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124 .\" ========================================================================
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125 .\"
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126 .IX Title "SIMILARITYMATRICESFINGERPRINTS 1"
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127 .TH SIMILARITYMATRICESFINGERPRINTS 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 SimilarityMatricesFingerprints.pl \- Calculate similarity matrices 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 SimilarityMatricesFingerprints.pl SDFile(s) FPFile(s) TextFile(s)...
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137 .PP
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138 SimilarityMatricesFingerprints.pl [\fB\-\-alpha\fR \fInumber\fR] [\fB\-\-beta\fR \fInumber\fR]
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139 [\fB\-b, \-\-BitVectorComparisonMode\fR \fIAll | \*(L"TanimotoSimilarity,[ TverskySimilarity, ... ]\*(R"\fR]
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140 [\fB\-c, \-\-ColMode\fR \fIColNum | ColLabel\fR] [\fB\-\-CompoundIDCol\fR \fIcol number | col name\fR]
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141 [\fB\-\-CompoundIDPrefix\fR \fItext\fR] [\fB\-\-CompoundIDField\fR \fIDataFieldName\fR]
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142 [\fB\-\-CompoundIDMode\fR \fIDataField | MolName | LabelPrefix | MolNameOrLabelPrefix\fR]
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143 [\fB\-d, \-\-detail\fR \fIInfoLevel\fR] [\fB\-f, \-\-fast\fR] [\fB\-\-FingerprintsCol\fR \fIcol number | col name\fR]
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144 [\fB\-\-FingerprintsField\fR \fIFieldLabel\fR] [\fB\-h, \-\-help\fR] [\fB\-\-InDelim\fR \fIcomma | semicolon\fR]
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145 [\fB\-\-InputDataMode\fR \fILoadInMemory | ScanFile\fR]
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146 [\fB\-m, \-\-mode\fR \fIAutoDetect | FingerprintsBitVectorString | FingerprintsVectorString\fR]
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147 [\fB\-\-OutDelim\fR \fIcomma | tab | semicolon\fR] [\fB\-\-OutMatrixFormat\fR \fIRowsAndColumns | IDPairsAndValue\fR]
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148 [\fB\-\-OutMatrixType\fR \fIFullMatrix | UpperTriangularMatrix | LowerTriangularMatrix\fR]
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149 [\fB\-o, \-\-overwrite\fR] [\fB\-p, \-\-precision\fR \fInumber\fR]
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150 [\fB\-q, \-\-quote\fR \fIYes | No\fR] [\fB\-r, \-\-root\fR \fIRootName\fR]
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151 [\fB\-v, \-\-VectorComparisonMode\fR \fIAll | \*(L"TanimotoSimilairy, [ ManhattanDistance, ...]\*(R"\fR]
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152 [\fB\-\-VectorComparisonFormulism\fR \fIAll | \*(L"AlgebraicForm, [BinaryForm, SetTheoreticForm]\*(R"\fR]
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153 [\fB\-w, \-\-WorkingDir\fR dirname] SDFile(s) FPFile(s) TextFile(s)...
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154 .SH "DESCRIPTION"
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155 .IX Header "DESCRIPTION"
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156 Calculate similarity matrices using fingerprint bit-vector or vector strings data in \fI\s-1SD\s0, \s-1FP\s0
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157 and \s-1CSV/TSV\s0\fR text file(s) and generate \s-1CSV/TSV\s0 text file(s) containing values for specified
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158 similarity and distance coefficients.
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159 .PP
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160 The scripts SimilarityMatrixSDFiles.pl and SimilarityMatrixTextFiles.pl have been removed from the
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161 current release of MayaChemTools and their functionality merged with this script.
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162 .PP
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163 The valid \fISDFile\fR extensions are \fI.sdf\fR and \fI.sd\fR. All \s-1SD\s0 files in a current directory
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164 can be specified either by \fI*.sdf\fR or the current directory name.
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165 .PP
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166 The valid \fIFPFile\fR extensions are \fI.fpf\fR and \fI.fp\fR. All \s-1FP\s0 files in a current directory
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167 can be specified either by \fI*.fpf\fR or the current directory name.
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168 .PP
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169 The valid \fITextFile\fR extensions are \fI.csv\fR and \fI.tsv\fR for comma/semicolon and tab
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170 delimited text files respectively. All other file names are ignored. All text files in a
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171 current directory can be specified by \fI*.csv\fR, \fI*.tsv\fR, or the current directory
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172 name. The \fB\-\-indelim\fR option determines the format of \fITextFile(s)\fR. Any file
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173 which doesn't correspond to the format indicated by \fB\-\-indelim\fR option is ignored.
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174 .PP
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175 Example of \fI\s-1FP\s0\fR file containing fingerprints bit-vector string data:
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176 .PP
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177 .Vb 10
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178 \& #
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179 \& # Package = MayaChemTools 7.4
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180 \& # ReleaseDate = Oct 21, 2010
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181 \& #
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182 \& # TimeStamp = Mon Mar 7 15:14:01 2011
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183 \& #
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184 \& # FingerprintsStringType = FingerprintsBitVector
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185 \& #
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186 \& # Description = PathLengthBits:AtomicInvariantsAtomTypes:MinLength1:...
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187 \& # Size = 1024
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188 \& # BitStringFormat = HexadecimalString
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189 \& # BitsOrder = Ascending
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190 \& #
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191 \& Cmpd1 9c8460989ec8a49913991a6603130b0a19e8051c89184414953800cc21510...
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192 \& Cmpd2 000000249400840040100042011001001980410c000000001010088001120...
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193 \& ... ...
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194 \& ... ..
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195 .Ve
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196 .PP
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197 Example of \fI\s-1FP\s0\fR file containing fingerprints vector string data:
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198 .PP
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199 .Vb 10
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200 \& #
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201 \& # Package = MayaChemTools 7.4
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202 \& # ReleaseDate = Oct 21, 2010
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203 \& #
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204 \& # TimeStamp = Mon Mar 7 15:14:01 2011
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205 \& #
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206 \& # FingerprintsStringType = FingerprintsVector
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207 \& #
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208 \& # Description = PathLengthBits:AtomicInvariantsAtomTypes:MinLength1:...
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209 \& # VectorStringFormat = IDsAndValuesString
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210 \& # VectorValuesType = NumericalValues
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211 \& #
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212 \& 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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213 \& 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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214 \& 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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215 \& 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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216 \& 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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217 \& O C CC=O CCCC CCCN CCCO CCNC CNC=N CNC=O CNCN CCCC=O CCCCC CCCCN CC...;
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218 \& 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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219 \& 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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220 \& ... ...
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221 \& ... ...
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222 .Ve
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223 .PP
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224 Example of \fI\s-1SD\s0\fR file containing fingerprints bit-vector string data:
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225 .PP
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226 .Vb 10
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227 \& ... ...
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228 \& ... ...
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229 \& $$$$
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230 \& ... ...
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231 \& ... ...
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232 \& ... ...
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233 \& 41 44 0 0 0 0 0 0 0 0999 V2000
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234 \& \-3.3652 1.4499 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
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235 \& ... ...
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236 \& 2 3 1 0 0 0 0
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237 \& ... ...
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238 \& M END
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239 \& > <CmpdID>
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240 \& Cmpd1
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241 \&
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242 \& > <PathLengthFingerprints>
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243 \& FingerprintsBitVector;PathLengthBits:AtomicInvariantsAtomTypes:MinLengt
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244 \& h1:MaxLength8;1024;HexadecimalString;Ascending;9c8460989ec8a49913991a66
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245 \& 03130b0a19e8051c89184414953800cc2151082844a201042800130860308e8204d4028
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246 \& 00831048940e44281c00060449a5000ac80c894114e006321264401600846c050164462
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247 \& 08190410805000304a10205b0100e04c0038ba0fad0209c0ca8b1200012268b61c0026a
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248 \& aa0660a11014a011d46
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249 \&
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250 \& $$$$
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251 \& ... ...
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252 \& ... ...
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253 .Ve
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254 .PP
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255 Example of \s-1CSV\s0 \fIText\fR file containing fingerprints bit-vector string data:
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256 .PP
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257 .Vb 7
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258 \& "CompoundID","PathLengthFingerprints"
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259 \& "Cmpd1","FingerprintsBitVector;PathLengthBits:AtomicInvariantsAtomTypes
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260 \& :MinLength1:MaxLength8;1024;HexadecimalString;Ascending;9c8460989ec8a4
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261 \& 9913991a6603130b0a19e8051c89184414953800cc2151082844a20104280013086030
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262 \& 8e8204d402800831048940e44281c00060449a5000ac80c894114e006321264401..."
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263 \& ... ...
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264 \& ... ...
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265 .Ve
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266 .PP
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267 The current release of MayaChemTools supports the following types of fingerprint
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268 bit-vector and vector strings:
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269 .PP
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270 .Vb 6
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271 \& FingerprintsVector;AtomNeighborhoods:AtomicInvariantsAtomTypes:MinRadi
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272 \& us0:MaxRadius2;41;AlphaNumericalValues;ValuesString;NR0\-C.X1.BO1.H3\-AT
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273 \& 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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274 \& 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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275 \& TC1 NR0\-C.X2.BO2.H2\-ATC1:NR1\-C.X2.BO2.H2\-ATC1:NR1\-C.X3.BO3.H1\-ATC1:NR2
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276 \& \-C.X2.BO2.H2\-ATC1:NR2\-N.X3.BO3\-ATC1:NR2\-O.X1.BO1.H1\-ATC1 NR0\-C.X2.B...
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277 \&
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278 \& FingerprintsVector;AtomTypesCount:AtomicInvariantsAtomTypes:ArbitraryS
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279 \& ize;10;NumericalValues;IDsAndValuesString;C.X1.BO1.H3 C.X2.BO2.H2 C.X2
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280 \& .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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281 \& O.X1.BO2;2 4 14 3 10 1 1 1 3 2
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282 \&
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283 \& FingerprintsVector;AtomTypesCount:SLogPAtomTypes:ArbitrarySize;16;Nume
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284 \& ricalValues;IDsAndValuesString;C1 C10 C11 C14 C18 C20 C21 C22 C5 CS F
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285 \& 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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286 \&
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287 \& FingerprintsVector;AtomTypesCount:SLogPAtomTypes:FixedSize;67;OrderedN
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288 \& umericalValues;IDsAndValuesString;C1 C2 C3 C4 C5 C6 C7 C8 C9 C10 C11 C
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289 \& 12 C13 C14 C15 C16 C17 C18 C19 C20 C21 C22 C23 C24 C25 C26 C27 CS N1 N
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290 \& 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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291 \& 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
|
|
|
292 \& 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...
|
|
|
293 \&
|
|
|
294 \& FingerprintsVector;EStateIndicies:ArbitrarySize;11;NumericalValues;IDs
|
|
|
295 \& AndValuesString;SaaCH SaasC SaasN SdO SdssC SsCH3 SsF SsOH SssCH2 SssN
|
|
|
296 \& H SsssCH;24.778 4.387 1.993 25.023 \-1.435 3.975 14.006 29.759 \-0.073 3
|
|
|
297 \& .024 \-2.270
|
|
|
298 \&
|
|
|
299 \& FingerprintsVector;EStateIndicies:FixedSize;87;OrderedNumericalValues;
|
|
|
300 \& ValuesString;0 0 0 0 0 0 0 3.975 0 \-0.073 0 0 24.778 \-2.270 0 0 \-1.435
|
|
|
301 \& 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
|
|
|
302 \& 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
|
|
|
303 \& 0 0 0 0 0 0 0 0 0 0 0 0 0 0
|
|
|
304 \&
|
|
|
305 \& FingerprintsVector;ExtendedConnectivity:AtomicInvariantsAtomTypes:Radi
|
|
|
306 \& us2;60;AlphaNumericalValues;ValuesString;73555770 333564680 352413391
|
|
|
307 \& 666191900 1001270906 1371674323 1481469939 1977749791 2006158649 21414
|
|
|
308 \& 08799 49532520 64643108 79385615 96062769 273726379 564565671 85514103
|
|
|
309 \& 5 906706094 988546669 1018231313 1032696425 1197507444 1331250018 1338
|
|
|
310 \& 532734 1455473691 1607485225 1609687129 1631614296 1670251330 17303...
|
|
|
311 \&
|
|
|
312 \& FingerprintsVector;ExtendedConnectivityCount:AtomicInvariantsAtomTypes
|
|
|
313 \& :Radius2;60;NumericalValues;IDsAndValuesString;73555770 333564680 3524
|
|
|
314 \& 13391 666191900 1001270906 1371674323 1481469939 1977749791 2006158649
|
|
|
315 \& 2141408799 49532520 64643108 79385615 96062769 273726379 564565671...;
|
|
|
316 \& 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
|
|
|
317 \& 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
|
|
|
318 \&
|
|
|
319 \& FingerprintsBitVector;ExtendedConnectivityBits:AtomicInvariantsAtomTyp
|
|
|
320 \& es:Radius2;1024;BinaryString;Ascending;0000000000000000000000000000100
|
|
|
321 \& 0000000001010000000110000011000000000000100000000000000000000000100001
|
|
|
322 \& 1000000110000000000000000000000000010011000000000000000000000000010000
|
|
|
323 \& 0000000000000000000000000010000000000000000001000000000000000000000000
|
|
|
324 \& 0000000000010000100001000000000000101000000000000000100000000000000...
|
|
|
325 \&
|
|
|
326 \& FingerprintsVector;ExtendedConnectivity:FunctionalClassAtomTypes:Radiu
|
|
|
327 \& s2;57;AlphaNumericalValues;ValuesString;24769214 508787397 850393286 8
|
|
|
328 \& 62102353 981185303 1231636850 1649386610 1941540674 263599683 32920567
|
|
|
329 \& 1 571109041 639579325 683993318 723853089 810600886 885767127 90326012
|
|
|
330 \& 7 958841485 981022393 1126908698 1152248391 1317567065 1421489994 1455
|
|
|
331 \& 632544 1557272891 1826413669 1983319256 2015750777 2029559552 20404...
|
|
|
332 \&
|
|
|
333 \& FingerprintsVector;ExtendedConnectivity:EStateAtomTypes:Radius2;62;Alp
|
|
|
334 \& haNumericalValues;ValuesString;25189973 528584866 662581668 671034184
|
|
|
335 \& 926543080 1347067490 1738510057 1759600920 2034425745 2097234755 21450
|
|
|
336 \& 44754 96779665 180364292 341712110 345278822 386540408 387387308 50430
|
|
|
337 \& 1706 617094135 771528807 957666640 997798220 1158349170 1291258082 134
|
|
|
338 \& 1138533 1395329837 1420277211 1479584608 1486476397 1487556246 1566...
|
|
|
339 \&
|
|
|
340 \& FingerprintsBitVector;MACCSKeyBits;166;BinaryString;Ascending;00000000
|
|
|
341 \& 0000000000000000000000000000000001001000010010000000010010000000011100
|
|
|
342 \& 0100101010111100011011000100110110000011011110100110111111111111011111
|
|
|
343 \& 11111111111110111000
|
|
|
344 \&
|
|
|
345 \& FingerprintsBitVector;MACCSKeyBits;322;BinaryString;Ascending;11101011
|
|
|
346 \& 1110011111100101111111000111101100110000000000000011100010000000000000
|
|
|
347 \& 0000000000000000000000000000000000000000000000101000000000000000000000
|
|
|
348 \& 0000000000000000000000000000000000000000000000000000000000000000000000
|
|
|
349 \& 0000000000000000000000000000000000000011000000000000000000000000000000
|
|
|
350 \& 0000000000000000000000000000000000000000
|
|
|
351 \&
|
|
|
352 \& FingerprintsVector;MACCSKeyCount;166;OrderedNumericalValues;ValuesStri
|
|
|
353 \& 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
|
|
|
354 \& 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
|
|
|
355 \& 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
|
|
|
356 \& 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
|
|
|
357 \& 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
|
|
|
358 \&
|
|
|
359 \& FingerprintsVector;MACCSKeyCount;322;OrderedNumericalValues;ValuesStri
|
|
|
360 \& 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
|
|
|
361 \& 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
|
|
|
362 \& 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
|
|
|
363 \& 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
|
|
|
364 \& 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 ...
|
|
|
365 \&
|
|
|
366 \& FingerprintsBitVector;PathLengthBits:AtomicInvariantsAtomTypes:MinLeng
|
|
|
367 \& th1:MaxLength8;1024;BinaryString;Ascending;001000010011010101011000110
|
|
|
368 \& 0100010101011000101001011100110001000010001001101000001001001001001000
|
|
|
369 \& 0010110100000111001001000001001010100100100000000011000000101001011100
|
|
|
370 \& 0010000001000101010100000100111100110111011011011000000010110111001101
|
|
|
371 \& 0101100011000000010001000011000010100011101100001000001000100000000...
|
|
|
372 \&
|
|
|
373 \& FingerprintsVector;PathLengthCount:AtomicInvariantsAtomTypes:MinLength
|
|
|
374 \& 1:MaxLength8;432;NumericalValues;IDsAndValuesPairsString;C.X1.BO1.H3 2
|
|
|
375 \& 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
|
|
|
376 \& 2.BO2.H1 1 N.X3.BO3 1 O.X1.BO1.H1 3 O.X1.BO2 2 C.X1.BO1.H3C.X3.BO3.H1
|
|
|
377 \& 2 C.X2.BO2.H2C.X2.BO2.H2 1 C.X2.BO2.H2C.X3.BO3.H1 4 C.X2.BO2.H2C.X3.BO
|
|
|
378 \& 4 1 C.X2.BO2.H2N.X3.BO3 1 C.X2.BO3.H1:C.X2.BO3.H1 10 C.X2.BO3.H1:C....
|
|
|
379 \&
|
|
|
380 \& FingerprintsVector;PathLengthCount:MMFF94AtomTypes:MinLength1:MaxLengt
|
|
|
381 \& h8;463;NumericalValues;IDsAndValuesPairsString;C5A 2 C5B 2 C=ON 1 CB 1
|
|
|
382 \& 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
|
|
|
383 \& 5 2 C5ACB 1 C5ACR 1 C5B:C5B 1 C5BC=ON 1 C5BCB 1 C=ON=O=CN 1 C=ONNC=O 1
|
|
|
384 \& CB:CB 18 CBF 1 CBNC=O 1 COO=O=CO 1 COOCR 1 COOOC=O 1 CRCR 7 CRN5 1 CR
|
|
|
385 \& OR 2 C5A:C5B:C5B 2 C5A:C5BC=ON 1 C5A:C5BCB 1 C5A:N5:C5A 1 C5A:N5CR ...
|
|
|
386 \&
|
|
|
387 \& FingerprintsVector;TopologicalAtomPairs:AtomicInvariantsAtomTypes:MinD
|
|
|
388 \& istance1:MaxDistance10;223;NumericalValues;IDsAndValuesString;C.X1.BO1
|
|
|
389 \& .H3\-D1\-C.X3.BO3.H1 C.X2.BO2.H2\-D1\-C.X2.BO2.H2 C.X2.BO2.H2\-D1\-C.X3.BO3.
|
|
|
390 \& H1 C.X2.BO2.H2\-D1\-C.X3.BO4 C.X2.BO2.H2\-D1\-N.X3.BO3 C.X2.BO3.H1\-D1\-...;
|
|
|
391 \& 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
|
|
|
392 \& 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...
|
|
|
393 \&
|
|
|
394 \& FingerprintsVector;TopologicalAtomPairs:FunctionalClassAtomTypes:MinDi
|
|
|
395 \& stance1:MaxDistance10;144;NumericalValues;IDsAndValuesString;Ar\-D1\-Ar
|
|
|
396 \& Ar\-D1\-Ar.HBA Ar\-D1\-HBD Ar\-D1\-Hal Ar\-D1\-None Ar.HBA\-D1\-None HBA\-D1\-NI H
|
|
|
397 \& BA\-D1\-None HBA.HBD\-D1\-NI HBA.HBD\-D1\-None HBD\-D1\-None NI\-D1\-None No...;
|
|
|
398 \& 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
|
|
|
399 \& 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 ...
|
|
|
400 \&
|
|
|
401 \& FingerprintsVector;TopologicalAtomTorsions:AtomicInvariantsAtomTypes;3
|
|
|
402 \& 3;NumericalValues;IDsAndValuesString;C.X1.BO1.H3\-C.X3.BO3.H1\-C.X3.BO4\-
|
|
|
403 \& C.X3.BO4 C.X1.BO1.H3\-C.X3.BO3.H1\-C.X3.BO4\-N.X3.BO3 C.X2.BO2.H2\-C.X2.BO
|
|
|
404 \& 2.H2\-C.X3.BO3.H1\-C.X2.BO2.H2 C.X2.BO2.H2\-C.X2.BO2.H2\-C.X3.BO3.H1\-O...;
|
|
|
405 \& 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
|
|
|
406 \&
|
|
|
407 \& FingerprintsVector;TopologicalAtomTorsions:EStateAtomTypes;36;Numerica
|
|
|
408 \& lValues;IDsAndValuesString;aaCH\-aaCH\-aaCH\-aaCH aaCH\-aaCH\-aaCH\-aasC aaC
|
|
|
409 \& H\-aaCH\-aasC\-aaCH aaCH\-aaCH\-aasC\-aasC aaCH\-aaCH\-aasC\-sF aaCH\-aaCH\-aasC\-
|
|
|
410 \& ssNH aaCH\-aasC\-aasC\-aasC aaCH\-aasC\-aasC\-aasN aaCH\-aasC\-ssNH\-dssC a...;
|
|
|
411 \& 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
|
|
|
412 \&
|
|
|
413 \& FingerprintsVector;TopologicalAtomTriplets:AtomicInvariantsAtomTypes:M
|
|
|
414 \& inDistance1:MaxDistance10;3096;NumericalValues;IDsAndValuesString;C.X1
|
|
|
415 \& .BO1.H3\-D1\-C.X1.BO1.H3\-D1\-C.X3.BO3.H1\-D2 C.X1.BO1.H3\-D1\-C.X2.BO2.H2\-D1
|
|
|
416 \& 0\-C.X3.BO4\-D9 C.X1.BO1.H3\-D1\-C.X2.BO2.H2\-D3\-N.X3.BO3\-D4 C.X1.BO1.H3\-D1
|
|
|
417 \& \-C.X2.BO2.H2\-D4\-C.X2.BO2.H2\-D5 C.X1.BO1.H3\-D1\-C.X2.BO2.H2\-D6\-C.X3....;
|
|
|
418 \& 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
|
|
|
419 \& 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...
|
|
|
420 \&
|
|
|
421 \& FingerprintsVector;TopologicalAtomTriplets:SYBYLAtomTypes:MinDistance1
|
|
|
422 \& :MaxDistance10;2332;NumericalValues;IDsAndValuesString;C.2\-D1\-C.2\-D9\-C
|
|
|
423 \& .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\-
|
|
|
424 \& 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
|
|
|
425 \& \-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.
|
|
|
426 \& 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...
|
|
|
427 \&
|
|
|
428 \& FingerprintsVector;TopologicalPharmacophoreAtomPairs:ArbitrarySize:Min
|
|
|
429 \& Distance1:MaxDistance10;54;NumericalValues;IDsAndValuesString;H\-D1\-H H
|
|
|
430 \& \-D1\-NI HBA\-D1\-NI HBD\-D1\-NI H\-D2\-H H\-D2\-HBA H\-D2\-HBD HBA\-D2\-HBA HBA\-D2\-
|
|
|
431 \& 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
|
|
|
432 \& BA H\-D4\-HBD HBA\-D4\-HBA HBA\-D4\-HBD HBD\-D4\-HBD H\-D5\-H H\-D5\-HBA H\-D5\-...;
|
|
|
433 \& 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
|
|
|
434 \& 3 4 1 37 10 8 1 35 10 9 3 3 1 28 7 7 4 18 16 12 5 1 2 1
|
|
|
435 \&
|
|
|
436 \& FingerprintsVector;TopologicalPharmacophoreAtomPairs:FixedSize:MinDist
|
|
|
437 \& ance1:MaxDistance10;150;OrderedNumericalValues;ValuesString;18 0 0 1 0
|
|
|
438 \& 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
|
|
|
439 \& 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
|
|
|
440 \& 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
|
|
|
441 \& 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...
|
|
|
442 \&
|
|
|
443 \& FingerprintsVector;TopologicalPharmacophoreAtomTriplets:ArbitrarySize:
|
|
|
444 \& MinDistance1:MaxDistance10;696;NumericalValues;IDsAndValuesString;Ar1\-
|
|
|
445 \& Ar1\-Ar1 Ar1\-Ar1\-H1 Ar1\-Ar1\-HBA1 Ar1\-Ar1\-HBD1 Ar1\-H1\-H1 Ar1\-H1\-HBA1 Ar1
|
|
|
446 \& \-H1\-HBD1 Ar1\-HBA1\-HBD1 H1\-H1\-H1 H1\-H1\-HBA1 H1\-H1\-HBD1 H1\-HBA1\-HBA1 H1\-
|
|
|
447 \& HBA1\-HBD1 H1\-HBA1\-NI1 H1\-HBD1\-NI1 HBA1\-HBA1\-NI1 HBA1\-HBD1\-NI1 Ar1\-...;
|
|
|
448 \& 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
|
|
|
449 \& 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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|
|
450 \& 119 123 24 15 185 202 41 25 22 17 3 5 85 95 18 11 23 17 3 1 1 6 4 ...
|
|
|
451 \&
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|
|
452 \& FingerprintsVector;TopologicalPharmacophoreAtomTriplets:FixedSize:MinD
|
|
|
453 \& istance1:MaxDistance10;2692;OrderedNumericalValues;ValuesString;46 106
|
|
|
454 \& 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
|
|
|
455 \& 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
|
|
|
456 \& 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
|
|
|
457 \& 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 ...
|
|
|
458 .Ve
|
|
|
459 .SH "OPTIONS"
|
|
|
460 .IX Header "OPTIONS"
|
|
|
461 .IP "\fB\-\-alpha\fR \fInumber\fR" 4
|
|
|
462 .IX Item "--alpha number"
|
|
|
463 Value of alpha parameter for calculating \fITversky\fR similarity coefficient specified for
|
|
|
464 \&\fB\-b, \-\-BitVectorComparisonMode\fR option. It corresponds to weights assigned for bits set
|
|
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465 to \*(L"1\*(R" in a pair of fingerprint bit-vectors during the calculation of similarity coefficient. Possible
|
|
|
466 values: \fI0 to 1\fR. Default value: <0.5>.
|
|
|
467 .IP "\fB\-\-beta\fR \fInumber\fR" 4
|
|
|
468 .IX Item "--beta number"
|
|
|
469 Value of beta parameter for calculating \fIWeightedTanimoto\fR and \fIWeightedTversky\fR
|
|
|
470 similarity coefficients specified for \fB\-b, \-\-BitVectorComparisonMode\fR option. It is used to
|
|
|
471 weight the contributions of bits set to \*(L"0\*(R" during the calculation of similarity coefficients. Possible
|
|
|
472 values: \fI0 to 1\fR. Default value of <1> makes \fIWeightedTanimoto\fR and \fIWeightedTversky\fR
|
|
|
473 equivalent to \fITanimoto\fR and \fITversky\fR.
|
|
|
474 .ie n .IP "\fB\-b, \-\-BitVectorComparisonMode\fR \fIAll | ""TanimotoSimilarity,[TverskySimilarity,...]""\fR" 4
|
|
|
475 .el .IP "\fB\-b, \-\-BitVectorComparisonMode\fR \fIAll | ``TanimotoSimilarity,[TverskySimilarity,...]''\fR" 4
|
|
|
476 .IX Item "-b, --BitVectorComparisonMode All | TanimotoSimilarity,[TverskySimilarity,...]"
|
|
|
477 Specify what similarity coefficients to use for calculating similarity matrices for fingerprints bit-vector
|
|
|
478 strings data values in \fITextFile(s)\fR: calculate similarity matrices for all supported similarity
|
|
|
479 coefficients or specify a comma delimited list of similarity coefficients. Possible values:
|
|
|
480 \&\fIAll | "TanimotoSimilarity,[TverskySimilarity,...]\fR. Default: \fITanimotoSimilarity\fR
|
|
|
481 .Sp
|
|
|
482 \&\fIAll\fR uses complete list of supported similarity coefficients: \fIBaroniUrbaniSimilarity, BuserSimilarity,
|
|
|
483 CosineSimilarity, DiceSimilarity, DennisSimilarity, ForbesSimilarity, FossumSimilarity, HamannSimilarity, JacardSimilarity,
|
|
|
484 Kulczynski1Similarity, Kulczynski2Similarity, MatchingSimilarity, McConnaugheySimilarity, OchiaiSimilarity,
|
|
|
485 PearsonSimilarity, RogersTanimotoSimilarity, RussellRaoSimilarity, SimpsonSimilarity, SkoalSneath1Similarity,
|
|
|
486 SkoalSneath2Similarity, SkoalSneath3Similarity, TanimotoSimilarity, TverskySimilarity, YuleSimilarity,
|
|
|
487 WeightedTanimotoSimilarity, WeightedTverskySimilarity\fR. These similarity coefficients are described below.
|
|
|
488 .Sp
|
|
|
489 For two fingerprint bit-vectors A and B of same size, let:
|
|
|
490 .Sp
|
|
|
491 .Vb 4
|
|
|
492 \& Na = Number of bits set to "1" in A
|
|
|
493 \& Nb = Number of bits set to "1" in B
|
|
|
494 \& Nc = Number of bits set to "1" in both A and B
|
|
|
495 \& Nd = Number of bits set to "0" in both A and B
|
|
|
496 \&
|
|
|
497 \& Nt = Number of bits set to "1" or "0" in A or B (Size of A or B)
|
|
|
498 \& Nt = Na + Nb \- Nc + Nd
|
|
|
499 \&
|
|
|
500 \& Na \- Nc = Number of bits set to "1" in A but not in B
|
|
|
501 \& Nb \- Nc = Number of bits set to "1" in B but not in A
|
|
|
502 .Ve
|
|
|
503 .Sp
|
|
|
504 Then, various similarity coefficients [ Ref. 40 \- 42 ] for a pair of bit-vectors A and B are
|
|
|
505 defined as follows:
|
|
|
506 .Sp
|
|
|
507 \&\fIBaroniUrbaniSimilarity\fR: ( \s-1SQRT\s0( Nc * Nd ) + Nc ) / ( \s-1SQRT\s0 ( Nc * Nd ) + Nc + ( Na \- Nc ) + ( Nb \- Nc ) ) ( same as Buser )
|
|
|
508 .Sp
|
|
|
509 \&\fIBuserSimilarity\fR: ( \s-1SQRT\s0 ( Nc * Nd ) + Nc ) / ( \s-1SQRT\s0 ( Nc * Nd ) + Nc + ( Na \- Nc ) + ( Nb \- Nc ) ) ( same as BaroniUrbani )
|
|
|
510 .Sp
|
|
|
511 \&\fICosineSimilarity\fR: Nc / \s-1SQRT\s0 ( Na * Nb ) (same as Ochiai)
|
|
|
512 .Sp
|
|
|
513 \&\fIDiceSimilarity\fR: (2 * Nc) / ( Na + Nb )
|
|
|
514 .Sp
|
|
|
515 \&\fIDennisSimilarity\fR: ( Nc * Nd \- ( ( Na \- Nc ) * ( Nb \- Nc ) ) ) / \s-1SQRT\s0 ( Nt * Na * Nb)
|
|
|
516 .Sp
|
|
|
517 \&\fIForbesSimilarity\fR: ( Nt * Nc ) / ( Na * Nb )
|
|
|
518 .Sp
|
|
|
519 \&\fIFossumSimilarity\fR: ( Nt * ( ( Nc \- 1/2 ) ** 2 ) / ( Na * Nb )
|
|
|
520 .Sp
|
|
|
521 \&\fIHamannSimilarity\fR: ( ( Nc + Nd ) \- ( Na \- Nc ) \- ( Nb \- Nc ) ) / Nt
|
|
|
522 .Sp
|
|
|
523 \&\fIJaccardSimilarity\fR: Nc / ( ( Na \- Nc) + ( Nb \- Nc ) + Nc ) = Nc / ( Na + Nb \- Nc ) (same as Tanimoto)
|
|
|
524 .Sp
|
|
|
525 \&\fIKulczynski1Similarity\fR: Nc / ( ( Na \- Nc ) + ( Nb \- Nc) ) = Nc / ( Na + Nb \- 2Nc )
|
|
|
526 .Sp
|
|
|
527 \&\fIKulczynski2Similarity\fR: ( ( Nc / 2 ) * ( 2 * Nc + ( Na \- Nc ) + ( Nb \- Nc) ) ) / ( ( Nc + ( Na \- Nc ) ) * ( Nc + ( Nb \- Nc ) ) ) = 0.5 * ( Nc / Na + Nc / Nb )
|
|
|
528 .Sp
|
|
|
529 \&\fIMatchingSimilarity\fR: ( Nc + Nd ) / Nt
|
|
|
530 .Sp
|
|
|
531 \&\fIMcConnaugheySimilarity\fR: ( Nc ** 2 \- ( Na \- Nc ) * ( Nb \- Nc) ) / ( Na * Nb )
|
|
|
532 .Sp
|
|
|
533 \&\fIOchiaiSimilarity\fR: Nc / \s-1SQRT\s0 ( Na * Nb ) (same as Cosine)
|
|
|
534 .Sp
|
|
|
535 \&\fIPearsonSimilarity\fR: ( ( Nc * Nd ) \- ( ( Na \- Nc ) * ( Nb \- Nc ) ) / \s-1SQRT\s0 ( Na * Nb * ( Na \- Nc + Nd ) * ( Nb \- Nc + Nd ) )
|
|
|
536 .Sp
|
|
|
537 \&\fIRogersTanimotoSimilarity\fR: ( Nc + Nd ) / ( ( Na \- Nc) + ( Nb \- Nc) + Nt) = ( Nc + Nd ) / ( Na + Nb \- 2Nc + Nt)
|
|
|
538 .Sp
|
|
|
539 \&\fIRussellRaoSimilarity\fR: Nc / Nt
|
|
|
540 .Sp
|
|
|
541 \&\fISimpsonSimilarity\fR: Nc / \s-1MIN\s0 ( Na, Nb)
|
|
|
542 .Sp
|
|
|
543 \&\fISkoalSneath1Similarity\fR: Nc / ( Nc + 2 * ( Na \- Nc) + 2 * ( Nb \- Nc) ) = Nc / ( 2 * Na + 2 * Nb \- 3 * Nc )
|
|
|
544 .Sp
|
|
|
545 \&\fISkoalSneath2Similarity\fR: ( 2 * Nc + 2 * Nd ) / ( Nc + Nd + Nt )
|
|
|
546 .Sp
|
|
|
547 \&\fISkoalSneath3Similarity\fR: ( Nc + Nd ) / ( ( Na \- Nc ) + ( Nb \- Nc ) ) = ( Nc + Nd ) / ( Na + Nb \- 2 * Nc )
|
|
|
548 .Sp
|
|
|
549 \&\fITanimotoSimilarity\fR: Nc / ( ( Na \- Nc) + ( Nb \- Nc ) + Nc ) = Nc / ( Na + Nb \- Nc ) (same as Jaccard)
|
|
|
550 .Sp
|
|
|
551 \&\fITverskySimilarity\fR: Nc / ( alpha * ( Na \- Nc ) + ( 1 \- alpha) * ( Nb \- Nc) + Nc ) = Nc / ( alpha * ( Na \- Nb ) + Nb)
|
|
|
552 .Sp
|
|
|
553 \&\fIYuleSimilarity\fR: ( ( Nc * Nd ) \- ( ( Na \- Nc ) * ( Nb \- Nc ) ) ) / ( ( Nc * Nd ) + ( ( Na \- Nc ) * ( Nb \- Nc ) ) )
|
|
|
554 .Sp
|
|
|
555 Values of Tanimoto/Jaccard and Tversky coefficients are dependent on only those bit which
|
|
|
556 are set to \*(L"1\*(R" in both A and B. In order to take into account all bit positions, modified versions
|
|
|
557 of Tanimoto [ Ref. 42 ] and Tversky [ Ref. 43 ] have been developed.
|
|
|
558 .Sp
|
|
|
559 Let:
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|
|
560 .Sp
|
|
|
561 .Vb 3
|
|
|
562 \& Na\*(Aq = Number of bits set to "0" in A
|
|
|
563 \& Nb\*(Aq = Number of bits set to "0" in B
|
|
|
564 \& Nc\*(Aq = Number of bits set to "0" in both A and B
|
|
|
565 .Ve
|
|
|
566 .Sp
|
|
|
567 Tanimoto': Nc' / ( ( Na' \- Nc') + ( Nb' \- Nc' ) + Nc' ) = Nc' / ( Na' + Nb' \- Nc' )
|
|
|
568 .Sp
|
|
|
569 Tversky': Nc' / ( alpha * ( Na' \- Nc' ) + ( 1 \- alpha) * ( Nb' \- Nc' ) + Nc' ) = Nc' / ( alpha * ( Na' \- Nb' ) + Nb')
|
|
|
570 .Sp
|
|
|
571 Then:
|
|
|
572 .Sp
|
|
|
573 \&\fIWeightedTanimotoSimilarity\fR = beta * Tanimoto + (1 \- beta) * Tanimoto'
|
|
|
574 .Sp
|
|
|
575 \&\fIWeightedTverskySimilarity\fR = beta * Tversky + (1 \- beta) * Tversky'
|
|
|
576 .IP "\fB\-c, \-\-ColMode\fR \fIColNum | ColLabel\fR" 4
|
|
|
577 .IX Item "-c, --ColMode ColNum | ColLabel"
|
|
|
578 Specify how columns are identified in \fITextFile(s)\fR: using column number or column
|
|
|
579 label. Possible values: \fIColNum or ColLabel\fR. Default value: \fIColNum\fR.
|
|
|
580 .IP "\fB\-\-CompoundIDCol\fR \fIcol number | col name\fR" 4
|
|
|
581 .IX Item "--CompoundIDCol col number | col name"
|
|
|
582 This value is \fB\-c, \-\-ColMode\fR mode specific. It specifies input \fITextFile(s)\fR column to use for
|
|
|
583 generating compound \s-1ID\s0 for similarity matrices in output \fITextFile(s)\fR. Possible values: \fIcol number
|
|
|
584 or col label\fR. Default value: \fIfirst column containing the word compoundID in its column label or sequentially
|
|
|
585 generated IDs\fR.
|
|
|
586 .IP "\fB\-\-CompoundIDPrefix\fR \fItext\fR" 4
|
|
|
587 .IX Item "--CompoundIDPrefix text"
|
|
|
588 Specify compound \s-1ID\s0 prefix to use during sequential generation of compound IDs for input \fISDFile(s)\fR
|
|
|
589 and \fITextFile(s)\fR. Default value: \fICmpd\fR. The default value generates compound IDs which look
|
|
|
590 like Cmpd<Number>.
|
|
|
591 .Sp
|
|
|
592 For input \fISDFile(s)\fR, this value is only used during \fILabelPrefix | MolNameOrLabelPrefix\fR values
|
|
|
593 of \fB\-\-CompoundIDMode\fR option; otherwise, it's ignored.
|
|
|
594 .Sp
|
|
|
595 Examples for \fILabelPrefix\fR or \fIMolNameOrLabelPrefix\fR value of \fB\-\-CompoundIDMode\fR:
|
|
|
596 .Sp
|
|
|
597 .Vb 1
|
|
|
598 \& Compound
|
|
|
599 .Ve
|
|
|
600 .Sp
|
|
|
601 The values specified above generates compound IDs which correspond to Compound<Number>
|
|
|
602 instead of default value of Cmpd<Number>.
|
|
|
603 .IP "\fB\-\-CompoundIDField\fR \fIDataFieldName\fR" 4
|
|
|
604 .IX Item "--CompoundIDField DataFieldName"
|
|
|
605 Specify input \fISDFile(s)\fR datafield label for generating compound IDs. This value is only used
|
|
|
606 during \fIDataField\fR value of \fB\-\-CompoundIDMode\fR option.
|
|
|
607 .Sp
|
|
|
608 Examples for \fIDataField\fR value of \fB\-\-CompoundIDMode\fR:
|
|
|
609 .Sp
|
|
|
610 .Vb 2
|
|
|
611 \& MolID
|
|
|
612 \& ExtReg
|
|
|
613 .Ve
|
|
|
614 .IP "\fB\-\-CompoundIDMode\fR \fIDataField | MolName | LabelPrefix | MolNameOrLabelPrefix\fR" 4
|
|
|
615 .IX Item "--CompoundIDMode DataField | MolName | LabelPrefix | MolNameOrLabelPrefix"
|
|
|
616 Specify how to generate compound IDs from input \fISDFile(s)\fR for similarity matrix \s-1CSV/TSV\s0 text
|
|
|
617 file(s): use a \fISDFile(s)\fR datafield value; use molname line from \fISDFile(s)\fR; generate a sequential \s-1ID\s0
|
|
|
618 with specific prefix; use combination of both MolName and LabelPrefix with usage of LabelPrefix values
|
|
|
619 for empty molname lines.
|
|
|
620 .Sp
|
|
|
621 Possible values: \fIDataField | MolName | LabelPrefix | MolNameOrLabelPrefix\fR.
|
|
|
622 Default: \fILabelPrefix\fR.
|
|
|
623 .Sp
|
|
|
624 For \fIMolNameAndLabelPrefix\fR value of \fB\-\-CompoundIDMode\fR, molname line in \fISDFile(s)\fR takes
|
|
|
625 precedence over sequential compound IDs generated using \fILabelPrefix\fR and only empty molname
|
|
|
626 values are replaced with sequential compound IDs.
|
|
|
627 .IP "\fB\-d, \-\-detail\fR \fIInfoLevel\fR" 4
|
|
|
628 .IX Item "-d, --detail InfoLevel"
|
|
|
629 Level of information to print about lines being ignored. Default: \fI1\fR. Possible values:
|
|
|
630 \&\fI1, 2 or 3\fR.
|
|
|
631 .IP "\fB\-f, \-\-fast\fR" 4
|
|
|
632 .IX Item "-f, --fast"
|
|
|
633 In this mode, fingerprints columns specified using \fB\-\-FingerprintsCol\fR for \fITextFile(s)\fR and
|
|
|
634 \&\fB\-\-FingerprintsField\fR for \fISDFile(s)\fR are assumed to contain valid fingerprints data and no
|
|
|
635 checking is performed before calculating similarity matrices. By default, fingerprints data is
|
|
|
636 validated before computing pairwise similarity and distance coefficients.
|
|
|
637 .IP "\fB\-\-FingerprintsCol\fR \fIcol number | col name\fR" 4
|
|
|
638 .IX Item "--FingerprintsCol col number | col name"
|
|
|
639 This value is \fB\-c, \-\-colmode\fR specific. It specifies fingerprints column to use during
|
|
|
640 calculation similarity matrices for \fITextFile(s)\fR. Possible values: \fIcol number or col label\fR.
|
|
|
641 Default value: \fIfirst column containing the word Fingerprints in its column label\fR.
|
|
|
642 .IP "\fB\-\-FingerprintsField\fR \fIFieldLabel\fR" 4
|
|
|
643 .IX Item "--FingerprintsField FieldLabel"
|
|
|
644 Fingerprints field label to use during calculation similarity matrices for \fISDFile(s)\fR.
|
|
|
645 Default value: \fIfirst data field label containing the word Fingerprints in its label\fR
|
|
|
646 .IP "\fB\-h, \-\-help\fR" 4
|
|
|
647 .IX Item "-h, --help"
|
|
|
648 Print this help message.
|
|
|
649 .IP "\fB\-\-InDelim\fR \fIcomma | semicolon\fR" 4
|
|
|
650 .IX Item "--InDelim comma | semicolon"
|
|
|
651 Input delimiter for \s-1CSV\s0 \fITextFile(s)\fR. Possible values: \fIcomma or semicolon\fR.
|
|
|
652 Default value: \fIcomma\fR. For \s-1TSV\s0 files, this option is ignored and \fItab\fR is used as a
|
|
|
653 delimiter.
|
|
|
654 .IP "\fB\-\-InputDataMode\fR \fILoadInMemory | ScanFile\fR" 4
|
|
|
655 .IX Item "--InputDataMode LoadInMemory | ScanFile"
|
|
|
656 Specify how fingerprints bit-vector or vector strings data from \fI\s-1SD\s0, \s-1FP\s0 and \s-1CSV/TSV\s0\fR
|
|
|
657 fingerprint file(s) is processed: Retrieve, process and load all available fingerprints
|
|
|
658 data in memory; Retrieve and process data for fingerprints one at a time. Possible values
|
|
|
659 : \fILoadInMemory | ScanFile\fR. Default: \fILoadInMemory\fR.
|
|
|
660 .Sp
|
|
|
661 During \fILoadInMemory\fR value of \fB\-\-InputDataMode\fR, fingerprints bit-vector or vector
|
|
|
662 strings data from input file is retrieved, processed, and loaded into memory all at once
|
|
|
663 as fingerprints objects for generation for similarity matrices.
|
|
|
664 .Sp
|
|
|
665 During \fIScanFile\fR value of \fB\-\-InputDataMode\fR, multiple passes over the input fingerprints
|
|
|
666 file are performed to retrieve and process fingerprints bit-vector or vector strings data one at
|
|
|
667 a time to generate fingerprints objects used during generation of similarity matrices. A temporary
|
|
|
668 copy of the input fingerprints file is made at the start and deleted after generating the matrices.
|
|
|
669 .Sp
|
|
|
670 \&\fIScanFile\fR value of \fB\-\-InputDataMode\fR allows processing of arbitrary large fingerprints files
|
|
|
671 without any additional memory requirement.
|
|
|
672 .IP "\fB\-m, \-\-mode\fR \fIAutoDetect | FingerprintsBitVectorString | FingerprintsVectorString\fR" 4
|
|
|
673 .IX Item "-m, --mode AutoDetect | FingerprintsBitVectorString | FingerprintsVectorString"
|
|
|
674 Format of fingerprint strings data in \fITextFile(s)\fR: automatically detect format of fingerprints
|
|
|
675 string created by MayaChemTools fingerprints generation scripts or explicitly specify its format.
|
|
|
676 Possible values: \fIAutoDetect | FingerprintsBitVectorString | FingerprintsVectorString\fR. Default
|
|
|
677 value: \fIAutoDetect\fR.
|
|
|
678 .IP "\fB\-\-OutDelim\fR \fIcomma | tab | semicolon\fR" 4
|
|
|
679 .IX Item "--OutDelim comma | tab | semicolon"
|
|
|
680 Delimiter for output \s-1CSV/TSV\s0 text file(s). Possible values: \fIcomma, tab, or semicolon\fR
|
|
|
681 Default value: \fIcomma\fR.
|
|
|
682 .IP "\fB\-\-OutMatrixFormat\fR \fIRowsAndColumns | IDPairsAndValue\fR" 4
|
|
|
683 .IX Item "--OutMatrixFormat RowsAndColumns | IDPairsAndValue"
|
|
|
684 Specify how similarity or distance values calculated for fingerprints vector and bit-vector strings
|
|
|
685 are written to the output \s-1CSV/TSV\s0 text file(s): Generate text files containing rows and columns
|
|
|
686 with their labels corresponding to compound IDs and each matrix element value corresponding to
|
|
|
687 similarity or distance between corresponding compounds; Generate text files containing rows containing
|
|
|
688 compoundIDs for two compounds followed by similarity or distance value between these compounds.
|
|
|
689 .Sp
|
|
|
690 Possible values: \fIRowsAndColumns, or IDPairsAndValue\fR. Default value: \fIRowsAndColumns\fR.
|
|
|
691 .Sp
|
|
|
692 The value of \fB\-\-OutMatrixFormat\fR in conjunction with \fB\-\-OutMatrixType\fR determines type
|
|
|
693 of data written to output files and allows generation of up to 6 different output data formats:
|
|
|
694 .Sp
|
|
|
695 .Vb 1
|
|
|
696 \& OutMatrixFormat OutMatrixType
|
|
|
697 \&
|
|
|
698 \& RowsAndColumns FullMatrix [ DEFAULT ]
|
|
|
699 \& RowsAndColumns UpperTriangularMatrix
|
|
|
700 \& RowsAndColumns LowerTriangularMatrix
|
|
|
701 \&
|
|
|
702 \& IDPairsAndValue FullMatrix
|
|
|
703 \& IDPairsAndValue UpperTriangularMatrix
|
|
|
704 \& IDPairsAndValue LowerTriangularMatrix
|
|
|
705 .Ve
|
|
|
706 .Sp
|
|
|
707 Example of data in output file for \fIRowsAndColumns\fR \fB\-\-OutMatrixFormat\fR value for
|
|
|
708 \&\fIFullMatrix\fR valueof \fB\-\-OutMatrixType\fR:
|
|
|
709 .Sp
|
|
|
710 .Vb 10
|
|
|
711 \& "","Cmpd1","Cmpd2","Cmpd3","Cmpd4","Cmpd5","Cmpd6",... ...
|
|
|
712 \& "Cmpd1","1","0.04","0.25","0.13","0.11","0.2",... ...
|
|
|
713 \& "Cmpd2","0.04","1","0.06","0.05","0.19","0.07",... ...
|
|
|
714 \& "Cmpd3","0.25","0.06","1","0.12","0.22","0.25",... ...
|
|
|
715 \& "Cmpd4","0.13","0.05","0.12","1","0.11","0.13",... ...
|
|
|
716 \& "Cmpd5","0.11","0.19","0.22","0.11","1","0.17",... ...
|
|
|
717 \& "Cmpd6","0.2","0.07","0.25","0.13","0.17","1",... ...
|
|
|
718 \& ... ... ..
|
|
|
719 \& ... ... ..
|
|
|
720 \& ... ... ..
|
|
|
721 .Ve
|
|
|
722 .Sp
|
|
|
723 Example of data in output file for \fIRowsAndColumns\fR \fB\-\-OutMatrixFormat\fR value for
|
|
|
724 \&\fIUpperTriangularMatrix\fR value of \fB\-\-OutMatrixType\fR:
|
|
|
725 .Sp
|
|
|
726 .Vb 10
|
|
|
727 \& "","Cmpd1","Cmpd2","Cmpd3","Cmpd4","Cmpd5","Cmpd6",... ...
|
|
|
728 \& "Cmpd1","1","0.04","0.25","0.13","0.11","0.2",... ...
|
|
|
729 \& "Cmpd2","1","0.06","0.05","0.19","0.07",... ...
|
|
|
730 \& "Cmpd3","1","0.12","0.22","0.25",... ...
|
|
|
731 \& "Cmpd4","1","0.11","0.13",... ...
|
|
|
732 \& "Cmpd5","1","0.17",... ...
|
|
|
733 \& "Cmpd6","1",... ...
|
|
|
734 \& ... ... ..
|
|
|
735 \& ... ... ..
|
|
|
736 \& ... ... ..
|
|
|
737 .Ve
|
|
|
738 .Sp
|
|
|
739 Example of data in output file for \fIRowsAndColumns\fR \fB\-\-OutMatrixFormat\fR value for
|
|
|
740 \&\fILowerTriangularMatrix\fR value of \fB\-\-OutMatrixType\fR:
|
|
|
741 .Sp
|
|
|
742 .Vb 10
|
|
|
743 \& "","Cmpd1","Cmpd2","Cmpd3","Cmpd4","Cmpd5","Cmpd6",... ...
|
|
|
744 \& "Cmpd1","1"
|
|
|
745 \& "Cmpd2","0.04","1"
|
|
|
746 \& "Cmpd3","0.25","0.06","1"
|
|
|
747 \& "Cmpd4","0.13","0.05","0.12","1"
|
|
|
748 \& "Cmpd5","0.11","0.19","0.22","0.11","1"
|
|
|
749 \& "Cmpd6","0.2","0.07","0.25","0.13","0.17","1"
|
|
|
750 \& ... ... ..
|
|
|
751 \& ... ... ..
|
|
|
752 \& ... ... ..
|
|
|
753 .Ve
|
|
|
754 .Sp
|
|
|
755 Example of data in output file for \fIIDPairsAndValue\fR \fB\-\-OutMatrixFormat\fR value for
|
|
|
756 <FullMatrix> value of \fBOutMatrixType\fR:
|
|
|
757 .Sp
|
|
|
758 .Vb 10
|
|
|
759 \& "CmpdID1","CmpdID2","Coefficient Value"
|
|
|
760 \& "Cmpd1","Cmpd1","1"
|
|
|
761 \& "Cmpd1","Cmpd2","0.04"
|
|
|
762 \& "Cmpd1","Cmpd3","0.25"
|
|
|
763 \& "Cmpd1","Cmpd4","0.13"
|
|
|
764 \& ... ... ...
|
|
|
765 \& ... ... ...
|
|
|
766 \& ... ... ...
|
|
|
767 \& "Cmpd2","Cmpd1","0.04"
|
|
|
768 \& "Cmpd2","Cmpd2","1"
|
|
|
769 \& "Cmpd2","Cmpd3","0.06"
|
|
|
770 \& "Cmpd2","Cmpd4","0.05"
|
|
|
771 \& ... ... ...
|
|
|
772 \& ... ... ...
|
|
|
773 \& ... ... ...
|
|
|
774 \& "Cmpd3","Cmpd1","0.25"
|
|
|
775 \& "Cmpd3","Cmpd2","0.06"
|
|
|
776 \& "Cmpd3","Cmpd3","1"
|
|
|
777 \& "Cmpd3","Cmpd4","0.12"
|
|
|
778 \& ... ... ...
|
|
|
779 \& ... ... ...
|
|
|
780 \& ... ... ...
|
|
|
781 .Ve
|
|
|
782 .Sp
|
|
|
783 Example of data in output file for \fIIDPairsAndValue\fR \fB\-\-OutMatrixFormat\fR value for
|
|
|
784 <UpperTriangularMatrix> value of \fB\-\-OutMatrixType\fR:
|
|
|
785 .Sp
|
|
|
786 .Vb 10
|
|
|
787 \& "CmpdID1","CmpdID2","Coefficient Value"
|
|
|
788 \& "Cmpd1","Cmpd1","1"
|
|
|
789 \& "Cmpd1","Cmpd2","0.04"
|
|
|
790 \& "Cmpd1","Cmpd3","0.25"
|
|
|
791 \& "Cmpd1","Cmpd4","0.13"
|
|
|
792 \& ... ... ...
|
|
|
793 \& ... ... ...
|
|
|
794 \& ... ... ...
|
|
|
795 \& "Cmpd2","Cmpd2","1"
|
|
|
796 \& "Cmpd2","Cmpd3","0.06"
|
|
|
797 \& "Cmpd2","Cmpd4","0.05"
|
|
|
798 \& ... ... ...
|
|
|
799 \& ... ... ...
|
|
|
800 \& ... ... ...
|
|
|
801 \& "Cmpd3","Cmpd3","1"
|
|
|
802 \& "Cmpd3","Cmpd4","0.12"
|
|
|
803 \& ... ... ...
|
|
|
804 \& ... ... ...
|
|
|
805 \& ... ... ...
|
|
|
806 .Ve
|
|
|
807 .Sp
|
|
|
808 Example of data in output file for \fIIDPairsAndValue\fR \fB\-\-OutMatrixFormat\fR value for
|
|
|
809 <LowerTriangularMatrix> value of \fB\-\-OutMatrixType\fR:
|
|
|
810 .Sp
|
|
|
811 .Vb 10
|
|
|
812 \& "CmpdID1","CmpdID2","Coefficient Value"
|
|
|
813 \& "Cmpd1","Cmpd1","1"
|
|
|
814 \& "Cmpd2","Cmpd1","0.04"
|
|
|
815 \& "Cmpd2","Cmpd2","1"
|
|
|
816 \& "Cmpd3","Cmpd1","0.25"
|
|
|
817 \& "Cmpd3","Cmpd2","0.06"
|
|
|
818 \& "Cmpd3","Cmpd3","1"
|
|
|
819 \& "Cmpd4","Cmpd1","0.13"
|
|
|
820 \& "Cmpd4","Cmpd2","0.05"
|
|
|
821 \& "Cmpd4","Cmpd3","0.12"
|
|
|
822 \& "Cmpd4","Cmpd4","1"
|
|
|
823 \& ... ... ...
|
|
|
824 \& ... ... ...
|
|
|
825 \& ... ... ...
|
|
|
826 .Ve
|
|
|
827 .IP "\fB\-\-OutMatrixType\fR \fIFullMatrix | UpperTriangularMatrix | LowerTriangularMatrix\fR" 4
|
|
|
828 .IX Item "--OutMatrixType FullMatrix | UpperTriangularMatrix | LowerTriangularMatrix"
|
|
|
829 Type of similarity or distance matrix to calculate for fingerprints vector and bit-vector strings:
|
|
|
830 Calculate full matrix; Calculate lower triangular matrix including diagonal; Calculate upper triangular
|
|
|
831 matrix including diagonal.
|
|
|
832 .Sp
|
|
|
833 Possible values: \fIFullMatrix, UpperTriangularMatrix, or LowerTriangularMatrix\fR. Default value:
|
|
|
834 \&\fIFullMatrix\fR.
|
|
|
835 .Sp
|
|
|
836 The value of \fB\-\-OutMatrixType\fR in conjunction with \fB\-\-OutMatrixFormat\fR determines type
|
|
|
837 of data written to output files.
|
|
|
838 .IP "\fB\-o, \-\-overwrite\fR" 4
|
|
|
839 .IX Item "-o, --overwrite"
|
|
|
840 Overwrite existing files
|
|
|
841 .IP "\fB\-p, \-\-precision\fR \fInumber\fR" 4
|
|
|
842 .IX Item "-p, --precision number"
|
|
|
843 Precision of calculated values in the output file. Default: up to \fI2\fR decimal places.
|
|
|
844 Valid values: positive integers.
|
|
|
845 .IP "\fB\-q, \-\-quote\fR \fIYes | No\fR" 4
|
|
|
846 .IX Item "-q, --quote Yes | No"
|
|
|
847 Put quote around column values in output \s-1CSV/TSV\s0 text file(s). Possible values:
|
|
|
848 \&\fIYes or No\fR. Default value: \fIYes\fR.
|
|
|
849 .IP "\fB\-r, \-\-root\fR \fIRootName\fR" 4
|
|
|
850 .IX Item "-r, --root RootName"
|
|
|
851 New file name is generated using the root: <Root><BitVectorComparisonMode>.<Ext> or
|
|
|
852 <Root><VectorComparisonMode><VectorComparisonFormulism>.<Ext>.
|
|
|
853 The csv, and tsv <Ext> values are used for comma/semicolon, and tab delimited text files
|
|
|
854 respectively. This option is ignored for multiple input files.
|
|
|
855 .ie n .IP "\fB\-v, \-\-VectorComparisonMode\fR \fIAll | ""TanimotoSimilarity,[ManhattanDistance,...]""\fR" 4
|
|
|
856 .el .IP "\fB\-v, \-\-VectorComparisonMode\fR \fIAll | ``TanimotoSimilarity,[ManhattanDistance,...]''\fR" 4
|
|
|
857 .IX Item "-v, --VectorComparisonMode All | TanimotoSimilarity,[ManhattanDistance,...]"
|
|
|
858 Specify what similarity or distance coefficients to use for calculating similarity matrices for
|
|
|
859 fingerprint vector strings data values in \fITextFile(s)\fR: calculate similarity matrices for all
|
|
|
860 supported similarity and distance coefficients or specify a comma delimited list of similarity
|
|
|
861 and distance coefficients. Possible values: \fIAll | \*(L"TanimotoSimilairy,[ManhattanDistance,..]\*(R"\fR.
|
|
|
862 Default: \fITanimotoSimilarity\fR.
|
|
|
863 .Sp
|
|
|
864 The value of \fB\-v, \-\-VectorComparisonMode\fR, in conjunction with \fB\-\-VectorComparisonFormulism\fR,
|
|
|
865 decides which type of similarity and distance coefficient formulism gets used.
|
|
|
866 .Sp
|
|
|
867 \&\fIAll\fR uses complete list of supported similarity and distance coefficients: \fICosineSimilarity,
|
|
|
868 CzekanowskiSimilarity, DiceSimilarity, OchiaiSimilarity, JaccardSimilarity, SorensonSimilarity, TanimotoSimilarity,
|
|
|
869 CityBlockDistance, EuclideanDistance, HammingDistance, ManhattanDistance, SoergelDistance\fR. These
|
|
|
870 similarity and distance coefficients are described below.
|
|
|
871 .Sp
|
|
|
872 \&\fBFingerprintsVector.pm\fR module, used to calculate similarity and distance coefficients,
|
|
|
873 provides support to perform comparison between vectors containing three different types of
|
|
|
874 values:
|
|
|
875 .Sp
|
|
|
876 Type I: OrderedNumericalValues
|
|
|
877 .Sp
|
|
|
878 .Vb 3
|
|
|
879 \& . Size of two vectors are same
|
|
|
880 \& . Vectors contain real values in a specific order. For example: MACCS keys
|
|
|
881 \& count, Topological pharmnacophore atom pairs and so on.
|
|
|
882 .Ve
|
|
|
883 .Sp
|
|
|
884 Type \s-1II:\s0 UnorderedNumericalValues
|
|
|
885 .Sp
|
|
|
886 .Vb 3
|
|
|
887 \& . Size of two vectors might not be same
|
|
|
888 \& . Vectors contain unordered real value identified by value IDs. For example:
|
|
|
889 \& Toplogical atom pairs, Topological atom torsions and so on
|
|
|
890 .Ve
|
|
|
891 .Sp
|
|
|
892 Type \s-1III:\s0 AlphaNumericalValues
|
|
|
893 .Sp
|
|
|
894 .Vb 3
|
|
|
895 \& . Size of two vectors might not be same
|
|
|
896 \& . Vectors contain unordered alphanumerical values. For example: Extended
|
|
|
897 \& connectivity fingerprints, atom neighborhood fingerprints.
|
|
|
898 .Ve
|
|
|
899 .Sp
|
|
|
900 Before performing similarity or distance calculations between vectors containing UnorderedNumericalValues
|
|
|
901 or AlphaNumericalValues, the vectors are transformed into vectors containing unique OrderedNumericalValues
|
|
|
902 using value IDs for UnorderedNumericalValues and values itself for AlphaNumericalValues.
|
|
|
903 .Sp
|
|
|
904 Three forms of similarity and distance calculation between two vectors, specified using \fB\-\-VectorComparisonFormulism\fR
|
|
|
905 option, are supported: \fIAlgebraicForm, BinaryForm or SetTheoreticForm\fR.
|
|
|
906 .Sp
|
|
|
907 For \fIBinaryForm\fR, the ordered list of processed final vector values containing the value or
|
|
|
908 count of each unique value type is simply converted into a binary vector containing 1s and 0s
|
|
|
909 corresponding to presence or absence of values before calculating similarity or distance between
|
|
|
910 two vectors.
|
|
|
911 .Sp
|
|
|
912 For two fingerprint vectors A and B of same size containing OrderedNumericalValues, let:
|
|
|
913 .Sp
|
|
|
914 .Vb 1
|
|
|
915 \& N = Number values in A or B
|
|
|
916 \&
|
|
|
917 \& Xa = Values of vector A
|
|
|
918 \& Xb = Values of vector B
|
|
|
919 \&
|
|
|
920 \& Xai = Value of ith element in A
|
|
|
921 \& Xbi = Value of ith element in B
|
|
|
922 \&
|
|
|
923 \& SUM = Sum of i over N values
|
|
|
924 .Ve
|
|
|
925 .Sp
|
|
|
926 For SetTheoreticForm of calculation between two vectors, let:
|
|
|
927 .Sp
|
|
|
928 .Vb 2
|
|
|
929 \& SetIntersectionXaXb = SUM ( MIN ( Xai, Xbi ) )
|
|
|
930 \& SetDifferenceXaXb = SUM ( Xai ) + SUM ( Xbi ) \- SUM ( MIN ( Xai, Xbi ) )
|
|
|
931 .Ve
|
|
|
932 .Sp
|
|
|
933 For BinaryForm of calculation between two vectors, let:
|
|
|
934 .Sp
|
|
|
935 .Vb 5
|
|
|
936 \& Na = Number of bits set to "1" in A = SUM ( Xai )
|
|
|
937 \& Nb = Number of bits set to "1" in B = SUM ( Xbi )
|
|
|
938 \& Nc = Number of bits set to "1" in both A and B = SUM ( Xai * Xbi )
|
|
|
939 \& Nd = Number of bits set to "0" in both A and B
|
|
|
940 \& = SUM ( 1 \- Xai \- Xbi + Xai * Xbi)
|
|
|
941 \&
|
|
|
942 \& N = Number of bits set to "1" or "0" in A or B = Size of A or B = Na + Nb \- Nc + Nd
|
|
|
943 .Ve
|
|
|
944 .Sp
|
|
|
945 Additionally, for BinaryForm various values also correspond to:
|
|
|
946 .Sp
|
|
|
947 .Vb 4
|
|
|
948 \& Na = | Xa |
|
|
|
949 \& Nb = | Xb |
|
|
|
950 \& Nc = | SetIntersectionXaXb |
|
|
|
951 \& Nd = N \- | SetDifferenceXaXb |
|
|
|
952 \&
|
|
|
953 \& | SetDifferenceXaXb | = N \- Nd = Na + Nb \- Nc + Nd \- Nd = Na + Nb \- Nc
|
|
|
954 \& = | Xa | + | Xb | \- | SetIntersectionXaXb |
|
|
|
955 .Ve
|
|
|
956 .Sp
|
|
|
957 Various similarity and distance coefficients [ Ref 40, Ref 62, Ref 64 ] for a pair of vectors A and B
|
|
|
958 in \fIAlgebraicForm, BinaryForm and SetTheoreticForm\fR are defined as follows:
|
|
|
959 .Sp
|
|
|
960 \&\fBCityBlockDistance\fR: ( same as HammingDistance and ManhattanDistance)
|
|
|
961 .Sp
|
|
|
962 \&\fIAlgebraicForm\fR: \s-1SUM\s0 ( \s-1ABS\s0 ( Xai \- Xbi ) )
|
|
|
963 .Sp
|
|
|
964 \&\fIBinaryForm\fR: ( Na \- Nc ) + ( Nb \- Nc ) = Na + Nb \- 2 * Nc
|
|
|
965 .Sp
|
|
|
966 \&\fISetTheoreticForm\fR: | SetDifferenceXaXb | \- | SetIntersectionXaXb | = \s-1SUM\s0 ( Xai ) + \s-1SUM\s0 ( Xbi ) \- 2 * ( \s-1SUM\s0 ( \s-1MIN\s0 ( Xai, Xbi ) ) )
|
|
|
967 .Sp
|
|
|
968 \&\fBCosineSimilarity\fR: ( same as OchiaiSimilarityCoefficient)
|
|
|
969 .Sp
|
|
|
970 \&\fIAlgebraicForm\fR: \s-1SUM\s0 ( Xai * Xbi ) / \s-1SQRT\s0 ( \s-1SUM\s0 ( Xai ** 2) * \s-1SUM\s0 ( Xbi ** 2) )
|
|
|
971 .Sp
|
|
|
972 \&\fIBinaryForm\fR: Nc / \s-1SQRT\s0 ( Na * Nb)
|
|
|
973 .Sp
|
|
|
974 \&\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 ) )
|
|
|
975 .Sp
|
|
|
976 \&\fBCzekanowskiSimilarity\fR: ( same as DiceSimilarity and SorensonSimilarity)
|
|
|
977 .Sp
|
|
|
978 \&\fIAlgebraicForm\fR: ( 2 * ( \s-1SUM\s0 ( Xai * Xbi ) ) ) / ( \s-1SUM\s0 ( Xai ** 2) + \s-1SUM\s0 ( Xbi **2 ) )
|
|
|
979 .Sp
|
|
|
980 \&\fIBinaryForm\fR: 2 * Nc / ( Na + Nb )
|
|
|
981 .Sp
|
|
|
982 \&\fISetTheoreticForm\fR: 2 * | SetIntersectionXaXb | / ( |Xa| + |Xb| ) = 2 * ( \s-1SUM\s0 ( \s-1MIN\s0 ( Xai, Xbi ) ) ) / ( \s-1SUM\s0 ( Xai ) + \s-1SUM\s0 ( Xbi ) )
|
|
|
983 .Sp
|
|
|
984 \&\fBDiceSimilarity\fR: ( same as CzekanowskiSimilarity and SorensonSimilarity)
|
|
|
985 .Sp
|
|
|
986 \&\fIAlgebraicForm\fR: ( 2 * ( \s-1SUM\s0 ( Xai * Xbi ) ) ) / ( \s-1SUM\s0 ( Xai ** 2) + \s-1SUM\s0 ( Xbi **2 ) )
|
|
|
987 .Sp
|
|
|
988 \&\fIBinaryForm\fR: 2 * Nc / ( Na + Nb )
|
|
|
989 .Sp
|
|
|
990 \&\fISetTheoreticForm\fR: 2 * | SetIntersectionXaXb | / ( |Xa| + |Xb| ) = 2 * ( \s-1SUM\s0 ( \s-1MIN\s0 ( Xai, Xbi ) ) ) / ( \s-1SUM\s0 ( Xai ) + \s-1SUM\s0 ( Xbi ) )
|
|
|
991 .Sp
|
|
|
992 \&\fBEuclideanDistance\fR:
|
|
|
993 .Sp
|
|
|
994 \&\fIAlgebraicForm\fR: \s-1SQRT\s0 ( \s-1SUM\s0 ( ( ( Xai \- Xbi ) ** 2 ) ) )
|
|
|
995 .Sp
|
|
|
996 \&\fIBinaryForm\fR: \s-1SQRT\s0 ( ( Na \- Nc ) + ( Nb \- Nc ) ) = \s-1SQRT\s0 ( Na + Nb \- 2 * Nc )
|
|
|
997 .Sp
|
|
|
998 \&\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 ) ) ) )
|
|
|
999 .Sp
|
|
|
1000 \&\fBHammingDistance\fR: ( same as CityBlockDistance and ManhattanDistance)
|
|
|
1001 .Sp
|
|
|
1002 \&\fIAlgebraicForm\fR: \s-1SUM\s0 ( \s-1ABS\s0 ( Xai \- Xbi ) )
|
|
|
1003 .Sp
|
|
|
1004 \&\fIBinaryForm\fR: ( Na \- Nc ) + ( Nb \- Nc ) = Na + Nb \- 2 * Nc
|
|
|
1005 .Sp
|
|
|
1006 \&\fISetTheoreticForm\fR: | SetDifferenceXaXb | \- | SetIntersectionXaXb | = \s-1SUM\s0 ( Xai ) + \s-1SUM\s0 ( Xbi ) \- 2 * ( \s-1SUM\s0 ( \s-1MIN\s0 ( Xai, Xbi ) ) )
|
|
|
1007 .Sp
|
|
|
1008 \&\fBJaccardSimilarity\fR: ( same as TanimotoSimilarity)
|
|
|
1009 .Sp
|
|
|
1010 \&\fIAlgebraicForm\fR: \s-1SUM\s0 ( Xai * Xbi ) / ( \s-1SUM\s0 ( Xai ** 2 ) + \s-1SUM\s0 ( Xbi ** 2 ) \- \s-1SUM\s0 ( Xai * Xbi ) )
|
|
|
1011 .Sp
|
|
|
1012 \&\fIBinaryForm\fR: Nc / ( ( Na \- Nc ) + ( Nb \- Nc ) + Nc ) = Nc / ( Na + Nb \- Nc )
|
|
|
1013 .Sp
|
|
|
1014 \&\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 ) ) )
|
|
|
1015 .Sp
|
|
|
1016 \&\fBManhattanDistance\fR: ( same as CityBlockDistance and HammingDistance)
|
|
|
1017 .Sp
|
|
|
1018 \&\fIAlgebraicForm\fR: \s-1SUM\s0 ( \s-1ABS\s0 ( Xai \- Xbi ) )
|
|
|
1019 .Sp
|
|
|
1020 \&\fIBinaryForm\fR: ( Na \- Nc ) + ( Nb \- Nc ) = Na + Nb \- 2 * Nc
|
|
|
1021 .Sp
|
|
|
1022 \&\fISetTheoreticForm\fR: | SetDifferenceXaXb | \- | SetIntersectionXaXb | = \s-1SUM\s0 ( Xai ) + \s-1SUM\s0 ( Xbi ) \- 2 * ( \s-1SUM\s0 ( \s-1MIN\s0 ( Xai, Xbi ) ) )
|
|
|
1023 .Sp
|
|
|
1024 \&\fBOchiaiSimilarity\fR: ( same as CosineSimilarity)
|
|
|
1025 .Sp
|
|
|
1026 \&\fIAlgebraicForm\fR: \s-1SUM\s0 ( Xai * Xbi ) / \s-1SQRT\s0 ( \s-1SUM\s0 ( Xai ** 2) * \s-1SUM\s0 ( Xbi ** 2) )
|
|
|
1027 .Sp
|
|
|
1028 \&\fIBinaryForm\fR: Nc / \s-1SQRT\s0 ( Na * Nb)
|
|
|
1029 .Sp
|
|
|
1030 \&\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 ) )
|
|
|
1031 .Sp
|
|
|
1032 \&\fBSorensonSimilarity\fR: ( same as CzekanowskiSimilarity and DiceSimilarity)
|
|
|
1033 .Sp
|
|
|
1034 \&\fIAlgebraicForm\fR: ( 2 * ( \s-1SUM\s0 ( Xai * Xbi ) ) ) / ( \s-1SUM\s0 ( Xai ** 2) + \s-1SUM\s0 ( Xbi **2 ) )
|
|
|
1035 .Sp
|
|
|
1036 \&\fIBinaryForm\fR: 2 * Nc / ( Na + Nb )
|
|
|
1037 .Sp
|
|
|
1038 \&\fISetTheoreticForm\fR: 2 * | SetIntersectionXaXb | / ( |Xa| + |Xb| ) = 2 * ( \s-1SUM\s0 ( \s-1MIN\s0 ( Xai, Xbi ) ) ) / ( \s-1SUM\s0 ( Xai ) + \s-1SUM\s0 ( Xbi ) )
|
|
|
1039 .Sp
|
|
|
1040 \&\fBSoergelDistance\fR:
|
|
|
1041 .Sp
|
|
|
1042 \&\fIAlgebraicForm\fR: \s-1SUM\s0 ( \s-1ABS\s0 ( Xai \- Xbi ) ) / \s-1SUM\s0 ( \s-1MAX\s0 ( Xai, Xbi ) )
|
|
|
1043 .Sp
|
|
|
1044 \&\fIBinaryForm\fR: 1 \- Nc / ( Na + Nb \- Nc ) = ( Na + Nb \- 2 * Nc ) / ( Na + Nb \- Nc )
|
|
|
1045 .Sp
|
|
|
1046 \&\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 ) ) )
|
|
|
1047 .Sp
|
|
|
1048 \&\fBTanimotoSimilarity\fR: ( same as JaccardSimilarity)
|
|
|
1049 .Sp
|
|
|
1050 \&\fIAlgebraicForm\fR: \s-1SUM\s0 ( Xai * Xbi ) / ( \s-1SUM\s0 ( Xai ** 2 ) + \s-1SUM\s0 ( Xbi ** 2 ) \- \s-1SUM\s0 ( Xai * Xbi ) )
|
|
|
1051 .Sp
|
|
|
1052 \&\fIBinaryForm\fR: Nc / ( ( Na \- Nc ) + ( Nb \- Nc ) + Nc ) = Nc / ( Na + Nb \- Nc )
|
|
|
1053 .Sp
|
|
|
1054 \&\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 ) ) )
|
|
|
1055 .ie n .IP "\fB\-\-VectorComparisonFormulism\fR \fIAll | ""AlgebraicForm,[BinaryForm,SetTheoreticForm]""\fR" 4
|
|
|
1056 .el .IP "\fB\-\-VectorComparisonFormulism\fR \fIAll | ``AlgebraicForm,[BinaryForm,SetTheoreticForm]''\fR" 4
|
|
|
1057 .IX Item "--VectorComparisonFormulism All | AlgebraicForm,[BinaryForm,SetTheoreticForm]"
|
|
|
1058 Specify fingerprints vector comparison formulism to use for calculation similarity and distance
|
|
|
1059 coefficients during \fB\-v, \-\-VectorComparisonMode\fR: use all supported comparison formulisms
|
|
|
1060 or specify a comma delimited. Possible values: \fIAll | \*(L"AlgebraicForm,[BinaryForm,SetTheoreticForm]\*(R"\fR.
|
|
|
1061 Default value: \fIAlgebraicForm\fR.
|
|
|
1062 .Sp
|
|
|
1063 \&\fIAll\fR uses all three forms of supported vector comparison formulism for values of \fB\-v, \-\-VectorComparisonMode\fR
|
|
|
1064 option.
|
|
|
1065 .Sp
|
|
|
1066 For fingerprint vector strings containing \fBAlphaNumericalValues\fR data values \- \fBExtendedConnectivityFingerprints\fR,
|
|
|
1067 \&\fBAtomNeighborhoodsFingerprints\fR and so on \- all three formulism result in same value during similarity and distance
|
|
|
1068 calculations.
|
|
|
1069 .IP "\fB\-w, \-\-WorkingDir\fR \fIDirName\fR" 4
|
|
|
1070 .IX Item "-w, --WorkingDir DirName"
|
|
|
1071 Location of working directory. Default: current directory.
|
|
|
1072 .SH "EXAMPLES"
|
|
|
1073 .IX Header "EXAMPLES"
|
|
|
1074 To generate a similarity matrix corresponding to Tanimoto similarity coefficient for fingerprints
|
|
|
1075 bit-vector strings data corresponding to supported fingerprints in text file present in a column
|
|
|
1076 name containing Fingerprint substring by loading all fingerprints data into memory and create a
|
|
|
1077 SampleFPHexTanimotoSimilarity.csv file containing compound IDs retrieved from column name
|
|
|
1078 containing CompoundID substring, type:
|
|
|
1079 .PP
|
|
|
1080 .Vb 1
|
|
|
1081 \& % SimilarityMatricesFingerprints.pl \-o SampleFPHex.csv
|
|
|
1082 .Ve
|
|
|
1083 .PP
|
|
|
1084 To generate a similarity matrix corresponding to Tanimoto similarity coefficient for fingerprints
|
|
|
1085 bit-vector strings data corresponding to supported fingerprints in \s-1SD\s0 File present in a data field
|
|
|
1086 with Fingerprint substring in its label by loading all fingerprints data into memory and create a
|
|
|
1087 SampleFPHexTanimotoSimilarity.csv file containing sequentially generated compound IDs with
|
|
|
1088 Cmpd prefix, type:
|
|
|
1089 .PP
|
|
|
1090 .Vb 1
|
|
|
1091 \& % SimilarityMatricesFingerprints.pl \-o SampleFPHex.sdf
|
|
|
1092 .Ve
|
|
|
1093 .PP
|
|
|
1094 To generate a similarity matrix corresponding to Tanimoto similarity coefficient for fingerprints
|
|
|
1095 bit-vector strings data corresponding to supported fingerprints in \s-1FP\s0 file by loading all fingerprints
|
|
|
1096 data into memory and create a SampleFPHexTanimotoSimilarity.csv file along with compound IDs
|
|
|
1097 retrieved from \s-1FP\s0 file, type:
|
|
|
1098 .PP
|
|
|
1099 .Vb 1
|
|
|
1100 \& % SimilarityMatricesFingerprints.pl \-o SampleFPHex.fpf
|
|
|
1101 .Ve
|
|
|
1102 .PP
|
|
|
1103 To generate a lower triangular similarity matrix corresponding to Tanimoto similarity coefficient for
|
|
|
1104 fingerprints bit-vector strings data corresponding to supported fingerprints in text file present in a
|
|
|
1105 column name containing Fingerprint substring by loading all fingerprints data into memory and create
|
|
|
1106 a SampleFPHexTanimotoSimilarity.csv file containing compound IDs retrieved from column name
|
|
|
1107 containing CompoundID substring, type:
|
|
|
1108 .PP
|
|
|
1109 .Vb 3
|
|
|
1110 \& % SimilarityMatricesFingerprints.pl \-o \-\-InputDataMode LoadInMemory
|
|
|
1111 \& \-\-OutMatrixFormat RowsAndColumns \-\-OutMatrixType LowerTriangularMatrix
|
|
|
1112 \& SampleFPHex.csv
|
|
|
1113 .Ve
|
|
|
1114 .PP
|
|
|
1115 To generate a upper triangular similarity matrix corresponding to Tanimoto similarity coefficient for
|
|
|
1116 fingerprints bit-vector strings data corresponding to supported fingerprints in text file present in a
|
|
|
1117 column name containing Fingerprint substring by loading all fingerprints data into memory and create
|
|
|
1118 a SampleFPHexTanimotoSimilarity.csv file in IDPairsAndValue format containing compound IDs retrieved
|
|
|
1119 from column name containing CompoundID substring, type:
|
|
|
1120 .PP
|
|
|
1121 .Vb 3
|
|
|
1122 \& % SimilarityMatricesFingerprints.pl \-o \-\-InputDataMode LoadInMemory
|
|
|
1123 \& \-\-OutMatrixFormat IDPairsAndValue \-\-OutMatrixType UpperTriangularMatrix
|
|
|
1124 \& SampleFPHex.csv
|
|
|
1125 .Ve
|
|
|
1126 .PP
|
|
|
1127 To generate a full similarity matrix corresponding to Tanimoto similarity coefficient for fingerprints
|
|
|
1128 bit-vector strings data corresponding to supported fingerprints in text file present in a column
|
|
|
1129 name containing Fingerprint substring by scanning file without loading all fingerprints data into memory
|
|
|
1130 and create a SampleFPHexTanimotoSimilarity.csv file containing compound IDs retrieved from
|
|
|
1131 column name containing CompoundID substring, type:
|
|
|
1132 .PP
|
|
|
1133 .Vb 3
|
|
|
1134 \& % SimilarityMatricesFingerprints.pl \-o \-\-InputDataMode ScanFile
|
|
|
1135 \& \-\-OutMatrixFormat RowsAndColumns \-\-OutMatrixType FullMatrix
|
|
|
1136 \& SampleFPHex.csv
|
|
|
1137 .Ve
|
|
|
1138 .PP
|
|
|
1139 To generate a lower triangular similarity matrix corresponding to Tanimoto similarity coefficient for
|
|
|
1140 fingerprints bit-vector strings data corresponding to supported fingerprints in text file present in a
|
|
|
1141 column name containing Fingerprint substring by scanning file without loading all fingerprints data into
|
|
|
1142 memory and create a SampleFPHexTanimotoSimilarity.csv file in IDPairsAndValue format containing
|
|
|
1143 compound IDs retrieved from column name containing CompoundID substring, type:
|
|
|
1144 .PP
|
|
|
1145 .Vb 3
|
|
|
1146 \& % SimilarityMatricesFingerprints.pl \-o \-\-InputDataMode ScanFile
|
|
|
1147 \& \-\-OutMatrixFormat IDPairsAndValue \-\-OutMatrixType LowerTriangularMatrix
|
|
|
1148 \& SampleFPHex.csv
|
|
|
1149 .Ve
|
|
|
1150 .PP
|
|
|
1151 To generate a similarity matrix corresponding to Tanimoto similarity coefficient using algebraic formulism
|
|
|
1152 for fingerprints vector strings data corresponding to supported fingerprints in text file present in a column name
|
|
|
1153 containing Fingerprint substring and create a SampleFPCountTanimotoSimilarityAlgebraicForm.csv file
|
|
|
1154 containing compound IDs retrieved from column name containing CompoundID substring, type:
|
|
|
1155 .PP
|
|
|
1156 .Vb 1
|
|
|
1157 \& % SimilarityMatricesFingerprints.pl \-o SampleFPCount.csv
|
|
|
1158 .Ve
|
|
|
1159 .PP
|
|
|
1160 To generate a similarity matrix corresponding to Tanimoto similarity coefficient using algebraic formulism
|
|
|
1161 for fingerprints vector strings data corresponding to supported fingerprints in \s-1SD\s0 file present in a data field with
|
|
|
1162 Fingerprint substring in its label and create a SampleFPCountTanimotoSimilarityAlgebraicForm.csv file
|
|
|
1163 containing sequentially generated compound IDs with Cmpd prefix, type:
|
|
|
1164 .PP
|
|
|
1165 .Vb 1
|
|
|
1166 \& % SimilarityMatricesFingerprints.pl \-o SampleFPCount.sdf
|
|
|
1167 .Ve
|
|
|
1168 .PP
|
|
|
1169 To generate a similarity matrix corresponding to Tanimoto similarity coefficient using algebraic formulism
|
|
|
1170 vector strings data corresponding to supported fingerprints in \s-1FP\s0 file and create a
|
|
|
1171 SampleFPCountTanimotoSimilarityAlgebraicForm.csv file along with compound IDs retrieved from \s-1FP\s0 file, type:
|
|
|
1172 .PP
|
|
|
1173 .Vb 1
|
|
|
1174 \& % SimilarityMatricesFingerprints.pl \-o SampleFPCount.fpf
|
|
|
1175 .Ve
|
|
|
1176 .PP
|
|
|
1177 To generate a similarity matrix corresponding to Tanimoto similarity coefficient for fingerprints
|
|
|
1178 bit-vector strings data corresponding to supported fingerprints in text file present in a column name
|
|
|
1179 containing Fingerprint substring and create a SampleFPHexTanimotoSimilarity.csv file in
|
|
|
1180 IDPairsAndValue format containing compound IDs retrieved from column name containing
|
|
|
1181 CompoundID substring, type:
|
|
|
1182 .PP
|
|
|
1183 .Vb 2
|
|
|
1184 \& % SimilarityMatricesFingerprints.pl \-\-OutMatrixFormat IDPairsAndValue \-o
|
|
|
1185 \& SampleFPHex.csv
|
|
|
1186 .Ve
|
|
|
1187 .PP
|
|
|
1188 To generate a similarity matrix corresponding to Tanimoto similarity coefficient for fingerprints
|
|
|
1189 bit-vector strings data corresponding to supported fingerprints in \s-1SD\s0 file present in a data field with
|
|
|
1190 Fingerprint substring in its label and create a SampleFPHexTanimotoSimilarity.csv file in
|
|
|
1191 IDPairsAndValue format containing sequentially generated compound IDs with Cmpd prefix,
|
|
|
1192 type:
|
|
|
1193 .PP
|
|
|
1194 .Vb 2
|
|
|
1195 \& % SimilarityMatricesFingerprints.pl \-\-OutMatrixFormat IDPairsAndValue \-o
|
|
|
1196 \& SampleFPHex.sdf
|
|
|
1197 .Ve
|
|
|
1198 .PP
|
|
|
1199 To generate a similarity matrix corresponding to Tanimoto similarity coefficient for fingerprints
|
|
|
1200 bit-vector strings data corresponding to supported fingerprints in \s-1FP\s0 file and create a
|
|
|
1201 SampleFPHexTanimotoSimilarity.csv file in IDPairsAndValue format along with compound IDs retrieved
|
|
|
1202 from \s-1FP\s0 file, type:
|
|
|
1203 .PP
|
|
|
1204 .Vb 2
|
|
|
1205 \& % SimilarityMatricesFingerprints.pl \-\-OutMatrixFormat IDPairsAndValue \-o
|
|
|
1206 \& SampleFPHex.fpf
|
|
|
1207 .Ve
|
|
|
1208 .PP
|
|
|
1209 To generate a similarity matrix corresponding to Tanimoto similarity coefficient for fingerprints
|
|
|
1210 bit-vector strings data corresponding to supported fingerprints in \s-1SD\s0 file present in a data field with
|
|
|
1211 Fingerprint substring in its label and create a SampleFPHexTanimotoSimilarity.csv file
|
|
|
1212 containing compound IDs from mol name line, type:
|
|
|
1213 .PP
|
|
|
1214 .Vb 2
|
|
|
1215 \& % SimilarityMatricesFingerprints.pl \-\-CompoundIDMode MolName \-o
|
|
|
1216 \& SampleFPHex.sdf
|
|
|
1217 .Ve
|
|
|
1218 .PP
|
|
|
1219 To generate a similarity matrix corresponding to Tanimoto similarity coefficient for fingerprints
|
|
|
1220 bit-vector strings data corresponding to supported fingerprints present in a data field with
|
|
|
1221 Fingerprint substring in its label and create a SampleFPHexTanimotoSimilarity.csv file
|
|
|
1222 containing compound IDs from data field name Mol_ID, type:
|
|
|
1223 .PP
|
|
|
1224 .Vb 2
|
|
|
1225 \& % SimilarityMatricesFingerprints.pl \-\-CompoundIDMode DataField
|
|
|
1226 \& \-\-CompoundIDField Mol_ID \-o SampleFPBin.sdf
|
|
|
1227 .Ve
|
|
|
1228 .PP
|
|
|
1229 To generate similarity matrices corresponding to Buser, Dice and Tanimoto similarity coefficient
|
|
|
1230 for fingerprints bit-vector strings data corresponding to supported fingerprints present in a column
|
|
|
1231 name containing Fingerprint substring and create SampleFPBin[CoefficientName]Similarity.csv files
|
|
|
1232 containing compound IDs retrieved from column name containing CompoundID substring, type:
|
|
|
1233 .PP
|
|
|
1234 .Vb 2
|
|
|
1235 \& % SimilarityMatricesFingerprints.pl \-b "BuserSimilarity,DiceSimilarity,
|
|
|
1236 \& TanimotoSimilarity" \-o SampleFPBin.csv
|
|
|
1237 .Ve
|
|
|
1238 .PP
|
|
|
1239 To generate similarity matrices corresponding to Buser, Dice and Tanimoto similarity coefficient
|
|
|
1240 for fingerprints bit-vector strings data corresponding to supported fingerprints present in a data field with
|
|
|
1241 Fingerprint substring in its label and create SampleFPBin[CoefficientName]Similarity.csv files
|
|
|
1242 containing sequentially generated compound IDs with Cmpd prefix, type:
|
|
|
1243 .PP
|
|
|
1244 .Vb 2
|
|
|
1245 \& % SimilarityMatricesFingerprints.pl \-b "BuserSimilarity,DiceSimilarity,
|
|
|
1246 \& TanimotoSimilarity" \-o SampleFPBin.sdf
|
|
|
1247 .Ve
|
|
|
1248 .PP
|
|
|
1249 To generate similarity matrices corresponding to CityBlock distance and Tanimoto similarity coefficients using
|
|
|
1250 algebraic formulism for fingerprints vector strings data corresponding to supported fingerprints present in
|
|
|
1251 a column name containing Fingerprint substring and create SampleFPCount[CoefficientName]AlgebraicForm.csv
|
|
|
1252 files containing compound IDs retrieved from column name containing CompoundID substring, type:
|
|
|
1253 .PP
|
|
|
1254 .Vb 2
|
|
|
1255 \& % SimilarityMatricesFingerprints.pl \-v "CityBlockDistance,
|
|
|
1256 \& TanimotoSimilarity" \-o SampleFPCount.csv
|
|
|
1257 .Ve
|
|
|
1258 .PP
|
|
|
1259 To generate similarity matrices corresponding to CityBlock distance and Tanimoto similarity coefficients using
|
|
|
1260 algebraic formulism for fingerprints vector strings data corresponding to supported fingerprints present in
|
|
|
1261 a data field with Fingerprint substring in its label and create SampleFPCount[CoefficientName]AlgebraicForm.csv
|
|
|
1262 files containing sequentially generated compound IDs with Cmpd prefix, type:
|
|
|
1263 .PP
|
|
|
1264 .Vb 2
|
|
|
1265 \& % SimilarityMatricesFingerprints.pl \-v "CityBlockDistance,
|
|
|
1266 \& TanimotoSimilarity" \-o SampleFPCount.sdf
|
|
|
1267 .Ve
|
|
|
1268 .PP
|
|
|
1269 To generate similarity matrices corresponding to CityBlock distance Tanimoto similarity coefficients using
|
|
|
1270 binary formulism for fingerprints vector strings data corresponding to supported fingerprints present in
|
|
|
1271 a column name containing Fingerprint substring and create SampleFPCount[CoefficientName]Binary.csv
|
|
|
1272 files containing compound IDs retrieved from column name containing CompoundID substring, type:
|
|
|
1273 .PP
|
|
|
1274 .Vb 3
|
|
|
1275 \& % SimilarityMatricesFingerprints.pl \-v "CityBlockDistance,
|
|
|
1276 \& TanimotoSimilarity" \-\-VectorComparisonFormulism BinaryForm \-o
|
|
|
1277 \& SampleFPCount.csv
|
|
|
1278 .Ve
|
|
|
1279 .PP
|
|
|
1280 To generate similarity matrices corresponding to CityBlock distance Tanimoto similarity coefficients using
|
|
|
1281 binary formulism for fingerprints vector strings data corresponding to supported fingerprints present in
|
|
|
1282 a data field with Fingerprint substring in its label and create SampleFPCount[CoefficientName]Binary.csv
|
|
|
1283 files containing sequentially generated compound IDs with Cmpd prefix, type:
|
|
|
1284 .PP
|
|
|
1285 .Vb 3
|
|
|
1286 \& % SimilarityMatricesFingerprints.pl \-v "CityBlockDistance,
|
|
|
1287 \& TanimotoSimilarity" \-\-VectorComparisonFormulism BinaryForm \-o
|
|
|
1288 \& SampleFPCount.sdf
|
|
|
1289 .Ve
|
|
|
1290 .PP
|
|
|
1291 To generate similarity matrices corresponding to CityBlock distance Tanimoto similarity coefficients using
|
|
|
1292 all supported comparison formulisms for fingerprints vector strings data corresponding to supported
|
|
|
1293 fingerprints present in a column name containing Fingerprint substring and create
|
|
|
1294 SampleFPCount[CoefficientName][FormulismName].csv files containing compound IDs retrieved from column
|
|
|
1295 name containing CompoundID substring, type:
|
|
|
1296 .PP
|
|
|
1297 .Vb 2
|
|
|
1298 \& % SimilarityMatricesFingerprints.pl \-v "CityBlockDistance,
|
|
|
1299 \& TanimotoSimilarity" \-\-VectorComparisonFormulism All \-o SampleFPCount.csv
|
|
|
1300 .Ve
|
|
|
1301 .PP
|
|
|
1302 To generate similarity matrices corresponding to CityBlock distance Tanimoto similarity coefficients using
|
|
|
1303 all supported comparison formulisms for fingerprints vector strings data corresponding to supported
|
|
|
1304 fingerprints present in a data field with Fingerprint substring in its label and create
|
|
|
1305 SampleFPCount[CoefficientName][FormulismName].csv files containing sequentially generated
|
|
|
1306 compound IDs with Cmpd prefix, type:
|
|
|
1307 .PP
|
|
|
1308 .Vb 2
|
|
|
1309 \& % SimilarityMatricesFingerprints.pl \-v "CityBlockDistance,TanimotoSimilarity"
|
|
|
1310 \& \-\-VectorComparisonFormulism All \-o SampleFPCount.sdf
|
|
|
1311 .Ve
|
|
|
1312 .PP
|
|
|
1313 To generate similarity matrices corresponding to all available similarity coefficient for fingerprints
|
|
|
1314 bit-vector strings data corresponding to supported fingerprints present in a column name
|
|
|
1315 containing Fingerprint substring and create SampleFPHex[CoefficientName].csv files
|
|
|
1316 containing compound IDs retrieved from column name containing CompoundID substring, type:
|
|
|
1317 .PP
|
|
|
1318 .Vb 2
|
|
|
1319 \& % SimilarityMatricesFingerprints.pl \-m AutoDetect \-\-BitVectorComparisonMode
|
|
|
1320 \& All \-\-alpha 0.5 \-beta 0.5 \-o SampleFPHex.csv
|
|
|
1321 .Ve
|
|
|
1322 .PP
|
|
|
1323 To generate similarity matrices corresponding to all available similarity coefficient for fingerprints
|
|
|
1324 bit-vector strings data corresponding to supported fingerprints present in a data field with Fingerprint
|
|
|
1325 substring in its label and create SampleFPHex[CoefficientName].csv files containing sequentially
|
|
|
1326 generated compound IDs with Cmpd prefix, type
|
|
|
1327 .PP
|
|
|
1328 .Vb 2
|
|
|
1329 \& % SimilarityMatricesFingerprints.pl \-m AutoDetect \-\-BitVectorComparisonMode
|
|
|
1330 \& All \-\-alpha 0.5 \-beta 0.5 \-o SampleFPHex.sdf
|
|
|
1331 .Ve
|
|
|
1332 .PP
|
|
|
1333 To generate similarity matrices corresponding to all available similarity and distance coefficients using
|
|
|
1334 all comparison formulism for fingerprints vector strings data corresponding to supported fingerprints
|
|
|
1335 present in a column name containing Fingerprint substring and create
|
|
|
1336 SampleFPCount[CoefficientName][FormulismName].csv files containing compound IDs
|
|
|
1337 retrieved from column name containing CompoundID substring, type:
|
|
|
1338 .PP
|
|
|
1339 .Vb 2
|
|
|
1340 \& % SimilarityMatricesFingerprints.pl \-m AutoDetect \-\-VectorComparisonMode
|
|
|
1341 \& All \-\-VectorComparisonFormulism All \-o SampleFPCount.csv
|
|
|
1342 .Ve
|
|
|
1343 .PP
|
|
|
1344 To generate similarity matrices corresponding to all available similarity and distance coefficients using
|
|
|
1345 all comparison formulism for fingerprints vector strings data corresponding to supported fingerprints
|
|
|
1346 present in a data field with Fingerprint substring in its label and create
|
|
|
1347 SampleFPCount[CoefficientName][FormulismName].csv files containing sequentially generated
|
|
|
1348 compound IDs with Cmpd prefix, type:
|
|
|
1349 .PP
|
|
|
1350 .Vb 2
|
|
|
1351 \& % SimilarityMatricesFingerprints.pl \-m AutoDetect \-\-VectorComparisonMode
|
|
|
1352 \& All \-\-VectorComparisonFormulism All \-o SampleFPCount.sdf
|
|
|
1353 .Ve
|
|
|
1354 .PP
|
|
|
1355 To generate a similarity matrix corresponding to Tanimoto similarity coefficient for fingerprints
|
|
|
1356 bit-vector strings data corresponding to supported fingerprints present in a column number 2
|
|
|
1357 and create a SampleFPHexTanimotoSimilarity.csv file containing compound IDs retrieved column
|
|
|
1358 number 1, type:
|
|
|
1359 .PP
|
|
|
1360 .Vb 2
|
|
|
1361 \& % SimilarityMatricesFingerprints.pl \-\-ColMode ColNum \-\-CompoundIDCol 1
|
|
|
1362 \& \-\-FingerprintsCol 2 \-o SampleFPHex.csv
|
|
|
1363 .Ve
|
|
|
1364 .PP
|
|
|
1365 To generate a similarity matrix corresponding to Tanimoto similarity coefficient for fingerprints
|
|
|
1366 bit-vector strings data corresponding to supported fingerprints present in a data field name
|
|
|
1367 Fingerprints and create a SampleFPHexTanimotoSimilarity.csv file containing compound IDs
|
|
|
1368 present in data field name Mol_ID, type:
|
|
|
1369 .PP
|
|
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1370 .Vb 2
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1371 \& % SimilarityMatricesFingerprints.pl \-\-FingerprintsField Fingerprints
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1372 \& \-\-CompoundIDMode DataField \-\-CompoundIDField Mol_ID \-o SampleFPHex.sdf
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1373 .Ve
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1374 .PP
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1375 To generate a similarity matrix corresponding to Tversky similarity coefficient for fingerprints
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1376 bit-vector strings data corresponding to supported fingerprints present in a column named Fingerprints
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1377 and create a SampleFPHexTverskySimilarity.tsv file containing compound IDs retrieved column named
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1378 CompoundID, type:
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1379 .PP
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1380 .Vb 4
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1381 \& % SimilarityMatricesFingerprints.pl \-\-BitVectorComparisonMode
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1382 \& TverskySimilarity \-\-alpha 0.5 \-\-ColMode ColLabel \-\-CompoundIDCol
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1383 \& CompoundID \-\-FingerprintsCol Fingerprints \-\-OutDelim Tab \-\-quote No
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1384 \& \-o SampleFPHex.csv
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1385 .Ve
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1386 .PP
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1387 To generate a similarity matrix corresponding to Tanimoto similarity coefficient for fingerprints
|
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1388 bit-vector strings data corresponding to supported fingerprints present in a data field
|
|
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1389 with Fingerprint substring in its label and create a SampleFPHexTanimotoSimilarity.csv file
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1390 containing compound IDs from molname line or sequentially generated compound IDs
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1391 with Mol prefix, type:
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1392 .PP
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1393 .Vb 2
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1394 \& % SimilarityMatricesFingerprints.pl \-\-CompoundIDMode MolnameOrLabelPrefix
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1395 \& \-\-CompoundIDPrefix Mol \-o SampleFPHex.sdf
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1396 .Ve
|
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1397 .PP
|
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1398 To generate a similarity matrix corresponding to Tanimoto similarity coefficient for fingerprints
|
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|
1399 bit-vector strings data corresponding to supported fingerprints present in a data field with
|
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1400 Fingerprint substring in its label and create a SampleFPHexTanimotoSimilarity.tsv file
|
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1401 containing sequentially generated compound IDs with Cmpd prefix, type:
|
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1402 .PP
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1403 .Vb 1
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1404 \& % SimilarityMatricesFingerprints.pl \-OutDelim Tab \-\-quote No \-o SampleFPHex.sdf
|
|
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1405 .Ve
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1406 .SH "AUTHOR"
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1407 .IX Header "AUTHOR"
|
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|
1408 Manish Sud <msud@san.rr.com>
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1409 .SH "SEE ALSO"
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1410 .IX Header "SEE ALSO"
|
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1411 InfoFingerprintsFiles.pl, SimilaritySearchingFingerprints.pl, AtomNeighborhoodsFingerprints.pl,
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1412 ExtendedConnectivityFingerprints.pl, MACCSKeysFingerprints.pl, PathLengthFingerprints.pl,
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1413 TopologicalAtomPairsFingerprints.pl, TopologicalAtomTorsionsFingerprints.pl,
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1414 TopologicalPharmacophoreAtomPairsFingerprints.pl, TopologicalPharmacophoreAtomTripletsFingerprints.pl
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1415 .SH "COPYRIGHT"
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|
1416 .IX Header "COPYRIGHT"
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1417 Copyright (C) 2015 Manish Sud. All rights reserved.
|
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1418 .PP
|
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|
1419 This file is part of MayaChemTools.
|
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1420 .PP
|
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|
1421 MayaChemTools is free software; you can redistribute it and/or modify it under
|
|
|
1422 the terms of the \s-1GNU\s0 Lesser General Public License as published by the Free
|
|
|
1423 Software Foundation; either version 3 of the License, or (at your option)
|
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1424 any later version.
|
