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| author | deepakjadmin |
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| date | Wed, 20 Jan 2016 09:23:18 -0500 |
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| 124 .\" ======================================================================== | |
| 125 .\" | |
| 126 .IX Title "SIMILARITYSEARCHINGFINGERPRINTS 1" | |
| 127 .TH SIMILARITYSEARCHINGFINGERPRINTS 1 "2015-03-29" "perl v5.14.2" "MayaChemTools" | |
| 128 .\" For nroff, turn off justification. Always turn off hyphenation; it makes | |
| 129 .\" way too many mistakes in technical documents. | |
| 130 .if n .ad l | |
| 131 .nh | |
| 132 .SH "NAME" | |
| 133 SimilaritySearchingFingerprints.pl \- Perform similarity search using fingerprints strings data in SD, FP and CSV/TSV text file(s) | |
| 134 .SH "SYNOPSIS" | |
| 135 .IX Header "SYNOPSIS" | |
| 136 SimilaritySearchingFingerprints.pl ReferenceFPFile DatabaseFPFile | |
| 137 .PP | |
| 138 SimilaritySearchingFingerprints.pl [\fB\-\-alpha\fR \fInumber\fR] [\fB\-\-beta\fR \fInumber\fR] | |
| 139 [\fB\-b, \-\-BitVectorComparisonMode\fR \fITanimotoSimilarity | TverskySimilarity | ...\fR] | |
| 140 [\fB\-\-DatabaseColMode\fR \fIColNum | ColLabel\fR] [\fB\-\-DatabaseCompoundIDCol\fR \fIcol number | col name\fR] | |
| 141 [\fB\-\-DatabaseCompoundIDPrefix\fR \fItext\fR] [\fB\-\-DatabaseCompoundIDField\fR \fIDataFieldName\fR] | |
| 142 [\fB\-\-DatabaseCompoundIDMode\fR \fIDataField | MolName | LabelPrefix | MolNameOrLabelPrefix\fR] | |
| 143 [\fB\-\-DatabaseDataCols\fR \fI\*(L"DataColNum1, DataColNum2,... \*(R" | DataColLabel1, DataCoLabel2,... "\fR] | |
| 144 [\fB\-\-DatabaseDataColsMode\fR \fIAll | Specify | CompoundID\fR] [\fB\-\-DatabaseDataFields\fR \fI\*(L"FieldLabel1, FieldLabel2,... \*(R"\fR] | |
| 145 [\fB\-\-DatabaseDataFieldsMode\fR \fIAll | Common | Specify | CompoundID\fR] | |
| 146 [\fB\-\-DatabaseFingerprintsCol\fR \fIcol number | col name\fR] [\fB\-\-DatabaseFingerprintsField\fR \fIFieldLabel\fR] | |
| 147 []\fB\-\-DistanceCutoff\fR \fInumber\fR] [\fB\-d, \-\-detail\fR \fIInfoLevel\fR] [\fB\-f, \-\-fast\fR] | |
| 148 [\fB\-\-FingerprintsMode\fR \fIAutoDetect | FingerprintsBitVectorString | FingerprintsVectorString\fR] | |
| 149 [\fB\-g, \-\-GroupFusionRule\fR \fIMax, Mean, Median, Min, Sum, Euclidean\fR] [\fB\-\-GroupFusionApplyCutoff\fR \fIYes | No\fR] | |
| 150 [\fB\-h, \-\-help\fR] [\fB\-\-InDelim\fR \fIcomma | semicolon\fR] [\fB\-k, \-\-KNN\fR \fIall | number\fR] | |
| 151 [\fB\-m, \-\-mode\fR \fIIndividualReference | MultipleReferences\fR] | |
| 152 [\fB\-n, \-\-NumOfSimilarMolecules\fR \fInumber\fR] [\fB\-\-OutDelim\fR \fIcomma | tab | semicolon\fR] | |
| 153 [\fB\-\-output\fR \fI\s-1SD\s0 | text | both\fR] [\fB\-o, \-\-overwrite\fR] | |
| 154 [\fB\-p, \-\-PercentSimilarMolecules\fR \fInumber\fR] [\fB\-\-precision\fR \fInumber\fR] [\fB\-q, \-\-quote\fR \fIYes | No\fR] | |
| 155 [\fB\-\-ReferenceColMode\fR \fIColNum | ColLabel\fR] [\fB\-\-ReferenceCompoundIDCol\fR \fIcol number | col name\fR] | |
| 156 [\fB\-\-ReferenceCompoundIDPrefix\fR \fItext\fR] [\fB\-\-ReferenceCompoundIDField\fR \fIDataFieldName\fR] | |
| 157 [\fB\-\-ReferenceCompoundIDMode\fR \fIDataField | MolName | LabelPrefix | MolNameOrLabelPrefix\fR] | |
| 158 [\fB\-\-ReferenceFingerprintsCol\fR \fIcol number | col name\fR] [\fB\-\-ReferenceFingerprintsField\fR \fIFieldLabel\fR] | |
| 159 [\fB\-r, \-\-root\fR \fIRootName\fR] [\fB\-s, \-\-SearchMode\fR \fISimilaritySearch | DissimilaritySearch\fR] | |
| 160 [\fB\-\-SimilarCountMode\fR \fINumOfSimilar | PercentSimilar\fR] [\fB\-\-SimilarityCutoff\fR \fInumber\fR] | |
| 161 [\fB\-v, \-\-VectorComparisonMode\fR \fITanimotoSimilairy | ... | ManhattanDistance | ...\fR] | |
| 162 [\fB\-\-VectorComparisonFormulism\fR \fIAlgebraicForm | BinaryForm | SetTheoreticForm\fR] | |
| 163 [\fB\-w, \-\-WorkingDir\fR dirname] ReferenceFingerprintsFile DatabaseFingerprintsFile | |
| 164 .SH "DESCRIPTION" | |
| 165 .IX Header "DESCRIPTION" | |
| 166 Perform molecular similarity search [ Ref 94\-113 ] using fingerprint bit-vector or vector strings | |
| 167 data in \fI\s-1SD\s0, \s-1FP\s0, or \s-1CSV/TSV\s0 text\fR files corresponding to \fIReferenceFingerprintsFile\fR and | |
| 168 \&\fIDatabaseFingerprintsFile\fR, and generate \s-1SD\s0 and \s-1CSV/TSV\s0 text file(s) containing database | |
| 169 molecules which are similar to reference molecule(s). The reference molecules are also referred | |
| 170 to as query or seed molecules and database molecules as target molecules in the literature. | |
| 171 .PP | |
| 172 The current release of MayaChemTools supports two types of similarity search modes: | |
| 173 \&\fIIndividualReference or MultipleReferences\fR. For default value of \fIMultipleReferences\fR for \fB\-m, \-\-mode\fR | |
| 174 option, reference molecules are considered as a set and \fB\-g, \-\-GroupFusionRule\fR is used to calculate | |
| 175 similarity of a database molecule against reference molecules set. The group fusion rule is also | |
| 176 referred to as data fusion of consensus scoring in the literature. However, for \fIIndividualReference\fR | |
| 177 value of \fB\-m, \-\-mode\fR option, reference molecules are treated as individual molecules and each reference | |
| 178 molecule is compared against a database molecule by itself to identify similar molecules. | |
| 179 .PP | |
| 180 The molecular dissimilarity search can also be performed using \fIDissimilaritySearch\fR value for | |
| 181 \&\fB\-s, \-\-SearchMode\fR option. During dissimilarity search or usage of distance comparison coefficient | |
| 182 in similarity similarity search, the meaning of fingerprints comparison value is automatically reversed | |
| 183 as shown below: | |
| 184 .PP | |
| 185 .Vb 1 | |
| 186 \& SeachMode ComparisonCoefficient ResultsSort ComparisonValues | |
| 187 \& | |
| 188 \& Similarity SimilarityCoefficient Descending Higher value imples | |
| 189 \& high similarity | |
| 190 \& Similarity DistanceCoefficient Ascending Lower value implies | |
| 191 \& high similarity | |
| 192 \& | |
| 193 \& Dissimilarity SimilarityCoefficient Ascending Lower value implies | |
| 194 \& high dissimilarity | |
| 195 \& Dissimilarity DistanceCoefficient Descending Higher value implies | |
| 196 \& high dissimilarity | |
| 197 .Ve | |
| 198 .PP | |
| 199 During \fIIndividualReference\fR value of \fB\-m, \-\-Mode\fR option for similarity search, fingerprints bit-vector | |
| 200 or vector string of each reference molecule is compared with database molecules using specified | |
| 201 similarity or distance coefficients to identify most similar molecules for each reference molecule. | |
| 202 Based on value of \fB\-\-SimilarCountMode\fR, up to \fB\-\-n, \-\-NumOfSimilarMolecules\fR or \fB\-p, | |
| 203 \&\-\-PercentSimilarMolecules\fR at specified \fB\-\-SimilarityCutoff\fR or \fB\-\-DistanceCutoff\fR are | |
| 204 identified for each reference molecule. | |
| 205 .PP | |
| 206 During \fIMultipleReferences\fR value \fB\-m, \-\-mode\fR option for similarity search, all reference molecules | |
| 207 are considered as a set and \fB\-g, \-\-GroupFusionRule\fR is used to calculate similarity of a database | |
| 208 molecule against reference molecules set either using all reference molecules or number of k\-nearest | |
| 209 neighbors (k\-NN) to a database molecule specified using \fB\-k, \-\-kNN\fR. The fingerprints bit-vector | |
| 210 or vector string of each reference molecule in a set is compared with a database molecule using | |
| 211 a similarity or distance coefficient specified via \fB\-b, \-\-BitVectorComparisonMode\fR or \fB\-v, | |
| 212 \&\-\-VectorComparisonMode\fR. The reference molecules whose comparison values with a database | |
| 213 molecule fall outside specified \fB\-\-SimilarityCutoff\fR or \fB\-\-DistanceCutoff\fR are ignored during \fIYes\fR | |
| 214 value of \fB\-\-GroupFusionApplyCutoff\fR. The specified \fB\-g, \-\-GroupFusionRule\fR is applied to | |
| 215 \&\fB\-k, \-\-kNN\fR reference molecules to calculate final similarity value between a database molecule | |
| 216 and reference molecules set. | |
| 217 .PP | |
| 218 The input fingerprints \fI\s-1SD\s0, \s-1FP\s0, or Text (\s-1CSV/TSV\s0)\fR files for \fIReferenceFingerprintsFile\fR and | |
| 219 \&\fIDatabaseTextFile\fR must contain valid fingerprint bit-vector or vector strings data corresponding to | |
| 220 same type of fingerprints. | |
| 221 .PP | |
| 222 The valid fingerprints \fISDFile\fR extensions are \fI.sdf\fR and \fI.sd\fR. The valid fingerprints \fIFPFile\fR | |
| 223 extensions are \fI.fpf\fR and \fI.fp\fR. The valid fingerprints \fITextFile (\s-1CSV/TSV\s0)\fR extensions are | |
| 224 \&\fI.csv\fR and \fI.tsv\fR for comma/semicolon and tab delimited text files respectively. The \fB\-\-indelim\fR | |
| 225 option determines the format of \fITextFile\fR. Any file which doesn't correspond to the format indicated | |
| 226 by \fB\-\-indelim\fR option is ignored. | |
| 227 .PP | |
| 228 Example of \fI\s-1FP\s0\fR file containing fingerprints bit-vector string data: | |
| 229 .PP | |
| 230 .Vb 10 | |
| 231 \& # | |
| 232 \& # Package = MayaChemTools 7.4 | |
| 233 \& # ReleaseDate = Oct 21, 2010 | |
| 234 \& # | |
| 235 \& # TimeStamp = Mon Mar 7 15:14:01 2011 | |
| 236 \& # | |
| 237 \& # FingerprintsStringType = FingerprintsBitVector | |
| 238 \& # | |
| 239 \& # Description = PathLengthBits:AtomicInvariantsAtomTypes:MinLength1:... | |
| 240 \& # Size = 1024 | |
| 241 \& # BitStringFormat = HexadecimalString | |
| 242 \& # BitsOrder = Ascending | |
| 243 \& # | |
| 244 \& Cmpd1 9c8460989ec8a49913991a6603130b0a19e8051c89184414953800cc21510... | |
| 245 \& Cmpd2 000000249400840040100042011001001980410c000000001010088001120... | |
| 246 \& ... ... | |
| 247 \& ... .. | |
| 248 .Ve | |
| 249 .PP | |
| 250 Example of \fI\s-1FP\s0\fR file containing fingerprints vector string data: | |
| 251 .PP | |
| 252 .Vb 10 | |
| 253 \& # | |
| 254 \& # Package = MayaChemTools 7.4 | |
| 255 \& # ReleaseDate = Oct 21, 2010 | |
| 256 \& # | |
| 257 \& # TimeStamp = Mon Mar 7 15:14:01 2011 | |
| 258 \& # | |
| 259 \& # FingerprintsStringType = FingerprintsVector | |
| 260 \& # | |
| 261 \& # Description = PathLengthBits:AtomicInvariantsAtomTypes:MinLength1:... | |
| 262 \& # VectorStringFormat = IDsAndValuesString | |
| 263 \& # VectorValuesType = NumericalValues | |
| 264 \& # | |
| 265 \& 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: | |
| 266 \& 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...; | |
| 267 \& 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 | |
| 268 \& 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 ... | |
| 269 \& 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 | |
| 270 \& O C CC=O CCCC CCCN CCCO CCNC CNC=N CNC=O CNCN CCCC=O CCCCC CCCCN CC...; | |
| 271 \& 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 | |
| 272 \& 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 ... | |
| 273 \& ... ... | |
| 274 \& ... ... | |
| 275 .Ve | |
| 276 .PP | |
| 277 Example of \fI\s-1SD\s0\fR file containing fingerprints bit-vector string data: | |
| 278 .PP | |
| 279 .Vb 10 | |
| 280 \& ... ... | |
| 281 \& ... ... | |
| 282 \& $$$$ | |
| 283 \& ... ... | |
| 284 \& ... ... | |
| 285 \& ... ... | |
| 286 \& 41 44 0 0 0 0 0 0 0 0999 V2000 | |
| 287 \& \-3.3652 1.4499 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 | |
| 288 \& ... ... | |
| 289 \& 2 3 1 0 0 0 0 | |
| 290 \& ... ... | |
| 291 \& M END | |
| 292 \& > <CmpdID> | |
| 293 \& Cmpd1 | |
| 294 \& | |
| 295 \& > <PathLengthFingerprints> | |
| 296 \& FingerprintsBitVector;PathLengthBits:AtomicInvariantsAtomTypes:MinLengt | |
| 297 \& h1:MaxLength8;1024;HexadecimalString;Ascending;9c8460989ec8a49913991a66 | |
| 298 \& 03130b0a19e8051c89184414953800cc2151082844a201042800130860308e8204d4028 | |
| 299 \& 00831048940e44281c00060449a5000ac80c894114e006321264401600846c050164462 | |
| 300 \& 08190410805000304a10205b0100e04c0038ba0fad0209c0ca8b1200012268b61c0026a | |
| 301 \& aa0660a11014a011d46 | |
| 302 \& | |
| 303 \& $$$$ | |
| 304 \& ... ... | |
| 305 \& ... ... | |
| 306 .Ve | |
| 307 .PP | |
| 308 Example of \s-1CSV\s0 \fITextFile\fR containing fingerprints bit-vector string data: | |
| 309 .PP | |
| 310 .Vb 7 | |
| 311 \& "CompoundID","PathLengthFingerprints" | |
| 312 \& "Cmpd1","FingerprintsBitVector;PathLengthBits:AtomicInvariantsAtomTypes | |
| 313 \& :MinLength1:MaxLength8;1024;HexadecimalString;Ascending;9c8460989ec8a4 | |
| 314 \& 9913991a6603130b0a19e8051c89184414953800cc2151082844a20104280013086030 | |
| 315 \& 8e8204d402800831048940e44281c00060449a5000ac80c894114e006321264401..." | |
| 316 \& ... ... | |
| 317 \& ... ... | |
| 318 .Ve | |
| 319 .PP | |
| 320 The current release of MayaChemTools supports the following types of fingerprint | |
| 321 bit-vector and vector strings: | |
| 322 .PP | |
| 323 .Vb 6 | |
| 324 \& FingerprintsVector;AtomNeighborhoods:AtomicInvariantsAtomTypes:MinRadi | |
| 325 \& us0:MaxRadius2;41;AlphaNumericalValues;ValuesString;NR0\-C.X1.BO1.H3\-AT | |
| 326 \& C1:NR1\-C.X3.BO3.H1\-ATC1:NR2\-C.X1.BO1.H3\-ATC1:NR2\-C.X3.BO4\-ATC1 NR0\-C.X | |
| 327 \& 1.BO1.H3\-ATC1:NR1\-C.X3.BO3.H1\-ATC1:NR2\-C.X1.BO1.H3\-ATC1:NR2\-C.X3.BO4\-A | |
| 328 \& TC1 NR0\-C.X2.BO2.H2\-ATC1:NR1\-C.X2.BO2.H2\-ATC1:NR1\-C.X3.BO3.H1\-ATC1:NR2 | |
| 329 \& \-C.X2.BO2.H2\-ATC1:NR2\-N.X3.BO3\-ATC1:NR2\-O.X1.BO1.H1\-ATC1 NR0\-C.X2.B... | |
| 330 \& | |
| 331 \& FingerprintsVector;AtomTypesCount:AtomicInvariantsAtomTypes:ArbitraryS | |
| 332 \& ize;10;NumericalValues;IDsAndValuesString;C.X1.BO1.H3 C.X2.BO2.H2 C.X2 | |
| 333 \& .BO3.H1 C.X3.BO3.H1 C.X3.BO4 F.X1.BO1 N.X2.BO2.H1 N.X3.BO3 O.X1.BO1.H1 | |
| 334 \& O.X1.BO2;2 4 14 3 10 1 1 1 3 2 | |
| 335 \& | |
| 336 \& FingerprintsVector;AtomTypesCount:SLogPAtomTypes:ArbitrarySize;16;Nume | |
| 337 \& ricalValues;IDsAndValuesString;C1 C10 C11 C14 C18 C20 C21 C22 C5 CS F | |
| 338 \& N11 N4 O10 O2 O9;5 1 1 1 14 4 2 1 2 2 1 1 1 1 3 1 | |
| 339 \& | |
| 340 \& FingerprintsVector;AtomTypesCount:SLogPAtomTypes:FixedSize;67;OrderedN | |
| 341 \& umericalValues;IDsAndValuesString;C1 C2 C3 C4 C5 C6 C7 C8 C9 C10 C11 C | |
| 342 \& 12 C13 C14 C15 C16 C17 C18 C19 C20 C21 C22 C23 C24 C25 C26 C27 CS N1 N | |
| 343 \& 2 N3 N4 N5 N6 N7 N8 N9 N10 N11 N12 N13 N14 NS O1 O2 O3 O4 O5 O6 O7 O8 | |
| 344 \& 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 | |
| 345 \& 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... | |
| 346 \& | |
| 347 \& FingerprintsVector;EStateIndicies:ArbitrarySize;11;NumericalValues;IDs | |
| 348 \& AndValuesString;SaaCH SaasC SaasN SdO SdssC SsCH3 SsF SsOH SssCH2 SssN | |
| 349 \& H SsssCH;24.778 4.387 1.993 25.023 \-1.435 3.975 14.006 29.759 \-0.073 3 | |
| 350 \& .024 \-2.270 | |
| 351 \& | |
| 352 \& FingerprintsVector;EStateIndicies:FixedSize;87;OrderedNumericalValues; | |
| 353 \& ValuesString;0 0 0 0 0 0 0 3.975 0 \-0.073 0 0 24.778 \-2.270 0 0 \-1.435 | |
| 354 \& 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 | |
| 355 \& 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 | |
| 356 \& 0 0 0 0 0 0 0 0 0 0 0 0 0 0 | |
| 357 \& | |
| 358 \& FingerprintsVector;ExtendedConnectivity:AtomicInvariantsAtomTypes:Radi | |
| 359 \& us2;60;AlphaNumericalValues;ValuesString;73555770 333564680 352413391 | |
| 360 \& 666191900 1001270906 1371674323 1481469939 1977749791 2006158649 21414 | |
| 361 \& 08799 49532520 64643108 79385615 96062769 273726379 564565671 85514103 | |
| 362 \& 5 906706094 988546669 1018231313 1032696425 1197507444 1331250018 1338 | |
| 363 \& 532734 1455473691 1607485225 1609687129 1631614296 1670251330 17303... | |
| 364 \& | |
| 365 \& FingerprintsVector;ExtendedConnectivityCount:AtomicInvariantsAtomTypes | |
| 366 \& :Radius2;60;NumericalValues;IDsAndValuesString;73555770 333564680 3524 | |
| 367 \& 13391 666191900 1001270906 1371674323 1481469939 1977749791 2006158649 | |
| 368 \& 2141408799 49532520 64643108 79385615 96062769 273726379 564565671...; | |
| 369 \& 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 | |
| 370 \& 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 | |
| 371 \& | |
| 372 \& FingerprintsBitVector;ExtendedConnectivityBits:AtomicInvariantsAtomTyp | |
| 373 \& es:Radius2;1024;BinaryString;Ascending;0000000000000000000000000000100 | |
| 374 \& 0000000001010000000110000011000000000000100000000000000000000000100001 | |
| 375 \& 1000000110000000000000000000000000010011000000000000000000000000010000 | |
| 376 \& 0000000000000000000000000010000000000000000001000000000000000000000000 | |
| 377 \& 0000000000010000100001000000000000101000000000000000100000000000000... | |
| 378 \& | |
| 379 \& FingerprintsVector;ExtendedConnectivity:FunctionalClassAtomTypes:Radiu | |
| 380 \& s2;57;AlphaNumericalValues;ValuesString;24769214 508787397 850393286 8 | |
| 381 \& 62102353 981185303 1231636850 1649386610 1941540674 263599683 32920567 | |
| 382 \& 1 571109041 639579325 683993318 723853089 810600886 885767127 90326012 | |
| 383 \& 7 958841485 981022393 1126908698 1152248391 1317567065 1421489994 1455 | |
| 384 \& 632544 1557272891 1826413669 1983319256 2015750777 2029559552 20404... | |
| 385 \& | |
| 386 \& FingerprintsVector;ExtendedConnectivity:EStateAtomTypes:Radius2;62;Alp | |
| 387 \& haNumericalValues;ValuesString;25189973 528584866 662581668 671034184 | |
| 388 \& 926543080 1347067490 1738510057 1759600920 2034425745 2097234755 21450 | |
| 389 \& 44754 96779665 180364292 341712110 345278822 386540408 387387308 50430 | |
| 390 \& 1706 617094135 771528807 957666640 997798220 1158349170 1291258082 134 | |
| 391 \& 1138533 1395329837 1420277211 1479584608 1486476397 1487556246 1566... | |
| 392 \& | |
| 393 \& FingerprintsBitVector;MACCSKeyBits;166;BinaryString;Ascending;00000000 | |
| 394 \& 0000000000000000000000000000000001001000010010000000010010000000011100 | |
| 395 \& 0100101010111100011011000100110110000011011110100110111111111111011111 | |
| 396 \& 11111111111110111000 | |
| 397 \& | |
| 398 \& FingerprintsBitVector;MACCSKeyBits;322;BinaryString;Ascending;11101011 | |
| 399 \& 1110011111100101111111000111101100110000000000000011100010000000000000 | |
| 400 \& 0000000000000000000000000000000000000000000000101000000000000000000000 | |
| 401 \& 0000000000000000000000000000000000000000000000000000000000000000000000 | |
| 402 \& 0000000000000000000000000000000000000011000000000000000000000000000000 | |
| 403 \& 0000000000000000000000000000000000000000 | |
| 404 \& | |
| 405 \& FingerprintsVector;MACCSKeyCount;166;OrderedNumericalValues;ValuesStri | |
| 406 \& 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 | |
| 407 \& 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 | |
| 408 \& 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 | |
| 409 \& 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 | |
| 410 \& 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 | |
| 411 \& | |
| 412 \& FingerprintsVector;MACCSKeyCount;322;OrderedNumericalValues;ValuesStri | |
| 413 \& 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 | |
| 414 \& 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 | |
| 415 \& 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 | |
| 416 \& 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 | |
| 417 \& 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 ... | |
| 418 \& | |
| 419 \& FingerprintsBitVector;PathLengthBits:AtomicInvariantsAtomTypes:MinLeng | |
| 420 \& th1:MaxLength8;1024;BinaryString;Ascending;001000010011010101011000110 | |
| 421 \& 0100010101011000101001011100110001000010001001101000001001001001001000 | |
| 422 \& 0010110100000111001001000001001010100100100000000011000000101001011100 | |
| 423 \& 0010000001000101010100000100111100110111011011011000000010110111001101 | |
| 424 \& 0101100011000000010001000011000010100011101100001000001000100000000... | |
| 425 \& | |
| 426 \& FingerprintsVector;PathLengthCount:AtomicInvariantsAtomTypes:MinLength | |
| 427 \& 1:MaxLength8;432;NumericalValues;IDsAndValuesPairsString;C.X1.BO1.H3 2 | |
| 428 \& 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 | |
| 429 \& 2.BO2.H1 1 N.X3.BO3 1 O.X1.BO1.H1 3 O.X1.BO2 2 C.X1.BO1.H3C.X3.BO3.H1 | |
| 430 \& 2 C.X2.BO2.H2C.X2.BO2.H2 1 C.X2.BO2.H2C.X3.BO3.H1 4 C.X2.BO2.H2C.X3.BO | |
| 431 \& 4 1 C.X2.BO2.H2N.X3.BO3 1 C.X2.BO3.H1:C.X2.BO3.H1 10 C.X2.BO3.H1:C.... | |
| 432 \& | |
| 433 \& FingerprintsVector;PathLengthCount:MMFF94AtomTypes:MinLength1:MaxLengt | |
| 434 \& h8;463;NumericalValues;IDsAndValuesPairsString;C5A 2 C5B 2 C=ON 1 CB 1 | |
| 435 \& 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 | |
| 436 \& 5 2 C5ACB 1 C5ACR 1 C5B:C5B 1 C5BC=ON 1 C5BCB 1 C=ON=O=CN 1 C=ONNC=O 1 | |
| 437 \& CB:CB 18 CBF 1 CBNC=O 1 COO=O=CO 1 COOCR 1 COOOC=O 1 CRCR 7 CRN5 1 CR | |
| 438 \& OR 2 C5A:C5B:C5B 2 C5A:C5BC=ON 1 C5A:C5BCB 1 C5A:N5:C5A 1 C5A:N5CR ... | |
| 439 \& | |
| 440 \& FingerprintsVector;TopologicalAtomPairs:AtomicInvariantsAtomTypes:MinD | |
| 441 \& istance1:MaxDistance10;223;NumericalValues;IDsAndValuesString;C.X1.BO1 | |
| 442 \& .H3\-D1\-C.X3.BO3.H1 C.X2.BO2.H2\-D1\-C.X2.BO2.H2 C.X2.BO2.H2\-D1\-C.X3.BO3. | |
| 443 \& H1 C.X2.BO2.H2\-D1\-C.X3.BO4 C.X2.BO2.H2\-D1\-N.X3.BO3 C.X2.BO3.H1\-D1\-...; | |
| 444 \& 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 | |
| 445 \& 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... | |
| 446 \& | |
| 447 \& FingerprintsVector;TopologicalAtomPairs:FunctionalClassAtomTypes:MinDi | |
| 448 \& stance1:MaxDistance10;144;NumericalValues;IDsAndValuesString;Ar\-D1\-Ar | |
| 449 \& Ar\-D1\-Ar.HBA Ar\-D1\-HBD Ar\-D1\-Hal Ar\-D1\-None Ar.HBA\-D1\-None HBA\-D1\-NI H | |
| 450 \& BA\-D1\-None HBA.HBD\-D1\-NI HBA.HBD\-D1\-None HBD\-D1\-None NI\-D1\-None No...; | |
| 451 \& 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 | |
| 452 \& 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 ... | |
| 453 \& | |
| 454 \& FingerprintsVector;TopologicalAtomTorsions:AtomicInvariantsAtomTypes;3 | |
| 455 \& 3;NumericalValues;IDsAndValuesString;C.X1.BO1.H3\-C.X3.BO3.H1\-C.X3.BO4\- | |
| 456 \& C.X3.BO4 C.X1.BO1.H3\-C.X3.BO3.H1\-C.X3.BO4\-N.X3.BO3 C.X2.BO2.H2\-C.X2.BO | |
| 457 \& 2.H2\-C.X3.BO3.H1\-C.X2.BO2.H2 C.X2.BO2.H2\-C.X2.BO2.H2\-C.X3.BO3.H1\-O...; | |
| 458 \& 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 | |
| 459 \& | |
| 460 \& FingerprintsVector;TopologicalAtomTorsions:EStateAtomTypes;36;Numerica | |
| 461 \& lValues;IDsAndValuesString;aaCH\-aaCH\-aaCH\-aaCH aaCH\-aaCH\-aaCH\-aasC aaC | |
| 462 \& H\-aaCH\-aasC\-aaCH aaCH\-aaCH\-aasC\-aasC aaCH\-aaCH\-aasC\-sF aaCH\-aaCH\-aasC\- | |
| 463 \& ssNH aaCH\-aasC\-aasC\-aasC aaCH\-aasC\-aasC\-aasN aaCH\-aasC\-ssNH\-dssC a...; | |
| 464 \& 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 | |
| 465 \& | |
| 466 \& FingerprintsVector;TopologicalAtomTriplets:AtomicInvariantsAtomTypes:M | |
| 467 \& inDistance1:MaxDistance10;3096;NumericalValues;IDsAndValuesString;C.X1 | |
| 468 \& .BO1.H3\-D1\-C.X1.BO1.H3\-D1\-C.X3.BO3.H1\-D2 C.X1.BO1.H3\-D1\-C.X2.BO2.H2\-D1 | |
| 469 \& 0\-C.X3.BO4\-D9 C.X1.BO1.H3\-D1\-C.X2.BO2.H2\-D3\-N.X3.BO3\-D4 C.X1.BO1.H3\-D1 | |
| 470 \& \-C.X2.BO2.H2\-D4\-C.X2.BO2.H2\-D5 C.X1.BO1.H3\-D1\-C.X2.BO2.H2\-D6\-C.X3....; | |
| 471 \& 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 | |
| 472 \& 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... | |
| 473 \& | |
| 474 \& FingerprintsVector;TopologicalAtomTriplets:SYBYLAtomTypes:MinDistance1 | |
| 475 \& :MaxDistance10;2332;NumericalValues;IDsAndValuesString;C.2\-D1\-C.2\-D9\-C | |
| 476 \& .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\- | |
| 477 \& 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 | |
| 478 \& \-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. | |
| 479 \& 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... | |
| 480 \& | |
| 481 \& FingerprintsVector;TopologicalPharmacophoreAtomPairs:ArbitrarySize:Min | |
| 482 \& Distance1:MaxDistance10;54;NumericalValues;IDsAndValuesString;H\-D1\-H H | |
| 483 \& \-D1\-NI HBA\-D1\-NI HBD\-D1\-NI H\-D2\-H H\-D2\-HBA H\-D2\-HBD HBA\-D2\-HBA HBA\-D2\- | |
| 484 \& 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 | |
| 485 \& BA H\-D4\-HBD HBA\-D4\-HBA HBA\-D4\-HBD HBD\-D4\-HBD H\-D5\-H H\-D5\-HBA H\-D5\-...; | |
| 486 \& 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 | |
| 487 \& 3 4 1 37 10 8 1 35 10 9 3 3 1 28 7 7 4 18 16 12 5 1 2 1 | |
| 488 \& | |
| 489 \& FingerprintsVector;TopologicalPharmacophoreAtomPairs:FixedSize:MinDist | |
| 490 \& ance1:MaxDistance10;150;OrderedNumericalValues;ValuesString;18 0 0 1 0 | |
| 491 \& 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 | |
| 492 \& 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 | |
| 493 \& 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 | |
| 494 \& 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... | |
| 495 \& | |
| 496 \& FingerprintsVector;TopologicalPharmacophoreAtomTriplets:ArbitrarySize: | |
| 497 \& MinDistance1:MaxDistance10;696;NumericalValues;IDsAndValuesString;Ar1\- | |
| 498 \& Ar1\-Ar1 Ar1\-Ar1\-H1 Ar1\-Ar1\-HBA1 Ar1\-Ar1\-HBD1 Ar1\-H1\-H1 Ar1\-H1\-HBA1 Ar1 | |
| 499 \& \-H1\-HBD1 Ar1\-HBA1\-HBD1 H1\-H1\-H1 H1\-H1\-HBA1 H1\-H1\-HBD1 H1\-HBA1\-HBA1 H1\- | |
| 500 \& HBA1\-HBD1 H1\-HBA1\-NI1 H1\-HBD1\-NI1 HBA1\-HBA1\-NI1 HBA1\-HBD1\-NI1 Ar1\-...; | |
| 501 \& 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 | |
| 502 \& 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 | |
| 503 \& 119 123 24 15 185 202 41 25 22 17 3 5 85 95 18 11 23 17 3 1 1 6 4 ... | |
| 504 \& | |
| 505 \& FingerprintsVector;TopologicalPharmacophoreAtomTriplets:FixedSize:MinD | |
| 506 \& istance1:MaxDistance10;2692;OrderedNumericalValues;ValuesString;46 106 | |
| 507 \& 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 | |
| 508 \& 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 | |
| 509 \& 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 | |
| 510 \& 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 ... | |
| 511 .Ve | |
| 512 .SH "OPTIONS" | |
| 513 .IX Header "OPTIONS" | |
| 514 .IP "\fB\-\-alpha\fR \fInumber\fR" 4 | |
| 515 .IX Item "--alpha number" | |
| 516 Value of alpha parameter for calculating \fITversky\fR similarity coefficient specified for | |
| 517 \&\fB\-b, \-\-BitVectorComparisonMode\fR option. It corresponds to weights assigned for bits set | |
| 518 to \*(L"1\*(R" in a pair of fingerprint bit-vectors during the calculation of similarity coefficient. Possible | |
| 519 values: \fI0 to 1\fR. Default value: <0.5>. | |
| 520 .IP "\fB\-\-beta\fR \fInumber\fR" 4 | |
| 521 .IX Item "--beta number" | |
| 522 Value of beta parameter for calculating \fIWeightedTanimoto\fR and \fIWeightedTversky\fR | |
| 523 similarity coefficients specified for \fB\-b, \-\-BitVectorComparisonMode\fR option. It is used to | |
| 524 weight the contributions of bits set to \*(L"0\*(R" during the calculation of similarity coefficients. Possible | |
| 525 values: \fI0 to 1\fR. Default value of <1> makes \fIWeightedTanimoto\fR and \fIWeightedTversky\fR | |
| 526 equivalent to \fITanimoto\fR and \fITversky\fR. | |
| 527 .IP "\fB\-b, \-\-BitVectorComparisonMode\fR \fITanimotoSimilarity | TverskySimilarity | ...\fR" 4 | |
| 528 .IX Item "-b, --BitVectorComparisonMode TanimotoSimilarity | TverskySimilarity | ..." | |
| 529 Specify what similarity coefficient to use for calculating similarity between fingerprints bit-vector | |
| 530 string data values in \fIReferenceFingerprintsFile\fR and \fIDatabaseFingerprintsFile\fR during similarity | |
| 531 search. Possible values: \fITanimotoSimilarity | TverskySimilarity | ...\fR. Default: \fITanimotoSimilarity\fR | |
| 532 .Sp | |
| 533 The current release supports the following similarity coefficients: \fIBaroniUrbaniSimilarity, BuserSimilarity, | |
| 534 CosineSimilarity, DiceSimilarity, DennisSimilarity, ForbesSimilarity, FossumSimilarity, HamannSimilarity, JacardSimilarity, | |
| 535 Kulczynski1Similarity, Kulczynski2Similarity, MatchingSimilarity, McConnaugheySimilarity, OchiaiSimilarity, | |
| 536 PearsonSimilarity, RogersTanimotoSimilarity, RussellRaoSimilarity, SimpsonSimilarity, SkoalSneath1Similarity, | |
| 537 SkoalSneath2Similarity, SkoalSneath3Similarity, TanimotoSimilarity, TverskySimilarity, YuleSimilarity, | |
| 538 WeightedTanimotoSimilarity, WeightedTverskySimilarity\fR. These similarity coefficients are described below. | |
| 539 .Sp | |
| 540 For two fingerprint bit-vectors A and B of same size, let: | |
| 541 .Sp | |
| 542 .Vb 4 | |
| 543 \& Na = Number of bits set to "1" in A | |
| 544 \& Nb = Number of bits set to "1" in B | |
| 545 \& Nc = Number of bits set to "1" in both A and B | |
| 546 \& Nd = Number of bits set to "0" in both A and B | |
| 547 \& | |
| 548 \& Nt = Number of bits set to "1" or "0" in A or B (Size of A or B) | |
| 549 \& Nt = Na + Nb \- Nc + Nd | |
| 550 \& | |
| 551 \& Na \- Nc = Number of bits set to "1" in A but not in B | |
| 552 \& Nb \- Nc = Number of bits set to "1" in B but not in A | |
| 553 .Ve | |
| 554 .Sp | |
| 555 Then, various similarity coefficients [ Ref. 40 \- 42 ] for a pair of bit-vectors A and B are | |
| 556 defined as follows: | |
| 557 .Sp | |
| 558 \&\fIBaroniUrbaniSimilarity\fR: ( \s-1SQRT\s0( Nc * Nd ) + Nc ) / ( \s-1SQRT\s0 ( Nc * Nd ) + Nc + ( Na \- Nc ) + ( Nb \- Nc ) ) ( same as Buser ) | |
| 559 .Sp | |
| 560 \&\fIBuserSimilarity\fR: ( \s-1SQRT\s0 ( Nc * Nd ) + Nc ) / ( \s-1SQRT\s0 ( Nc * Nd ) + Nc + ( Na \- Nc ) + ( Nb \- Nc ) ) ( same as BaroniUrbani ) | |
| 561 .Sp | |
| 562 \&\fICosineSimilarity\fR: Nc / \s-1SQRT\s0 ( Na * Nb ) (same as Ochiai) | |
| 563 .Sp | |
| 564 \&\fIDiceSimilarity\fR: (2 * Nc) / ( Na + Nb ) | |
| 565 .Sp | |
| 566 \&\fIDennisSimilarity\fR: ( Nc * Nd \- ( ( Na \- Nc ) * ( Nb \- Nc ) ) ) / \s-1SQRT\s0 ( Nt * Na * Nb) | |
| 567 .Sp | |
| 568 \&\fIForbesSimilarity\fR: ( Nt * Nc ) / ( Na * Nb ) | |
| 569 .Sp | |
| 570 \&\fIFossumSimilarity\fR: ( Nt * ( ( Nc \- 1/2 ) ** 2 ) / ( Na * Nb ) | |
| 571 .Sp | |
| 572 \&\fIHamannSimilarity\fR: ( ( Nc + Nd ) \- ( Na \- Nc ) \- ( Nb \- Nc ) ) / Nt | |
| 573 .Sp | |
| 574 \&\fIJaccardSimilarity\fR: Nc / ( ( Na \- Nc) + ( Nb \- Nc ) + Nc ) = Nc / ( Na + Nb \- Nc ) (same as Tanimoto) | |
| 575 .Sp | |
| 576 \&\fIKulczynski1Similarity\fR: Nc / ( ( Na \- Nc ) + ( Nb \- Nc) ) = Nc / ( Na + Nb \- 2Nc ) | |
| 577 .Sp | |
| 578 \&\fIKulczynski2Similarity\fR: ( ( Nc / 2 ) * ( 2 * Nc + ( Na \- Nc ) + ( Nb \- Nc) ) ) / ( ( Nc + ( Na \- Nc ) ) * ( Nc + ( Nb \- Nc ) ) ) = 0.5 * ( Nc / Na + Nc / Nb ) | |
| 579 .Sp | |
| 580 \&\fIMatchingSimilarity\fR: ( Nc + Nd ) / Nt | |
| 581 .Sp | |
| 582 \&\fIMcConnaugheySimilarity\fR: ( Nc ** 2 \- ( Na \- Nc ) * ( Nb \- Nc) ) / ( Na * Nb ) | |
| 583 .Sp | |
| 584 \&\fIOchiaiSimilarity\fR: Nc / \s-1SQRT\s0 ( Na * Nb ) (same as Cosine) | |
| 585 .Sp | |
| 586 \&\fIPearsonSimilarity\fR: ( ( Nc * Nd ) \- ( ( Na \- Nc ) * ( Nb \- Nc ) ) / \s-1SQRT\s0 ( Na * Nb * ( Na \- Nc + Nd ) * ( Nb \- Nc + Nd ) ) | |
| 587 .Sp | |
| 588 \&\fIRogersTanimotoSimilarity\fR: ( Nc + Nd ) / ( ( Na \- Nc) + ( Nb \- Nc) + Nt) = ( Nc + Nd ) / ( Na + Nb \- 2Nc + Nt) | |
| 589 .Sp | |
| 590 \&\fIRussellRaoSimilarity\fR: Nc / Nt | |
| 591 .Sp | |
| 592 \&\fISimpsonSimilarity\fR: Nc / \s-1MIN\s0 ( Na, Nb) | |
| 593 .Sp | |
| 594 \&\fISkoalSneath1Similarity\fR: Nc / ( Nc + 2 * ( Na \- Nc) + 2 * ( Nb \- Nc) ) = Nc / ( 2 * Na + 2 * Nb \- 3 * Nc ) | |
| 595 .Sp | |
| 596 \&\fISkoalSneath2Similarity\fR: ( 2 * Nc + 2 * Nd ) / ( Nc + Nd + Nt ) | |
| 597 .Sp | |
| 598 \&\fISkoalSneath3Similarity\fR: ( Nc + Nd ) / ( ( Na \- Nc ) + ( Nb \- Nc ) ) = ( Nc + Nd ) / ( Na + Nb \- 2 * Nc ) | |
| 599 .Sp | |
| 600 \&\fITanimotoSimilarity\fR: Nc / ( ( Na \- Nc) + ( Nb \- Nc ) + Nc ) = Nc / ( Na + Nb \- Nc ) (same as Jaccard) | |
| 601 .Sp | |
| 602 \&\fITverskySimilarity\fR: Nc / ( alpha * ( Na \- Nc ) + ( 1 \- alpha) * ( Nb \- Nc) + Nc ) = Nc / ( alpha * ( Na \- Nb ) + Nb) | |
| 603 .Sp | |
| 604 \&\fIYuleSimilarity\fR: ( ( Nc * Nd ) \- ( ( Na \- Nc ) * ( Nb \- Nc ) ) ) / ( ( Nc * Nd ) + ( ( Na \- Nc ) * ( Nb \- Nc ) ) ) | |
| 605 .Sp | |
| 606 Values of Tanimoto/Jaccard and Tversky coefficients are dependent on only those bit which | |
| 607 are set to \*(L"1\*(R" in both A and B. In order to take into account all bit positions, modified versions | |
| 608 of Tanimoto [ Ref. 42 ] and Tversky [ Ref. 43 ] have been developed. | |
| 609 .Sp | |
| 610 Let: | |
| 611 .Sp | |
| 612 .Vb 3 | |
| 613 \& Na\*(Aq = Number of bits set to "0" in A | |
| 614 \& Nb\*(Aq = Number of bits set to "0" in B | |
| 615 \& Nc\*(Aq = Number of bits set to "0" in both A and B | |
| 616 .Ve | |
| 617 .Sp | |
| 618 Tanimoto': Nc' / ( ( Na' \- Nc') + ( Nb' \- Nc' ) + Nc' ) = Nc' / ( Na' + Nb' \- Nc' ) | |
| 619 .Sp | |
| 620 Tversky': Nc' / ( alpha * ( Na' \- Nc' ) + ( 1 \- alpha) * ( Nb' \- Nc' ) + Nc' ) = Nc' / ( alpha * ( Na' \- Nb' ) + Nb') | |
| 621 .Sp | |
| 622 Then: | |
| 623 .Sp | |
| 624 \&\fIWeightedTanimotoSimilarity\fR = beta * Tanimoto + (1 \- beta) * Tanimoto' | |
| 625 .Sp | |
| 626 \&\fIWeightedTverskySimilarity\fR = beta * Tversky + (1 \- beta) * Tversky' | |
| 627 .IP "\fB\-\-DatabaseColMode\fR \fIColNum | ColLabel\fR" 4 | |
| 628 .IX Item "--DatabaseColMode ColNum | ColLabel" | |
| 629 Specify how columns are identified in database fingerprints \fITextFile\fR: using column | |
| 630 number or column label. Possible values: \fIColNum or ColLabel\fR. Default value: \fIColNum\fR. | |
| 631 .IP "\fB\-\-DatabaseCompoundIDCol\fR \fIcol number | col name\fR" 4 | |
| 632 .IX Item "--DatabaseCompoundIDCol col number | col name" | |
| 633 This value is \fB\-\-DatabaseColMode\fR mode specific. It specifies column to use for retrieving compound | |
| 634 \&\s-1ID\s0 from database fingerprints \fITextFile\fR during similarity and dissimilarity search for output \s-1SD\s0 and | |
| 635 \&\s-1CSV/TSV\s0 text files. Possible values: \fIcol number or col label\fR. Default value: \fIfirst column containing | |
| 636 the word compoundID in its column label or sequentially generated IDs\fR. | |
| 637 .Sp | |
| 638 This is only used for \fICompoundID\fR value of \fB\-\-DatabaseDataColsMode\fR option. | |
| 639 .IP "\fB\-\-DatabaseCompoundIDPrefix\fR \fItext\fR" 4 | |
| 640 .IX Item "--DatabaseCompoundIDPrefix text" | |
| 641 Specify compound \s-1ID\s0 prefix to use during sequential generation of compound IDs for database fingerprints | |
| 642 \&\fISDFile\fR and \fITextFile\fR. Default value: \fICmpd\fR. The default value generates compound IDs which look | |
| 643 like Cmpd<Number>. | |
| 644 .Sp | |
| 645 For database fingerprints \fISDFile\fR, this value is only used during \fILabelPrefix | MolNameOrLabelPrefix\fR | |
| 646 values of \fB\-\-DatabaseCompoundIDMode\fR option; otherwise, it's ignored. | |
| 647 .Sp | |
| 648 Examples for \fILabelPrefix\fR or \fIMolNameOrLabelPrefix\fR value of \fB\-\-DatabaseCompoundIDMode\fR: | |
| 649 .Sp | |
| 650 .Vb 1 | |
| 651 \& Compound | |
| 652 .Ve | |
| 653 .Sp | |
| 654 The values specified above generates compound IDs which correspond to Compound<Number> | |
| 655 instead of default value of Cmpd<Number>. | |
| 656 .IP "\fB\-\-DatabaseCompoundIDField\fR \fIDataFieldName\fR" 4 | |
| 657 .IX Item "--DatabaseCompoundIDField DataFieldName" | |
| 658 Specify database fingerprints \fISDFile\fR datafield label for generating compound IDs. This value is | |
| 659 only used during \fIDataField\fR value of \fB\-\-DatabaseCompoundIDMode\fR option. | |
| 660 .Sp | |
| 661 Examples for \fIDataField\fR value of \fB\-\-DatabaseCompoundIDMode\fR: | |
| 662 .Sp | |
| 663 .Vb 2 | |
| 664 \& MolID | |
| 665 \& ExtReg | |
| 666 .Ve | |
| 667 .IP "\fB\-\-DatabaseCompoundIDMode\fR \fIDataField | MolName | LabelPrefix | MolNameOrLabelPrefix\fR" 4 | |
| 668 .IX Item "--DatabaseCompoundIDMode DataField | MolName | LabelPrefix | MolNameOrLabelPrefix" | |
| 669 Specify how to generate compound IDs from database fingerprints \fISDFile\fR during similarity and | |
| 670 dissimilarity search for output \s-1SD\s0 and \s-1CSV/TSV\s0 text files: use a \fISDFile\fR datafield value; use | |
| 671 molname line from \fISDFile\fR; generate a sequential \s-1ID\s0 with specific prefix; use combination of both | |
| 672 MolName and LabelPrefix with usage of LabelPrefix values for empty molname lines. | |
| 673 .Sp | |
| 674 Possible values: \fIDataField | MolName | LabelPrefix | MolNameOrLabelPrefix\fR. | |
| 675 Default: \fILabelPrefix\fR. | |
| 676 .Sp | |
| 677 For \fIMolNameAndLabelPrefix\fR value of \fB\-\-DatabaseCompoundIDMode\fR, molname line in \fISDFile\fR takes | |
| 678 precedence over sequential compound IDs generated using \fILabelPrefix\fR and only empty molname | |
| 679 values are replaced with sequential compound IDs. | |
| 680 .Sp | |
| 681 This is only used for \fICompoundID\fR value of \fB\-\-DatabaseDataFieldsMode\fR option. | |
| 682 .ie n .IP "\fB\-\-DatabaseDataCols\fR \fI""DataColNum1,DataColNum2,... "" | DataColLabel1,DataCoLabel2,... ""\fR" 4 | |
| 683 .el .IP "\fB\-\-DatabaseDataCols\fR \fI``DataColNum1,DataColNum2,... '' | DataColLabel1,DataCoLabel2,... ""\fR" 4 | |
| 684 .IX Item "--DatabaseDataCols DataColNum1,DataColNum2,... | DataColLabel1,DataCoLabel2,... """ | |
| 685 This value is \fB\-\-DatabaseColMode\fR mode specific. It is a comma delimited list of database fingerprints | |
| 686 \&\fITextFile\fR data column numbers or labels to extract and write to \s-1SD\s0 and \s-1CSV/TSV\s0 text files along with | |
| 687 other information for \fI\s-1SD\s0 | text | both\fR values of \fB\-\-output\fR option. | |
| 688 .Sp | |
| 689 This is only used for \fISpecify\fR value of \fB\-\-DatabaseDataColsMode\fR option. | |
| 690 .Sp | |
| 691 Examples: | |
| 692 .Sp | |
| 693 .Vb 2 | |
| 694 \& 1,2,3 | |
| 695 \& CompoundName,MolWt | |
| 696 .Ve | |
| 697 .IP "\fB\-\-DatabaseDataColsMode\fR \fIAll | Specify | CompoundID\fR" 4 | |
| 698 .IX Item "--DatabaseDataColsMode All | Specify | CompoundID" | |
| 699 Specify how data columns from database fingerprints \fITextFile\fR are transferred to output \s-1SD\s0 and | |
| 700 \&\s-1CSV/TSV\s0 text files along with other information for \fI\s-1SD\s0 | text | both\fR values of \fB\-\-output\fR option: | |
| 701 transfer all data columns; extract specified data columns; generate a compound \s-1ID\s0 database compound | |
| 702 prefix. Possible values: \fIAll | Specify | CompoundID\fR. Default value: \fICompoundID\fR. | |
| 703 .ie n .IP "\fB\-\-DatabaseDataFields\fR \fI""FieldLabel1,FieldLabel2,... ""\fR" 4 | |
| 704 .el .IP "\fB\-\-DatabaseDataFields\fR \fI``FieldLabel1,FieldLabel2,... ''\fR" 4 | |
| 705 .IX Item "--DatabaseDataFields FieldLabel1,FieldLabel2,... " | |
| 706 Comma delimited list of database fingerprints \fISDFile\fR data fields to extract and write to \s-1SD\s0 | |
| 707 and \s-1CSV/TSV\s0 text files along with other information for \fI\s-1SD\s0 | text | both\fR values of | |
| 708 \&\fB\-\-output\fR option. | |
| 709 .Sp | |
| 710 This is only used for \fISpecify\fR value of \fB\-\-DatabaseDataFieldsMode\fR option. | |
| 711 .Sp | |
| 712 Examples: | |
| 713 .Sp | |
| 714 .Vb 2 | |
| 715 \& Extreg | |
| 716 \& MolID,CompoundName | |
| 717 .Ve | |
| 718 .IP "\fB\-\-DatabaseDataFieldsMode\fR \fIAll | Common | Specify | CompoundID\fR" 4 | |
| 719 .IX Item "--DatabaseDataFieldsMode All | Common | Specify | CompoundID" | |
| 720 Specify how data fields from database fingerprints \fISDFile\fR are transferred to output \s-1SD\s0 and | |
| 721 \&\s-1CSV/TSV\s0 text files along with other information for \fI\s-1SD\s0 | text | both\fR values of \fB\-\-output\fR | |
| 722 option: transfer all \s-1SD\s0 data field; transfer \s-1SD\s0 data files common to all compounds; extract | |
| 723 specified data fields; generate a compound \s-1ID\s0 using molname line, a compound prefix, or a | |
| 724 combination of both. Possible values: \fIAll | Common | specify | CompoundID\fR. Default value: | |
| 725 \&\fICompoundID\fR. | |
| 726 .IP "\fB\-\-DatabaseFingerprintsCol\fR \fIcol number | col name\fR" 4 | |
| 727 .IX Item "--DatabaseFingerprintsCol col number | col name" | |
| 728 This value is \fB\-\-DatabaseColMode\fR specific. It specifies fingerprints column to use during similarity | |
| 729 and dissimilarity search for database fingerprints \fITextFile\fR. Possible values: \fIcol number or col label\fR. | |
| 730 Default value: \fIfirst column containing the word Fingerprints in its column label\fR. | |
| 731 .IP "\fB\-\-DatabaseFingerprintsField\fR \fIFieldLabel\fR" 4 | |
| 732 .IX Item "--DatabaseFingerprintsField FieldLabel" | |
| 733 Fingerprints field label to use during similarity and dissimilarity search for database fingerprints \fISDFile\fR. | |
| 734 Default value: \fIfirst data field label containing the word Fingerprints in its label\fR | |
| 735 .IP "\fB\-\-DistanceCutoff\fR \fInumber\fR" 4 | |
| 736 .IX Item "--DistanceCutoff number" | |
| 737 Distance cutoff value to use during comparison of distance value between a pair of database | |
| 738 and reference molecule calculated by distance comparison methods for fingerprints vector | |
| 739 string data values. Possible values: \fIAny valid number\fR. Default value: \fI10\fR. | |
| 740 .Sp | |
| 741 The comparison value between a pair of database and reference molecule must meet the cutoff | |
| 742 criterion as shown below: | |
| 743 .Sp | |
| 744 .Vb 1 | |
| 745 \& SeachMode CutoffCriterion ComparisonValues | |
| 746 \& | |
| 747 \& Similarity <= Lower value implies high similarity | |
| 748 \& Dissimilarity >= Higher value implies high dissimilarity | |
| 749 .Ve | |
| 750 .Sp | |
| 751 This option is only used during distance coefficients values of \fB\-v, \-\-VectorComparisonMode\fR | |
| 752 option. | |
| 753 .Sp | |
| 754 This option is ignored during \fINo\fR value of \fB\-\-GroupFusionApplyCutoff\fR for \fIMultipleReferences\fR | |
| 755 \&\fB\-m, \-\-mode\fR. | |
| 756 .IP "\fB\-d, \-\-detail\fR \fIInfoLevel\fR" 4 | |
| 757 .IX Item "-d, --detail InfoLevel" | |
| 758 Level of information to print about lines being ignored. Default: \fI1\fR. Possible values: | |
| 759 \&\fI1, 2 or 3\fR. | |
| 760 .IP "\fB\-f, \-\-fast\fR" 4 | |
| 761 .IX Item "-f, --fast" | |
| 762 In this mode, fingerprints columns specified using \fB\-\-FingerprintsCol\fR for reference and database | |
| 763 fingerprints \fITextFile(s)\fR, and \fB\-\-FingerprintsField\fR for reference and database fingerprints \fISDFile(s)\fR | |
| 764 are assumed to contain valid fingerprints data and no checking is performed before performing similarity | |
| 765 and dissimilarity search. By default, fingerprints data is validated before computing pairwise similarity and | |
| 766 distance coefficients. | |
| 767 .IP "\fB\-\-FingerprintsMode\fR \fIAutoDetect | FingerprintsBitVectorString | FingerprintsVectorString\fR" 4 | |
| 768 .IX Item "--FingerprintsMode AutoDetect | FingerprintsBitVectorString | FingerprintsVectorString" | |
| 769 Format of fingerprint strings data in reference and database fingerprints \fI\s-1SD\s0, \s-1FP\s0, or Text (\s-1CSV/TSV\s0)\fR | |
| 770 files: automatically detect format of fingerprints string created by MayaChemTools fingerprints | |
| 771 generation scripts or explicitly specify its format. Possible values: \fIAutoDetect | FingerprintsBitVectorString | | |
| 772 FingerprintsVectorString\fR. Default value: \fIAutoDetect\fR. | |
| 773 .IP "\fB\-g, \-\-GroupFusionRule\fR \fIMax, Min, Mean, Median, Sum, Euclidean\fR" 4 | |
| 774 .IX Item "-g, --GroupFusionRule Max, Min, Mean, Median, Sum, Euclidean" | |
| 775 Specify what group fusion [ Ref 94\-97, Ref 100, Ref 105 ] rule to use for calculating similarity of | |
| 776 a database molecule against a set of reference molecules during \fIMultipleReferences\fR value of | |
| 777 similarity search \fB\-m, \-\-mode\fR. Possible values: \fIMax, Min, Mean, Median, Sum, Euclidean\fR. Default | |
| 778 value: \fIMax\fR. \fIMean\fR value corresponds to average or arithmetic mean. The group fusion rule is | |
| 779 also referred to as data fusion of consensus scoring in the literature. | |
| 780 .Sp | |
| 781 For a reference molecules set and a database molecule, let: | |
| 782 .Sp | |
| 783 .Vb 1 | |
| 784 \& N = Number of reference molecules in a set | |
| 785 \& | |
| 786 \& i = ith reference reference molecule in a set | |
| 787 \& n = Nth reference reference molecule in a set | |
| 788 \& | |
| 789 \& d = dth database molecule | |
| 790 \& | |
| 791 \& Crd = Fingerprints comparison value between rth reference and dth database | |
| 792 \& molecule \- similarity/dissimilarity comparison using similarity or | |
| 793 \& distance coefficient | |
| 794 .Ve | |
| 795 .Sp | |
| 796 Then, various group fusion rules to calculate fused similarity between a database molecule and | |
| 797 reference molecules set are defined as follows: | |
| 798 .Sp | |
| 799 \&\fBMax\fR: \s-1MAX\s0 ( C1d, C2d, ..., Cid, ..., Cnd ) | |
| 800 .Sp | |
| 801 \&\fBMin\fR: \s-1MIN\s0 ( C1d, C2d, ..., Cid, ..., Cnd ) | |
| 802 .Sp | |
| 803 \&\fBMean\fR: \s-1SUM\s0 ( C1d, C2d, ..., Cid, ..., Cnd ) / N | |
| 804 .Sp | |
| 805 \&\fBMedian\fR: \s-1MEDIAN\s0 ( C1d, C2d, ..., Cid, ..., Cnd ) | |
| 806 .Sp | |
| 807 \&\fBSum\fR: \s-1SUM\s0 ( C1d, C2d, ..., Cid, ..., Cnd ) | |
| 808 .Sp | |
| 809 \&\fBEuclidean\fR: \s-1SQRT\s0( \s-1SUM\s0( C1d ** 2, C2d ** 2, ..., Cid ** 2, ..., Cnd *** 2) ) | |
| 810 .Sp | |
| 811 The fingerprints bit-vector or vector string of each reference molecule in a set is compared | |
| 812 with a database molecule using a similarity or distance coefficient specified via \fB\-b, | |
| 813 \&\-\-BitVectorComparisonMode\fR or \fB\-v, \-\-VectorComparisonMode\fR. The reference molecules | |
| 814 whose comparison values with a database molecule fall outside specified \fB\-\-SimilarityCutoff\fR | |
| 815 or \fB\-\-DistanceCutoff\fR are ignored during \fIYes\fR value of \fB\-\-GroupFusionApplyCutoff\fR. The | |
| 816 specified \fB\-g, \-\-GroupFusionRule\fR is applied to \fB\-k, \-\-kNN\fR reference molecules to calculate | |
| 817 final fused similarity value between a database molecule and reference molecules set. | |
| 818 .Sp | |
| 819 During dissimilarity search or usage of distance comparison coefficient in similarity search, | |
| 820 the meaning of fingerprints comaprison value is automatically reversed as shown below: | |
| 821 .Sp | |
| 822 .Vb 1 | |
| 823 \& SeachMode ComparisonCoefficient ComparisonValues | |
| 824 \& | |
| 825 \& Similarity SimilarityCoefficient Higher value imples high similarity | |
| 826 \& Similarity DistanceCoefficient Lower value implies high similarity | |
| 827 \& | |
| 828 \& Dissimilarity SimilarityCoefficient Lower value implies high | |
| 829 \& dissimilarity | |
| 830 \& Dissimilarity DistanceCoefficient Higher value implies high | |
| 831 \& dissimilarity | |
| 832 .Ve | |
| 833 .Sp | |
| 834 Consequently, \fIMax\fR implies highest and lowest comparison value for usage of similarity and | |
| 835 distance coefficient respectively during similarity search. And it corresponds to lowest and highest | |
| 836 comparison value for usage of similarity and distance coefficient respectively during dissimilarity | |
| 837 search. During \fIMin\fR fusion rule, the highest and lowest comparison values are appropriately | |
| 838 reversed. | |
| 839 .IP "\fB\-\-GroupFusionApplyCutoff\fR \fIYes | No\fR" 4 | |
| 840 .IX Item "--GroupFusionApplyCutoff Yes | No" | |
| 841 Specify whether to apply \fB\-\-SimilarityCutoff\fR or \fB\-\-DistanceCutoff\fR values during application | |
| 842 of \fB\-g, \-\-GroupFusionRule\fR to reference molecules set. Possible values: \fIYes or No\fR. Default | |
| 843 value: \fIYes\fR. | |
| 844 .Sp | |
| 845 During \fIYes\fR value of \fB\-\-GroupFusionApplyCutoff\fR, the reference molecules whose comparison | |
| 846 values with a database molecule fall outside specified \fB\-\-SimilarityCutoff\fR or \fB\-\-DistanceCutoff\fR | |
| 847 are not used to calculate final fused similarity value between a database molecule and reference | |
| 848 molecules set. | |
| 849 .IP "\fB\-h, \-\-help\fR" 4 | |
| 850 .IX Item "-h, --help" | |
| 851 Print this help message. | |
| 852 .IP "\fB\-\-InDelim\fR \fIcomma | semicolon\fR" 4 | |
| 853 .IX Item "--InDelim comma | semicolon" | |
| 854 Input delimiter for reference and database fingerprints \s-1CSV\s0 \fITextFile(s)\fR. Possible values: | |
| 855 \&\fIcomma or semicolon\fR. Default value: \fIcomma\fR. For \s-1TSV\s0 files, this option is ignored | |
| 856 and \fItab\fR is used as a delimiter. | |
| 857 .IP "\fB\-k, \-\-kNN\fR \fIall | number\fR" 4 | |
| 858 .IX Item "-k, --kNN all | number" | |
| 859 Number of k\-nearest neighbors (k\-NN) reference molecules to use during \fB\-g, \-\-GroupFusionRule\fR | |
| 860 for calculating similarity of a database molecule against a set of reference molecules. Possible values: | |
| 861 \&\fIall | positive integers\fR. Default: \fIall\fR. | |
| 862 .Sp | |
| 863 After ranking similarity values between a database molecule and reference molecules during | |
| 864 \&\fIMultipleReferences\fR value of similarity search \fB\-m, \-\-mode\fR option, a top \fB\-k, \-\-KNN\fR reference | |
| 865 molecule are selected and used during \fB\-g, \-\-GroupFusionRule\fR. | |
| 866 .Sp | |
| 867 This option is \fB\-s, \-\-SearchMode\fR dependent: It corresponds to dissimilar molecules during | |
| 868 \&\fIDissimilaritySearch\fR value of \fB\-s, \-\-SearchMode\fR option. | |
| 869 .IP "\fB\-m, \-\-mode\fR \fIIndividualReference | MultipleReferences\fR" 4 | |
| 870 .IX Item "-m, --mode IndividualReference | MultipleReferences" | |
| 871 Specify how to treat reference molecules in \fIReferenceFingerprintsFile\fR during similarity search: | |
| 872 Treat each reference molecule individually during similarity search or perform similarity | |
| 873 search by treating multiple reference molecules as a set. Possible values: \fIIndividualReference | |
| 874 | MultipleReferences\fR. Default value: \fIMultipleReferences\fR. | |
| 875 .Sp | |
| 876 During \fIIndividualReference\fR value of \fB\-m, \-\-Mode\fR for similarity search, fingerprints bit-vector | |
| 877 or vector string of each reference molecule is compared with database molecules using specified | |
| 878 similarity or distance coefficients to identify most similar molecules for each reference molecule. | |
| 879 Based on value of \fB\-\-SimilarCountMode\fR, upto \fB\-\-n, NumOfSimilarMolecules\fR or \fB\-p, | |
| 880 \&\-\-PercentSimilarMolecules\fR at specified <\-\-SimilarityCutoff> or \fB\-\-DistanceCutoff\fR are | |
| 881 identified for each reference molecule. | |
| 882 .Sp | |
| 883 During \fIMultipleReferences\fR value \fB\-m, \-\-mode\fR for similarity search, all reference molecules | |
| 884 are considered as a set and \fB\-g, \-\-GroupFusionRule\fR is used to calculate similarity of a database | |
| 885 molecule against reference molecules set either using all reference molecules or number of k\-nearest | |
| 886 neighbors (k\-NN) to a database molecule specified using \fB\-k, \-\-kNN\fR. The fingerprints bit-vector | |
| 887 or vector string of each reference molecule in a set is compared with a database molecule using | |
| 888 a similarity or distance coefficient specified via \fB\-b, \-\-BitVectorComparisonMode\fR or \fB\-v, | |
| 889 \&\-\-VectorComparisonMode\fR. The reference molecules whose comparison values with a database | |
| 890 molecule fall outside specified \fB\-\-SimilarityCutoff\fR or \fB\-\-DistanceCutoff\fR are ignored. The | |
| 891 specified \fB\-g, \-\-GroupFusionRule\fR is applied to rest of \fB\-k, \-\-kNN\fR reference molecules to calculate | |
| 892 final similarity value between a database molecule and reference molecules set. | |
| 893 .Sp | |
| 894 The meaning of similarity and distance is automatically reversed during \fIDissimilaritySearch\fR value | |
| 895 of \fB\-s, \-\-SearchMode\fR along with appropriate handling of \fB\-\-SimilarityCutoff\fR or | |
| 896 \&\fB\-\-DistanceCutoff\fR values. | |
| 897 .IP "\fB\-n, \-\-NumOfSimilarMolecules\fR \fInumber\fR" 4 | |
| 898 .IX Item "-n, --NumOfSimilarMolecules number" | |
| 899 Maximum number of most similar database molecules to find for each reference molecule or set of | |
| 900 reference molecules based on \fIIndividualReference\fR or \fIMultipleReferences\fR value of similarity | |
| 901 search \fB\-m, \-\-mode\fR option. Default: \fI10\fR. Valid values: positive integers. | |
| 902 .Sp | |
| 903 This option is ignored during \fIPercentSimilar\fR value of \fB\-\-SimilarCountMode\fR option. | |
| 904 .Sp | |
| 905 This option is \fB\-s, \-\-SearchMode\fR dependent: It corresponds to dissimilar molecules during | |
| 906 \&\fIDissimilaritySearch\fR value of \fB\-s, \-\-SearchMode\fR option. | |
| 907 .IP "\fB\-\-OutDelim\fR \fIcomma | tab | semicolon\fR" 4 | |
| 908 .IX Item "--OutDelim comma | tab | semicolon" | |
| 909 Delimiter for output \s-1CSV/TSV\s0 text file. Possible values: \fIcomma, tab, or semicolon\fR | |
| 910 Default value: \fIcomma\fR. | |
| 911 .IP "\fB\-\-output\fR \fI\s-1SD\s0 | text | both\fR" 4 | |
| 912 .IX Item "--output SD | text | both" | |
| 913 Type of output files to generate. Possible values: \fI\s-1SD\s0, text, or both\fR. Default value: \fItext\fR. | |
| 914 .IP "\fB\-o, \-\-overwrite\fR" 4 | |
| 915 .IX Item "-o, --overwrite" | |
| 916 Overwrite existing files | |
| 917 .IP "\fB\-p, \-\-PercentSimilarMolecules\fR \fInumber\fR" 4 | |
| 918 .IX Item "-p, --PercentSimilarMolecules number" | |
| 919 Maximum percent of mosy similar database molecules to find for each reference molecule or set of | |
| 920 reference molecules based on \fIIndividualReference\fR or \fIMultipleReferences\fR value of similarity | |
| 921 search \fB\-m, \-\-mode\fR option. Default: \fI1\fR percent of database molecules. Valid values: non-zero values | |
| 922 in between \fI0 to 100\fR. | |
| 923 .Sp | |
| 924 This option is ignored during \fINumOfSimilar\fR value of \fB\-\-SimilarCountMode\fR option. | |
| 925 .Sp | |
| 926 During \fIPercentSimilar\fR value of \fB\-\-SimilarCountMode\fR option, the number of molecules | |
| 927 in \fIDatabaseFingerprintsFile\fR is counted and number of similar molecules correspond to | |
| 928 \&\fB\-\-PercentSimilarMolecules\fR of the total number of database molecules. | |
| 929 .Sp | |
| 930 This option is \fB\-s, \-\-SearchMode\fR dependent: It corresponds to dissimilar molecules during | |
| 931 \&\fIDissimilaritySearch\fR value of \fB\-s, \-\-SearchMode\fR option. | |
| 932 .IP "\fB\-\-precision\fR \fInumber\fR" 4 | |
| 933 .IX Item "--precision number" | |
| 934 Precision of calculated similarity values for comparison and generating output files. Default: up to \fI2\fR | |
| 935 decimal places. Valid values: positive integers. | |
| 936 .IP "\fB\-q, \-\-quote\fR \fIYes | No\fR" 4 | |
| 937 .IX Item "-q, --quote Yes | No" | |
| 938 Put quote around column values in output \s-1CSV/TSV\s0 text file. Possible values: | |
| 939 \&\fIYes or No\fR. Default value: \fIYes\fR. | |
| 940 .IP "\fB\-\-ReferenceColMode\fR \fIColNum | ColLabel\fR" 4 | |
| 941 .IX Item "--ReferenceColMode ColNum | ColLabel" | |
| 942 Specify how columns are identified in reference fingerprints \fITextFile\fR: using column | |
| 943 number or column label. Possible values: \fIColNum or ColLabel\fR. Default value: \fIColNum\fR. | |
| 944 .IP "\fB\-\-ReferenceCompoundIDCol\fR \fIcol number | col name\fR" 4 | |
| 945 .IX Item "--ReferenceCompoundIDCol col number | col name" | |
| 946 This value is \fB\-\-ReferenceColMode\fR mode specific. It specifies column to use for retrieving compound | |
| 947 \&\s-1ID\s0 from reference fingerprints \fITextFile\fR during similarity and dissimilarity search for output \s-1SD\s0 and \s-1CSV/TSV\s0 | |
| 948 text files. Possible values: \fIcol number or col label\fR. Default value: \fIfirst column containing the word compoundID | |
| 949 in its column label or sequentially generated IDs\fR. | |
| 950 .IP "\fB\-\-ReferenceCompoundIDPrefix\fR \fItext\fR" 4 | |
| 951 .IX Item "--ReferenceCompoundIDPrefix text" | |
| 952 Specify compound \s-1ID\s0 prefix to use during sequential generation of compound IDs for reference fingerprints | |
| 953 \&\fISDFile\fR and \fITextFile\fR. Default value: \fICmpd\fR. The default value generates compound IDs which looks | |
| 954 like Cmpd<Number>. | |
| 955 .Sp | |
| 956 For reference fingerprints \fISDFile\fR, this value is only used during \fILabelPrefix | MolNameOrLabelPrefix\fR | |
| 957 values of \fB\-\-ReferenceCompoundIDMode\fR option; otherwise, it's ignored. | |
| 958 .Sp | |
| 959 Examples for \fILabelPrefix\fR or \fIMolNameOrLabelPrefix\fR value of \fB\-\-DatabaseCompoundIDMode\fR: | |
| 960 .Sp | |
| 961 .Vb 1 | |
| 962 \& Compound | |
| 963 .Ve | |
| 964 .Sp | |
| 965 The values specified above generates compound IDs which correspond to Compound<Number> | |
| 966 instead of default value of Cmpd<Number>. | |
| 967 .IP "\fB\-\-ReferenceCompoundIDField\fR \fIDataFieldName\fR" 4 | |
| 968 .IX Item "--ReferenceCompoundIDField DataFieldName" | |
| 969 Specify reference fingerprints \fISDFile\fR datafield label for generating compound IDs. | |
| 970 This value is only used during \fIDataField\fR value of \fB\-\-ReferenceCompoundIDMode\fR option. | |
| 971 .Sp | |
| 972 Examples for \fIDataField\fR value of \fB\-\-ReferenceCompoundIDMode\fR: | |
| 973 .Sp | |
| 974 .Vb 2 | |
| 975 \& MolID | |
| 976 \& ExtReg | |
| 977 .Ve | |
| 978 .IP "\fB\-\-ReferenceCompoundIDMode\fR \fIDataField | MolName | LabelPrefix | MolNameOrLabelPrefix\fR" 4 | |
| 979 .IX Item "--ReferenceCompoundIDMode DataField | MolName | LabelPrefix | MolNameOrLabelPrefix" | |
| 980 Specify how to generate compound IDs from reference fingerprints \fISDFile\fR during similarity and | |
| 981 dissimilarity search for output \s-1SD\s0 and \s-1CSV/TSV\s0 text files: use a \fISDFile\fR datafield value; use | |
| 982 molname line from \fISDFile\fR; generate a sequential \s-1ID\s0 with specific prefix; use combination of both | |
| 983 MolName and LabelPrefix with usage of LabelPrefix values for empty molname lines. | |
| 984 .Sp | |
| 985 Possible values: \fIDataField | MolName | LabelPrefix | MolNameOrLabelPrefix\fR. | |
| 986 Default: \fILabelPrefix\fR. | |
| 987 .Sp | |
| 988 For \fIMolNameAndLabelPrefix\fR value of \fB\-\-ReferenceCompoundIDMode\fR, molname line in \fISDFiles\fR | |
| 989 takes precedence over sequential compound IDs generated using \fILabelPrefix\fR and only empty molname | |
| 990 values are replaced with sequential compound IDs. | |
| 991 .IP "\fB\-\-ReferenceFingerprintsCol\fR \fIcol number | col name\fR" 4 | |
| 992 .IX Item "--ReferenceFingerprintsCol col number | col name" | |
| 993 This value is \fB\-\-ReferenceColMode\fR specific. It specifies fingerprints column to use during similarity | |
| 994 and dissimilarity search for reference fingerprints \fITextFile\fR. Possible values: \fIcol number or col label\fR. | |
| 995 Default value: \fIfirst column containing the word Fingerprints in its column label\fR. | |
| 996 .IP "\fB\-\-ReferenceFingerprintsField\fR \fIFieldLabel\fR" 4 | |
| 997 .IX Item "--ReferenceFingerprintsField FieldLabel" | |
| 998 Fingerprints field label to use during similarity and dissimilarity search for reference fingerprints \fISDFile\fR. | |
| 999 Default value: \fIfirst data field label containing the word Fingerprints in its label\fR | |
| 1000 .IP "\fB\-r, \-\-root\fR \fIRootName\fR" 4 | |
| 1001 .IX Item "-r, --root RootName" | |
| 1002 New file name is generated using the root: <Root>.<Ext>. Default for new file name: | |
| 1003 <ReferenceFileName>SimilaritySearching.<Ext>. The output file type determines <Ext> | |
| 1004 value. The sdf, csv, and tsv <Ext> values are used for \s-1SD\s0, comma/semicolon, and tab delimited | |
| 1005 text files respectively. | |
| 1006 .IP "\fB\-s, \-\-SearchMode\fR \fISimilaritySearch | DissimilaritySearch\fR" 4 | |
| 1007 .IX Item "-s, --SearchMode SimilaritySearch | DissimilaritySearch" | |
| 1008 Specify how to find molecules from database molecules for individual reference molecules or | |
| 1009 set of reference molecules: Find similar molecules or dissimilar molecules from database molecules. | |
| 1010 Possible values: \fISimilaritySearch | DissimilaritySearch\fR. Default value: \fISimilaritySearch\fR. | |
| 1011 .Sp | |
| 1012 During \fIDissimilaritySearch\fR value of \fB\-s, \-\-SearchMode\fR option, the meaning of the following | |
| 1013 options is switched and they correspond to dissimilar molecules instead of similar molecules: | |
| 1014 \&\fB\-\-SimilarCountMode\fR, \fB\-n, \-\-NumOfSimilarMolecules\fR, \fB\-\-PercentSimilarMolecules\fR, | |
| 1015 \&\fB\-k, \-\-kNN\fR. | |
| 1016 .IP "\fB\-\-SimilarCountMode\fR \fINumOfSimilar | PercentSimilar\fR" 4 | |
| 1017 .IX Item "--SimilarCountMode NumOfSimilar | PercentSimilar" | |
| 1018 Specify method used to count similar molecules found from database molecules for individual | |
| 1019 reference molecules or set of reference molecules: Find number of similar molecules or percent | |
| 1020 of similar molecules from database molecules. Possible values: \fINumOfSimilar | PercentSimilar\fR. | |
| 1021 Default value: \fINumOfSimilar\fR. | |
| 1022 .Sp | |
| 1023 The values for number of similar molecules and percent similar molecules are specified | |
| 1024 using options \fB\-n, NumOfSimilarMolecule\fR and \fB\-\-PercentSimilarMolecules\fR. | |
| 1025 .Sp | |
| 1026 This option is \fB\-s, \-\-SearchMode\fR dependent: It corresponds to dissimilar molecules during | |
| 1027 \&\fIDissimilaritySearch\fR value of \fB\-s, \-\-SearchMode\fR option. | |
| 1028 .IP "\fB\-\-SimilarityCutoff\fR \fInumber\fR" 4 | |
| 1029 .IX Item "--SimilarityCutoff number" | |
| 1030 Similarity cutoff value to use during comparison of similarity value between a pair of database | |
| 1031 and reference molecules calculated by similarity comparison methods for fingerprints bit-vector | |
| 1032 vector strings data values. Possible values: \fIAny valid number\fR. Default value: \fI0.75\fR. | |
| 1033 .Sp | |
| 1034 The comparison value between a pair of database and reference molecule must meet the cutoff | |
| 1035 criterion as shown below: | |
| 1036 .Sp | |
| 1037 .Vb 1 | |
| 1038 \& SeachMode CutoffCriterion ComparisonValues | |
| 1039 \& | |
| 1040 \& Similarity >= Higher value implies high similarity | |
| 1041 \& Dissimilarity <= Lower value implies high dissimilarity | |
| 1042 .Ve | |
| 1043 .Sp | |
| 1044 This option is ignored during \fINo\fR value of \fB\-\-GroupFusionApplyCutoff\fR for \fIMultipleReferences\fR | |
| 1045 \&\fB\-m, \-\-mode\fR. | |
| 1046 .Sp | |
| 1047 This option is \fB\-s, \-\-SearchMode\fR dependent: It corresponds to dissimilar molecules during | |
| 1048 \&\fIDissimilaritySearch\fR value of \fB\-s, \-\-SearchMode\fR option. | |
| 1049 .IP "\fB\-v, \-\-VectorComparisonMode\fR \fISupportedSimilarityName | SupportedDistanceName\fR" 4 | |
| 1050 .IX Item "-v, --VectorComparisonMode SupportedSimilarityName | SupportedDistanceName" | |
| 1051 Specify what similarity or distance coefficient to use for calculating similarity between fingerprint | |
| 1052 vector strings data values in \fIReferenceFingerprintsFile\fR and \fIDatabaseFingerprintsFile\fR during | |
| 1053 similarity search. Possible values: \fITanimotoSimilairy | ... | ManhattanDistance | ...\fR. Default | |
| 1054 value: \fITanimotoSimilarity\fR. | |
| 1055 .Sp | |
| 1056 The value of \fB\-v, \-\-VectorComparisonMode\fR, in conjunction with \fB\-\-VectorComparisonFormulism\fR, | |
| 1057 decides which type of similarity and distance coefficient formulism gets used. | |
| 1058 .Sp | |
| 1059 The current releases supports the following similarity and distance coefficients: \fICosineSimilarity, | |
| 1060 CzekanowskiSimilarity, DiceSimilarity, OchiaiSimilarity, JaccardSimilarity, SorensonSimilarity, TanimotoSimilarity, | |
| 1061 CityBlockDistance, EuclideanDistance, HammingDistance, ManhattanDistance, SoergelDistance\fR. These | |
| 1062 similarity and distance coefficients are described below. | |
| 1063 .Sp | |
| 1064 \&\fBFingerprintsVector.pm\fR module, used to calculate similarity and distance coefficients, | |
| 1065 provides support to perform comparison between vectors containing three different types of | |
| 1066 values: | |
| 1067 .Sp | |
| 1068 Type I: OrderedNumericalValues | |
| 1069 .Sp | |
| 1070 .Vb 3 | |
| 1071 \& . Size of two vectors are same | |
| 1072 \& . Vectors contain real values in a specific order. For example: MACCS keys | |
| 1073 \& count, Topological pharmnacophore atom pairs and so on. | |
| 1074 .Ve | |
| 1075 .Sp | |
| 1076 Type \s-1II:\s0 UnorderedNumericalValues | |
| 1077 .Sp | |
| 1078 .Vb 3 | |
| 1079 \& . Size of two vectors might not be same | |
| 1080 \& . Vectors contain unordered real value identified by value IDs. For example: | |
| 1081 \& Toplogical atom pairs, Topological atom torsions and so on | |
| 1082 .Ve | |
| 1083 .Sp | |
| 1084 Type \s-1III:\s0 AlphaNumericalValues | |
| 1085 .Sp | |
| 1086 .Vb 3 | |
| 1087 \& . Size of two vectors might not be same | |
| 1088 \& . Vectors contain unordered alphanumerical values. For example: Extended | |
| 1089 \& connectivity fingerprints, atom neighborhood fingerprints. | |
| 1090 .Ve | |
| 1091 .Sp | |
| 1092 Before performing similarity or distance calculations between vectors containing UnorderedNumericalValues | |
| 1093 or AlphaNumericalValues, the vectors are transformed into vectors containing unique OrderedNumericalValues | |
| 1094 using value IDs for UnorderedNumericalValues and values itself for AlphaNumericalValues. | |
| 1095 .Sp | |
| 1096 Three forms of similarity and distance calculation between two vectors, specified using \fB\-\-VectorComparisonFormulism\fR | |
| 1097 option, are supported: \fIAlgebraicForm, BinaryForm or SetTheoreticForm\fR. | |
| 1098 .Sp | |
| 1099 For \fIBinaryForm\fR, the ordered list of processed final vector values containing the value or | |
| 1100 count of each unique value type is simply converted into a binary vector containing 1s and 0s | |
| 1101 corresponding to presence or absence of values before calculating similarity or distance between | |
| 1102 two vectors. | |
| 1103 .Sp | |
| 1104 For two fingerprint vectors A and B of same size containing OrderedNumericalValues, let: | |
| 1105 .Sp | |
| 1106 .Vb 1 | |
| 1107 \& N = Number values in A or B | |
| 1108 \& | |
| 1109 \& Xa = Values of vector A | |
| 1110 \& Xb = Values of vector B | |
| 1111 \& | |
| 1112 \& Xai = Value of ith element in A | |
| 1113 \& Xbi = Value of ith element in B | |
| 1114 \& | |
| 1115 \& SUM = Sum of i over N values | |
| 1116 .Ve | |
| 1117 .Sp | |
| 1118 For SetTheoreticForm of calculation between two vectors, let: | |
| 1119 .Sp | |
| 1120 .Vb 2 | |
| 1121 \& SetIntersectionXaXb = SUM ( MIN ( Xai, Xbi ) ) | |
| 1122 \& SetDifferenceXaXb = SUM ( Xai ) + SUM ( Xbi ) \- SUM ( MIN ( Xai, Xbi ) ) | |
| 1123 .Ve | |
| 1124 .Sp | |
| 1125 For BinaryForm of calculation between two vectors, let: | |
| 1126 .Sp | |
| 1127 .Vb 5 | |
| 1128 \& Na = Number of bits set to "1" in A = SUM ( Xai ) | |
| 1129 \& Nb = Number of bits set to "1" in B = SUM ( Xbi ) | |
| 1130 \& Nc = Number of bits set to "1" in both A and B = SUM ( Xai * Xbi ) | |
| 1131 \& Nd = Number of bits set to "0" in both A and B | |
| 1132 \& = SUM ( 1 \- Xai \- Xbi + Xai * Xbi) | |
| 1133 \& | |
| 1134 \& N = Number of bits set to "1" or "0" in A or B = Size of A or B = Na + Nb \- Nc + Nd | |
| 1135 .Ve | |
| 1136 .Sp | |
| 1137 Additionally, for BinaryForm various values also correspond to: | |
| 1138 .Sp | |
| 1139 .Vb 4 | |
| 1140 \& Na = | Xa | | |
| 1141 \& Nb = | Xb | | |
| 1142 \& Nc = | SetIntersectionXaXb | | |
| 1143 \& Nd = N \- | SetDifferenceXaXb | | |
| 1144 \& | |
| 1145 \& | SetDifferenceXaXb | = N \- Nd = Na + Nb \- Nc + Nd \- Nd = Na + Nb \- Nc | |
| 1146 \& = | Xa | + | Xb | \- | SetIntersectionXaXb | | |
| 1147 .Ve | |
| 1148 .Sp | |
| 1149 Various similarity and distance coefficients [ Ref 40, Ref 62, Ref 64 ] for a pair of vectors A and B | |
| 1150 in \fIAlgebraicForm, BinaryForm and SetTheoreticForm\fR are defined as follows: | |
| 1151 .Sp | |
| 1152 \&\fBCityBlockDistance\fR: ( same as HammingDistance and ManhattanDistance) | |
| 1153 .Sp | |
| 1154 \&\fIAlgebraicForm\fR: \s-1SUM\s0 ( \s-1ABS\s0 ( Xai \- Xbi ) ) | |
| 1155 .Sp | |
| 1156 \&\fIBinaryForm\fR: ( Na \- Nc ) + ( Nb \- Nc ) = Na + Nb \- 2 * Nc | |
| 1157 .Sp | |
| 1158 \&\fISetTheoreticForm\fR: | SetDifferenceXaXb | \- | SetIntersectionXaXb | = \s-1SUM\s0 ( Xai ) + \s-1SUM\s0 ( Xbi ) \- 2 * ( \s-1SUM\s0 ( \s-1MIN\s0 ( Xai, Xbi ) ) ) | |
| 1159 .Sp | |
| 1160 \&\fBCosineSimilarity\fR: ( same as OchiaiSimilarityCoefficient) | |
| 1161 .Sp | |
| 1162 \&\fIAlgebraicForm\fR: \s-1SUM\s0 ( Xai * Xbi ) / \s-1SQRT\s0 ( \s-1SUM\s0 ( Xai ** 2) * \s-1SUM\s0 ( Xbi ** 2) ) | |
| 1163 .Sp | |
| 1164 \&\fIBinaryForm\fR: Nc / \s-1SQRT\s0 ( Na * Nb) | |
| 1165 .Sp | |
| 1166 \&\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 ) ) | |
| 1167 .Sp | |
| 1168 \&\fBCzekanowskiSimilarity\fR: ( same as DiceSimilarity and SorensonSimilarity) | |
| 1169 .Sp | |
| 1170 \&\fIAlgebraicForm\fR: ( 2 * ( \s-1SUM\s0 ( Xai * Xbi ) ) ) / ( \s-1SUM\s0 ( Xai ** 2) + \s-1SUM\s0 ( Xbi **2 ) ) | |
| 1171 .Sp | |
| 1172 \&\fIBinaryForm\fR: 2 * Nc / ( Na + Nb ) | |
| 1173 .Sp | |
| 1174 \&\fISetTheoreticForm\fR: 2 * | SetIntersectionXaXb | / ( |Xa| + |Xb| ) = 2 * ( \s-1SUM\s0 ( \s-1MIN\s0 ( Xai, Xbi ) ) ) / ( \s-1SUM\s0 ( Xai ) + \s-1SUM\s0 ( Xbi ) ) | |
| 1175 .Sp | |
| 1176 \&\fBDiceSimilarity\fR: ( same as CzekanowskiSimilarity and SorensonSimilarity) | |
| 1177 .Sp | |
| 1178 \&\fIAlgebraicForm\fR: ( 2 * ( \s-1SUM\s0 ( Xai * Xbi ) ) ) / ( \s-1SUM\s0 ( Xai ** 2) + \s-1SUM\s0 ( Xbi **2 ) ) | |
| 1179 .Sp | |
| 1180 \&\fIBinaryForm\fR: 2 * Nc / ( Na + Nb ) | |
| 1181 .Sp | |
| 1182 \&\fISetTheoreticForm\fR: 2 * | SetIntersectionXaXb | / ( |Xa| + |Xb| ) = 2 * ( \s-1SUM\s0 ( \s-1MIN\s0 ( Xai, Xbi ) ) ) / ( \s-1SUM\s0 ( Xai ) + \s-1SUM\s0 ( Xbi ) ) | |
| 1183 .Sp | |
| 1184 \&\fBEuclideanDistance\fR: | |
| 1185 .Sp | |
| 1186 \&\fIAlgebraicForm\fR: \s-1SQRT\s0 ( \s-1SUM\s0 ( ( ( Xai \- Xbi ) ** 2 ) ) ) | |
| 1187 .Sp | |
| 1188 \&\fIBinaryForm\fR: \s-1SQRT\s0 ( ( Na \- Nc ) + ( Nb \- Nc ) ) = \s-1SQRT\s0 ( Na + Nb \- 2 * Nc ) | |
| 1189 .Sp | |
| 1190 \&\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 ) ) ) ) | |
| 1191 .Sp | |
| 1192 \&\fBHammingDistance\fR: ( same as CityBlockDistance and ManhattanDistance) | |
| 1193 .Sp | |
| 1194 \&\fIAlgebraicForm\fR: \s-1SUM\s0 ( \s-1ABS\s0 ( Xai \- Xbi ) ) | |
| 1195 .Sp | |
| 1196 \&\fIBinaryForm\fR: ( Na \- Nc ) + ( Nb \- Nc ) = Na + Nb \- 2 * Nc | |
| 1197 .Sp | |
| 1198 \&\fISetTheoreticForm\fR: | SetDifferenceXaXb | \- | SetIntersectionXaXb | = \s-1SUM\s0 ( Xai ) + \s-1SUM\s0 ( Xbi ) \- 2 * ( \s-1SUM\s0 ( \s-1MIN\s0 ( Xai, Xbi ) ) ) | |
| 1199 .Sp | |
| 1200 \&\fBJaccardSimilarity\fR: ( same as TanimotoSimilarity) | |
| 1201 .Sp | |
| 1202 \&\fIAlgebraicForm\fR: \s-1SUM\s0 ( Xai * Xbi ) / ( \s-1SUM\s0 ( Xai ** 2 ) + \s-1SUM\s0 ( Xbi ** 2 ) \- \s-1SUM\s0 ( Xai * Xbi ) ) | |
| 1203 .Sp | |
| 1204 \&\fIBinaryForm\fR: Nc / ( ( Na \- Nc ) + ( Nb \- Nc ) + Nc ) = Nc / ( Na + Nb \- Nc ) | |
| 1205 .Sp | |
| 1206 \&\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 ) ) ) | |
| 1207 .Sp | |
| 1208 \&\fBManhattanDistance\fR: ( same as CityBlockDistance and HammingDistance) | |
| 1209 .Sp | |
| 1210 \&\fIAlgebraicForm\fR: \s-1SUM\s0 ( \s-1ABS\s0 ( Xai \- Xbi ) ) | |
| 1211 .Sp | |
| 1212 \&\fIBinaryForm\fR: ( Na \- Nc ) + ( Nb \- Nc ) = Na + Nb \- 2 * Nc | |
| 1213 .Sp | |
| 1214 \&\fISetTheoreticForm\fR: | SetDifferenceXaXb | \- | SetIntersectionXaXb | = \s-1SUM\s0 ( Xai ) + \s-1SUM\s0 ( Xbi ) \- 2 * ( \s-1SUM\s0 ( \s-1MIN\s0 ( Xai, Xbi ) ) ) | |
| 1215 .Sp | |
| 1216 \&\fBOchiaiSimilarity\fR: ( same as CosineSimilarity) | |
| 1217 .Sp | |
| 1218 \&\fIAlgebraicForm\fR: \s-1SUM\s0 ( Xai * Xbi ) / \s-1SQRT\s0 ( \s-1SUM\s0 ( Xai ** 2) * \s-1SUM\s0 ( Xbi ** 2) ) | |
| 1219 .Sp | |
| 1220 \&\fIBinaryForm\fR: Nc / \s-1SQRT\s0 ( Na * Nb) | |
| 1221 .Sp | |
| 1222 \&\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 ) ) | |
| 1223 .Sp | |
| 1224 \&\fBSorensonSimilarity\fR: ( same as CzekanowskiSimilarity and DiceSimilarity) | |
| 1225 .Sp | |
| 1226 \&\fIAlgebraicForm\fR: ( 2 * ( \s-1SUM\s0 ( Xai * Xbi ) ) ) / ( \s-1SUM\s0 ( Xai ** 2) + \s-1SUM\s0 ( Xbi **2 ) ) | |
| 1227 .Sp | |
| 1228 \&\fIBinaryForm\fR: 2 * Nc / ( Na + Nb ) | |
| 1229 .Sp | |
| 1230 \&\fISetTheoreticForm\fR: 2 * | SetIntersectionXaXb | / ( |Xa| + |Xb| ) = 2 * ( \s-1SUM\s0 ( \s-1MIN\s0 ( Xai, Xbi ) ) ) / ( \s-1SUM\s0 ( Xai ) + \s-1SUM\s0 ( Xbi ) ) | |
| 1231 .Sp | |
| 1232 \&\fBSoergelDistance\fR: | |
| 1233 .Sp | |
| 1234 \&\fIAlgebraicForm\fR: \s-1SUM\s0 ( \s-1ABS\s0 ( Xai \- Xbi ) ) / \s-1SUM\s0 ( \s-1MAX\s0 ( Xai, Xbi ) ) | |
| 1235 .Sp | |
| 1236 \&\fIBinaryForm\fR: 1 \- Nc / ( Na + Nb \- Nc ) = ( Na + Nb \- 2 * Nc ) / ( Na + Nb \- Nc ) | |
| 1237 .Sp | |
| 1238 \&\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 ) ) ) | |
| 1239 .Sp | |
| 1240 \&\fBTanimotoSimilarity\fR: ( same as JaccardSimilarity) | |
| 1241 .Sp | |
| 1242 \&\fIAlgebraicForm\fR: \s-1SUM\s0 ( Xai * Xbi ) / ( \s-1SUM\s0 ( Xai ** 2 ) + \s-1SUM\s0 ( Xbi ** 2 ) \- \s-1SUM\s0 ( Xai * Xbi ) ) | |
| 1243 .Sp | |
| 1244 \&\fIBinaryForm\fR: Nc / ( ( Na \- Nc ) + ( Nb \- Nc ) + Nc ) = Nc / ( Na + Nb \- Nc ) | |
| 1245 .Sp | |
| 1246 \&\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 ) ) ) | |
| 1247 .IP "\fB\-\-VectorComparisonFormulism\fR \fIAlgebraicForm | BinaryForm | SetTheoreticForm\fR" 4 | |
| 1248 .IX Item "--VectorComparisonFormulism AlgebraicForm | BinaryForm | SetTheoreticForm" | |
| 1249 Specify fingerprints vector comparison formulism to use for calculation similarity and distance | |
| 1250 coefficients during \fB\-v, \-\-VectorComparisonMode\fR. Possible values: \fIAlgebraicForm | BinaryForm | | |
| 1251 SetTheoreticForm\fR. Default value: \fIAlgebraicForm\fR. | |
| 1252 .Sp | |
| 1253 For fingerprint vector strings containing \fBAlphaNumericalValues\fR data values \- \fBExtendedConnectivityFingerprints\fR, | |
| 1254 \&\fBAtomNeighborhoodsFingerprints\fR and so on \- all three formulism result in same value during similarity and distance | |
| 1255 calculations. | |
| 1256 .IP "\fB\-w, \-\-WorkingDir\fR \fIDirName\fR" 4 | |
| 1257 .IX Item "-w, --WorkingDir DirName" | |
| 1258 Location of working directory. Default: current directory. | |
| 1259 .SH "EXAMPLES" | |
| 1260 .IX Header "EXAMPLES" | |
| 1261 To perform similarity search using Tanimoto coefficient by treating all reference molecules as a set | |
| 1262 to find 10 most similar database molecules with application of Max group fusion rule and similarity | |
| 1263 cutoff to supported fingerprints strings data in \s-1SD\s0 fingerprints files present in a data fields with | |
| 1264 Fingerprint substring in their labels, and create a ReferenceFPHexSimilaritySearching.csv file containing | |
| 1265 sequentially generated database compound IDs with Cmpd prefix, type: | |
| 1266 .PP | |
| 1267 .Vb 2 | |
| 1268 \& % SimilaritySearchingFingerprints.pl \-o ReferenceSampleFPHex.sdf | |
| 1269 \& DatabaseSampleFPHex.sdf | |
| 1270 .Ve | |
| 1271 .PP | |
| 1272 To perform similarity search using Tanimoto coefficient by treating all reference molecules as a set | |
| 1273 to find 10 most similar database molecules with application of Max group fusion rule and similarity | |
| 1274 cutoff to supported fingerprints strings data in \s-1FP\s0 fingerprints files, and create a | |
| 1275 SimilaritySearchResults.csv file containing database compound IDs retireved from \s-1FP\s0 file, type: | |
| 1276 .PP | |
| 1277 .Vb 2 | |
| 1278 \& % SimilaritySearchingFingerprints.pl \-r SimilaritySearchResults \-o | |
| 1279 \& ReferenceSampleFPBin.fpf DatabaseSampleFPBin.fpf | |
| 1280 .Ve | |
| 1281 .PP | |
| 1282 To perform similarity search using Tanimoto coefficient by treating all reference molecules as a set | |
| 1283 to find 10 most similar database database molecules with application of Max group fusion rule and | |
| 1284 similarity cutoff to supported fingerprints strings data in text fingerprints files present in a column | |
| 1285 names containing Fingerprint substring in their names, and create a ReferenceFPHexSimilaritySearching.csv | |
| 1286 file containing database compound IDs retireved column name containing CompoundID substring or | |
| 1287 sequentially generated compound IDs, type: | |
| 1288 .PP | |
| 1289 .Vb 2 | |
| 1290 \& % SimilaritySearchingFingerprints.pl \-o ReferenceSampleFPCount.csv | |
| 1291 \& DatabaseSampleFPCount.csv | |
| 1292 .Ve | |
| 1293 .PP | |
| 1294 To perform similarity search using Tanimoto coefficient by treating reference molecules as individual molecules | |
| 1295 to find 10 most similar database molecules for each reference molecule with application of similarity cutoff to | |
| 1296 supported fingerprints strings data in \s-1SD\s0 fingerprints files present in a data fields with Fingerprint substring | |
| 1297 in their labels, and create a ReferenceFPHexSimilaritySearching.csv file containing sequentially generated | |
| 1298 reference and database compound IDs with Cmpd prefix, type: | |
| 1299 .PP | |
| 1300 .Vb 2 | |
| 1301 \& % SimilaritySearchingFingerprints.pl \-mode IndividualReference \-o | |
| 1302 \& ReferenceSampleFPHex.sdf DatabaseSampleFPHex.sdf | |
| 1303 .Ve | |
| 1304 .PP | |
| 1305 To perform similarity search using Tanimoto coefficient by treating reference molecules as individual molecules | |
| 1306 to find 10 most similar database molecules for each reference molecule with application of similarity cutoff to | |
| 1307 supported fingerprints strings data in \s-1FP\s0 fingerprints files, and create a ReferenceFPHexSimilaritySearching.csv | |
| 1308 file containing references and database compound IDs retireved from \s-1FP\s0 file, type: | |
| 1309 .PP | |
| 1310 .Vb 2 | |
| 1311 \& % SimilaritySearchingFingerprints.pl \-mode IndividualReference \-o | |
| 1312 \& ReferenceSampleFPHex.fpf DatabaseSampleFPHex.fpf | |
| 1313 .Ve | |
| 1314 .PP | |
| 1315 To perform similarity search using Tanimoto coefficient by treating reference molecules as individual molecules | |
| 1316 to find 10 most similar database molecules for each reference molecule with application of similarity cutoff to | |
| 1317 supported fingerprints strings data in text fingerprints files present in a column names containing Fingerprint | |
| 1318 substring in their names, and create a ReferenceFPHexSimilaritySearching.csv file containing reference and | |
| 1319 database compound IDs retrieved column name containing CompoundID substring or sequentially generated | |
| 1320 compound IDs, type: | |
| 1321 .PP | |
| 1322 .Vb 2 | |
| 1323 \& % SimilaritySearchingFingerprints.pl \-mode IndividualReference \-o | |
| 1324 \& ReferenceSampleFPHex.csv DatabaseSampleFPHex.csv | |
| 1325 .Ve | |
| 1326 .PP | |
| 1327 To perform dissimilarity search using Tanimoto coefficient by treating all reference molecules as a set | |
| 1328 to find 10 most dissimilar database molecules with application of Max group fusion rule and similarity | |
| 1329 cutoff to supported fingerprints strings data in \s-1SD\s0 fingerprints files present in a data fields with | |
| 1330 Fingerprint substring in their labels, and create a ReferenceFPHexSimilaritySearching.csv file containing | |
| 1331 sequentially generated database compound IDs with Cmpd prefix, type: | |
| 1332 .PP | |
| 1333 .Vb 2 | |
| 1334 \& % SimilaritySearchingFingerprints.pl \-\-mode MultipleReferences \-\-SearchMode | |
| 1335 \& DissimilaritySearch \-o ReferenceSampleFPHex.sdf DatabaseSampleFPHex.sdf | |
| 1336 .Ve | |
| 1337 .PP | |
| 1338 To perform similarity search using CityBlock distance by treating reference molecules as individual molecules | |
| 1339 to find 10 most similar database molecules for each reference molecule with application of distance cutoff | |
| 1340 to supported vector fingerprints strings data in \s-1SD\s0 fingerprints files present in a data fields with Fingerprint | |
| 1341 substring in their labels, and create a ReferenceFPHexSimilaritySearching.csv file containing sequentially generated | |
| 1342 reference and database compound IDs with Cmpd prefix, type: | |
| 1343 .PP | |
| 1344 .Vb 4 | |
| 1345 \& % SimilaritySearchingFingerprints.pl \-mode IndividualReference | |
| 1346 \& \-\-VectorComparisonMode CityBlockDistance \-\-VectorComparisonFormulism | |
| 1347 \& AlgebraicForm \-\-DistanceCutoff 10 \-o | |
| 1348 \& ReferenceSampleFPCount.sdf DatabaseSampleFPCount.sdf | |
| 1349 .Ve | |
| 1350 .PP | |
| 1351 To perform similarity search using Tanimoto coefficient by treating all reference molecules as a set | |
| 1352 to find 100 most similar database molecules with application of Mean group fusion rule to to top 10 | |
| 1353 reference molecules with in similarity cutoff of 0.75 to supported fingerprints strings data in \s-1FP\s0 fingerprints | |
| 1354 files, and create a ReferenceFPHexSimilaritySearching.csv file containing database compound IDs retrieved | |
| 1355 from \s-1FP\s0 file, type: | |
| 1356 .PP | |
| 1357 .Vb 6 | |
| 1358 \& % SimilaritySearchingFingerprints.pl \-\-mode MultipleReferences \-\-SearchMode | |
| 1359 \& SimilaritySearch \-\-BitVectorComparisonMode TanimotoSimilarity | |
| 1360 \& \-\-GroupFusionRule Mean \-\-GroupFusionApplyCutoff Yes \-\-kNN 10 | |
| 1361 \& \-\-SimilarityCutoff 0.75 \-\-SimilarCountMode NumOfSimilar | |
| 1362 \& \-\-NumOfSimilarMolecules 100 \-o | |
| 1363 \& ReferenceSampleFPHex.fpf DatabaseSampleFPHex.fpf | |
| 1364 .Ve | |
| 1365 .PP | |
| 1366 To perform similarity search using Tanimoto coefficient by treating reference molecules as individual molecules | |
| 1367 to find 2 percent of most similar database molecules for each reference molecule with application of similarity | |
| 1368 cutoff of 0.85 to supported fingerprints strings data in text fingerprints files present in specific columns and | |
| 1369 create a ReferenceFPHexSimilaritySearching.csv file containing reference and database compoundIDs retrieved | |
| 1370 from specific columns, type: | |
| 1371 .PP | |
| 1372 .Vb 8 | |
| 1373 \& % SimilaritySearchingFingerprints.pl \-\-mode IndividualReference \-\-SearchMode | |
| 1374 \& SimilaritySearch \-\-BitVectorComparisonMode TanimotoSimilarity | |
| 1375 \& \-\-ReferenceColMode ColLabel \-\-ReferenceFingerprintsCol Fingerprints | |
| 1376 \& \-\-ReferenceCompoundIDCol CompoundID \-\-DatabaseColMode Collabel | |
| 1377 \& \-\-DatabaseCompoundIDCol CompoundID \-\-DatabaseFingerprintsCol | |
| 1378 \& Fingerprints \-\-SimilarityCutoff 0.85 \-\-SimilarCountMode PercentSimilar | |
| 1379 \& \-\-PercentSimilarMolecules 2 \-o | |
| 1380 \& ReferenceSampleFPHex.csv DatabaseSampleFPHex.csv | |
| 1381 .Ve | |
| 1382 .PP | |
| 1383 To perform similarity search using Tanimoto coefficient by treating reference molecules as individual molecules | |
| 1384 to find top 50 most similar database molecules for each reference molecule with application of similarity | |
| 1385 cutoff of 0.85 to supported fingerprints strings data in \s-1SD\s0 fingerprints files present in specific data fields and | |
| 1386 create both ReferenceFPHexSimilaritySearching.csv and ReferenceFPHexSimilaritySearching.sdf files containing | |
| 1387 reference and database compoundIDs retrieved from specific data fields, type: | |
| 1388 .PP | |
| 1389 .Vb 9 | |
| 1390 \& % SimilaritySearchingFingerprints.pl \-\-mode IndividualReference \-\-SearchMode | |
| 1391 \& SimilaritySearch \-\-BitVectorComparisonMode TanimotoSimilarity | |
| 1392 \& \-\-ReferenceFingerprintsField Fingerprints | |
| 1393 \& \-\-DatabaseFingerprintsField Fingerprints | |
| 1394 \& \-\-ReferenceCompoundIDMode DataField \-\-ReferenceCompoundIDField CmpdID | |
| 1395 \& \-\-DatabaseCompoundIDMode DataField \-\-DatabaseCompoundIDField CmpdID | |
| 1396 \& \-\-SimilarityCutoff 0.85 \-\-SimilarCountMode NumOfSimilar | |
| 1397 \& \-\-NumOfSimilarMolecules 50 \-\-output both \-o | |
| 1398 \& ReferenceSampleFPHex.sdf DatabaseSampleFPHex.sdf | |
| 1399 .Ve | |
| 1400 .PP | |
| 1401 To perform similarity search using Tanimoto coefficient by treating reference molecules as individual molecules | |
| 1402 to find 1 percent of most similar database molecules for each reference molecule with application of similarity | |
| 1403 cutoff to supported fingerprints strings data in \s-1SD\s0 fingerprints files present in specific data field labels, and create | |
| 1404 both ReferenceFPHexSimilaritySearching.csv ReferenceFPHexSimilaritySearching.sdf files containing reference and | |
| 1405 database compound IDs retrieved from specific data field labels along with other specific data for database | |
| 1406 molecules, type: | |
| 1407 .PP | |
| 1408 .Vb 10 | |
| 1409 \& % SimilaritySearchingFingerprints.pl \-\-mode IndividualReference \-\-SearchMode | |
| 1410 \& SimilaritySearch \-\-BitVectorComparisonMode TanimotoSimilarity | |
| 1411 \& \-\-ReferenceFingerprintsField Fingerprints | |
| 1412 \& \-\-DatabaseFingerprintsField Fingerprints | |
| 1413 \& \-\-ReferenceCompoundIDMode DataField \-\-ReferenceCompoundIDField CmpdID | |
| 1414 \& \-\-DatabaseCompoundIDMode DataField \-\-DatabaseCompoundIDField CmpdID | |
| 1415 \& \-\-DatabaseDataFieldsMode Specify \-\-DatabaseDataFields "TPSA,SLogP" | |
| 1416 \& \-\-SimilarityCutoff 0.75 \-\-SimilarCountMode PercentSimilar | |
| 1417 \& \-\-PercentSimilarMolecules 1 \-\-output both \-\-OutDelim comma \-\-quote Yes | |
| 1418 \& \-\-precision 3 \-o ReferenceSampleFPHex.sdf DatabaseSampleFPHex.sdf | |
| 1419 .Ve | |
| 1420 .SH "AUTHOR" | |
| 1421 .IX Header "AUTHOR" | |
| 1422 Manish Sud <msud@san.rr.com> | |
| 1423 .SH "SEE ALSO" | |
| 1424 .IX Header "SEE ALSO" | |
| 1425 InfoFingerprintsFiles.pl, SimilarityMatricesFingerprints.pl, AtomNeighborhoodsFingerprints.pl, | |
| 1426 ExtendedConnectivityFingerprints.pl, MACCSKeysFingerprints.pl, PathLengthFingerprints.pl, | |
| 1427 TopologicalAtomPairsFingerprints.pl, TopologicalAtomTorsionsFingerprints.pl, | |
| 1428 TopologicalPharmacophoreAtomPairsFingerprints.pl, TopologicalPharmacophoreAtomTripletsFingerprints.pl | |
| 1429 .SH "COPYRIGHT" | |
| 1430 .IX Header "COPYRIGHT" | |
| 1431 Copyright (C) 2015 Manish Sud. All rights reserved. | |
| 1432 .PP | |
| 1433 This file is part of MayaChemTools. | |
| 1434 .PP | |
| 1435 MayaChemTools is free software; you can redistribute it and/or modify it under | |
| 1436 the terms of the \s-1GNU\s0 Lesser General Public License as published by the Free | |
| 1437 Software Foundation; either version 3 of the License, or (at your option) | |
| 1438 any later version. |