       1 #!/usr/bin/perl -w
       2 #
       3 # File: ExtendedConnectivityFingerprints.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 "$FindBin::Bin/../lib";
      28 use Getopt::Long;
      29 use File::Basename;
      30 use Text::ParseWords;
      31 use Benchmark;
      32 use FileUtil;
      33 use TextUtil;
      34 use SDFileUtil;
      35 use MoleculeFileIO;
      36 use FileIO::FingerprintsSDFileIO;
      37 use FileIO::FingerprintsTextFileIO;
      38 use FileIO::FingerprintsFPFileIO;
      39 use AtomTypes::AtomicInvariantsAtomTypes;
      40 use AtomTypes::FunctionalClassAtomTypes;
      41 use Fingerprints::ExtendedConnectivityFingerprints;
      42
      43 my($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     GenerateExtendedConnectivityFingerprints($FileIndex);
      81   }
      82 }
      83 print "\n$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 GenerateExtendedConnectivityFingerprints {
      94   my($FileIndex) = @_;
      95   my($CmpdCount, $IgnoredCmpdCount, $SDFile, $MoleculeFileIO, $Molecule, $ExtendedConnectivityFingerprints, $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     $ExtendedConnectivityFingerprints = GenerateMoleculeFingerprints($Molecule);
     121     if (!$ExtendedConnectivityFingerprints) {
     122       $IgnoredCmpdCount++;
     123       ProcessIgnoredCompound('FingerprintsGenerationFailed', $CmpdCount, $Molecule);
     124       next COMPOUND;
     125     }
     126
     127     WriteDataToOutputFiles($FileIndex, $CmpdCount, $Molecule, $ExtendedConnectivityFingerprints, $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} =~ /^(ExtendedConnectivity|ExtendedConnectivityCount)$/i) {
     218     %FingerprintsFileIOParams = ('Mode' => 'Write', 'Overwrite' => $OptionsInfo{OverwriteFiles}, 'FingerprintsStringMode' => 'FingerprintsVectorString', 'VectorStringFormat' => $OptionsInfo{VectorStringFormat});
     219   }
     220   elsif ($OptionsInfo{Mode} =~ /^ExtendedConnectivityBits$/i) {
     221     %FingerprintsFileIOParams = ('Mode' => 'Write', 'Overwrite' => $OptionsInfo{OverwriteFiles}, 'FingerprintsStringMode' => 'FingerprintsBitVectorString', 'BitStringFormat' => $OptionsInfo{BitStringFormat}, 'BitsOrder' => $OptionsInfo{BitsOrder});
     222   }
     223
     224   if ($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, $ExtendedConnectivityFingerprints, $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     $NewFPSDFileIO->WriteFingerprints($ExtendedConnectivityFingerprints, $CmpdString);
     268   }
     269
     270   if ($NewFPTextFileIO) {
     271     my($ColValuesRef);
     272
     273     $ColValuesRef = SetupFPTextFileCoulmnValues($FileIndex, $CmpdCount, $Molecule, $DataFieldLabelAndValuesRef);
     274     $NewFPTextFileIO->WriteFingerprints($ExtendedConnectivityFingerprints, $ColValuesRef);
     275   }
     276
     277   if ($NewFPFileIO) {
     278     my($CompoundID);
     279
     280     $CompoundID = SetupCmpdIDForOutputFiles($CmpdCount, $Molecule, $DataFieldLabelAndValuesRef);
     281     $NewFPFileIO->WriteFingerprints($ExtendedConnectivityFingerprints, $CompoundID);
     282   }
     283 }
     284
     285 # Generate approriate column labels for FPText output file...
     286 #
     287 sub SetupFPTextFileCoulmnLabels {
     288   my($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($ExtendedConnectivityFingerprints);
     364
     365   if ($OptionsInfo{KeepLargestComponent}) {
     366     $Molecule->KeepLargestComponent();
     367   }
     368   if (!$Molecule->DetectRings()) {
     369     return undef;
     370   }
     371   $Molecule->SetAromaticityModel($OptionsInfo{AromaticityModel});
     372   $Molecule->DetectAromaticity();
     373
     374   $ExtendedConnectivityFingerprints = undef;
     375   if ($OptionsInfo{Mode} =~ /^(ExtendedConnectivity|ExtendedConnectivityCount)$/i ) {
     376     $ExtendedConnectivityFingerprints = new Fingerprints::ExtendedConnectivityFingerprints('Type' => $OptionsInfo{Mode}, 'Molecule' => $Molecule, 'NeighborhoodRadius' => $OptionsInfo{NeighborhoodRadius}, 'AtomIdentifierType' => $OptionsInfo{AtomIdentifierType});
     377   }
     378   elsif ($OptionsInfo{Mode} =~ /^ExtendedConnectivityBits$/i) {
     379     $ExtendedConnectivityFingerprints = new Fingerprints::ExtendedConnectivityFingerprints('Type' => $OptionsInfo{Mode}, 'Molecule' => $Molecule, 'NeighborhoodRadius' => $OptionsInfo{NeighborhoodRadius}, 'AtomIdentifierType' => $OptionsInfo{AtomIdentifierType}, 'Size' => $OptionsInfo{Size}, 'UsePerlCoreRandom' => $OptionsInfo{UsePerlCoreRandom});
     380   }
     381   else {
     382     die "Error: The value specified, $Options{mode}, for option \"-m, --mode\" is not valid. Allowed values: ExtendedConnectivity,  ExtendedConnectivityCount or ExtendedConnectivityBits\n";
     383   }
     384   SetAtomIdentifierTypeValuesToUse($ExtendedConnectivityFingerprints);
     385
     386   # Generate fingerprints...
     387   $ExtendedConnectivityFingerprints->GenerateFingerprints();
     388
     389   # Make sure fingerprints generation is successful...
     390   if (!$ExtendedConnectivityFingerprints->IsFingerprintsGenerationSuccessful()) {
     391     return undef;
     392   }
     393
     394   return $ExtendedConnectivityFingerprints;
     395 }
     396
     397 # Set atom identifier type to use for generating fingerprints...
     398 #
     399 sub SetAtomIdentifierTypeValuesToUse {
     400   my($ExtendedConnectivityFingerprints) = @_;
     401
     402   if ($OptionsInfo{AtomIdentifierType} =~ /^AtomicInvariantsAtomTypes$/i) {
     403     $ExtendedConnectivityFingerprints->SetAtomicInvariantsToUse(\@{$OptionsInfo{AtomicInvariantsToUse}});
     404   }
     405   elsif ($OptionsInfo{AtomIdentifierType} =~ /^FunctionalClassAtomTypes$/i) {
     406     $ExtendedConnectivityFingerprints->SetFunctionalClassesToUse(\@{$OptionsInfo{FunctionalClassesToUse}});
     407   }
     408   elsif ($OptionsInfo{AtomIdentifierType} =~ /^(DREIDINGAtomTypes|EStateAtomTypes|MMFF94AtomTypes|SLogPAtomTypes|SYBYLAtomTypes|TPSAAtomTypes|UFFAtomTypes)$/i) {
     409     # Nothing to do for now...
     410   }
     411   else {
     412     die "Error: The value specified, $Options{atomidentifiertype}, for option \"-a, --AtomIdentifierType\" is not valid. Supported atom identifier types in current release of MayaChemTools: AtomicInvariantsAtomTypes, DREIDINGAtomTypes, EStateAtomTypes, FunctionalClassAtomTypes, MMFF94AtomTypes, SLogPAtomTypes, SYBYLAtomTypes, TPSAAtomTypes, UFFAtomTypes\n";
     413   }
     414 }
     415
     416 # Retrieve information about SD files...
     417 #
     418 sub RetrieveSDFilesInfo {
     419   my($SDFile, $Index, $FileDir, $FileExt, $FileName, $OutFileRoot, $TextOutFileExt, $SDOutFileExt, $FPOutFileExt, $NewSDFileName, $NewFPFileName, $NewTextFileName, $CheckDataField, $CollectDataFields, $AllDataFieldsRef, $CommonDataFieldsRef);
     420
     421   %SDFilesInfo = ();
     422   @{$SDFilesInfo{FileOkay}} = ();
     423   @{$SDFilesInfo{OutFileRoot}} = ();
     424   @{$SDFilesInfo{SDOutFileNames}} = ();
     425   @{$SDFilesInfo{FPOutFileNames}} = ();
     426   @{$SDFilesInfo{TextOutFileNames}} = ();
     427   @{$SDFilesInfo{AllDataFieldsRef}} = ();
     428   @{$SDFilesInfo{CommonDataFieldsRef}} = ();
     429
     430   $CheckDataField = ($OptionsInfo{TextOutput} && ($OptionsInfo{DataFieldsMode} =~ /^CompoundID$/i) && ($OptionsInfo{CompoundIDMode} =~ /^DataField$/i)) ? 1 : 0;
     431   $CollectDataFields = ($OptionsInfo{TextOutput} && ($OptionsInfo{DataFieldsMode} =~ /^(All|Common)$/i)) ? 1 : 0;
     432
     433   FILELIST: for $Index (0 .. $#SDFilesList) {
     434     $SDFile = $SDFilesList[$Index];
     435
     436     $SDFilesInfo{FileOkay}[$Index] = 0;
     437     $SDFilesInfo{OutFileRoot}[$Index] = '';
     438     $SDFilesInfo{SDOutFileNames}[$Index] = '';
     439     $SDFilesInfo{FPOutFileNames}[$Index] = '';
     440     $SDFilesInfo{TextOutFileNames}[$Index] = '';
     441
     442     $SDFile = $SDFilesList[$Index];
     443     if (!(-e $SDFile)) {
     444       warn "Warning: Ignoring file $SDFile: It doesn't exist\n";
     445       next FILELIST;
     446     }
     447     if (!CheckFileType($SDFile, "sd sdf")) {
     448       warn "Warning: Ignoring file $SDFile: It's not a SD file\n";
     449       next FILELIST;
     450     }
     451
     452     if ($CheckDataField) {
     453       # Make sure data field exists in SD file..
     454       my($CmpdString, $SpecifiedDataField, @CmpdLines, %DataFieldValues);
     455
     456       @CmpdLines = ();
     457       open SDFILE, "$SDFile" or die "Error: Couldn't open $SDFile: $! \n";
     458       $CmpdString = ReadCmpdString(\*SDFILE);
     459       close SDFILE;
     460       @CmpdLines = split "\n", $CmpdString;
     461       %DataFieldValues = GetCmpdDataHeaderLabelsAndValues(\@CmpdLines);
     462       $SpecifiedDataField = $OptionsInfo{CompoundID};
     463       if (!exists $DataFieldValues{$SpecifiedDataField}) {
     464         warn "Warning: Ignoring file $SDFile: Data field value, $SpecifiedDataField, using  \"--CompoundID\" option in \"DataField\" \"--CompoundIDMode\" doesn't exist\n";
     465         next FILELIST;
     466       }
     467     }
     468
     469     $AllDataFieldsRef = '';
     470     $CommonDataFieldsRef = '';
     471     if ($CollectDataFields) {
     472       my($CmpdCount);
     473       open SDFILE, "$SDFile" or die "Error: Couldn't open $SDFile: $! \n";
     474       ($CmpdCount, $AllDataFieldsRef, $CommonDataFieldsRef) = GetAllAndCommonCmpdDataHeaderLabels(\*SDFILE);
     475       close SDFILE;
     476     }
     477
     478     # Setup output file names...
     479     $FileDir = ""; $FileName = ""; $FileExt = "";
     480     ($FileDir, $FileName, $FileExt) = ParseFileName($SDFile);
     481
     482     $TextOutFileExt = "csv";
     483     if ($Options{outdelim} =~ /^tab$/i) {
     484       $TextOutFileExt = "tsv";
     485     }
     486     $SDOutFileExt = $FileExt;
     487     $FPOutFileExt = "fpf";
     488
     489     if ($OptionsInfo{OutFileRoot} && (@SDFilesList == 1)) {
     490       my ($RootFileDir, $RootFileName, $RootFileExt) = ParseFileName($OptionsInfo{OutFileRoot});
     491       if ($RootFileName && $RootFileExt) {
     492         $FileName = $RootFileName;
     493       }
     494       else {
     495         $FileName = $OptionsInfo{OutFileRoot};
     496       }
     497       $OutFileRoot = $FileName;
     498     }
     499     else {
     500       $OutFileRoot = "${FileName}ExtendedConnectivityFP";
     501     }
     502
     503     $NewSDFileName = "${OutFileRoot}.${SDOutFileExt}";
     504     $NewFPFileName = "${OutFileRoot}.${FPOutFileExt}";
     505     $NewTextFileName = "${OutFileRoot}.${TextOutFileExt}";
     506
     507     if ($OptionsInfo{SDOutput}) {
     508       if ($SDFile =~ /$NewSDFileName/i) {
     509         warn "Warning: Ignoring input file $SDFile: Same output, $NewSDFileName, and input file names.\n";
     510         print "Specify a different name using \"-r --root\" option or use default name.\n";
     511         next FILELIST;
     512       }
     513     }
     514
     515     if (!$OptionsInfo{OverwriteFiles}) {
     516       # Check SD and text outout files...
     517       if ($OptionsInfo{SDOutput}) {
     518         if (-e $NewSDFileName) {
     519           warn "Warning: Ignoring file $SDFile: The file $NewSDFileName already exists\n";
     520           next FILELIST;
     521         }
     522       }
     523       if ($OptionsInfo{FPOutput}) {
     524         if (-e $NewFPFileName) {
     525           warn "Warning: Ignoring file $SDFile: The file $NewFPFileName already exists\n";
     526           next FILELIST;
     527         }
     528       }
     529       if ($OptionsInfo{TextOutput}) {
     530         if (-e $NewTextFileName) {
     531           warn "Warning: Ignoring file $SDFile: The file $NewTextFileName already exists\n";
     532           next FILELIST;
     533         }
     534       }
     535     }
     536
     537     $SDFilesInfo{FileOkay}[$Index] = 1;
     538
     539     $SDFilesInfo{OutFileRoot}[$Index] = $OutFileRoot;
     540     $SDFilesInfo{SDOutFileNames}[$Index] = $NewSDFileName;
     541     $SDFilesInfo{FPOutFileNames}[$Index] = $NewFPFileName;
     542     $SDFilesInfo{TextOutFileNames}[$Index] = $NewTextFileName;
     543
     544     $SDFilesInfo{AllDataFieldsRef}[$Index] = $AllDataFieldsRef;
     545     $SDFilesInfo{CommonDataFieldsRef}[$Index] = $CommonDataFieldsRef;
     546   }
     547 }
     548
     549 # Process option values...
     550 sub ProcessOptions {
     551   %OptionsInfo = ();
     552
     553   ProcessAtomIdentifierTypeOptions();
     554
     555   $OptionsInfo{AromaticityModel} = $Options{aromaticitymodel};
     556
     557   $OptionsInfo{BitsOrder} = $Options{bitsorder};
     558   $OptionsInfo{BitStringFormat} = $Options{bitstringformat};
     559
     560   $OptionsInfo{CompoundIDMode} = $Options{compoundidmode};
     561   $OptionsInfo{CompoundIDLabel} = $Options{compoundidlabel};
     562   $OptionsInfo{DataFieldsMode} = $Options{datafieldsmode};
     563
     564   my(@SpecifiedDataFields);
     565   @SpecifiedDataFields = ();
     566
     567   @{$OptionsInfo{SpecifiedDataFields}} = ();
     568   $OptionsInfo{CompoundID} = '';
     569
     570   if ($Options{datafieldsmode} =~ /^CompoundID$/i) {
     571     if ($Options{compoundidmode} =~ /^DataField$/i) {
     572       if (!$Options{compoundid}) {
     573         die "Error: You must specify a value for \"--CompoundID\" option in \"DataField\" \"--CompoundIDMode\". \n";
     574       }
     575       $OptionsInfo{CompoundID} = $Options{compoundid};
     576     }
     577     elsif ($Options{compoundidmode} =~ /^(LabelPrefix|MolNameOrLabelPrefix)$/i) {
     578       $OptionsInfo{CompoundID} = $Options{compoundid} ? $Options{compoundid} : 'Cmpd';
     579     }
     580   }
     581   elsif ($Options{datafieldsmode} =~ /^Specify$/i) {
     582     if (!$Options{datafields}) {
     583       die "Error: You must specify a value for \"--DataFields\" option in \"Specify\" \"-d, --DataFieldsMode\". \n";
     584     }
     585     @SpecifiedDataFields = split /\,/, $Options{datafields};
     586     push @{$OptionsInfo{SpecifiedDataFields}}, @SpecifiedDataFields;
     587   }
     588
     589   $OptionsInfo{FingerprintsLabel} = $Options{fingerprintslabel} ? $Options{fingerprintslabel} : 'ExtendedConnectivityFingerprints';
     590
     591   $OptionsInfo{Filter} = ($Options{filter} =~ /^Yes$/i) ? 1 : 0;
     592
     593   $OptionsInfo{KeepLargestComponent} = ($Options{keeplargestcomponent} =~ /^Yes$/i) ? 1 : 0;
     594
     595   $OptionsInfo{Mode} = $Options{mode};
     596
     597   $OptionsInfo{NeighborhoodRadius} = $Options{neighborhoodradius};
     598
     599   $OptionsInfo{UsePerlCoreRandom} = ($Options{useperlcorerandom} =~ /^Yes$/i) ? 1 : 0;
     600
     601   $OptionsInfo{Output} = $Options{output};
     602   $OptionsInfo{SDOutput} = ($Options{output} =~ /^(SD|All)$/i) ? 1 : 0;
     603   $OptionsInfo{FPOutput} = ($Options{output} =~ /^(FP|All)$/i) ? 1 : 0;
     604   $OptionsInfo{TextOutput} = ($Options{output} =~ /^(Text|All)$/i) ? 1 : 0;
     605
     606   $OptionsInfo{OutDelim} = $Options{outdelim};
     607   $OptionsInfo{OutQuote} = ($Options{quote} =~ /^Yes$/i) ? 1 : 0;
     608
     609   $OptionsInfo{OverwriteFiles} = $Options{overwrite} ? 1 : 0;
     610   $OptionsInfo{OutFileRoot} = $Options{root} ? $Options{root} : 0;
     611
     612   my($Size, $MinSize, $MaxSize);
     613   $MinSize = 32;
     614   $MaxSize = 2**32;
     615   $Size = $Options{size};
     616   if (!(IsPositiveInteger($Size) && $Size >= $MinSize && $Size <= $MaxSize && IsNumberPowerOfNumber($Size, 2))) {
     617     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";
     618   }
     619   $OptionsInfo{Size} = $Size;
     620
     621   # Setup default vector string format...
     622   #
     623   my($VectorStringFormat);
     624   $VectorStringFormat = '';
     625   if ($Options{vectorstringformat}) {
     626     $VectorStringFormat = $Options{vectorstringformat};
     627   }
     628   else {
     629     $VectorStringFormat = ($Options{mode} =~ /^ExtendedConnectivity$/) ? "ValuesString" : "IDsAndValuesString";
     630   }
     631   $OptionsInfo{VectorStringFormat} = $VectorStringFormat;
     632 }
     633
     634 # Process atom identifier type and related options...
     635 #
     636 sub ProcessAtomIdentifierTypeOptions {
     637
     638   $OptionsInfo{AtomIdentifierType} = $Options{atomidentifiertype};
     639
     640   if ($Options{atomidentifiertype} =~ /^AtomicInvariantsAtomTypes$/i) {
     641     ProcessAtomicInvariantsToUseOption();
     642   }
     643   elsif ($Options{atomidentifiertype} =~ /^FunctionalClassAtomTypes$/i) {
     644     ProcessFunctionalClassesToUse();
     645   }
     646   elsif ($Options{atomidentifiertype} =~ /^(DREIDINGAtomTypes|EStateAtomTypes|MMFF94AtomTypes|SLogPAtomTypes|SYBYLAtomTypes|TPSAAtomTypes|UFFAtomTypes)$/i) {
     647     # Nothing to do for now...
     648   }
     649   else {
     650     die "Error: The value specified, $Options{atomidentifiertype}, for option \"-a, --AtomIdentifierType\" is not valid. Supported atom identifier types in current release of MayaChemTools: AtomicInvariantsAtomTypes, DREIDINGAtomTypes, EStateAtomTypes, FunctionalClassAtomTypes, MMFF94AtomTypes, SLogPAtomTypes, SYBYLAtomTypes, TPSAAtomTypes, UFFAtomTypes\n";
     651   }
     652 }
     653
     654 # Process specified atomic invariants to use...
     655 #
     656 sub ProcessAtomicInvariantsToUseOption {
     657   my($AtomicInvariant, $AtomSymbolSpecified, @AtomicInvariantsWords);
     658
     659   @{$OptionsInfo{AtomicInvariantsToUse}} = ();
     660   if (IsEmpty($Options{atomicinvariantstouse})) {
     661     die "Error: Atomic invariants value specified using \"--AtomicInvariantsToUse\" option is empty\n";
     662   }
     663   $AtomSymbolSpecified = 0;
     664   @AtomicInvariantsWords = split /\,/, $Options{atomicinvariantstouse};
     665   for $AtomicInvariant (@AtomicInvariantsWords) {
     666     if (!AtomTypes::AtomicInvariantsAtomTypes::IsAtomicInvariantAvailable($AtomicInvariant)) {
     667       die "Error: Atomic invariant specified, $AtomicInvariant, using \"--AtomicInvariantsToUse\" option is not valid...\n ";
     668     }
     669     if ($AtomicInvariant =~ /^(AS|AtomSymbol)$/i) {
     670       $AtomSymbolSpecified = 1;
     671     }
     672     push @{$OptionsInfo{AtomicInvariantsToUse}}, $AtomicInvariant;
     673   }
     674   if (!$AtomSymbolSpecified) {
     675     die "Error: Atomic invariant, AS or AtomSymbol, must be specified as using \"--AtomicInvariantsToUse\" option...\n ";
     676   }
     677 }
     678
     679 # Process specified functional classes invariants to use...
     680 #
     681 sub ProcessFunctionalClassesToUse {
     682   my($FunctionalClass, @FunctionalClassesToUseWords);
     683
     684   @{$OptionsInfo{FunctionalClassesToUse}} = ();
     685   if (IsEmpty($Options{functionalclassestouse})) {
     686     die "Error: Functional classes value specified using \"--FunctionalClassesToUse\" option is empty\n";
     687   }
     688   @FunctionalClassesToUseWords = split /\,/, $Options{functionalclassestouse};
     689   for $FunctionalClass (@FunctionalClassesToUseWords) {
     690     if (!AtomTypes::FunctionalClassAtomTypes::IsFunctionalClassAvailable($FunctionalClass)) {
     691       die "Error: Functional class specified, $FunctionalClass, using \"--FunctionalClassesToUse\" option is not valid...\n ";
     692     }
     693     push @{$OptionsInfo{FunctionalClassesToUse}}, $FunctionalClass;
     694   }
     695 }
     696
     697 # Setup script usage  and retrieve command line arguments specified using various options...
     698 sub SetupScriptUsage {
     699
     700   # Retrieve all the options...
     701   %Options = ();
     702
     703   $Options{aromaticitymodel} = 'MayaChemToolsAromaticityModel';
     704
     705   $Options{atomidentifiertype} = 'AtomicInvariantsAtomTypes';
     706   $Options{atomicinvariantstouse} = 'AS,X,BO,H,FC,MN';
     707   $Options{functionalclassestouse} = 'HBD,HBA,PI,NI,Ar,Hal';
     708
     709   $Options{bitsorder} = 'Ascending';
     710   $Options{bitstringformat} = 'HexadecimalString';
     711
     712   $Options{compoundidmode} = 'LabelPrefix';
     713   $Options{compoundidlabel} = 'CompoundID';
     714   $Options{datafieldsmode} = 'CompoundID';
     715
     716   $Options{filter} = 'Yes';
     717
     718   $Options{keeplargestcomponent} = 'Yes';
     719
     720   $Options{mode} = 'ExtendedConnectivity';
     721
     722   $Options{neighborhoodradius} = 2;
     723
     724   $Options{useperlcorerandom} = 'yes';
     725
     726   $Options{output} = 'text';
     727   $Options{outdelim} = 'comma';
     728   $Options{quote} = 'yes';
     729
     730   $Options{size} = 1024;
     731
     732   $Options{vectorstringformat} = '';
     733
     734   if (!GetOptions(\%Options, "aromaticitymodel=s", "atomidentifiertype|a=s", "atomicinvariantstouse=s", "functionalclassestouse=s", "bitsorder=s", "bitstringformat|b=s", "compoundid=s", "compoundidlabel=s", "compoundidmode=s", "datafields=s", "datafieldsmode|d=s", "filter|f=s", "fingerprintslabel=s",  "help|h", "keeplargestcomponent|k=s",  "mode|m=s", "neighborhoodradius|n=s", "outdelim=s", "output=s", "overwrite|o", "quote|q=s", "root|r=s", "size|s=i", "useperlcorerandom=s", "vectorstringformat|v=s", "workingdir|w=s")) {
     735     die "\nTo get a list of valid options and their values, use \"$ScriptName -h\" or\n\"perl -S $ScriptName -h\" command and try again...\n";
     736   }
     737   if ($Options{workingdir}) {
     738     if (! -d $Options{workingdir}) {
     739       die "Error: The value specified, $Options{workingdir}, for option \"-w --workingdir\" is not a directory name.\n";
     740     }
     741     chdir $Options{workingdir} or die "Error: Couldn't chdir $Options{workingdir}: $! \n";
     742   }
     743   if (!Molecule::IsSupportedAromaticityModel($Options{aromaticitymodel})) {
     744     my(@SupportedModels) = Molecule::GetSupportedAromaticityModels();
     745     die "Error: The value specified, $Options{aromaticitymodel}, for option \"--AromaticityModel\" is not valid. Supported aromaticity models in current release of MayaChemTools: @SupportedModels\n";
     746   }
     747   if ($Options{atomidentifiertype} !~ /^(AtomicInvariantsAtomTypes|FunctionalClassAtomTypes|DREIDINGAtomTypes|EStateAtomTypes|MMFF94AtomTypes|SLogPAtomTypes|SYBYLAtomTypes|TPSAAtomTypes|UFFAtomTypes)$/i) {
     748     die "Error: The value specified, $Options{atomidentifiertype}, for option \"-a, --AtomIdentifierType\" is not valid. Supported atom identifier types in current release of MayaChemTools: AtomicInvariantsAtomTypes, FunctionalClassAtomTypes, DREIDINGAtomTypes, EStateAtomTypes, MMFF94AtomTypes, SLogPAtomTypes, SYBYLAtomTypes, TPSAAtomTypes, UFFAtomTypes\n";
     749   }
     750   if ($Options{bitsorder} !~ /^(Ascending|Descending)$/i) {
     751     die "Error: The value specified, $Options{bitsorder}, for option \"--BitsOrder\" is not valid. Allowed values: Ascending or Descending\n";
     752   }
     753   if ($Options{bitstringformat} !~ /^(BinaryString|HexadecimalString)$/i) {
     754     die "Error: The value specified, $Options{bitstringformat}, for option \"-b, --bitstringformat\" is not valid. Allowed values: BinaryString or HexadecimalString\n";
     755   }
     756   if ($Options{compoundidmode} !~ /^(DataField|MolName|LabelPrefix|MolNameOrLabelPrefix)$/i) {
     757     die "Error: The value specified, $Options{compoundidmode}, for option \"--CompoundIDMode\" is not valid. Allowed values: DataField, MolName, LabelPrefix or MolNameOrLabelPrefix\n";
     758   }
     759   if ($Options{datafieldsmode} !~ /^(All|Common|Specify|CompoundID)$/i) {
     760     die "Error: The value specified, $Options{datafieldsmode}, for option \"-d, --DataFieldsMode\" is not valid. Allowed values: All, Common, Specify or CompoundID\n";
     761   }
     762   if ($Options{filter} !~ /^(Yes|No)$/i) {
     763     die "Error: The value specified, $Options{filter}, for option \"-f, --Filter\" is not valid. Allowed values: Yes or No\n";
     764   }
     765   if ($Options{keeplargestcomponent} !~ /^(Yes|No)$/i) {
     766     die "Error: The value specified, $Options{keeplargestcomponent}, for option \"-k, --KeepLargestComponent\" is not valid. Allowed values: Yes or No\n";
     767   }
     768   if ($Options{mode} !~ /^(ExtendedConnectivity|ExtendedConnectivityCount|ExtendedConnectivityBits)$/i) {
     769     die "Error: The value specified, $Options{mode}, for option \"-m, --mode\" is not valid. Allowed values: ExtendedConnectivity, ExtendedConnecticityCount, or ExtendedConnectivityBits\n";
     770   }
     771   if (!(IsInteger($Options{neighborhoodradius}) && ($Options{neighborhoodradius} >= 0))) {
     772     die "Error: The value specified, $Options{neighborhoodradius}, for option \"-n, --NeighborhoodRadius\" is not valid. Allowed values: >= 0 \n";
     773   }
     774   if ($Options{output} !~ /^(SD|FP|text|all)$/i) {
     775     die "Error: The value specified, $Options{output}, for option \"--output\" is not valid. Allowed values: SD, FP, text, or all\n";
     776   }
     777   if ($Options{outdelim} !~ /^(comma|semicolon|tab)$/i) {
     778     die "Error: The value specified, $Options{outdelim}, for option \"--outdelim\" is not valid. Allowed values: comma, tab, or semicolon\n";
     779   }
     780   if ($Options{quote} !~ /^(Yes|No)$/i) {
     781     die "Error: The value specified, $Options{quote}, for option \"-q --quote\" is not valid. Allowed values: Yes or No\n";
     782   }
     783   if (!IsPositiveInteger($Options{size})) {
     784     die "Error: The value specified, $Options{size}, for option \"-s, --size\" is not valid. Allowed values: > 0 \n";
     785   }
     786   if ($Options{outdelim} =~ /semicolon/i && $Options{quote} =~ /^No$/i) {
     787     die "Error: The value specified, $Options{quote}, for option \"-q --quote\" is not allowed with, semicolon value of \"--outdelim\" option: Fingerprints string use semicolon as delimiter for various data fields and must be quoted.\n";
     788   }
     789   if ($Options{useperlcorerandom} !~ /^(Yes|No)$/i) {
     790     die "Error: The value specified, $Options{useperlcorerandom}, for option \"--UsePerlCoreRandom\" is not valid. Allowed values: Yes or No\n";
     791   }
     792   if ($Options{vectorstringformat} && $Options{vectorstringformat} !~ /^(ValuesString|IDsAndValuesString|IDsAndValuesPairsString|ValuesAndIDsString|ValuesAndIDsPairsString)$/i) {
     793     die "Error: The value specified, $Options{vectorstringformat}, for option \"-v, --VectorStringFormat\" is not valid. Allowed values: ValuesString, IDsAndValuesString, IDsAndValuesPairsString, ValuesAndIDsString or ValuesAndIDsPairsString\n";
     794   }
     795 }
     796