.BO3.H1 C.X3.BO4 F.X1.BO1 N.X2.BO2.H1 N.X3.BO3 O.X1.BO1.H1 | |
| 151 O.X1.BO2;2 4 14 3 10 1 1 1 3 2 | |
| 152 | |
| 153 FingerprintsVector;AtomTypesCount:SLogPAtomTypes:ArbitrarySize;16;Nume | |
| 154 ricalValues;IDsAndValuesString;C1 C10 C11 C14 C18 C20 C21 C22 C5 CS F | |
| 155 N11 N4 O10 O2 O9;5 1 1 1 14 4 2 1 2 2 1 1 1 1 3 1 | |
| 156 | |
| 157 FingerprintsVector;AtomTypesCount:SLogPAtomTypes:FixedSize;67;OrderedN | |
| 158 umericalValues;IDsAndValuesString;C1 C2 C3 C4 C5 C6 C7 C8 C9 C10 C11 C | |
| 159 12 C13 C14 C15 C16 C17 C18 C19 C20 C21 C22 C23 C24 C25 C26 C27 CS N1 N | |
| 160 2 N3 N4 N5 N6 N7 N8 N9 N10 N11 N12 N13 N14 NS O1 O2 O3 O4 O5 O6 O7 O8 | |
| 161 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 | |
| 162 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... | |
| 163 | |
| 164 FingerprintsVector;EStateIndicies:ArbitrarySize;11;NumericalValues;IDs | |
| 165 AndValuesString;SaaCH SaasC SaasN SdO SdssC SsCH3 SsF SsOH SssCH2 SssN | |
| 166 H SsssCH;24.778 4.387 1.993 25.023 -1.435 3.975 14.006 29.759 -0.073 3 | |
| 167 .024 -2.270 | |
| 168 | |
| 169 FingerprintsVector;EStateIndicies:FixedSize;87;OrderedNumericalValues; | |
| 170 ValuesString;0 0 0 0 0 0 0 3.975 0 -0.073 0 0 24.778 -2.270 0 0 -1.435 | |
| 171 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 | |
| 172 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 | |
| 173 0 0 0 0 0 0 0 0 0 0 0 0 0 0 | |
| 174 | |
| 175 FingerprintsVector;ExtendedConnectivity:AtomicInvariantsAtomTypes:Radi | |
| 176 us2;60;AlphaNumericalValues;ValuesString;73555770 333564680 352413391 | |
| 177 666191900 1001270906 1371674323 1481469939 1977749791 2006158649 21414 | |
| 178 08799 49532520 64643108 79385615 96062769 273726379 564565671 85514103 | |
| 179 5 906706094 988546669 1018231313 1032696425 1197507444 1331250018 1338 | |
| 180 532734 1455473691 1607485225 1609687129 1631614296 1670251330 17303... | |
| 181 | |
| 182 FingerprintsVector;ExtendedConnectivityCount:AtomicInvariantsAtomTypes | |
| 183 :Radius2;60;NumericalValues;IDsAndValuesString;73555770 333564680 3524 | |
| 184 13391 666191900 1001270906 1371674323 1481469939 1977749791 2006158649 | |
| 185 2141408799 49532520 64643108 79385615 96062769 273726379 564565671...; | |
| 186 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 | |
| 187 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 | |
| 188 | |
| 189 FingerprintsBitVector;ExtendedConnectivityBits:AtomicInvariantsAtomTyp | |
| 190 es:Radius2;1024;BinaryString;Ascending;0000000000000000000000000000100 | |
| 191 0000000001010000000110000011000000000000100000000000000000000000100001 | |
| 192 1000000110000000000000000000000000010011000000000000000000000000010000 | |
| 193 0000000000000000000000000010000000000000000001000000000000000000000000 | |
| 194 0000000000010000100001000000000000101000000000000000100000000000000... | |
| 195 | |
| 196 FingerprintsVector;ExtendedConnectivity:FunctionalClassAtomTypes:Radiu | |
| 197 s2;57;AlphaNumericalValues;ValuesString;24769214 508787397 850393286 8 | |
| 198 62102353 981185303 1231636850 1649386610 1941540674 263599683 32920567 | |
| 199 1 571109041 639579325 683993318 723853089 810600886 885767127 90326012 | |
| 200 7 958841485 981022393 1126908698 1152248391 1317567065 1421489994 1455 | |
| 201 632544 1557272891 1826413669 1983319256 2015750777 2029559552 20404... | |
| 202 | |
| 203 FingerprintsVector;ExtendedConnectivity:EStateAtomTypes:Radius2;62;Alp | |
| 204 haNumericalValues;ValuesString;25189973 528584866 662581668 671034184 | |
| 205 926543080 1347067490 1738510057 1759600920 2034425745 2097234755 21450 | |
| 206 44754 96779665 180364292 341712110 345278822 386540408 387387308 50430 | |
| 207 1706 617094135 771528807 957666640 997798220 1158349170 1291258082 134 | |
| 208 1138533 1395329837 1420277211 1479584608 1486476397 1487556246 1566... | |
| 209 | |
| 210 FingerprintsBitVector;MACCSKeyBits;166;BinaryString;Ascending;00000000 | |
| 211 0000000000000000000000000000000001001000010010000000010010000000011100 | |
| 212 0100101010111100011011000100110110000011011110100110111111111111011111 | |
| 213 11111111111110111000 | |
| 214 | |
| 215 FingerprintsBitVector;MACCSKeyBits;322;BinaryString;Ascending;11101011 | |
| 216 1110011111100101111111000111101100110000000000000011100010000000000000 | |
| 217 0000000000000000000000000000000000000000000000101000000000000000000000 | |
| 218 0000000000000000000000000000000000000000000000000000000000000000000000 | |
| 219 0000000000000000000000000000000000000011000000000000000000000000000000 | |
| 220 0000000000000000000000000000000000000000 | |
| 221 | |
| 222 FingerprintsVector;MACCSKeyCount;166;OrderedNumericalValues;ValuesStri | |
| 223 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 | |
| 224 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 | |
| 225 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 | |
| 226 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 | |
| 227 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 | |
| 228 | |
| 229 FingerprintsVector;MACCSKeyCount;322;OrderedNumericalValues;ValuesStri | |
| 230 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 | |
| 231 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 | |
| 232 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 | |
| 233 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 | |
| 234 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 ... | |
| 235 | |
| 236 FingerprintsBitVector;PathLengthBits:AtomicInvariantsAtomTypes:MinLeng | |
| 237 th1:MaxLength8;1024;BinaryString;Ascending;001000010011010101011000110 | |
| 238 0100010101011000101001011100110001000010001001101000001001001001001000 | |
| 239 0010110100000111001001000001001010100100100000000011000000101001011100 | |
| 240 0010000001000101010100000100111100110111011011011000000010110111001101 | |
| 241 0101100011000000010001000011000010100011101100001000001000100000000... | |
| 242 | |
| 243 FingerprintsVector;PathLengthCount:AtomicInvariantsAtomTypes:MinLength | |
| 244 1:MaxLength8;432;NumericalValues;IDsAndValuesPairsString;C.X1.BO1.H3 2 | |
| 245 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 | |
| 246 2.BO2.H1 1 N.X3.BO3 1 O.X1.BO1.H1 3 O.X1.BO2 2 C.X1.BO1.H3C.X3.BO3.H1 | |
| 247 2 C.X2.BO2.H2C.X2.BO2.H2 1 C.X2.BO2.H2C.X3.BO3.H1 4 C.X2.BO2.H2C.X3.BO | |
| 248 4 1 C.X2.BO2.H2N.X3.BO3 1 C.X2.BO3.H1:C.X2.BO3.H1 10 C.X2.BO3.H1:C.... | |
| 249 | |
| 250 FingerprintsVector;PathLengthCount:MMFF94AtomTypes:MinLength1:MaxLengt | |
| 251 h8;463;NumericalValues;IDsAndValuesPairsString;C5A 2 C5B 2 C=ON 1 CB 1 | |
| 252 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 | |
| 253 5 2 C5ACB 1 C5ACR 1 C5B:C5B 1 C5BC=ON 1 C5BCB 1 C=ON=O=CN 1 C=ONNC=O 1 | |
| 254 CB:CB 18 CBF 1 CBNC=O 1 COO=O=CO 1 COOCR 1 COOOC=O 1 CRCR 7 CRN5 1 CR | |
| 255 OR 2 C5A:C5B:C5B 2 C5A:C5BC=ON 1 C5A:C5BCB 1 C5A:N5:C5A 1 C5A:N5CR ... | |
| 256 | |
| 257 FingerprintsVector;TopologicalAtomPairs:AtomicInvariantsAtomTypes:MinD | |
| 258 istance1:MaxDistance10;223;NumericalValues;IDsAndValuesString;C.X1.BO1 | |
| 259 .H3-D1-C.X3.BO3.H1 C.X2.BO2.H2-D1-C.X2.BO2.H2 C.X2.BO2.H2-D1-C.X3.BO3. | |
| 260 H1 C.X2.BO2.H2-D1-C.X3.BO4 C.X2.BO2.H2-D1-N.X3.BO3 C.X2.BO3.H1-D1-...; | |
| 261 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 | |
| 262 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... | |
| 263 | |
| 264 FingerprintsVector;TopologicalAtomPairs:FunctionalClassAtomTypes:MinDi | |
| 265 stance1:MaxDistance10;144;NumericalValues;IDsAndValuesString;Ar-D1-Ar | |
| 266 Ar-D1-Ar.HBA Ar-D1-HBD Ar-D1-Hal Ar-D1-None Ar.HBA-D1-None HBA-D1-NI H | |
| 267 BA-D1-None HBA.HBD-D1-NI HBA.HBD-D1-None HBD-D1-None NI-D1-None No...; | |
| 268 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 | |
| 269 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 ... | |
| 270 | |
| 271 FingerprintsVector;TopologicalAtomTorsions:AtomicInvariantsAtomTypes;3 | |
| 272 3;NumericalValues;IDsAndValuesString;C.X1.BO1.H3-C.X3.BO3.H1-C.X3.BO4- | |
| 273 C.X3.BO4 C.X1.BO1.H3-C.X3.BO3.H1-C.X3.BO4-N.X3.BO3 C.X2.BO2.H2-C.X2.BO | |
| 274 2.H2-C.X3.BO3.H1-C.X2.BO2.H2 C.X2.BO2.H2-C.X2.BO2.H2-C.X3.BO3.H1-O...; | |
| 275 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 | |
| 276 | |
| 277 FingerprintsVector;TopologicalAtomTorsions:EStateAtomTypes;36;Numerica | |
| 278 lValues;IDsAndValuesString;aaCH-aaCH-aaCH-aaCH aaCH-aaCH-aaCH-aasC aaC | |
| 279 H-aaCH-aasC-aaCH aaCH-aaCH-aasC-aasC aaCH-aaCH-aasC-sF aaCH-aaCH-aasC- | |
| 280 ssNH aaCH-aasC-aasC-aasC aaCH-aasC-aasC-aasN aaCH-aasC-ssNH-dssC a...; | |
| 281 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 | |
| 282 | |
| 283 FingerprintsVector;TopologicalAtomTriplets:AtomicInvariantsAtomTypes:M | |
| 284 inDistance1:MaxDistance10;3096;NumericalValues;IDsAndValuesString;C.X1 | |
| 285 .BO1.H3-D1-C.X1.BO1.H3-D1-C.X3.BO3.H1-D2 C.X1.BO1.H3-D1-C.X2.BO2.H2-D1 | |
| 286 0-C.X3.BO4-D9 C.X1.BO1.H3-D1-C.X2.BO2.H2-D3-N.X3.BO3-D4 C.X1.BO1.H3-D1 | |
| 287 -C.X2.BO2.H2-D4-C.X2.BO2.H2-D5 C.X1.BO1.H3-D1-C.X2.BO2.H2-D6-C.X3....; | |
| 288 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 | |
| 289 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... | |
| 290 | |
| 291 FingerprintsVector;TopologicalAtomTriplets:SYBYLAtomTypes:MinDistance1 | |
| 292 :MaxDistance10;2332;NumericalValues;IDsAndValuesString;C.2-D1-C.2-D9-C | |
| 293 .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- | |
| 294 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 | |
| 295 -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. | |
| 296 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... | |
| 297 | |
| 298 FingerprintsVector;TopologicalPharmacophoreAtomPairs:ArbitrarySize:Min | |
| 299 Distance1:MaxDistance10;54;NumericalValues;IDsAndValuesString;H-D1-H H | |
| 300 -D1-NI HBA-D1-NI HBD-D1-NI H-D2-H H-D2-HBA H-D2-HBD HBA-D2-HBA HBA-D2- | |
| 301 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 | |
| 302 BA H-D4-HBD HBA-D4-HBA HBA-D4-HBD HBD-D4-HBD H-D5-H H-D5-HBA H-D5-...; | |
| 303 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 | |
| 304 3 4 1 37 10 8 1 35 10 9 3 3 1 28 7 7 4 18 16 12 5 1 2 1 | |
| 305 | |
| 306 FingerprintsVector;TopologicalPharmacophoreAtomPairs:FixedSize:MinDist | |
| 307 ance1:MaxDistance10;150;OrderedNumericalValues;ValuesString;18 0 0 1 0 | |
| 308 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 | |
| 309 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 | |
| 310 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 | |
| 311 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... | |
| 312 | |
| 313 FingerprintsVector;TopologicalPharmacophoreAtomTriplets:ArbitrarySize: | |
| 314 MinDistance1:MaxDistance10;696;NumericalValues;IDsAndValuesString;Ar1- | |
| 315 Ar1-Ar1 Ar1-Ar1-H1 Ar1-Ar1-HBA1 Ar1-Ar1-HBD1 Ar1-H1-H1 Ar1-H1-HBA1 Ar1 | |
| 316 -H1-HBD1 Ar1-HBA1-HBD1 H1-H1-H1 H1-H1-HBA1 H1-H1-HBD1 H1-HBA1-HBA1 H1- | |
| 317 HBA1-HBD1 H1-HBA1-NI1 H1-HBD1-NI1 HBA1-HBA1-NI1 HBA1-HBD1-NI1 Ar1-...; | |
| 318 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 | |
| 319 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 | |
| 320 119 123 24 15 185 202 41 25 22 17 3 5 85 95 18 11 23 17 3 1 1 6 4 ... | |
| 321 | |
| 322 FingerprintsVector;TopologicalPharmacophoreAtomTriplets:FixedSize:MinD | |
| 323 istance1:MaxDistance10;2692;OrderedNumericalValues;ValuesString;46 106 | |
| 324 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 | |
| 325 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 | |
| 326 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 | |
| 327 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 ... | |
| 328 | |
| 329 OPTIONS | |
| 330 --alpha *number* | |
| 331 Value of alpha parameter for calculating *Tversky* similarity | |
| 332 coefficient specified for -b, --BitVectorComparisonMode option. It | |
| 333 corresponds to weights assigned for bits set to "1" in a pair of | |
| 334 fingerprint bit-vectors during the calculation of similarity | |
| 335 coefficient. Possible values: *0 to 1*. Default value: <0.5>. | |
| 336 | |
| 337 --beta *number* | |
| 338 Value of beta parameter for calculating *WeightedTanimoto* and | |
| 339 *WeightedTversky* similarity coefficients specified for -b, | |
| 340 --BitVectorComparisonMode option. It is used to weight the | |
| 341 contributions of bits set to "0" during the calculation of | |
| 342 similarity coefficients. Possible values: *0 to 1*. Default value of | |
| 343 <1> makes *WeightedTanimoto* and *WeightedTversky* equivalent to | |
| 344 *Tanimoto* and *Tversky*. | |
| 345 | |
| 346 -b, --BitVectorComparisonMode *All | | |
| 347 "TanimotoSimilarity,[TverskySimilarity,...]"* | |
| 348 Specify what similarity coefficients to use for calculating | |
| 349 similarity matrices for fingerprints bit-vector strings data values | |
| 350 in *TextFile(s)*: calculate similarity matrices for all supported | |
| 351 similarity coefficients or specify a comma delimited list of | |
| 352 similarity coefficients. Possible values: *All | | |
| 353 "TanimotoSimilarity,[TverskySimilarity,...]*. Default: | |
| 354 *TanimotoSimilarity* | |
| 355 | |
| 356 *All* uses complete list of supported similarity coefficients: | |
| 357 *BaroniUrbaniSimilarity, BuserSimilarity, CosineSimilarity, | |
| 358 DiceSimilarity, DennisSimilarity, ForbesSimilarity, | |
| 359 FossumSimilarity, HamannSimilarity, JacardSimilarity, | |
| 360 Kulczynski1Similarity, Kulczynski2Similarity, MatchingSimilarity, | |
| 361 McConnaugheySimilarity, OchiaiSimilarity, PearsonSimilarity, | |
| 362 RogersTanimotoSimilarity, RussellRaoSimilarity, SimpsonSimilarity, | |
| 363 SkoalSneath1Similarity, SkoalSneath2Similarity, | |
| 364 SkoalSneath3Similarity, TanimotoSimilarity, TverskySimilarity, | |
| 365 YuleSimilarity, WeightedTanimotoSimilarity, | |
| 366 WeightedTverskySimilarity*. These similarity coefficients are | |
| 367 described below. | |
| 368 | |
| 369 For two fingerprint bit-vectors A and B of same size, let: | |
| 370 | |
| 371 Na = Number of bits set to "1" in A | |
| 372 Nb = Number of bits set to "1" in B | |
| 373 Nc = Number of bits set to "1" in both A and B | |
| 374 Nd = Number of bits set to "0" in both A and B | |
| 375 | |
| 376 Nt = Number of bits set to "1" or "0" in A or B (Size of A or B) | |
| 377 Nt = Na + Nb - Nc + Nd | |
| 378 | |
| 379 Na - Nc = Number of bits set to "1" in A but not in B | |
| 380 Nb - Nc = Number of bits set to "1" in B but not in A | |
| 381 | |
| 382 Then, various similarity coefficients [ Ref. 40 - 42 ] for a pair of | |
| 383 bit-vectors A and B are defined as follows: | |
| 384 | |
| 385 *BaroniUrbaniSimilarity*: ( SQRT( Nc * Nd ) + Nc ) / ( SQRT ( Nc * | |
| 386 Nd ) + Nc + ( Na - Nc ) + ( Nb - Nc ) ) ( same as Buser ) | |
| 387 | |
| 388 *BuserSimilarity*: ( SQRT ( Nc * Nd ) + Nc ) / ( SQRT ( Nc * Nd ) + | |
| 389 Nc + ( Na - Nc ) + ( Nb - Nc ) ) ( same as BaroniUrbani ) | |
| 390 | |
| 391 *CosineSimilarity*: Nc / SQRT ( Na * Nb ) (same as Ochiai) | |
| 392 | |
| 393 *DiceSimilarity*: (2 * Nc) / ( Na + Nb ) | |
| 394 | |
| 395 *DennisSimilarity*: ( Nc * Nd - ( ( Na - Nc ) * ( Nb - Nc ) ) ) / | |
| 396 SQRT ( Nt * Na * Nb) | |
| 397 | |
| 398 *ForbesSimilarity*: ( Nt * Nc ) / ( Na * Nb ) | |
| 399 | |
| 400 *FossumSimilarity*: ( Nt * ( ( Nc - 1/2 ) ** 2 ) / ( Na * Nb ) | |
| 401 | |
| 402 *HamannSimilarity*: ( ( Nc + Nd ) - ( Na - Nc ) - ( Nb - Nc ) ) / Nt | |
| 403 | |
| 404 *JaccardSimilarity*: Nc / ( ( Na - Nc) + ( Nb - Nc ) + Nc ) = Nc / ( | |
| 405 Na + Nb - Nc ) (same as Tanimoto) | |
| 406 | |
| 407 *Kulczynski1Similarity*: Nc / ( ( Na - Nc ) + ( Nb - Nc) ) = Nc / ( | |
| 408 Na + Nb - 2Nc ) | |
| 409 | |
| 410 *Kulczynski2Similarity*: ( ( Nc / 2 ) * ( 2 * Nc + ( Na - Nc ) + ( | |
| 411 Nb - Nc) ) ) / ( ( Nc + ( Na - Nc ) ) * ( Nc + ( Nb - Nc ) ) ) = 0.5 | |
| 412 * ( Nc / Na + Nc / Nb ) | |
| 413 | |
| 414 *MatchingSimilarity*: ( Nc + Nd ) / Nt | |
| 415 | |
| 416 *McConnaugheySimilarity*: ( Nc ** 2 - ( Na - Nc ) * ( Nb - Nc) ) / ( | |
| 417 Na * Nb ) | |
| 418 | |
| 419 *OchiaiSimilarity*: Nc / SQRT ( Na * Nb ) (same as Cosine) | |
| 420 | |
| 421 *PearsonSimilarity*: ( ( Nc * Nd ) - ( ( Na - Nc ) * ( Nb - Nc ) ) / | |
| 422 SQRT ( Na * Nb * ( Na - Nc + Nd ) * ( Nb - Nc + Nd ) ) | |
| 423 | |
| 424 *RogersTanimotoSimilarity*: ( Nc + Nd ) / ( ( Na - Nc) + ( Nb - Nc) | |
| 425 + Nt) = ( Nc + Nd ) / ( Na + Nb - 2Nc + Nt) | |
| 426 | |
| 427 *RussellRaoSimilarity*: Nc / Nt | |
| 428 | |
| 429 *SimpsonSimilarity*: Nc / MIN ( Na, Nb) | |
| 430 | |
| 431 *SkoalSneath1Similarity*: Nc / ( Nc + 2 * ( Na - Nc) + 2 * ( Nb - | |
| 432 Nc) ) = Nc / ( 2 * Na + 2 * Nb - 3 * Nc ) | |
| 433 | |
| 434 *SkoalSneath2Similarity*: ( 2 * Nc + 2 * Nd ) / ( Nc + Nd + Nt ) | |
| 435 | |
| 436 *SkoalSneath3Similarity*: ( Nc + Nd ) / ( ( Na - Nc ) + ( Nb - Nc ) | |
| 437 ) = ( Nc + Nd ) / ( Na + Nb - 2 * Nc ) | |
| 438 | |
| 439 *TanimotoSimilarity*: Nc / ( ( Na - Nc) + ( Nb - Nc ) + Nc ) = Nc / | |
| 440 ( Na + Nb - Nc ) (same as Jaccard) | |
| 441 | |
| 442 *TverskySimilarity*: Nc / ( alpha * ( Na - Nc ) + ( 1 - alpha) * ( | |
| 443 Nb - Nc) + Nc ) = Nc / ( alpha * ( Na - Nb ) + Nb) | |
| 444 | |
| 445 *YuleSimilarity*: ( ( Nc * Nd ) - ( ( Na - Nc ) * ( Nb - Nc ) ) ) / | |
| 446 ( ( Nc * Nd ) + ( ( Na - Nc ) * ( Nb - Nc ) ) ) | |
| 447 | |
| 448 Values of Tanimoto/Jaccard and Tversky coefficients are dependent on | |
| 449 only those bit which are set to "1" in both A and B. In order to | |
| 450 take into account all bit positions, modified versions of Tanimoto [ | |
| 451 Ref. 42 ] and Tversky [ Ref. 43 ] have been developed. | |
| 452 | |
| 453 Let: | |
| 454 | |
| 455 Na' = Number of bits set to "0" in A | |
| 456 Nb' = Number of bits set to "0" in B | |
| 457 Nc' = Number of bits set to "0" in both A and B | |
| 458 | |
| 459 Tanimoto': Nc' / ( ( Na' - Nc') + ( Nb' - Nc' ) + Nc' ) = Nc' / ( | |
| 460 Na' + Nb' - Nc' ) | |
| 461 | |
| 462 Tversky': Nc' / ( alpha * ( Na' - Nc' ) + ( 1 - alpha) * ( Nb' - Nc' | |
| 463 ) + Nc' ) = Nc' / ( alpha * ( Na' - Nb' ) + Nb') | |
| 464 | |
| 465 Then: | |
| 466 | |
| 467 *WeightedTanimotoSimilarity* = beta * Tanimoto + (1 - beta) * | |
| 468 Tanimoto' | |
| 469 | |
| 470 *WeightedTverskySimilarity* = beta * Tversky + (1 - beta) * Tversky' | |
| 471 | |
| 472 -c, --ColMode *ColNum | ColLabel* | |
| 473 Specify how columns are identified in *TextFile(s)*: using column | |
| 474 number or column label. Possible values: *ColNum or ColLabel*. | |
| 475 Default value: *ColNum*. | |
| 476 | |
| 477 --CompoundIDCol *col number | col name* | |
| 478 This value is -c, --ColMode mode specific. It specifies input | |
| 479 *TextFile(s)* column to use for generating compound ID for | |
| 480 similarity matrices in output *TextFile(s)*. Possible values: *col | |
| 481 number or col label*. Default value: *first column containing the | |
| 482 word compoundID in its column label or sequentially generated IDs*. | |
| 483 | |
| 484 --CompoundIDPrefix *text* | |
| 485 Specify compound ID prefix to use during sequential generation of | |
| 486 compound IDs for input *SDFile(s)* and *TextFile(s)*. Default value: | |
| 487 *Cmpd*. The default value generates compound IDs which look like | |
| 488 Cmpd<Number>. | |
| 489 | |
| 490 For input *SDFile(s)*, this value is only used during *LabelPrefix | | |
| 491 MolNameOrLabelPrefix* values of --CompoundIDMode option; otherwise, | |
| 492 it's ignored. | |
| 493 | |
| 494 Examples for *LabelPrefix* or *MolNameOrLabelPrefix* value of | |
| 495 --CompoundIDMode: | |
| 496 | |
| 497 Compound | |
| 498 | |
| 499 The values specified above generates compound IDs which correspond | |
| 500 to Compound<Number> instead of default value of Cmpd<Number>. | |
| 501 | |
| 502 --CompoundIDField *DataFieldName* | |
| 503 Specify input *SDFile(s)* datafield label for generating compound | |
| 504 IDs. This value is only used during *DataField* value of | |
| 505 --CompoundIDMode option. | |
| 506 | |
| 507 Examples for *DataField* value of --CompoundIDMode: | |
| 508 | |
| 509 MolID | |
| 510 ExtReg | |
| 511 | |
| 512 --CompoundIDMode *DataField | MolName | LabelPrefix | | |
| 513 MolNameOrLabelPrefix* | |
| 514 Specify how to generate compound IDs from input *SDFile(s)* for | |
| 515 similarity matrix CSV/TSV text file(s): use a *SDFile(s)* datafield | |
| 516 value; use molname line from *SDFile(s)*; generate a sequential ID | |
| 517 with specific prefix; use combination of both MolName and | |
| 518 LabelPrefix with usage of LabelPrefix values for empty molname | |
| 519 lines. | |
| 520 | |
| 521 Possible values: *DataField | MolName | LabelPrefix | | |
| 522 MolNameOrLabelPrefix*. Default: *LabelPrefix*. | |
| 523 | |
| 524 For *MolNameAndLabelPrefix* value of --CompoundIDMode, molname line | |
| 525 in *SDFile(s)* takes precedence over sequential compound IDs | |
| 526 generated using *LabelPrefix* and only empty molname values are | |
| 527 replaced with sequential compound IDs. | |
| 528 | |
| 529 -d, --detail *InfoLevel* | |
| 530 Level of information to print about lines being ignored. Default: | |
| 531 *1*. Possible values: *1, 2 or 3*. | |
| 532 | |
| 533 -f, --fast | |
| 534 In this mode, fingerprints columns specified using --FingerprintsCol | |
| 535 for *TextFile(s)* and --FingerprintsField for *SDFile(s)* are | |
| 536 assumed to contain valid fingerprints data and no checking is | |
| 537 performed before calculating similarity matrices. By default, | |
| 538 fingerprints data is validated before computing pairwise similarity | |
| 539 and distance coefficients. | |
| 540 | |
| 541 --FingerprintsCol *col number | col name* | |
| 542 This value is -c, --colmode specific. It specifies fingerprints | |
| 543 column to use during calculation similarity matrices for | |
| 544 *TextFile(s)*. Possible values: *col number or col label*. Default | |
| 545 value: *first column containing the word Fingerprints in its column | |
| 546 label*. | |
| 547 | |
| 548 --FingerprintsField *FieldLabel* | |
| 549 Fingerprints field label to use during calculation similarity | |
| 550 matrices for *SDFile(s)*. Default value: *first data field label | |
| 551 containing the word Fingerprints in its label* | |
| 552 | |
| 553 -h, --help | |
| 554 Print this help message. | |
| 555 | |
| 556 --InDelim *comma | semicolon* | |
| 557 Input delimiter for CSV *TextFile(s)*. Possible values: *comma or | |
| 558 semicolon*. Default value: *comma*. For TSV files, this option is | |
| 559 ignored and *tab* is used as a delimiter. | |
| 560 | |
| 561 --InputDataMode *LoadInMemory | ScanFile* | |
| 562 Specify how fingerprints bit-vector or vector strings data from *SD, | |
| 563 FP and CSV/TSV* fingerprint file(s) is processed: Retrieve, process | |
| 564 and load all available fingerprints data in memory; Retrieve and | |
| 565 process data for fingerprints one at a time. Possible values : | |
| 566 *LoadInMemory | ScanFile*. Default: *LoadInMemory*. | |
| 567 | |
| 568 During *LoadInMemory* value of --InputDataMode, fingerprints | |
| 569 bit-vector or vector strings data from input file is retrieved, | |
| 570 processed, and loaded into memory all at once as fingerprints | |
| 571 objects for generation for similarity matrices. | |
| 572 | |
| 573 During *ScanFile* value of --InputDataMode, multiple passes over the | |
| 574 input fingerprints file are performed to retrieve and process | |
| 575 fingerprints bit-vector or vector strings data one at a time to | |
| 576 generate fingerprints objects used during generation of similarity | |
| 577 matrices. A temporary copy of the input fingerprints file is made at | |
| 578 the start and deleted after generating the matrices. | |
| 579 | |
| 580 *ScanFile* value of --InputDataMode allows processing of arbitrary | |
| 581 large fingerprints files without any additional memory requirement. | |
| 582 | |
| 583 -m, --mode *AutoDetect | FingerprintsBitVectorString | | |
| 584 FingerprintsVectorString* | |
| 585 Format of fingerprint strings data in *TextFile(s)*: automatically | |
| 586 detect format of fingerprints string created by MayaChemTools | |
| 587 fingerprints generation scripts or explicitly specify its format. | |
| 588 Possible values: *AutoDetect | FingerprintsBitVectorString | | |
| 589 FingerprintsVectorString*. Default value: *AutoDetect*. | |
| 590 | |
| 591 --OutDelim *comma | tab | semicolon* | |
| 592 Delimiter for output CSV/TSV text file(s). Possible values: *comma, | |
| 593 tab, or semicolon* Default value: *comma*. | |
| 594 | |
| 595 --OutMatrixFormat *RowsAndColumns | IDPairsAndValue* | |
| 596 Specify how similarity or distance values calculated for | |
| 597 fingerprints vector and bit-vector strings are written to the output | |
| 598 CSV/TSV text file(s): Generate text files containing rows and | |
| 599 columns with their labels corresponding to compound IDs and each | |
| 600 matrix element value corresponding to similarity or distance between | |
| 601 corresponding compounds; Generate text files containing rows | |
| 602 containing compoundIDs for two compounds followed by similarity or | |
| 603 distance value between these compounds. | |
| 604 | |
| 605 Possible values: *RowsAndColumns, or IDPairsAndValue*. Default | |
| 606 value: *RowsAndColumns*. | |
| 607 | |
| 608 The value of --OutMatrixFormat in conjunction with --OutMatrixType | |
| 609 determines type of data written to output files and allows | |
| 610 generation of up to 6 different output data formats: | |
| 611 | |
| 612 OutMatrixFormat OutMatrixType | |
| 613 | |
| 614 RowsAndColumns FullMatrix [ DEFAULT ] | |
| 615 RowsAndColumns UpperTriangularMatrix | |
| 616 RowsAndColumns LowerTriangularMatrix | |
| 617 | |
| 618 IDPairsAndValue FullMatrix | |
| 619 IDPairsAndValue UpperTriangularMatrix | |
| 620 IDPairsAndValue LowerTriangularMatrix | |
| 621 | |
| 622 Example of data in output file for *RowsAndColumns* | |
| 623 --OutMatrixFormat value for *FullMatrix* valueof --OutMatrixType: | |
| 624 | |
| 625 "","Cmpd1","Cmpd2","Cmpd3","Cmpd4","Cmpd5","Cmpd6",... ... | |
| 626 "Cmpd1","1","0.04","0.25","0.13","0.11","0.2",... ... | |
| 627 "Cmpd2","0.04","1","0.06","0.05","0.19","0.07",... ... | |
| 628 "Cmpd3","0.25","0.06","1","0.12","0.22","0.25",... ... | |
| 629 "Cmpd4","0.13","0.05","0.12","1","0.11","0.13",... ... | |
| 630 "Cmpd5","0.11","0.19","0.22","0.11","1","0.17",... ... | |
| 631 "Cmpd6","0.2","0.07","0.25","0.13","0.17","1",... ... | |
| 632 ... ... .. | |
| 633 ... ... .. | |
| 634 ... ... .. | |
| 635 | |
| 636 Example of data in output file for *RowsAndColumns* | |
| 637 --OutMatrixFormat value for *UpperTriangularMatrix* value of | |
| 638 --OutMatrixType: | |
| 639 | |
| 640 "","Cmpd1","Cmpd2","Cmpd3","Cmpd4","Cmpd5","Cmpd6",... ... | |
| 641 "Cmpd1","1","0.04","0.25","0.13","0.11","0.2",... ... | |
| 642 "Cmpd2","1","0.06","0.05","0.19","0.07",... ... | |
| 643 "Cmpd3","1","0.12","0.22","0.25",... ... | |
| 644 "Cmpd4","1","0.11","0.13",... ... | |
| 645 "Cmpd5","1","0.17",... ... | |
| 646 "Cmpd6","1",... ... | |
| 647 ... ... .. | |
| 648 ... ... .. | |
| 649 ... ... .. | |
| 650 | |
| 651 Example of data in output file for *RowsAndColumns* | |
| 652 --OutMatrixFormat value for *LowerTriangularMatrix* value of | |
| 653 --OutMatrixType: | |
| 654 | |
| 655 "","Cmpd1","Cmpd2","Cmpd3","Cmpd4","Cmpd5","Cmpd6",... ... | |
| 656 "Cmpd1","1" | |
| 657 "Cmpd2","0.04","1" | |
| 658 "Cmpd3","0.25","0.06","1" | |
| 659 "Cmpd4","0.13","0.05","0.12","1" | |
| 660 "Cmpd5","0.11","0.19","0.22","0.11","1" | |
| 661 "Cmpd6","0.2","0.07","0.25","0.13","0.17","1" | |
| 662 ... ... .. | |
| 663 ... ... .. | |
| 664 ... ... .. | |
| 665 | |
| 666 Example of data in output file for *IDPairsAndValue* | |
| 667 --OutMatrixFormat value for <FullMatrix> value of OutMatrixType: | |
| 668 | |
| 669 "CmpdID1","CmpdID2","Coefficient Value" | |
| 670 "Cmpd1","Cmpd1","1" | |
| 671 "Cmpd1","Cmpd2","0.04" | |
| 672 "Cmpd1","Cmpd3","0.25" | |
| 673 "Cmpd1","Cmpd4","0.13" | |
| 674 ... ... ... | |
| 675 ... ... ... | |
| 676 ... ... ... | |
| 677 "Cmpd2","Cmpd1","0.04" | |
| 678 "Cmpd2","Cmpd2","1" | |
| 679 "Cmpd2","Cmpd3","0.06" | |
| 680 "Cmpd2","Cmpd4","0.05" | |
| 681 ... ... ... | |
| 682 ... ... ... | |
| 683 ... ... ... | |
| 684 "Cmpd3","Cmpd1","0.25" | |
| 685 "Cmpd3","Cmpd2","0.06" | |
| 686 "Cmpd3","Cmpd3","1" | |
| 687 "Cmpd3","Cmpd4","0.12" | |
| 688 ... ... ... | |
| 689 ... ... ... | |
| 690 ... ... ... | |
| 691 | |
| 692 Example of data in output file for *IDPairsAndValue* | |
| 693 --OutMatrixFormat value for <UpperTriangularMatrix> value of | |
| 694 --OutMatrixType: | |
| 695 | |
| 696 "CmpdID1","CmpdID2","Coefficient Value" | |
| 697 "Cmpd1","Cmpd1","1" | |
| 698 "Cmpd1","Cmpd2","0.04" | |
| 699 "Cmpd1","Cmpd3","0.25" | |
| 700 "Cmpd1","Cmpd4","0.13" | |
| 701 ... ... ... | |
| 702 ... ... ... | |
| 703 ... ... ... | |
| 704 "Cmpd2","Cmpd2","1" | |
| 705 "Cmpd2","Cmpd3","0.06" | |
| 706 "Cmpd2","Cmpd4","0.05" | |
| 707 ... ... ... | |
| 708 ... ... ... | |
| 709 ... ... ... | |
| 710 "Cmpd3","Cmpd3","1" | |
| 711 "Cmpd3","Cmpd4","0.12" | |
| 712 ... ... ... | |
| 713 ... ... ... | |
| 714 ... ... ... | |
| 715 | |
| 716 Example of data in output file for *IDPairsAndValue* | |
| 717 --OutMatrixFormat value for <LowerTriangularMatrix> value of | |
| 718 --OutMatrixType: | |
| 719 | |
| 720 "CmpdID1","CmpdID2","Coefficient Value" | |
| 721 "Cmpd1","Cmpd1","1" | |
| 722 "Cmpd2","Cmpd1","0.04" | |
| 723 "Cmpd2","Cmpd2","1" | |
| 724 "Cmpd3","Cmpd1","0.25" | |
| 725 "Cmpd3","Cmpd2","0.06" | |
| 726 "Cmpd3","Cmpd3","1" | |
| 727 "Cmpd4","Cmpd1","0.13" | |
| 728 "Cmpd4","Cmpd2","0.05" | |
| 729 "Cmpd4","Cmpd3","0.12" | |
| 730 "Cmpd4","Cmpd4","1" | |
| 731 ... ... ... | |
| 732 ... ... ... | |
| 733 ... ... ... | |
| 734 | |
| 735 --OutMatrixType *FullMatrix | UpperTriangularMatrix | | |
| 736 LowerTriangularMatrix* | |
| 737 Type of similarity or distance matrix to calculate for fingerprints | |
| 738 vector and bit-vector strings: Calculate full matrix; Calculate | |
| 739 lower triangular matrix including diagonal; Calculate upper | |
| 740 triangular matrix including diagonal. | |
| 741 | |
| 742 Possible values: *FullMatrix, UpperTriangularMatrix, or | |
| 743 LowerTriangularMatrix*. Default value: *FullMatrix*. | |
| 744 | |
| 745 The value of --OutMatrixType in conjunction with --OutMatrixFormat | |
| 746 determines type of data written to output files. | |
| 747 | |
| 748 -o, --overwrite | |
| 749 Overwrite existing files | |
| 750 | |
| 751 -p, --precision *number* | |
| 752 Precision of calculated values in the output file. Default: up to | |
| 753 *2* decimal places. Valid values: positive integers. | |
| 754 | |
| 755 -q, --quote *Yes | No* | |
| 756 Put quote around column values in output CSV/TSV text file(s). | |
| 757 Possible values: *Yes or No*. Default value: *Yes*. | |
| 758 | |
| 759 -r, --root *RootName* | |
| 760 New file name is generated using the root: | |
| 761 <Root><BitVectorComparisonMode>.<Ext> or | |
| 762 <Root><VectorComparisonMode><VectorComparisonFormulism>.<Ext>. The | |
| 763 csv, and tsv <Ext> values are used for comma/semicolon, and tab | |
| 764 delimited text files respectively. This option is ignored for | |
| 765 multiple input files. | |
| 766 | |
| 767 -v, --VectorComparisonMode *All | | |
| 768 "TanimotoSimilarity,[ManhattanDistance,...]"* | |
| 769 Specify what similarity or distance coefficients to use for | |
| 770 calculating similarity matrices for fingerprint vector strings data | |
| 771 values in *TextFile(s)*: calculate similarity matrices for all | |
| 772 supported similarity and distance coefficients or specify a comma | |
| 773 delimited list of similarity and distance coefficients. Possible | |
| 774 values: *All | "TanimotoSimilairy,[ManhattanDistance,..]"*. Default: | |
| 775 *TanimotoSimilarity*. | |
| 776 | |
| 777 The value of -v, --VectorComparisonMode, in conjunction with | |
| 778 --VectorComparisonFormulism, decides which type of similarity and | |
| 779 distance coefficient formulism gets used. | |
| 780 | |
| 781 *All* uses complete list of supported similarity and distance | |
| 782 coefficients: *CosineSimilarity, CzekanowskiSimilarity, | |
| 783 DiceSimilarity, OchiaiSimilarity, JaccardSimilarity, | |
| 784 SorensonSimilarity, TanimotoSimilarity, CityBlockDistance, | |
| 785 EuclideanDistance, HammingDistance, ManhattanDistance, | |
| 786 SoergelDistance*. These similarity and distance coefficients are | |
| 787 described below. | |
| 788 | |
| 789 FingerprintsVector.pm module, used to calculate similarity and | |
| 790 distance coefficients, provides support to perform comparison | |
| 791 between vectors containing three different types of values: | |
| 792 | |
| 793 Type I: OrderedNumericalValues | |
| 794 | |
| 795 . Size of two vectors are same | |
| 796 . Vectors contain real values in a specific order. For example: MACCS keys | |
| 797 count, Topological pharmnacophore atom pairs and so on. | |
| 798 | |
| 799 Type II: UnorderedNumericalValues | |
| 800 | |
| 801 . Size of two vectors might not be same | |
| 802 . Vectors contain unordered real value identified by value IDs. For example: | |
| 803 Toplogical atom pairs, Topological atom torsions and so on | |
| 804 | |
| 805 Type III: AlphaNumericalValues | |
| 806 | |
| 807 . Size of two vectors might not be same | |
| 808 . Vectors contain unordered alphanumerical values. For example: Extended | |
| 809 connectivity fingerprints, atom neighborhood fingerprints. | |
| 810 | |
| 811 Before performing similarity or distance calculations between | |
| 812 vectors containing UnorderedNumericalValues or AlphaNumericalValues, | |
| 813 the vectors are transformed into vectors containing unique | |
| 814 OrderedNumericalValues using value IDs for UnorderedNumericalValues | |
| 815 and values itself for AlphaNumericalValues. | |
| 816 | |
| 817 Three forms of similarity and distance calculation between two | |
| 818 vectors, specified using --VectorComparisonFormulism option, are | |
| 819 supported: *AlgebraicForm, BinaryForm or SetTheoreticForm*. | |
| 820 | |
| 821 For *BinaryForm*, the ordered list of processed final vector values | |
| 822 containing the value or count of each unique value type is simply | |
| 823 converted into a binary vector containing 1s and 0s corresponding to | |
| 824 presence or absence of values before calculating similarity or | |
| 825 distance between two vectors. | |
| 826 | |
| 827 For two fingerprint vectors A and B of same size containing | |
| 828 OrderedNumericalValues, let: | |
| 829 | |
| 830 N = Number values in A or B | |
| 831 | |
| 832 Xa = Values of vector A | |
| 833 Xb = Values of vector B | |
| 834 | |
| 835 Xai = Value of ith element in A | |
| 836 Xbi = Value of ith element in B | |
| 837 | |
| 838 SUM = Sum of i over N values | |
| 839 | |
| 840 For SetTheoreticForm of calculation between two vectors, let: | |
| 841 | |
| 842 SetIntersectionXaXb = SUM ( MIN ( Xai, Xbi ) ) | |
| 843 SetDifferenceXaXb = SUM ( Xai ) + SUM ( Xbi ) - SUM ( MIN ( Xai, Xbi ) ) | |
| 844 | |
| 845 For BinaryForm of calculation between two vectors, let: | |
| 846 | |
| 847 Na = Number of bits set to "1" in A = SUM ( Xai ) | |
| 848 Nb = Number of bits set to "1" in B = SUM ( Xbi ) | |
| 849 Nc = Number of bits set to "1" in both A and B = SUM ( Xai * Xbi ) | |
| 850 Nd = Number of bits set to "0" in both A and B | |
| 851 = SUM ( 1 - Xai - Xbi + Xai * Xbi) | |
| 852 | |
| 853 N = Number of bits set to "1" or "0" in A or B = Size of A or B = Na + Nb - Nc + Nd | |
| 854 | |
| 855 Additionally, for BinaryForm various values also correspond to: | |
| 856 | |
| 857 Na = | Xa | | |
| 858 Nb = | Xb | | |
| 859 Nc = | SetIntersectionXaXb | | |
| 860 Nd = N - | SetDifferenceXaXb | | |
| 861 | |
| 862 | SetDifferenceXaXb | = N - Nd = Na + Nb - Nc + Nd - Nd = Na + Nb - Nc | |
| 863 = | Xa | + | Xb | - | SetIntersectionXaXb | | |
| 864 | |
| 865 Various similarity and distance coefficients [ Ref 40, Ref 62, Ref | |
| 866 64 ] for a pair of vectors A and B in *AlgebraicForm, BinaryForm and | |
| 867 SetTheoreticForm* are defined as follows: | |
| 868 | |
| 869 CityBlockDistance: ( same as HammingDistance and ManhattanDistance) | |
| 870 | |
| 871 *AlgebraicForm*: SUM ( ABS ( Xai - Xbi ) ) | |
| 872 | |
| 873 *BinaryForm*: ( Na - Nc ) + ( Nb - Nc ) = Na + Nb - 2 * Nc | |
| 874 | |
| 875 *SetTheoreticForm*: | SetDifferenceXaXb | - | SetIntersectionXaXb | | |
| 876 = SUM ( Xai ) + SUM ( Xbi ) - 2 * ( SUM ( MIN ( Xai, Xbi ) ) ) | |
| 877 | |
| 878 CosineSimilarity: ( same as OchiaiSimilarityCoefficient) | |
| 879 | |
| 880 *AlgebraicForm*: SUM ( Xai * Xbi ) / SQRT ( SUM ( Xai ** 2) * SUM ( | |
| 881 Xbi ** 2) ) | |
| 882 | |
| 883 *BinaryForm*: Nc / SQRT ( Na * Nb) | |
| 884 | |
| 885 *SetTheoreticForm*: | SetIntersectionXaXb | / SQRT ( |Xa| * |Xb| ) = | |
| 886 SUM ( MIN ( Xai, Xbi ) ) / SQRT ( SUM ( Xai ) * SUM ( Xbi ) ) | |
| 887 | |
| 888 CzekanowskiSimilarity: ( same as DiceSimilarity and | |
| 889 SorensonSimilarity) | |
| 890 | |
| 891 *AlgebraicForm*: ( 2 * ( SUM ( Xai * Xbi ) ) ) / ( SUM ( Xai ** 2) + | |
| 892 SUM ( Xbi **2 ) ) | |
| 893 | |
| 894 *BinaryForm*: 2 * Nc / ( Na + Nb ) | |
| 895 | |
| 896 *SetTheoreticForm*: 2 * | SetIntersectionXaXb | / ( |Xa| + |Xb| ) = | |
| 897 2 * ( SUM ( MIN ( Xai, Xbi ) ) ) / ( SUM ( Xai ) + SUM ( Xbi ) ) | |
| 898 | |
| 899 DiceSimilarity: ( same as CzekanowskiSimilarity and | |
| 900 SorensonSimilarity) | |
| 901 | |
| 902 *AlgebraicForm*: ( 2 * ( SUM ( Xai * Xbi ) ) ) / ( SUM ( Xai ** 2) + | |
| 903 SUM ( Xbi **2 ) ) | |
| 904 | |
| 905 *BinaryForm*: 2 * Nc / ( Na + Nb ) | |
| 906 | |
| 907 *SetTheoreticForm*: 2 * | SetIntersectionXaXb | / ( |Xa| + |Xb| ) = | |
| 908 2 * ( SUM ( MIN ( Xai, Xbi ) ) ) / ( SUM ( Xai ) + SUM ( Xbi ) ) | |
| 909 | |
| 910 EuclideanDistance: | |
| 911 | |
| 912 *AlgebraicForm*: SQRT ( SUM ( ( ( Xai - Xbi ) ** 2 ) ) ) | |
| 913 | |
| 914 *BinaryForm*: SQRT ( ( Na - Nc ) + ( Nb - Nc ) ) = SQRT ( Na + Nb - | |
| 915 2 * Nc ) | |
| 916 | |
| 917 *SetTheoreticForm*: SQRT ( | SetDifferenceXaXb | - | | |
| 918 SetIntersectionXaXb | ) = SQRT ( SUM ( Xai ) + SUM ( Xbi ) - 2 * ( | |
| 919 SUM ( MIN ( Xai, Xbi ) ) ) ) | |
| 920 | |
| 921 HammingDistance: ( same as CityBlockDistance and ManhattanDistance) | |
| 922 | |
| 923 *AlgebraicForm*: SUM ( ABS ( Xai - Xbi ) ) | |
| 924 | |
| 925 *BinaryForm*: ( Na - Nc ) + ( Nb - Nc ) = Na + Nb - 2 * Nc | |
| 926 | |
| 927 *SetTheoreticForm*: | SetDifferenceXaXb | - | SetIntersectionXaXb | | |
| 928 = SUM ( Xai ) + SUM ( Xbi ) - 2 * ( SUM ( MIN ( Xai, Xbi ) ) ) | |
| 929 | |
| 930 JaccardSimilarity: ( same as TanimotoSimilarity) | |
| 931 | |
| 932 *AlgebraicForm*: SUM ( Xai * Xbi ) / ( SUM ( Xai ** 2 ) + SUM ( Xbi | |
| 933 ** 2 ) - SUM ( Xai * Xbi ) ) | |
| 934 | |
| 935 *BinaryForm*: Nc / ( ( Na - Nc ) + ( Nb - Nc ) + Nc ) = Nc / ( Na + | |
| 936 Nb - Nc ) | |
| 937 | |
| 938 *SetTheoreticForm*: | SetIntersectionXaXb | / | SetDifferenceXaXb | | |
| 939 = SUM ( MIN ( Xai, Xbi ) ) / ( SUM ( Xai ) + SUM ( Xbi ) - SUM ( MIN | |
| 940 ( Xai, Xbi ) ) ) | |
| 941 | |
| 942 ManhattanDistance: ( same as CityBlockDistance and HammingDistance) | |
| 943 | |
| 944 *AlgebraicForm*: SUM ( ABS ( Xai - Xbi ) ) | |
| 945 | |
| 946 *BinaryForm*: ( Na - Nc ) + ( Nb - Nc ) = Na + Nb - 2 * Nc | |
| 947 | |
| 948 *SetTheoreticForm*: | SetDifferenceXaXb | - | SetIntersectionXaXb | | |
| 949 = SUM ( Xai ) + SUM ( Xbi ) - 2 * ( SUM ( MIN ( Xai, Xbi ) ) ) | |
| 950 | |
| 951 OchiaiSimilarity: ( same as CosineSimilarity) | |
| 952 | |
| 953 *AlgebraicForm*: SUM ( Xai * Xbi ) / SQRT ( SUM ( Xai ** 2) * SUM ( | |
| 954 Xbi ** 2) ) | |
| 955 | |
| 956 *BinaryForm*: Nc / SQRT ( Na * Nb) | |
| 957 | |
| 958 *SetTheoreticForm*: | SetIntersectionXaXb | / SQRT ( |Xa| * |Xb| ) = | |
| 959 SUM ( MIN ( Xai, Xbi ) ) / SQRT ( SUM ( Xai ) * SUM ( Xbi ) ) | |
| 960 | |
| 961 SorensonSimilarity: ( same as CzekanowskiSimilarity and | |
| 962 DiceSimilarity) | |
| 963 | |
| 964 *AlgebraicForm*: ( 2 * ( SUM ( Xai * Xbi ) ) ) / ( SUM ( Xai ** 2) + | |
| 965 SUM ( Xbi **2 ) ) | |
| 966 | |
| 967 *BinaryForm*: 2 * Nc / ( Na + Nb ) | |
| 968 | |
| 969 *SetTheoreticForm*: 2 * | SetIntersectionXaXb | / ( |Xa| + |Xb| ) = | |
| 970 2 * ( SUM ( MIN ( Xai, Xbi ) ) ) / ( SUM ( Xai ) + SUM ( Xbi ) ) | |
| 971 | |
| 972 SoergelDistance: | |
| 973 | |
| 974 *AlgebraicForm*: SUM ( ABS ( Xai - Xbi ) ) / SUM ( MAX ( Xai, Xbi ) | |
| 975 ) | |
| 976 | |
| 977 *BinaryForm*: 1 - Nc / ( Na + Nb - Nc ) = ( Na + Nb - 2 * Nc ) / ( | |
| 978 Na + Nb - Nc ) | |
| 979 | |
| 980 *SetTheoreticForm*: ( | SetDifferenceXaXb | - | SetIntersectionXaXb | |
| 981 | ) / | SetDifferenceXaXb | = ( SUM ( Xai ) + SUM ( Xbi ) - 2 * ( | |
| 982 SUM ( MIN ( Xai, Xbi ) ) ) ) / ( SUM ( Xai ) + SUM ( Xbi ) - SUM ( | |
| 983 MIN ( Xai, Xbi ) ) ) | |
| 984 | |
| 985 TanimotoSimilarity: ( same as JaccardSimilarity) | |
| 986 | |
| 987 *AlgebraicForm*: SUM ( Xai * Xbi ) / ( SUM ( Xai ** 2 ) + SUM ( Xbi | |
| 988 ** 2 ) - SUM ( Xai * Xbi ) ) | |
| 989 | |
| 990 *BinaryForm*: Nc / ( ( Na - Nc ) + ( Nb - Nc ) + Nc ) = Nc / ( Na + | |
| 991 Nb - Nc ) | |
| 992 | |
| 993 *SetTheoreticForm*: | SetIntersectionXaXb | / | SetDifferenceXaXb | | |
| 994 = SUM ( MIN ( Xai, Xbi ) ) / ( SUM ( Xai ) + SUM ( Xbi ) - SUM ( MIN | |
| 995 ( Xai, Xbi ) ) ) | |
| 996 | |
| 997 --VectorComparisonFormulism *All | | |
| 998 "AlgebraicForm,[BinaryForm,SetTheoreticForm]"* | |
| 999 Specify fingerprints vector comparison formulism to use for | |
| 1000 calculation similarity and distance coefficients during -v, | |
| 1001 --VectorComparisonMode: use all supported comparison formulisms or | |
| 1002 specify a comma delimited. Possible values: *All | | |
| 1003 "AlgebraicForm,[BinaryForm,SetTheoreticForm]"*. Default value: | |
| 1004 *AlgebraicForm*. | |
| 1005 | |
| 1006 *All* uses all three forms of supported vector comparison formulism | |
| 1007 for values of -v, --VectorComparisonMode option. | |
| 1008 | |
| 1009 For fingerprint vector strings containing AlphaNumericalValues data | |
| 1010 values - ExtendedConnectivityFingerprints, | |
| 1011 AtomNeighborhoodsFingerprints and so on - all three formulism result | |
| 1012 in same value during similarity and distance calculations. | |
| 1013 | |
| 1014 -w, --WorkingDir *DirName* | |
| 1015 Location of working directory. Default: current directory. | |
| 1016 | |
| 1017 EXAMPLES | |
| 1018 To generate a similarity matrix corresponding to Tanimoto similarity | |
| 1019 coefficient for fingerprints bit-vector strings data corresponding to | |
| 1020 supported fingerprints in text file present in a column name containing | |
| 1021 Fingerprint substring by loading all fingerprints data into memory and | |
| 1022 create a SampleFPHexTanimotoSimilarity.csv file containing compound IDs | |
| 1023 retrieved from column name containing CompoundID substring, type: | |
| 1024 | |
| 1025 % SimilarityMatricesFingerprints.pl -o SampleFPHex.csv | |
| 1026 | |
| 1027 To generate a similarity matrix corresponding to Tanimoto similarity | |
| 1028 coefficient for fingerprints bit-vector strings data corresponding to | |
| 1029 supported fingerprints in SD File present in a data field with | |
| 1030 Fingerprint substring in its label by loading all fingerprints data into | |
| 1031 memory and create a SampleFPHexTanimotoSimilarity.csv file containing | |
| 1032 sequentially generated compound IDs with Cmpd prefix, type: | |
| 1033 | |
| 1034 % SimilarityMatricesFingerprints.pl -o SampleFPHex.sdf | |
| 1035 | |
| 1036 To generate a similarity matrix corresponding to Tanimoto similarity | |
| 1037 coefficient for fingerprints bit-vector strings data corresponding to | |
| 1038 supported fingerprints in FP file by loading all fingerprints data into | |
| 1039 memory and create a SampleFPHexTanimotoSimilarity.csv file along with | |
| 1040 compound IDs retrieved from FP file, type: | |
| 1041 | |
| 1042 % SimilarityMatricesFingerprints.pl -o SampleFPHex.fpf | |
| 1043 | |
| 1044 To generate a lower triangular similarity matrix corresponding to | |
| 1045 Tanimoto similarity coefficient for fingerprints bit-vector strings data | |
| 1046 corresponding to supported fingerprints in text file present in a column | |
| 1047 name containing Fingerprint substring by loading all fingerprints data | |
| 1048 into memory and create a SampleFPHexTanimotoSimilarity.csv file | |
| 1049 containing compound IDs retrieved from column name containing CompoundID | |
| 1050 substring, type: | |
| 1051 | |
| 1052 % SimilarityMatricesFingerprints.pl -o --InputDataMode LoadInMemory | |
| 1053 --OutMatrixFormat RowsAndColumns --OutMatrixType LowerTriangularMatrix | |
| 1054 SampleFPHex.csv | |
| 1055 | |
| 1056 To generate a upper triangular similarity matrix corresponding to | |
| 1057 Tanimoto similarity coefficient for fingerprints bit-vector strings data | |
| 1058 corresponding to supported fingerprints in text file present in a column | |
| 1059 name containing Fingerprint substring by loading all fingerprints data | |
| 1060 into memory and create a SampleFPHexTanimotoSimilarity.csv file in | |
| 1061 IDPairsAndValue format containing compound IDs retrieved from column | |
| 1062 name containing CompoundID substring, type: | |
| 1063 | |
| 1064 % SimilarityMatricesFingerprints.pl -o --InputDataMode LoadInMemory | |
| 1065 --OutMatrixFormat IDPairsAndValue --OutMatrixType UpperTriangularMatrix | |
| 1066 SampleFPHex.csv | |
| 1067 | |
| 1068 To generate a full similarity matrix corresponding to Tanimoto | |
| 1069 similarity coefficient for fingerprints bit-vector strings data | |
| 1070 corresponding to supported fingerprints in text file present in a column | |
| 1071 name containing Fingerprint substring by scanning file without loading | |
| 1072 all fingerprints data into memory and create a | |
| 1073 SampleFPHexTanimotoSimilarity.csv file containing compound IDs retrieved | |
| 1074 from column name containing CompoundID substring, type: | |
| 1075 | |
| 1076 % SimilarityMatricesFingerprints.pl -o --InputDataMode ScanFile | |
| 1077 --OutMatrixFormat RowsAndColumns --OutMatrixType FullMatrix | |
| 1078 SampleFPHex.csv | |
| 1079 | |
| 1080 To generate a lower triangular similarity matrix corresponding to | |
| 1081 Tanimoto similarity coefficient for fingerprints bit-vector strings data | |
| 1082 corresponding to supported fingerprints in text file present in a column | |
| 1083 name containing Fingerprint substring by scanning file without loading | |
| 1084 all fingerprints data into memory and create a | |
| 1085 SampleFPHexTanimotoSimilarity.csv file in IDPairsAndValue format | |
| 1086 containing compound IDs retrieved from column name containing CompoundID | |
| 1087 substring, type: | |
| 1088 | |
| 1089 % SimilarityMatricesFingerprints.pl -o --InputDataMode ScanFile | |
| 1090 --OutMatrixFormat IDPairsAndValue --OutMatrixType LowerTriangularMatrix | |
| 1091 SampleFPHex.csv | |
| 1092 | |
| 1093 To generate a similarity matrix corresponding to Tanimoto similarity | |
| 1094 coefficient using algebraic formulism for fingerprints vector strings | |
| 1095 data corresponding to supported fingerprints in text file present in a | |
| 1096 column name containing Fingerprint substring and create a | |
| 1097 SampleFPCountTanimotoSimilarityAlgebraicForm.csv file containing | |
| 1098 compound IDs retrieved from column name containing CompoundID substring, | |
| 1099 type: | |
| 1100 | |
| 1101 % SimilarityMatricesFingerprints.pl -o SampleFPCount.csv | |
| 1102 | |
| 1103 To generate a similarity matrix corresponding to Tanimoto similarity | |
| 1104 coefficient using algebraic formulism for fingerprints vector strings | |
| 1105 data corresponding to supported fingerprints in SD file present in a | |
| 1106 data field with Fingerprint substring in its label and create a | |
| 1107 SampleFPCountTanimotoSimilarityAlgebraicForm.csv file containing | |
| 1108 sequentially generated compound IDs with Cmpd prefix, type: | |
| 1109 | |
| 1110 % SimilarityMatricesFingerprints.pl -o SampleFPCount.sdf | |
| 1111 | |
| 1112 To generate a similarity matrix corresponding to Tanimoto similarity | |
| 1113 coefficient using algebraic formulism vector strings data corresponding | |
| 1114 to supported fingerprints in FP file and create a | |
| 1115 SampleFPCountTanimotoSimilarityAlgebraicForm.csv file along with | |
| 1116 compound IDs retrieved from FP file, type: | |
| 1117 | |
| 1118 % SimilarityMatricesFingerprints.pl -o SampleFPCount.fpf | |
| 1119 | |
| 1120 To generate a similarity matrix corresponding to Tanimoto similarity | |
| 1121 coefficient for fingerprints bit-vector strings data corresponding to | |
| 1122 supported fingerprints in text file present in a column name containing | |
| 1123 Fingerprint substring and create a SampleFPHexTanimotoSimilarity.csv | |
| 1124 file in IDPairsAndValue format containing compound IDs retrieved from | |
| 1125 column name containing CompoundID substring, type: | |
| 1126 | |
| 1127 % SimilarityMatricesFingerprints.pl --OutMatrixFormat IDPairsAndValue -o | |
| 1128 SampleFPHex.csv | |
| 1129 | |
| 1130 To generate a similarity matrix corresponding to Tanimoto similarity | |
| 1131 coefficient for fingerprints bit-vector strings data corresponding to | |
| 1132 supported fingerprints in SD file present in a data field with | |
| 1133 Fingerprint substring in its label and create a | |
| 1134 SampleFPHexTanimotoSimilarity.csv file in IDPairsAndValue format | |
| 1135 containing sequentially generated compound IDs with Cmpd prefix, type: | |
| 1136 | |
| 1137 % SimilarityMatricesFingerprints.pl --OutMatrixFormat IDPairsAndValue -o | |
| 1138 SampleFPHex.sdf | |
| 1139 | |
| 1140 To generate a similarity matrix corresponding to Tanimoto similarity | |
| 1141 coefficient for fingerprints bit-vector strings data corresponding to | |
| 1142 supported fingerprints in FP file and create a | |
| 1143 SampleFPHexTanimotoSimilarity.csv file in IDPairsAndValue format along | |
| 1144 with compound IDs retrieved from FP file, type: | |
| 1145 | |
| 1146 % SimilarityMatricesFingerprints.pl --OutMatrixFormat IDPairsAndValue -o | |
| 1147 SampleFPHex.fpf | |
| 1148 | |
| 1149 To generate a similarity matrix corresponding to Tanimoto similarity | |
| 1150 coefficient for fingerprints bit-vector strings data corresponding to | |
| 1151 supported fingerprints in SD file present in a data field with | |
| 1152 Fingerprint substring in its label and create a | |
| 1153 SampleFPHexTanimotoSimilarity.csv file containing compound IDs from mol | |
| 1154 name line, type: | |
| 1155 | |
| 1156 % SimilarityMatricesFingerprints.pl --CompoundIDMode MolName -o | |
| 1157 SampleFPHex.sdf | |
| 1158 | |
| 1159 To generate a similarity matrix corresponding to Tanimoto similarity | |
| 1160 coefficient for fingerprints bit-vector strings data corresponding to | |
| 1161 supported fingerprints present in a data field with Fingerprint | |
| 1162 substring in its label and create a SampleFPHexTanimotoSimilarity.csv | |
| 1163 file containing compound IDs from data field name Mol_ID, type: | |
| 1164 | |
| 1165 % SimilarityMatricesFingerprints.pl --CompoundIDMode DataField | |
| 1166 --CompoundIDField Mol_ID -o SampleFPBin.sdf | |
| 1167 | |
| 1168 To generate similarity matrices corresponding to Buser, Dice and | |
| 1169 Tanimoto similarity coefficient for fingerprints bit-vector strings data | |
| 1170 corresponding to supported fingerprints present in a column name | |
| 1171 containing Fingerprint substring and create | |
| 1172 SampleFPBin[CoefficientName]Similarity.csv files containing compound IDs | |
| 1173 retrieved from column name containing CompoundID substring, type: | |
| 1174 | |
| 1175 % SimilarityMatricesFingerprints.pl -b "BuserSimilarity,DiceSimilarity, | |
| 1176 TanimotoSimilarity" -o SampleFPBin.csv | |
| 1177 | |
| 1178 To generate similarity matrices corresponding to Buser, Dice and | |
| 1179 Tanimoto similarity coefficient for fingerprints bit-vector strings data | |
| 1180 corresponding to supported fingerprints present in a data field with | |
| 1181 Fingerprint substring in its label and create | |
| 1182 SampleFPBin[CoefficientName]Similarity.csv files containing sequentially | |
| 1183 generated compound IDs with Cmpd prefix, type: | |
| 1184 | |
| 1185 % SimilarityMatricesFingerprints.pl -b "BuserSimilarity,DiceSimilarity, | |
| 1186 TanimotoSimilarity" -o SampleFPBin.sdf | |
| 1187 | |
| 1188 To generate similarity matrices corresponding to CityBlock distance and | |
| 1189 Tanimoto similarity coefficients using algebraic formulism for | |
| 1190 fingerprints vector strings data corresponding to supported fingerprints | |
| 1191 present in a column name containing Fingerprint substring and create | |
| 1192 SampleFPCount[CoefficientName]AlgebraicForm.csv files containing | |
| 1193 compound IDs retrieved from column name containing CompoundID substring, | |
| 1194 type: | |
| 1195 | |
| 1196 % SimilarityMatricesFingerprints.pl -v "CityBlockDistance, | |
| 1197 TanimotoSimilarity" -o SampleFPCount.csv | |
| 1198 | |
| 1199 To generate similarity matrices corresponding to CityBlock distance and | |
| 1200 Tanimoto similarity coefficients using algebraic formulism for | |
| 1201 fingerprints vector strings data corresponding to supported fingerprints | |
| 1202 present in a data field with Fingerprint substring in its label and | |
| 1203 create SampleFPCount[CoefficientName]AlgebraicForm.csv files containing | |
| 1204 sequentially generated compound IDs with Cmpd prefix, type: | |
| 1205 | |
| 1206 % SimilarityMatricesFingerprints.pl -v "CityBlockDistance, | |
| 1207 TanimotoSimilarity" -o SampleFPCount.sdf | |
| 1208 | |
| 1209 To generate similarity matrices corresponding to CityBlock distance | |
| 1210 Tanimoto similarity coefficients using binary formulism for fingerprints | |
| 1211 vector strings data corresponding to supported fingerprints present in a | |
| 1212 column name containing Fingerprint substring and create | |
| 1213 SampleFPCount[CoefficientName]Binary.csv files containing compound IDs | |
| 1214 retrieved from column name containing CompoundID substring, type: | |
| 1215 | |
| 1216 % SimilarityMatricesFingerprints.pl -v "CityBlockDistance, | |
| 1217 TanimotoSimilarity" --VectorComparisonFormulism BinaryForm -o | |
| 1218 SampleFPCount.csv | |
| 1219 | |
| 1220 To generate similarity matrices corresponding to CityBlock distance | |
| 1221 Tanimoto similarity coefficients using binary formulism for fingerprints | |
| 1222 vector strings data corresponding to supported fingerprints present in a | |
| 1223 data field with Fingerprint substring in its label and create | |
| 1224 SampleFPCount[CoefficientName]Binary.csv files containing sequentially | |
| 1225 generated compound IDs with Cmpd prefix, type: | |
| 1226 | |
| 1227 % SimilarityMatricesFingerprints.pl -v "CityBlockDistance, | |
| 1228 TanimotoSimilarity" --VectorComparisonFormulism BinaryForm -o | |
| 1229 SampleFPCount.sdf | |
| 1230 | |
| 1231 To generate similarity matrices corresponding to CityBlock distance | |
| 1232 Tanimoto similarity coefficients using all supported comparison | |
| 1233 formulisms for fingerprints vector strings data corresponding to | |
| 1234 supported fingerprints present in a column name containing Fingerprint | |
| 1235 substring and create SampleFPCount[CoefficientName][FormulismName].csv | |
| 1236 files containing compound IDs retrieved from column name containing | |
| 1237 CompoundID substring, type: | |
| 1238 | |
| 1239 % SimilarityMatricesFingerprints.pl -v "CityBlockDistance, | |
| 1240 TanimotoSimilarity" --VectorComparisonFormulism All -o SampleFPCount.csv | |
| 1241 | |
| 1242 To generate similarity matrices corresponding to CityBlock distance | |
| 1243 Tanimoto similarity coefficients using all supported comparison | |
| 1244 formulisms for fingerprints vector strings data corresponding to | |
| 1245 supported fingerprints present in a data field with Fingerprint | |
| 1246 substring in its label and create | |
| 1247 SampleFPCount[CoefficientName][FormulismName].csv files containing | |
| 1248 sequentially generated compound IDs with Cmpd prefix, type: | |
| 1249 | |
| 1250 % SimilarityMatricesFingerprints.pl -v "CityBlockDistance,TanimotoSimilarity" | |
| 1251 --VectorComparisonFormulism All -o SampleFPCount.sdf | |
| 1252 | |
| 1253 To generate similarity matrices corresponding to all available | |
| 1254 similarity coefficient for fingerprints bit-vector strings data | |
| 1255 corresponding to supported fingerprints present in a column name | |
| 1256 containing Fingerprint substring and create | |
| 1257 SampleFPHex[CoefficientName].csv files containing compound IDs retrieved | |
| 1258 from column name containing CompoundID substring, type: | |
| 1259 | |
| 1260 % SimilarityMatricesFingerprints.pl -m AutoDetect --BitVectorComparisonMode | |
| 1261 All --alpha 0.5 -beta 0.5 -o SampleFPHex.csv | |
| 1262 | |
| 1263 To generate similarity matrices corresponding to all available | |
| 1264 similarity coefficient for fingerprints bit-vector strings data | |
| 1265 corresponding to supported fingerprints present in a data field with | |
| 1266 Fingerprint substring in its label and create | |
| 1267 SampleFPHex[CoefficientName].csv files containing sequentially generated | |
| 1268 compound IDs with Cmpd prefix, type | |
| 1269 | |
| 1270 % SimilarityMatricesFingerprints.pl -m AutoDetect --BitVectorComparisonMode | |
| 1271 All --alpha 0.5 -beta 0.5 -o SampleFPHex.sdf | |
| 1272 | |
| 1273 To generate similarity matrices corresponding to all available | |
| 1274 similarity and distance coefficients using all comparison formulism for | |
| 1275 fingerprints vector strings data corresponding to supported fingerprints | |
| 1276 present in a column name containing Fingerprint substring and create | |
| 1277 SampleFPCount[CoefficientName][FormulismName].csv files containing | |
| 1278 compound IDs retrieved from column name containing CompoundID substring, | |
| 1279 type: | |
| 1280 | |
| 1281 % SimilarityMatricesFingerprints.pl -m AutoDetect --VectorComparisonMode | |
| 1282 All --VectorComparisonFormulism All -o SampleFPCount.csv | |
| 1283 | |
| 1284 To generate similarity matrices corresponding to all available | |
| 1285 similarity and distance coefficients using all comparison formulism for | |
| 1286 fingerprints vector strings data corresponding to supported fingerprints | |
| 1287 present in a data field with Fingerprint substring in its label and | |
| 1288 create SampleFPCount[CoefficientName][FormulismName].csv files | |
| 1289 containing sequentially generated compound IDs with Cmpd prefix, type: | |
| 1290 | |
| 1291 % SimilarityMatricesFingerprints.pl -m AutoDetect --VectorComparisonMode | |
| 1292 All --VectorComparisonFormulism All -o SampleFPCount.sdf | |
| 1293 | |
| 1294 To generate a similarity matrix corresponding to Tanimoto similarity | |
| 1295 coefficient for fingerprints bit-vector strings data corresponding to | |
| 1296 supported fingerprints present in a column number 2 and create a | |
| 1297 SampleFPHexTanimotoSimilarity.csv file containing compound IDs retrieved | |
| 1298 column number 1, type: | |
| 1299 | |
| 1300 % SimilarityMatricesFingerprints.pl --ColMode ColNum --CompoundIDCol 1 | |
| 1301 --FingerprintsCol 2 -o SampleFPHex.csv | |
| 1302 | |
| 1303 To generate a similarity matrix corresponding to Tanimoto similarity | |
| 1304 coefficient for fingerprints bit-vector strings data corresponding to | |
| 1305 supported fingerprints present in a data field name Fingerprints and | |
| 1306 create a SampleFPHexTanimotoSimilarity.csv file containing compound IDs | |
| 1307 present in data field name Mol_ID, type: | |
| 1308 | |
| 1309 % SimilarityMatricesFingerprints.pl --FingerprintsField Fingerprints | |
| 1310 --CompoundIDMode DataField --CompoundIDField Mol_ID -o SampleFPHex.sdf | |
| 1311 | |
| 1312 To generate a similarity matrix corresponding to Tversky similarity | |
| 1313 coefficient for fingerprints bit-vector strings data corresponding to | |
| 1314 supported fingerprints present in a column named Fingerprints and create | |
| 1315 a SampleFPHexTverskySimilarity.tsv file containing compound IDs | |
| 1316 retrieved column named CompoundID, type: | |
| 1317 | |
| 1318 % SimilarityMatricesFingerprints.pl --BitVectorComparisonMode | |
| 1319 TverskySimilarity --alpha 0.5 --ColMode ColLabel --CompoundIDCol | |
| 1320 CompoundID --FingerprintsCol Fingerprints --OutDelim Tab --quote No | |
| 1321 -o SampleFPHex.csv | |
| 1322 | |
| 1323 To generate a similarity matrix corresponding to Tanimoto similarity | |
| 1324 coefficient for fingerprints bit-vector strings data corresponding to | |
| 1325 supported fingerprints present in a data field with Fingerprint | |
| 1326 substring in its label and create a SampleFPHexTanimotoSimilarity.csv | |
| 1327 file containing compound IDs from molname line or sequentially generated | |
| 1328 compound IDs with Mol prefix, type: | |
| 1329 | |
| 1330 % SimilarityMatricesFingerprints.pl --CompoundIDMode MolnameOrLabelPrefix | |
| 1331 --CompoundIDPrefix Mol -o SampleFPHex.sdf | |
| 1332 | |
| 1333 To generate a similarity matrix corresponding to Tanimoto similarity | |
| 1334 coefficient for fingerprints bit-vector strings data corresponding to | |
| 1335 supported fingerprints present in a data field with Fingerprint | |
| 1336 substring in its label and create a SampleFPHexTanimotoSimilarity.tsv | |
| 1337 file containing sequentially generated compound IDs with Cmpd prefix, | |
| 1338 type: | |
| 1339 | |
| 1340 % SimilarityMatricesFingerprints.pl -OutDelim Tab --quote No -o SampleFPHex.sdf | |
| 1341 | |
| 1342 AUTHOR | |
| 1343 Manish Sud <msud@san.rr.com> | |
| 1344 | |
| 1345 SEE ALSO | |
| 1346 InfoFingerprintsFiles.pl, SimilaritySearchingFingerprints.pl, | |
| 1347 AtomNeighborhoodsFingerprints.pl, ExtendedConnectivityFingerprints.pl, | |
| 1348 MACCSKeysFingerprints.pl, PathLengthFingerprints.pl, | |
| 1349 TopologicalAtomPairsFingerprints.pl, | |
| 1350 TopologicalAtomTorsionsFingerprints.pl, | |
| 1351 TopologicalPharmacophoreAtomPairsFingerprints.pl, | |
| 1352 TopologicalPharmacophoreAtomTripletsFingerprints.pl | |
| 1353 | |
| 1354 COPYRIGHT | |
| 1355 Copyright (C) 2015 Manish Sud. All rights reserved. | |
| 1356 | |
| 1357 This file is part of MayaChemTools. | |
| 1358 | |
| 1359 MayaChemTools is free software; you can redistribute it and/or modify it | |
| 1360 under the terms of the GNU Lesser General Public License as published by | |
| 1361 the Free Software Foundation; either version 3 of the License, or (at | |
| 1362 your option) any later version. | |
| 1363 |