       1 #!/usr/bin/perl -w
       2 #
       3 # File: PathLengthFingerprints.pl
       4 # Author: Manish Sud <msud@san.rr.com>
       5 #
       6 # Copyright (C) 2018 Manish Sud. All rights reserved.
       7 #
       8 # This file is part of MayaChemTools.
       9 #
      10 # MayaChemTools is free software; you can redistribute it and/or modify it under
      11 # the terms of the GNU Lesser General Public License as published by the Free
      12 # Software Foundation; either version 3 of the License, or (at your option) any
      13 # later version.
      14 #
      15 # MayaChemTools is distributed in the hope that it will be useful, but without
      16 # any warranty; without even the implied warranty of merchantability of fitness
      17 # for a particular purpose.  See the GNU Lesser General Public License for more
      18 # details.
      19 #
      20 # You should have received a copy of the GNU Lesser General Public License
      21 # along with MayaChemTools; if not, see <http://www.gnu.org/licenses/> or
      22 # write to the Free Software Foundation Inc., 59 Temple Place, Suite 330,
      23 # Boston, MA, 02111-1307, USA.
      24 #
      25
      26 use strict;
      27 use FindBin; use lib "$FindBin::Bin/../lib";
      28 use Getopt::Long;
      29 use File::Basename;
      30 use Text::ParseWords;
      31 use Benchmark;
      32 use FileUtil;
      33 use TextUtil;
      34 use SDFileUtil;
      35 use MoleculeFileIO;
      36 use FileIO::FingerprintsSDFileIO;
      37 use FileIO::FingerprintsTextFileIO;
      38 use FileIO::FingerprintsFPFileIO;
      39 use AtomTypes::AtomicInvariantsAtomTypes;
      40 use AtomTypes::FunctionalClassAtomTypes;
      41 use Fingerprints::PathLengthFingerprints;
      42
      43 my($ScriptName, %Options, $StartTime, $EndTime, $TotalTime);
      44
      45 # Autoflush STDOUT
      46 $| = 1;
      47
      48 # Starting message...
      49 $ScriptName = basename($0);
      50 print "\n$ScriptName: Starting...\n\n";
      51 $StartTime = new Benchmark;
      52
      53 # Get the options and setup script...
      54 SetupScriptUsage();
      55 if ($Options{help} || @ARGV < 1) {
      56   die GetUsageFromPod("$FindBin::Bin/$ScriptName");
      57 }
      58
      59 my(@SDFilesList);
      60 @SDFilesList = ExpandFileNames(\@ARGV, "sdf sd");
      61
      62 # Process options...
      63 print "Processing options...\n";
      64 my(%OptionsInfo);
      65 ProcessOptions();
      66
      67 # Setup information about input files...
      68 print "Checking input SD file(s)...\n";
      69 my(%SDFilesInfo);
      70 RetrieveSDFilesInfo();
      71
      72 # Process input files..
      73 my($FileIndex);
      74 if (@SDFilesList > 1) {
      75   print "\nProcessing SD files...\n";
      76 }
      77 for $FileIndex (0 .. $#SDFilesList) {
      78   if ($SDFilesInfo{FileOkay}[$FileIndex]) {
      79     print "\nProcessing file $SDFilesList[$FileIndex]...\n";
      80     GeneratePathLengthFingerprints($FileIndex);
      81   }
      82 }
      83 print "\n$ScriptName:Done...\n\n";
      84
      85 $EndTime = new Benchmark;
      86 $TotalTime = timediff ($EndTime, $StartTime);
      87 print "Total time: ", timestr($TotalTime), "\n";
      88
      89 ###############################################################################
      90
      91 # Generate fingerprints for a SD file...
      92 #
      93 sub GeneratePathLengthFingerprints {
      94   my($FileIndex) = @_;
      95   my($CmpdCount, $IgnoredCmpdCount, $SDFile, $MoleculeFileIO, $Molecule, $PathLengthFingerprints, $NewFPSDFileIO, $NewFPTextFileIO, $NewFPFileIO);
      96
      97   $SDFile = $SDFilesList[$FileIndex];
      98
      99   # Setup output files...
     100   #
     101   ($NewFPSDFileIO, $NewFPTextFileIO, $NewFPFileIO) = SetupAndOpenOutputFiles($FileIndex);
     102
     103   $MoleculeFileIO = new MoleculeFileIO('Name' => $SDFile);
     104   $MoleculeFileIO->Open();
     105
     106   $CmpdCount = 0;
     107   $IgnoredCmpdCount = 0;
     108
     109   COMPOUND: while ($Molecule = $MoleculeFileIO->ReadMolecule()) {
     110     $CmpdCount++;
     111
     112     # Filter compound data before calculating fingerprints...
     113     if ($OptionsInfo{Filter}) {
     114       if (CheckAndFilterCompound($CmpdCount, $Molecule)) {
     115         $IgnoredCmpdCount++;
     116         next COMPOUND;
     117       }
     118     }
     119
     120     $PathLengthFingerprints = GenerateMoleculeFingerprints($Molecule);
     121     if (!$PathLengthFingerprints) {
     122       $IgnoredCmpdCount++;
     123       ProcessIgnoredCompound('FingerprintsGenerationFailed', $CmpdCount, $Molecule);
     124       next COMPOUND;
     125     }
     126
     127     WriteDataToOutputFiles($FileIndex, $CmpdCount, $Molecule, $PathLengthFingerprints, $NewFPSDFileIO, $NewFPTextFileIO, $NewFPFileIO);
     128   }
     129   $MoleculeFileIO->Close();
     130
     131   if ($NewFPSDFileIO) {
     132     $NewFPSDFileIO->Close();
     133   }
     134   if ($NewFPTextFileIO) {
     135     $NewFPTextFileIO->Close();
     136   }
     137   if ($NewFPFileIO) {
     138     $NewFPFileIO->Close();
     139   }
     140
     141   WriteFingerprintsGenerationSummaryStatistics($CmpdCount, $IgnoredCmpdCount);
     142 }
     143
     144 # Process compound being ignored due to problems in fingerprints geneation...
     145 #
     146 sub ProcessIgnoredCompound {
     147   my($Mode, $CmpdCount, $Molecule) = @_;
     148   my($CmpdID, $DataFieldLabelAndValuesRef);
     149
     150   $DataFieldLabelAndValuesRef = $Molecule->GetDataFieldLabelAndValues();
     151   $CmpdID = SetupCmpdIDForOutputFiles($CmpdCount, $Molecule, $DataFieldLabelAndValuesRef);
     152
     153   MODE: {
     154     if ($Mode =~ /^ContainsNonElementalData$/i) {
     155       warn "\nWarning: Ignoring compound record number $CmpdCount with ID $CmpdID: Compound contains atom data corresponding to non-elemental atom symbol(s)...\n\n";
     156       next MODE;
     157     }
     158
     159     if ($Mode =~ /^ContainsNoElementalData$/i) {
     160       warn "\nWarning: Ignoring compound record number $CmpdCount with ID $CmpdID: Compound contains no atom data...\n\n";
     161       next MODE;
     162     }
     163
     164     if ($Mode =~ /^FingerprintsGenerationFailed$/i) {
     165       warn "\nWarning: Ignoring compound record number $CmpdCount with ID $CmpdID: Fingerprints generation didn't succeed...\n\n";
     166       next MODE;
     167     }
     168     warn "\nWarning: Ignoring compound record number $CmpdCount with ID $CmpdID: Fingerprints generation didn't succeed...\n\n";
     169   }
     170 }
     171
     172 # Check and filter compounds....
     173 #
     174 sub CheckAndFilterCompound {
     175   my($CmpdCount, $Molecule) = @_;
     176   my($ElementCount, $NonElementCount);
     177
     178   ($ElementCount, $NonElementCount) = $Molecule->GetNumOfElementsAndNonElements();
     179
     180   if ($NonElementCount) {
     181     ProcessIgnoredCompound('ContainsNonElementalData', $CmpdCount, $Molecule);
     182     return 1;
     183   }
     184
     185   if (!$ElementCount) {
     186     ProcessIgnoredCompound('ContainsNoElementalData', $CmpdCount, $Molecule);
     187     return 1;
     188   }
     189
     190   return 0;
     191 }
     192
     193 # Write out compounds fingerprints generation summary statistics...
     194 #
     195 sub WriteFingerprintsGenerationSummaryStatistics {
     196   my($CmpdCount, $IgnoredCmpdCount) = @_;
     197   my($ProcessedCmpdCount);
     198
     199   $ProcessedCmpdCount = $CmpdCount - $IgnoredCmpdCount;
     200
     201   print "\nNumber of compounds: $CmpdCount\n";
     202   print "Number of compounds processed successfully during fingerprints generation: $ProcessedCmpdCount\n";
     203   print "Number of compounds ignored during fingerprints generation: $IgnoredCmpdCount\n";
     204 }
     205
     206 # Open output files...
     207 #
     208 sub SetupAndOpenOutputFiles {
     209   my($FileIndex) = @_;
     210   my($NewFPSDFile, $NewFPFile, $NewFPTextFile, $NewFPSDFileIO, $NewFPTextFileIO, $NewFPFileIO, %FingerprintsFileIOParams);
     211
     212   ($NewFPSDFileIO, $NewFPTextFileIO, $NewFPFileIO) = (undef) x 3;
     213
     214   # Setup common parameters for fingerprints file IO objects...
     215   #
     216   %FingerprintsFileIOParams = ();
     217   if ($OptionsInfo{Mode} =~ /^PathLengthBits$/i) {
     218     %FingerprintsFileIOParams = ('Mode' => 'Write', 'Overwrite' => $OptionsInfo{OverwriteFiles}, 'FingerprintsStringMode' => 'FingerprintsBitVectorString', 'BitStringFormat' => $OptionsInfo{BitStringFormat}, 'BitsOrder' => $OptionsInfo{BitsOrder});
     219   }
     220   elsif ($OptionsInfo{Mode} =~ /^PathLengthCount$/i) {
     221     %FingerprintsFileIOParams = ('Mode' => 'Write', 'Overwrite' => $OptionsInfo{OverwriteFiles}, 'FingerprintsStringMode' => 'FingerprintsVectorString', 'VectorStringFormat' => $OptionsInfo{VectorStringFormat});
     222   }
     223
     224   if ($OptionsInfo{SDOutput}) {
     225     $NewFPSDFile = $SDFilesInfo{SDOutFileNames}[$FileIndex];
     226     print "Generating SD file $NewFPSDFile...\n";
     227     $NewFPSDFileIO = new FileIO::FingerprintsSDFileIO('Name' => $NewFPSDFile, %FingerprintsFileIOParams, 'FingerprintsFieldLabel' => $OptionsInfo{FingerprintsLabel});
     228     $NewFPSDFileIO->Open();
     229   }
     230
     231   if ($OptionsInfo{FPOutput}) {
     232     $NewFPFile = $SDFilesInfo{FPOutFileNames}[$FileIndex];
     233     print "Generating FP file $NewFPFile...\n";
     234     $NewFPFileIO = new FileIO::FingerprintsFPFileIO('Name' => $NewFPFile, %FingerprintsFileIOParams);
     235     $NewFPFileIO->Open();
     236   }
     237
     238   if ($OptionsInfo{TextOutput}) {
     239     my($ColLabelsRef);
     240
     241     $NewFPTextFile = $SDFilesInfo{TextOutFileNames}[$FileIndex];
     242     $ColLabelsRef = SetupFPTextFileCoulmnLabels($FileIndex);
     243
     244     print "Generating text file $NewFPTextFile...\n";
     245     $NewFPTextFileIO = new FileIO::FingerprintsTextFileIO('Name' => $NewFPTextFile, %FingerprintsFileIOParams, 'DataColLabels' => $ColLabelsRef, 'OutDelim' => $OptionsInfo{OutDelim}, 'OutQuote' => $OptionsInfo{OutQuote});
     246     $NewFPTextFileIO->Open();
     247   }
     248
     249   return ($NewFPSDFileIO, $NewFPTextFileIO, $NewFPFileIO);
     250 }
     251
     252 # Write fingerpritns and other data to appropriate output files...
     253 #
     254 sub WriteDataToOutputFiles {
     255   my($FileIndex, $CmpdCount, $Molecule, $PathLengthFingerprints, $NewFPSDFileIO, $NewFPTextFileIO, $NewFPFileIO) = @_;
     256   my($DataFieldLabelAndValuesRef);
     257
     258   $DataFieldLabelAndValuesRef = undef;
     259   if ($NewFPTextFileIO || $NewFPFileIO) {
     260     $DataFieldLabelAndValuesRef = $Molecule->GetDataFieldLabelAndValues();
     261   }
     262
     263   if ($NewFPSDFileIO) {
     264     my($CmpdString);
     265
     266     $CmpdString = $Molecule->GetInputMoleculeString();
     267     $NewFPSDFileIO->WriteFingerprints($PathLengthFingerprints, $CmpdString);
     268   }
     269
     270   if ($NewFPTextFileIO) {
     271     my($ColValuesRef);
     272
     273     $ColValuesRef = SetupFPTextFileCoulmnValues($FileIndex, $CmpdCount, $Molecule, $DataFieldLabelAndValuesRef);
     274     $NewFPTextFileIO->WriteFingerprints($PathLengthFingerprints, $ColValuesRef);
     275   }
     276
     277   if ($NewFPFileIO) {
     278     my($CompoundID);
     279
     280     $CompoundID = SetupCmpdIDForOutputFiles($CmpdCount, $Molecule, $DataFieldLabelAndValuesRef);
     281     $NewFPFileIO->WriteFingerprints($PathLengthFingerprints, $CompoundID);
     282   }
     283 }
     284
     285 # Generate approriate column labels for FPText output file...
     286 #
     287 sub SetupFPTextFileCoulmnLabels {
     288   my($FileIndex) = @_;
     289   my($Line, @ColLabels);
     290
     291   @ColLabels = ();
     292   if ($OptionsInfo{DataFieldsMode} =~ /^All$/i) {
     293     push @ColLabels, @{$SDFilesInfo{AllDataFieldsRef}[$FileIndex]};
     294   }
     295   elsif ($OptionsInfo{DataFieldsMode} =~ /^Common$/i) {
     296     push @ColLabels, @{$SDFilesInfo{CommonDataFieldsRef}[$FileIndex]};
     297   }
     298   elsif ($OptionsInfo{DataFieldsMode} =~ /^Specify$/i) {
     299     push @ColLabels, @{$OptionsInfo{SpecifiedDataFields}};
     300   }
     301   elsif ($OptionsInfo{DataFieldsMode} =~ /^CompoundID$/i) {
     302     push @ColLabels, $OptionsInfo{CompoundIDLabel};
     303   }
     304   # Add fingerprints label...
     305   push @ColLabels, $OptionsInfo{FingerprintsLabel};
     306
     307   return \@ColLabels;
     308 }
     309
     310 # Generate column values FPText output file..
     311 #
     312 sub SetupFPTextFileCoulmnValues {
     313   my($FileIndex, $CmpdCount, $Molecule, $DataFieldLabelAndValuesRef) = @_;
     314   my(@ColValues);
     315
     316   @ColValues = ();
     317   if ($OptionsInfo{DataFieldsMode} =~ /^CompoundID$/i) {
     318     push @ColValues, SetupCmpdIDForOutputFiles($CmpdCount, $Molecule, $DataFieldLabelAndValuesRef);
     319   }
     320   elsif ($OptionsInfo{DataFieldsMode} =~ /^All$/i) {
     321     @ColValues = map { exists $DataFieldLabelAndValuesRef->{$_} ? $DataFieldLabelAndValuesRef->{$_} : ''} @{$SDFilesInfo{AllDataFieldsRef}[$FileIndex]};
     322   }
     323   elsif ($OptionsInfo{DataFieldsMode} =~ /^Common$/i) {
     324     @ColValues = map { exists $DataFieldLabelAndValuesRef->{$_} ? $DataFieldLabelAndValuesRef->{$_} : ''} @{$SDFilesInfo{CommonDataFieldsRef}[$FileIndex]};
     325   }
     326   elsif ($OptionsInfo{DataFieldsMode} =~ /^Specify$/i) {
     327     @ColValues = map { exists $DataFieldLabelAndValuesRef->{$_} ? $DataFieldLabelAndValuesRef->{$_} : ''} @{$OptionsInfo{SpecifiedDataFields}};
     328   }
     329
     330   return \@ColValues;
     331 }
     332
     333 # Generate compound ID for FP and FPText output files..
     334 #
     335 sub SetupCmpdIDForOutputFiles {
     336   my($CmpdCount, $Molecule, $DataFieldLabelAndValuesRef) = @_;
     337   my($CmpdID);
     338
     339   $CmpdID = '';
     340   if ($OptionsInfo{CompoundIDMode} =~ /^MolNameOrLabelPrefix$/i) {
     341     my($MolName);
     342     $MolName = $Molecule->GetName();
     343     $CmpdID = $MolName ? $MolName : "$OptionsInfo{CompoundID}${CmpdCount}";
     344   }
     345   elsif ($OptionsInfo{CompoundIDMode} =~ /^LabelPrefix$/i) {
     346     $CmpdID = "$OptionsInfo{CompoundID}${CmpdCount}";
     347   }
     348   elsif ($OptionsInfo{CompoundIDMode} =~ /^DataField$/i) {
     349     my($SpecifiedDataField);
     350     $SpecifiedDataField = $OptionsInfo{CompoundID};
     351     $CmpdID = exists $DataFieldLabelAndValuesRef->{$SpecifiedDataField} ? $DataFieldLabelAndValuesRef->{$SpecifiedDataField} : '';
     352   }
     353   elsif ($OptionsInfo{CompoundIDMode} =~ /^MolName$/i) {
     354     $CmpdID = $Molecule->GetName();
     355   }
     356   return $CmpdID;
     357 }
     358
     359 # Generate fingerprints for molecule...
     360 #
     361 sub GenerateMoleculeFingerprints {
     362   my($Molecule) = @_;
     363   my($PathLengthFingerprints);
     364
     365   if ($OptionsInfo{KeepLargestComponent}) {
     366     $Molecule->KeepLargestComponent();
     367   }
     368   if ($OptionsInfo{IgnoreHydrogens}) {
     369     $Molecule->DeleteHydrogens();
     370   }
     371
     372   if ($OptionsInfo{DetectAromaticity}) {
     373     if (!$Molecule->DetectRings()) {
     374       return undef;
     375     }
     376     $Molecule->SetAromaticityModel($OptionsInfo{AromaticityModel});
     377     $Molecule->DetectAromaticity();
     378   }
     379
     380   $PathLengthFingerprints = undef;
     381   if ($OptionsInfo{Mode} =~ /^PathLengthBits$/i) {
     382     $PathLengthFingerprints = GeneratePathLengthBitsFingerprints($Molecule);
     383   }
     384   elsif ($OptionsInfo{Mode} =~ /^PathLengthCount$/i) {
     385     $PathLengthFingerprints = GeneratePathLengthCountFingerprints($Molecule);
     386   }
     387   else {
     388     die "Error: The value specified, $Options{mode}, for option \"-m, --mode\" is not valid. Allowed values: PathLengthBits or PathLengthCount\n";
     389   }
     390
     391   return $PathLengthFingerprints;
     392 }
     393
     394 # Generate pathlength bits finerprints for molecule...
     395 #
     396 sub GeneratePathLengthBitsFingerprints {
     397   my($Molecule) = @_;
     398   my($PathLengthFingerprints);
     399
     400   $PathLengthFingerprints = new Fingerprints::PathLengthFingerprints('Molecule' => $Molecule, 'Type' => 'PathLengthBits', 'AtomIdentifierType' => $OptionsInfo{AtomIdentifierType}, 'NumOfBitsToSetPerPath' => $OptionsInfo{NumOfBitsToSetPerPath}, 'Size' => $OptionsInfo{Size}, 'MinLength' => $OptionsInfo{MinPathLength}, 'MaxLength' => $OptionsInfo{MaxPathLength}, 'AllowRings' => $OptionsInfo{AllowRings}, 'AllowSharedBonds' => $OptionsInfo{AllowSharedBonds}, 'UseBondSymbols' => $OptionsInfo{UseBondSymbols}, 'UseUniquePaths' => $OptionsInfo{UseUniquePaths}, 'UsePerlCoreRandom' => $OptionsInfo{UsePerlCoreRandom});
     401
     402   # Set atom identifier type...
     403   SetAtomIdentifierTypeValuesToUse($PathLengthFingerprints);
     404
     405   # Generate fingerprints...
     406   $PathLengthFingerprints->GenerateFingerprints();
     407
     408   # Make sure fingerprints generation is successful...
     409   if (!$PathLengthFingerprints->IsFingerprintsGenerationSuccessful()) {
     410     return undef;
     411   }
     412
     413   if ($OptionsInfo{Fold}) {
     414     my($CheckSizeValue) = 0;
     415     $PathLengthFingerprints->FoldFingerprintsBySize($OptionsInfo{FoldedSize}, $CheckSizeValue);
     416   }
     417
     418   return $PathLengthFingerprints;
     419 }
     420
     421 # Generate pathlength count finerprints for molecule...
     422 #
     423 sub GeneratePathLengthCountFingerprints {
     424   my($Molecule) = @_;
     425   my($PathLengthFingerprints);
     426
     427   $PathLengthFingerprints = new Fingerprints::PathLengthFingerprints('Molecule' => $Molecule, 'Type' => 'PathLengthCount', 'AtomIdentifierType' => $OptionsInfo{AtomIdentifierType}, 'MinLength' => $OptionsInfo{MinPathLength}, 'MaxLength' => $OptionsInfo{MaxPathLength}, 'AllowRings' => $OptionsInfo{AllowRings}, 'AllowSharedBonds' => $OptionsInfo{AllowSharedBonds}, 'UseBondSymbols' => $OptionsInfo{UseBondSymbols}, 'UseUniquePaths' => $OptionsInfo{UseUniquePaths});
     428
     429   # Set atom identifier type...
     430   SetAtomIdentifierTypeValuesToUse($PathLengthFingerprints);
     431
     432   # Generate fingerprints...
     433   $PathLengthFingerprints->GenerateFingerprints();
     434
     435   # Make sure fingerprints generation is successful...
     436   if (!$PathLengthFingerprints->IsFingerprintsGenerationSuccessful()) {
     437     return undef;
     438   }
     439   return $PathLengthFingerprints;
     440 }
     441
     442 # Set atom identifier type to use for generating path strings...
     443 #
     444 sub SetAtomIdentifierTypeValuesToUse {
     445   my($PathLengthFingerprints) = @_;
     446
     447   if ($OptionsInfo{AtomIdentifierType} =~ /^AtomicInvariantsAtomTypes$/i) {
     448     $PathLengthFingerprints->SetAtomicInvariantsToUse(\@{$OptionsInfo{AtomicInvariantsToUse}});
     449   }
     450   elsif ($OptionsInfo{AtomIdentifierType} =~ /^FunctionalClassAtomTypes$/i) {
     451     $PathLengthFingerprints->SetFunctionalClassesToUse(\@{$OptionsInfo{FunctionalClassesToUse}});
     452   }
     453   elsif ($OptionsInfo{AtomIdentifierType} =~ /^(DREIDINGAtomTypes|EStateAtomTypes|MMFF94AtomTypes|SLogPAtomTypes|SYBYLAtomTypes|TPSAAtomTypes|UFFAtomTypes)$/i) {
     454     # Nothing to do for now...
     455   }
     456   else {
     457     die "Error: The value specified, $Options{atomidentifiertype}, for option \"-a, --AtomIdentifierType\" is not valid. Supported atom identifier types in current release of MayaChemTools: AtomicInvariantsAtomTypes, DREIDINGAtomTypes, EStateAtomTypes, FunctionalClassAtomTypes, MMFF94AtomTypes, SLogPAtomTypes, SYBYLAtomTypes, TPSAAtomTypes, UFFAtomTypes\n";
     458   }
     459 }
     460
     461 # Retrieve information about SD files...
     462 #
     463 sub RetrieveSDFilesInfo {
     464   my($SDFile, $Index, $FileDir, $FileExt, $FileName, $OutFileRoot, $TextOutFileExt, $SDOutFileExt, $FPOutFileExt, $NewSDFileName, $NewFPFileName, $NewTextFileName, $CheckDataField, $CollectDataFields, $AllDataFieldsRef, $CommonDataFieldsRef);
     465
     466   %SDFilesInfo = ();
     467   @{$SDFilesInfo{FileOkay}} = ();
     468   @{$SDFilesInfo{OutFileRoot}} = ();
     469   @{$SDFilesInfo{SDOutFileNames}} = ();
     470   @{$SDFilesInfo{FPOutFileNames}} = ();
     471   @{$SDFilesInfo{TextOutFileNames}} = ();
     472   @{$SDFilesInfo{AllDataFieldsRef}} = ();
     473   @{$SDFilesInfo{CommonDataFieldsRef}} = ();
     474
     475   $CheckDataField = ($OptionsInfo{TextOutput} && ($OptionsInfo{DataFieldsMode} =~ /^CompoundID$/i) && ($OptionsInfo{CompoundIDMode} =~ /^DataField$/i)) ? 1 : 0;
     476   $CollectDataFields = ($OptionsInfo{TextOutput} && ($OptionsInfo{DataFieldsMode} =~ /^(All|Common)$/i)) ? 1 : 0;
     477
     478   FILELIST: for $Index (0 .. $#SDFilesList) {
     479     $SDFile = $SDFilesList[$Index];
     480
     481     $SDFilesInfo{FileOkay}[$Index] = 0;
     482     $SDFilesInfo{OutFileRoot}[$Index] = '';
     483     $SDFilesInfo{SDOutFileNames}[$Index] = '';
     484     $SDFilesInfo{FPOutFileNames}[$Index] = '';
     485     $SDFilesInfo{TextOutFileNames}[$Index] = '';
     486
     487     $SDFile = $SDFilesList[$Index];
     488     if (!(-e $SDFile)) {
     489       warn "Warning: Ignoring file $SDFile: It doesn't exist\n";
     490       next FILELIST;
     491     }
     492     if (!CheckFileType($SDFile, "sd sdf")) {
     493       warn "Warning: Ignoring file $SDFile: It's not a SD file\n";
     494       next FILELIST;
     495     }
     496
     497     if ($CheckDataField) {
     498       # Make sure data field exists in SD file..
     499       my($CmpdString, $SpecifiedDataField, @CmpdLines, %DataFieldValues);
     500
     501       @CmpdLines = ();
     502       open SDFILE, "$SDFile" or die "Error: Couldn't open $SDFile: $! \n";
     503       $CmpdString = ReadCmpdString(\*SDFILE);
     504       close SDFILE;
     505       @CmpdLines = split "\n", $CmpdString;
     506       %DataFieldValues = GetCmpdDataHeaderLabelsAndValues(\@CmpdLines);
     507       $SpecifiedDataField = $OptionsInfo{CompoundID};
     508       if (!exists $DataFieldValues{$SpecifiedDataField}) {
     509         warn "Warning: Ignoring file $SDFile: Data field value, $SpecifiedDataField, using  \"--CompoundID\" option in \"DataField\" \"--CompoundIDMode\" doesn't exist\n";
     510         next FILELIST;
     511       }
     512     }
     513
     514     $AllDataFieldsRef = '';
     515     $CommonDataFieldsRef = '';
     516     if ($CollectDataFields) {
     517       my($CmpdCount);
     518       open SDFILE, "$SDFile" or die "Error: Couldn't open $SDFile: $! \n";
     519       ($CmpdCount, $AllDataFieldsRef, $CommonDataFieldsRef) = GetAllAndCommonCmpdDataHeaderLabels(\*SDFILE);
     520       close SDFILE;
     521     }
     522
     523     # Setup output file names...
     524     $FileDir = ""; $FileName = ""; $FileExt = "";
     525     ($FileDir, $FileName, $FileExt) = ParseFileName($SDFile);
     526
     527     $TextOutFileExt = "csv";
     528     if ($Options{outdelim} =~ /^tab$/i) {
     529       $TextOutFileExt = "tsv";
     530     }
     531     $SDOutFileExt = $FileExt;
     532     $FPOutFileExt = "fpf";
     533
     534     if ($OptionsInfo{OutFileRoot} && (@SDFilesList == 1)) {
     535       my ($RootFileDir, $RootFileName, $RootFileExt) = ParseFileName($OptionsInfo{OutFileRoot});
     536       if ($RootFileName && $RootFileExt) {
     537         $FileName = $RootFileName;
     538       }
     539       else {
     540         $FileName = $OptionsInfo{OutFileRoot};
     541       }
     542       $OutFileRoot = $FileName;
     543     }
     544     else {
     545       $OutFileRoot = "${FileName}PathLengthFP";
     546     }
     547
     548     $NewSDFileName = "${OutFileRoot}.${SDOutFileExt}";
     549     $NewFPFileName = "${OutFileRoot}.${FPOutFileExt}";
     550     $NewTextFileName = "${OutFileRoot}.${TextOutFileExt}";
     551
     552     if ($OptionsInfo{SDOutput}) {
     553       if ($SDFile =~ /$NewSDFileName/i) {
     554         warn "Warning: Ignoring input file $SDFile: Same output, $NewSDFileName, and input file names.\n";
     555         print "Specify a different name using \"-r --root\" option or use default name.\n";
     556         next FILELIST;
     557       }
     558     }
     559
     560     if (!$OptionsInfo{OverwriteFiles}) {
     561       # Check SD, FP and text outout files...
     562       if ($OptionsInfo{SDOutput}) {
     563         if (-e $NewSDFileName) {
     564           warn "Warning: Ignoring file $SDFile: The file $NewSDFileName already exists\n";
     565           next FILELIST;
     566         }
     567       }
     568       if ($OptionsInfo{FPOutput}) {
     569         if (-e $NewFPFileName) {
     570           warn "Warning: Ignoring file $SDFile: The file $NewFPFileName already exists\n";
     571           next FILELIST;
     572         }
     573       }
     574       if ($OptionsInfo{TextOutput}) {
     575         if (-e $NewTextFileName) {
     576           warn "Warning: Ignoring file $SDFile: The file $NewTextFileName already exists\n";
     577           next FILELIST;
     578         }
     579       }
     580     }
     581
     582     $SDFilesInfo{FileOkay}[$Index] = 1;
     583
     584     $SDFilesInfo{OutFileRoot}[$Index] = $OutFileRoot;
     585     $SDFilesInfo{SDOutFileNames}[$Index] = $NewSDFileName;
     586     $SDFilesInfo{FPOutFileNames}[$Index] = $NewFPFileName;
     587     $SDFilesInfo{TextOutFileNames}[$Index] = $NewTextFileName;
     588
     589     $SDFilesInfo{AllDataFieldsRef}[$Index] = $AllDataFieldsRef;
     590     $SDFilesInfo{CommonDataFieldsRef}[$Index] = $CommonDataFieldsRef;
     591   }
     592 }
     593
     594 # Process option values...
     595 sub ProcessOptions {
     596   %OptionsInfo = ();
     597
     598   $OptionsInfo{Mode} = $Options{mode};
     599   $OptionsInfo{AromaticityModel} = $Options{aromaticitymodel};
     600   $OptionsInfo{PathMode} = $Options{pathmode};
     601
     602   ProcessAtomIdentifierTypeOptions();
     603
     604   $OptionsInfo{BitsOrder} = $Options{bitsorder};
     605   $OptionsInfo{BitStringFormat} = $Options{bitstringformat};
     606
     607   $OptionsInfo{CompoundIDMode} = $Options{compoundidmode};
     608   $OptionsInfo{CompoundIDLabel} = $Options{compoundidlabel};
     609   $OptionsInfo{DataFieldsMode} = $Options{datafieldsmode};
     610
     611   my(@SpecifiedDataFields);
     612   @SpecifiedDataFields = ();
     613
     614   @{$OptionsInfo{SpecifiedDataFields}} = ();
     615   $OptionsInfo{CompoundID} = '';
     616
     617   if ($Options{datafieldsmode} =~ /^CompoundID$/i) {
     618     if ($Options{compoundidmode} =~ /^DataField$/i) {
     619       if (!$Options{compoundid}) {
     620         die "Error: You must specify a value for \"--CompoundID\" option in \"DataField\" \"--CompoundIDMode\". \n";
     621       }
     622       $OptionsInfo{CompoundID} = $Options{compoundid};
     623     }
     624     elsif ($Options{compoundidmode} =~ /^(LabelPrefix|MolNameOrLabelPrefix)$/i) {
     625       $OptionsInfo{CompoundID} = $Options{compoundid} ? $Options{compoundid} : 'Cmpd';
     626     }
     627   }
     628   elsif ($Options{datafieldsmode} =~ /^Specify$/i) {
     629     if (!$Options{datafields}) {
     630       die "Error: You must specify a value for \"--DataFields\" option in \"Specify\" \"-d, --DataFieldsMode\". \n";
     631     }
     632     @SpecifiedDataFields = split /\,/, $Options{datafields};
     633     push @{$OptionsInfo{SpecifiedDataFields}}, @SpecifiedDataFields;
     634   }
     635
     636   if ($Options{atomidentifiertype} !~ /^AtomicInvariantsAtomTypes$/i) {
     637     if ($Options{detectaromaticity} =~ /^No$/i) {
     638       die "Error: The value specified, $Options{detectaromaticity}, for option \"--DetectAromaticity\" is not valid. No value is only allowed during AtomicInvariantsAtomTypes value for \"-a, --AtomIdentifierType\" \n";
     639     }
     640   }
     641   $OptionsInfo{DetectAromaticity} = ($Options{detectaromaticity} =~ /^Yes$/i) ? 1 : 0;
     642
     643   $OptionsInfo{Filter} = ($Options{filter} =~ /^Yes$/i) ? 1 : 0;
     644
     645   $OptionsInfo{FingerprintsLabel} = $Options{fingerprintslabel} ? $Options{fingerprintslabel} : 'PathLengthFingerprints';
     646
     647   my($Size, $MinSize, $MaxSize);
     648   $MinSize = 32;
     649   $MaxSize = 2**32;
     650   $Size = $Options{size};
     651   if (!(IsPositiveInteger($Size) && $Size >= $MinSize && $Size <= $MaxSize && IsNumberPowerOfNumber($Size, 2))) {
     652     die "Error: Invalid size value, $Size, for \"-s, --size\" option. Allowed values: power of 2, >= minimum size of $MinSize, and <= maximum size of $MaxSize.\n";
     653   }
     654   $OptionsInfo{Size} = $Size;
     655
     656   $OptionsInfo{Fold} = ($Options{fold} =~ /^Yes$/i) ? 1 : 0;
     657   my($FoldedSize);
     658   $FoldedSize = $Options{foldedsize};
     659   if ($Options{fold} =~ /^Yes$/i) {
     660     if (!(IsPositiveInteger($FoldedSize) && $FoldedSize < $Size && IsNumberPowerOfNumber($FoldedSize, 2))) {
     661       die "Error: Invalid folded size value, $FoldedSize, for \"--FoldedSize\" option. Allowed values: power of 2, >= minimum size of $MinSize, and < size value of $Size.\n";
     662     }
     663   }
     664   $OptionsInfo{FoldedSize} = $FoldedSize;
     665
     666   $OptionsInfo{IgnoreHydrogens} = ($Options{ignorehydrogens} =~ /^Yes$/i) ? 1 : 0;
     667   $OptionsInfo{KeepLargestComponent} = ($Options{keeplargestcomponent} =~ /^Yes$/i) ? 1 : 0;
     668
     669   my($MinPathLength, $MaxPathLength);
     670   $MinPathLength = $Options{minpathlength};
     671   $MaxPathLength = $Options{maxpathlength};
     672   if (!IsPositiveInteger($MinPathLength)) {
     673     die "Error: Invalid path length value, $MinPathLength, for \"--MinPathLength\" option. Allowed values: > 0\n";
     674   }
     675   if (!IsPositiveInteger($MaxPathLength)) {
     676     die "Error: Invalid path length value, $MaxPathLength, for \"--MinPathLength\" option. Allowed values: > 0\n";
     677   }
     678   if ($MinPathLength >= $MaxPathLength) {
     679     die "Error: Invalid minimum and maximum path length values, $MinPathLength and $MaxPathLength, for \"--MinPathLength\"  and \"--MaxPathLength\"options. Allowed values: minimum path length value must be smaller than maximum path length value.\n";
     680   }
     681   $OptionsInfo{MinPathLength} = $MinPathLength;
     682   $OptionsInfo{MaxPathLength} = $MaxPathLength;
     683
     684   my($NumOfBitsToSetPerPath);
     685   $NumOfBitsToSetPerPath = $Options{numofbitstosetperpath};
     686   if (!IsPositiveInteger($MaxPathLength)) {
     687     die "Error: Invalid  value, $NumOfBitsToSetPerPath, for \"-n, --NumOfBitsToSetPerPath\" option. Allowed values: > 0\n";
     688   }
     689   if ($NumOfBitsToSetPerPath >= $Size) {
     690     die "Error: Invalid  value, $NumOfBitsToSetPerPath, for \"-n, --NumOfBitsToSetPerPath\" option. Allowed values: It must be less than the size, $Size, of the fingerprint bit-string.\n";
     691   }
     692   $OptionsInfo{NumOfBitsToSetPerPath} = $NumOfBitsToSetPerPath;
     693
     694   $OptionsInfo{Output} = $Options{output};
     695   $OptionsInfo{SDOutput} = ($Options{output} =~ /^(SD|All)$/i) ? 1 : 0;
     696   $OptionsInfo{FPOutput} = ($Options{output} =~ /^(FP|All)$/i) ? 1 : 0;
     697   $OptionsInfo{TextOutput} = ($Options{output} =~ /^(Text|All)$/i) ? 1 : 0;
     698
     699   $OptionsInfo{OutDelim} = $Options{outdelim};
     700   $OptionsInfo{OutQuote} = ($Options{quote} =~ /^Yes$/i) ? 1 : 0;
     701
     702   $OptionsInfo{OverwriteFiles} = $Options{overwrite} ? 1 : 0;
     703   $OptionsInfo{OutFileRoot} = $Options{root} ? $Options{root} : 0;
     704
     705   $OptionsInfo{UseBondSymbols} = ($Options{usebondsymbols} =~ /^Yes$/i) ? 1 : 0;
     706
     707   $OptionsInfo{UsePerlCoreRandom} = ($Options{useperlcorerandom} =~ /^Yes$/i) ? 1 : 0;
     708
     709   $OptionsInfo{UseUniquePaths} = ($Options{useuniquepaths} =~ /^Yes$/i) ? 1 : 0;
     710
     711   $OptionsInfo{VectorStringFormat} = $Options{vectorstringformat};
     712
     713   # Setup parameters used during generation of fingerprints by PathLengthFingerprints class...
     714   my($AllowRings, $AllowSharedBonds);
     715   $AllowRings = 1;
     716   $AllowSharedBonds = 1;
     717   MODE: {
     718     if ($Options{pathmode} =~ /^AtomPathsWithoutRings$/i) { $AllowSharedBonds = 0; $AllowRings = 0; last MODE;}
     719     if ($Options{pathmode} =~ /^AtomPathsWithRings$/i) { $AllowSharedBonds = 0; $AllowRings = 1; last MODE;}
     720     if ($Options{pathmode} =~ /^AllAtomPathsWithoutRings$/i) { $AllowSharedBonds = 1; $AllowRings = 0; last MODE;}
     721     if ($Options{pathmode} =~ /^AllAtomPathsWithRings$/i) { $AllowSharedBonds = 1; $AllowRings = 1; last MODE;}
     722     die "Error: ProcessOptions: mode value, $Options{pathmode}, is not supported.\n";
     723   }
     724   $OptionsInfo{AllowRings} = $AllowRings;
     725   $OptionsInfo{AllowSharedBonds} = $AllowSharedBonds;
     726 }
     727
     728 # Process atom identifier type and related options...
     729 #
     730 sub ProcessAtomIdentifierTypeOptions {
     731
     732   $OptionsInfo{AtomIdentifierType} = $Options{atomidentifiertype};
     733
     734   if ($Options{atomidentifiertype} =~ /^AtomicInvariantsAtomTypes$/i) {
     735     ProcessAtomicInvariantsToUseOption();
     736   }
     737   elsif ($Options{atomidentifiertype} =~ /^FunctionalClassAtomTypes$/i) {
     738     ProcessFunctionalClassesToUse();
     739   }
     740   elsif ($OptionsInfo{AtomIdentifierType} =~ /^(DREIDINGAtomTypes|EStateAtomTypes|MMFF94AtomTypes|SLogPAtomTypes|SYBYLAtomTypes|TPSAAtomTypes|UFFAtomTypes)$/i) {
     741     # Nothing to do for now...
     742   }
     743   else {
     744     die "Error: The value specified, $Options{atomidentifiertype}, for option \"-a, --AtomIdentifierType\" is not valid. Supported atom identifier types in current release of MayaChemTools: AtomicInvariantsAtomTypes, DREIDINGAtomTypes, EStateAtomTypes, FunctionalClassAtomTypes, MMFF94AtomTypes, SLogPAtomTypes, SYBYLAtomTypes, TPSAAtomTypes, UFFAtomTypes\n";
     745   }
     746 }
     747
     748 # Process specified atomic invariants to use...
     749 #
     750 sub ProcessAtomicInvariantsToUseOption {
     751   my($AtomicInvariant, $AtomSymbolSpecified, @AtomicInvariantsWords);
     752
     753   @{$OptionsInfo{AtomicInvariantsToUse}} = ();
     754   if (IsEmpty($Options{atomicinvariantstouse})) {
     755     die "Error: Atomic invariants value specified using \"--AtomicInvariantsToUse\" option is empty\n";
     756   }
     757   $AtomSymbolSpecified = 0;
     758   @AtomicInvariantsWords = split /\,/, $Options{atomicinvariantstouse};
     759   for $AtomicInvariant (@AtomicInvariantsWords) {
     760     if (!AtomTypes::AtomicInvariantsAtomTypes::IsAtomicInvariantAvailable($AtomicInvariant)) {
     761       die "Error: Atomic invariant specified, $AtomicInvariant, using \"--AtomicInvariantsToUse\" option is not valid...\n ";
     762     }
     763     if ($AtomicInvariant =~ /^(AS|AtomSymbol)$/i) {
     764       $AtomSymbolSpecified = 1;
     765     }
     766     push @{$OptionsInfo{AtomicInvariantsToUse}}, $AtomicInvariant;
     767   }
     768   if (!$AtomSymbolSpecified) {
     769     die "Error: Atomic invariant, AS or AtomSymbol, must be specified as using \"--AtomicInvariantsToUse\" option...\n ";
     770   }
     771 }
     772
     773 # Process specified functional classes invariants to use...
     774 #
     775 sub ProcessFunctionalClassesToUse {
     776   my($FunctionalClass, @FunctionalClassesToUseWords);
     777
     778   @{$OptionsInfo{FunctionalClassesToUse}} = ();
     779   if (IsEmpty($Options{functionalclassestouse})) {
     780     die "Error: Functional classes value specified using \"--FunctionalClassesToUse\" option is empty\n";
     781   }
     782   @FunctionalClassesToUseWords = split /\,/, $Options{functionalclassestouse};
     783   for $FunctionalClass (@FunctionalClassesToUseWords) {
     784     if (!AtomTypes::FunctionalClassAtomTypes::IsFunctionalClassAvailable($FunctionalClass)) {
     785       die "Error: Functional class specified, $FunctionalClass, using \"--FunctionalClassesToUse\" option is not valid...\n ";
     786     }
     787     push @{$OptionsInfo{FunctionalClassesToUse}}, $FunctionalClass;
     788   }
     789 }
     790
     791 # Setup script usage  and retrieve command line arguments specified using various options...
     792 sub SetupScriptUsage {
     793
     794   # Retrieve all the options...
     795   %Options = ();
     796
     797   $Options{aromaticitymodel} = 'MayaChemToolsAromaticityModel';
     798
     799   $Options{atomidentifiertype} = 'AtomicInvariantsAtomTypes';
     800   $Options{atomicinvariantstouse} = 'AS';
     801
     802   $Options{functionalclassestouse} = 'HBD,HBA,PI,NI,Ar,Hal';
     803
     804   $Options{bitsorder} = 'Ascending';
     805   $Options{bitstringformat} = 'HexadecimalString';
     806
     807   $Options{compoundidmode} = 'LabelPrefix';
     808   $Options{compoundidlabel} = 'CompoundID';
     809   $Options{datafieldsmode} = 'CompoundID';
     810   $Options{detectaromaticity} = 'Yes';
     811
     812   $Options{filter} = 'Yes';
     813
     814   $Options{fold} = 'No';
     815   $Options{foldedsize} = 256;
     816
     817   $Options{ignorehydrogens} = 'Yes';
     818   $Options{keeplargestcomponent} = 'Yes';
     819
     820   $Options{mode} = 'PathLengthBits';
     821   $Options{pathmode} = 'AllAtomPathsWithRings';
     822
     823   $Options{minpathlength} = 1;
     824   $Options{maxpathlength} = 8;
     825
     826   $Options{numofbitstosetperpath} = 1;
     827
     828   $Options{output} = 'text';
     829   $Options{outdelim} = 'comma';
     830   $Options{quote} = 'yes';
     831
     832   $Options{size} = 1024;
     833
     834   $Options{usebondsymbols} = 'yes';
     835   $Options{useperlcorerandom} = 'yes';
     836   $Options{useuniquepaths} = 'yes';
     837
     838   $Options{vectorstringformat} = 'IDsAndValuesString';
     839
     840   if (!GetOptions(\%Options, "aromaticitymodel=s", "atomidentifiertype|a=s", "atomicinvariantstouse=s", "functionalclassestouse=s", "bitsorder=s", "bitstringformat|b=s", "compoundid=s", "compoundidlabel=s", "compoundidmode=s", "datafields=s", "datafieldsmode|d=s", "detectaromaticity=s", "filter|f=s", "fingerprintslabel=s", "fold=s", "foldedsize=i", "help|h", "ignorehydrogens|i=s", "keeplargestcomponent|k=s", "mode|m=s", "minpathlength=i", "maxpathlength=i", "numofbitstosetperpath|n=i", "outdelim=s", "output=s", "overwrite|o", "pathmode|p=s", "quote|q=s", "root|r=s", "size|s=i", "usebondsymbols|u=s", "useperlcorerandom=s", "useuniquepaths=s", "vectorstringformat|v=s", "workingdir|w=s")) {
     841     die "\nTo get a list of valid options and their values, use \"$ScriptName -h\" or\n\"perl -S $ScriptName -h\" command and try again...\n";
     842   }
     843   if ($Options{workingdir}) {
     844     if (! -d $Options{workingdir}) {
     845       die "Error: The value specified, $Options{workingdir}, for option \"-w --workingdir\" is not a directory name.\n";
     846     }
     847     chdir $Options{workingdir} or die "Error: Couldn't chdir $Options{workingdir}: $! \n";
     848   }
     849   if (!Molecule::IsSupportedAromaticityModel($Options{aromaticitymodel})) {
     850     my(@SupportedModels) = Molecule::GetSupportedAromaticityModels();
     851     die "Error: The value specified, $Options{aromaticitymodel}, for option \"--AromaticityModel\" is not valid. Supported aromaticity models in current release of MayaChemTools: @SupportedModels\n";
     852   }
     853   if ($Options{atomidentifiertype} !~ /^(AtomicInvariantsAtomTypes|DREIDINGAtomTypes|EStateAtomTypes|FunctionalClassAtomTypes|MMFF94AtomTypes|SLogPAtomTypes|SYBYLAtomTypes|TPSAAtomTypes|UFFAtomTypes)$/i) {
     854     die "Error: The value specified, $Options{atomidentifiertype}, for option \"-a, --AtomIdentifierType\" is not valid. Supported atom identifier types in current release of MayaChemTools: AtomicInvariantsAtomTypes, DREIDINGAtomTypes, EStateAtomTypes, FunctionalClassAtomTypes, MMFF94AtomTypes, SLogPAtomTypes, SYBYLAtomTypes, TPSAAtomTypes, UFFAtomTypes\n";
     855   }
     856   if ($Options{bitsorder} !~ /^(Ascending|Descending)$/i) {
     857     die "Error: The value specified, $Options{bitsorder}, for option \"--BitsOrder\" is not valid. Allowed values: Ascending or Descending\n";
     858   }
     859   if ($Options{bitstringformat} !~ /^(BinaryString|HexadecimalString)$/i) {
     860     die "Error: The value specified, $Options{bitstringformat}, for option \"-b, --bitstringformat\" is not valid. Allowed values: BinaryString or HexadecimalString\n";
     861   }
     862   if ($Options{compoundidmode} !~ /^(DataField|MolName|LabelPrefix|MolNameOrLabelPrefix)$/i) {
     863     die "Error: The value specified, $Options{compoundidmode}, for option \"--CompoundIDMode\" is not valid. Allowed values: DataField, MolName, LabelPrefix or MolNameOrLabelPrefix\n";
     864   }
     865   if ($Options{datafieldsmode} !~ /^(All|Common|Specify|CompoundID)$/i) {
     866     die "Error: The value specified, $Options{datafieldsmode}, for option \"-d, --DataFieldsMode\" is not valid. Allowed values: All, Common, Specify or CompoundID\n";
     867   }
     868   if ($Options{detectaromaticity} !~ /^(Yes|No)$/i) {
     869     die "Error: The value specified, $Options{detectaromaticity}, for option \"--DetectAromaticity\" is not valid. Allowed values: Yes or No\n";
     870   }
     871   if ($Options{filter} !~ /^(Yes|No)$/i) {
     872     die "Error: The value specified, $Options{filter}, for option \"-f, --Filter\" is not valid. Allowed values: Yes or No\n";
     873   }
     874   if ($Options{fold} !~ /^(Yes|No)$/i) {
     875     die "Error: The value specified, $Options{fold}, for option \"--fold\" is not valid. Allowed values: Yes or No\n";
     876   }
     877   if (!IsPositiveInteger($Options{foldedsize})) {
     878     die "Error: The value specified, $Options{foldedsize}, for option \"--FoldedSize\" is not valid. Allowed values: > 0 \n";
     879   }
     880   if ($Options{ignorehydrogens} !~ /^(Yes|No)$/i) {
     881     die "Error: The value specified, $Options{ignorehydrogens}, for option \"-i, --IgnoreHydrogens\" is not valid. Allowed values: Yes or No\n";
     882   }
     883   if ($Options{keeplargestcomponent} !~ /^(Yes|No)$/i) {
     884     die "Error: The value specified, $Options{keeplargestcomponent}, for option \"-k, --KeepLargestComponent\" is not valid. Allowed values: Yes or No\n";
     885   }
     886   if ($Options{mode} !~ /^(PathLengthBits|PathLengthCount)$/i) {
     887     die "Error: The value specified, $Options{mode}, for option \"-m, --mode\" is not valid. Allowed values: PathLengthBits or PathLengthCount\n";
     888   }
     889   if (!IsPositiveInteger($Options{minpathlength})) {
     890     die "Error: The value specified, $Options{minpathlength}, for option \"--MinPathLength\" is not valid. Allowed values: > 0 \n";
     891   }
     892   if (!IsPositiveInteger($Options{numofbitstosetperpath})) {
     893     die "Error: The value specified, $Options{NumOfBitsToSetPerPath}, for option \"--NumOfBitsToSetPerPath\" is not valid. Allowed values: > 0 \n";
     894   }
     895   if (!IsPositiveInteger($Options{maxpathlength})) {
     896     die "Error: The value specified, $Options{maxpathlength}, for option \"--MaxPathLength\" is not valid. Allowed values: > 0 \n";
     897   }
     898   if ($Options{output} !~ /^(SD|FP|text|all)$/i) {
     899     die "Error: The value specified, $Options{output}, for option \"--output\" is not valid. Allowed values: SD, FP, text, or all\n";
     900   }
     901   if ($Options{outdelim} !~ /^(comma|semicolon|tab)$/i) {
     902     die "Error: The value specified, $Options{outdelim}, for option \"--outdelim\" is not valid. Allowed values: comma, tab, or semicolon\n";
     903   }
     904   if ($Options{pathmode} !~ /^(AtomPathsWithoutRings|AtomPathsWithRings|AllAtomPathsWithoutRings|AllAtomPathsWithRings)$/i) {
     905     die "Error: The value specified, $Options{pathmode}, for option \"-m, --PathMode\" is not valid. Allowed values: AtomPathsWithoutRings, AtomPathsWithRings, AllAtomPathsWithoutRings or AllAtomPathsWithRings\n";
     906   }
     907   if ($Options{quote} !~ /^(Yes|No)$/i) {
     908     die "Error: The value specified, $Options{quote}, for option \"-q --quote\" is not valid. Allowed values: Yes or No\n";
     909   }
     910   if ($Options{outdelim} =~ /semicolon/i && $Options{quote} =~ /^No$/i) {
     911     die "Error: The value specified, $Options{quote}, for option \"-q --quote\" is not allowed with, semicolon value of \"--outdelim\" option: Fingerprints string use semicolon as delimiter for various data fields and must be quoted.\n";
     912   }
     913
     914   if (!IsPositiveInteger($Options{size})) {
     915     die "Error: The value specified, $Options{size}, for option \"-s, --size\" is not valid. Allowed values: > 0 \n";
     916   }
     917   if ($Options{usebondsymbols} !~ /^(Yes|No)$/i) {
     918     die "Error: The value specified, $Options{usebondsymbols}, for option \"-u, --UseBondSymbols\" is not valid. Allowed values: Yes or No\n";
     919   }
     920   if ($Options{useperlcorerandom} !~ /^(Yes|No)$/i) {
     921     die "Error: The value specified, $Options{useperlcorerandom}, for option \"--UsePerlCoreRandom\" is not valid. Allowed values: Yes or No\n";
     922   }
     923   if ($Options{useuniquepaths} !~ /^(Yes|No)$/i) {
     924     die "Error: The value specified, $Options{useuniquepaths}, for option \"--UseUniquePaths\" is not valid. Allowed values: Yes or No\n";
     925   }
     926   if ($Options{vectorstringformat} !~ /^(IDsAndValuesString|IDsAndValuesPairsString|ValuesAndIDsString|ValuesAndIDsPairsString)$/i) {
     927     die "Error: The value specified, $Options{vectorstringformat}, for option \"-v, --VectorStringFormat\" is not valid. Allowed values: IDsAndValuesString, IDsAndValuesPairsString, ValuesAndIDsString or ValuesAndIDsPairsString\n";
     928   }
     929 }
     930