1 #!/usr/bin/perl -w 2 # 3 # $RCSfile: EStateIndiciesFingerprints.pl,v $ 4 # $Date: 2015/02/28 20:46:19 $ 5 # $Revision: 1.23 $ 6 # 7 # Author: Manish Sud <msud@san.rr.com> 8 # 9 # Copyright (C) 2015 Manish Sud. All rights reserved. 10 # 11 # This file is part of MayaChemTools. 12 # 13 # MayaChemTools is free software; you can redistribute it and/or modify it under 14 # the terms of the GNU Lesser General Public License as published by the Free 15 # Software Foundation; either version 3 of the License, or (at your option) any 16 # later version. 17 # 18 # MayaChemTools is distributed in the hope that it will be useful, but without 19 # any warranty; without even the implied warranty of merchantability of fitness 20 # for a particular purpose. See the GNU Lesser General Public License for more 21 # details. 22 # 23 # You should have received a copy of the GNU Lesser General Public License 24 # along with MayaChemTools; if not, see <http://www.gnu.org/licenses/> or 25 # write to the Free Software Foundation Inc., 59 Temple Place, Suite 330, 26 # Boston, MA, 02111-1307, USA. 27 # 28 29 use strict; 30 use FindBin; use lib "$FindBin::Bin/../lib"; 31 use Getopt::Long; 32 use File::Basename; 33 use Text::ParseWords; 34 use Benchmark; 35 use FileUtil; 36 use TextUtil; 37 use SDFileUtil; 38 use MoleculeFileIO; 39 use FileIO::FingerprintsSDFileIO; 40 use FileIO::FingerprintsTextFileIO; 41 use FileIO::FingerprintsFPFileIO; 42 use AtomTypes::EStateAtomTypes; 43 use Fingerprints::EStateIndiciesFingerprints; 44 45 my($ScriptName, %Options, $StartTime, $EndTime, $TotalTime); 46 47 # Autoflush STDOUT 48 $| = 1; 49 50 # Starting message... 51 $ScriptName = basename($0); 52 print "\n$ScriptName: Starting...\n\n"; 53 $StartTime = new Benchmark; 54 55 # Get the options and setup script... 56 SetupScriptUsage(); 57 if ($Options{help} || @ARGV < 1) { 58 die GetUsageFromPod("$FindBin::Bin/$ScriptName"); 59 } 60 61 my(@SDFilesList); 62 @SDFilesList = ExpandFileNames(\@ARGV, "sdf sd"); 63 64 # Process options... 65 print "Processing options...\n"; 66 my(%OptionsInfo); 67 ProcessOptions(); 68 69 # Setup information about input files... 70 print "Checking input SD file(s)...\n"; 71 my(%SDFilesInfo); 72 RetrieveSDFilesInfo(); 73 74 # Process input files.. 75 my($FileIndex); 76 if (@SDFilesList > 1) { 77 print "\nProcessing SD files...\n"; 78 } 79 for $FileIndex (0 .. $#SDFilesList) { 80 if ($SDFilesInfo{FileOkay}[$FileIndex]) { 81 print "\nProcessing file $SDFilesList[$FileIndex]...\n"; 82 GenerateEStateIndiciesFingerprints($FileIndex); 83 } 84 } 85 print "\n$ScriptName:Done...\n\n"; 86 87 $EndTime = new Benchmark; 88 $TotalTime = timediff ($EndTime, $StartTime); 89 print "Total time: ", timestr($TotalTime), "\n"; 90 91 ############################################################################### 92 93 # Generate fingerprints for a SD file... 94 # 95 sub GenerateEStateIndiciesFingerprints { 96 my($FileIndex) = @_; 97 my($CmpdCount, $IgnoredCmpdCount, $SDFile, $MoleculeFileIO, $Molecule, $EStateIndiciesFingerprints, $NewFPSDFileIO, $NewFPTextFileIO, $NewFPFileIO); 98 99 $SDFile = $SDFilesList[$FileIndex]; 100 101 # Setup output files... 102 # 103 ($NewFPSDFileIO, $NewFPTextFileIO, $NewFPFileIO) = SetupAndOpenOutputFiles($FileIndex); 104 105 $MoleculeFileIO = new MoleculeFileIO('Name' => $SDFile); 106 $MoleculeFileIO->Open(); 107 108 $CmpdCount = 0; 109 $IgnoredCmpdCount = 0; 110 111 COMPOUND: while ($Molecule = $MoleculeFileIO->ReadMolecule()) { 112 $CmpdCount++; 113 114 # Filter compound data before calculating fingerprints... 115 if ($OptionsInfo{Filter}) { 116 if (CheckAndFilterCompound($CmpdCount, $Molecule)) { 117 $IgnoredCmpdCount++; 118 next COMPOUND; 119 } 120 } 121 122 $EStateIndiciesFingerprints = GenerateMoleculeFingerprints($Molecule); 123 if (!$EStateIndiciesFingerprints) { 124 $IgnoredCmpdCount++; 125 ProcessIgnoredCompound('FingerprintsGenerationFailed', $CmpdCount, $Molecule); 126 next COMPOUND; 127 } 128 129 WriteDataToOutputFiles($FileIndex, $CmpdCount, $Molecule, $EStateIndiciesFingerprints, $NewFPSDFileIO, $NewFPTextFileIO, $NewFPFileIO); 130 } 131 $MoleculeFileIO->Close(); 132 133 if ($NewFPSDFileIO) { 134 $NewFPSDFileIO->Close(); 135 } 136 if ($NewFPTextFileIO) { 137 $NewFPTextFileIO->Close(); 138 } 139 if ($NewFPFileIO) { 140 $NewFPFileIO->Close(); 141 } 142 143 WriteFingerprintsGenerationSummaryStatistics($CmpdCount, $IgnoredCmpdCount); 144 } 145 146 # Process compound being ignored due to problems in fingerprints geneation... 147 # 148 sub ProcessIgnoredCompound { 149 my($Mode, $CmpdCount, $Molecule) = @_; 150 my($CmpdID, $DataFieldLabelAndValuesRef); 151 152 $DataFieldLabelAndValuesRef = $Molecule->GetDataFieldLabelAndValues(); 153 $CmpdID = SetupCmpdIDForOutputFiles($CmpdCount, $Molecule, $DataFieldLabelAndValuesRef); 154 155 MODE: { 156 if ($Mode =~ /^ContainsNonElementalData$/i) { 157 warn "\nWarning: Ignoring compound record number $CmpdCount with ID $CmpdID: Compound contains atom data corresponding to non-elemental atom symbol(s)...\n\n"; 158 next MODE; 159 } 160 161 if ($Mode =~ /^ContainsNoElementalData$/i) { 162 warn "\nWarning: Ignoring compound record number $CmpdCount with ID $CmpdID: Compound contains no atom data...\n\n"; 163 next MODE; 164 } 165 166 if ($Mode =~ /^FingerprintsGenerationFailed$/i) { 167 warn "\nWarning: Ignoring compound record number $CmpdCount with ID $CmpdID: Fingerprints generation didn't succeed...\n\n"; 168 next MODE; 169 } 170 warn "\nWarning: Ignoring compound record number $CmpdCount with ID $CmpdID: Fingerprints generation didn't succeed...\n\n"; 171 } 172 } 173 174 # Check and filter compounds.... 175 # 176 sub CheckAndFilterCompound { 177 my($CmpdCount, $Molecule) = @_; 178 my($ElementCount, $NonElementCount); 179 180 ($ElementCount, $NonElementCount) = $Molecule->GetNumOfElementsAndNonElements(); 181 182 if ($NonElementCount) { 183 ProcessIgnoredCompound('ContainsNonElementalData', $CmpdCount, $Molecule); 184 return 1; 185 } 186 187 if (!$ElementCount) { 188 ProcessIgnoredCompound('ContainsNoElementalData', $CmpdCount, $Molecule); 189 return 1; 190 } 191 192 return 0; 193 } 194 195 # Write out compounds fingerprints generation summary statistics... 196 # 197 sub WriteFingerprintsGenerationSummaryStatistics { 198 my($CmpdCount, $IgnoredCmpdCount) = @_; 199 my($ProcessedCmpdCount); 200 201 $ProcessedCmpdCount = $CmpdCount - $IgnoredCmpdCount; 202 203 print "\nNumber of compounds: $CmpdCount\n"; 204 print "Number of compounds processed successfully during fingerprints generation: $ProcessedCmpdCount\n"; 205 print "Number of compounds ignored during fingerprints generation: $IgnoredCmpdCount\n"; 206 } 207 208 # Open output files... 209 # 210 sub SetupAndOpenOutputFiles { 211 my($FileIndex) = @_; 212 my($NewFPSDFile, $NewFPFile, $NewFPTextFile, $NewFPSDFileIO, $NewFPTextFileIO, $NewFPFileIO, %FingerprintsFileIOParams); 213 214 ($NewFPSDFileIO, $NewFPTextFileIO, $NewFPFileIO) = (undef) x 3; 215 216 # Setup common parameters for fingerprints file IO objects... 217 # 218 %FingerprintsFileIOParams = (); 219 %FingerprintsFileIOParams = ('Mode' => 'Write', 'Overwrite' => $OptionsInfo{OverwriteFiles}, 'FingerprintsStringMode' => 'FingerprintsVectorString', 'VectorStringFormat' => $OptionsInfo{VectorStringFormat}); 220 221 if ($OptionsInfo{SDOutput}) { 222 $NewFPSDFile = $SDFilesInfo{SDOutFileNames}[$FileIndex]; 223 print "Generating SD file $NewFPSDFile...\n"; 224 $NewFPSDFileIO = new FileIO::FingerprintsSDFileIO('Name' => $NewFPSDFile, %FingerprintsFileIOParams, 'FingerprintsFieldLabel' => $OptionsInfo{FingerprintsLabel}); 225 $NewFPSDFileIO->Open(); 226 } 227 228 if ($OptionsInfo{FPOutput}) { 229 $NewFPFile = $SDFilesInfo{FPOutFileNames}[$FileIndex]; 230 print "Generating FP file $NewFPFile...\n"; 231 $NewFPFileIO = new FileIO::FingerprintsFPFileIO('Name' => $NewFPFile, %FingerprintsFileIOParams); 232 $NewFPFileIO->Open(); 233 } 234 235 if ($OptionsInfo{TextOutput}) { 236 my($ColLabelsRef); 237 238 $NewFPTextFile = $SDFilesInfo{TextOutFileNames}[$FileIndex]; 239 $ColLabelsRef = SetupFPTextFileCoulmnLabels($FileIndex); 240 241 print "Generating text file $NewFPTextFile...\n"; 242 $NewFPTextFileIO = new FileIO::FingerprintsTextFileIO('Name' => $NewFPTextFile, %FingerprintsFileIOParams, 'DataColLabels' => $ColLabelsRef, 'OutDelim' => $OptionsInfo{OutDelim}, 'OutQuote' => $OptionsInfo{OutQuote}); 243 $NewFPTextFileIO->Open(); 244 } 245 246 return ($NewFPSDFileIO, $NewFPTextFileIO, $NewFPFileIO); 247 } 248 249 # Write fingerpritns and other data to appropriate output files... 250 # 251 sub WriteDataToOutputFiles { 252 my($FileIndex, $CmpdCount, $Molecule, $EStateIndiciesFingerprints, $NewFPSDFileIO, $NewFPTextFileIO, $NewFPFileIO) = @_; 253 my($DataFieldLabelAndValuesRef); 254 255 $DataFieldLabelAndValuesRef = undef; 256 if ($NewFPTextFileIO || $NewFPFileIO) { 257 $DataFieldLabelAndValuesRef = $Molecule->GetDataFieldLabelAndValues(); 258 } 259 260 if ($NewFPSDFileIO) { 261 my($CmpdString); 262 263 $CmpdString = $Molecule->GetInputMoleculeString(); 264 $NewFPSDFileIO->WriteFingerprints($EStateIndiciesFingerprints, $CmpdString); 265 } 266 267 if ($NewFPTextFileIO) { 268 my($ColValuesRef); 269 270 $ColValuesRef = SetupFPTextFileCoulmnValues($FileIndex, $CmpdCount, $Molecule, $DataFieldLabelAndValuesRef); 271 $NewFPTextFileIO->WriteFingerprints($EStateIndiciesFingerprints, $ColValuesRef); 272 } 273 274 if ($NewFPFileIO) { 275 my($CompoundID); 276 277 $CompoundID = SetupCmpdIDForOutputFiles($CmpdCount, $Molecule, $DataFieldLabelAndValuesRef); 278 $NewFPFileIO->WriteFingerprints($EStateIndiciesFingerprints, $CompoundID); 279 } 280 281 } 282 283 # Generate approriate column labels for FPText output file... 284 # 285 sub SetupFPTextFileCoulmnLabels { 286 my($FileIndex) = @_; 287 my($Line, @ColLabels); 288 289 @ColLabels = (); 290 if ($OptionsInfo{DataFieldsMode} =~ /^All$/i) { 291 push @ColLabels, @{$SDFilesInfo{AllDataFieldsRef}[$FileIndex]}; 292 } 293 elsif ($OptionsInfo{DataFieldsMode} =~ /^Common$/i) { 294 push @ColLabels, @{$SDFilesInfo{CommonDataFieldsRef}[$FileIndex]}; 295 } 296 elsif ($OptionsInfo{DataFieldsMode} =~ /^Specify$/i) { 297 push @ColLabels, @{$OptionsInfo{SpecifiedDataFields}}; 298 } 299 elsif ($OptionsInfo{DataFieldsMode} =~ /^CompoundID$/i) { 300 push @ColLabels, $OptionsInfo{CompoundIDLabel}; 301 } 302 # Add fingerprints label... 303 push @ColLabels, $OptionsInfo{FingerprintsLabel}; 304 305 return \@ColLabels; 306 } 307 308 # Generate column values FPText output file.. 309 # 310 sub SetupFPTextFileCoulmnValues { 311 my($FileIndex, $CmpdCount, $Molecule, $DataFieldLabelAndValuesRef) = @_; 312 my(@ColValues); 313 314 @ColValues = (); 315 if ($OptionsInfo{DataFieldsMode} =~ /^CompoundID$/i) { 316 push @ColValues, SetupCmpdIDForOutputFiles($CmpdCount, $Molecule, $DataFieldLabelAndValuesRef); 317 } 318 elsif ($OptionsInfo{DataFieldsMode} =~ /^All$/i) { 319 @ColValues = map { exists $DataFieldLabelAndValuesRef->{$_} ? $DataFieldLabelAndValuesRef->{$_} : ''} @{$SDFilesInfo{AllDataFieldsRef}[$FileIndex]}; 320 } 321 elsif ($OptionsInfo{DataFieldsMode} =~ /^Common$/i) { 322 @ColValues = map { exists $DataFieldLabelAndValuesRef->{$_} ? $DataFieldLabelAndValuesRef->{$_} : ''} @{$SDFilesInfo{CommonDataFieldsRef}[$FileIndex]}; 323 } 324 elsif ($OptionsInfo{DataFieldsMode} =~ /^Specify$/i) { 325 @ColValues = map { exists $DataFieldLabelAndValuesRef->{$_} ? $DataFieldLabelAndValuesRef->{$_} : ''} @{$OptionsInfo{SpecifiedDataFields}}; 326 } 327 328 return \@ColValues; 329 } 330 331 # Generate compound ID for FP and FPText output files.. 332 # 333 sub SetupCmpdIDForOutputFiles { 334 my($CmpdCount, $Molecule, $DataFieldLabelAndValuesRef) = @_; 335 my($CmpdID); 336 337 $CmpdID = ''; 338 if ($OptionsInfo{CompoundIDMode} =~ /^MolNameOrLabelPrefix$/i) { 339 my($MolName); 340 $MolName = $Molecule->GetName(); 341 $CmpdID = $MolName ? $MolName : "$OptionsInfo{CompoundID}${CmpdCount}"; 342 } 343 elsif ($OptionsInfo{CompoundIDMode} =~ /^LabelPrefix$/i) { 344 $CmpdID = "$OptionsInfo{CompoundID}${CmpdCount}"; 345 } 346 elsif ($OptionsInfo{CompoundIDMode} =~ /^DataField$/i) { 347 my($SpecifiedDataField); 348 $SpecifiedDataField = $OptionsInfo{CompoundID}; 349 $CmpdID = exists $DataFieldLabelAndValuesRef->{$SpecifiedDataField} ? $DataFieldLabelAndValuesRef->{$SpecifiedDataField} : ''; 350 } 351 elsif ($OptionsInfo{CompoundIDMode} =~ /^MolName$/i) { 352 $CmpdID = $Molecule->GetName(); 353 } 354 return $CmpdID; 355 } 356 357 # Generate fingerprints for molecule... 358 # 359 sub GenerateMoleculeFingerprints { 360 my($Molecule) = @_; 361 my($EStateIndiciesFingerprints); 362 363 if ($OptionsInfo{KeepLargestComponent}) { 364 $Molecule->KeepLargestComponent(); 365 } 366 if (!$Molecule->DetectRings()) { 367 return undef; 368 } 369 $Molecule->SetAromaticityModel($OptionsInfo{AromaticityModel}); 370 $Molecule->DetectAromaticity(); 371 372 $EStateIndiciesFingerprints = new Fingerprints::EStateIndiciesFingerprints('Molecule' => $Molecule, 'EStateAtomTypesSetToUse' => $OptionsInfo{EStateAtomTypesSetToUse}, 'ValuesPrecision' => $OptionsInfo{ValuesPrecision}); 373 374 # Generate E-state indicies fingerprints... 375 $EStateIndiciesFingerprints->GenerateFingerprints(); 376 377 # Make sure E-state indicies fingerprints generation is successful... 378 if (!$EStateIndiciesFingerprints->IsFingerprintsGenerationSuccessful()) { 379 return undef; 380 } 381 382 return $EStateIndiciesFingerprints; 383 } 384 385 # Retrieve information about SD files... 386 # 387 sub RetrieveSDFilesInfo { 388 my($SDFile, $Index, $FileDir, $FileExt, $FileName, $OutFileRoot, $TextOutFileExt, $SDOutFileExt, $FPOutFileExt, $NewSDFileName, $NewFPFileName, $NewTextFileName, $CheckDataField, $CollectDataFields, $AllDataFieldsRef, $CommonDataFieldsRef); 389 390 %SDFilesInfo = (); 391 @{$SDFilesInfo{FileOkay}} = (); 392 @{$SDFilesInfo{OutFileRoot}} = (); 393 @{$SDFilesInfo{SDOutFileNames}} = (); 394 @{$SDFilesInfo{FPOutFileNames}} = (); 395 @{$SDFilesInfo{TextOutFileNames}} = (); 396 @{$SDFilesInfo{AllDataFieldsRef}} = (); 397 @{$SDFilesInfo{CommonDataFieldsRef}} = (); 398 399 $CheckDataField = ($OptionsInfo{TextOutput} && ($OptionsInfo{DataFieldsMode} =~ /^CompoundID$/i) && ($OptionsInfo{CompoundIDMode} =~ /^DataField$/i)) ? 1 : 0; 400 $CollectDataFields = ($OptionsInfo{TextOutput} && ($OptionsInfo{DataFieldsMode} =~ /^(All|Common)$/i)) ? 1 : 0; 401 402 FILELIST: for $Index (0 .. $#SDFilesList) { 403 $SDFile = $SDFilesList[$Index]; 404 405 $SDFilesInfo{FileOkay}[$Index] = 0; 406 $SDFilesInfo{OutFileRoot}[$Index] = ''; 407 $SDFilesInfo{SDOutFileNames}[$Index] = ''; 408 $SDFilesInfo{FPOutFileNames}[$Index] = ''; 409 $SDFilesInfo{TextOutFileNames}[$Index] = ''; 410 411 $SDFile = $SDFilesList[$Index]; 412 if (!(-e $SDFile)) { 413 warn "Warning: Ignoring file $SDFile: It doesn't exist\n"; 414 next FILELIST; 415 } 416 if (!CheckFileType($SDFile, "sd sdf")) { 417 warn "Warning: Ignoring file $SDFile: It's not a SD file\n"; 418 next FILELIST; 419 } 420 421 if ($CheckDataField) { 422 # Make sure data field exists in SD file.. 423 my($CmpdString, $SpecifiedDataField, @CmpdLines, %DataFieldValues); 424 425 @CmpdLines = (); 426 open SDFILE, "$SDFile" or die "Error: Couldn't open $SDFile: $! \n"; 427 $CmpdString = ReadCmpdString(\*SDFILE); 428 close SDFILE; 429 @CmpdLines = split "\n", $CmpdString; 430 %DataFieldValues = GetCmpdDataHeaderLabelsAndValues(\@CmpdLines); 431 $SpecifiedDataField = $OptionsInfo{CompoundID}; 432 if (!exists $DataFieldValues{$SpecifiedDataField}) { 433 warn "Warning: Ignoring file $SDFile: Data field value, $SpecifiedDataField, using \"--CompoundID\" option in \"DataField\" \"--CompoundIDMode\" doesn't exist\n"; 434 next FILELIST; 435 } 436 } 437 438 $AllDataFieldsRef = ''; 439 $CommonDataFieldsRef = ''; 440 if ($CollectDataFields) { 441 my($CmpdCount); 442 open SDFILE, "$SDFile" or die "Error: Couldn't open $SDFile: $! \n"; 443 ($CmpdCount, $AllDataFieldsRef, $CommonDataFieldsRef) = GetAllAndCommonCmpdDataHeaderLabels(\*SDFILE); 444 close SDFILE; 445 } 446 447 # Setup output file names... 448 $FileDir = ""; $FileName = ""; $FileExt = ""; 449 ($FileDir, $FileName, $FileExt) = ParseFileName($SDFile); 450 451 $TextOutFileExt = "csv"; 452 if ($Options{outdelim} =~ /^tab$/i) { 453 $TextOutFileExt = "tsv"; 454 } 455 $SDOutFileExt = $FileExt; 456 $FPOutFileExt = "fpf"; 457 458 if ($OptionsInfo{OutFileRoot} && (@SDFilesList == 1)) { 459 my ($RootFileDir, $RootFileName, $RootFileExt) = ParseFileName($OptionsInfo{OutFileRoot}); 460 if ($RootFileName && $RootFileExt) { 461 $FileName = $RootFileName; 462 } 463 else { 464 $FileName = $OptionsInfo{OutFileRoot}; 465 } 466 $OutFileRoot = $FileName; 467 } 468 else { 469 $OutFileRoot = "${FileName}EStateIndiciesFP"; 470 } 471 472 $NewSDFileName = "${OutFileRoot}.${SDOutFileExt}"; 473 $NewFPFileName = "${OutFileRoot}.${FPOutFileExt}"; 474 $NewTextFileName = "${OutFileRoot}.${TextOutFileExt}"; 475 476 if ($OptionsInfo{SDOutput}) { 477 if ($SDFile =~ /$NewSDFileName/i) { 478 warn "Warning: Ignoring input file $SDFile: Same output, $NewSDFileName, and input file names.\n"; 479 print "Specify a different name using \"-r --root\" option or use default name.\n"; 480 next FILELIST; 481 } 482 } 483 484 if (!$OptionsInfo{OverwriteFiles}) { 485 # Check SD and text outout files... 486 if ($OptionsInfo{SDOutput}) { 487 if (-e $NewSDFileName) { 488 warn "Warning: Ignoring file $SDFile: The file $NewSDFileName already exists\n"; 489 next FILELIST; 490 } 491 } 492 if ($OptionsInfo{FPOutput}) { 493 if (-e $NewFPFileName) { 494 warn "Warning: Ignoring file $SDFile: The file $NewFPFileName already exists\n"; 495 next FILELIST; 496 } 497 } 498 if ($OptionsInfo{TextOutput}) { 499 if (-e $NewTextFileName) { 500 warn "Warning: Ignoring file $SDFile: The file $NewTextFileName already exists\n"; 501 next FILELIST; 502 } 503 } 504 } 505 506 $SDFilesInfo{FileOkay}[$Index] = 1; 507 508 $SDFilesInfo{OutFileRoot}[$Index] = $OutFileRoot; 509 $SDFilesInfo{SDOutFileNames}[$Index] = $NewSDFileName; 510 $SDFilesInfo{FPOutFileNames}[$Index] = $NewFPFileName; 511 $SDFilesInfo{TextOutFileNames}[$Index] = $NewTextFileName; 512 513 $SDFilesInfo{AllDataFieldsRef}[$Index] = $AllDataFieldsRef; 514 $SDFilesInfo{CommonDataFieldsRef}[$Index] = $CommonDataFieldsRef; 515 } 516 } 517 518 # Process option values... 519 sub ProcessOptions { 520 %OptionsInfo = (); 521 522 $OptionsInfo{AromaticityModel} = $Options{aromaticitymodel}; 523 524 $OptionsInfo{EStateAtomTypesSetToUse} = $Options{estateatomtypessettouse} ? $Options{estateatomtypessettouse} : 'ArbitrarySize'; 525 526 $OptionsInfo{CompoundIDMode} = $Options{compoundidmode}; 527 $OptionsInfo{CompoundIDLabel} = $Options{compoundidlabel}; 528 $OptionsInfo{DataFieldsMode} = $Options{datafieldsmode}; 529 530 my(@SpecifiedDataFields); 531 @SpecifiedDataFields = (); 532 533 @{$OptionsInfo{SpecifiedDataFields}} = (); 534 $OptionsInfo{CompoundID} = ''; 535 536 if ($Options{datafieldsmode} =~ /^CompoundID$/i) { 537 if ($Options{compoundidmode} =~ /^DataField$/i) { 538 if (!$Options{compoundid}) { 539 die "Error: You must specify a value for \"--CompoundID\" option in \"DataField\" \"--CompoundIDMode\". \n"; 540 } 541 $OptionsInfo{CompoundID} = $Options{compoundid}; 542 } 543 elsif ($Options{compoundidmode} =~ /^(LabelPrefix|MolNameOrLabelPrefix)$/i) { 544 $OptionsInfo{CompoundID} = $Options{compoundid} ? $Options{compoundid} : 'Cmpd'; 545 } 546 } 547 elsif ($Options{datafieldsmode} =~ /^Specify$/i) { 548 if (!$Options{datafields}) { 549 die "Error: You must specify a value for \"--DataFields\" option in \"Specify\" \"-d, --DataFieldsMode\". \n"; 550 } 551 @SpecifiedDataFields = split /\,/, $Options{datafields}; 552 push @{$OptionsInfo{SpecifiedDataFields}}, @SpecifiedDataFields; 553 } 554 555 $OptionsInfo{FingerprintsLabel} = $Options{fingerprintslabel} ? $Options{fingerprintslabel} : 'EStateIndiciesFingerprints'; 556 557 $OptionsInfo{Filter} = ($Options{filter} =~ /^Yes$/i) ? 1 : 0; 558 559 if ($Options{fingerprintslabelmode} =~ /^FingerprintsLabelWithIDs$/) { 560 if ($Options{estateatomtypessettouse} =~ /^FixedSize$/i) { 561 # Append E-state atom types for non-hydrogen atoms to the fingerprints label... 562 my($AtomType, @IDs); 563 @IDs = (); 564 for $AtomType (@{AtomTypes::EStateAtomTypes::GetAllPossibleEStateNonHydrogenAtomTypes()}) { 565 push @IDs, "S${AtomType}"; 566 } 567 $OptionsInfo{FingerprintsLabel} .= "; EStateAtomTypes: " . TextUtil::JoinWords(\@IDs, " ", 0); 568 } 569 } 570 $OptionsInfo{FingerprintsLabelMode} = $Options{fingerprintslabelmode}; 571 572 $OptionsInfo{KeepLargestComponent} = ($Options{keeplargestcomponent} =~ /^Yes$/i) ? 1 : 0; 573 574 $OptionsInfo{Output} = $Options{output}; 575 $OptionsInfo{SDOutput} = ($Options{output} =~ /^(SD|All)$/i) ? 1 : 0; 576 $OptionsInfo{FPOutput} = ($Options{output} =~ /^(FP|All)$/i) ? 1 : 0; 577 $OptionsInfo{TextOutput} = ($Options{output} =~ /^(Text|All)$/i) ? 1 : 0; 578 579 $OptionsInfo{OutDelim} = $Options{outdelim}; 580 $OptionsInfo{OutQuote} = ($Options{quote} =~ /^Yes$/i) ? 1 : 0; 581 582 $OptionsInfo{OverwriteFiles} = $Options{overwrite} ? 1 : 0; 583 $OptionsInfo{OutFileRoot} = $Options{root} ? $Options{root} : 0; 584 585 # Precision for E-state indicies... 586 $OptionsInfo{ValuesPrecision} = $Options{valuesprecision}; 587 588 # Setup default vector string format... 589 my($VectorStringFormat); 590 $VectorStringFormat = ''; 591 if ($Options{vectorstringformat}) { 592 $VectorStringFormat = $Options{vectorstringformat}; 593 } 594 else { 595 $VectorStringFormat = ($Options{estateatomtypessettouse} =~ /^FixedSize$/) ? "ValuesString" : "IDsAndValuesString"; 596 } 597 $OptionsInfo{VectorStringFormat} = $VectorStringFormat; 598 } 599 600 # Setup script usage and retrieve command line arguments specified using various options... 601 sub SetupScriptUsage { 602 603 # Retrieve all the options... 604 %Options = (); 605 606 $Options{aromaticitymodel} = 'MayaChemToolsAromaticityModel'; 607 608 $Options{compoundidmode} = 'LabelPrefix'; 609 $Options{compoundidlabel} = 'CompoundID'; 610 $Options{datafieldsmode} = 'CompoundID'; 611 612 $Options{filter} = 'Yes'; 613 614 $Options{estateatomtypessettouse} = 'ArbitrarySize'; 615 616 $Options{fingerprintslabelmode} = 'FingerprintsLabelOnly'; 617 $Options{keeplargestcomponent} = 'Yes'; 618 619 $Options{output} = 'text'; 620 $Options{outdelim} = 'comma'; 621 $Options{quote} = 'yes'; 622 623 $Options{valuesprecision} = 3; 624 625 $Options{vectorstringformat} = ''; 626 627 if (!GetOptions(\%Options, "aromaticitymodel=s", "compoundid=s", "compoundidlabel=s", "compoundidmode=s", "datafields=s", "datafieldsmode|d=s", "estateatomtypessettouse|e=s", "filter|f=s", "fingerprintslabelmode=s", "fingerprintslabel=s", "help|h", "keeplargestcomponent|k=s", "outdelim=s", "output=s", "overwrite|o", "quote|q=s", "root|r=s", "valuesprecision=s", "vectorstringformat|v=s", "workingdir|w=s")) { 628 die "\nTo get a list of valid options and their values, use \"$ScriptName -h\" or\n\"perl -S $ScriptName -h\" command and try again...\n"; 629 } 630 if ($Options{workingdir}) { 631 if (! -d $Options{workingdir}) { 632 die "Error: The value specified, $Options{workingdir}, for option \"-w --workingdir\" is not a directory name.\n"; 633 } 634 chdir $Options{workingdir} or die "Error: Couldn't chdir $Options{workingdir}: $! \n"; 635 } 636 if (!Molecule::IsSupportedAromaticityModel($Options{aromaticitymodel})) { 637 my(@SupportedModels) = Molecule::GetSupportedAromaticityModels(); 638 die "Error: The value specified, $Options{aromaticitymodel}, for option \"--AromaticityModel\" is not valid. Supported aromaticity models in current release of MayaChemTools: @SupportedModels\n"; 639 } 640 if ($Options{compoundidmode} !~ /^(DataField|MolName|LabelPrefix|MolNameOrLabelPrefix)$/i) { 641 die "Error: The value specified, $Options{compoundidmode}, for option \"--CompoundIDMode\" is not valid. Allowed values: DataField, MolName, LabelPrefix or MolNameOrLabelPrefix\n"; 642 } 643 if ($Options{datafieldsmode} !~ /^(All|Common|Specify|CompoundID)$/i) { 644 die "Error: The value specified, $Options{datafieldsmode}, for option \"-d, --DataFieldsMode\" is not valid. Allowed values: All, Common, Specify or CompoundID\n"; 645 } 646 if ($Options{estateatomtypessettouse} && $Options{estateatomtypessettouse} !~ /^(ArbitrarySize|FixedSize)$/) { 647 die "Error: The value specified, $Options{estateatomtypessettouse}, for option \"-e, --EStateAtomTypesSetToUse\" is not valid. Allowed values: ArbitrarySize or FixedSize\n"; 648 } 649 if ($Options{filter} !~ /^(Yes|No)$/i) { 650 die "Error: The value specified, $Options{filter}, for option \"-f, --Filter\" is not valid. Allowed values: Yes or No\n"; 651 } 652 if ($Options{fingerprintslabelmode} !~ /^(FingerprintsLabelOnly|FingerprintsLabelWithIDs)$/i) { 653 die "Error: The value specified, $Options{fingerprintslabelmode}, for option \"--FingerprintsLabelMode\" is not valid. Allowed values: FingerprintsLabelOnly or FingerprintsLabelWithIDs\n"; 654 } 655 if ($Options{keeplargestcomponent} !~ /^(Yes|No)$/i) { 656 die "Error: The value specified, $Options{keeplargestcomponent}, for option \"-k, --KeepLargestComponent\" is not valid. Allowed values: Yes or No\n"; 657 } 658 if ($Options{output} !~ /^(SD|FP|text|all)$/i) { 659 die "Error: The value specified, $Options{output}, for option \"--output\" is not valid. Allowed values: SD, FP, text, or all\n"; 660 } 661 if ($Options{outdelim} !~ /^(comma|semicolon|tab)$/i) { 662 die "Error: The value specified, $Options{outdelim}, for option \"--outdelim\" is not valid. Allowed values: comma, tab, or semicolon\n"; 663 } 664 if ($Options{quote} !~ /^(Yes|No)$/i) { 665 die "Error: The value specified, $Options{quote}, for option \"-q --quote\" is not valid. Allowed values: Yes or No\n"; 666 } 667 if ($Options{outdelim} =~ /semicolon/i && $Options{quote} =~ /^No$/i) { 668 die "Error: The value specified, $Options{quote}, for option \"-q --quote\" is not allowed with, semicolon value of \"--outdelim\" option: Fingerprints string use semicolon as delimiter for various data fields and must be quoted.\n"; 669 } 670 if (!IsPositiveInteger($Options{valuesprecision})) { 671 die "Error: The value specified, $Options{valuesprecision}, for option \"--ValuesPrecision\" is not valid. Allowed values: > 0 \n"; 672 } 673 if ($Options{vectorstringformat} && $Options{vectorstringformat} !~ /^(ValuesString|IDsAndValuesString|IDsAndValuesPairsString|ValuesAndIDsString|ValuesAndIDsPairsString)$/i) { 674 die "Error: The value specified, $Options{vectorstringformat}, for option \"-v, --VectorStringFormat\" is not valid. Allowed values: ValuesString, IDsAndValuesString, IDsAndValuesPairsString, ValuesAndIDsString or ValuesAndIDsPairsString\n"; 675 } 676 } 677