MayaChemTools

   1 #!/usr/bin/perl -w
   2 #
   3 # $RCSfile: TopologicalAtomTripletsFingerprints.pl,v $
   4 # $Date: 2015/02/28 20:46:23 $
   5 # $Revision: 1.21 $
   6 #
   7 # Author: Manish Sud <msud@san.rr.com>
   8 #
   9 # Copyright (C) 2015 Manish Sud. All rights reserved.
  10 #
  11 # This file is part of MayaChemTools.
  12 #
  13 # MayaChemTools is free software; you can redistribute it and/or modify it under
  14 # the terms of the GNU Lesser General Public License as published by the Free
  15 # Software Foundation; either version 3 of the License, or (at your option) any
  16 # later version.
  17 #
  18 # MayaChemTools is distributed in the hope that it will be useful, but without
  19 # any warranty; without even the implied warranty of merchantability of fitness
  20 # for a particular purpose.  See the GNU Lesser General Public License for more
  21 # details.
  22 #
  23 # You should have received a copy of the GNU Lesser General Public License
  24 # along with MayaChemTools; if not, see <http://www.gnu.org/licenses/> or
  25 # write to the Free Software Foundation Inc., 59 Temple Place, Suite 330,
  26 # Boston, MA, 02111-1307, USA.
  27 #
  28 
  29 use strict;
  30 use FindBin; use lib "$FindBin::Bin/../lib";
  31 use Getopt::Long;
  32 use File::Basename;
  33 use Text::ParseWords;
  34 use Benchmark;
  35 use FileUtil;
  36 use TextUtil;
  37 use SDFileUtil;
  38 use MoleculeFileIO;
  39 use FileIO::FingerprintsSDFileIO;
  40 use FileIO::FingerprintsTextFileIO;
  41 use FileIO::FingerprintsFPFileIO;
  42 use AtomTypes::AtomicInvariantsAtomTypes;
  43 use AtomTypes::FunctionalClassAtomTypes;
  44 use Fingerprints::TopologicalAtomTripletsFingerprints;
  45 
  46 my($ScriptName, %Options, $StartTime, $EndTime, $TotalTime);
  47 
  48 # Autoflush STDOUT
  49 $| = 1;
  50 
  51 # Starting message...
  52 $ScriptName = basename($0);
  53 print "\n$ScriptName: Starting...\n\n";
  54 $StartTime = new Benchmark;
  55 
  56 # Get the options and setup script...
  57 SetupScriptUsage();
  58 if ($Options{help} || @ARGV < 1) {
  59   die GetUsageFromPod("$FindBin::Bin/$ScriptName");
  60 }
  61 
  62 my(@SDFilesList);
  63 @SDFilesList = ExpandFileNames(\@ARGV, "sdf sd");
  64 
  65 # Process options...
  66 print "Processing options...\n";
  67 my(%OptionsInfo);
  68 ProcessOptions();
  69 
  70 # Setup information about input files...
  71 print "Checking input SD file(s)...\n";
  72 my(%SDFilesInfo);
  73 RetrieveSDFilesInfo();
  74 
  75 # Process input files..
  76 my($FileIndex);
  77 if (@SDFilesList > 1) {
  78   print "\nProcessing SD files...\n";
  79 }
  80 for $FileIndex (0 .. $#SDFilesList) {
  81   if ($SDFilesInfo{FileOkay}[$FileIndex]) {
  82     print "\nProcessing file $SDFilesList[$FileIndex]...\n";
  83     GenerateTopologicalAtomTripletsFingerprints($FileIndex);
  84   }
  85 }
  86 print "\n$ScriptName:Done...\n\n";
  87 
  88 $EndTime = new Benchmark;
  89 $TotalTime = timediff ($EndTime, $StartTime);
  90 print "Total time: ", timestr($TotalTime), "\n";
  91 
  92 ###############################################################################
  93 
  94 # Generate fingerprints for a SD file...
  95 #
  96 sub GenerateTopologicalAtomTripletsFingerprints {
  97   my($FileIndex) = @_;
  98   my($CmpdCount, $IgnoredCmpdCount, $SDFile, $MoleculeFileIO, $Molecule, $TopologicalAtomTripletsFingerprints, $NewFPSDFileIO, $NewFPTextFileIO, $NewFPFileIO);
  99 
 100   $SDFile = $SDFilesList[$FileIndex];
 101 
 102   # Setup output files...
 103   #
 104   ($NewFPSDFileIO, $NewFPTextFileIO, $NewFPFileIO) = SetupAndOpenOutputFiles($FileIndex);
 105 
 106   $MoleculeFileIO = new MoleculeFileIO('Name' => $SDFile);
 107   $MoleculeFileIO->Open();
 108 
 109   $CmpdCount = 0;
 110   $IgnoredCmpdCount = 0;
 111 
 112   COMPOUND: while ($Molecule = $MoleculeFileIO->ReadMolecule()) {
 113     $CmpdCount++;
 114 
 115     # Filter compound data before calculating fingerprints...
 116     if ($OptionsInfo{Filter}) {
 117       if (CheckAndFilterCompound($CmpdCount, $Molecule)) {
 118         $IgnoredCmpdCount++;
 119         next COMPOUND;
 120       }
 121     }
 122 
 123     $TopologicalAtomTripletsFingerprints = GenerateMoleculeFingerprints($Molecule);
 124     if (!$TopologicalAtomTripletsFingerprints) {
 125       $IgnoredCmpdCount++;
 126       ProcessIgnoredCompound('FingerprintsGenerationFailed', $CmpdCount, $Molecule);
 127       next COMPOUND;
 128     }
 129 
 130     WriteDataToOutputFiles($FileIndex, $CmpdCount, $Molecule, $TopologicalAtomTripletsFingerprints, $NewFPSDFileIO, $NewFPTextFileIO, $NewFPFileIO);
 131   }
 132   $MoleculeFileIO->Close();
 133 
 134   if ($NewFPSDFileIO) {
 135     $NewFPSDFileIO->Close();
 136   }
 137   if ($NewFPTextFileIO) {
 138     $NewFPTextFileIO->Close();
 139   }
 140   if ($NewFPFileIO) {
 141     $NewFPFileIO->Close();
 142   }
 143 
 144   WriteFingerprintsGenerationSummaryStatistics($CmpdCount, $IgnoredCmpdCount);
 145 }
 146 
 147 # Process compound being ignored due to problems in fingerprints geneation...
 148 #
 149 sub ProcessIgnoredCompound {
 150   my($Mode, $CmpdCount, $Molecule) = @_;
 151   my($CmpdID, $DataFieldLabelAndValuesRef);
 152 
 153   $DataFieldLabelAndValuesRef = $Molecule->GetDataFieldLabelAndValues();
 154   $CmpdID = SetupCmpdIDForOutputFiles($CmpdCount, $Molecule, $DataFieldLabelAndValuesRef);
 155 
 156   MODE: {
 157     if ($Mode =~ /^ContainsNonElementalData$/i) {
 158       warn "\nWarning: Ignoring compound record number $CmpdCount with ID $CmpdID: Compound contains atom data corresponding to non-elemental atom symbol(s)...\n\n";
 159       next MODE;
 160     }
 161 
 162     if ($Mode =~ /^ContainsNoElementalData$/i) {
 163       warn "\nWarning: Ignoring compound record number $CmpdCount with ID $CmpdID: Compound contains no atom data...\n\n";
 164       next MODE;
 165     }
 166 
 167     if ($Mode =~ /^FingerprintsGenerationFailed$/i) {
 168       warn "\nWarning: Ignoring compound record number $CmpdCount with ID $CmpdID: Fingerprints generation didn't succeed...\n\n";
 169       next MODE;
 170     }
 171     warn "\nWarning: Ignoring compound record number $CmpdCount with ID $CmpdID: Fingerprints generation didn't succeed...\n\n";
 172   }
 173 }
 174 
 175 # Check and filter compounds....
 176 #
 177 sub CheckAndFilterCompound {
 178   my($CmpdCount, $Molecule) = @_;
 179   my($ElementCount, $NonElementCount);
 180 
 181   ($ElementCount, $NonElementCount) = $Molecule->GetNumOfElementsAndNonElements();
 182 
 183   if ($NonElementCount) {
 184     ProcessIgnoredCompound('ContainsNonElementalData', $CmpdCount, $Molecule);
 185     return 1;
 186   }
 187 
 188   if (!$ElementCount) {
 189     ProcessIgnoredCompound('ContainsNoElementalData', $CmpdCount, $Molecule);
 190     return 1;
 191   }
 192 
 193   return 0;
 194 }
 195 
 196 # Write out compounds fingerprints generation summary statistics...
 197 #
 198 sub WriteFingerprintsGenerationSummaryStatistics {
 199   my($CmpdCount, $IgnoredCmpdCount) = @_;
 200   my($ProcessedCmpdCount);
 201 
 202   $ProcessedCmpdCount = $CmpdCount - $IgnoredCmpdCount;
 203 
 204   print "\nNumber of compounds: $CmpdCount\n";
 205   print "Number of compounds processed successfully during fingerprints generation: $ProcessedCmpdCount\n";
 206   print "Number of compounds ignored during fingerprints generation: $IgnoredCmpdCount\n";
 207 }
 208 
 209 # Open output files...
 210 #
 211 sub SetupAndOpenOutputFiles {
 212   my($FileIndex) = @_;
 213   my($NewFPSDFile, $NewFPFile, $NewFPTextFile, $NewFPSDFileIO, $NewFPTextFileIO, $NewFPFileIO, %FingerprintsFileIOParams);
 214 
 215   ($NewFPSDFileIO, $NewFPTextFileIO, $NewFPFileIO) = (undef) x 3;
 216 
 217   # Setup common parameters for fingerprints file IO objects...
 218   #
 219   %FingerprintsFileIOParams = ('Mode' => 'Write', 'Overwrite' => $OptionsInfo{OverwriteFiles}, 'FingerprintsStringMode' => 'FingerprintsVectorString', 'VectorStringFormat' => $OptionsInfo{VectorStringFormat});
 220 
 221   if ($OptionsInfo{SDOutput}) {
 222     $NewFPSDFile = $SDFilesInfo{SDOutFileNames}[$FileIndex];
 223     print "Generating SD file $NewFPSDFile...\n";
 224     $NewFPSDFileIO = new FileIO::FingerprintsSDFileIO('Name' => $NewFPSDFile, %FingerprintsFileIOParams, 'FingerprintsFieldLabel' => $OptionsInfo{FingerprintsLabel});
 225     $NewFPSDFileIO->Open();
 226   }
 227 
 228   if ($OptionsInfo{FPOutput}) {
 229     $NewFPFile = $SDFilesInfo{FPOutFileNames}[$FileIndex];
 230     print "Generating FP file $NewFPFile...\n";
 231     $NewFPFileIO = new FileIO::FingerprintsFPFileIO('Name' => $NewFPFile, %FingerprintsFileIOParams);
 232     $NewFPFileIO->Open();
 233   }
 234 
 235   if ($OptionsInfo{TextOutput}) {
 236     my($ColLabelsRef);
 237 
 238     $NewFPTextFile = $SDFilesInfo{TextOutFileNames}[$FileIndex];
 239     $ColLabelsRef = SetupFPTextFileCoulmnLabels($FileIndex);
 240 
 241     print "Generating text file $NewFPTextFile...\n";
 242     $NewFPTextFileIO = new FileIO::FingerprintsTextFileIO('Name' => $NewFPTextFile, %FingerprintsFileIOParams, 'DataColLabels' => $ColLabelsRef, 'OutDelim' => $OptionsInfo{OutDelim}, 'OutQuote' => $OptionsInfo{OutQuote});
 243     $NewFPTextFileIO->Open();
 244   }
 245 
 246   return ($NewFPSDFileIO, $NewFPTextFileIO, $NewFPFileIO);
 247 }
 248 
 249 # Write fingerpritns and other data to appropriate output files...
 250 #
 251 sub WriteDataToOutputFiles {
 252   my($FileIndex, $CmpdCount, $Molecule, $TopologicalAtomTripletsFingerprints, $NewFPSDFileIO, $NewFPTextFileIO, $NewFPFileIO) = @_;
 253   my($DataFieldLabelAndValuesRef);
 254 
 255   $DataFieldLabelAndValuesRef = undef;
 256   if ($NewFPTextFileIO || $NewFPFileIO) {
 257     $DataFieldLabelAndValuesRef = $Molecule->GetDataFieldLabelAndValues();
 258   }
 259 
 260   if ($NewFPSDFileIO) {
 261     my($CmpdString);
 262 
 263     $CmpdString = $Molecule->GetInputMoleculeString();
 264     $NewFPSDFileIO->WriteFingerprints($TopologicalAtomTripletsFingerprints, $CmpdString);
 265   }
 266 
 267   if ($NewFPTextFileIO) {
 268     my($ColValuesRef);
 269 
 270     $ColValuesRef = SetupFPTextFileCoulmnValues($FileIndex, $CmpdCount, $Molecule, $DataFieldLabelAndValuesRef);
 271     $NewFPTextFileIO->WriteFingerprints($TopologicalAtomTripletsFingerprints, $ColValuesRef);
 272   }
 273 
 274   if ($NewFPFileIO) {
 275     my($CompoundID);
 276 
 277     $CompoundID = SetupCmpdIDForOutputFiles($CmpdCount, $Molecule, $DataFieldLabelAndValuesRef);
 278     $NewFPFileIO->WriteFingerprints($TopologicalAtomTripletsFingerprints, $CompoundID);
 279   }
 280 }
 281 
 282 # Generate approriate column labels for FPText output file...
 283 #
 284 sub SetupFPTextFileCoulmnLabels {
 285   my($FileIndex) = @_;
 286   my($Line, @ColLabels);
 287 
 288   @ColLabels = ();
 289   if ($OptionsInfo{DataFieldsMode} =~ /^All$/i) {
 290     push @ColLabels, @{$SDFilesInfo{AllDataFieldsRef}[$FileIndex]};
 291   }
 292   elsif ($OptionsInfo{DataFieldsMode} =~ /^Common$/i) {
 293     push @ColLabels, @{$SDFilesInfo{CommonDataFieldsRef}[$FileIndex]};
 294   }
 295   elsif ($OptionsInfo{DataFieldsMode} =~ /^Specify$/i) {
 296     push @ColLabels, @{$OptionsInfo{SpecifiedDataFields}};
 297   }
 298   elsif ($OptionsInfo{DataFieldsMode} =~ /^CompoundID$/i) {
 299     push @ColLabels, $OptionsInfo{CompoundIDLabel};
 300   }
 301   # Add fingerprints label...
 302   push @ColLabels, $OptionsInfo{FingerprintsLabel};
 303 
 304   return \@ColLabels;
 305 }
 306 
 307 # Generate column values FPText output file..
 308 #
 309 sub SetupFPTextFileCoulmnValues {
 310   my($FileIndex, $CmpdCount, $Molecule, $DataFieldLabelAndValuesRef) = @_;
 311   my(@ColValues);
 312 
 313   @ColValues = ();
 314   if ($OptionsInfo{DataFieldsMode} =~ /^CompoundID$/i) {
 315     push @ColValues, SetupCmpdIDForOutputFiles($CmpdCount, $Molecule, $DataFieldLabelAndValuesRef);
 316   }
 317   elsif ($OptionsInfo{DataFieldsMode} =~ /^All$/i) {
 318     @ColValues = map { exists $DataFieldLabelAndValuesRef->{$_} ? $DataFieldLabelAndValuesRef->{$_} : ''} @{$SDFilesInfo{AllDataFieldsRef}[$FileIndex]};
 319   }
 320   elsif ($OptionsInfo{DataFieldsMode} =~ /^Common$/i) {
 321     @ColValues = map { exists $DataFieldLabelAndValuesRef->{$_} ? $DataFieldLabelAndValuesRef->{$_} : ''} @{$SDFilesInfo{CommonDataFieldsRef}[$FileIndex]};
 322   }
 323   elsif ($OptionsInfo{DataFieldsMode} =~ /^Specify$/i) {
 324     @ColValues = map { exists $DataFieldLabelAndValuesRef->{$_} ? $DataFieldLabelAndValuesRef->{$_} : ''} @{$OptionsInfo{SpecifiedDataFields}};
 325   }
 326 
 327   return \@ColValues;
 328 }
 329 
 330 # Generate compound ID for FP and FPText output files..
 331 #
 332 sub SetupCmpdIDForOutputFiles {
 333   my($CmpdCount, $Molecule, $DataFieldLabelAndValuesRef) = @_;
 334   my($CmpdID);
 335 
 336   $CmpdID = '';
 337   if ($OptionsInfo{CompoundIDMode} =~ /^MolNameOrLabelPrefix$/i) {
 338     my($MolName);
 339     $MolName = $Molecule->GetName();
 340     $CmpdID = $MolName ? $MolName : "$OptionsInfo{CompoundID}${CmpdCount}";
 341   }
 342   elsif ($OptionsInfo{CompoundIDMode} =~ /^LabelPrefix$/i) {
 343     $CmpdID = "$OptionsInfo{CompoundID}${CmpdCount}";
 344   }
 345   elsif ($OptionsInfo{CompoundIDMode} =~ /^DataField$/i) {
 346     my($SpecifiedDataField);
 347     $SpecifiedDataField = $OptionsInfo{CompoundID};
 348     $CmpdID = exists $DataFieldLabelAndValuesRef->{$SpecifiedDataField} ? $DataFieldLabelAndValuesRef->{$SpecifiedDataField} : '';
 349   }
 350   elsif ($OptionsInfo{CompoundIDMode} =~ /^MolName$/i) {
 351     $CmpdID = $Molecule->GetName();
 352   }
 353   return $CmpdID;
 354 }
 355 
 356 # Generate fingerprints for molecule...
 357 #
 358 sub GenerateMoleculeFingerprints {
 359   my($Molecule) = @_;
 360   my($TopologicalAtomTripletsFingerprints);
 361 
 362   if ($OptionsInfo{KeepLargestComponent}) {
 363     $Molecule->KeepLargestComponent();
 364   }
 365   if (!$Molecule->DetectRings()) {
 366     return undef;
 367   }
 368   $Molecule->SetAromaticityModel($OptionsInfo{AromaticityModel});
 369   $Molecule->DetectAromaticity();
 370 
 371   $TopologicalAtomTripletsFingerprints = new Fingerprints::TopologicalAtomTripletsFingerprints('Molecule' => $Molecule, 'MinDistance' => $OptionsInfo{MinDistance},  'MaxDistance' => $OptionsInfo{MaxDistance}, 'UseTriangleInequality' => $OptionsInfo{UseTriangleInequality}, 'AtomIdentifierType' => $OptionsInfo{AtomIdentifierType});
 372   SetAtomIdentifierTypeValuesToUse($TopologicalAtomTripletsFingerprints);
 373 
 374   # Generate fingerprints...
 375   $TopologicalAtomTripletsFingerprints->GenerateFingerprints();
 376 
 377   # Make sure fingerprints generation is successful...
 378   if (!$TopologicalAtomTripletsFingerprints->IsFingerprintsGenerationSuccessful()) {
 379     return undef;
 380   }
 381 
 382   return $TopologicalAtomTripletsFingerprints;
 383 }
 384 
 385 # Set atom identifier type to use for generating fingerprints...
 386 #
 387 sub SetAtomIdentifierTypeValuesToUse {
 388   my($TopologicalAtomTripletsFingerprints) = @_;
 389 
 390   if ($OptionsInfo{AtomIdentifierType} =~ /^AtomicInvariantsAtomTypes$/i) {
 391     $TopologicalAtomTripletsFingerprints->SetAtomicInvariantsToUse(\@{$OptionsInfo{AtomicInvariantsToUse}});
 392   }
 393   elsif ($OptionsInfo{AtomIdentifierType} =~ /^FunctionalClassAtomTypes$/i) {
 394     $TopologicalAtomTripletsFingerprints->SetFunctionalClassesToUse(\@{$OptionsInfo{FunctionalClassesToUse}});
 395   }
 396   elsif ($OptionsInfo{AtomIdentifierType} =~ /^(DREIDINGAtomTypes|EStateAtomTypes|MMFF94AtomTypes|SLogPAtomTypes|SYBYLAtomTypes|TPSAAtomTypes|UFFAtomTypes)$/i) {
 397     # Nothing to do for now...
 398   }
 399   else {
 400     die "Error: The value specified, $Options{atomidentifiertype}, for option \"-a, --AtomIdentifierType\" is not valid. Supported atom identifier types in current release of MayaChemTools: AtomicInvariantsAtomTypes, DREIDINGAtomTypes, EStateAtomTypes, FunctionalClassAtomTypes, MMFF94AtomTypes, SLogPAtomTypes, SYBYLAtomTypes, TPSAAtomTypes, UFFAtomTypes\n";
 401   }
 402 }
 403 
 404 # Retrieve information about SD files...
 405 #
 406 sub RetrieveSDFilesInfo {
 407   my($SDFile, $Index, $FileDir, $FileExt, $FileName, $OutFileRoot, $TextOutFileExt, $SDOutFileExt, $FPOutFileExt, $NewSDFileName, $NewFPFileName, $NewTextFileName, $CheckDataField, $CollectDataFields, $AllDataFieldsRef, $CommonDataFieldsRef);
 408 
 409   %SDFilesInfo = ();
 410   @{$SDFilesInfo{FileOkay}} = ();
 411   @{$SDFilesInfo{OutFileRoot}} = ();
 412   @{$SDFilesInfo{SDOutFileNames}} = ();
 413   @{$SDFilesInfo{FPOutFileNames}} = ();
 414   @{$SDFilesInfo{TextOutFileNames}} = ();
 415   @{$SDFilesInfo{AllDataFieldsRef}} = ();
 416   @{$SDFilesInfo{CommonDataFieldsRef}} = ();
 417 
 418   $CheckDataField = ($OptionsInfo{TextOutput} && ($OptionsInfo{DataFieldsMode} =~ /^CompoundID$/i) && ($OptionsInfo{CompoundIDMode} =~ /^DataField$/i)) ? 1 : 0;
 419   $CollectDataFields = ($OptionsInfo{TextOutput} && ($OptionsInfo{DataFieldsMode} =~ /^(All|Common)$/i)) ? 1 : 0;
 420 
 421   FILELIST: for $Index (0 .. $#SDFilesList) {
 422     $SDFile = $SDFilesList[$Index];
 423 
 424     $SDFilesInfo{FileOkay}[$Index] = 0;
 425     $SDFilesInfo{OutFileRoot}[$Index] = '';
 426     $SDFilesInfo{SDOutFileNames}[$Index] = '';
 427     $SDFilesInfo{FPOutFileNames}[$Index] = '';
 428     $SDFilesInfo{TextOutFileNames}[$Index] = '';
 429 
 430     $SDFile = $SDFilesList[$Index];
 431     if (!(-e $SDFile)) {
 432       warn "Warning: Ignoring file $SDFile: It doesn't exist\n";
 433       next FILELIST;
 434     }
 435     if (!CheckFileType($SDFile, "sd sdf")) {
 436       warn "Warning: Ignoring file $SDFile: It's not a SD file\n";
 437       next FILELIST;
 438     }
 439 
 440     if ($CheckDataField) {
 441       # Make sure data field exists in SD file..
 442       my($CmpdString, $SpecifiedDataField, @CmpdLines, %DataFieldValues);
 443 
 444       @CmpdLines = ();
 445       open SDFILE, "$SDFile" or die "Error: Couldn't open $SDFile: $! \n";
 446       $CmpdString = ReadCmpdString(\*SDFILE);
 447       close SDFILE;
 448       @CmpdLines = split "\n", $CmpdString;
 449       %DataFieldValues = GetCmpdDataHeaderLabelsAndValues(\@CmpdLines);
 450       $SpecifiedDataField = $OptionsInfo{CompoundID};
 451       if (!exists $DataFieldValues{$SpecifiedDataField}) {
 452         warn "Warning: Ignoring file $SDFile: Data field value, $SpecifiedDataField, using  \"--CompoundID\" option in \"DataField\" \"--CompoundIDMode\" doesn't exist\n";
 453         next FILELIST;
 454       }
 455     }
 456 
 457     $AllDataFieldsRef = '';
 458     $CommonDataFieldsRef = '';
 459     if ($CollectDataFields) {
 460       my($CmpdCount);
 461       open SDFILE, "$SDFile" or die "Error: Couldn't open $SDFile: $! \n";
 462       ($CmpdCount, $AllDataFieldsRef, $CommonDataFieldsRef) = GetAllAndCommonCmpdDataHeaderLabels(\*SDFILE);
 463       close SDFILE;
 464     }
 465 
 466     # Setup output file names...
 467     $FileDir = ""; $FileName = ""; $FileExt = "";
 468     ($FileDir, $FileName, $FileExt) = ParseFileName($SDFile);
 469 
 470     $TextOutFileExt = "csv";
 471     if ($Options{outdelim} =~ /^tab$/i) {
 472       $TextOutFileExt = "tsv";
 473     }
 474     $SDOutFileExt = $FileExt;
 475     $FPOutFileExt = "fpf";
 476 
 477     if ($OptionsInfo{OutFileRoot} && (@SDFilesList == 1)) {
 478       my ($RootFileDir, $RootFileName, $RootFileExt) = ParseFileName($OptionsInfo{OutFileRoot});
 479       if ($RootFileName && $RootFileExt) {
 480         $FileName = $RootFileName;
 481       }
 482       else {
 483         $FileName = $OptionsInfo{OutFileRoot};
 484       }
 485       $OutFileRoot = $FileName;
 486     }
 487     else {
 488       $OutFileRoot = "${FileName}TopologicalAtomTripletsFP";
 489     }
 490 
 491     $NewSDFileName = "${OutFileRoot}.${SDOutFileExt}";
 492     $NewFPFileName = "${OutFileRoot}.${FPOutFileExt}";
 493     $NewTextFileName = "${OutFileRoot}.${TextOutFileExt}";
 494 
 495     if ($OptionsInfo{SDOutput}) {
 496       if ($SDFile =~ /$NewSDFileName/i) {
 497         warn "Warning: Ignoring input file $SDFile: Same output, $NewSDFileName, and input file names.\n";
 498         print "Specify a different name using \"-r --root\" option or use default name.\n";
 499         next FILELIST;
 500       }
 501     }
 502 
 503     if (!$OptionsInfo{OverwriteFiles}) {
 504       # Check SD and text outout files...
 505       if ($OptionsInfo{SDOutput}) {
 506         if (-e $NewSDFileName) {
 507           warn "Warning: Ignoring file $SDFile: The file $NewSDFileName already exists\n";
 508           next FILELIST;
 509         }
 510       }
 511       if ($OptionsInfo{FPOutput}) {
 512         if (-e $NewFPFileName) {
 513           warn "Warning: Ignoring file $SDFile: The file $NewFPFileName already exists\n";
 514           next FILELIST;
 515         }
 516       }
 517       if ($OptionsInfo{TextOutput}) {
 518         if (-e $NewTextFileName) {
 519           warn "Warning: Ignoring file $SDFile: The file $NewTextFileName already exists\n";
 520           next FILELIST;
 521         }
 522       }
 523     }
 524 
 525     $SDFilesInfo{FileOkay}[$Index] = 1;
 526 
 527     $SDFilesInfo{OutFileRoot}[$Index] = $OutFileRoot;
 528     $SDFilesInfo{SDOutFileNames}[$Index] = $NewSDFileName;
 529     $SDFilesInfo{FPOutFileNames}[$Index] = $NewFPFileName;
 530     $SDFilesInfo{TextOutFileNames}[$Index] = $NewTextFileName;
 531 
 532     $SDFilesInfo{AllDataFieldsRef}[$Index] = $AllDataFieldsRef;
 533     $SDFilesInfo{CommonDataFieldsRef}[$Index] = $CommonDataFieldsRef;
 534   }
 535 }
 536 
 537 # Process option values...
 538 sub ProcessOptions {
 539   %OptionsInfo = ();
 540 
 541   ProcessAtomIdentifierTypeOptions();
 542 
 543   $OptionsInfo{AromaticityModel} = $Options{aromaticitymodel};
 544 
 545   $OptionsInfo{CompoundIDMode} = $Options{compoundidmode};
 546   $OptionsInfo{CompoundIDLabel} = $Options{compoundidlabel};
 547   $OptionsInfo{DataFieldsMode} = $Options{datafieldsmode};
 548 
 549   my(@SpecifiedDataFields);
 550   @SpecifiedDataFields = ();
 551 
 552   @{$OptionsInfo{SpecifiedDataFields}} = ();
 553   $OptionsInfo{CompoundID} = '';
 554 
 555   if ($Options{datafieldsmode} =~ /^CompoundID$/i) {
 556     if ($Options{compoundidmode} =~ /^DataField$/i) {
 557       if (!$Options{compoundid}) {
 558         die "Error: You must specify a value for \"--CompoundID\" option in \"DataField\" \"--CompoundIDMode\". \n";
 559       }
 560       $OptionsInfo{CompoundID} = $Options{compoundid};
 561     }
 562     elsif ($Options{compoundidmode} =~ /^(LabelPrefix|MolNameOrLabelPrefix)$/i) {
 563       $OptionsInfo{CompoundID} = $Options{compoundid} ? $Options{compoundid} : 'Cmpd';
 564     }
 565   }
 566   elsif ($Options{datafieldsmode} =~ /^Specify$/i) {
 567     if (!$Options{datafields}) {
 568       die "Error: You must specify a value for \"--DataFields\" option in \"Specify\" \"-d, --DataFieldsMode\". \n";
 569     }
 570     @SpecifiedDataFields = split /\,/, $Options{datafields};
 571     push @{$OptionsInfo{SpecifiedDataFields}}, @SpecifiedDataFields;
 572   }
 573 
 574   $OptionsInfo{Filter} = ($Options{filter} =~ /^Yes$/i) ? 1 : 0;
 575 
 576   $OptionsInfo{FingerprintsLabel} = $Options{fingerprintslabel} ? $Options{fingerprintslabel} : 'TopologicalAtomTripletsFingerprints';
 577 
 578   $OptionsInfo{KeepLargestComponent} = ($Options{keeplargestcomponent} =~ /^Yes$/i) ? 1 : 0;
 579 
 580   $OptionsInfo{MinDistance} = $Options{mindistance};
 581   $OptionsInfo{MaxDistance} = $Options{maxdistance};
 582 
 583   $OptionsInfo{Output} = $Options{output};
 584   $OptionsInfo{SDOutput} = ($Options{output} =~ /^(SD|All)$/i) ? 1 : 0;
 585   $OptionsInfo{FPOutput} = ($Options{output} =~ /^(FP|All)$/i) ? 1 : 0;
 586   $OptionsInfo{TextOutput} = ($Options{output} =~ /^(Text|All)$/i) ? 1 : 0;
 587 
 588   $OptionsInfo{OutDelim} = $Options{outdelim};
 589   $OptionsInfo{OutQuote} = ($Options{quote} =~ /^Yes$/i) ? 1 : 0;
 590 
 591   $OptionsInfo{OverwriteFiles} = $Options{overwrite} ? 1 : 0;
 592   $OptionsInfo{OutFileRoot} = $Options{root} ? $Options{root} : 0;
 593 
 594   $OptionsInfo{UseTriangleInequality} = ($Options{usetriangleinequality} =~ /^Yes$/i) ? 1 : 0;
 595 
 596   $OptionsInfo{VectorStringFormat} = $Options{vectorstringformat};
 597 }
 598 
 599 # Process atom identifier type and related options...
 600 #
 601 sub ProcessAtomIdentifierTypeOptions {
 602 
 603   $OptionsInfo{AtomIdentifierType} = $Options{atomidentifiertype};
 604 
 605   if ($Options{atomidentifiertype} =~ /^AtomicInvariantsAtomTypes$/i) {
 606     ProcessAtomicInvariantsToUseOption();
 607   }
 608   elsif ($Options{atomidentifiertype} =~ /^FunctionalClassAtomTypes$/i) {
 609     ProcessFunctionalClassesToUse();
 610   }
 611   elsif ($OptionsInfo{AtomIdentifierType} =~ /^(DREIDINGAtomTypes|EStateAtomTypes|MMFF94AtomTypes|SLogPAtomTypes|SYBYLAtomTypes|TPSAAtomTypes|UFFAtomTypes)$/i) {
 612     # Nothing to do for now...
 613   }
 614   else {
 615     die "Error: The value specified, $Options{atomidentifiertype}, for option \"-a, --AtomIdentifierType\" is not valid. Supported atom identifier types in current release of MayaChemTools: AtomicInvariantsAtomTypes, DREIDINGAtomTypes, EStateAtomTypes, FunctionalClassAtomTypes, MMFF94AtomTypes, SLogPAtomTypes, SYBYLAtomTypes, TPSAAtomTypes, UFFAtomTypes\n";
 616   }
 617 }
 618 
 619 # Process specified atomic invariants to use...
 620 #
 621 sub ProcessAtomicInvariantsToUseOption {
 622   my($AtomicInvariant, $AtomSymbolSpecified, @AtomicInvariantsWords);
 623 
 624   @{$OptionsInfo{AtomicInvariantsToUse}} = ();
 625   if (IsEmpty($Options{atomicinvariantstouse})) {
 626     die "Error: Atomic invariants value specified using \"--AtomicInvariantsToUse\" option is empty\n";
 627   }
 628   $AtomSymbolSpecified = 0;
 629   @AtomicInvariantsWords = split /\,/, $Options{atomicinvariantstouse};
 630   for $AtomicInvariant (@AtomicInvariantsWords) {
 631     if (!AtomTypes::AtomicInvariantsAtomTypes::IsAtomicInvariantAvailable($AtomicInvariant)) {
 632       die "Error: Atomic invariant specified, $AtomicInvariant, using \"--AtomicInvariantsToUse\" option is not valid...\n ";
 633     }
 634     if ($AtomicInvariant =~ /^(AS|AtomSymbol)$/i) {
 635       $AtomSymbolSpecified = 1;
 636     }
 637     push @{$OptionsInfo{AtomicInvariantsToUse}}, $AtomicInvariant;
 638   }
 639   if (!$AtomSymbolSpecified) {
 640     die "Error: Atomic invariant, AS or AtomSymbol, must be specified as using \"--AtomicInvariantsToUse\" option...\n ";
 641   }
 642 }
 643 
 644 # Process specified functional classes invariants to use...
 645 #
 646 sub ProcessFunctionalClassesToUse {
 647   my($FunctionalClass, @FunctionalClassesToUseWords);
 648 
 649   @{$OptionsInfo{FunctionalClassesToUse}} = ();
 650   if (IsEmpty($Options{functionalclassestouse})) {
 651     die "Error: Functional classes value specified using \"--FunctionalClassesToUse\" option is empty\n";
 652   }
 653   @FunctionalClassesToUseWords = split /\,/, $Options{functionalclassestouse};
 654   for $FunctionalClass (@FunctionalClassesToUseWords) {
 655     if (!AtomTypes::FunctionalClassAtomTypes::IsFunctionalClassAvailable($FunctionalClass)) {
 656       die "Error: Functional class specified, $FunctionalClass, using \"--FunctionalClassesToUse\" option is not valid...\n ";
 657     }
 658     push @{$OptionsInfo{FunctionalClassesToUse}}, $FunctionalClass;
 659   }
 660 }
 661 
 662 # Setup script usage  and retrieve command line arguments specified using various options...
 663 sub SetupScriptUsage {
 664 
 665   # Retrieve all the options...
 666   %Options = ();
 667 
 668   $Options{aromaticitymodel} = 'MayaChemToolsAromaticityModel';
 669 
 670   $Options{atomidentifiertype} = 'AtomicInvariantsAtomTypes';
 671   $Options{atomicinvariantstouse} = 'AS,X,BO,H,FC';
 672 
 673   $Options{functionalclassestouse} = 'HBD,HBA,PI,NI,Ar,Hal';
 674 
 675   $Options{compoundidmode} = 'LabelPrefix';
 676   $Options{compoundidlabel} = 'CompoundID';
 677   $Options{datafieldsmode} = 'CompoundID';
 678 
 679   $Options{filter} = 'Yes';
 680 
 681   $Options{keeplargestcomponent} = 'Yes';
 682 
 683   $Options{mindistance} = 1;
 684   $Options{maxdistance} = 10;
 685 
 686   $Options{output} = 'text';
 687   $Options{outdelim} = 'comma';
 688   $Options{quote} = 'yes';
 689 
 690   $Options{usetriangleinequality} = 'No';
 691 
 692   $Options{vectorstringformat} = 'IDsAndValuesString';
 693 
 694   if (!GetOptions(\%Options, "aromaticitymodel=s", "atomidentifiertype|a=s", "atomicinvariantstouse=s", "functionalclassestouse=s", "compoundid=s", "compoundidlabel=s", "compoundidmode=s", "datafields=s", "datafieldsmode|d=s", "filter|f=s", "fingerprintslabel=s",  "help|h", "keeplargestcomponent|k=s",  "mindistance=s", "maxdistance=s", "outdelim=s", "output=s", "overwrite|o", "quote|q=s", "root|r=s", , "usetriangleinequality|u=s", "vectorstringformat|v=s", "workingdir|w=s")) {
 695     die "\nTo get a list of valid options and their values, use \"$ScriptName -h\" or\n\"perl -S $ScriptName -h\" command and try again...\n";
 696   }
 697   if ($Options{workingdir}) {
 698     if (! -d $Options{workingdir}) {
 699       die "Error: The value specified, $Options{workingdir}, for option \"-w --workingdir\" is not a directory name.\n";
 700     }
 701     chdir $Options{workingdir} or die "Error: Couldn't chdir $Options{workingdir}: $! \n";
 702   }
 703   if (!Molecule::IsSupportedAromaticityModel($Options{aromaticitymodel})) {
 704     my(@SupportedModels) = Molecule::GetSupportedAromaticityModels();
 705     die "Error: The value specified, $Options{aromaticitymodel}, for option \"--AromaticityModel\" is not valid. Supported aromaticity models in current release of MayaChemTools: @SupportedModels\n";
 706   }
 707   if ($Options{atomidentifiertype} !~ /^(AtomicInvariantsAtomTypes|DREIDINGAtomTypes|EStateAtomTypes|FunctionalClassAtomTypes|MMFF94AtomTypes|SLogPAtomTypes|SYBYLAtomTypes|TPSAAtomTypes|UFFAtomTypes)$/i) {
 708     die "Error: The value specified, $Options{atomidentifiertype}, for option \"-a, --AtomIdentifierType\" is not valid. Supported atom identifier types in current release of MayaChemTools: AtomicInvariantsAtomTypes, DREIDINGAtomTypes, EStateAtomTypes, FunctionalClassAtomTypes, MMFF94AtomTypes, SLogPAtomTypes, SYBYLAtomTypes, TPSAAtomTypes, UFFAtomTypes\n";
 709   }
 710   if ($Options{compoundidmode} !~ /^(DataField|MolName|LabelPrefix|MolNameOrLabelPrefix)$/i) {
 711     die "Error: The value specified, $Options{compoundidmode}, for option \"--CompoundIDMode\" is not valid. Allowed values: DataField, MolName, LabelPrefix or MolNameOrLabelPrefix\n";
 712   }
 713   if ($Options{datafieldsmode} !~ /^(All|Common|Specify|CompoundID)$/i) {
 714     die "Error: The value specified, $Options{datafieldsmode}, for option \"-d, --DataFieldsMode\" is not valid. Allowed values: All, Common, Specify or CompoundID\n";
 715   }
 716   if ($Options{filter} !~ /^(Yes|No)$/i) {
 717     die "Error: The value specified, $Options{filter}, for option \"-f, --Filter\" is not valid. Allowed values: Yes or No\n";
 718   }
 719   if ($Options{keeplargestcomponent} !~ /^(Yes|No)$/i) {
 720     die "Error: The value specified, $Options{keeplargestcomponent}, for option \"-k, --KeepLargestComponent\" is not valid. Allowed values: Yes or No\n";
 721   }
 722   if (!IsPositiveInteger($Options{mindistance})) {
 723     die "Error: The value specified, $Options{mindistance}, for option \"--MinDistance\" is not valid. Allowed values: > 0 \n";
 724   }
 725   if (!IsPositiveInteger($Options{maxdistance})) {
 726     die "Error: The value specified, $Options{maxdistance}, for option \"--MaxDistance\" is not valid. Allowed values: > 0 \n";
 727   }
 728   if ($Options{mindistance} > $Options{maxdistance}) {
 729     die "Error: The value specified, specified, $Options{mindistance}, for option \"--MinDistance\" must be less than the value specified, $Options{maxdistance}, for option \"--MaxDistance\" \n";
 730   }
 731   if ($Options{output} !~ /^(SD|FP|text|all)$/i) {
 732     die "Error: The value specified, $Options{output}, for option \"--output\" is not valid. Allowed values: SD, FP, text, or all\n";
 733   }
 734   if ($Options{outdelim} !~ /^(comma|semicolon|tab)$/i) {
 735     die "Error: The value specified, $Options{outdelim}, for option \"--outdelim\" is not valid. Allowed values: comma, tab, or semicolon\n";
 736   }
 737   if ($Options{quote} !~ /^(Yes|No)$/i) {
 738     die "Error: The value specified, $Options{quote}, for option \"-q --quote\" is not valid. Allowed values: Yes or No\n";
 739   }
 740   if ($Options{outdelim} =~ /semicolon/i && $Options{quote} =~ /^No$/i) {
 741     die "Error: The value specified, $Options{quote}, for option \"-q --quote\" is not allowed with, semicolon value of \"--outdelim\" option: Fingerprints string use semicolon as delimiter for various data fields and must be quoted.\n";
 742   }
 743   if ($Options{usetriangleinequality} !~ /^(Yes|No)$/i) {
 744     die "Error: The value specified, $Options{usetriangleinequality}, for option \"-u, --UseTriangleInequality\" is not valid. Allowed values: Yes or No\n";
 745   }
 746   if ($Options{vectorstringformat} !~ /^(IDsAndValuesString|IDsAndValuesPairsString|ValuesAndIDsString|ValuesAndIDsPairsString)$/i) {
 747     die "Error: The value specified, $Options{vectorstringformat}, for option \"-v, --VectorStringFormat\" is not valid. Allowed values: IDsAndValuesString, IDsAndValuesPairsString, ValuesAndIDsString or ValuesAndIDsPairsString\n";
 748   }
 749 }
 750