Mercurial > repos > deepakjadmin > mayatool3_test2
comparison bin/TopologicalAtomTripletsFingerprints.pl @ 0:4816e4a8ae95 draft default tip
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| author | deepakjadmin |
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| date | Wed, 20 Jan 2016 09:23:18 -0500 |
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| -1:000000000000 | 0:4816e4a8ae95 |
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| 1 #!/usr/bin/perl -w | |
| 2 # | |
| 3 # $RCSfile: TopologicalAtomTripletsFingerprints.pl,v $ | |
| 4 # $Date: 2015/02/28 20:46:23 $ | |
| 5 # $Revision: 1.21 $ | |
| 6 # | |
| 7 # Author: Manish Sud <msud@san.rr.com> | |
| 8 # | |
| 9 # Copyright (C) 2015 Manish Sud. All rights reserved. | |
| 10 # | |
| 11 # This file is part of MayaChemTools. | |
| 12 # | |
| 13 # MayaChemTools is free software; you can redistribute it and/or modify it under | |
| 14 # the terms of the GNU Lesser General Public License as published by the Free | |
| 15 # Software Foundation; either version 3 of the License, or (at your option) any | |
| 16 # later version. | |
| 17 # | |
| 18 # MayaChemTools is distributed in the hope that it will be useful, but without | |
| 19 # any warranty; without even the implied warranty of merchantability of fitness | |
| 20 # for a particular purpose. See the GNU Lesser General Public License for more | |
| 21 # details. | |
| 22 # | |
| 23 # You should have received a copy of the GNU Lesser General Public License | |
| 24 # along with MayaChemTools; if not, see <http://www.gnu.org/licenses/> or | |
| 25 # write to the Free Software Foundation Inc., 59 Temple Place, Suite 330, | |
| 26 # Boston, MA, 02111-1307, USA. | |
| 27 # | |
| 28 | |
| 29 use strict; | |
| 30 use FindBin; use lib "$FindBin::Bin/../lib"; | |
| 31 use Getopt::Long; | |
| 32 use File::Basename; | |
| 33 use Text::ParseWords; | |
| 34 use Benchmark; | |
| 35 use FileUtil; | |
| 36 use TextUtil; | |
| 37 use SDFileUtil; | |
| 38 use MoleculeFileIO; | |
| 39 use FileIO::FingerprintsSDFileIO; | |
| 40 use FileIO::FingerprintsTextFileIO; | |
| 41 use FileIO::FingerprintsFPFileIO; | |
| 42 use AtomTypes::AtomicInvariantsAtomTypes; | |
| 43 use AtomTypes::FunctionalClassAtomTypes; | |
| 44 use Fingerprints::TopologicalAtomTripletsFingerprints; | |
| 45 | |
| 46 my($ScriptName, %Options, $StartTime, $EndTime, $TotalTime); | |
| 47 | |
| 48 # Autoflush STDOUT | |
| 49 $| = 1; | |
| 50 | |
| 51 # Starting message... | |
| 52 $ScriptName = basename($0); | |
| 53 print "\n$ScriptName: Starting...\n\n"; | |
| 54 $StartTime = new Benchmark; | |
| 55 | |
| 56 # Get the options and setup script... | |
| 57 SetupScriptUsage(); | |
| 58 if ($Options{help} || @ARGV < 1) { | |
| 59 die GetUsageFromPod("$FindBin::Bin/$ScriptName"); | |
| 60 } | |
| 61 | |
| 62 my(@SDFilesList); | |
| 63 @SDFilesList = ExpandFileNames(\@ARGV, "sdf sd"); | |
| 64 | |
| 65 # Process options... | |
| 66 print "Processing options...\n"; | |
| 67 my(%OptionsInfo); | |
| 68 ProcessOptions(); | |
| 69 | |
| 70 # Setup information about input files... | |
| 71 print "Checking input SD file(s)...\n"; | |
| 72 my(%SDFilesInfo); | |
| 73 RetrieveSDFilesInfo(); | |
| 74 | |
| 75 # Process input files.. | |
| 76 my($FileIndex); | |
| 77 if (@SDFilesList > 1) { | |
| 78 print "\nProcessing SD files...\n"; | |
| 79 } | |
| 80 for $FileIndex (0 .. $#SDFilesList) { | |
| 81 if ($SDFilesInfo{FileOkay}[$FileIndex]) { | |
| 82 print "\nProcessing file $SDFilesList[$FileIndex]...\n"; | |
| 83 GenerateTopologicalAtomTripletsFingerprints($FileIndex); | |
| 84 } | |
| 85 } | |
| 86 print "\n$ScriptName:Done...\n\n"; | |
| 87 | |
| 88 $EndTime = new Benchmark; | |
| 89 $TotalTime = timediff ($EndTime, $StartTime); | |
| 90 print "Total time: ", timestr($TotalTime), "\n"; | |
| 91 | |
| 92 ############################################################################### | |
| 93 | |
| 94 # Generate fingerprints for a SD file... | |
| 95 # | |
| 96 sub GenerateTopologicalAtomTripletsFingerprints { | |
| 97 my($FileIndex) = @_; | |
| 98 my($CmpdCount, $IgnoredCmpdCount, $SDFile, $MoleculeFileIO, $Molecule, $TopologicalAtomTripletsFingerprints, $NewFPSDFileIO, $NewFPTextFileIO, $NewFPFileIO); | |
| 99 | |
| 100 $SDFile = $SDFilesList[$FileIndex]; | |
| 101 | |
| 102 # Setup output files... | |
| 103 # | |
| 104 ($NewFPSDFileIO, $NewFPTextFileIO, $NewFPFileIO) = SetupAndOpenOutputFiles($FileIndex); | |
| 105 | |
| 106 $MoleculeFileIO = new MoleculeFileIO('Name' => $SDFile); | |
| 107 $MoleculeFileIO->Open(); | |
| 108 | |
| 109 $CmpdCount = 0; | |
| 110 $IgnoredCmpdCount = 0; | |
| 111 | |
| 112 COMPOUND: while ($Molecule = $MoleculeFileIO->ReadMolecule()) { | |
| 113 $CmpdCount++; | |
| 114 | |
| 115 # Filter compound data before calculating fingerprints... | |
| 116 if ($OptionsInfo{Filter}) { | |
| 117 if (CheckAndFilterCompound($CmpdCount, $Molecule)) { | |
| 118 $IgnoredCmpdCount++; | |
| 119 next COMPOUND; | |
| 120 } | |
| 121 } | |
| 122 | |
| 123 $TopologicalAtomTripletsFingerprints = GenerateMoleculeFingerprints($Molecule); | |
| 124 if (!$TopologicalAtomTripletsFingerprints) { | |
| 125 $IgnoredCmpdCount++; | |
| 126 ProcessIgnoredCompound('FingerprintsGenerationFailed', $CmpdCount, $Molecule); | |
| 127 next COMPOUND; | |
| 128 } | |
| 129 | |
| 130 WriteDataToOutputFiles($FileIndex, $CmpdCount, $Molecule, $TopologicalAtomTripletsFingerprints, $NewFPSDFileIO, $NewFPTextFileIO, $NewFPFileIO); | |
| 131 } | |
| 132 $MoleculeFileIO->Close(); | |
| 133 | |
| 134 if ($NewFPSDFileIO) { | |
| 135 $NewFPSDFileIO->Close(); | |
| 136 } | |
| 137 if ($NewFPTextFileIO) { | |
| 138 $NewFPTextFileIO->Close(); | |
| 139 } | |
| 140 if ($NewFPFileIO) { | |
| 141 $NewFPFileIO->Close(); | |
| 142 } | |
| 143 | |
| 144 WriteFingerprintsGenerationSummaryStatistics($CmpdCount, $IgnoredCmpdCount); | |
| 145 } | |
| 146 | |
| 147 # Process compound being ignored due to problems in fingerprints geneation... | |
| 148 # | |
| 149 sub ProcessIgnoredCompound { | |
| 150 my($Mode, $CmpdCount, $Molecule) = @_; | |
| 151 my($CmpdID, $DataFieldLabelAndValuesRef); | |
| 152 | |
| 153 $DataFieldLabelAndValuesRef = $Molecule->GetDataFieldLabelAndValues(); | |
| 154 $CmpdID = SetupCmpdIDForOutputFiles($CmpdCount, $Molecule, $DataFieldLabelAndValuesRef); | |
| 155 | |
| 156 MODE: { | |
| 157 if ($Mode =~ /^ContainsNonElementalData$/i) { | |
| 158 warn "\nWarning: Ignoring compound record number $CmpdCount with ID $CmpdID: Compound contains atom data corresponding to non-elemental atom symbol(s)...\n\n"; | |
| 159 next MODE; | |
| 160 } | |
| 161 | |
| 162 if ($Mode =~ /^ContainsNoElementalData$/i) { | |
| 163 warn "\nWarning: Ignoring compound record number $CmpdCount with ID $CmpdID: Compound contains no atom data...\n\n"; | |
| 164 next MODE; | |
| 165 } | |
| 166 | |
| 167 if ($Mode =~ /^FingerprintsGenerationFailed$/i) { | |
| 168 warn "\nWarning: Ignoring compound record number $CmpdCount with ID $CmpdID: Fingerprints generation didn't succeed...\n\n"; | |
| 169 next MODE; | |
| 170 } | |
| 171 warn "\nWarning: Ignoring compound record number $CmpdCount with ID $CmpdID: Fingerprints generation didn't succeed...\n\n"; | |
| 172 } | |
| 173 } | |
| 174 | |
| 175 # Check and filter compounds.... | |
| 176 # | |
| 177 sub CheckAndFilterCompound { | |
| 178 my($CmpdCount, $Molecule) = @_; | |
| 179 my($ElementCount, $NonElementCount); | |
| 180 | |
| 181 ($ElementCount, $NonElementCount) = $Molecule->GetNumOfElementsAndNonElements(); | |
| 182 | |
| 183 if ($NonElementCount) { | |
| 184 ProcessIgnoredCompound('ContainsNonElementalData', $CmpdCount, $Molecule); | |
| 185 return 1; | |
| 186 } | |
| 187 | |
| 188 if (!$ElementCount) { | |
| 189 ProcessIgnoredCompound('ContainsNoElementalData', $CmpdCount, $Molecule); | |
| 190 return 1; | |
| 191 } | |
| 192 | |
| 193 return 0; | |
| 194 } | |
| 195 | |
| 196 # Write out compounds fingerprints generation summary statistics... | |
| 197 # | |
| 198 sub WriteFingerprintsGenerationSummaryStatistics { | |
| 199 my($CmpdCount, $IgnoredCmpdCount) = @_; | |
| 200 my($ProcessedCmpdCount); | |
| 201 | |
| 202 $ProcessedCmpdCount = $CmpdCount - $IgnoredCmpdCount; | |
| 203 | |
| 204 print "\nNumber of compounds: $CmpdCount\n"; | |
| 205 print "Number of compounds processed successfully during fingerprints generation: $ProcessedCmpdCount\n"; | |
| 206 print "Number of compounds ignored during fingerprints generation: $IgnoredCmpdCount\n"; | |
| 207 } | |
| 208 | |
| 209 # Open output files... | |
| 210 # | |
| 211 sub SetupAndOpenOutputFiles { | |
| 212 my($FileIndex) = @_; | |
| 213 my($NewFPSDFile, $NewFPFile, $NewFPTextFile, $NewFPSDFileIO, $NewFPTextFileIO, $NewFPFileIO, %FingerprintsFileIOParams); | |
| 214 | |
| 215 ($NewFPSDFileIO, $NewFPTextFileIO, $NewFPFileIO) = (undef) x 3; | |
| 216 | |
| 217 # Setup common parameters for fingerprints file IO objects... | |
| 218 # | |
| 219 %FingerprintsFileIOParams = ('Mode' => 'Write', 'Overwrite' => $OptionsInfo{OverwriteFiles}, 'FingerprintsStringMode' => 'FingerprintsVectorString', 'VectorStringFormat' => $OptionsInfo{VectorStringFormat}); | |
| 220 | |
| 221 if ($OptionsInfo{SDOutput}) { | |
| 222 $NewFPSDFile = $SDFilesInfo{SDOutFileNames}[$FileIndex]; | |
| 223 print "Generating SD file $NewFPSDFile...\n"; | |
| 224 $NewFPSDFileIO = new FileIO::FingerprintsSDFileIO('Name' => $NewFPSDFile, %FingerprintsFileIOParams, 'FingerprintsFieldLabel' => $OptionsInfo{FingerprintsLabel}); | |
| 225 $NewFPSDFileIO->Open(); | |
| 226 } | |
| 227 | |
| 228 if ($OptionsInfo{FPOutput}) { | |
| 229 $NewFPFile = $SDFilesInfo{FPOutFileNames}[$FileIndex]; | |
| 230 print "Generating FP file $NewFPFile...\n"; | |
| 231 $NewFPFileIO = new FileIO::FingerprintsFPFileIO('Name' => $NewFPFile, %FingerprintsFileIOParams); | |
| 232 $NewFPFileIO->Open(); | |
| 233 } | |
| 234 | |
| 235 if ($OptionsInfo{TextOutput}) { | |
| 236 my($ColLabelsRef); | |
| 237 | |
| 238 $NewFPTextFile = $SDFilesInfo{TextOutFileNames}[$FileIndex]; | |
| 239 $ColLabelsRef = SetupFPTextFileCoulmnLabels($FileIndex); | |
| 240 | |
| 241 print "Generating text file $NewFPTextFile...\n"; | |
| 242 $NewFPTextFileIO = new FileIO::FingerprintsTextFileIO('Name' => $NewFPTextFile, %FingerprintsFileIOParams, 'DataColLabels' => $ColLabelsRef, 'OutDelim' => $OptionsInfo{OutDelim}, 'OutQuote' => $OptionsInfo{OutQuote}); | |
| 243 $NewFPTextFileIO->Open(); | |
| 244 } | |
| 245 | |
| 246 return ($NewFPSDFileIO, $NewFPTextFileIO, $NewFPFileIO); | |
| 247 } | |
| 248 | |
| 249 # Write fingerpritns and other data to appropriate output files... | |
| 250 # | |
| 251 sub WriteDataToOutputFiles { | |
| 252 my($FileIndex, $CmpdCount, $Molecule, $TopologicalAtomTripletsFingerprints, $NewFPSDFileIO, $NewFPTextFileIO, $NewFPFileIO) = @_; | |
| 253 my($DataFieldLabelAndValuesRef); | |
| 254 | |
| 255 $DataFieldLabelAndValuesRef = undef; | |
| 256 if ($NewFPTextFileIO || $NewFPFileIO) { | |
| 257 $DataFieldLabelAndValuesRef = $Molecule->GetDataFieldLabelAndValues(); | |
| 258 } | |
| 259 | |
| 260 if ($NewFPSDFileIO) { | |
| 261 my($CmpdString); | |
| 262 | |
| 263 $CmpdString = $Molecule->GetInputMoleculeString(); | |
| 264 $NewFPSDFileIO->WriteFingerprints($TopologicalAtomTripletsFingerprints, $CmpdString); | |
| 265 } | |
| 266 | |
| 267 if ($NewFPTextFileIO) { | |
| 268 my($ColValuesRef); | |
| 269 | |
| 270 $ColValuesRef = SetupFPTextFileCoulmnValues($FileIndex, $CmpdCount, $Molecule, $DataFieldLabelAndValuesRef); | |
| 271 $NewFPTextFileIO->WriteFingerprints($TopologicalAtomTripletsFingerprints, $ColValuesRef); | |
| 272 } | |
| 273 | |
| 274 if ($NewFPFileIO) { | |
| 275 my($CompoundID); | |
| 276 | |
| 277 $CompoundID = SetupCmpdIDForOutputFiles($CmpdCount, $Molecule, $DataFieldLabelAndValuesRef); | |
| 278 $NewFPFileIO->WriteFingerprints($TopologicalAtomTripletsFingerprints, $CompoundID); | |
| 279 } | |
| 280 } | |
| 281 | |
| 282 # Generate approriate column labels for FPText output file... | |
| 283 # | |
| 284 sub SetupFPTextFileCoulmnLabels { | |
| 285 my($FileIndex) = @_; | |
| 286 my($Line, @ColLabels); | |
| 287 | |
| 288 @ColLabels = (); | |
| 289 if ($OptionsInfo{DataFieldsMode} =~ /^All$/i) { | |
| 290 push @ColLabels, @{$SDFilesInfo{AllDataFieldsRef}[$FileIndex]}; | |
| 291 } | |
| 292 elsif ($OptionsInfo{DataFieldsMode} =~ /^Common$/i) { | |
| 293 push @ColLabels, @{$SDFilesInfo{CommonDataFieldsRef}[$FileIndex]}; | |
| 294 } | |
| 295 elsif ($OptionsInfo{DataFieldsMode} =~ /^Specify$/i) { | |
| 296 push @ColLabels, @{$OptionsInfo{SpecifiedDataFields}}; | |
| 297 } | |
| 298 elsif ($OptionsInfo{DataFieldsMode} =~ /^CompoundID$/i) { | |
| 299 push @ColLabels, $OptionsInfo{CompoundIDLabel}; | |
| 300 } | |
| 301 # Add fingerprints label... | |
| 302 push @ColLabels, $OptionsInfo{FingerprintsLabel}; | |
| 303 | |
| 304 return \@ColLabels; | |
| 305 } | |
| 306 | |
| 307 # Generate column values FPText output file.. | |
| 308 # | |
| 309 sub SetupFPTextFileCoulmnValues { | |
| 310 my($FileIndex, $CmpdCount, $Molecule, $DataFieldLabelAndValuesRef) = @_; | |
| 311 my(@ColValues); | |
| 312 | |
| 313 @ColValues = (); | |
| 314 if ($OptionsInfo{DataFieldsMode} =~ /^CompoundID$/i) { | |
| 315 push @ColValues, SetupCmpdIDForOutputFiles($CmpdCount, $Molecule, $DataFieldLabelAndValuesRef); | |
| 316 } | |
| 317 elsif ($OptionsInfo{DataFieldsMode} =~ /^All$/i) { | |
| 318 @ColValues = map { exists $DataFieldLabelAndValuesRef->{$_} ? $DataFieldLabelAndValuesRef->{$_} : ''} @{$SDFilesInfo{AllDataFieldsRef}[$FileIndex]}; | |
| 319 } | |
| 320 elsif ($OptionsInfo{DataFieldsMode} =~ /^Common$/i) { | |
| 321 @ColValues = map { exists $DataFieldLabelAndValuesRef->{$_} ? $DataFieldLabelAndValuesRef->{$_} : ''} @{$SDFilesInfo{CommonDataFieldsRef}[$FileIndex]}; | |
| 322 } | |
| 323 elsif ($OptionsInfo{DataFieldsMode} =~ /^Specify$/i) { | |
| 324 @ColValues = map { exists $DataFieldLabelAndValuesRef->{$_} ? $DataFieldLabelAndValuesRef->{$_} : ''} @{$OptionsInfo{SpecifiedDataFields}}; | |
| 325 } | |
| 326 | |
| 327 return \@ColValues; | |
| 328 } | |
| 329 | |
| 330 # Generate compound ID for FP and FPText output files.. | |
| 331 # | |
| 332 sub SetupCmpdIDForOutputFiles { | |
| 333 my($CmpdCount, $Molecule, $DataFieldLabelAndValuesRef) = @_; | |
| 334 my($CmpdID); | |
| 335 | |
| 336 $CmpdID = ''; | |
| 337 if ($OptionsInfo{CompoundIDMode} =~ /^MolNameOrLabelPrefix$/i) { | |
| 338 my($MolName); | |
| 339 $MolName = $Molecule->GetName(); | |
| 340 $CmpdID = $MolName ? $MolName : "$OptionsInfo{CompoundID}${CmpdCount}"; | |
| 341 } | |
| 342 elsif ($OptionsInfo{CompoundIDMode} =~ /^LabelPrefix$/i) { | |
| 343 $CmpdID = "$OptionsInfo{CompoundID}${CmpdCount}"; | |
| 344 } | |
| 345 elsif ($OptionsInfo{CompoundIDMode} =~ /^DataField$/i) { | |
| 346 my($SpecifiedDataField); | |
| 347 $SpecifiedDataField = $OptionsInfo{CompoundID}; | |
| 348 $CmpdID = exists $DataFieldLabelAndValuesRef->{$SpecifiedDataField} ? $DataFieldLabelAndValuesRef->{$SpecifiedDataField} : ''; | |
| 349 } | |
| 350 elsif ($OptionsInfo{CompoundIDMode} =~ /^MolName$/i) { | |
| 351 $CmpdID = $Molecule->GetName(); | |
| 352 } | |
| 353 return $CmpdID; | |
| 354 } | |
| 355 | |
| 356 # Generate fingerprints for molecule... | |
| 357 # | |
| 358 sub GenerateMoleculeFingerprints { | |
| 359 my($Molecule) = @_; | |
| 360 my($TopologicalAtomTripletsFingerprints); | |
| 361 | |
| 362 if ($OptionsInfo{KeepLargestComponent}) { | |
| 363 $Molecule->KeepLargestComponent(); | |
| 364 } | |
| 365 if (!$Molecule->DetectRings()) { | |
| 366 return undef; | |
| 367 } | |
| 368 $Molecule->SetAromaticityModel($OptionsInfo{AromaticityModel}); | |
| 369 $Molecule->DetectAromaticity(); | |
| 370 | |
| 371 $TopologicalAtomTripletsFingerprints = new Fingerprints::TopologicalAtomTripletsFingerprints('Molecule' => $Molecule, 'MinDistance' => $OptionsInfo{MinDistance}, 'MaxDistance' => $OptionsInfo{MaxDistance}, 'UseTriangleInequality' => $OptionsInfo{UseTriangleInequality}, 'AtomIdentifierType' => $OptionsInfo{AtomIdentifierType}); | |
| 372 SetAtomIdentifierTypeValuesToUse($TopologicalAtomTripletsFingerprints); | |
| 373 | |
| 374 # Generate fingerprints... | |
| 375 $TopologicalAtomTripletsFingerprints->GenerateFingerprints(); | |
| 376 | |
| 377 # Make sure fingerprints generation is successful... | |
| 378 if (!$TopologicalAtomTripletsFingerprints->IsFingerprintsGenerationSuccessful()) { | |
| 379 return undef; | |
| 380 } | |
| 381 | |
| 382 return $TopologicalAtomTripletsFingerprints; | |
| 383 } | |
| 384 | |
| 385 # Set atom identifier type to use for generating fingerprints... | |
| 386 # | |
| 387 sub SetAtomIdentifierTypeValuesToUse { | |
| 388 my($TopologicalAtomTripletsFingerprints) = @_; | |
| 389 | |
| 390 if ($OptionsInfo{AtomIdentifierType} =~ /^AtomicInvariantsAtomTypes$/i) { | |
| 391 $TopologicalAtomTripletsFingerprints->SetAtomicInvariantsToUse(\@{$OptionsInfo{AtomicInvariantsToUse}}); | |
| 392 } | |
| 393 elsif ($OptionsInfo{AtomIdentifierType} =~ /^FunctionalClassAtomTypes$/i) { | |
| 394 $TopologicalAtomTripletsFingerprints->SetFunctionalClassesToUse(\@{$OptionsInfo{FunctionalClassesToUse}}); | |
| 395 } | |
| 396 elsif ($OptionsInfo{AtomIdentifierType} =~ /^(DREIDINGAtomTypes|EStateAtomTypes|MMFF94AtomTypes|SLogPAtomTypes|SYBYLAtomTypes|TPSAAtomTypes|UFFAtomTypes)$/i) { | |
| 397 # Nothing to do for now... | |
| 398 } | |
| 399 else { | |
| 400 die "Error: The value specified, $Options{atomidentifiertype}, for option \"-a, --AtomIdentifierType\" is not valid. Supported atom identifier types in current release of MayaChemTools: AtomicInvariantsAtomTypes, DREIDINGAtomTypes, EStateAtomTypes, FunctionalClassAtomTypes, MMFF94AtomTypes, SLogPAtomTypes, SYBYLAtomTypes, TPSAAtomTypes, UFFAtomTypes\n"; | |
| 401 } | |
| 402 } | |
| 403 | |
| 404 # Retrieve information about SD files... | |
| 405 # | |
| 406 sub RetrieveSDFilesInfo { | |
| 407 my($SDFile, $Index, $FileDir, $FileExt, $FileName, $OutFileRoot, $TextOutFileExt, $SDOutFileExt, $FPOutFileExt, $NewSDFileName, $NewFPFileName, $NewTextFileName, $CheckDataField, $CollectDataFields, $AllDataFieldsRef, $CommonDataFieldsRef); | |
| 408 | |
| 409 %SDFilesInfo = (); | |
| 410 @{$SDFilesInfo{FileOkay}} = (); | |
| 411 @{$SDFilesInfo{OutFileRoot}} = (); | |
| 412 @{$SDFilesInfo{SDOutFileNames}} = (); | |
| 413 @{$SDFilesInfo{FPOutFileNames}} = (); | |
| 414 @{$SDFilesInfo{TextOutFileNames}} = (); | |
| 415 @{$SDFilesInfo{AllDataFieldsRef}} = (); | |
| 416 @{$SDFilesInfo{CommonDataFieldsRef}} = (); | |
| 417 | |
| 418 $CheckDataField = ($OptionsInfo{TextOutput} && ($OptionsInfo{DataFieldsMode} =~ /^CompoundID$/i) && ($OptionsInfo{CompoundIDMode} =~ /^DataField$/i)) ? 1 : 0; | |
| 419 $CollectDataFields = ($OptionsInfo{TextOutput} && ($OptionsInfo{DataFieldsMode} =~ /^(All|Common)$/i)) ? 1 : 0; | |
| 420 | |
| 421 FILELIST: for $Index (0 .. $#SDFilesList) { | |
| 422 $SDFile = $SDFilesList[$Index]; | |
| 423 | |
| 424 $SDFilesInfo{FileOkay}[$Index] = 0; | |
| 425 $SDFilesInfo{OutFileRoot}[$Index] = ''; | |
| 426 $SDFilesInfo{SDOutFileNames}[$Index] = ''; | |
| 427 $SDFilesInfo{FPOutFileNames}[$Index] = ''; | |
| 428 $SDFilesInfo{TextOutFileNames}[$Index] = ''; | |
| 429 | |
| 430 $SDFile = $SDFilesList[$Index]; | |
| 431 if (!(-e $SDFile)) { | |
| 432 warn "Warning: Ignoring file $SDFile: It doesn't exist\n"; | |
| 433 next FILELIST; | |
| 434 } | |
| 435 if (!CheckFileType($SDFile, "sd sdf")) { | |
| 436 warn "Warning: Ignoring file $SDFile: It's not a SD file\n"; | |
| 437 next FILELIST; | |
| 438 } | |
| 439 | |
| 440 if ($CheckDataField) { | |
| 441 # Make sure data field exists in SD file.. | |
| 442 my($CmpdString, $SpecifiedDataField, @CmpdLines, %DataFieldValues); | |
| 443 | |
| 444 @CmpdLines = (); | |
| 445 open SDFILE, "$SDFile" or die "Error: Couldn't open $SDFile: $! \n"; | |
| 446 $CmpdString = ReadCmpdString(\*SDFILE); | |
| 447 close SDFILE; | |
| 448 @CmpdLines = split "\n", $CmpdString; | |
| 449 %DataFieldValues = GetCmpdDataHeaderLabelsAndValues(\@CmpdLines); | |
| 450 $SpecifiedDataField = $OptionsInfo{CompoundID}; | |
| 451 if (!exists $DataFieldValues{$SpecifiedDataField}) { | |
| 452 warn "Warning: Ignoring file $SDFile: Data field value, $SpecifiedDataField, using \"--CompoundID\" option in \"DataField\" \"--CompoundIDMode\" doesn't exist\n"; | |
| 453 next FILELIST; | |
| 454 } | |
| 455 } | |
| 456 | |
| 457 $AllDataFieldsRef = ''; | |
| 458 $CommonDataFieldsRef = ''; | |
| 459 if ($CollectDataFields) { | |
| 460 my($CmpdCount); | |
| 461 open SDFILE, "$SDFile" or die "Error: Couldn't open $SDFile: $! \n"; | |
| 462 ($CmpdCount, $AllDataFieldsRef, $CommonDataFieldsRef) = GetAllAndCommonCmpdDataHeaderLabels(\*SDFILE); | |
| 463 close SDFILE; | |
| 464 } | |
| 465 | |
| 466 # Setup output file names... | |
| 467 $FileDir = ""; $FileName = ""; $FileExt = ""; | |
| 468 ($FileDir, $FileName, $FileExt) = ParseFileName($SDFile); | |
| 469 | |
| 470 $TextOutFileExt = "csv"; | |
| 471 if ($Options{outdelim} =~ /^tab$/i) { | |
| 472 $TextOutFileExt = "tsv"; | |
| 473 } | |
| 474 $SDOutFileExt = $FileExt; | |
| 475 $FPOutFileExt = "fpf"; | |
| 476 | |
| 477 if ($OptionsInfo{OutFileRoot} && (@SDFilesList == 1)) { | |
| 478 my ($RootFileDir, $RootFileName, $RootFileExt) = ParseFileName($OptionsInfo{OutFileRoot}); | |
| 479 if ($RootFileName && $RootFileExt) { | |
| 480 $FileName = $RootFileName; | |
| 481 } | |
| 482 else { | |
| 483 $FileName = $OptionsInfo{OutFileRoot}; | |
| 484 } | |
| 485 $OutFileRoot = $FileName; | |
| 486 } | |
| 487 else { | |
| 488 $OutFileRoot = "${FileName}TopologicalAtomTripletsFP"; | |
| 489 } | |
| 490 | |
| 491 $NewSDFileName = "${OutFileRoot}.${SDOutFileExt}"; | |
| 492 $NewFPFileName = "${OutFileRoot}.${FPOutFileExt}"; | |
| 493 $NewTextFileName = "${OutFileRoot}.${TextOutFileExt}"; | |
| 494 | |
| 495 if ($OptionsInfo{SDOutput}) { | |
| 496 if ($SDFile =~ /$NewSDFileName/i) { | |
| 497 warn "Warning: Ignoring input file $SDFile: Same output, $NewSDFileName, and input file names.\n"; | |
| 498 print "Specify a different name using \"-r --root\" option or use default name.\n"; | |
| 499 next FILELIST; | |
| 500 } | |
| 501 } | |
| 502 | |
| 503 if (!$OptionsInfo{OverwriteFiles}) { | |
| 504 # Check SD and text outout files... | |
| 505 if ($OptionsInfo{SDOutput}) { | |
| 506 if (-e $NewSDFileName) { | |
| 507 warn "Warning: Ignoring file $SDFile: The file $NewSDFileName already exists\n"; | |
| 508 next FILELIST; | |
| 509 } | |
| 510 } | |
| 511 if ($OptionsInfo{FPOutput}) { | |
| 512 if (-e $NewFPFileName) { | |
| 513 warn "Warning: Ignoring file $SDFile: The file $NewFPFileName already exists\n"; | |
| 514 next FILELIST; | |
| 515 } | |
| 516 } | |
| 517 if ($OptionsInfo{TextOutput}) { | |
| 518 if (-e $NewTextFileName) { | |
| 519 warn "Warning: Ignoring file $SDFile: The file $NewTextFileName already exists\n"; | |
| 520 next FILELIST; | |
| 521 } | |
| 522 } | |
| 523 } | |
| 524 | |
| 525 $SDFilesInfo{FileOkay}[$Index] = 1; | |
| 526 | |
| 527 $SDFilesInfo{OutFileRoot}[$Index] = $OutFileRoot; | |
| 528 $SDFilesInfo{SDOutFileNames}[$Index] = $NewSDFileName; | |
| 529 $SDFilesInfo{FPOutFileNames}[$Index] = $NewFPFileName; | |
| 530 $SDFilesInfo{TextOutFileNames}[$Index] = $NewTextFileName; | |
| 531 | |
| 532 $SDFilesInfo{AllDataFieldsRef}[$Index] = $AllDataFieldsRef; | |
| 533 $SDFilesInfo{CommonDataFieldsRef}[$Index] = $CommonDataFieldsRef; | |
| 534 } | |
| 535 } | |
| 536 | |
| 537 # Process option values... | |
| 538 sub ProcessOptions { | |
| 539 %OptionsInfo = (); | |
| 540 | |
| 541 ProcessAtomIdentifierTypeOptions(); | |
| 542 | |
| 543 $OptionsInfo{AromaticityModel} = $Options{aromaticitymodel}; | |
| 544 | |
| 545 $OptionsInfo{CompoundIDMode} = $Options{compoundidmode}; | |
| 546 $OptionsInfo{CompoundIDLabel} = $Options{compoundidlabel}; | |
| 547 $OptionsInfo{DataFieldsMode} = $Options{datafieldsmode}; | |
| 548 | |
| 549 my(@SpecifiedDataFields); | |
| 550 @SpecifiedDataFields = (); | |
| 551 | |
| 552 @{$OptionsInfo{SpecifiedDataFields}} = (); | |
| 553 $OptionsInfo{CompoundID} = ''; | |
| 554 | |
| 555 if ($Options{datafieldsmode} =~ /^CompoundID$/i) { | |
| 556 if ($Options{compoundidmode} =~ /^DataField$/i) { | |
| 557 if (!$Options{compoundid}) { | |
| 558 die "Error: You must specify a value for \"--CompoundID\" option in \"DataField\" \"--CompoundIDMode\". \n"; | |
| 559 } | |
| 560 $OptionsInfo{CompoundID} = $Options{compoundid}; | |
| 561 } | |
| 562 elsif ($Options{compoundidmode} =~ /^(LabelPrefix|MolNameOrLabelPrefix)$/i) { | |
| 563 $OptionsInfo{CompoundID} = $Options{compoundid} ? $Options{compoundid} : 'Cmpd'; | |
| 564 } | |
| 565 } | |
| 566 elsif ($Options{datafieldsmode} =~ /^Specify$/i) { | |
| 567 if (!$Options{datafields}) { | |
| 568 die "Error: You must specify a value for \"--DataFields\" option in \"Specify\" \"-d, --DataFieldsMode\". \n"; | |
| 569 } | |
| 570 @SpecifiedDataFields = split /\,/, $Options{datafields}; | |
| 571 push @{$OptionsInfo{SpecifiedDataFields}}, @SpecifiedDataFields; | |
| 572 } | |
| 573 | |
| 574 $OptionsInfo{Filter} = ($Options{filter} =~ /^Yes$/i) ? 1 : 0; | |
| 575 | |
| 576 $OptionsInfo{FingerprintsLabel} = $Options{fingerprintslabel} ? $Options{fingerprintslabel} : 'TopologicalAtomTripletsFingerprints'; | |
| 577 | |
| 578 $OptionsInfo{KeepLargestComponent} = ($Options{keeplargestcomponent} =~ /^Yes$/i) ? 1 : 0; | |
| 579 | |
| 580 $OptionsInfo{MinDistance} = $Options{mindistance}; | |
| 581 $OptionsInfo{MaxDistance} = $Options{maxdistance}; | |
| 582 | |
| 583 $OptionsInfo{Output} = $Options{output}; | |
| 584 $OptionsInfo{SDOutput} = ($Options{output} =~ /^(SD|All)$/i) ? 1 : 0; | |
| 585 $OptionsInfo{FPOutput} = ($Options{output} =~ /^(FP|All)$/i) ? 1 : 0; | |
| 586 $OptionsInfo{TextOutput} = ($Options{output} =~ /^(Text|All)$/i) ? 1 : 0; | |
| 587 | |
| 588 $OptionsInfo{OutDelim} = $Options{outdelim}; | |
| 589 $OptionsInfo{OutQuote} = ($Options{quote} =~ /^Yes$/i) ? 1 : 0; | |
| 590 | |
| 591 $OptionsInfo{OverwriteFiles} = $Options{overwrite} ? 1 : 0; | |
| 592 $OptionsInfo{OutFileRoot} = $Options{root} ? $Options{root} : 0; | |
| 593 | |
| 594 $OptionsInfo{UseTriangleInequality} = ($Options{usetriangleinequality} =~ /^Yes$/i) ? 1 : 0; | |
| 595 | |
| 596 $OptionsInfo{VectorStringFormat} = $Options{vectorstringformat}; | |
| 597 } | |
| 598 | |
| 599 # Process atom identifier type and related options... | |
| 600 # | |
| 601 sub ProcessAtomIdentifierTypeOptions { | |
| 602 | |
| 603 $OptionsInfo{AtomIdentifierType} = $Options{atomidentifiertype}; | |
| 604 | |
| 605 if ($Options{atomidentifiertype} =~ /^AtomicInvariantsAtomTypes$/i) { | |
| 606 ProcessAtomicInvariantsToUseOption(); | |
| 607 } | |
| 608 elsif ($Options{atomidentifiertype} =~ /^FunctionalClassAtomTypes$/i) { | |
| 609 ProcessFunctionalClassesToUse(); | |
| 610 } | |
| 611 elsif ($OptionsInfo{AtomIdentifierType} =~ /^(DREIDINGAtomTypes|EStateAtomTypes|MMFF94AtomTypes|SLogPAtomTypes|SYBYLAtomTypes|TPSAAtomTypes|UFFAtomTypes)$/i) { | |
| 612 # Nothing to do for now... | |
| 613 } | |
| 614 else { | |
| 615 die "Error: The value specified, $Options{atomidentifiertype}, for option \"-a, --AtomIdentifierType\" is not valid. Supported atom identifier types in current release of MayaChemTools: AtomicInvariantsAtomTypes, DREIDINGAtomTypes, EStateAtomTypes, FunctionalClassAtomTypes, MMFF94AtomTypes, SLogPAtomTypes, SYBYLAtomTypes, TPSAAtomTypes, UFFAtomTypes\n"; | |
| 616 } | |
| 617 } | |
| 618 | |
| 619 # Process specified atomic invariants to use... | |
| 620 # | |
| 621 sub ProcessAtomicInvariantsToUseOption { | |
| 622 my($AtomicInvariant, $AtomSymbolSpecified, @AtomicInvariantsWords); | |
| 623 | |
| 624 @{$OptionsInfo{AtomicInvariantsToUse}} = (); | |
| 625 if (IsEmpty($Options{atomicinvariantstouse})) { | |
| 626 die "Error: Atomic invariants value specified using \"--AtomicInvariantsToUse\" option is empty\n"; | |
| 627 } | |
| 628 $AtomSymbolSpecified = 0; | |
| 629 @AtomicInvariantsWords = split /\,/, $Options{atomicinvariantstouse}; | |
| 630 for $AtomicInvariant (@AtomicInvariantsWords) { | |
| 631 if (!AtomTypes::AtomicInvariantsAtomTypes::IsAtomicInvariantAvailable($AtomicInvariant)) { | |
| 632 die "Error: Atomic invariant specified, $AtomicInvariant, using \"--AtomicInvariantsToUse\" option is not valid...\n "; | |
| 633 } | |
| 634 if ($AtomicInvariant =~ /^(AS|AtomSymbol)$/i) { | |
| 635 $AtomSymbolSpecified = 1; | |
| 636 } | |
| 637 push @{$OptionsInfo{AtomicInvariantsToUse}}, $AtomicInvariant; | |
| 638 } | |
| 639 if (!$AtomSymbolSpecified) { | |
| 640 die "Error: Atomic invariant, AS or AtomSymbol, must be specified as using \"--AtomicInvariantsToUse\" option...\n "; | |
| 641 } | |
| 642 } | |
| 643 | |
| 644 # Process specified functional classes invariants to use... | |
| 645 # | |
| 646 sub ProcessFunctionalClassesToUse { | |
| 647 my($FunctionalClass, @FunctionalClassesToUseWords); | |
| 648 | |
| 649 @{$OptionsInfo{FunctionalClassesToUse}} = (); | |
| 650 if (IsEmpty($Options{functionalclassestouse})) { | |
| 651 die "Error: Functional classes value specified using \"--FunctionalClassesToUse\" option is empty\n"; | |
| 652 } | |
| 653 @FunctionalClassesToUseWords = split /\,/, $Options{functionalclassestouse}; | |
| 654 for $FunctionalClass (@FunctionalClassesToUseWords) { | |
| 655 if (!AtomTypes::FunctionalClassAtomTypes::IsFunctionalClassAvailable($FunctionalClass)) { | |
| 656 die "Error: Functional class specified, $FunctionalClass, using \"--FunctionalClassesToUse\" option is not valid...\n "; | |
| 657 } | |
| 658 push @{$OptionsInfo{FunctionalClassesToUse}}, $FunctionalClass; | |
| 659 } | |
| 660 } | |
| 661 | |
| 662 # Setup script usage and retrieve command line arguments specified using various options... | |
| 663 sub SetupScriptUsage { | |
| 664 | |
| 665 # Retrieve all the options... | |
| 666 %Options = (); | |
| 667 | |
| 668 $Options{aromaticitymodel} = 'MayaChemToolsAromaticityModel'; | |
| 669 | |
| 670 $Options{atomidentifiertype} = 'AtomicInvariantsAtomTypes'; | |
| 671 $Options{atomicinvariantstouse} = 'AS,X,BO,H,FC'; | |
| 672 | |
| 673 $Options{functionalclassestouse} = 'HBD,HBA,PI,NI,Ar,Hal'; | |
| 674 | |
| 675 $Options{compoundidmode} = 'LabelPrefix'; | |
| 676 $Options{compoundidlabel} = 'CompoundID'; | |
| 677 $Options{datafieldsmode} = 'CompoundID'; | |
| 678 | |
| 679 $Options{filter} = 'Yes'; | |
| 680 | |
| 681 $Options{keeplargestcomponent} = 'Yes'; | |
| 682 | |
| 683 $Options{mindistance} = 1; | |
| 684 $Options{maxdistance} = 10; | |
| 685 | |
| 686 $Options{output} = 'text'; | |
| 687 $Options{outdelim} = 'comma'; | |
| 688 $Options{quote} = 'yes'; | |
| 689 | |
| 690 $Options{usetriangleinequality} = 'No'; | |
| 691 | |
| 692 $Options{vectorstringformat} = 'IDsAndValuesString'; | |
| 693 | |
| 694 if (!GetOptions(\%Options, "aromaticitymodel=s", "atomidentifiertype|a=s", "atomicinvariantstouse=s", "functionalclassestouse=s", "compoundid=s", "compoundidlabel=s", "compoundidmode=s", "datafields=s", "datafieldsmode|d=s", "filter|f=s", "fingerprintslabel=s", "help|h", "keeplargestcomponent|k=s", "mindistance=s", "maxdistance=s", "outdelim=s", "output=s", "overwrite|o", "quote|q=s", "root|r=s", , "usetriangleinequality|u=s", "vectorstringformat|v=s", "workingdir|w=s")) { | |
| 695 die "\nTo get a list of valid options and their values, use \"$ScriptName -h\" or\n\"perl -S $ScriptName -h\" command and try again...\n"; | |
| 696 } | |
| 697 if ($Options{workingdir}) { | |
| 698 if (! -d $Options{workingdir}) { | |
| 699 die "Error: The value specified, $Options{workingdir}, for option \"-w --workingdir\" is not a directory name.\n"; | |
| 700 } | |
| 701 chdir $Options{workingdir} or die "Error: Couldn't chdir $Options{workingdir}: $! \n"; | |
| 702 } | |
| 703 if (!Molecule::IsSupportedAromaticityModel($Options{aromaticitymodel})) { | |
| 704 my(@SupportedModels) = Molecule::GetSupportedAromaticityModels(); | |
| 705 die "Error: The value specified, $Options{aromaticitymodel}, for option \"--AromaticityModel\" is not valid. Supported aromaticity models in current release of MayaChemTools: @SupportedModels\n"; | |
| 706 } | |
| 707 if ($Options{atomidentifiertype} !~ /^(AtomicInvariantsAtomTypes|DREIDINGAtomTypes|EStateAtomTypes|FunctionalClassAtomTypes|MMFF94AtomTypes|SLogPAtomTypes|SYBYLAtomTypes|TPSAAtomTypes|UFFAtomTypes)$/i) { | |
| 708 die "Error: The value specified, $Options{atomidentifiertype}, for option \"-a, --AtomIdentifierType\" is not valid. Supported atom identifier types in current release of MayaChemTools: AtomicInvariantsAtomTypes, DREIDINGAtomTypes, EStateAtomTypes, FunctionalClassAtomTypes, MMFF94AtomTypes, SLogPAtomTypes, SYBYLAtomTypes, TPSAAtomTypes, UFFAtomTypes\n"; | |
| 709 } | |
| 710 if ($Options{compoundidmode} !~ /^(DataField|MolName|LabelPrefix|MolNameOrLabelPrefix)$/i) { | |
| 711 die "Error: The value specified, $Options{compoundidmode}, for option \"--CompoundIDMode\" is not valid. Allowed values: DataField, MolName, LabelPrefix or MolNameOrLabelPrefix\n"; | |
| 712 } | |
| 713 if ($Options{datafieldsmode} !~ /^(All|Common|Specify|CompoundID)$/i) { | |
| 714 die "Error: The value specified, $Options{datafieldsmode}, for option \"-d, --DataFieldsMode\" is not valid. Allowed values: All, Common, Specify or CompoundID\n"; | |
| 715 } | |
| 716 if ($Options{filter} !~ /^(Yes|No)$/i) { | |
| 717 die "Error: The value specified, $Options{filter}, for option \"-f, --Filter\" is not valid. Allowed values: Yes or No\n"; | |
| 718 } | |
| 719 if ($Options{keeplargestcomponent} !~ /^(Yes|No)$/i) { | |
| 720 die "Error: The value specified, $Options{keeplargestcomponent}, for option \"-k, --KeepLargestComponent\" is not valid. Allowed values: Yes or No\n"; | |
| 721 } | |
| 722 if (!IsPositiveInteger($Options{mindistance})) { | |
| 723 die "Error: The value specified, $Options{mindistance}, for option \"--MinDistance\" is not valid. Allowed values: > 0 \n"; | |
| 724 } | |
| 725 if (!IsPositiveInteger($Options{maxdistance})) { | |
| 726 die "Error: The value specified, $Options{maxdistance}, for option \"--MaxDistance\" is not valid. Allowed values: > 0 \n"; | |
| 727 } | |
| 728 if ($Options{mindistance} > $Options{maxdistance}) { | |
| 729 die "Error: The value specified, specified, $Options{mindistance}, for option \"--MinDistance\" must be less than the value specified, $Options{maxdistance}, for option \"--MaxDistance\" \n"; | |
| 730 } | |
| 731 if ($Options{output} !~ /^(SD|FP|text|all)$/i) { | |
| 732 die "Error: The value specified, $Options{output}, for option \"--output\" is not valid. Allowed values: SD, FP, text, or all\n"; | |
| 733 } | |
| 734 if ($Options{outdelim} !~ /^(comma|semicolon|tab)$/i) { | |
| 735 die "Error: The value specified, $Options{outdelim}, for option \"--outdelim\" is not valid. Allowed values: comma, tab, or semicolon\n"; | |
| 736 } | |
| 737 if ($Options{quote} !~ /^(Yes|No)$/i) { | |
| 738 die "Error: The value specified, $Options{quote}, for option \"-q --quote\" is not valid. Allowed values: Yes or No\n"; | |
| 739 } | |
| 740 if ($Options{outdelim} =~ /semicolon/i && $Options{quote} =~ /^No$/i) { | |
| 741 die "Error: The value specified, $Options{quote}, for option \"-q --quote\" is not allowed with, semicolon value of \"--outdelim\" option: Fingerprints string use semicolon as delimiter for various data fields and must be quoted.\n"; | |
| 742 } | |
| 743 if ($Options{usetriangleinequality} !~ /^(Yes|No)$/i) { | |
| 744 die "Error: The value specified, $Options{usetriangleinequality}, for option \"-u, --UseTriangleInequality\" is not valid. Allowed values: Yes or No\n"; | |
| 745 } | |
| 746 if ($Options{vectorstringformat} !~ /^(IDsAndValuesString|IDsAndValuesPairsString|ValuesAndIDsString|ValuesAndIDsPairsString)$/i) { | |
| 747 die "Error: The value specified, $Options{vectorstringformat}, for option \"-v, --VectorStringFormat\" is not valid. Allowed values: IDsAndValuesString, IDsAndValuesPairsString, ValuesAndIDsString or ValuesAndIDsPairsString\n"; | |
| 748 } | |
| 749 } | |
| 750 | |
| 751 __END__ | |
| 752 | |
| 753 =head1 NAME | |
| 754 | |
| 755 TopologicalAtomTripletsFingerprints.pl - Generate topological atom triplets fingerprints for SD files | |
| 756 | |
| 757 =head1 SYNOPSIS | |
| 758 | |
| 759 TopologicalAtomTripletsFingerprints.pl SDFile(s)... | |
| 760 | |
| 761 TopologicalAtomTripletsFingerprints.pl [B<--AromaticityModel> I<AromaticityModelType>] | |
| 762 [B<-a, --AtomIdentifierType> I<AtomicInvariantsAtomTypes>] | |
| 763 [B<--AtomicInvariantsToUse> I<"AtomicInvariant,AtomicInvariant...">] | |
| 764 [B<--FunctionalClassesToUse> I<"FunctionalClass1,FunctionalClass2...">] | |
| 765 [B<--CompoundID> I<DataFieldName or LabelPrefixString>] [B<--CompoundIDLabel> I<text>] | |
| 766 [B<--CompoundIDMode>] [B<--DataFields> I<"FieldLabel1,FieldLabel2,...">] | |
| 767 [B<-d, --DataFieldsMode> I<All | Common | Specify | CompoundID>] [B<-f, --Filter> I<Yes | No>] | |
| 768 [B<--FingerprintsLabel> I<text>] [B<-h, --help>] [B<-k, --KeepLargestComponent> I<Yes | No>] | |
| 769 [B<--MinDistance> I<number>] [B<--MaxDistance> I<number>] | |
| 770 [B<--OutDelim> I<comma | tab | semicolon>] [B<--output> I<SD | FP | text | all>] [B<-o, --overwrite>] | |
| 771 [B<-q, --quote> I<Yes | No>] [B<-r, --root> I<RootName>] [B<-u, --UseTriangleInequality> I<Yes | No>] | |
| 772 [B<-v, --VectorStringFormat> I<ValuesString, IDsAndValuesString | IDsAndValuesPairsString | ValuesAndIDsString | ValuesAndIDsPairsString>] | |
| 773 [B<-w, --WorkingDir> dirname] SDFile(s)... | |
| 774 | |
| 775 =head1 DESCRIPTION | |
| 776 | |
| 777 Generate topological atom triplets fingerprints for I<SDFile(s)> and create | |
| 778 appropriate SD, FP or CSV/TSV text file(s) containing fingerprints vector strings corresponding to | |
| 779 molecular fingerprints. | |
| 780 | |
| 781 Multiple SDFile names are separated by spaces. The valid file extensions are I<.sdf> | |
| 782 and I<.sd>. All other file names are ignored. All the SD files in a current directory | |
| 783 can be specified either by I<*.sdf> or the current directory name. | |
| 784 | |
| 785 The current release of MayaChemTools supports generation of topological atom triplets | |
| 786 fingerprints corresponding to following B<-a, --AtomIdentifierTypes>: | |
| 787 | |
| 788 AtomicInvariantsAtomTypes, DREIDINGAtomTypes, EStateAtomTypes, | |
| 789 FunctionalClassAtomTypes, MMFF94AtomTypes, SLogPAtomTypes, | |
| 790 SYBYLAtomTypes, TPSAAtomTypes, UFFAtomTypes | |
| 791 | |
| 792 Based on the values specified for B<-a, --AtomIdentifierType> and B<--AtomicInvariantsToUse>, | |
| 793 initial atom types are assigned to all non-hydrogen atoms in a molecule. Using the distance | |
| 794 matrix for the molecule and initial atom types assigned to non-hydrogen atoms, all unique atom | |
| 795 pairs within B<--MinDistance> and B<--MaxDistance> are identified and counted. An atom triplet | |
| 796 identifier is generated for each unique atom triplet; the format of the atom triplet identifier is: | |
| 797 | |
| 798 <ATx>-Dyz-<ATy>-Dxz-<ATz>-Dxy | |
| 799 | |
| 800 ATx, ATy, ATz: Atom types assigned to atom x, atom y, and atom z | |
| 801 Dxy: Distance between atom x and atom y | |
| 802 Dxz: Distance between atom x and atom z | |
| 803 Dyz: Distance between atom y and atom z | |
| 804 | |
| 805 where <AT1>-D23 <= <AT2>-D13 <= <AT3>-D12 | |
| 806 | |
| 807 The atom triplet identifiers for all unique atom triplets corresponding to non-hydrogen atoms constitute | |
| 808 topological atom triplets fingerprints of the molecule. | |
| 809 | |
| 810 Example of I<SD> file containing topological atom triplets fingerprints string data: | |
| 811 | |
| 812 ... ... | |
| 813 ... ... | |
| 814 $$$$ | |
| 815 ... ... | |
| 816 ... ... | |
| 817 ... ... | |
| 818 41 44 0 0 0 0 0 0 0 0999 V2000 | |
| 819 -3.3652 1.4499 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 | |
| 820 ... ... | |
| 821 2 3 1 0 0 0 0 | |
| 822 ... ... | |
| 823 M END | |
| 824 > <CmpdID> | |
| 825 Cmpd1 | |
| 826 | |
| 827 > <TopologicalAtomTripletsFingerprints> | |
| 828 FingerprintsVector;TopologicalAtomTriplets:AtomicInvariantsAtomTypes:Mi | |
| 829 nDistance1:MaxDistance10;3096;NumericalValues;IDsAndValuesString;C.X1.B | |
| 830 O1.H3-D1-C.X1.BO1.H3-D1-C.X3.BO3.H1-D2 C.X1.BO1.H3-D1-C.X2.BO2.H2-D10-C | |
| 831 .X3.BO4-D9 C.X1.BO1.H3-D1-C.X2.BO2.H2-D3-N.X3.BO3-D4 C.X1.BO1.H3-D1...; | |
| 832 1 2 2 2 2 2 2 2 8 8 4 8 4 4 2 2 2 2 4 2 2 2 4 2 2 2 2 1 2 2 4 4 4 2 2 2 | |
| 833 4 4 4 8 4 4 2 4 4 4 2 4 4 2 2 2 2 2 2 2 2 1 2 2 2 2 2 2 2 2 2 2 8 8 ... | |
| 834 | |
| 835 $$$$ | |
| 836 ... ... | |
| 837 ... ... | |
| 838 | |
| 839 Example of I<FP> file containing topological atom triplets fingerprints string data: | |
| 840 | |
| 841 # | |
| 842 # Package = MayaChemTools 7.4 | |
| 843 # Release Date = Oct 21, 2010 | |
| 844 # | |
| 845 # TimeStamp = Fri Mar 11 15:24:01 2011 | |
| 846 # | |
| 847 # FingerprintsStringType = FingerprintsVector | |
| 848 # | |
| 849 # Description = TopologicalAtomTriplets:AtomicInvariantsAtomTypes:Mi... | |
| 850 # VectorStringFormat = IDsAndValuesString | |
| 851 # VectorValuesType = NumericalValues | |
| 852 # | |
| 853 Cmpd1 3096;C.X1.BO1.H3-D1-C.X1.BO1.H3-D1-C.X3.BO3.H1-D2...;1 2 2 2 2... | |
| 854 Cmpd2 1093;C.X1.BO1.H3-D1-C.X1.BO1.H3-D3-C.X2.BO2.H2-D4...;2 2 2 2 2... | |
| 855 ... ... | |
| 856 ... .. | |
| 857 | |
| 858 Example of CSV I<Text> file containing topological atom triplets fingerprints string data: | |
| 859 | |
| 860 "CompoundID","TopologicalAtomTripletsFingerprints" | |
| 861 "Cmpd1","FingerprintsVector;TopologicalAtomTriplets:AtomicInvariantsAto | |
| 862 mTypes:MinDistance1:MaxDistance10;3096;NumericalValues;IDsAndValuesStri | |
| 863 ng;C.X1.BO1.H3-D1-C.X1.BO1.H3-D1-C.X3.BO3.H1-D2 C.X1.BO1.H3-D1-C.X2.BO2 | |
| 864 .H2-D10-C.X3.BO4-D9 C.X1.BO1.H3-D1-C.X2.BO2.H2-D3-N.X3.BO3-D4 C.X1....; | |
| 865 1 2 2 2 2 2 2 2 8 8 4 8 4 4 2 2 2 2 4 2 2 2 4 2 2 2 2 1 2 2 4 4 4 2 2 2 | |
| 866 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 8 ... | |
| 867 ... ... | |
| 868 ... ... | |
| 869 | |
| 870 The current release of MayaChemTools generates the following types of topological atom triplets | |
| 871 fingerprints vector strings: | |
| 872 | |
| 873 FingerprintsVector;TopologicalAtomTriplets:AtomicInvariantsAtomTypes:M | |
| 874 inDistance1:MaxDistance10;3096;NumericalValues;IDsAndValuesString;C.X1 | |
| 875 .BO1.H3-D1-C.X1.BO1.H3-D1-C.X3.BO3.H1-D2 C.X1.BO1.H3-D1-C.X2.BO2.H2-D1 | |
| 876 0-C.X3.BO4-D9 C.X1.BO1.H3-D1-C.X2.BO2.H2-D3-N.X3.BO3-D4 C.X1.BO1.H3-D1 | |
| 877 -C.X2.BO2.H2-D4-C.X2.BO2.H2-D5 C.X1.BO1.H3-D1-C.X2.BO2.H2-D6-C.X3....; | |
| 878 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 | |
| 879 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... | |
| 880 | |
| 881 FingerprintsVector;TopologicalAtomTriplets:AtomicInvariantsAtomTypes:M | |
| 882 inDistance1:MaxDistance10;3096;NumericalValues;IDsAndValuesPairsString | |
| 883 ;C.X1.BO1.H3-D1-C.X1.BO1.H3-D1-C.X3.BO3.H1-D2 1 C.X1.BO1.H3-D1-C.X2.BO | |
| 884 2.H2-D10-C.X3.BO4-D9 2 C.X1.BO1.H3-D1-C.X2.BO2.H2-D3-N.X3.BO3-D4 2 C.X | |
| 885 1.BO1.H3-D1-C.X2.BO2.H2-D4-C.X2.BO2.H2-D5 2 C.X1.BO1.H3-D1-C.X2.BO2.H2 | |
| 886 -D6-C.X3.BO3.H1-D5 2 C.X1.BO1.H3-D1-C.X2.BO2.H2-D6-C.X3.BO3.H1-D7 2... | |
| 887 | |
| 888 FingerprintsVector;TopologicalAtomTriplets:DREIDINGAtomTypes:MinDistan | |
| 889 ce1:MaxDistance10;2377;NumericalValues;IDsAndValuesString;C_2-D1-C_2-D | |
| 890 9-C_3-D10 C_2-D1-C_2-D9-C_R-D10 C_2-D1-C_3-D1-C_3-D2 C_2-D1-C_3-D10-C_ | |
| 891 3-D9 C_2-D1-C_3-D2-C_3-D3 C_2-D1-C_3-D2-C_R-D3 C_2-D1-C_3-D3-C_3-D4 C_ | |
| 892 2-D1-C_3-D3-N_R-D4 C_2-D1-C_3-D3-O_3-D2 C_2-D1-C_3-D4-C_3-D5 C_2-D...; | |
| 893 1 1 1 2 1 1 3 1 1 2 2 1 1 1 1 1 1 1 1 2 1 3 4 5 1 1 6 4 2 2 3 1 1 1 2 | |
| 894 2 1 2 1 1 2 2 2 1 2 1 2 1 1 3 3 2 6 4 2 1 1 1 2 2 1 1 1 1 1 1 1 1 1... | |
| 895 | |
| 896 FingerprintsVector;TopologicalAtomTriplets:EStateAtomTypes:MinDistance | |
| 897 1:MaxDistance10;3298;NumericalValues;IDsAndValuesString;aaCH-D1-aaCH-D | |
| 898 1-aaCH-D2 aaCH-D1-aaCH-D1-aasC-D2 aaCH-D1-aaCH-D10-aaCH-D9 aaCH-D1-aaC | |
| 899 H-D10-aasC-D9 aaCH-D1-aaCH-D2-aaCH-D3 aaCH-D1-aaCH-D2-aasC-D1 aaCH-D1- | |
| 900 aaCH-D2-aasC-D3 aaCH-D1-aaCH-D3-aasC-D2 aaCH-D1-aaCH-D4-aasC-D5 aa...; | |
| 901 6 4 24 4 16 8 8 4 8 8 8 12 10 14 4 16 24 4 12 2 2 4 1 10 2 2 15 2 2 2 | |
| 902 2 2 2 14 4 2 2 2 2 1 2 10 2 2 4 1 2 4 8 3 3 3 4 6 4 2 2 3 3 1 1 1 2 1 | |
| 903 2 2 4 2 3 2 1 2 4 5 3 2 2 1 2 4 3 2 8 12 6 2 2 4 4 7 1 4 2 4 2 2 2 ... | |
| 904 | |
| 905 FingerprintsVector;TopologicalAtomTriplets:FunctionalClassAtomTypes:Mi | |
| 906 nDistance1:MaxDistance10;2182;NumericalValues;IDsAndValuesString;Ar-D1 | |
| 907 -Ar-D1-Ar-D2 Ar-D1-Ar-D1-Ar.HBA-D2 Ar-D1-Ar-D10-Ar-D9 Ar-D1-Ar-D10-Hal | |
| 908 -D9 Ar-D1-Ar-D2-Ar-D2 Ar-D1-Ar-D2-Ar-D3 Ar-D1-Ar-D2-Ar.HBA-D1 Ar-D1-Ar | |
| 909 -D2-Ar.HBA-D2 Ar-D1-Ar-D2-Ar.HBA-D3 Ar-D1-Ar-D2-HBD-D1 Ar-D1-Ar-D2...; | |
| 910 27 1 32 2 2 63 3 2 1 2 1 2 3 1 1 40 3 1 2 2 2 2 4 2 2 47 4 2 2 1 2 1 5 | |
| 911 2 2 51 4 3 1 3 1 9 1 1 50 3 3 4 1 9 50 2 2 3 3 5 45 1 1 1 2 1 2 2 3 3 | |
| 912 4 4 3 2 1 1 3 4 5 5 3 1 2 3 2 3 5 7 2 7 3 7 1 1 2 2 2 2 3 1 4 3 1 2... | |
| 913 | |
| 914 FingerprintsVector;TopologicalAtomTriplets:MMFF94AtomTypes:MinDistance | |
| 915 1:MaxDistance10;2966;NumericalValues;IDsAndValuesString;C5A-D1-C5A-D1- | |
| 916 N5-D2 C5A-D1-C5A-D2-C5B-D2 C5A-D1-C5A-D3-CB-D2 C5A-D1-C5A-D3-CR-D2 C5A | |
| 917 -D1-C5B-D1-C5B-D2 C5A-D1-C5B-D2-C=ON-D1 C5A-D1-C5B-D2-CB-D1 C5A-D1-C5B | |
| 918 -D3-C=ON-D2 C5A-D1-C5B-D3-CB-D2 C5A-D1-C=ON-D3-NC=O-D2 C5A-D1-C=ON-D3- | |
| 919 O=CN-D2 C5A-D1-C=ON-D4-NC=O-D3 C5A-D1-C=ON-D4-O=CN-D3 C5A-D1-CB-D1-... | |
| 920 | |
| 921 FingerprintsVector;TopologicalAtomTriplets:SLogPAtomTypes:MinDistance1 | |
| 922 :MaxDistance10;3710;NumericalValues;IDsAndValuesString;C1-D1-C1-D1-C11 | |
| 923 -D2 C1-D1-C1-D1-CS-D2 C1-D1-C1-D10-C5-D9 C1-D1-C1-D3-C10-D2 C1-D1-C1-D | |
| 924 3-C5-D2 C1-D1-C1-D3-CS-D2 C1-D1-C1-D3-CS-D4 C1-D1-C1-D4-C10-D5 C1-D1-C | |
| 925 1-D4-C11-D5 C1-D1-C1-D5-C10-D4 C1-D1-C1-D5-C5-D4 C1-D1-C1-D6-C11-D7 C1 | |
| 926 -D1-C1-D6-CS-D5 C1-D1-C1-D6-CS-D7 C1-D1-C1-D8-C11-D9 C1-D1-C1-D8-CS... | |
| 927 | |
| 928 FingerprintsVector;TopologicalAtomTriplets:SYBYLAtomTypes:MinDistance1 | |
| 929 :MaxDistance10;2332;NumericalValues;IDsAndValuesString;C.2-D1-C.2-D9-C | |
| 930 .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- | |
| 931 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 | |
| 932 -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. | |
| 933 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... | |
| 934 | |
| 935 FingerprintsVector;TopologicalAtomTriplets:TPSAAtomTypes:MinDistance1: | |
| 936 MaxDistance10;1007;NumericalValues;IDsAndValuesString;N21-D1-N7-D3-Non | |
| 937 e-D4 N21-D1-N7-D5-None-D4 N21-D1-None-D1-None-D2 N21-D1-None-D2-None-D | |
| 938 2 N21-D1-None-D2-None-D3 N21-D1-None-D3-None-D4 N21-D1-None-D4-None-D5 | |
| 939 N21-D1-None-D4-O3-D3 N21-D1-None-D4-O4-D3 N21-D1-None-D5-None-D6 N21- | |
| 940 D1-None-D6-None-D7 N21-D1-None-D6-O4-D5 N21-D1-None-D7-None-D8 N21-... | |
| 941 | |
| 942 FingerprintsVector;TopologicalAtomTriplets:UFFAtomTypes:MinDistance1:M | |
| 943 axDistance10;2377;NumericalValues;IDsAndValuesString;C_2-D1-C_2-D9-C_3 | |
| 944 -D10 C_2-D1-C_2-D9-C_R-D10 C_2-D1-C_3-D1-C_3-D2 C_2-D1-C_3-D10-C_3-D9 | |
| 945 C_2-D1-C_3-D2-C_3-D3 C_2-D1-C_3-D2-C_R-D3 C_2-D1-C_3-D3-C_3-D4 C_2-D1- | |
| 946 C_3-D3-N_R-D4 C_2-D1-C_3-D3-O_3-D2 C_2-D1-C_3-D4-C_3-D5 C_2-D1-C_3-D5- | |
| 947 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-C_3-... | |
| 948 | |
| 949 =head1 OPTIONS | |
| 950 | |
| 951 =over 4 | |
| 952 | |
| 953 =item B<--AromaticityModel> I<MDLAromaticityModel | TriposAromaticityModel | MMFFAromaticityModel | ChemAxonBasicAromaticityModel | ChemAxonGeneralAromaticityModel | DaylightAromaticityModel | MayaChemToolsAromaticityModel> | |
| 954 | |
| 955 Specify aromaticity model to use during detection of aromaticity. Possible values in the current | |
| 956 release are: I<MDLAromaticityModel, TriposAromaticityModel, MMFFAromaticityModel, | |
| 957 ChemAxonBasicAromaticityModel, ChemAxonGeneralAromaticityModel, DaylightAromaticityModel | |
| 958 or MayaChemToolsAromaticityModel>. Default value: I<MayaChemToolsAromaticityModel>. | |
| 959 | |
| 960 The supported aromaticity model names along with model specific control parameters | |
| 961 are defined in B<AromaticityModelsData.csv>, which is distributed with the current release | |
| 962 and is available under B<lib/data> directory. B<Molecule.pm> module retrieves data from | |
| 963 this file during class instantiation and makes it available to method B<DetectAromaticity> | |
| 964 for detecting aromaticity corresponding to a specific model. | |
| 965 | |
| 966 =item B<-a, --AtomIdentifierType> I<AtomicInvariantsAtomTypes | DREIDINGAtomTypes | EStateAtomTypes | FunctionalClassAtomTypes | MMFF94AtomTypes | SLogPAtomTypes | SYBYLAtomTypes | TPSAAtomTypes | UFFAtomTypes> | |
| 967 | |
| 968 Specify atom identifier type to use for assignment of initial atom identifier to non-hydrogen | |
| 969 atoms during calculation of topological atom triplets fingerprints. Possible values in the current | |
| 970 release are: I<AtomicInvariantsAtomTypes, DREIDINGAtomTypes, EStateAtomTypes, | |
| 971 FunctionalClassAtomTypes, MMFF94AtomTypes, SLogPAtomTypes, SYBYLAtomTypes, | |
| 972 TPSAAtomTypes, UFFAtomTypes>. Default value: I<AtomicInvariantsAtomTypes>. | |
| 973 | |
| 974 =item B<--AtomicInvariantsToUse> I<"AtomicInvariant,AtomicInvariant..."> | |
| 975 | |
| 976 This value is used during I<AtomicInvariantsAtomTypes> value of B<a, --AtomIdentifierType> | |
| 977 option. It's a list of comma separated valid atomic invariant atom types. | |
| 978 | |
| 979 Possible values for atomic invariants are: I<AS, X, BO, LBO, SB, DB, TB, | |
| 980 H, Ar, RA, FC, MN, SM>. Default value: I<AS,X,BO,H,FC>. | |
| 981 | |
| 982 The atomic invariants abbreviations correspond to: | |
| 983 | |
| 984 AS = Atom symbol corresponding to element symbol | |
| 985 | |
| 986 X<n> = Number of non-hydrogen atom neighbors or heavy atoms | |
| 987 BO<n> = Sum of bond orders to non-hydrogen atom neighbors or heavy atoms | |
| 988 LBO<n> = Largest bond order of non-hydrogen atom neighbors or heavy atoms | |
| 989 SB<n> = Number of single bonds to non-hydrogen atom neighbors or heavy atoms | |
| 990 DB<n> = Number of double bonds to non-hydrogen atom neighbors or heavy atoms | |
| 991 TB<n> = Number of triple bonds to non-hydrogen atom neighbors or heavy atoms | |
| 992 H<n> = Number of implicit and explicit hydrogens for atom | |
| 993 Ar = Aromatic annotation indicating whether atom is aromatic | |
| 994 RA = Ring atom annotation indicating whether atom is a ring | |
| 995 FC<+n/-n> = Formal charge assigned to atom | |
| 996 MN<n> = Mass number indicating isotope other than most abundant isotope | |
| 997 SM<n> = Spin multiplicity of atom. Possible values: 1 (singlet), 2 (doublet) or | |
| 998 3 (triplet) | |
| 999 | |
| 1000 Atom type generated by AtomTypes::AtomicInvariantsAtomTypes class corresponds to: | |
| 1001 | |
| 1002 AS.X<n>.BO<n>.LBO<n>.<SB><n>.<DB><n>.<TB><n>.H<n>.Ar.RA.FC<+n/-n>.MN<n>.SM<n> | |
| 1003 | |
| 1004 Except for AS which is a required atomic invariant in atom types, all other atomic invariants are | |
| 1005 optional. Atom type specification doesn't include atomic invariants with zero or undefined values. | |
| 1006 | |
| 1007 In addition to usage of abbreviations for specifying atomic invariants, the following descriptive words | |
| 1008 are also allowed: | |
| 1009 | |
| 1010 X : NumOfNonHydrogenAtomNeighbors or NumOfHeavyAtomNeighbors | |
| 1011 BO : SumOfBondOrdersToNonHydrogenAtoms or SumOfBondOrdersToHeavyAtoms | |
| 1012 LBO : LargestBondOrderToNonHydrogenAtoms or LargestBondOrderToHeavyAtoms | |
| 1013 SB : NumOfSingleBondsToNonHydrogenAtoms or NumOfSingleBondsToHeavyAtoms | |
| 1014 DB : NumOfDoubleBondsToNonHydrogenAtoms or NumOfDoubleBondsToHeavyAtoms | |
| 1015 TB : NumOfTripleBondsToNonHydrogenAtoms or NumOfTripleBondsToHeavyAtoms | |
| 1016 H : NumOfImplicitAndExplicitHydrogens | |
| 1017 Ar : Aromatic | |
| 1018 RA : RingAtom | |
| 1019 FC : FormalCharge | |
| 1020 MN : MassNumber | |
| 1021 SM : SpinMultiplicity | |
| 1022 | |
| 1023 I<AtomTypes::AtomicInvariantsAtomTypes> module is used to assign atomic invariant | |
| 1024 atom types. | |
| 1025 | |
| 1026 =item B<--FunctionalClassesToUse> I<"FunctionalClass1,FunctionalClass2..."> | |
| 1027 | |
| 1028 This value is used during I<FunctionalClassAtomTypes> value of B<a, --AtomIdentifierType> | |
| 1029 option. It's a list of comma separated valid functional classes. | |
| 1030 | |
| 1031 Possible values for atom functional classes are: I<Ar, CA, H, HBA, HBD, Hal, NI, PI, RA>. | |
| 1032 Default value [ Ref 24 ]: I<HBD,HBA,PI,NI,Ar,Hal>. | |
| 1033 | |
| 1034 The functional class abbreviations correspond to: | |
| 1035 | |
| 1036 HBD: HydrogenBondDonor | |
| 1037 HBA: HydrogenBondAcceptor | |
| 1038 PI : PositivelyIonizable | |
| 1039 NI : NegativelyIonizable | |
| 1040 Ar : Aromatic | |
| 1041 Hal : Halogen | |
| 1042 H : Hydrophobic | |
| 1043 RA : RingAtom | |
| 1044 CA : ChainAtom | |
| 1045 | |
| 1046 Functional class atom type specification for an atom corresponds to: | |
| 1047 | |
| 1048 Ar.CA.H.HBA.HBD.Hal.NI.PI.RA | |
| 1049 | |
| 1050 I<AtomTypes::FunctionalClassAtomTypes> module is used to assign functional class atom | |
| 1051 types. It uses following definitions [ Ref 60-61, Ref 65-66 ]: | |
| 1052 | |
| 1053 HydrogenBondDonor: NH, NH2, OH | |
| 1054 HydrogenBondAcceptor: N[!H], O | |
| 1055 PositivelyIonizable: +, NH2 | |
| 1056 NegativelyIonizable: -, C(=O)OH, S(=O)OH, P(=O)OH | |
| 1057 | |
| 1058 =item B<--CompoundID> I<DataFieldName or LabelPrefixString> | |
| 1059 | |
| 1060 This value is B<--CompoundIDMode> specific and indicates how compound ID is generated. | |
| 1061 | |
| 1062 For I<DataField> value of B<--CompoundIDMode> option, it corresponds to datafield label name | |
| 1063 whose value is used as compound ID; otherwise, it's a prefix string used for generating compound | |
| 1064 IDs like LabelPrefixString<Number>. Default value, I<Cmpd>, generates compound IDs which | |
| 1065 look like Cmpd<Number>. | |
| 1066 | |
| 1067 Examples for I<DataField> value of B<--CompoundIDMode>: | |
| 1068 | |
| 1069 MolID | |
| 1070 ExtReg | |
| 1071 | |
| 1072 Examples for I<LabelPrefix> or I<MolNameOrLabelPrefix> value of B<--CompoundIDMode>: | |
| 1073 | |
| 1074 Compound | |
| 1075 | |
| 1076 The value specified above generates compound IDs which correspond to Compound<Number> | |
| 1077 instead of default value of Cmpd<Number>. | |
| 1078 | |
| 1079 =item B<--CompoundIDLabel> I<text> | |
| 1080 | |
| 1081 Specify compound ID column label for CSV/TSV text file(s) used during I<CompoundID> value | |
| 1082 of B<--DataFieldsMode> option. Default value: I<CompoundID>. | |
| 1083 | |
| 1084 =item B<--CompoundIDMode> I<DataField | MolName | LabelPrefix | MolNameOrLabelPrefix> | |
| 1085 | |
| 1086 Specify how to generate compound IDs and write to FP or CSV/TSV text file(s) along with generated | |
| 1087 fingerprints for I<FP | text | all> values of B<--output> option: use a I<SDFile(s)> datafield value; | |
| 1088 use molname line from I<SDFile(s)>; generate a sequential ID with specific prefix; use combination | |
| 1089 of both MolName and LabelPrefix with usage of LabelPrefix values for empty molname lines. | |
| 1090 | |
| 1091 Possible values: I<DataField | MolName | LabelPrefix | MolNameOrLabelPrefix>. | |
| 1092 Default value: I<LabelPrefix>. | |
| 1093 | |
| 1094 For I<MolNameAndLabelPrefix> value of B<--CompoundIDMode>, molname line in I<SDFile(s)> takes | |
| 1095 precedence over sequential compound IDs generated using I<LabelPrefix> and only empty molname | |
| 1096 values are replaced with sequential compound IDs. | |
| 1097 | |
| 1098 This is only used for I<CompoundID> value of B<--DataFieldsMode> option. | |
| 1099 | |
| 1100 =item B<--DataFields> I<"FieldLabel1,FieldLabel2,..."> | |
| 1101 | |
| 1102 Comma delimited list of I<SDFiles(s)> data fields to extract and write to CSV/TSV text file(s) along | |
| 1103 with generated fingerprints for I<text | all> values of B<--output> option. | |
| 1104 | |
| 1105 This is only used for I<Specify> value of B<--DataFieldsMode> option. | |
| 1106 | |
| 1107 Examples: | |
| 1108 | |
| 1109 Extreg | |
| 1110 MolID,CompoundName | |
| 1111 | |
| 1112 =item B<-d, --DataFieldsMode> I<All | Common | Specify | CompoundID> | |
| 1113 | |
| 1114 Specify how data fields in I<SDFile(s)> are transferred to output CSV/TSV text file(s) along | |
| 1115 with generated fingerprints for I<text | all> values of B<--output> option: transfer all SD | |
| 1116 data field; transfer SD data files common to all compounds; extract specified data fields; | |
| 1117 generate a compound ID using molname line, a compound prefix, or a combination of both. | |
| 1118 Possible values: I<All | Common | specify | CompoundID>. Default value: I<CompoundID>. | |
| 1119 | |
| 1120 =item B<-f, --Filter> I<Yes | No> | |
| 1121 | |
| 1122 Specify whether to check and filter compound data in SDFile(s). Possible values: I<Yes or No>. | |
| 1123 Default value: I<Yes>. | |
| 1124 | |
| 1125 By default, compound data is checked before calculating fingerprints and compounds containing | |
| 1126 atom data corresponding to non-element symbols or no atom data are ignored. | |
| 1127 | |
| 1128 =item B<--FingerprintsLabel> I<text> | |
| 1129 | |
| 1130 SD data label or text file column label to use for fingerprints string in output SD or | |
| 1131 CSV/TSV text file(s) specified by B<--output>. Default value: I<TopologicalAtomTripletsFingerprints>. | |
| 1132 | |
| 1133 =item B<-h, --help> | |
| 1134 | |
| 1135 Print this help message. | |
| 1136 | |
| 1137 =item B<-k, --KeepLargestComponent> I<Yes | No> | |
| 1138 | |
| 1139 Generate fingerprints for only the largest component in molecule. Possible values: | |
| 1140 I<Yes or No>. Default value: I<Yes>. | |
| 1141 | |
| 1142 For molecules containing multiple connected components, fingerprints can be generated | |
| 1143 in two different ways: use all connected components or just the largest connected | |
| 1144 component. By default, all atoms except for the largest connected component are | |
| 1145 deleted before generation of fingerprints. | |
| 1146 | |
| 1147 =item B<--MinDistance> I<number> | |
| 1148 | |
| 1149 Minimum bond distance between atom triplets for generating topological atom triplets. Default value: | |
| 1150 I<1>. Valid values: positive integers and less than B<--MaxDistance>. | |
| 1151 | |
| 1152 =item B<--MaxDistance> I<number> | |
| 1153 | |
| 1154 Maximum bond distance between atom triplets for generating topological atom triplets. Default value: | |
| 1155 I<10>. Valid values: positive integers and greater than B<--MinDistance>. | |
| 1156 | |
| 1157 =item B<--OutDelim> I<comma | tab | semicolon> | |
| 1158 | |
| 1159 Delimiter for output CSV/TSV text file(s). Possible values: I<comma, tab, or semicolon> | |
| 1160 Default value: I<comma> | |
| 1161 | |
| 1162 =item B<--output> I<SD | FP | text | all> | |
| 1163 | |
| 1164 Type of output files to generate. Possible values: I<SD, FP, text, or all>. Default value: I<text>. | |
| 1165 | |
| 1166 =item B<-o, --overwrite> | |
| 1167 | |
| 1168 Overwrite existing files. | |
| 1169 | |
| 1170 =item B<-q, --quote> I<Yes | No> | |
| 1171 | |
| 1172 Put quote around column values in output CSV/TSV text file(s). Possible values: | |
| 1173 I<Yes or No>. Default value: I<Yes>. | |
| 1174 | |
| 1175 =item B<-r, --root> I<RootName> | |
| 1176 | |
| 1177 New file name is generated using the root: <Root>.<Ext>. Default for new file names: | |
| 1178 <SDFileName><TopologicalAtomTripletsFP>.<Ext>. The file type determines <Ext> value. | |
| 1179 The sdf, fpf, csv, and tsv <Ext> values are used for SD, FP, comma/semicolon, and tab | |
| 1180 delimited text files, respectively.This option is ignored for multiple input files. | |
| 1181 | |
| 1182 =item B<-u, --UseTriangleInequality> I<Yes | No> | |
| 1183 | |
| 1184 Specify whether to imply triangle distance inequality test to distances between atom pairs in | |
| 1185 atom triplets during generation of atom triplets generation. Possible values: I<Yes or No>. | |
| 1186 Default value: I<No>. | |
| 1187 | |
| 1188 Triangle distance inequality test implies that distance or binned distance between any two atom | |
| 1189 pairs in an atom triplet must be less than the sum of distances or binned distances between other | |
| 1190 two atoms pairs and greater than the difference of their distances. | |
| 1191 | |
| 1192 For atom triplet ATx-Dyz-ATy-Dxz-ATz-Dxy to satisfy triangle inequality: | |
| 1193 | |
| 1194 Dyz > |Dxz - Dxy| and Dyz < Dxz + Dxy | |
| 1195 Dxz > |Dyz - Dxy| and Dyz < Dyz + Dxy | |
| 1196 Dxy > |Dyz - Dxz| and Dxy < Dyz + Dxz | |
| 1197 | |
| 1198 =item B<-v, --VectorStringFormat> I<IDsAndValuesString | IDsAndValuesPairsString | ValuesAndIDsString | ValuesAndIDsPairsString> | |
| 1199 | |
| 1200 Format of fingerprints vector string data in output SD, FP or CSV/TSV text file(s) specified by | |
| 1201 B<--output> option. Possible values: I<IDsAndValuesString | IDsAndValuesPairsString | ValuesAndIDsString | | |
| 1202 ValuesAndIDsPairsString>. Default value: I<IDsAndValuesString>. | |
| 1203 | |
| 1204 Examples: | |
| 1205 | |
| 1206 | |
| 1207 FingerprintsVector;TopologicalAtomTriplets:AtomicInvariantsAtomTypes:M | |
| 1208 inDistance1:MaxDistance10;3096;NumericalValues;IDsAndValuesString;C.X1 | |
| 1209 .BO1.H3-D1-C.X1.BO1.H3-D1-C.X3.BO3.H1-D2 C.X1.BO1.H3-D1-C.X2.BO2.H2-D1 | |
| 1210 0-C.X3.BO4-D9 C.X1.BO1.H3-D1-C.X2.BO2.H2-D3-N.X3.BO3-D4 C.X1.BO1.H3-D1 | |
| 1211 -C.X2.BO2.H2-D4-C.X2.BO2.H2-D5 C.X1.BO1.H3-D1-C.X2.BO2.H2-D6-C.X3....; | |
| 1212 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 | |
| 1213 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... | |
| 1214 | |
| 1215 FingerprintsVector;TopologicalAtomTriplets:AtomicInvariantsAtomTypes:M | |
| 1216 inDistance1:MaxDistance10;3096;NumericalValues;IDsAndValuesPairsString | |
| 1217 ;C.X1.BO1.H3-D1-C.X1.BO1.H3-D1-C.X3.BO3.H1-D2 1 C.X1.BO1.H3-D1-C.X2.BO | |
| 1218 2.H2-D10-C.X3.BO4-D9 2 C.X1.BO1.H3-D1-C.X2.BO2.H2-D3-N.X3.BO3-D4 2 C.X | |
| 1219 1.BO1.H3-D1-C.X2.BO2.H2-D4-C.X2.BO2.H2-D5 2 C.X1.BO1.H3-D1-C.X2.BO2.H2 | |
| 1220 -D6-C.X3.BO3.H1-D5 2 C.X1.BO1.H3-D1-C.X2.BO2.H2-D6-C.X3.BO3.H1-D7 2... | |
| 1221 | |
| 1222 =item B<-w, --WorkingDir> I<DirName> | |
| 1223 | |
| 1224 Location of working directory. Default value: current directory. | |
| 1225 | |
| 1226 =back | |
| 1227 | |
| 1228 =head1 EXAMPLES | |
| 1229 | |
| 1230 To generate topological atom triplets fingerprints corresponding to bond distances from 1 through | |
| 1231 10 using atomic invariants atom types in IDsAndValuesString format and create a SampleTATFP.csv | |
| 1232 file containing sequential compound IDs along with fingerprints vector strings data, type: | |
| 1233 | |
| 1234 % TopologicalAtomTripletsFingerprints.pl -r SampleTATFP -o Sample.sdf | |
| 1235 | |
| 1236 To generate topological atom triplets fingerprints corresponding to bond distances from 1 through | |
| 1237 10 using atomic invariants atom types in IDsAndValuesString format and create SampleTATFP.sdf, | |
| 1238 SampleTATFP.fpf and SampleTATFP.csv files containing sequential compound IDs in CSV file along | |
| 1239 with fingerprints vector strings data, type: | |
| 1240 | |
| 1241 % TopologicalAtomTripletsFingerprints.pl --output all -r SampleTATFP | |
| 1242 -o Sample.sdf | |
| 1243 | |
| 1244 To generate topological atom triplets fingerprints corresponding to bond distances from 1 through | |
| 1245 10 using atomic invariants atom types in IDsAndValuesPairsString format and create a SampleTATFP.csv | |
| 1246 file containing sequential compound IDs along with fingerprints vector strings data, type: | |
| 1247 | |
| 1248 % TopologicalAtomTripletsFingerprints.pl --VectorStringFormat | |
| 1249 IDsAndValuesPairsString -r SampleTATFP -o Sample.sdf | |
| 1250 | |
| 1251 To generate topological atom triplets fingerprints corresponding to bond distances from 1 through | |
| 1252 10 using DREIDING atom types in IDsAndValuesString format and create a SampleTATFP.csv | |
| 1253 file containing sequential compound IDs along with fingerprints vector strings data, type: | |
| 1254 | |
| 1255 % TopologicalAtomTripletsFingerprints.pl -a DREIDINGAtomTypes | |
| 1256 -r SampleTATFP -o Sample.sdf | |
| 1257 | |
| 1258 To generate topological atom triplets fingerprints corresponding to bond distances from 1 through | |
| 1259 10 using E-state atom types in IDsAndValuesString format and create a SampleTATFP.csv | |
| 1260 file containing sequential compound IDs along with fingerprints vector strings data, type: | |
| 1261 | |
| 1262 % TopologicalAtomTripletsFingerprints.pl -a EStateAtomTypes | |
| 1263 -r SampleTATFP -o Sample.sdf | |
| 1264 | |
| 1265 To generate topological atom triplets fingerprints corresponding to bond distances from 1 through | |
| 1266 10 using functional class atom types in IDsAndValuesString format and create a SampleTATFP.csv | |
| 1267 file containing sequential compound IDs along with fingerprints vector strings data, type: | |
| 1268 | |
| 1269 % TopologicalAtomTripletsFingerprints.pl -a FunctionalClassAtomTypes | |
| 1270 -r SampleTATFP -o Sample.sdf | |
| 1271 | |
| 1272 To generate topological atom triplets fingerprints corresponding to bond distances from 1 through | |
| 1273 10 using DREIDING atom types in IDsAndValuesString format and create a SampleTATFP.csv | |
| 1274 file containing sequential compound IDs along with fingerprints vector strings data, type: | |
| 1275 | |
| 1276 % TopologicalAtomTripletsFingerprints.pl -a DREIDINGAtomTypes | |
| 1277 -r SampleTATFP -o Sample.sdf | |
| 1278 | |
| 1279 To generate topological atom triplets fingerprints corresponding to bond distances from 1 through | |
| 1280 10 using MM94 atom types in IDsAndValuesString format and create a SampleTATFP.csv | |
| 1281 file containing sequential compound IDs along with fingerprints vector strings data, type: | |
| 1282 | |
| 1283 % TopologicalAtomTripletsFingerprints.pl -a MMFF94AtomTypes | |
| 1284 -r SampleTATFP -o Sample.sdf | |
| 1285 | |
| 1286 To generate topological atom triplets fingerprints corresponding to bond distances from 1 through | |
| 1287 10 using SLogP atom types in IDsAndValuesString format and create a SampleTATFP.csv | |
| 1288 file containing sequential compound IDs along with fingerprints vector strings data, type: | |
| 1289 | |
| 1290 % TopologicalAtomTripletsFingerprints.pl -a SLogPAtomTypes | |
| 1291 -r SampleTATFP -o Sample.sdf | |
| 1292 | |
| 1293 To generate topological atom triplets fingerprints corresponding to bond distances from 1 through | |
| 1294 10 using SYBYL atom types in IDsAndValuesString format and create a SampleTATFP.csv | |
| 1295 file containing sequential compound IDs along with fingerprints vector strings data, type: | |
| 1296 | |
| 1297 % TopologicalAtomTripletsFingerprints.pl -a SYBYLAtomTypes | |
| 1298 -r SampleTATFP -o Sample.sdf | |
| 1299 | |
| 1300 To generate topological atom triplets fingerprints corresponding to bond distances from 1 through | |
| 1301 10 using TPSA atom types in IDsAndValuesString format and create a SampleTATFP.csv | |
| 1302 file containing sequential compound IDs along with fingerprints vector strings data, type: | |
| 1303 | |
| 1304 % TopologicalAtomTripletsFingerprints.pl -a TPSAAtomTypes | |
| 1305 -r SampleTATFP -o Sample.sdf | |
| 1306 | |
| 1307 To generate topological atom triplets fingerprints corresponding to bond distances from 1 through | |
| 1308 10 using UFF atom types in IDsAndValuesString format and create a SampleTATFP.csv | |
| 1309 file containing sequential compound IDs along with fingerprints vector strings data, type: | |
| 1310 | |
| 1311 % TopologicalAtomTripletsFingerprints.pl -a UFFAtomTypes | |
| 1312 -r SampleTATFP -o Sample.sdf | |
| 1313 | |
| 1314 To generate topological atom triplets fingerprints corresponding to bond distances from 1 through | |
| 1315 6 using atomic invariants atom types in IDsAndValuesString format and create a SampleTATFP.csv | |
| 1316 file containing sequential compound IDs along with fingerprints vector strings data, type: | |
| 1317 | |
| 1318 % TopologicalAtomTripletsFingerprints.pl -a AtomicInvariantsAtomTypes | |
| 1319 --MinDistance 1 --MaxDistance 6 -r SampleTATFP -o Sample.sdf | |
| 1320 | |
| 1321 To generate topological atom triplets fingerprints corresponding to bond distances from 1 through | |
| 1322 10 using only AS,X atomic invariants atom types in IDsAndValuesString format and create a | |
| 1323 SampleTATFP.csv file containing sequential compound IDs along with fingerprints vector strings | |
| 1324 data, type: | |
| 1325 | |
| 1326 % TopologicalAtomTripletsFingerprints.pl -a AtomicInvariantsAtomTypes | |
| 1327 --AtomicInvariantsToUse "AS,X" --MinDistance 1 --MaxDistance 6 | |
| 1328 -r SampleTATFP -o Sample.sdf | |
| 1329 | |
| 1330 To generate topological atom triplets fingerprints corresponding to bond distances from 1 through | |
| 1331 10 using atomic invariants atom types in IDsAndValuesString format and create a SampleTATFP.csv | |
| 1332 file containing compound ID from molecule name line along with fingerprints vector strings | |
| 1333 data, type: | |
| 1334 | |
| 1335 % TopologicalAtomTripletsFingerprints.pl -a AtomicInvariantsAtomTypes | |
| 1336 --DataFieldsMode CompoundID -CompoundIDMode MolName | |
| 1337 -r SampleTATFP -o Sample.sdf | |
| 1338 | |
| 1339 To generate topological atom triplets fingerprints corresponding to bond distances from 1 through | |
| 1340 10 using atomic invariants atom types in IDsAndValuesString format and create a SampleTATFP.csv | |
| 1341 file containing compound IDs using specified data field along with fingerprints vector strings | |
| 1342 data, type: | |
| 1343 | |
| 1344 % TopologicalAtomTripletsFingerprints.pl -a AtomicInvariantsAtomTypes | |
| 1345 --DataFieldsMode CompoundID -CompoundIDMode DataField --CompoundID | |
| 1346 Mol_ID -r SampleTATFP -o Sample.sdf | |
| 1347 | |
| 1348 To generate topological atom triplets fingerprints corresponding to bond distances from 1 through | |
| 1349 10 using atomic invariants atom types in IDsAndValuesString format and create a SampleTATFP.csv | |
| 1350 file containing compound ID using combination of molecule name line and an explicit compound | |
| 1351 prefix along with fingerprints vector strings data, type: | |
| 1352 | |
| 1353 % TopologicalAtomTripletsFingerprints.pl -a AtomicInvariantsAtomTypes | |
| 1354 --DataFieldsMode CompoundID -CompoundIDMode MolnameOrLabelPrefix | |
| 1355 --CompoundID Cmpd --CompoundIDLabel MolID -r SampleTATFP -o Sample.sdf | |
| 1356 | |
| 1357 To generate topological atom triplets fingerprints corresponding to bond distances from 1 through | |
| 1358 10 using atomic invariants atom types in IDsAndValuesString format and create a SampleTATFP.csv | |
| 1359 file containing specific data fields columns along with fingerprints vector strings | |
| 1360 data, type: | |
| 1361 | |
| 1362 % TopologicalAtomTripletsFingerprints.pl -a AtomicInvariantsAtomTypes | |
| 1363 --DataFieldsMode Specify --DataFields Mol_ID -r SampleTATFP | |
| 1364 -o Sample.sdf | |
| 1365 | |
| 1366 To generate topological atom triplets fingerprints corresponding to bond distances from 1 through | |
| 1367 10 using atomic invariants atom types in IDsAndValuesString format and create a SampleTATFP.csv | |
| 1368 file containing common data fields columns along with fingerprints vector strings | |
| 1369 data, type: | |
| 1370 | |
| 1371 % TopologicalAtomTripletsFingerprints.pl -a AtomicInvariantsAtomTypes | |
| 1372 --DataFieldsMode Common -r SampleTATFP -o Sample.sdf | |
| 1373 | |
| 1374 To generate topological atom triplets fingerprints corresponding to bond distances from 1 through | |
| 1375 10 using atomic invariants atom types in IDsAndValuesString format and create SampleTATFP.sdf, | |
| 1376 SampleTATFP.fpf and SampleTATFP.csv files containing all data fields columns in CSV file along with | |
| 1377 fingerprints data, type: | |
| 1378 | |
| 1379 % TopologicalAtomTripletsFingerprints.pl -a AtomicInvariantsAtomTypes | |
| 1380 --DataFieldsMode All --output all -r SampleTATFP | |
| 1381 -o Sample.sdf | |
| 1382 | |
| 1383 =head1 AUTHOR | |
| 1384 | |
| 1385 Manish Sud <msud@san.rr.com> | |
| 1386 | |
| 1387 =head1 SEE ALSO | |
| 1388 | |
| 1389 InfoFingerprintsFiles.pl, SimilarityMatricesFingerprints.pl, AtomNeighborhoodsFingerprints.pl, | |
| 1390 ExtendedConnectivityFingerprints.pl, MACCSKeysFingerprints.pl, | |
| 1391 PathLengthFingerprints.pl, TopologicalAtomTorsionsFingerprints.pl, | |
| 1392 TopologicalPharmacophoreAtomPairsFingerprints.pl, TopologicalPharmacophoreAtomTripletsFingerprints.pl | |
| 1393 | |
| 1394 =head1 COPYRIGHT | |
| 1395 | |
| 1396 Copyright (C) 2015 Manish Sud. All rights reserved. | |
| 1397 | |
| 1398 This file is part of MayaChemTools. | |
| 1399 | |
| 1400 MayaChemTools is free software; you can redistribute it and/or modify it under | |
| 1401 the terms of the GNU Lesser General Public License as published by the Free | |
| 1402 Software Foundation; either version 3 of the License, or (at your option) | |
| 1403 any later version. | |
| 1404 | |
| 1405 =cut |