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