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124 .\" ========================================================================
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125 .\"
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126 .IX Title "SIMILARITYSEARCHINGFINGERPRINTS 1"
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127 .TH SIMILARITYSEARCHINGFINGERPRINTS 1 "2015-03-29" "perl v5.14.2" "MayaChemTools"
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128 .\" For nroff, turn off justification. Always turn off hyphenation; it makes
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129 .\" way too many mistakes in technical documents.
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130 .if n .ad l
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131 .nh
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132 .SH "NAME"
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133 SimilaritySearchingFingerprints.pl \- Perform similarity search using fingerprints strings data in SD, FP and CSV/TSV text file(s)
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134 .SH "SYNOPSIS"
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135 .IX Header "SYNOPSIS"
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136 SimilaritySearchingFingerprints.pl ReferenceFPFile DatabaseFPFile
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137 .PP
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138 SimilaritySearchingFingerprints.pl [\fB\-\-alpha\fR \fInumber\fR] [\fB\-\-beta\fR \fInumber\fR]
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139 [\fB\-b, \-\-BitVectorComparisonMode\fR \fITanimotoSimilarity | TverskySimilarity | ...\fR]
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140 [\fB\-\-DatabaseColMode\fR \fIColNum | ColLabel\fR] [\fB\-\-DatabaseCompoundIDCol\fR \fIcol number | col name\fR]
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141 [\fB\-\-DatabaseCompoundIDPrefix\fR \fItext\fR] [\fB\-\-DatabaseCompoundIDField\fR \fIDataFieldName\fR]
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142 [\fB\-\-DatabaseCompoundIDMode\fR \fIDataField | MolName | LabelPrefix | MolNameOrLabelPrefix\fR]
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143 [\fB\-\-DatabaseDataCols\fR \fI\*(L"DataColNum1, DataColNum2,... \*(R" | DataColLabel1, DataCoLabel2,... "\fR]
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144 [\fB\-\-DatabaseDataColsMode\fR \fIAll | Specify | CompoundID\fR] [\fB\-\-DatabaseDataFields\fR \fI\*(L"FieldLabel1, FieldLabel2,... \*(R"\fR]
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145 [\fB\-\-DatabaseDataFieldsMode\fR \fIAll | Common | Specify | CompoundID\fR]
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146 [\fB\-\-DatabaseFingerprintsCol\fR \fIcol number | col name\fR] [\fB\-\-DatabaseFingerprintsField\fR \fIFieldLabel\fR]
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147 []\fB\-\-DistanceCutoff\fR \fInumber\fR] [\fB\-d, \-\-detail\fR \fIInfoLevel\fR] [\fB\-f, \-\-fast\fR]
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148 [\fB\-\-FingerprintsMode\fR \fIAutoDetect | FingerprintsBitVectorString | FingerprintsVectorString\fR]
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149 [\fB\-g, \-\-GroupFusionRule\fR \fIMax, Mean, Median, Min, Sum, Euclidean\fR] [\fB\-\-GroupFusionApplyCutoff\fR \fIYes | No\fR]
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150 [\fB\-h, \-\-help\fR] [\fB\-\-InDelim\fR \fIcomma | semicolon\fR] [\fB\-k, \-\-KNN\fR \fIall | number\fR]
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151 [\fB\-m, \-\-mode\fR \fIIndividualReference | MultipleReferences\fR]
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152 [\fB\-n, \-\-NumOfSimilarMolecules\fR \fInumber\fR] [\fB\-\-OutDelim\fR \fIcomma | tab | semicolon\fR]
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153 [\fB\-\-output\fR \fI\s-1SD\s0 | text | both\fR] [\fB\-o, \-\-overwrite\fR]
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154 [\fB\-p, \-\-PercentSimilarMolecules\fR \fInumber\fR] [\fB\-\-precision\fR \fInumber\fR] [\fB\-q, \-\-quote\fR \fIYes | No\fR]
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155 [\fB\-\-ReferenceColMode\fR \fIColNum | ColLabel\fR] [\fB\-\-ReferenceCompoundIDCol\fR \fIcol number | col name\fR]
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156 [\fB\-\-ReferenceCompoundIDPrefix\fR \fItext\fR] [\fB\-\-ReferenceCompoundIDField\fR \fIDataFieldName\fR]
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157 [\fB\-\-ReferenceCompoundIDMode\fR \fIDataField | MolName | LabelPrefix | MolNameOrLabelPrefix\fR]
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158 [\fB\-\-ReferenceFingerprintsCol\fR \fIcol number | col name\fR] [\fB\-\-ReferenceFingerprintsField\fR \fIFieldLabel\fR]
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159 [\fB\-r, \-\-root\fR \fIRootName\fR] [\fB\-s, \-\-SearchMode\fR \fISimilaritySearch | DissimilaritySearch\fR]
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160 [\fB\-\-SimilarCountMode\fR \fINumOfSimilar | PercentSimilar\fR] [\fB\-\-SimilarityCutoff\fR \fInumber\fR]
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161 [\fB\-v, \-\-VectorComparisonMode\fR \fITanimotoSimilairy | ... | ManhattanDistance | ...\fR]
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162 [\fB\-\-VectorComparisonFormulism\fR \fIAlgebraicForm | BinaryForm | SetTheoreticForm\fR]
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163 [\fB\-w, \-\-WorkingDir\fR dirname] ReferenceFingerprintsFile DatabaseFingerprintsFile
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164 .SH "DESCRIPTION"
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165 .IX Header "DESCRIPTION"
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166 Perform molecular similarity search [ Ref 94\-113 ] using fingerprint bit-vector or vector strings
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167 data in \fI\s-1SD\s0, \s-1FP\s0, or \s-1CSV/TSV\s0 text\fR files corresponding to \fIReferenceFingerprintsFile\fR and
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168 \&\fIDatabaseFingerprintsFile\fR, and generate \s-1SD\s0 and \s-1CSV/TSV\s0 text file(s) containing database
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169 molecules which are similar to reference molecule(s). The reference molecules are also referred
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170 to as query or seed molecules and database molecules as target molecules in the literature.
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171 .PP
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172 The current release of MayaChemTools supports two types of similarity search modes:
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173 \&\fIIndividualReference or MultipleReferences\fR. For default value of \fIMultipleReferences\fR for \fB\-m, \-\-mode\fR
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174 option, reference molecules are considered as a set and \fB\-g, \-\-GroupFusionRule\fR is used to calculate
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175 similarity of a database molecule against reference molecules set. The group fusion rule is also
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176 referred to as data fusion of consensus scoring in the literature. However, for \fIIndividualReference\fR
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177 value of \fB\-m, \-\-mode\fR option, reference molecules are treated as individual molecules and each reference
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178 molecule is compared against a database molecule by itself to identify similar molecules.
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179 .PP
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180 The molecular dissimilarity search can also be performed using \fIDissimilaritySearch\fR value for
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181 \&\fB\-s, \-\-SearchMode\fR option. During dissimilarity search or usage of distance comparison coefficient
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182 in similarity similarity search, the meaning of fingerprints comparison value is automatically reversed
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183 as shown below:
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184 .PP
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185 .Vb 1
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186 \& SeachMode ComparisonCoefficient ResultsSort ComparisonValues
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187 \&
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188 \& Similarity SimilarityCoefficient Descending Higher value imples
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189 \& high similarity
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190 \& Similarity DistanceCoefficient Ascending Lower value implies
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191 \& high similarity
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192 \&
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193 \& Dissimilarity SimilarityCoefficient Ascending Lower value implies
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194 \& high dissimilarity
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195 \& Dissimilarity DistanceCoefficient Descending Higher value implies
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196 \& high dissimilarity
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197 .Ve
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198 .PP
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199 During \fIIndividualReference\fR value of \fB\-m, \-\-Mode\fR option for similarity search, fingerprints bit-vector
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200 or vector string of each reference molecule is compared with database molecules using specified
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201 similarity or distance coefficients to identify most similar molecules for each reference molecule.
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202 Based on value of \fB\-\-SimilarCountMode\fR, up to \fB\-\-n, \-\-NumOfSimilarMolecules\fR or \fB\-p,
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203 \&\-\-PercentSimilarMolecules\fR at specified \fB\-\-SimilarityCutoff\fR or \fB\-\-DistanceCutoff\fR are
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204 identified for each reference molecule.
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205 .PP
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206 During \fIMultipleReferences\fR value \fB\-m, \-\-mode\fR option for similarity search, all reference molecules
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207 are considered as a set and \fB\-g, \-\-GroupFusionRule\fR is used to calculate similarity of a database
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208 molecule against reference molecules set either using all reference molecules or number of k\-nearest
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209 neighbors (k\-NN) to a database molecule specified using \fB\-k, \-\-kNN\fR. The fingerprints bit-vector
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210 or vector string of each reference molecule in a set is compared with a database molecule using
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211 a similarity or distance coefficient specified via \fB\-b, \-\-BitVectorComparisonMode\fR or \fB\-v,
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212 \&\-\-VectorComparisonMode\fR. The reference molecules whose comparison values with a database
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213 molecule fall outside specified \fB\-\-SimilarityCutoff\fR or \fB\-\-DistanceCutoff\fR are ignored during \fIYes\fR
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214 value of \fB\-\-GroupFusionApplyCutoff\fR. The specified \fB\-g, \-\-GroupFusionRule\fR is applied to
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215 \&\fB\-k, \-\-kNN\fR reference molecules to calculate final similarity value between a database molecule
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216 and reference molecules set.
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217 .PP
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218 The input fingerprints \fI\s-1SD\s0, \s-1FP\s0, or Text (\s-1CSV/TSV\s0)\fR files for \fIReferenceFingerprintsFile\fR and
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219 \&\fIDatabaseTextFile\fR must contain valid fingerprint bit-vector or vector strings data corresponding to
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220 same type of fingerprints.
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221 .PP
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222 The valid fingerprints \fISDFile\fR extensions are \fI.sdf\fR and \fI.sd\fR. The valid fingerprints \fIFPFile\fR
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223 extensions are \fI.fpf\fR and \fI.fp\fR. The valid fingerprints \fITextFile (\s-1CSV/TSV\s0)\fR extensions are
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224 \&\fI.csv\fR and \fI.tsv\fR for comma/semicolon and tab delimited text files respectively. The \fB\-\-indelim\fR
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225 option determines the format of \fITextFile\fR. Any file which doesn't correspond to the format indicated
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226 by \fB\-\-indelim\fR option is ignored.
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227 .PP
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228 Example of \fI\s-1FP\s0\fR file containing fingerprints bit-vector string data:
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229 .PP
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230 .Vb 10
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231 \& #
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232 \& # Package = MayaChemTools 7.4
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233 \& # ReleaseDate = Oct 21, 2010
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234 \& #
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235 \& # TimeStamp = Mon Mar 7 15:14:01 2011
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236 \& #
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237 \& # FingerprintsStringType = FingerprintsBitVector
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238 \& #
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239 \& # Description = PathLengthBits:AtomicInvariantsAtomTypes:MinLength1:...
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240 \& # Size = 1024
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241 \& # BitStringFormat = HexadecimalString
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242 \& # BitsOrder = Ascending
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243 \& #
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244 \& Cmpd1 9c8460989ec8a49913991a6603130b0a19e8051c89184414953800cc21510...
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245 \& Cmpd2 000000249400840040100042011001001980410c000000001010088001120...
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246 \& ... ...
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247 \& ... ..
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248 .Ve
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249 .PP
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250 Example of \fI\s-1FP\s0\fR file containing fingerprints vector string data:
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251 .PP
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252 .Vb 10
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253 \& #
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254 \& # Package = MayaChemTools 7.4
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255 \& # ReleaseDate = Oct 21, 2010
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256 \& #
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257 \& # TimeStamp = Mon Mar 7 15:14:01 2011
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258 \& #
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259 \& # FingerprintsStringType = FingerprintsVector
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260 \& #
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261 \& # Description = PathLengthBits:AtomicInvariantsAtomTypes:MinLength1:...
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262 \& # VectorStringFormat = IDsAndValuesString
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263 \& # VectorValuesType = NumericalValues
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264 \& #
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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:
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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...;
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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
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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 ...
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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
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270 \& O C CC=O CCCC CCCN CCCO CCNC CNC=N CNC=O CNCN CCCC=O CCCCC CCCCN CC...;
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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
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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 ...
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273 \& ... ...
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274 \& ... ...
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275 .Ve
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276 .PP
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277 Example of \fI\s-1SD\s0\fR file containing fingerprints bit-vector string data:
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278 .PP
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279 .Vb 10
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280 \& ... ...
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281 \& ... ...
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282 \& $$$$
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283 \& ... ...
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284 \& ... ...
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285 \& ... ...
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286 \& 41 44 0 0 0 0 0 0 0 0999 V2000
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287 \& \-3.3652 1.4499 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
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288 \& ... ...
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289 \& 2 3 1 0 0 0 0
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290 \& ... ...
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291 \& M END
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292 \& > <CmpdID>
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293 \& Cmpd1
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294 \&
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295 \& > <PathLengthFingerprints>
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296 \& FingerprintsBitVector;PathLengthBits:AtomicInvariantsAtomTypes:MinLengt
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297 \& h1:MaxLength8;1024;HexadecimalString;Ascending;9c8460989ec8a49913991a66
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298 \& 03130b0a19e8051c89184414953800cc2151082844a201042800130860308e8204d4028
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299 \& 00831048940e44281c00060449a5000ac80c894114e006321264401600846c050164462
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300 \& 08190410805000304a10205b0100e04c0038ba0fad0209c0ca8b1200012268b61c0026a
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301 \& aa0660a11014a011d46
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302 \&
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303 \& $$$$
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304 \& ... ...
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305 \& ... ...
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306 .Ve
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307 .PP
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308 Example of \s-1CSV\s0 \fITextFile\fR containing fingerprints bit-vector string data:
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309 .PP
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310 .Vb 7
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311 \& "CompoundID","PathLengthFingerprints"
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312 \& "Cmpd1","FingerprintsBitVector;PathLengthBits:AtomicInvariantsAtomTypes
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313 \& :MinLength1:MaxLength8;1024;HexadecimalString;Ascending;9c8460989ec8a4
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314 \& 9913991a6603130b0a19e8051c89184414953800cc2151082844a20104280013086030
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315 \& 8e8204d402800831048940e44281c00060449a5000ac80c894114e006321264401..."
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316 \& ... ...
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317 \& ... ...
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318 .Ve
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319 .PP
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320 The current release of MayaChemTools supports the following types of fingerprint
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321 bit-vector and vector strings:
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322 .PP
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323 .Vb 6
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324 \& FingerprintsVector;AtomNeighborhoods:AtomicInvariantsAtomTypes:MinRadi
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325 \& us0:MaxRadius2;41;AlphaNumericalValues;ValuesString;NR0\-C.X1.BO1.H3\-AT
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326 \& C1:NR1\-C.X3.BO3.H1\-ATC1:NR2\-C.X1.BO1.H3\-ATC1:NR2\-C.X3.BO4\-ATC1 NR0\-C.X
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327 \& 1.BO1.H3\-ATC1:NR1\-C.X3.BO3.H1\-ATC1:NR2\-C.X1.BO1.H3\-ATC1:NR2\-C.X3.BO4\-A
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328 \& TC1 NR0\-C.X2.BO2.H2\-ATC1:NR1\-C.X2.BO2.H2\-ATC1:NR1\-C.X3.BO3.H1\-ATC1:NR2
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329 \& \-C.X2.BO2.H2\-ATC1:NR2\-N.X3.BO3\-ATC1:NR2\-O.X1.BO1.H1\-ATC1 NR0\-C.X2.B...
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330 \&
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331 \& FingerprintsVector;AtomTypesCount:AtomicInvariantsAtomTypes:ArbitraryS
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332 \& ize;10;NumericalValues;IDsAndValuesString;C.X1.BO1.H3 C.X2.BO2.H2 C.X2
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333 \& .BO3.H1 C.X3.BO3.H1 C.X3.BO4 F.X1.BO1 N.X2.BO2.H1 N.X3.BO3 O.X1.BO1.H1
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334 \& O.X1.BO2;2 4 14 3 10 1 1 1 3 2
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335 \&
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336 \& FingerprintsVector;AtomTypesCount:SLogPAtomTypes:ArbitrarySize;16;Nume
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337 \& ricalValues;IDsAndValuesString;C1 C10 C11 C14 C18 C20 C21 C22 C5 CS F
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338 \& N11 N4 O10 O2 O9;5 1 1 1 14 4 2 1 2 2 1 1 1 1 3 1
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339 \&
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340 \& FingerprintsVector;AtomTypesCount:SLogPAtomTypes:FixedSize;67;OrderedN
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341 \& umericalValues;IDsAndValuesString;C1 C2 C3 C4 C5 C6 C7 C8 C9 C10 C11 C
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342 \& 12 C13 C14 C15 C16 C17 C18 C19 C20 C21 C22 C23 C24 C25 C26 C27 CS N1 N
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343 \& 2 N3 N4 N5 N6 N7 N8 N9 N10 N11 N12 N13 N14 NS O1 O2 O3 O4 O5 O6 O7 O8
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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
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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...
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346 \&
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347 \& FingerprintsVector;EStateIndicies:ArbitrarySize;11;NumericalValues;IDs
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348 \& AndValuesString;SaaCH SaasC SaasN SdO SdssC SsCH3 SsF SsOH SssCH2 SssN
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349 \& H SsssCH;24.778 4.387 1.993 25.023 \-1.435 3.975 14.006 29.759 \-0.073 3
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350 \& .024 \-2.270
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351 \&
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352 \& FingerprintsVector;EStateIndicies:FixedSize;87;OrderedNumericalValues;
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353 \& ValuesString;0 0 0 0 0 0 0 3.975 0 \-0.073 0 0 24.778 \-2.270 0 0 \-1.435
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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
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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
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356 \& 0 0 0 0 0 0 0 0 0 0 0 0 0 0
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357 \&
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358 \& FingerprintsVector;ExtendedConnectivity:AtomicInvariantsAtomTypes:Radi
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359 \& us2;60;AlphaNumericalValues;ValuesString;73555770 333564680 352413391
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360 \& 666191900 1001270906 1371674323 1481469939 1977749791 2006158649 21414
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361 \& 08799 49532520 64643108 79385615 96062769 273726379 564565671 85514103
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362 \& 5 906706094 988546669 1018231313 1032696425 1197507444 1331250018 1338
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363 \& 532734 1455473691 1607485225 1609687129 1631614296 1670251330 17303...
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364 \&
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365 \& FingerprintsVector;ExtendedConnectivityCount:AtomicInvariantsAtomTypes
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366 \& :Radius2;60;NumericalValues;IDsAndValuesString;73555770 333564680 3524
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367 \& 13391 666191900 1001270906 1371674323 1481469939 1977749791 2006158649
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368 \& 2141408799 49532520 64643108 79385615 96062769 273726379 564565671...;
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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
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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
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371 \&
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372 \& FingerprintsBitVector;ExtendedConnectivityBits:AtomicInvariantsAtomTyp
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373 \& es:Radius2;1024;BinaryString;Ascending;0000000000000000000000000000100
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374 \& 0000000001010000000110000011000000000000100000000000000000000000100001
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375 \& 1000000110000000000000000000000000010011000000000000000000000000010000
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376 \& 0000000000000000000000000010000000000000000001000000000000000000000000
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377 \& 0000000000010000100001000000000000101000000000000000100000000000000...
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378 \&
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379 \& FingerprintsVector;ExtendedConnectivity:FunctionalClassAtomTypes:Radiu
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380 \& s2;57;AlphaNumericalValues;ValuesString;24769214 508787397 850393286 8
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381 \& 62102353 981185303 1231636850 1649386610 1941540674 263599683 32920567
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382 \& 1 571109041 639579325 683993318 723853089 810600886 885767127 90326012
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383 \& 7 958841485 981022393 1126908698 1152248391 1317567065 1421489994 1455
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384 \& 632544 1557272891 1826413669 1983319256 2015750777 2029559552 20404...
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385 \&
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386 \& FingerprintsVector;ExtendedConnectivity:EStateAtomTypes:Radius2;62;Alp
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387 \& haNumericalValues;ValuesString;25189973 528584866 662581668 671034184
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388 \& 926543080 1347067490 1738510057 1759600920 2034425745 2097234755 21450
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389 \& 44754 96779665 180364292 341712110 345278822 386540408 387387308 50430
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390 \& 1706 617094135 771528807 957666640 997798220 1158349170 1291258082 134
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391 \& 1138533 1395329837 1420277211 1479584608 1486476397 1487556246 1566...
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392 \&
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393 \& FingerprintsBitVector;MACCSKeyBits;166;BinaryString;Ascending;00000000
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394 \& 0000000000000000000000000000000001001000010010000000010010000000011100
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395 \& 0100101010111100011011000100110110000011011110100110111111111111011111
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396 \& 11111111111110111000
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397 \&
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398 \& FingerprintsBitVector;MACCSKeyBits;322;BinaryString;Ascending;11101011
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399 \& 1110011111100101111111000111101100110000000000000011100010000000000000
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400 \& 0000000000000000000000000000000000000000000000101000000000000000000000
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401 \& 0000000000000000000000000000000000000000000000000000000000000000000000
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402 \& 0000000000000000000000000000000000000011000000000000000000000000000000
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403 \& 0000000000000000000000000000000000000000
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404 \&
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405 \& FingerprintsVector;MACCSKeyCount;166;OrderedNumericalValues;ValuesStri
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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
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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
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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
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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
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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
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411 \&
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412 \& FingerprintsVector;MACCSKeyCount;322;OrderedNumericalValues;ValuesStri
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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
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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
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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
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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
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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 ...
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418 \&
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419 \& FingerprintsBitVector;PathLengthBits:AtomicInvariantsAtomTypes:MinLeng
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420 \& th1:MaxLength8;1024;BinaryString;Ascending;001000010011010101011000110
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421 \& 0100010101011000101001011100110001000010001001101000001001001001001000
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422 \& 0010110100000111001001000001001010100100100000000011000000101001011100
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423 \& 0010000001000101010100000100111100110111011011011000000010110111001101
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424 \& 0101100011000000010001000011000010100011101100001000001000100000000...
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425 \&
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426 \& FingerprintsVector;PathLengthCount:AtomicInvariantsAtomTypes:MinLength
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427 \& 1:MaxLength8;432;NumericalValues;IDsAndValuesPairsString;C.X1.BO1.H3 2
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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
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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
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430 \& 2 C.X2.BO2.H2C.X2.BO2.H2 1 C.X2.BO2.H2C.X3.BO3.H1 4 C.X2.BO2.H2C.X3.BO
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431 \& 4 1 C.X2.BO2.H2N.X3.BO3 1 C.X2.BO3.H1:C.X2.BO3.H1 10 C.X2.BO3.H1:C....
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432 \&
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433 \& FingerprintsVector;PathLengthCount:MMFF94AtomTypes:MinLength1:MaxLengt
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434 \& h8;463;NumericalValues;IDsAndValuesPairsString;C5A 2 C5B 2 C=ON 1 CB 1
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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
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436 \& 5 2 C5ACB 1 C5ACR 1 C5B:C5B 1 C5BC=ON 1 C5BCB 1 C=ON=O=CN 1 C=ONNC=O 1
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437 \& CB:CB 18 CBF 1 CBNC=O 1 COO=O=CO 1 COOCR 1 COOOC=O 1 CRCR 7 CRN5 1 CR
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438 \& OR 2 C5A:C5B:C5B 2 C5A:C5BC=ON 1 C5A:C5BCB 1 C5A:N5:C5A 1 C5A:N5CR ...
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439 \&
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440 \& FingerprintsVector;TopologicalAtomPairs:AtomicInvariantsAtomTypes:MinD
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441 \& istance1:MaxDistance10;223;NumericalValues;IDsAndValuesString;C.X1.BO1
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442 \& .H3\-D1\-C.X3.BO3.H1 C.X2.BO2.H2\-D1\-C.X2.BO2.H2 C.X2.BO2.H2\-D1\-C.X3.BO3.
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443 \& H1 C.X2.BO2.H2\-D1\-C.X3.BO4 C.X2.BO2.H2\-D1\-N.X3.BO3 C.X2.BO3.H1\-D1\-...;
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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
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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...
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446 \&
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447 \& FingerprintsVector;TopologicalAtomPairs:FunctionalClassAtomTypes:MinDi
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448 \& stance1:MaxDistance10;144;NumericalValues;IDsAndValuesString;Ar\-D1\-Ar
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449 \& Ar\-D1\-Ar.HBA Ar\-D1\-HBD Ar\-D1\-Hal Ar\-D1\-None Ar.HBA\-D1\-None HBA\-D1\-NI H
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450 \& BA\-D1\-None HBA.HBD\-D1\-NI HBA.HBD\-D1\-None HBD\-D1\-None NI\-D1\-None No...;
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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
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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 ...
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453 \&
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454 \& FingerprintsVector;TopologicalAtomTorsions:AtomicInvariantsAtomTypes;3
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455 \& 3;NumericalValues;IDsAndValuesString;C.X1.BO1.H3\-C.X3.BO3.H1\-C.X3.BO4\-
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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
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457 \& 2.H2\-C.X3.BO3.H1\-C.X2.BO2.H2 C.X2.BO2.H2\-C.X2.BO2.H2\-C.X3.BO3.H1\-O...;
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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
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459 \&
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460 \& FingerprintsVector;TopologicalAtomTorsions:EStateAtomTypes;36;Numerica
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461 \& lValues;IDsAndValuesString;aaCH\-aaCH\-aaCH\-aaCH aaCH\-aaCH\-aaCH\-aasC aaC
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462 \& H\-aaCH\-aasC\-aaCH aaCH\-aaCH\-aasC\-aasC aaCH\-aaCH\-aasC\-sF aaCH\-aaCH\-aasC\-
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463 \& ssNH aaCH\-aasC\-aasC\-aasC aaCH\-aasC\-aasC\-aasN aaCH\-aasC\-ssNH\-dssC a...;
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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
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465 \&
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466 \& FingerprintsVector;TopologicalAtomTriplets:AtomicInvariantsAtomTypes:M
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467 \& inDistance1:MaxDistance10;3096;NumericalValues;IDsAndValuesString;C.X1
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468 \& .BO1.H3\-D1\-C.X1.BO1.H3\-D1\-C.X3.BO3.H1\-D2 C.X1.BO1.H3\-D1\-C.X2.BO2.H2\-D1
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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
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470 \& \-C.X2.BO2.H2\-D4\-C.X2.BO2.H2\-D5 C.X1.BO1.H3\-D1\-C.X2.BO2.H2\-D6\-C.X3....;
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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
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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...
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473 \&
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474 \& FingerprintsVector;TopologicalAtomTriplets:SYBYLAtomTypes:MinDistance1
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475 \& :MaxDistance10;2332;NumericalValues;IDsAndValuesString;C.2\-D1\-C.2\-D9\-C
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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\-
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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
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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.
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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...
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480 \&
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481 \& FingerprintsVector;TopologicalPharmacophoreAtomPairs:ArbitrarySize:Min
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482 \& Distance1:MaxDistance10;54;NumericalValues;IDsAndValuesString;H\-D1\-H H
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483 \& \-D1\-NI HBA\-D1\-NI HBD\-D1\-NI H\-D2\-H H\-D2\-HBA H\-D2\-HBD HBA\-D2\-HBA HBA\-D2\-
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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
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485 \& BA H\-D4\-HBD HBA\-D4\-HBA HBA\-D4\-HBD HBD\-D4\-HBD H\-D5\-H H\-D5\-HBA H\-D5\-...;
|
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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
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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
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488 \&
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489 \& FingerprintsVector;TopologicalPharmacophoreAtomPairs:FixedSize:MinDist
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490 \& ance1:MaxDistance10;150;OrderedNumericalValues;ValuesString;18 0 0 1 0
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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
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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
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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
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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...
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495 \&
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496 \& FingerprintsVector;TopologicalPharmacophoreAtomTriplets:ArbitrarySize:
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497 \& MinDistance1:MaxDistance10;696;NumericalValues;IDsAndValuesString;Ar1\-
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498 \& Ar1\-Ar1 Ar1\-Ar1\-H1 Ar1\-Ar1\-HBA1 Ar1\-Ar1\-HBD1 Ar1\-H1\-H1 Ar1\-H1\-HBA1 Ar1
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499 \& \-H1\-HBD1 Ar1\-HBA1\-HBD1 H1\-H1\-H1 H1\-H1\-HBA1 H1\-H1\-HBD1 H1\-HBA1\-HBA1 H1\-
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500 \& HBA1\-HBD1 H1\-HBA1\-NI1 H1\-HBD1\-NI1 HBA1\-HBA1\-NI1 HBA1\-HBD1\-NI1 Ar1\-...;
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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
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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
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503 \& 119 123 24 15 185 202 41 25 22 17 3 5 85 95 18 11 23 17 3 1 1 6 4 ...
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504 \&
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505 \& FingerprintsVector;TopologicalPharmacophoreAtomTriplets:FixedSize:MinD
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506 \& istance1:MaxDistance10;2692;OrderedNumericalValues;ValuesString;46 106
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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
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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
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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
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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 ...
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511 .Ve
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512 .SH "OPTIONS"
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513 .IX Header "OPTIONS"
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514 .IP "\fB\-\-alpha\fR \fInumber\fR" 4
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515 .IX Item "--alpha number"
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516 Value of alpha parameter for calculating \fITversky\fR similarity coefficient specified for
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517 \&\fB\-b, \-\-BitVectorComparisonMode\fR option. It corresponds to weights assigned for bits set
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518 to \*(L"1\*(R" in a pair of fingerprint bit-vectors during the calculation of similarity coefficient. Possible
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519 values: \fI0 to 1\fR. Default value: <0.5>.
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520 .IP "\fB\-\-beta\fR \fInumber\fR" 4
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521 .IX Item "--beta number"
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522 Value of beta parameter for calculating \fIWeightedTanimoto\fR and \fIWeightedTversky\fR
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523 similarity coefficients specified for \fB\-b, \-\-BitVectorComparisonMode\fR option. It is used to
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524 weight the contributions of bits set to \*(L"0\*(R" during the calculation of similarity coefficients. Possible
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525 values: \fI0 to 1\fR. Default value of <1> makes \fIWeightedTanimoto\fR and \fIWeightedTversky\fR
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526 equivalent to \fITanimoto\fR and \fITversky\fR.
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527 .IP "\fB\-b, \-\-BitVectorComparisonMode\fR \fITanimotoSimilarity | TverskySimilarity | ...\fR" 4
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528 .IX Item "-b, --BitVectorComparisonMode TanimotoSimilarity | TverskySimilarity | ..."
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529 Specify what similarity coefficient to use for calculating similarity between fingerprints bit-vector
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530 string data values in \fIReferenceFingerprintsFile\fR and \fIDatabaseFingerprintsFile\fR during similarity
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531 search. Possible values: \fITanimotoSimilarity | TverskySimilarity | ...\fR. Default: \fITanimotoSimilarity\fR
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532 .Sp
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533 The current release supports the following similarity coefficients: \fIBaroniUrbaniSimilarity, BuserSimilarity,
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|
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534 CosineSimilarity, DiceSimilarity, DennisSimilarity, ForbesSimilarity, FossumSimilarity, HamannSimilarity, JacardSimilarity,
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535 Kulczynski1Similarity, Kulczynski2Similarity, MatchingSimilarity, McConnaugheySimilarity, OchiaiSimilarity,
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|
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536 PearsonSimilarity, RogersTanimotoSimilarity, RussellRaoSimilarity, SimpsonSimilarity, SkoalSneath1Similarity,
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|
|
537 SkoalSneath2Similarity, SkoalSneath3Similarity, TanimotoSimilarity, TverskySimilarity, YuleSimilarity,
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|
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538 WeightedTanimotoSimilarity, WeightedTverskySimilarity\fR. These similarity coefficients are described below.
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539 .Sp
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|
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540 For two fingerprint bit-vectors A and B of same size, let:
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541 .Sp
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542 .Vb 4
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543 \& Na = Number of bits set to "1" in A
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544 \& Nb = Number of bits set to "1" in B
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|
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545 \& Nc = Number of bits set to "1" in both A and B
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546 \& Nd = Number of bits set to "0" in both A and B
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547 \&
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548 \& Nt = Number of bits set to "1" or "0" in A or B (Size of A or B)
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549 \& Nt = Na + Nb \- Nc + Nd
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550 \&
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551 \& Na \- Nc = Number of bits set to "1" in A but not in B
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552 \& Nb \- Nc = Number of bits set to "1" in B but not in A
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553 .Ve
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554 .Sp
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555 Then, various similarity coefficients [ Ref. 40 \- 42 ] for a pair of bit-vectors A and B are
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556 defined as follows:
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557 .Sp
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558 \&\fIBaroniUrbaniSimilarity\fR: ( \s-1SQRT\s0( Nc * Nd ) + Nc ) / ( \s-1SQRT\s0 ( Nc * Nd ) + Nc + ( Na \- Nc ) + ( Nb \- Nc ) ) ( same as Buser )
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559 .Sp
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560 \&\fIBuserSimilarity\fR: ( \s-1SQRT\s0 ( Nc * Nd ) + Nc ) / ( \s-1SQRT\s0 ( Nc * Nd ) + Nc + ( Na \- Nc ) + ( Nb \- Nc ) ) ( same as BaroniUrbani )
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561 .Sp
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|
562 \&\fICosineSimilarity\fR: Nc / \s-1SQRT\s0 ( Na * Nb ) (same as Ochiai)
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563 .Sp
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564 \&\fIDiceSimilarity\fR: (2 * Nc) / ( Na + Nb )
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565 .Sp
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566 \&\fIDennisSimilarity\fR: ( Nc * Nd \- ( ( Na \- Nc ) * ( Nb \- Nc ) ) ) / \s-1SQRT\s0 ( Nt * Na * Nb)
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567 .Sp
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568 \&\fIForbesSimilarity\fR: ( Nt * Nc ) / ( Na * Nb )
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569 .Sp
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570 \&\fIFossumSimilarity\fR: ( Nt * ( ( Nc \- 1/2 ) ** 2 ) / ( Na * Nb )
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571 .Sp
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572 \&\fIHamannSimilarity\fR: ( ( Nc + Nd ) \- ( Na \- Nc ) \- ( Nb \- Nc ) ) / Nt
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573 .Sp
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574 \&\fIJaccardSimilarity\fR: Nc / ( ( Na \- Nc) + ( Nb \- Nc ) + Nc ) = Nc / ( Na + Nb \- Nc ) (same as Tanimoto)
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575 .Sp
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576 \&\fIKulczynski1Similarity\fR: Nc / ( ( Na \- Nc ) + ( Nb \- Nc) ) = Nc / ( Na + Nb \- 2Nc )
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577 .Sp
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578 \&\fIKulczynski2Similarity\fR: ( ( Nc / 2 ) * ( 2 * Nc + ( Na \- Nc ) + ( Nb \- Nc) ) ) / ( ( Nc + ( Na \- Nc ) ) * ( Nc + ( Nb \- Nc ) ) ) = 0.5 * ( Nc / Na + Nc / Nb )
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579 .Sp
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580 \&\fIMatchingSimilarity\fR: ( Nc + Nd ) / Nt
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581 .Sp
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|
|
582 \&\fIMcConnaugheySimilarity\fR: ( Nc ** 2 \- ( Na \- Nc ) * ( Nb \- Nc) ) / ( Na * Nb )
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583 .Sp
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|
584 \&\fIOchiaiSimilarity\fR: Nc / \s-1SQRT\s0 ( Na * Nb ) (same as Cosine)
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585 .Sp
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586 \&\fIPearsonSimilarity\fR: ( ( Nc * Nd ) \- ( ( Na \- Nc ) * ( Nb \- Nc ) ) / \s-1SQRT\s0 ( Na * Nb * ( Na \- Nc + Nd ) * ( Nb \- Nc + Nd ) )
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587 .Sp
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588 \&\fIRogersTanimotoSimilarity\fR: ( Nc + Nd ) / ( ( Na \- Nc) + ( Nb \- Nc) + Nt) = ( Nc + Nd ) / ( Na + Nb \- 2Nc + Nt)
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589 .Sp
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590 \&\fIRussellRaoSimilarity\fR: Nc / Nt
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591 .Sp
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592 \&\fISimpsonSimilarity\fR: Nc / \s-1MIN\s0 ( Na, Nb)
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593 .Sp
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|
594 \&\fISkoalSneath1Similarity\fR: Nc / ( Nc + 2 * ( Na \- Nc) + 2 * ( Nb \- Nc) ) = Nc / ( 2 * Na + 2 * Nb \- 3 * Nc )
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595 .Sp
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|
|
596 \&\fISkoalSneath2Similarity\fR: ( 2 * Nc + 2 * Nd ) / ( Nc + Nd + Nt )
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|
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597 .Sp
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598 \&\fISkoalSneath3Similarity\fR: ( Nc + Nd ) / ( ( Na \- Nc ) + ( Nb \- Nc ) ) = ( Nc + Nd ) / ( Na + Nb \- 2 * Nc )
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599 .Sp
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600 \&\fITanimotoSimilarity\fR: Nc / ( ( Na \- Nc) + ( Nb \- Nc ) + Nc ) = Nc / ( Na + Nb \- Nc ) (same as Jaccard)
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|
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601 .Sp
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602 \&\fITverskySimilarity\fR: Nc / ( alpha * ( Na \- Nc ) + ( 1 \- alpha) * ( Nb \- Nc) + Nc ) = Nc / ( alpha * ( Na \- Nb ) + Nb)
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|
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603 .Sp
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|
604 \&\fIYuleSimilarity\fR: ( ( Nc * Nd ) \- ( ( Na \- Nc ) * ( Nb \- Nc ) ) ) / ( ( Nc * Nd ) + ( ( Na \- Nc ) * ( Nb \- Nc ) ) )
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605 .Sp
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|
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606 Values of Tanimoto/Jaccard and Tversky coefficients are dependent on only those bit which
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|
|
607 are set to \*(L"1\*(R" in both A and B. In order to take into account all bit positions, modified versions
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|
|
608 of Tanimoto [ Ref. 42 ] and Tversky [ Ref. 43 ] have been developed.
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609 .Sp
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610 Let:
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|
611 .Sp
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612 .Vb 3
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|
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613 \& Na\*(Aq = Number of bits set to "0" in A
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|
|
614 \& Nb\*(Aq = Number of bits set to "0" in B
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|
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615 \& Nc\*(Aq = Number of bits set to "0" in both A and B
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|
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616 .Ve
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617 .Sp
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618 Tanimoto': Nc' / ( ( Na' \- Nc') + ( Nb' \- Nc' ) + Nc' ) = Nc' / ( Na' + Nb' \- Nc' )
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619 .Sp
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620 Tversky': Nc' / ( alpha * ( Na' \- Nc' ) + ( 1 \- alpha) * ( Nb' \- Nc' ) + Nc' ) = Nc' / ( alpha * ( Na' \- Nb' ) + Nb')
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621 .Sp
|
|
|
622 Then:
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623 .Sp
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624 \&\fIWeightedTanimotoSimilarity\fR = beta * Tanimoto + (1 \- beta) * Tanimoto'
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|
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625 .Sp
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626 \&\fIWeightedTverskySimilarity\fR = beta * Tversky + (1 \- beta) * Tversky'
|
|
|
627 .IP "\fB\-\-DatabaseColMode\fR \fIColNum | ColLabel\fR" 4
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|
628 .IX Item "--DatabaseColMode ColNum | ColLabel"
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|
|
629 Specify how columns are identified in database fingerprints \fITextFile\fR: using column
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|
|
630 number or column label. Possible values: \fIColNum or ColLabel\fR. Default value: \fIColNum\fR.
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|
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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
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|
|
636 the word compoundID in its column label or sequentially generated IDs\fR.
|
|
|
637 .Sp
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|
|
638 This is only used for \fICompoundID\fR value of \fB\-\-DatabaseDataColsMode\fR option.
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|
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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
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|
642 \&\fISDFile\fR and \fITextFile\fR. Default value: \fICmpd\fR. The default value generates compound IDs which look
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643 like Cmpd<Number>.
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|
|
644 .Sp
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|
|
645 For database fingerprints \fISDFile\fR, this value is only used during \fILabelPrefix | MolNameOrLabelPrefix\fR
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|
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646 values of \fB\-\-DatabaseCompoundIDMode\fR option; otherwise, it's ignored.
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|
|
647 .Sp
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|
|
648 Examples for \fILabelPrefix\fR or \fIMolNameOrLabelPrefix\fR value of \fB\-\-DatabaseCompoundIDMode\fR:
|
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|
649 .Sp
|
|
|
650 .Vb 1
|
|
|
651 \& Compound
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|
|
652 .Ve
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|
653 .Sp
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|
|
654 The values specified above generates compound IDs which correspond to Compound<Number>
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|
655 instead of default value of Cmpd<Number>.
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|
|
656 .IP "\fB\-\-DatabaseCompoundIDField\fR \fIDataFieldName\fR" 4
|
|
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657 .IX Item "--DatabaseCompoundIDField DataFieldName"
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|
|
658 Specify database fingerprints \fISDFile\fR datafield label for generating compound IDs. This value is
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|
|
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
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|
|
667 .IP "\fB\-\-DatabaseCompoundIDMode\fR \fIDataField | MolName | LabelPrefix | MolNameOrLabelPrefix\fR" 4
|
|
|
668 .IX Item "--DatabaseCompoundIDMode DataField | MolName | LabelPrefix | MolNameOrLabelPrefix"
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|
|
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.
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|
|
675 Default: \fILabelPrefix\fR.
|
|
|
676 .Sp
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|
|
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:
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|
|
692 .Sp
|
|
|
693 .Vb 2
|
|
|
694 \& 1,2,3
|
|
|
695 \& CompoundName,MolWt
|
|
|
696 .Ve
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|
|
697 .IP "\fB\-\-DatabaseDataColsMode\fR \fIAll | Specify | CompoundID\fR" 4
|
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|
698 .IX Item "--DatabaseDataColsMode All | Specify | CompoundID"
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|
|
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:
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|
|
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.
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|
|
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.
|
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|
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
|
|
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1294 To perform similarity search using Tanimoto coefficient by treating reference molecules as individual molecules
|
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1295 to find 10 most similar database molecules for each reference molecule with application of similarity cutoff to
|
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1296 supported fingerprints strings data in \s-1SD\s0 fingerprints files present in a data fields with Fingerprint substring
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1297 in their labels, and create a ReferenceFPHexSimilaritySearching.csv file containing sequentially generated
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1298 reference and database compound IDs with Cmpd prefix, type:
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1299 .PP
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1300 .Vb 2
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1301 \& % SimilaritySearchingFingerprints.pl \-mode IndividualReference \-o
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1302 \& ReferenceSampleFPHex.sdf DatabaseSampleFPHex.sdf
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1303 .Ve
|
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1304 .PP
|
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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
|
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1308 file containing references and database compound IDs retireved from \s-1FP\s0 file, type:
|
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1309 .PP
|
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1310 .Vb 2
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1311 \& % SimilaritySearchingFingerprints.pl \-mode IndividualReference \-o
|
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1312 \& ReferenceSampleFPHex.fpf DatabaseSampleFPHex.fpf
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|
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1313 .Ve
|
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1314 .PP
|
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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
|
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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:
|
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1321 .PP
|
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|
1322 .Vb 2
|
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|
1323 \& % SimilaritySearchingFingerprints.pl \-mode IndividualReference \-o
|
|
|
1324 \& ReferenceSampleFPHex.csv DatabaseSampleFPHex.csv
|
|
|
1325 .Ve
|
|
|
1326 .PP
|
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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
|
|
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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.
|
