Mercurial > repos > deepakjadmin > mayatool3_test3
comparison mayachemtools/bin/MACCSKeysFingerprints.pl @ 0:73ae111cf86f draft
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| author | deepakjadmin |
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| date | Wed, 20 Jan 2016 11:55:01 -0500 |
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| -1:000000000000 | 0:73ae111cf86f |
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| 1 #!/usr/bin/perl -w | |
| 2 # | |
| 3 # $RCSfile: MACCSKeysFingerprints.pl,v $ | |
| 4 # $Date: 2015/02/28 20:46:20 $ | |
| 5 # $Revision: 1.31 $ | |
| 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 "$FindBin::Bin/../lib"; | |
| 31 use Getopt::Long; | |
| 32 use File::Basename; | |
| 33 use Text::ParseWords; | |
| 34 use Benchmark; | |
| 35 use FileUtil; | |
| 36 use TextUtil; | |
| 37 use SDFileUtil; | |
| 38 use MoleculeFileIO; | |
| 39 use FileIO::FingerprintsSDFileIO; | |
| 40 use FileIO::FingerprintsTextFileIO; | |
| 41 use FileIO::FingerprintsFPFileIO; | |
| 42 use Fingerprints::MACCSKeys; | |
| 43 | |
| 44 my($ScriptName, %Options, $StartTime, $EndTime, $TotalTime); | |
| 45 | |
| 46 # Autoflush STDOUT | |
| 47 $| = 1; | |
| 48 | |
| 49 # Starting message... | |
| 50 $ScriptName = basename($0); | |
| 51 print "\n$ScriptName: Starting...\n\n"; | |
| 52 $StartTime = new Benchmark; | |
| 53 | |
| 54 # Get the options and setup script... | |
| 55 SetupScriptUsage(); | |
| 56 if ($Options{help} || @ARGV < 1) { | |
| 57 die GetUsageFromPod("$FindBin::Bin/$ScriptName"); | |
| 58 } | |
| 59 | |
| 60 my(@SDFilesList); | |
| 61 @SDFilesList = ExpandFileNames(\@ARGV, "sdf sd"); | |
| 62 | |
| 63 # Process options... | |
| 64 print "Processing options...\n"; | |
| 65 my(%OptionsInfo); | |
| 66 ProcessOptions(); | |
| 67 | |
| 68 # Setup information about input files... | |
| 69 print "Checking input SD file(s)...\n"; | |
| 70 my(%SDFilesInfo); | |
| 71 RetrieveSDFilesInfo(); | |
| 72 | |
| 73 # Process input files.. | |
| 74 my($FileIndex); | |
| 75 if (@SDFilesList > 1) { | |
| 76 print "\nProcessing SD files...\n"; | |
| 77 } | |
| 78 for $FileIndex (0 .. $#SDFilesList) { | |
| 79 if ($SDFilesInfo{FileOkay}[$FileIndex]) { | |
| 80 print "\nProcessing file $SDFilesList[$FileIndex]...\n"; | |
| 81 GenerateMACCSKeysFingerprints($FileIndex); | |
| 82 } | |
| 83 } | |
| 84 print "\n$ScriptName:Done...\n\n"; | |
| 85 | |
| 86 $EndTime = new Benchmark; | |
| 87 $TotalTime = timediff ($EndTime, $StartTime); | |
| 88 print "Total time: ", timestr($TotalTime), "\n"; | |
| 89 | |
| 90 ############################################################################### | |
| 91 | |
| 92 # Generate fingerprints for a SD file... | |
| 93 # | |
| 94 sub GenerateMACCSKeysFingerprints { | |
| 95 my($FileIndex) = @_; | |
| 96 my($CmpdCount, $IgnoredCmpdCount, $SDFile, $MoleculeFileIO, $Molecule, $MACCSKeysFingerprints, $NewFPSDFileIO, $NewFPTextFileIO, $NewFPFileIO); | |
| 97 | |
| 98 $SDFile = $SDFilesList[$FileIndex]; | |
| 99 | |
| 100 # Setup output files... | |
| 101 # | |
| 102 ($NewFPSDFileIO, $NewFPTextFileIO, $NewFPFileIO) = SetupAndOpenOutputFiles($FileIndex); | |
| 103 | |
| 104 $MoleculeFileIO = new MoleculeFileIO('Name' => $SDFile); | |
| 105 $MoleculeFileIO->Open(); | |
| 106 | |
| 107 $CmpdCount = 0; | |
| 108 $IgnoredCmpdCount = 0; | |
| 109 | |
| 110 COMPOUND: while ($Molecule = $MoleculeFileIO->ReadMolecule()) { | |
| 111 $CmpdCount++; | |
| 112 | |
| 113 # Filter compound data before calculating fingerprints... | |
| 114 if ($OptionsInfo{Filter}) { | |
| 115 if (CheckAndFilterCompound($CmpdCount, $Molecule)) { | |
| 116 $IgnoredCmpdCount++; | |
| 117 next COMPOUND; | |
| 118 } | |
| 119 } | |
| 120 | |
| 121 $MACCSKeysFingerprints = GenerateMoleculeFingerprints($Molecule); | |
| 122 if (!$MACCSKeysFingerprints) { | |
| 123 $IgnoredCmpdCount++; | |
| 124 ProcessIgnoredCompound('FingerprintsGenerationFailed', $CmpdCount, $Molecule); | |
| 125 next COMPOUND; | |
| 126 } | |
| 127 | |
| 128 WriteDataToOutputFiles($FileIndex, $CmpdCount, $Molecule, $MACCSKeysFingerprints, $NewFPSDFileIO, $NewFPTextFileIO, $NewFPFileIO); | |
| 129 } | |
| 130 $MoleculeFileIO->Close(); | |
| 131 | |
| 132 if ($NewFPSDFileIO) { | |
| 133 $NewFPSDFileIO->Close(); | |
| 134 } | |
| 135 if ($NewFPTextFileIO) { | |
| 136 $NewFPTextFileIO->Close(); | |
| 137 } | |
| 138 if ($NewFPFileIO) { | |
| 139 $NewFPFileIO->Close(); | |
| 140 } | |
| 141 | |
| 142 WriteFingerprintsGenerationSummaryStatistics($CmpdCount, $IgnoredCmpdCount); | |
| 143 } | |
| 144 | |
| 145 # Process compound being ignored due to problems in fingerprints geneation... | |
| 146 # | |
| 147 sub ProcessIgnoredCompound { | |
| 148 my($Mode, $CmpdCount, $Molecule) = @_; | |
| 149 my($CmpdID, $DataFieldLabelAndValuesRef); | |
| 150 | |
| 151 $DataFieldLabelAndValuesRef = $Molecule->GetDataFieldLabelAndValues(); | |
| 152 $CmpdID = SetupCmpdIDForOutputFiles($CmpdCount, $Molecule, $DataFieldLabelAndValuesRef); | |
| 153 | |
| 154 MODE: { | |
| 155 if ($Mode =~ /^ContainsNonElementalData$/i) { | |
| 156 warn "\nWarning: Ignoring compound record number $CmpdCount with ID $CmpdID: Compound contains atom data corresponding to non-elemental atom symbol(s)...\n\n"; | |
| 157 next MODE; | |
| 158 } | |
| 159 | |
| 160 if ($Mode =~ /^ContainsNoElementalData$/i) { | |
| 161 warn "\nWarning: Ignoring compound record number $CmpdCount with ID $CmpdID: Compound contains no atom data...\n\n"; | |
| 162 next MODE; | |
| 163 } | |
| 164 | |
| 165 if ($Mode =~ /^FingerprintsGenerationFailed$/i) { | |
| 166 warn "\nWarning: Ignoring compound record number $CmpdCount with ID $CmpdID: Fingerprints generation didn't succeed...\n\n"; | |
| 167 next MODE; | |
| 168 } | |
| 169 warn "\nWarning: Ignoring compound record number $CmpdCount with ID $CmpdID: Fingerprints generation didn't succeed...\n\n"; | |
| 170 } | |
| 171 } | |
| 172 | |
| 173 # Check and filter compounds.... | |
| 174 # | |
| 175 sub CheckAndFilterCompound { | |
| 176 my($CmpdCount, $Molecule) = @_; | |
| 177 my($ElementCount, $NonElementCount); | |
| 178 | |
| 179 ($ElementCount, $NonElementCount) = $Molecule->GetNumOfElementsAndNonElements(); | |
| 180 | |
| 181 if ($NonElementCount) { | |
| 182 ProcessIgnoredCompound('ContainsNonElementalData', $CmpdCount, $Molecule); | |
| 183 return 1; | |
| 184 } | |
| 185 | |
| 186 if (!$ElementCount) { | |
| 187 ProcessIgnoredCompound('ContainsNoElementalData', $CmpdCount, $Molecule); | |
| 188 return 1; | |
| 189 } | |
| 190 | |
| 191 return 0; | |
| 192 } | |
| 193 | |
| 194 # Write out compounds fingerprints generation summary statistics... | |
| 195 # | |
| 196 sub WriteFingerprintsGenerationSummaryStatistics { | |
| 197 my($CmpdCount, $IgnoredCmpdCount) = @_; | |
| 198 my($ProcessedCmpdCount); | |
| 199 | |
| 200 $ProcessedCmpdCount = $CmpdCount - $IgnoredCmpdCount; | |
| 201 | |
| 202 print "\nNumber of compounds: $CmpdCount\n"; | |
| 203 print "Number of compounds processed successfully during fingerprints generation: $ProcessedCmpdCount\n"; | |
| 204 print "Number of compounds ignored during fingerprints generation: $IgnoredCmpdCount\n"; | |
| 205 } | |
| 206 | |
| 207 # Open output files... | |
| 208 # | |
| 209 sub SetupAndOpenOutputFiles { | |
| 210 my($FileIndex) = @_; | |
| 211 my($NewFPSDFile, $NewFPFile, $NewFPTextFile, $NewFPSDFileIO, $NewFPTextFileIO, $NewFPFileIO, %FingerprintsFileIOParams); | |
| 212 | |
| 213 ($NewFPSDFileIO, $NewFPTextFileIO, $NewFPFileIO) = (undef) x 3; | |
| 214 | |
| 215 # Setup common parameters for fingerprints file IO objects... | |
| 216 # | |
| 217 %FingerprintsFileIOParams = (); | |
| 218 if ($OptionsInfo{Mode} =~ /^MACCSKeyBits$/i) { | |
| 219 %FingerprintsFileIOParams = ('Mode' => 'Write', 'Overwrite' => $OptionsInfo{OverwriteFiles}, 'FingerprintsStringMode' => 'FingerprintsBitVectorString', 'BitStringFormat' => $OptionsInfo{BitStringFormat}, 'BitsOrder' => $OptionsInfo{BitsOrder}); | |
| 220 } | |
| 221 elsif ($OptionsInfo{Mode} =~ /^MACCSKeyCount$/i) { | |
| 222 %FingerprintsFileIOParams = ('Mode' => 'Write', 'Overwrite' => $OptionsInfo{OverwriteFiles}, 'FingerprintsStringMode' => 'FingerprintsVectorString', 'VectorStringFormat' => $OptionsInfo{VectorStringFormat}); | |
| 223 } | |
| 224 | |
| 225 if ($OptionsInfo{SDOutput}) { | |
| 226 $NewFPSDFile = $SDFilesInfo{SDOutFileNames}[$FileIndex]; | |
| 227 print "Generating SD file $NewFPSDFile...\n"; | |
| 228 $NewFPSDFileIO = new FileIO::FingerprintsSDFileIO('Name' => $NewFPSDFile, %FingerprintsFileIOParams, 'FingerprintsFieldLabel' => $OptionsInfo{FingerprintsLabel}); | |
| 229 $NewFPSDFileIO->Open(); | |
| 230 } | |
| 231 | |
| 232 if ($OptionsInfo{FPOutput}) { | |
| 233 $NewFPFile = $SDFilesInfo{FPOutFileNames}[$FileIndex]; | |
| 234 print "Generating FP file $NewFPFile...\n"; | |
| 235 $NewFPFileIO = new FileIO::FingerprintsFPFileIO('Name' => $NewFPFile, %FingerprintsFileIOParams); | |
| 236 $NewFPFileIO->Open(); | |
| 237 } | |
| 238 | |
| 239 if ($OptionsInfo{TextOutput}) { | |
| 240 my($ColLabelsRef); | |
| 241 | |
| 242 $NewFPTextFile = $SDFilesInfo{TextOutFileNames}[$FileIndex]; | |
| 243 $ColLabelsRef = SetupFPTextFileCoulmnLabels($FileIndex); | |
| 244 | |
| 245 print "Generating text file $NewFPTextFile...\n"; | |
| 246 $NewFPTextFileIO = new FileIO::FingerprintsTextFileIO('Name' => $NewFPTextFile, %FingerprintsFileIOParams, 'DataColLabels' => $ColLabelsRef, 'OutDelim' => $OptionsInfo{OutDelim}, 'OutQuote' => $OptionsInfo{OutQuote}); | |
| 247 $NewFPTextFileIO->Open(); | |
| 248 } | |
| 249 | |
| 250 return ($NewFPSDFileIO, $NewFPTextFileIO, $NewFPFileIO); | |
| 251 } | |
| 252 | |
| 253 # Write fingerpritns and other data to appropriate output files... | |
| 254 # | |
| 255 sub WriteDataToOutputFiles { | |
| 256 my($FileIndex, $CmpdCount, $Molecule, $MACCSKeysFingerprints, $NewFPSDFileIO, $NewFPTextFileIO, $NewFPFileIO) = @_; | |
| 257 my($DataFieldLabelAndValuesRef); | |
| 258 | |
| 259 $DataFieldLabelAndValuesRef = undef; | |
| 260 if ($NewFPTextFileIO || $NewFPFileIO) { | |
| 261 $DataFieldLabelAndValuesRef = $Molecule->GetDataFieldLabelAndValues(); | |
| 262 } | |
| 263 | |
| 264 if ($NewFPSDFileIO) { | |
| 265 my($CmpdString); | |
| 266 | |
| 267 $CmpdString = $Molecule->GetInputMoleculeString(); | |
| 268 $NewFPSDFileIO->WriteFingerprints($MACCSKeysFingerprints, $CmpdString); | |
| 269 } | |
| 270 | |
| 271 if ($NewFPTextFileIO) { | |
| 272 my($ColValuesRef); | |
| 273 | |
| 274 $ColValuesRef = SetupFPTextFileCoulmnValues($FileIndex, $CmpdCount, $Molecule, $DataFieldLabelAndValuesRef); | |
| 275 $NewFPTextFileIO->WriteFingerprints($MACCSKeysFingerprints, $ColValuesRef); | |
| 276 } | |
| 277 | |
| 278 if ($NewFPFileIO) { | |
| 279 my($CompoundID); | |
| 280 | |
| 281 $CompoundID = SetupCmpdIDForOutputFiles($CmpdCount, $Molecule, $DataFieldLabelAndValuesRef); | |
| 282 $NewFPFileIO->WriteFingerprints($MACCSKeysFingerprints, $CompoundID); | |
| 283 } | |
| 284 } | |
| 285 | |
| 286 # Generate approriate column labels for FPText output file... | |
| 287 # | |
| 288 sub SetupFPTextFileCoulmnLabels { | |
| 289 my($FileIndex) = @_; | |
| 290 my($Line, @ColLabels); | |
| 291 | |
| 292 @ColLabels = (); | |
| 293 if ($OptionsInfo{DataFieldsMode} =~ /^All$/i) { | |
| 294 push @ColLabels, @{$SDFilesInfo{AllDataFieldsRef}[$FileIndex]}; | |
| 295 } | |
| 296 elsif ($OptionsInfo{DataFieldsMode} =~ /^Common$/i) { | |
| 297 push @ColLabels, @{$SDFilesInfo{CommonDataFieldsRef}[$FileIndex]}; | |
| 298 } | |
| 299 elsif ($OptionsInfo{DataFieldsMode} =~ /^Specify$/i) { | |
| 300 push @ColLabels, @{$OptionsInfo{SpecifiedDataFields}}; | |
| 301 } | |
| 302 elsif ($OptionsInfo{DataFieldsMode} =~ /^CompoundID$/i) { | |
| 303 push @ColLabels, $OptionsInfo{CompoundIDLabel}; | |
| 304 } | |
| 305 # Add fingerprints label... | |
| 306 push @ColLabels, $OptionsInfo{FingerprintsLabel}; | |
| 307 | |
| 308 return \@ColLabels; | |
| 309 } | |
| 310 | |
| 311 # Generate column values FPText output file.. | |
| 312 # | |
| 313 sub SetupFPTextFileCoulmnValues { | |
| 314 my($FileIndex, $CmpdCount, $Molecule, $DataFieldLabelAndValuesRef) = @_; | |
| 315 my(@ColValues); | |
| 316 | |
| 317 @ColValues = (); | |
| 318 if ($OptionsInfo{DataFieldsMode} =~ /^CompoundID$/i) { | |
| 319 push @ColValues, SetupCmpdIDForOutputFiles($CmpdCount, $Molecule, $DataFieldLabelAndValuesRef); | |
| 320 } | |
| 321 elsif ($OptionsInfo{DataFieldsMode} =~ /^All$/i) { | |
| 322 @ColValues = map { exists $DataFieldLabelAndValuesRef->{$_} ? $DataFieldLabelAndValuesRef->{$_} : ''} @{$SDFilesInfo{AllDataFieldsRef}[$FileIndex]}; | |
| 323 } | |
| 324 elsif ($OptionsInfo{DataFieldsMode} =~ /^Common$/i) { | |
| 325 @ColValues = map { exists $DataFieldLabelAndValuesRef->{$_} ? $DataFieldLabelAndValuesRef->{$_} : ''} @{$SDFilesInfo{CommonDataFieldsRef}[$FileIndex]}; | |
| 326 } | |
| 327 elsif ($OptionsInfo{DataFieldsMode} =~ /^Specify$/i) { | |
| 328 @ColValues = map { exists $DataFieldLabelAndValuesRef->{$_} ? $DataFieldLabelAndValuesRef->{$_} : ''} @{$OptionsInfo{SpecifiedDataFields}}; | |
| 329 } | |
| 330 | |
| 331 return \@ColValues; | |
| 332 } | |
| 333 | |
| 334 # Generate compound ID for FP and FPText output files.. | |
| 335 # | |
| 336 sub SetupCmpdIDForOutputFiles { | |
| 337 my($CmpdCount, $Molecule, $DataFieldLabelAndValuesRef) = @_; | |
| 338 my($CmpdID); | |
| 339 | |
| 340 $CmpdID = ''; | |
| 341 if ($OptionsInfo{CompoundIDMode} =~ /^MolNameOrLabelPrefix$/i) { | |
| 342 my($MolName); | |
| 343 $MolName = $Molecule->GetName(); | |
| 344 $CmpdID = $MolName ? $MolName : "$OptionsInfo{CompoundID}${CmpdCount}"; | |
| 345 } | |
| 346 elsif ($OptionsInfo{CompoundIDMode} =~ /^LabelPrefix$/i) { | |
| 347 $CmpdID = "$OptionsInfo{CompoundID}${CmpdCount}"; | |
| 348 } | |
| 349 elsif ($OptionsInfo{CompoundIDMode} =~ /^DataField$/i) { | |
| 350 my($SpecifiedDataField); | |
| 351 $SpecifiedDataField = $OptionsInfo{CompoundID}; | |
| 352 $CmpdID = exists $DataFieldLabelAndValuesRef->{$SpecifiedDataField} ? $DataFieldLabelAndValuesRef->{$SpecifiedDataField} : ''; | |
| 353 } | |
| 354 elsif ($OptionsInfo{CompoundIDMode} =~ /^MolName$/i) { | |
| 355 $CmpdID = $Molecule->GetName(); | |
| 356 } | |
| 357 return $CmpdID; | |
| 358 } | |
| 359 | |
| 360 # Generate fingerprints for molecule... | |
| 361 # | |
| 362 sub GenerateMoleculeFingerprints { | |
| 363 my($Molecule) = @_; | |
| 364 my($MACCSKeysFingerprints); | |
| 365 | |
| 366 if ($OptionsInfo{KeepLargestComponent}) { | |
| 367 $Molecule->KeepLargestComponent(); | |
| 368 } | |
| 369 if (!$Molecule->DetectRings()) { | |
| 370 return undef; | |
| 371 } | |
| 372 $Molecule->SetAromaticityModel($OptionsInfo{AromaticityModel}); | |
| 373 $Molecule->DetectAromaticity(); | |
| 374 | |
| 375 $MACCSKeysFingerprints = undef; | |
| 376 if ($OptionsInfo{Mode} =~ /^MACCSKeyBits$/i) { | |
| 377 $MACCSKeysFingerprints = new Fingerprints::MACCSKeys('Molecule' => $Molecule, 'Type' => 'MACCSKeyBits', 'Size' => $OptionsInfo{Size}); | |
| 378 } | |
| 379 elsif ($OptionsInfo{Mode} =~ /^MACCSKeyCount$/i) { | |
| 380 $MACCSKeysFingerprints = new Fingerprints::MACCSKeys('Molecule' => $Molecule, 'Type' => 'MACCSKeyCount', 'Size' => $OptionsInfo{Size}); | |
| 381 } | |
| 382 else { | |
| 383 die "Error: The value specified, $Options{mode}, for option \"-m, --mode\" is not valid. Allowed values: MACCSKeyBits or MACCSKeyCount\n"; | |
| 384 } | |
| 385 $MACCSKeysFingerprints->GenerateMACCSKeys(); | |
| 386 | |
| 387 return $MACCSKeysFingerprints; | |
| 388 } | |
| 389 | |
| 390 # Retrieve information about SD files... | |
| 391 # | |
| 392 sub RetrieveSDFilesInfo { | |
| 393 my($SDFile, $Index, $FileDir, $FileExt, $FileName, $OutFileRoot, $TextOutFileExt, $SDOutFileExt, $FPOutFileExt, $NewSDFileName, $NewFPFileName, $NewTextFileName, $CheckDataField, $CollectDataFields, $AllDataFieldsRef, $CommonDataFieldsRef); | |
| 394 | |
| 395 %SDFilesInfo = (); | |
| 396 @{$SDFilesInfo{FileOkay}} = (); | |
| 397 @{$SDFilesInfo{OutFileRoot}} = (); | |
| 398 @{$SDFilesInfo{SDOutFileNames}} = (); | |
| 399 @{$SDFilesInfo{FPOutFileNames}} = (); | |
| 400 @{$SDFilesInfo{TextOutFileNames}} = (); | |
| 401 @{$SDFilesInfo{AllDataFieldsRef}} = (); | |
| 402 @{$SDFilesInfo{CommonDataFieldsRef}} = (); | |
| 403 | |
| 404 $CheckDataField = ($OptionsInfo{TextOutput} && ($OptionsInfo{DataFieldsMode} =~ /^CompoundID$/i) && ($OptionsInfo{CompoundIDMode} =~ /^DataField$/i)) ? 1 : 0; | |
| 405 $CollectDataFields = ($OptionsInfo{TextOutput} && ($OptionsInfo{DataFieldsMode} =~ /^(All|Common)$/i)) ? 1 : 0; | |
| 406 | |
| 407 FILELIST: for $Index (0 .. $#SDFilesList) { | |
| 408 $SDFile = $SDFilesList[$Index]; | |
| 409 | |
| 410 $SDFilesInfo{FileOkay}[$Index] = 0; | |
| 411 $SDFilesInfo{OutFileRoot}[$Index] = ''; | |
| 412 $SDFilesInfo{SDOutFileNames}[$Index] = ''; | |
| 413 $SDFilesInfo{FPOutFileNames}[$Index] = ''; | |
| 414 $SDFilesInfo{TextOutFileNames}[$Index] = ''; | |
| 415 | |
| 416 $SDFile = $SDFilesList[$Index]; | |
| 417 if (!(-e $SDFile)) { | |
| 418 warn "Warning: Ignoring file $SDFile: It doesn't exist\n"; | |
| 419 next FILELIST; | |
| 420 } | |
| 421 if (!CheckFileType($SDFile, "sd sdf")) { | |
| 422 warn "Warning: Ignoring file $SDFile: It's not a SD file\n"; | |
| 423 next FILELIST; | |
| 424 } | |
| 425 | |
| 426 if ($CheckDataField) { | |
| 427 # Make sure data field exists in SD file.. | |
| 428 my($CmpdString, $SpecifiedDataField, @CmpdLines, %DataFieldValues); | |
| 429 | |
| 430 @CmpdLines = (); | |
| 431 open SDFILE, "$SDFile" or die "Error: Couldn't open $SDFile: $! \n"; | |
| 432 $CmpdString = ReadCmpdString(\*SDFILE); | |
| 433 close SDFILE; | |
| 434 @CmpdLines = split "\n", $CmpdString; | |
| 435 %DataFieldValues = GetCmpdDataHeaderLabelsAndValues(\@CmpdLines); | |
| 436 $SpecifiedDataField = $OptionsInfo{CompoundID}; | |
| 437 if (!exists $DataFieldValues{$SpecifiedDataField}) { | |
| 438 warn "Warning: Ignoring file $SDFile: Data field value, $SpecifiedDataField, using \"--CompoundID\" option in \"DataField\" \"--CompoundIDMode\" doesn't exist\n"; | |
| 439 next FILELIST; | |
| 440 } | |
| 441 } | |
| 442 | |
| 443 $AllDataFieldsRef = ''; | |
| 444 $CommonDataFieldsRef = ''; | |
| 445 if ($CollectDataFields) { | |
| 446 my($CmpdCount); | |
| 447 open SDFILE, "$SDFile" or die "Error: Couldn't open $SDFile: $! \n"; | |
| 448 ($CmpdCount, $AllDataFieldsRef, $CommonDataFieldsRef) = GetAllAndCommonCmpdDataHeaderLabels(\*SDFILE); | |
| 449 close SDFILE; | |
| 450 } | |
| 451 | |
| 452 # Setup output file names... | |
| 453 $FileDir = ""; $FileName = ""; $FileExt = ""; | |
| 454 ($FileDir, $FileName, $FileExt) = ParseFileName($SDFile); | |
| 455 | |
| 456 $TextOutFileExt = "csv"; | |
| 457 if ($Options{outdelim} =~ /^tab$/i) { | |
| 458 $TextOutFileExt = "tsv"; | |
| 459 } | |
| 460 $SDOutFileExt = $FileExt; | |
| 461 $FPOutFileExt = "fpf"; | |
| 462 | |
| 463 if ($OptionsInfo{OutFileRoot} && (@SDFilesList == 1)) { | |
| 464 my ($RootFileDir, $RootFileName, $RootFileExt) = ParseFileName($OptionsInfo{OutFileRoot}); | |
| 465 if ($RootFileName && $RootFileExt) { | |
| 466 $FileName = $RootFileName; | |
| 467 } | |
| 468 else { | |
| 469 $FileName = $OptionsInfo{OutFileRoot}; | |
| 470 } | |
| 471 $OutFileRoot = $FileName; | |
| 472 } | |
| 473 else { | |
| 474 $OutFileRoot = "${FileName}MACCSKeysFP"; | |
| 475 } | |
| 476 | |
| 477 $NewSDFileName = "${OutFileRoot}.${SDOutFileExt}"; | |
| 478 $NewFPFileName = "${OutFileRoot}.${FPOutFileExt}"; | |
| 479 $NewTextFileName = "${OutFileRoot}.${TextOutFileExt}"; | |
| 480 | |
| 481 if ($OptionsInfo{SDOutput}) { | |
| 482 if ($SDFile =~ /$NewSDFileName/i) { | |
| 483 warn "Warning: Ignoring input file $SDFile: Same output, $NewSDFileName, and input file names.\n"; | |
| 484 print "Specify a different name using \"-r --root\" option or use default name.\n"; | |
| 485 next FILELIST; | |
| 486 } | |
| 487 } | |
| 488 | |
| 489 if (!$OptionsInfo{OverwriteFiles}) { | |
| 490 # Check SD and text outout files... | |
| 491 if ($OptionsInfo{SDOutput}) { | |
| 492 if (-e $NewSDFileName) { | |
| 493 warn "Warning: Ignoring file $SDFile: The file $NewSDFileName already exists\n"; | |
| 494 next FILELIST; | |
| 495 } | |
| 496 } | |
| 497 if ($OptionsInfo{FPOutput}) { | |
| 498 if (-e $NewFPFileName) { | |
| 499 warn "Warning: Ignoring file $SDFile: The file $NewFPFileName already exists\n"; | |
| 500 next FILELIST; | |
| 501 } | |
| 502 } | |
| 503 if ($OptionsInfo{TextOutput}) { | |
| 504 if (-e $NewTextFileName) { | |
| 505 warn "Warning: Ignoring file $SDFile: The file $NewTextFileName already exists\n"; | |
| 506 next FILELIST; | |
| 507 } | |
| 508 } | |
| 509 } | |
| 510 | |
| 511 $SDFilesInfo{FileOkay}[$Index] = 1; | |
| 512 | |
| 513 $SDFilesInfo{OutFileRoot}[$Index] = $OutFileRoot; | |
| 514 $SDFilesInfo{SDOutFileNames}[$Index] = $NewSDFileName; | |
| 515 $SDFilesInfo{FPOutFileNames}[$Index] = $NewFPFileName; | |
| 516 $SDFilesInfo{TextOutFileNames}[$Index] = $NewTextFileName; | |
| 517 | |
| 518 $SDFilesInfo{AllDataFieldsRef}[$Index] = $AllDataFieldsRef; | |
| 519 $SDFilesInfo{CommonDataFieldsRef}[$Index] = $CommonDataFieldsRef; | |
| 520 } | |
| 521 } | |
| 522 | |
| 523 # Process option values... | |
| 524 sub ProcessOptions { | |
| 525 %OptionsInfo = (); | |
| 526 | |
| 527 $OptionsInfo{Mode} = $Options{mode}; | |
| 528 $OptionsInfo{AromaticityModel} = $Options{aromaticitymodel}; | |
| 529 | |
| 530 $OptionsInfo{BitsOrder} = $Options{bitsorder}; | |
| 531 $OptionsInfo{BitStringFormat} = $Options{bitstringformat}; | |
| 532 | |
| 533 $OptionsInfo{CompoundIDMode} = $Options{compoundidmode}; | |
| 534 $OptionsInfo{CompoundIDLabel} = $Options{compoundidlabel}; | |
| 535 $OptionsInfo{DataFieldsMode} = $Options{datafieldsmode}; | |
| 536 | |
| 537 $OptionsInfo{Filter} = ($Options{filter} =~ /^Yes$/i) ? 1 : 0; | |
| 538 | |
| 539 my(@SpecifiedDataFields); | |
| 540 @SpecifiedDataFields = (); | |
| 541 | |
| 542 @{$OptionsInfo{SpecifiedDataFields}} = (); | |
| 543 $OptionsInfo{CompoundID} = ''; | |
| 544 | |
| 545 if ($Options{datafieldsmode} =~ /^CompoundID$/i) { | |
| 546 if ($Options{compoundidmode} =~ /^DataField$/i) { | |
| 547 if (!$Options{compoundid}) { | |
| 548 die "Error: You must specify a value for \"--CompoundID\" option in \"DataField\" \"--CompoundIDMode\". \n"; | |
| 549 } | |
| 550 $OptionsInfo{CompoundID} = $Options{compoundid}; | |
| 551 } | |
| 552 elsif ($Options{compoundidmode} =~ /^(LabelPrefix|MolNameOrLabelPrefix)$/i) { | |
| 553 $OptionsInfo{CompoundID} = $Options{compoundid} ? $Options{compoundid} : 'Cmpd'; | |
| 554 } | |
| 555 } | |
| 556 elsif ($Options{datafieldsmode} =~ /^Specify$/i) { | |
| 557 if (!$Options{datafields}) { | |
| 558 die "Error: You must specify a value for \"--DataFields\" option in \"Specify\" \"-d, --DataFieldsMode\". \n"; | |
| 559 } | |
| 560 @SpecifiedDataFields = split /\,/, $Options{datafields}; | |
| 561 push @{$OptionsInfo{SpecifiedDataFields}}, @SpecifiedDataFields; | |
| 562 } | |
| 563 | |
| 564 $OptionsInfo{FingerprintsLabel} = $Options{fingerprintslabel} ? $Options{fingerprintslabel} : 'MACCSKeysFingerprints'; | |
| 565 | |
| 566 $OptionsInfo{KeepLargestComponent} = ($Options{keeplargestcomponent} =~ /^Yes$/i) ? 1 : 0; | |
| 567 | |
| 568 $OptionsInfo{Output} = $Options{output}; | |
| 569 $OptionsInfo{SDOutput} = ($Options{output} =~ /^(SD|All)$/i) ? 1 : 0; | |
| 570 $OptionsInfo{FPOutput} = ($Options{output} =~ /^(FP|All)$/i) ? 1 : 0; | |
| 571 $OptionsInfo{TextOutput} = ($Options{output} =~ /^(Text|All)$/i) ? 1 : 0; | |
| 572 | |
| 573 $OptionsInfo{OutDelim} = $Options{outdelim}; | |
| 574 $OptionsInfo{OutQuote} = ($Options{quote} =~ /^Yes$/i) ? 1 : 0; | |
| 575 | |
| 576 $OptionsInfo{OverwriteFiles} = $Options{overwrite} ? 1 : 0; | |
| 577 $OptionsInfo{OutFileRoot} = $Options{root} ? $Options{root} : 0; | |
| 578 | |
| 579 $OptionsInfo{Size} = $Options{size}; | |
| 580 | |
| 581 $OptionsInfo{VectorStringFormat} = $Options{vectorstringformat}; | |
| 582 } | |
| 583 | |
| 584 # Setup script usage and retrieve command line arguments specified using various options... | |
| 585 sub SetupScriptUsage { | |
| 586 | |
| 587 # Retrieve all the options... | |
| 588 %Options = (); | |
| 589 | |
| 590 $Options{aromaticitymodel} = 'MayaChemToolsAromaticityModel'; | |
| 591 | |
| 592 $Options{bitsorder} = 'Ascending'; | |
| 593 $Options{bitstringformat} = 'BinaryString'; | |
| 594 | |
| 595 $Options{compoundidmode} = 'LabelPrefix'; | |
| 596 $Options{compoundidlabel} = 'CompoundID'; | |
| 597 $Options{datafieldsmode} = 'CompoundID'; | |
| 598 | |
| 599 $Options{filter} = 'Yes'; | |
| 600 | |
| 601 $Options{keeplargestcomponent} = 'Yes'; | |
| 602 | |
| 603 $Options{mode} = 'MACCSKeyBits'; | |
| 604 | |
| 605 $Options{output} = 'text'; | |
| 606 $Options{outdelim} = 'comma'; | |
| 607 $Options{quote} = 'yes'; | |
| 608 | |
| 609 $Options{size} = 166; | |
| 610 | |
| 611 $Options{vectorstringformat} = 'ValuesString'; | |
| 612 | |
| 613 if (!GetOptions(\%Options, "aromaticitymodel=s", "bitsorder=s", "bitstringformat|b=s", "compoundid=s", "compoundidlabel=s", "compoundidmode=s", "datafields=s", "datafieldsmode|d=s", "filter|f=s", "fingerprintslabel=s", "help|h", "keeplargestcomponent|k=s", "mode|m=s", "outdelim=s", "output=s", "overwrite|o", "quote|q=s", "root|r=s", "size|s=i", "vectorstringformat|v=s", "workingdir|w=s")) { | |
| 614 die "\nTo get a list of valid options and their values, use \"$ScriptName -h\" or\n\"perl -S $ScriptName -h\" command and try again...\n"; | |
| 615 } | |
| 616 if ($Options{workingdir}) { | |
| 617 if (! -d $Options{workingdir}) { | |
| 618 die "Error: The value specified, $Options{workingdir}, for option \"-w --workingdir\" is not a directory name.\n"; | |
| 619 } | |
| 620 chdir $Options{workingdir} or die "Error: Couldn't chdir $Options{workingdir}: $! \n"; | |
| 621 } | |
| 622 if (!Molecule::IsSupportedAromaticityModel($Options{aromaticitymodel})) { | |
| 623 my(@SupportedModels) = Molecule::GetSupportedAromaticityModels(); | |
| 624 die "Error: The value specified, $Options{aromaticitymodel}, for option \"--AromaticityModel\" is not valid. Supported aromaticity models in current release of MayaChemTools: @SupportedModels\n"; | |
| 625 } | |
| 626 if ($Options{bitsorder} !~ /^(Ascending|Descending)$/i) { | |
| 627 die "Error: The value specified, $Options{bitsorder}, for option \"--BitsOrder\" is not valid. Allowed values: Ascending or Descending\n"; | |
| 628 } | |
| 629 if ($Options{bitstringformat} !~ /^(BinaryString|HexadecimalString)$/i) { | |
| 630 die "Error: The value specified, $Options{bitstringformat}, for option \"-b, --bitstringformat\" is not valid. Allowed values: BinaryString or HexadecimalString\n"; | |
| 631 } | |
| 632 if ($Options{compoundidmode} !~ /^(DataField|MolName|LabelPrefix|MolNameOrLabelPrefix)$/i) { | |
| 633 die "Error: The value specified, $Options{compoundidmode}, for option \"--CompoundIDMode\" is not valid. Allowed values: DataField, MolName, LabelPrefix or MolNameOrLabelPrefix\n"; | |
| 634 } | |
| 635 if ($Options{datafieldsmode} !~ /^(All|Common|Specify|CompoundID)$/i) { | |
| 636 die "Error: The value specified, $Options{datafieldsmode}, for option \"-d, --DataFieldsMode\" is not valid. Allowed values: All, Common, Specify or CompoundID\n"; | |
| 637 } | |
| 638 if ($Options{filter} !~ /^(Yes|No)$/i) { | |
| 639 die "Error: The value specified, $Options{filter}, for option \"-f, --Filter\" is not valid. Allowed values: Yes or No\n"; | |
| 640 } | |
| 641 if ($Options{keeplargestcomponent} !~ /^(Yes|No)$/i) { | |
| 642 die "Error: The value specified, $Options{keeplargestcomponent}, for option \"-k, --KeepLargestComponent\" is not valid. Allowed values: Yes or No\n"; | |
| 643 } | |
| 644 if ($Options{mode} !~ /^(MACCSKeyBits|MACCSKeyCount)$/i) { | |
| 645 die "Error: The value specified, $Options{mode}, for option \"-m, --mode\" is not valid. Allowed values: MACCSKeyBits or MACCSKeyCount\n"; | |
| 646 } | |
| 647 if ($Options{output} !~ /^(SD|FP|text|all)$/i) { | |
| 648 die "Error: The value specified, $Options{output}, for option \"--output\" is not valid. Allowed values: SD, FP, text, or all\n"; | |
| 649 } | |
| 650 if ($Options{outdelim} !~ /^(comma|semicolon|tab)$/i) { | |
| 651 die "Error: The value specified, $Options{outdelim}, for option \"--outdelim\" is not valid. Allowed values: comma, tab, or semicolon\n"; | |
| 652 } | |
| 653 if ($Options{quote} !~ /^(Yes|No)$/i) { | |
| 654 die "Error: The value specified, $Options{quote}, for option \"-q --quote\" is not valid. Allowed values: Yes or No\n"; | |
| 655 } | |
| 656 if ($Options{outdelim} =~ /semicolon/i && $Options{quote} =~ /^No$/i) { | |
| 657 die "Error: The value specified, $Options{quote}, for option \"-q --quote\" is not allowed with, semicolon value of \"--outdelim\" option: Fingerprints string use semicolon as delimiter for various data fields and must be quoted.\n"; | |
| 658 } | |
| 659 if (!(IsPositiveInteger($Options{size}) && ($Options{size} == 166 || $Options{size} == 322))) { | |
| 660 die "Error: The value specified, $Options{size}, for option \"-s, --size\" is not valid. Allowed values: 166 or 322 \n"; | |
| 661 } | |
| 662 if ($Options{vectorstringformat} !~ /^(ValuesString|IDsAndValuesString|IDsAndValuesPairsString|ValuesAndIDsString|ValuesAndIDsPairsString)$/i) { | |
| 663 die "Error: The value specified, $Options{vectorstringformat}, for option \"-v, --VectorStringFormat\" is not valid. Allowed values: ValuesString, IDsAndValuesString, IDsAndValuesPairsString, ValuesAndIDsString or ValuesAndIDsPairsString\n"; | |
| 664 } | |
| 665 } | |
| 666 | |
| 667 __END__ | |
| 668 | |
| 669 =head1 NAME | |
| 670 | |
| 671 MACCSKeysFingerprints.pl - Generate MACCS key fingerprints for SD files | |
| 672 | |
| 673 =head1 SYNOPSIS | |
| 674 | |
| 675 MACCSKeysFingerprints.pl SDFile(s)... | |
| 676 | |
| 677 MACCSKeysFingerprints.pl [B<--AromaticityModel> I<AromaticityModelType>] | |
| 678 [B<--BitsOrder> I<Ascending | Descending>] | |
| 679 [B<-b, --BitStringFormat> I<BinaryString | HexadecimalString>] | |
| 680 [B<--CompoundID> I<DataFieldName or LabelPrefixString>] [B<--CompoundIDLabel> I<text>] | |
| 681 [B<--CompoundIDMode> I<DataField | MolName | LabelPrefix | MolNameOrLabelPrefix>] | |
| 682 [B<--DataFields> I<"FieldLabel1,FieldLabel2,...">] [B<-d, --DataFieldsMode> I<All | Common | Specify | CompoundID>] | |
| 683 [B<-f, --Filter> I<Yes | No>] [B<--FingerprintsLabel> I<text>] [B<-h, --help>] [B<-k, --KeepLargestComponent> I<Yes | No>] | |
| 684 [B<-m, --mode> I<MACCSKeyBits | MACCSKeyCount>] [B<--OutDelim> I<comma | tab | semicolon>] | |
| 685 [B<--output> I<SD | FP | text | all>] [B<-o, --overwrite>] | |
| 686 [B<-q, --quote> I<Yes | No>] [B<-r, --root> I<RootName>] [B<-s, --size> I<number>] | |
| 687 [B<-v, --VectorStringFormat> I<IDsAndValuesString | IDsAndValuesPairsString | ValuesAndIDsString | ValuesAndIDsPairsString>] | |
| 688 [B<-w, --WorkingDir> I<DirName>] | |
| 689 | |
| 690 =head1 DESCRIPTION | |
| 691 | |
| 692 Generate MACCS (Molecular ACCess System) keys fingerprints [ Ref 45-47 ] for I<SDFile(s)> | |
| 693 and create appropriate SD, FP or CSV/TSV text file(s) containing fingerprints bit-vector or | |
| 694 vector strings corresponding to molecular fingerprints. | |
| 695 | |
| 696 Multiple SDFile names are separated by spaces. The valid file extensions are I<.sdf> | |
| 697 and I<.sd>. All other file names are ignored. All the SD files in a current directory | |
| 698 can be specified either by I<*.sdf> or the current directory name. | |
| 699 | |
| 700 For each MACCS keys definition, atoms are processed to determine their membership to the key | |
| 701 and the appropriate molecular fingerprints strings are generated. An atom can belong to multiple | |
| 702 MACCS keys. | |
| 703 | |
| 704 For I<MACCSKeyBits> value of B<-m, --mode> option, a fingerprint bit-vector string containing | |
| 705 zeros and ones is generated and for I<MACCSKeyCount> value, a fingerprint vector string | |
| 706 corresponding to number of MACCS keys [ Ref 45-47 ] is generated. | |
| 707 | |
| 708 I<MACCSKeyBits | MACCSKeyCount> values for B<-m, --mode> option along with two possible | |
| 709 I<166 | 322> values of B<-s, --size> supports generation of four different types of MACCS | |
| 710 keys fingerprint: I<MACCS166KeyBits, MACCS166KeyCount, MACCS322KeyBits, MACCS322KeyCount>. | |
| 711 | |
| 712 Example of I<SD> file containing MAACS keys fingerprints string data: | |
| 713 | |
| 714 ... ... | |
| 715 ... ... | |
| 716 $$$$ | |
| 717 ... ... | |
| 718 ... ... | |
| 719 ... ... | |
| 720 41 44 0 0 0 0 0 0 0 0999 V2000 | |
| 721 -3.3652 1.4499 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 | |
| 722 ... ... | |
| 723 2 3 1 0 0 0 0 | |
| 724 ... ... | |
| 725 M END | |
| 726 > <CmpdID> | |
| 727 Cmpd1 | |
| 728 | |
| 729 > <MACCSKeysFingerprints> | |
| 730 FingerprintsBitVector;MACCSKeyBits;166;BinaryString;Ascending;000000000 | |
| 731 00000000000000000000000000000000100100001001000000001001000000001110001 | |
| 732 00101010111100011011000100110110000011011110100110111111111111011111111 | |
| 733 11111111110111000 | |
| 734 | |
| 735 $$$$ | |
| 736 ... ... | |
| 737 ... ... | |
| 738 | |
| 739 Example of I<FP> file containing MAACS keys fingerprints string data: | |
| 740 | |
| 741 # | |
| 742 # Package = MayaChemTools 7.4 | |
| 743 # Release Date = Oct 21, 2010 | |
| 744 # | |
| 745 # TimeStamp = Fri Mar 11 14:57:24 2011 | |
| 746 # | |
| 747 # FingerprintsStringType = FingerprintsBitVector | |
| 748 # | |
| 749 # Description = MACCSKeyBits | |
| 750 # Size = 166 | |
| 751 # BitStringFormat = BinaryString | |
| 752 # BitsOrder = Ascending | |
| 753 # | |
| 754 Cmpd1 00000000000000000000000000000000000000000100100001001000000001... | |
| 755 Cmpd2 00000000000000000000000010000000001000000010000000001000000000... | |
| 756 ... ... | |
| 757 ... .. | |
| 758 | |
| 759 Example of CSV I<Text> file containing MAACS keys fingerprints string data: | |
| 760 | |
| 761 "CompoundID","MACCSKeysFingerprints" | |
| 762 "Cmpd1","FingerprintsBitVector;MACCSKeyBits;166;BinaryString;Ascending; | |
| 763 00000000000000000000000000000000000000000100100001001000000001001000000 | |
| 764 00111000100101010111100011011000100110110000011011110100110111111111111 | |
| 765 01111111111111111110111000" | |
| 766 ... ... | |
| 767 ... ... | |
| 768 | |
| 769 The current release of MayaChemTools generates the following types of MACCS keys | |
| 770 fingerprints bit-vector and vector strings: | |
| 771 | |
| 772 FingerprintsBitVector;MACCSKeyBits;166;BinaryString;Ascending;00000000 | |
| 773 0000000000000000000000000000000001001000010010000000010010000000011100 | |
| 774 0100101010111100011011000100110110000011011110100110111111111111011111 | |
| 775 11111111111110111000 | |
| 776 | |
| 777 FingerprintsBitVector;MACCSKeyBits;166;HexadecimalString;Ascending;000 | |
| 778 000000021210210e845f8d8c60b79dffbffffd1 | |
| 779 | |
| 780 FingerprintsBitVector;MACCSKeyBits;322;BinaryString;Ascending;11101011 | |
| 781 1110011111100101111111000111101100110000000000000011100010000000000000 | |
| 782 0000000000000000000000000000000000000000000000101000000000000000000000 | |
| 783 0000000000000000000000000000000000000000000000000000000000000000000000 | |
| 784 0000000000000000000000000000000000000011000000000000000000000000000000 | |
| 785 0000000000000000000000000000000000000000 | |
| 786 | |
| 787 FingerprintsBitVector;MACCSKeyBits;322;HexadecimalString;Ascending;7d7 | |
| 788 e7af3edc000c1100000000000000500000000000000000000000000000000300000000 | |
| 789 000000000 | |
| 790 | |
| 791 FingerprintsVector;MACCSKeyCount;166;OrderedNumericalValues;ValuesStri | |
| 792 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 | |
| 793 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 | |
| 794 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 | |
| 795 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 | |
| 796 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 | |
| 797 | |
| 798 FingerprintsVector;MACCSKeyCount;322;OrderedNumericalValues;ValuesStri | |
| 799 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 | |
| 800 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 | |
| 801 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 | |
| 802 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 | |
| 803 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 ... | |
| 804 | |
| 805 =head1 OPTIONS | |
| 806 | |
| 807 =over 4 | |
| 808 | |
| 809 =item B<--AromaticityModel> I<MDLAromaticityModel | TriposAromaticityModel | MMFFAromaticityModel | ChemAxonBasicAromaticityModel | ChemAxonGeneralAromaticityModel | DaylightAromaticityModel | MayaChemToolsAromaticityModel> | |
| 810 | |
| 811 Specify aromaticity model to use during detection of aromaticity. Possible values in the current | |
| 812 release are: I<MDLAromaticityModel, TriposAromaticityModel, MMFFAromaticityModel, | |
| 813 ChemAxonBasicAromaticityModel, ChemAxonGeneralAromaticityModel, DaylightAromaticityModel | |
| 814 or MayaChemToolsAromaticityModel>. Default value: I<MayaChemToolsAromaticityModel>. | |
| 815 | |
| 816 The supported aromaticity model names along with model specific control parameters | |
| 817 are defined in B<AromaticityModelsData.csv>, which is distributed with the current release | |
| 818 and is available under B<lib/data> directory. B<Molecule.pm> module retrieves data from | |
| 819 this file during class instantiation and makes it available to method B<DetectAromaticity> | |
| 820 for detecting aromaticity corresponding to a specific model. | |
| 821 | |
| 822 =item B<--BitsOrder> I<Ascending | Descending> | |
| 823 | |
| 824 Bits order to use during generation of fingerprints bit-vector string for I<MACCSKeyBits> value of | |
| 825 B<-m, --mode> option. Possible values: I<Ascending, Descending>. Default: I<Ascending>. | |
| 826 | |
| 827 I<Ascending> bit order which corresponds to first bit in each byte as the lowest bit as | |
| 828 opposed to the highest bit. | |
| 829 | |
| 830 Internally, bits are stored in I<Ascending> order using Perl vec function. Regardless | |
| 831 of machine order, big-endian or little-endian, vec function always considers first | |
| 832 string byte as the lowest byte and first bit within each byte as the lowest bit. | |
| 833 | |
| 834 =item B<-b, --BitStringFormat> I<BinaryString | HexadecimalString> | |
| 835 | |
| 836 Format of fingerprints bit-vector string data in output SD, FP or CSV/TSV text file(s) specified by | |
| 837 B<--output> used during I<MACCSKeyBits> value of B<-m, --mode> option. Possible | |
| 838 values: I<BinaryString, HexadecimalString>. Default value: I<BinaryString>. | |
| 839 | |
| 840 I<BinaryString> corresponds to an ASCII string containing 1s and 0s. I<HexadecimalString> | |
| 841 contains bit values in ASCII hexadecimal format. | |
| 842 | |
| 843 Examples: | |
| 844 | |
| 845 FingerprintsBitVector;MACCSKeyBits;166;BinaryString;Ascending;00000000 | |
| 846 0000000000000000000000000000000001001000010010000000010010000000011100 | |
| 847 0100101010111100011011000100110110000011011110100110111111111111011111 | |
| 848 11111111111110111000 | |
| 849 | |
| 850 FingerprintsBitVector;MACCSKeyBits;166;HexadecimalString;Ascending;000 | |
| 851 000000021210210e845f8d8c60b79dffbffffd1 | |
| 852 | |
| 853 FingerprintsBitVector;MACCSKeyBits;322;BinaryString;Ascending;11101011 | |
| 854 1110011111100101111111000111101100110000000000000011100010000000000000 | |
| 855 0000000000000000000000000000000000000000000000101000000000000000000000 | |
| 856 0000000000000000000000000000000000000000000000000000000000000000000000 | |
| 857 0000000000000000000000000000000000000011000000000000000000000000000000 | |
| 858 0000000000000000000000000000000000000000 | |
| 859 | |
| 860 FingerprintsBitVector;MACCSKeyBits;322;HexadecimalString;Ascending;7d7 | |
| 861 e7af3edc000c1100000000000000500000000000000000000000000000000300000000 | |
| 862 000000000 | |
| 863 | |
| 864 =item B<--CompoundID> I<DataFieldName or LabelPrefixString> | |
| 865 | |
| 866 This value is B<--CompoundIDMode> specific and indicates how compound ID is generated. | |
| 867 | |
| 868 For I<DataField> value of B<--CompoundIDMode> option, it corresponds to datafield label name | |
| 869 whose value is used as compound ID; otherwise, it's a prefix string used for generating compound | |
| 870 IDs like LabelPrefixString<Number>. Default value, I<Cmpd>, generates compound IDs which | |
| 871 look like Cmpd<Number>. | |
| 872 | |
| 873 Examples for I<DataField> value of B<--CompoundIDMode>: | |
| 874 | |
| 875 MolID | |
| 876 ExtReg | |
| 877 | |
| 878 Examples for I<LabelPrefix> or I<MolNameOrLabelPrefix> value of B<--CompoundIDMode>: | |
| 879 | |
| 880 Compound | |
| 881 | |
| 882 The value specified above generates compound IDs which correspond to Compound<Number> | |
| 883 instead of default value of Cmpd<Number>. | |
| 884 | |
| 885 =item B<--CompoundIDLabel> I<text> | |
| 886 | |
| 887 Specify compound ID column label for FP or CSV/TSV text file(s) used during I<CompoundID> value | |
| 888 of B<--DataFieldsMode> option. Default: I<CompoundID>. | |
| 889 | |
| 890 =item B<--CompoundIDMode> I<DataField | MolName | LabelPrefix | MolNameOrLabelPrefix> | |
| 891 | |
| 892 Specify how to generate compound IDs and write to FP or CSV/TSV text file(s) along with generated | |
| 893 fingerprints for I<FP | text | all> values of B<--output> option: use a I<SDFile(s)> datafield value; | |
| 894 use molname line from I<SDFile(s)>; generate a sequential ID with specific prefix; use combination | |
| 895 of both MolName and LabelPrefix with usage of LabelPrefix values for empty molname lines. | |
| 896 | |
| 897 Possible values: I<DataField | MolName | LabelPrefix | MolNameOrLabelPrefix>. | |
| 898 Default: I<LabelPrefix>. | |
| 899 | |
| 900 For I<MolNameAndLabelPrefix> value of B<--CompoundIDMode>, molname line in I<SDFile(s)> takes | |
| 901 precedence over sequential compound IDs generated using I<LabelPrefix> and only empty molname | |
| 902 values are replaced with sequential compound IDs. | |
| 903 | |
| 904 This is only used for I<CompoundID> value of B<--DataFieldsMode> option. | |
| 905 | |
| 906 =item B<--DataFields> I<"FieldLabel1,FieldLabel2,..."> | |
| 907 | |
| 908 Comma delimited list of I<SDFiles(s)> data fields to extract and write to CSV/TSV text file(s) along | |
| 909 with generated fingerprints for I<text | all> values of B<--output> option. | |
| 910 | |
| 911 This is only used for I<Specify> value of B<--DataFieldsMode> option. | |
| 912 | |
| 913 Examples: | |
| 914 | |
| 915 Extreg | |
| 916 MolID,CompoundName | |
| 917 | |
| 918 =item B<-d, --DataFieldsMode> I<All | Common | Specify | CompoundID> | |
| 919 | |
| 920 Specify how data fields in I<SDFile(s)> are transferred to output CSV/TSV text file(s) along | |
| 921 with generated fingerprints for I<text | all> values of B<--output> option: transfer all SD | |
| 922 data field; transfer SD data files common to all compounds; extract specified data fields; | |
| 923 generate a compound ID using molname line, a compound prefix, or a combination of both. | |
| 924 Possible values: I<All | Common | specify | CompoundID>. Default value: I<CompoundID>. | |
| 925 | |
| 926 =item B<-f, --Filter> I<Yes | No> | |
| 927 | |
| 928 Specify whether to check and filter compound data in SDFile(s). Possible values: I<Yes or No>. | |
| 929 Default value: I<Yes>. | |
| 930 | |
| 931 By default, compound data is checked before calculating fingerprints and compounds containing | |
| 932 atom data corresponding to non-element symbols or no atom data are ignored. | |
| 933 | |
| 934 =item B<--FingerprintsLabel> I<text> | |
| 935 | |
| 936 SD data label or text file column label to use for fingerprints string in output SD or | |
| 937 CSV/TSV text file(s) specified by B<--output>. Default value: I<MACCSKeyFingerprints>. | |
| 938 | |
| 939 =item B<-h, --help> | |
| 940 | |
| 941 Print this help message. | |
| 942 | |
| 943 =item B<-k, --KeepLargestComponent> I<Yes | No> | |
| 944 | |
| 945 Generate fingerprints for only the largest component in molecule. Possible values: | |
| 946 I<Yes or No>. Default value: I<Yes>. | |
| 947 | |
| 948 For molecules containing multiple connected components, fingerprints can be generated | |
| 949 in two different ways: use all connected components or just the largest connected | |
| 950 component. By default, all atoms except for the largest connected component are | |
| 951 deleted before generation of fingerprints. | |
| 952 | |
| 953 =item B<-m, --mode> I<MACCSKeyBits | MACCSKeyCount> | |
| 954 | |
| 955 Specify type of MACCS keys [ Ref 45-47 ] fingerprints to generate for molecules in I<SDFile(s)>. | |
| 956 Possible values: I<MACCSKeyBits, MACCSKeyCount>. Default value: I<MACCSKeyBits>. | |
| 957 | |
| 958 For I<MACCSKeyBits> value of B<-m, --mode> option, a fingerprint bit-vector string containing | |
| 959 zeros and ones is generated and for I<MACCSKeyCount> value, a fingerprint vector string | |
| 960 corresponding to number of MACCS keys is generated. | |
| 961 | |
| 962 I<MACCSKeyBits | MACCSKeyCount> values for B<-m, --mode> option along with two possible | |
| 963 I<166 | 322> values of B<-s, --size> supports generation of four different types of MACCS | |
| 964 keys fingerprint: I<MACCS166KeyBits, MACCS166KeyCount, MACCS322KeyBits, MACCS322KeyCount>. | |
| 965 | |
| 966 Definition of MACCS keys uses the following atom and bond symbols to define atom and | |
| 967 bond environments: | |
| 968 | |
| 969 Atom symbols for 166 keys [ Ref 47 ]: | |
| 970 | |
| 971 A : Any valid periodic table element symbol | |
| 972 Q : Hetro atoms; any non-C or non-H atom | |
| 973 X : Halogens; F, Cl, Br, I | |
| 974 Z : Others; other than H, C, N, O, Si, P, S, F, Cl, Br, I | |
| 975 | |
| 976 Atom symbols for 322 keys [ Ref 46 ]: | |
| 977 | |
| 978 A : Any valid periodic table element symbol | |
| 979 Q : Hetro atoms; any non-C or non-H atom | |
| 980 X : Others; other than H, C, N, O, Si, P, S, F, Cl, Br, I | |
| 981 Z is neither defined nor used | |
| 982 | |
| 983 Bond types: | |
| 984 | |
| 985 - : Single | |
| 986 = : Double | |
| 987 T : Triple | |
| 988 # : Triple | |
| 989 ~ : Single or double query bond | |
| 990 % : An aromatic query bond | |
| 991 | |
| 992 None : Any bond type; no explicit bond specified | |
| 993 | |
| 994 $ : Ring bond; $ before a bond type specifies ring bond | |
| 995 ! : Chain or non-ring bond; ! before a bond type specifies chain bond | |
| 996 | |
| 997 @ : A ring linkage and the number following it specifies the | |
| 998 atoms position in the line, thus @1 means linked back to the first | |
| 999 atom in the list. | |
| 1000 | |
| 1001 Aromatic: Kekule or Arom5 | |
| 1002 | |
| 1003 Kekule: Bonds in 6-membered rings with alternate single/double bonds | |
| 1004 or perimeter bonds | |
| 1005 Arom5: Bonds in 5-membered rings with two double bonds and a hetro | |
| 1006 atom at the apex of the ring. | |
| 1007 | |
| 1008 MACCS 166 keys [ Ref 45-47 ] are defined as follows: | |
| 1009 | |
| 1010 Key Description | |
| 1011 | |
| 1012 1 ISOTOPE | |
| 1013 2 103 < ATOMIC NO. < 256 | |
| 1014 3 GROUP IVA,VA,VIA PERIODS 4-6 (Ge...) | |
| 1015 4 ACTINIDE | |
| 1016 5 GROUP IIIB,IVB (Sc...) | |
| 1017 6 LANTHANIDE | |
| 1018 7 GROUP VB,VIB,VIIB (V...) | |
| 1019 8 QAAA@1 | |
| 1020 9 GROUP VIII (Fe...) | |
| 1021 10 GROUP IIA (ALKALINE EARTH) | |
| 1022 11 4M RING | |
| 1023 12 GROUP IB,IIB (Cu...) | |
| 1024 13 ON(C)C | |
| 1025 14 S-S | |
| 1026 15 OC(O)O | |
| 1027 16 QAA@1 | |
| 1028 17 CTC | |
| 1029 18 GROUP IIIA (B...) | |
| 1030 19 7M RING | |
| 1031 20 SI | |
| 1032 21 C=C(Q)Q | |
| 1033 22 3M RING | |
| 1034 23 NC(O)O | |
| 1035 24 N-O | |
| 1036 25 NC(N)N | |
| 1037 26 C$=C($A)$A | |
| 1038 27 I | |
| 1039 28 QCH2Q | |
| 1040 29 P | |
| 1041 30 CQ(C)(C)A | |
| 1042 31 QX | |
| 1043 32 CSN | |
| 1044 33 NS | |
| 1045 34 CH2=A | |
| 1046 35 GROUP IA (ALKALI METAL) | |
| 1047 36 S HETEROCYCLE | |
| 1048 37 NC(O)N | |
| 1049 38 NC(C)N | |
| 1050 39 OS(O)O | |
| 1051 40 S-O | |
| 1052 41 CTN | |
| 1053 42 F | |
| 1054 43 QHAQH | |
| 1055 44 OTHER | |
| 1056 45 C=CN | |
| 1057 46 BR | |
| 1058 47 SAN | |
| 1059 48 OQ(O)O | |
| 1060 49 CHARGE | |
| 1061 50 C=C(C)C | |
| 1062 51 CSO | |
| 1063 52 NN | |
| 1064 53 QHAAAQH | |
| 1065 54 QHAAQH | |
| 1066 55 OSO | |
| 1067 56 ON(O)C | |
| 1068 57 O HETEROCYCLE | |
| 1069 58 QSQ | |
| 1070 59 Snot%A%A | |
| 1071 60 S=O | |
| 1072 61 AS(A)A | |
| 1073 62 A$A!A$A | |
| 1074 63 N=O | |
| 1075 64 A$A!S | |
| 1076 65 C%N | |
| 1077 66 CC(C)(C)A | |
| 1078 67 QS | |
| 1079 68 QHQH (&...) | |
| 1080 69 QQH | |
| 1081 70 QNQ | |
| 1082 71 NO | |
| 1083 72 OAAO | |
| 1084 73 S=A | |
| 1085 74 CH3ACH3 | |
| 1086 75 A!N$A | |
| 1087 76 C=C(A)A | |
| 1088 77 NAN | |
| 1089 78 C=N | |
| 1090 79 NAAN | |
| 1091 80 NAAAN | |
| 1092 81 SA(A)A | |
| 1093 82 ACH2QH | |
| 1094 83 QAAAA@1 | |
| 1095 84 NH2 | |
| 1096 85 CN(C)C | |
| 1097 86 CH2QCH2 | |
| 1098 87 X!A$A | |
| 1099 88 S | |
| 1100 89 OAAAO | |
| 1101 90 QHAACH2A | |
| 1102 91 QHAAACH2A | |
| 1103 92 OC(N)C | |
| 1104 93 QCH3 | |
| 1105 94 QN | |
| 1106 95 NAAO | |
| 1107 96 5M RING | |
| 1108 97 NAAAO | |
| 1109 98 QAAAAA@1 | |
| 1110 99 C=C | |
| 1111 100 ACH2N | |
| 1112 101 8M RING | |
| 1113 102 QO | |
| 1114 103 CL | |
| 1115 104 QHACH2A | |
| 1116 105 A$A($A)$A | |
| 1117 106 QA(Q)Q | |
| 1118 107 XA(A)A | |
| 1119 108 CH3AAACH2A | |
| 1120 109 ACH2O | |
| 1121 110 NCO | |
| 1122 111 NACH2A | |
| 1123 112 AA(A)(A)A | |
| 1124 113 Onot%A%A | |
| 1125 114 CH3CH2A | |
| 1126 115 CH3ACH2A | |
| 1127 116 CH3AACH2A | |
| 1128 117 NAO | |
| 1129 118 ACH2CH2A > 1 | |
| 1130 119 N=A | |
| 1131 120 HETEROCYCLIC ATOM > 1 (&...) | |
| 1132 121 N HETEROCYCLE | |
| 1133 122 AN(A)A | |
| 1134 123 OCO | |
| 1135 124 QQ | |
| 1136 125 AROMATIC RING > 1 | |
| 1137 126 A!O!A | |
| 1138 127 A$A!O > 1 (&...) | |
| 1139 128 ACH2AAACH2A | |
| 1140 129 ACH2AACH2A | |
| 1141 130 QQ > 1 (&...) | |
| 1142 131 QH > 1 | |
| 1143 132 OACH2A | |
| 1144 133 A$A!N | |
| 1145 134 X (HALOGEN) | |
| 1146 135 Nnot%A%A | |
| 1147 136 O=A > 1 | |
| 1148 137 HETEROCYCLE | |
| 1149 138 QCH2A > 1 (&...) | |
| 1150 139 OH | |
| 1151 140 O > 3 (&...) | |
| 1152 141 CH3 > 2 (&...) | |
| 1153 142 N > 1 | |
| 1154 143 A$A!O | |
| 1155 144 Anot%A%Anot%A | |
| 1156 145 6M RING > 1 | |
| 1157 146 O > 2 | |
| 1158 147 ACH2CH2A | |
| 1159 148 AQ(A)A | |
| 1160 149 CH3 > 1 | |
| 1161 150 A!A$A!A | |
| 1162 151 NH | |
| 1163 152 OC(C)C | |
| 1164 153 QCH2A | |
| 1165 154 C=O | |
| 1166 155 A!CH2!A | |
| 1167 156 NA(A)A | |
| 1168 157 C-O | |
| 1169 158 C-N | |
| 1170 159 O > 1 | |
| 1171 160 CH3 | |
| 1172 161 N | |
| 1173 162 AROMATIC | |
| 1174 163 6M RING | |
| 1175 164 O | |
| 1176 165 RING | |
| 1177 166 FRAGMENTS | |
| 1178 | |
| 1179 MACCS 322 keys set as defined in tables 1, 2 and 3 [ Ref 46 ] include: | |
| 1180 | |
| 1181 . 26 atom properties of type P, as listed in Table 1 | |
| 1182 . 32 one-atom environments, as listed in Table 3 | |
| 1183 . 264 atom-bond-atom combinations listed in Table 4 | |
| 1184 | |
| 1185 Total number of keys in three tables is : 322 | |
| 1186 | |
| 1187 Atom symbol, X, used for 322 keys [ Ref 46 ] doesn't refer to Halogens as it does for 166 keys. In | |
| 1188 order to keep the definition of 322 keys consistent with the published definitions, the symbol X is | |
| 1189 used to imply "others" atoms, but it's internally mapped to symbol X as defined for 166 keys | |
| 1190 during the generation of key values. | |
| 1191 | |
| 1192 Atom properties-based keys (26): | |
| 1193 | |
| 1194 Key Description | |
| 1195 1 A(AAA) or AA(A)A - atom with at least three neighbors | |
| 1196 2 Q - heteroatom | |
| 1197 3 Anot%not-A - atom involved in one or more multiple bonds, not aromatic | |
| 1198 4 A(AAAA) or AA(A)(A)A - atom with at least four neighbors | |
| 1199 5 A(QQ) or QA(Q) - atom with at least two heteroatom neighbors | |
| 1200 6 A(QQQ) or QA(Q)Q - atom with at least three heteroatom neighbors | |
| 1201 7 QH - heteroatom with at least one hydrogen attached | |
| 1202 8 CH2(AA) or ACH2A - carbon with at least two single bonds and at least | |
| 1203 two hydrogens attached | |
| 1204 9 CH3(A) or ACH3 - carbon with at least one single bond and at least three | |
| 1205 hydrogens attached | |
| 1206 10 Halogen | |
| 1207 11 A(-A-A-A) or A-A(-A)-A - atom has at least three single bonds | |
| 1208 12 AAAAAA@1 > 2 - atom is in at least two different six-membered rings | |
| 1209 13 A($A$A$A) or A$A($A)$A - atom has more than two ring bonds | |
| 1210 14 A$A!A$A - atom is at a ring/chain boundary. When a comparison is done | |
| 1211 with another atom the path passes through the chain bond. | |
| 1212 15 Anot%A%Anot%A - atom is at an aromatic/nonaromatic boundary. When a | |
| 1213 comparison is done with another atom the path | |
| 1214 passes through the aromatic bond. | |
| 1215 16 A!A!A - atom with more than one chain bond | |
| 1216 17 A!A$A!A - atom is at a ring/chain boundary. When a comparison is done | |
| 1217 with another atom the path passes through the ring bond. | |
| 1218 18 A%Anot%A%A - atom is at an aromatic/nonaromatic boundary. When a | |
| 1219 comparison is done with another atom the | |
| 1220 path passes through the nonaromatic bond. | |
| 1221 19 HETEROCYCLE - atom is a heteroatom in a ring. | |
| 1222 20 rare properties: atom with five or more neighbors, atom in | |
| 1223 four or more rings, or atom types other than | |
| 1224 H, C, N, O, S, F, Cl, Br, or I | |
| 1225 21 rare properties: atom has a charge, is an isotope, has two or | |
| 1226 more multiple bonds, or has a triple bond. | |
| 1227 22 N - nitrogen | |
| 1228 23 S - sulfur | |
| 1229 24 O - oxygen | |
| 1230 25 A(AA)A(A)A(AA) - atom has two neighbors, each with three or | |
| 1231 more neighbors (including the central atom). | |
| 1232 26 CHACH2 - atom has two hydrocarbon (CH2) neighbors | |
| 1233 | |
| 1234 Atomic environments properties-based keys (32): | |
| 1235 | |
| 1236 Key Description | |
| 1237 27 C(CC) | |
| 1238 28 C(CCC) | |
| 1239 29 C(CN) | |
| 1240 30 C(CCN) | |
| 1241 31 C(NN) | |
| 1242 32 C(NNC) | |
| 1243 33 C(NNN) | |
| 1244 34 C(CO) | |
| 1245 35 C(CCO) | |
| 1246 36 C(NO) | |
| 1247 37 C(NCO) | |
| 1248 38 C(NNO) | |
| 1249 39 C(OO) | |
| 1250 40 C(COO) | |
| 1251 41 C(NOO) | |
| 1252 42 C(OOO) | |
| 1253 43 Q(CC) | |
| 1254 44 Q(CCC) | |
| 1255 45 Q(CN) | |
| 1256 46 Q(CCN) | |
| 1257 47 Q(NN) | |
| 1258 48 Q(CNN) | |
| 1259 49 Q(NNN) | |
| 1260 50 Q(CO) | |
| 1261 51 Q(CCO) | |
| 1262 52 Q(NO) | |
| 1263 53 Q(CNO) | |
| 1264 54 Q(NNO) | |
| 1265 55 Q(OO) | |
| 1266 56 Q(COO) | |
| 1267 57 Q(NOO) | |
| 1268 58 Q(OOO) | |
| 1269 | |
| 1270 Note: The first symbol is the central atom, with atoms bonded to the central atom listed in | |
| 1271 parentheses. Q is any non-C, non-H atom. If only two atoms are in parentheses, there is | |
| 1272 no implication concerning the other atoms bonded to the central atom. | |
| 1273 | |
| 1274 Atom-Bond-Atom properties-based keys: (264) | |
| 1275 | |
| 1276 Key Description | |
| 1277 59 C-C | |
| 1278 60 C-N | |
| 1279 61 C-O | |
| 1280 62 C-S | |
| 1281 63 C-Cl | |
| 1282 64 C-P | |
| 1283 65 C-F | |
| 1284 66 C-Br | |
| 1285 67 C-Si | |
| 1286 68 C-I | |
| 1287 69 C-X | |
| 1288 70 N-N | |
| 1289 71 N-O | |
| 1290 72 N-S | |
| 1291 73 N-Cl | |
| 1292 74 N-P | |
| 1293 75 N-F | |
| 1294 76 N-Br | |
| 1295 77 N-Si | |
| 1296 78 N-I | |
| 1297 79 N-X | |
| 1298 80 O-O | |
| 1299 81 O-S | |
| 1300 82 O-Cl | |
| 1301 83 O-P | |
| 1302 84 O-F | |
| 1303 85 O-Br | |
| 1304 86 O-Si | |
| 1305 87 O-I | |
| 1306 88 O-X | |
| 1307 89 S-S | |
| 1308 90 S-Cl | |
| 1309 91 S-P | |
| 1310 92 S-F | |
| 1311 93 S-Br | |
| 1312 94 S-Si | |
| 1313 95 S-I | |
| 1314 96 S-X | |
| 1315 97 Cl-Cl | |
| 1316 98 Cl-P | |
| 1317 99 Cl-F | |
| 1318 100 Cl-Br | |
| 1319 101 Cl-Si | |
| 1320 102 Cl-I | |
| 1321 103 Cl-X | |
| 1322 104 P-P | |
| 1323 105 P-F | |
| 1324 106 P-Br | |
| 1325 107 P-Si | |
| 1326 108 P-I | |
| 1327 109 P-X | |
| 1328 110 F-F | |
| 1329 111 F-Br | |
| 1330 112 F-Si | |
| 1331 113 F-I | |
| 1332 114 F-X | |
| 1333 115 Br-Br | |
| 1334 116 Br-Si | |
| 1335 117 Br-I | |
| 1336 118 Br-X | |
| 1337 119 Si-Si | |
| 1338 120 Si-I | |
| 1339 121 Si-X | |
| 1340 122 I-I | |
| 1341 123 I-X | |
| 1342 124 X-X | |
| 1343 125 C=C | |
| 1344 126 C=N | |
| 1345 127 C=O | |
| 1346 128 C=S | |
| 1347 129 C=Cl | |
| 1348 130 C=P | |
| 1349 131 C=F | |
| 1350 132 C=Br | |
| 1351 133 C=Si | |
| 1352 134 C=I | |
| 1353 135 C=X | |
| 1354 136 N=N | |
| 1355 137 N=O | |
| 1356 138 N=S | |
| 1357 139 N=Cl | |
| 1358 140 N=P | |
| 1359 141 N=F | |
| 1360 142 N=Br | |
| 1361 143 N=Si | |
| 1362 144 N=I | |
| 1363 145 N=X | |
| 1364 146 O=O | |
| 1365 147 O=S | |
| 1366 148 O=Cl | |
| 1367 149 O=P | |
| 1368 150 O=F | |
| 1369 151 O=Br | |
| 1370 152 O=Si | |
| 1371 153 O=I | |
| 1372 154 O=X | |
| 1373 155 S=S | |
| 1374 156 S=Cl | |
| 1375 157 S=P | |
| 1376 158 S=F | |
| 1377 159 S=Br | |
| 1378 160 S=Si | |
| 1379 161 S=I | |
| 1380 162 S=X | |
| 1381 163 Cl=Cl | |
| 1382 164 Cl=P | |
| 1383 165 Cl=F | |
| 1384 166 Cl=Br | |
| 1385 167 Cl=Si | |
| 1386 168 Cl=I | |
| 1387 169 Cl=X | |
| 1388 170 P=P | |
| 1389 171 P=F | |
| 1390 172 P=Br | |
| 1391 173 P=Si | |
| 1392 174 P=I | |
| 1393 175 P=X | |
| 1394 176 F=F | |
| 1395 177 F=Br | |
| 1396 178 F=Si | |
| 1397 179 F=I | |
| 1398 180 F=X | |
| 1399 181 Br=Br | |
| 1400 182 Br=Si | |
| 1401 183 Br=I | |
| 1402 184 Br=X | |
| 1403 185 Si=Si | |
| 1404 186 Si=I | |
| 1405 187 Si=X | |
| 1406 188 I=I | |
| 1407 189 I=X | |
| 1408 190 X=X | |
| 1409 191 C#C | |
| 1410 192 C#N | |
| 1411 193 C#O | |
| 1412 194 C#S | |
| 1413 195 C#Cl | |
| 1414 196 C#P | |
| 1415 197 C#F | |
| 1416 198 C#Br | |
| 1417 199 C#Si | |
| 1418 200 C#I | |
| 1419 201 C#X | |
| 1420 202 N#N | |
| 1421 203 N#O | |
| 1422 204 N#S | |
| 1423 205 N#Cl | |
| 1424 206 N#P | |
| 1425 207 N#F | |
| 1426 208 N#Br | |
| 1427 209 N#Si | |
| 1428 210 N#I | |
| 1429 211 N#X | |
| 1430 212 O#O | |
| 1431 213 O#S | |
| 1432 214 O#Cl | |
| 1433 215 O#P | |
| 1434 216 O#F | |
| 1435 217 O#Br | |
| 1436 218 O#Si | |
| 1437 219 O#I | |
| 1438 220 O#X | |
| 1439 221 S#S | |
| 1440 222 S#Cl | |
| 1441 223 S#P | |
| 1442 224 S#F | |
| 1443 225 S#Br | |
| 1444 226 S#Si | |
| 1445 227 S#I | |
| 1446 228 S#X | |
| 1447 229 Cl#Cl | |
| 1448 230 Cl#P | |
| 1449 231 Cl#F | |
| 1450 232 Cl#Br | |
| 1451 233 Cl#Si | |
| 1452 234 Cl#I | |
| 1453 235 Cl#X | |
| 1454 236 P#P | |
| 1455 237 P#F | |
| 1456 238 P#Br | |
| 1457 239 P#Si | |
| 1458 240 P#I | |
| 1459 241 P#X | |
| 1460 242 F#F | |
| 1461 243 F#Br | |
| 1462 244 F#Si | |
| 1463 245 F#I | |
| 1464 246 F#X | |
| 1465 247 Br#Br | |
| 1466 248 Br#Si | |
| 1467 249 Br#I | |
| 1468 250 Br#X | |
| 1469 251 Si#Si | |
| 1470 252 Si#I | |
| 1471 253 Si#X | |
| 1472 254 I#I | |
| 1473 255 I#X | |
| 1474 256 X#X | |
| 1475 257 C$C | |
| 1476 258 C$N | |
| 1477 259 C$O | |
| 1478 260 C$S | |
| 1479 261 C$Cl | |
| 1480 262 C$P | |
| 1481 263 C$F | |
| 1482 264 C$Br | |
| 1483 265 C$Si | |
| 1484 266 C$I | |
| 1485 267 C$X | |
| 1486 268 N$N | |
| 1487 269 N$O | |
| 1488 270 N$S | |
| 1489 271 N$Cl | |
| 1490 272 N$P | |
| 1491 273 N$F | |
| 1492 274 N$Br | |
| 1493 275 N$Si | |
| 1494 276 N$I | |
| 1495 277 N$X | |
| 1496 278 O$O | |
| 1497 279 O$S | |
| 1498 280 O$Cl | |
| 1499 281 O$P | |
| 1500 282 O$F | |
| 1501 283 O$Br | |
| 1502 284 O$Si | |
| 1503 285 O$I | |
| 1504 286 O$X | |
| 1505 287 S$S | |
| 1506 288 S$Cl | |
| 1507 289 S$P | |
| 1508 290 S$F | |
| 1509 291 S$Br | |
| 1510 292 S$Si | |
| 1511 293 S$I | |
| 1512 294 S$X | |
| 1513 295 Cl$Cl | |
| 1514 296 Cl$P | |
| 1515 297 Cl$F | |
| 1516 298 Cl$Br | |
| 1517 299 Cl$Si | |
| 1518 300 Cl$I | |
| 1519 301 Cl$X | |
| 1520 302 P$P | |
| 1521 303 P$F | |
| 1522 304 P$Br | |
| 1523 305 P$Si | |
| 1524 306 P$I | |
| 1525 307 P$X | |
| 1526 308 F$F | |
| 1527 309 F$Br | |
| 1528 310 F$Si | |
| 1529 311 F$I | |
| 1530 312 F$X | |
| 1531 313 Br$Br | |
| 1532 314 Br$Si | |
| 1533 315 Br$I | |
| 1534 316 Br$X | |
| 1535 317 Si$Si | |
| 1536 318 Si$I | |
| 1537 319 Si$X | |
| 1538 320 I$I | |
| 1539 321 I$X | |
| 1540 322 X$X | |
| 1541 | |
| 1542 =item B<--OutDelim> I<comma | tab | semicolon> | |
| 1543 | |
| 1544 Delimiter for output CSV/TSV text file(s). Possible values: I<comma, tab, or semicolon> | |
| 1545 Default value: I<comma>. | |
| 1546 | |
| 1547 =item B<--output> I<SD | FP | text | all> | |
| 1548 | |
| 1549 Type of output files to generate. Possible values: I<SD, FP, text, or all>. Default value: I<text>. | |
| 1550 | |
| 1551 =item B<-o, --overwrite> | |
| 1552 | |
| 1553 Overwrite existing files. | |
| 1554 | |
| 1555 =item B<-q, --quote> I<Yes | No> | |
| 1556 | |
| 1557 Put quote around column values in output CSV/TSV text file(s). Possible values: | |
| 1558 I<Yes or No>. Default value: I<Yes>. | |
| 1559 | |
| 1560 =item B<-r, --root> I<RootName> | |
| 1561 | |
| 1562 New file name is generated using the root: <Root>.<Ext>. Default for new file | |
| 1563 names: <SDFileName><MACCSKeysFP>.<Ext>. The file type determines <Ext> value. | |
| 1564 The sdf, fpf, csv, and tsv <Ext> values are used for SD, FP, comma/semicolon, and tab | |
| 1565 delimited text files, respectively.This option is ignored for multiple input files. | |
| 1566 | |
| 1567 =item B<-s, --size> I<number> | |
| 1568 | |
| 1569 Size of MACCS keys [ Ref 45-47 ] set to use during fingerprints generation. Possible values: I<166 or 322>. | |
| 1570 Default value: I<166>. | |
| 1571 | |
| 1572 =item B<-v, --VectorStringFormat> I<ValuesString | IDsAndValuesString | IDsAndValuesPairsString | ValuesAndIDsString | ValuesAndIDsPairsString> | |
| 1573 | |
| 1574 Format of fingerprints vector string data in output SD, FP or CSV/TSV text file(s) specified by | |
| 1575 B<--output> used during I<MACCSKeyCount> value of B<-m, --mode> option. Possible | |
| 1576 values: I<ValuesString, IDsAndValuesString | IDsAndValuesPairsString | ValuesAndIDsString | | |
| 1577 ValuesAndIDsPairsString>. Defaultvalue: I<ValuesString>. | |
| 1578 | |
| 1579 Examples: | |
| 1580 | |
| 1581 FingerprintsVector;MACCSKeyCount;166;OrderedNumericalValues;ValuesStri | |
| 1582 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 | |
| 1583 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 | |
| 1584 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 | |
| 1585 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 | |
| 1586 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 | |
| 1587 | |
| 1588 FingerprintsVector;MACCSKeyCount;322;OrderedNumericalValues;ValuesStri | |
| 1589 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 | |
| 1590 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 | |
| 1591 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 | |
| 1592 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 | |
| 1593 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 ... | |
| 1594 | |
| 1595 =item B<-w, --WorkingDir> I<DirName> | |
| 1596 | |
| 1597 Location of working directory. Default: current directory. | |
| 1598 | |
| 1599 =back | |
| 1600 | |
| 1601 =head1 EXAMPLES | |
| 1602 | |
| 1603 To generate MACCS keys fingerprints of size 166 in binary bit-vector string format | |
| 1604 and create a SampleMACCS166FPBin.csv file containing sequential compound IDs along with | |
| 1605 fingerprints bit-vector strings data, type: | |
| 1606 | |
| 1607 % MACCSKeysFingerprints.pl -r SampleMACCS166FPBin -o Sample.sdf | |
| 1608 | |
| 1609 To generate MACCS keys fingerprints of size 166 in binary bit-vector string format | |
| 1610 and create SampleMACCS166FPBin.sdf, SampleMACCS166FPBin.csv and SampleMACCS166FPBin.csv | |
| 1611 files containing sequential compound IDs in CSV file along with fingerprints bit-vector strings data, type: | |
| 1612 | |
| 1613 % MACCSKeysFingerprints.pl --output all -r SampleMACCS166FPBin | |
| 1614 -o Sample.sdf | |
| 1615 | |
| 1616 To generate MACCS keys fingerprints of size 322 in binary bit-vector string format | |
| 1617 and create a SampleMACCS322FPBin.csv file containing sequential compound IDs along with | |
| 1618 fingerprints bit-vector strings data, type: | |
| 1619 | |
| 1620 % MACCSKeysFingerprints.pl -size 322 -r SampleMACCS322FPBin -o Sample.sdf | |
| 1621 | |
| 1622 To generate MACCS keys fingerprints of size 166 corresponding to count of keys in | |
| 1623 ValuesString format and create a SampleMACCS166FPCount.csv file containing sequential | |
| 1624 compound IDs along with fingerprints vector strings data, type: | |
| 1625 | |
| 1626 % MACCSKeysFingerprints.pl -m MACCSKeyCount -r SampleMACCS166FPCount | |
| 1627 -o Sample.sdf | |
| 1628 | |
| 1629 To generate MACCS keys fingerprints of size 322 corresponding to count of keys in | |
| 1630 ValuesString format and create a SampleMACCS322FPCount.csv file containing sequential | |
| 1631 compound IDs along with fingerprints vector strings data, type: | |
| 1632 | |
| 1633 % MACCSKeysFingerprints.pl -m MACCSKeyCount -size 322 | |
| 1634 -r SampleMACCS322FPCount -o Sample.sdf | |
| 1635 | |
| 1636 To generate MACCS keys fingerprints of size 166 in hexadecimal bit-vector string format with | |
| 1637 ascending bits order and create a SampleMACCS166FPHex.csv file containing compound IDs | |
| 1638 from MolName along with fingerprints bit-vector strings data, type: | |
| 1639 | |
| 1640 % MACCSKeysFingerprints.pl -m MACCSKeyBits --size 166 --BitStringFormat | |
| 1641 HexadecimalString --BitsOrder Ascending --DataFieldsMode CompoundID | |
| 1642 --CompoundIDMode MolName -r SampleMACCS166FPBin -o Sample.sdf | |
| 1643 | |
| 1644 To generate MACCS keys fingerprints of size 166 corresponding to count of keys in | |
| 1645 IDsAndValuesString format and create a SampleMACCS166FPCount.csv file containing | |
| 1646 compound IDs from MolName line along with fingerprints vector strings data, type: | |
| 1647 | |
| 1648 % MACCSKeysFingerprints.pl -m MACCSKeyCount --size 166 | |
| 1649 --VectorStringFormat IDsAndValuesString --DataFieldsMode CompoundID | |
| 1650 --CompoundIDMode MolName -r SampleMACCS166FPCount -o Sample.sdf | |
| 1651 | |
| 1652 To generate MACCS keys fingerprints of size 166 corresponding to count of keys in | |
| 1653 IDsAndValuesString format and create a SampleMACCS166FPCount.csv file containing | |
| 1654 compound IDs using specified data field along with fingerprints vector strings data, type: | |
| 1655 | |
| 1656 % MACCSKeysFingerprints.pl -m MACCSKeyCount --size 166 | |
| 1657 --VectorStringFormat IDsAndValuesString --DataFieldsMode CompoundID | |
| 1658 --CompoundIDMode DataField --CompoundID Mol_ID -r | |
| 1659 SampleMACCS166FPCount -o Sample.sdf | |
| 1660 | |
| 1661 To generate MACCS keys fingerprints of size 322 corresponding to count of keys in | |
| 1662 ValuesString format and create a SampleMACCS322FPCount.tsv file containing compound | |
| 1663 IDs derived from combination of molecule name line and an explicit compound prefix | |
| 1664 along with fingerprints vector strings data in a column labels MACCSKeyCountFP, type: | |
| 1665 | |
| 1666 % MACCSKeysFingerprints.pl -m MACCSKeyCount -size 322 --DataFieldsMode | |
| 1667 CompoundID --CompoundIDMode MolnameOrLabelPrefix --CompoundID Cmpd | |
| 1668 --CompoundIDLabel MolID --FingerprintsLabel MACCSKeyCountFP --OutDelim | |
| 1669 Tab -r SampleMACCS322FPCount -o Sample.sdf | |
| 1670 | |
| 1671 To generate MACCS keys fingerprints of size 166 corresponding to count of keys in | |
| 1672 ValuesString format and create a SampleMACCS166FPCount.csv file containing | |
| 1673 specific data fields columns along with fingerprints vector strings data, type: | |
| 1674 | |
| 1675 % MACCSKeysFingerprints.pl -m MACCSKeyCount --size 166 | |
| 1676 --VectorStringFormat ValuesString --DataFieldsMode Specify --DataFields | |
| 1677 Mol_ID -r SampleMACCS166FPCount -o Sample.sdf | |
| 1678 | |
| 1679 To generate MACCS keys fingerprints of size 322 corresponding to count of keys in | |
| 1680 ValuesString format and create a SampleMACCS322FPCount.csv file containing | |
| 1681 common data fields columns along with fingerprints vector strings data, type: | |
| 1682 | |
| 1683 % MACCSKeysFingerprints.pl -m MACCSKeyCount --size 322 | |
| 1684 --VectorStringFormat ValuesString --DataFieldsMode Common -r | |
| 1685 SampleMACCS322FPCount -o Sample.sdf | |
| 1686 | |
| 1687 To generate MACCS keys fingerprints of size 166 corresponding to count of keys in | |
| 1688 ValuesString format and create SampleMACCS166FPCount.sdf, SampleMACCS166FPCount.fpf and | |
| 1689 SampleMACCS166FPCount.csv files containing all data fields columns in CSV file | |
| 1690 along with fingerprints vector strings data, type: | |
| 1691 | |
| 1692 % MACCSKeysFingerprints.pl -m MACCSKeyCount --size 166 --output all | |
| 1693 --VectorStringFormat ValuesString --DataFieldsMode All -r | |
| 1694 SampleMACCS166FPCount -o Sample.sdf | |
| 1695 | |
| 1696 =head1 AUTHOR | |
| 1697 | |
| 1698 Manish Sud <msud@san.rr.com> | |
| 1699 | |
| 1700 =head1 SEE ALSO | |
| 1701 | |
| 1702 InfoFingerprintsFiles.pl, SimilarityMatricesFingerprints.pl, AtomNeighborhoodsFingerprints.pl, | |
| 1703 ExtendedConnectivityFingerprints.pl, PathLengthFingerprints.pl, | |
| 1704 TopologicalAtomPairsFingerprints.pl, TopologicalAtomTorsionsFingerprints.pl, | |
| 1705 TopologicalPharmacophoreAtomPairsFingerprints.pl, TopologicalPharmacophoreAtomTripletsFingerprints.pl | |
| 1706 | |
| 1707 =head1 COPYRIGHT | |
| 1708 | |
| 1709 Copyright (C) 2015 Manish Sud. All rights reserved. | |
| 1710 | |
| 1711 This file is part of MayaChemTools. | |
| 1712 | |
| 1713 MayaChemTools is free software; you can redistribute it and/or modify it under | |
| 1714 the terms of the GNU Lesser General Public License as published by the Free | |
| 1715 Software Foundation; either version 3 of the License, or (at your option) | |
| 1716 any later version. | |
| 1717 | |
| 1718 =cut |