       1 #!/usr/bin/perl -w
       2 #
       3 # $RCSfile: ExtendedConnectivityFingerprints.pl,v $
       4 # $Date: 2015/02/28 20:46:19 $
       5 # $Revision: 1.37 $
       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 "$FindBin::Bin/../lib";
      31 use Getopt::Long;
      32 use File::Basename;
      33 use Text::ParseWords;
      34 use Benchmark;
      35 use FileUtil;
      36 use TextUtil;
      37 use SDFileUtil;
      38 use MoleculeFileIO;
      39 use FileIO::FingerprintsSDFileIO;
      40 use FileIO::FingerprintsTextFileIO;
      41 use FileIO::FingerprintsFPFileIO;
      42 use AtomTypes::AtomicInvariantsAtomTypes;
      43 use AtomTypes::FunctionalClassAtomTypes;
      44 use Fingerprints::ExtendedConnectivityFingerprints;
      45
      46 my($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     GenerateExtendedConnectivityFingerprints($FileIndex);
      84   }
      85 }
      86 print "\n$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 GenerateExtendedConnectivityFingerprints {
      97   my($FileIndex) = @_;
      98   my($CmpdCount, $IgnoredCmpdCount, $SDFile, $MoleculeFileIO, $Molecule, $ExtendedConnectivityFingerprints, $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     $ExtendedConnectivityFingerprints = GenerateMoleculeFingerprints($Molecule);
     124     if (!$ExtendedConnectivityFingerprints) {
     125       $IgnoredCmpdCount++;
     126       ProcessIgnoredCompound('FingerprintsGenerationFailed', $CmpdCount, $Molecule);
     127       next COMPOUND;
     128     }
     129
     130     WriteDataToOutputFiles($FileIndex, $CmpdCount, $Molecule, $ExtendedConnectivityFingerprints, $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, $NewFPFileIO) = (undef) x 3;
     216
     217   # Setup common parameters for fingerprints file IO objects...
     218   #
     219   %FingerprintsFileIOParams = ();
     220   if ($OptionsInfo{Mode} =~ /^(ExtendedConnectivity|ExtendedConnectivityCount)$/i) {
     221     %FingerprintsFileIOParams = ('Mode' => 'Write', 'Overwrite' => $OptionsInfo{OverwriteFiles}, 'FingerprintsStringMode' => 'FingerprintsVectorString', 'VectorStringFormat' => $OptionsInfo{VectorStringFormat});
     222   }
     223   elsif ($OptionsInfo{Mode} =~ /^ExtendedConnectivityBits$/i) {
     224     %FingerprintsFileIOParams = ('Mode' => 'Write', 'Overwrite' => $OptionsInfo{OverwriteFiles}, 'FingerprintsStringMode' => 'FingerprintsBitVectorString', 'BitStringFormat' => $OptionsInfo{BitStringFormat}, 'BitsOrder' => $OptionsInfo{BitsOrder});
     225   }
     226
     227   if ($OptionsInfo{SDOutput}) {
     228     $NewFPSDFile = $SDFilesInfo{SDOutFileNames}[$FileIndex];
     229     print "Generating SD file $NewFPSDFile...\n";
     230     $NewFPSDFileIO = new FileIO::FingerprintsSDFileIO('Name' => $NewFPSDFile, %FingerprintsFileIOParams, 'FingerprintsFieldLabel' => $OptionsInfo{FingerprintsLabel});
     231     $NewFPSDFileIO->Open();
     232   }
     233
     234   if ($OptionsInfo{FPOutput}) {
     235     $NewFPFile = $SDFilesInfo{FPOutFileNames}[$FileIndex];
     236     print "Generating FP file $NewFPFile...\n";
     237     $NewFPFileIO = new FileIO::FingerprintsFPFileIO('Name' => $NewFPFile, %FingerprintsFileIOParams);
     238     $NewFPFileIO->Open();
     239   }
     240
     241   if ($OptionsInfo{TextOutput}) {
     242     my($ColLabelsRef);
     243
     244     $NewFPTextFile = $SDFilesInfo{TextOutFileNames}[$FileIndex];
     245     $ColLabelsRef = SetupFPTextFileCoulmnLabels($FileIndex);
     246
     247     print "Generating text file $NewFPTextFile...\n";
     248     $NewFPTextFileIO = new FileIO::FingerprintsTextFileIO('Name' => $NewFPTextFile, %FingerprintsFileIOParams, 'DataColLabels' => $ColLabelsRef, 'OutDelim' => $OptionsInfo{OutDelim}, 'OutQuote' => $OptionsInfo{OutQuote});
     249     $NewFPTextFileIO->Open();
     250   }
     251
     252   return ($NewFPSDFileIO, $NewFPTextFileIO, $NewFPFileIO);
     253 }
     254
     255 # Write fingerpritns and other data to appropriate output files...
     256 #
     257 sub WriteDataToOutputFiles {
     258   my($FileIndex, $CmpdCount, $Molecule, $ExtendedConnectivityFingerprints, $NewFPSDFileIO, $NewFPTextFileIO, $NewFPFileIO) = @_;
     259   my($DataFieldLabelAndValuesRef);
     260
     261   $DataFieldLabelAndValuesRef = undef;
     262   if ($NewFPTextFileIO || $NewFPFileIO) {
     263     $DataFieldLabelAndValuesRef = $Molecule->GetDataFieldLabelAndValues();
     264   }
     265
     266   if ($NewFPSDFileIO) {
     267     my($CmpdString);
     268
     269     $CmpdString = $Molecule->GetInputMoleculeString();
     270     $NewFPSDFileIO->WriteFingerprints($ExtendedConnectivityFingerprints, $CmpdString);
     271   }
     272
     273   if ($NewFPTextFileIO) {
     274     my($ColValuesRef);
     275
     276     $ColValuesRef = SetupFPTextFileCoulmnValues($FileIndex, $CmpdCount, $Molecule, $DataFieldLabelAndValuesRef);
     277     $NewFPTextFileIO->WriteFingerprints($ExtendedConnectivityFingerprints, $ColValuesRef);
     278   }
     279
     280   if ($NewFPFileIO) {
     281     my($CompoundID);
     282
     283     $CompoundID = SetupCmpdIDForOutputFiles($CmpdCount, $Molecule, $DataFieldLabelAndValuesRef);
     284     $NewFPFileIO->WriteFingerprints($ExtendedConnectivityFingerprints, $CompoundID);
     285   }
     286 }
     287
     288 # Generate approriate column labels for FPText output file...
     289 #
     290 sub SetupFPTextFileCoulmnLabels {
     291   my($FileIndex) = @_;
     292   my($Line, @ColLabels);
     293
     294   @ColLabels = ();
     295   if ($OptionsInfo{DataFieldsMode} =~ /^All$/i) {
     296     push @ColLabels, @{$SDFilesInfo{AllDataFieldsRef}[$FileIndex]};
     297   }
     298   elsif ($OptionsInfo{DataFieldsMode} =~ /^Common$/i) {
     299     push @ColLabels, @{$SDFilesInfo{CommonDataFieldsRef}[$FileIndex]};
     300   }
     301   elsif ($OptionsInfo{DataFieldsMode} =~ /^Specify$/i) {
     302     push @ColLabels, @{$OptionsInfo{SpecifiedDataFields}};
     303   }
     304   elsif ($OptionsInfo{DataFieldsMode} =~ /^CompoundID$/i) {
     305     push @ColLabels, $OptionsInfo{CompoundIDLabel};
     306   }
     307   # Add fingerprints label...
     308   push @ColLabels, $OptionsInfo{FingerprintsLabel};
     309
     310   return \@ColLabels;
     311 }
     312
     313 # Generate column values FPText output file..
     314 #
     315 sub SetupFPTextFileCoulmnValues {
     316   my($FileIndex, $CmpdCount, $Molecule, $DataFieldLabelAndValuesRef) = @_;
     317   my(@ColValues);
     318
     319   @ColValues = ();
     320   if ($OptionsInfo{DataFieldsMode} =~ /^CompoundID$/i) {
     321     push @ColValues, SetupCmpdIDForOutputFiles($CmpdCount, $Molecule, $DataFieldLabelAndValuesRef);
     322   }
     323   elsif ($OptionsInfo{DataFieldsMode} =~ /^All$/i) {
     324     @ColValues = map { exists $DataFieldLabelAndValuesRef->{$_} ? $DataFieldLabelAndValuesRef->{$_} : ''} @{$SDFilesInfo{AllDataFieldsRef}[$FileIndex]};
     325   }
     326   elsif ($OptionsInfo{DataFieldsMode} =~ /^Common$/i) {
     327     @ColValues = map { exists $DataFieldLabelAndValuesRef->{$_} ? $DataFieldLabelAndValuesRef->{$_} : ''} @{$SDFilesInfo{CommonDataFieldsRef}[$FileIndex]};
     328   }
     329   elsif ($OptionsInfo{DataFieldsMode} =~ /^Specify$/i) {
     330     @ColValues = map { exists $DataFieldLabelAndValuesRef->{$_} ? $DataFieldLabelAndValuesRef->{$_} : ''} @{$OptionsInfo{SpecifiedDataFields}};
     331   }
     332
     333   return \@ColValues;
     334 }
     335
     336 # Generate compound ID for FP and FPText output files..
     337 #
     338 sub SetupCmpdIDForOutputFiles {
     339   my($CmpdCount, $Molecule, $DataFieldLabelAndValuesRef) = @_;
     340   my($CmpdID);
     341
     342   $CmpdID = '';
     343   if ($OptionsInfo{CompoundIDMode} =~ /^MolNameOrLabelPrefix$/i) {
     344     my($MolName);
     345     $MolName = $Molecule->GetName();
     346     $CmpdID = $MolName ? $MolName : "$OptionsInfo{CompoundID}${CmpdCount}";
     347   }
     348   elsif ($OptionsInfo{CompoundIDMode} =~ /^LabelPrefix$/i) {
     349     $CmpdID = "$OptionsInfo{CompoundID}${CmpdCount}";
     350   }
     351   elsif ($OptionsInfo{CompoundIDMode} =~ /^DataField$/i) {
     352     my($SpecifiedDataField);
     353     $SpecifiedDataField = $OptionsInfo{CompoundID};
     354     $CmpdID = exists $DataFieldLabelAndValuesRef->{$SpecifiedDataField} ? $DataFieldLabelAndValuesRef->{$SpecifiedDataField} : '';
     355   }
     356   elsif ($OptionsInfo{CompoundIDMode} =~ /^MolName$/i) {
     357     $CmpdID = $Molecule->GetName();
     358   }
     359   return $CmpdID;
     360 }
     361
     362 # Generate fingerprints for molecule...
     363 #
     364 sub GenerateMoleculeFingerprints {
     365   my($Molecule) = @_;
     366   my($ExtendedConnectivityFingerprints);
     367
     368   if ($OptionsInfo{KeepLargestComponent}) {
     369     $Molecule->KeepLargestComponent();
     370   }
     371   if (!$Molecule->DetectRings()) {
     372     return undef;
     373   }
     374   $Molecule->SetAromaticityModel($OptionsInfo{AromaticityModel});
     375   $Molecule->DetectAromaticity();
     376
     377   $ExtendedConnectivityFingerprints = undef;
     378   if ($OptionsInfo{Mode} =~ /^(ExtendedConnectivity|ExtendedConnectivityCount)$/i ) {
     379     $ExtendedConnectivityFingerprints = new Fingerprints::ExtendedConnectivityFingerprints('Type' => $OptionsInfo{Mode}, 'Molecule' => $Molecule, 'NeighborhoodRadius' => $OptionsInfo{NeighborhoodRadius}, 'AtomIdentifierType' => $OptionsInfo{AtomIdentifierType});
     380   }
     381   elsif ($OptionsInfo{Mode} =~ /^ExtendedConnectivityBits$/i) {
     382     $ExtendedConnectivityFingerprints = new Fingerprints::ExtendedConnectivityFingerprints('Type' => $OptionsInfo{Mode}, 'Molecule' => $Molecule, 'NeighborhoodRadius' => $OptionsInfo{NeighborhoodRadius}, 'AtomIdentifierType' => $OptionsInfo{AtomIdentifierType}, 'Size' => $OptionsInfo{Size}, 'UsePerlCoreRandom' => $OptionsInfo{UsePerlCoreRandom});
     383   }
     384   else {
     385     die "Error: The value specified, $Options{mode}, for option \"-m, --mode\" is not valid. Allowed values: ExtendedConnectivity,  ExtendedConnectivityCount or ExtendedConnectivityBits\n";
     386   }
     387   SetAtomIdentifierTypeValuesToUse($ExtendedConnectivityFingerprints);
     388
     389   # Generate fingerprints...
     390   $ExtendedConnectivityFingerprints->GenerateFingerprints();
     391
     392   # Make sure fingerprints generation is successful...
     393   if (!$ExtendedConnectivityFingerprints->IsFingerprintsGenerationSuccessful()) {
     394     return undef;
     395   }
     396
     397   return $ExtendedConnectivityFingerprints;
     398 }
     399
     400 # Set atom identifier type to use for generating fingerprints...
     401 #
     402 sub SetAtomIdentifierTypeValuesToUse {
     403   my($ExtendedConnectivityFingerprints) = @_;
     404
     405   if ($OptionsInfo{AtomIdentifierType} =~ /^AtomicInvariantsAtomTypes$/i) {
     406     $ExtendedConnectivityFingerprints->SetAtomicInvariantsToUse(\@{$OptionsInfo{AtomicInvariantsToUse}});
     407   }
     408   elsif ($OptionsInfo{AtomIdentifierType} =~ /^FunctionalClassAtomTypes$/i) {
     409     $ExtendedConnectivityFingerprints->SetFunctionalClassesToUse(\@{$OptionsInfo{FunctionalClassesToUse}});
     410   }
     411   elsif ($OptionsInfo{AtomIdentifierType} =~ /^(DREIDINGAtomTypes|EStateAtomTypes|MMFF94AtomTypes|SLogPAtomTypes|SYBYLAtomTypes|TPSAAtomTypes|UFFAtomTypes)$/i) {
     412     # Nothing to do for now...
     413   }
     414   else {
     415     die "Error: The value specified, $Options{atomidentifiertype}, for option \"-a, --AtomIdentifierType\" is not valid. Supported atom identifier types in current release of MayaChemTools: AtomicInvariantsAtomTypes, DREIDINGAtomTypes, EStateAtomTypes, FunctionalClassAtomTypes, MMFF94AtomTypes, SLogPAtomTypes, SYBYLAtomTypes, TPSAAtomTypes, UFFAtomTypes\n";
     416   }
     417 }
     418
     419 # Retrieve information about SD files...
     420 #
     421 sub RetrieveSDFilesInfo {
     422   my($SDFile, $Index, $FileDir, $FileExt, $FileName, $OutFileRoot, $TextOutFileExt, $SDOutFileExt, $FPOutFileExt, $NewSDFileName, $NewFPFileName, $NewTextFileName, $CheckDataField, $CollectDataFields, $AllDataFieldsRef, $CommonDataFieldsRef);
     423
     424   %SDFilesInfo = ();
     425   @{$SDFilesInfo{FileOkay}} = ();
     426   @{$SDFilesInfo{OutFileRoot}} = ();
     427   @{$SDFilesInfo{SDOutFileNames}} = ();
     428   @{$SDFilesInfo{FPOutFileNames}} = ();
     429   @{$SDFilesInfo{TextOutFileNames}} = ();
     430   @{$SDFilesInfo{AllDataFieldsRef}} = ();
     431   @{$SDFilesInfo{CommonDataFieldsRef}} = ();
     432
     433   $CheckDataField = ($OptionsInfo{TextOutput} && ($OptionsInfo{DataFieldsMode} =~ /^CompoundID$/i) && ($OptionsInfo{CompoundIDMode} =~ /^DataField$/i)) ? 1 : 0;
     434   $CollectDataFields = ($OptionsInfo{TextOutput} && ($OptionsInfo{DataFieldsMode} =~ /^(All|Common)$/i)) ? 1 : 0;
     435
     436   FILELIST: for $Index (0 .. $#SDFilesList) {
     437     $SDFile = $SDFilesList[$Index];
     438
     439     $SDFilesInfo{FileOkay}[$Index] = 0;
     440     $SDFilesInfo{OutFileRoot}[$Index] = '';
     441     $SDFilesInfo{SDOutFileNames}[$Index] = '';
     442     $SDFilesInfo{FPOutFileNames}[$Index] = '';
     443     $SDFilesInfo{TextOutFileNames}[$Index] = '';
     444
     445     $SDFile = $SDFilesList[$Index];
     446     if (!(-e $SDFile)) {
     447       warn "Warning: Ignoring file $SDFile: It doesn't exist\n";
     448       next FILELIST;
     449     }
     450     if (!CheckFileType($SDFile, "sd sdf")) {
     451       warn "Warning: Ignoring file $SDFile: It's not a SD file\n";
     452       next FILELIST;
     453     }
     454
     455     if ($CheckDataField) {
     456       # Make sure data field exists in SD file..
     457       my($CmpdString, $SpecifiedDataField, @CmpdLines, %DataFieldValues);
     458
     459       @CmpdLines = ();
     460       open SDFILE, "$SDFile" or die "Error: Couldn't open $SDFile: $! \n";
     461       $CmpdString = ReadCmpdString(\*SDFILE);
     462       close SDFILE;
     463       @CmpdLines = split "\n", $CmpdString;
     464       %DataFieldValues = GetCmpdDataHeaderLabelsAndValues(\@CmpdLines);
     465       $SpecifiedDataField = $OptionsInfo{CompoundID};
     466       if (!exists $DataFieldValues{$SpecifiedDataField}) {
     467         warn "Warning: Ignoring file $SDFile: Data field value, $SpecifiedDataField, using  \"--CompoundID\" option in \"DataField\" \"--CompoundIDMode\" doesn't exist\n";
     468         next FILELIST;
     469       }
     470     }
     471
     472     $AllDataFieldsRef = '';
     473     $CommonDataFieldsRef = '';
     474     if ($CollectDataFields) {
     475       my($CmpdCount);
     476       open SDFILE, "$SDFile" or die "Error: Couldn't open $SDFile: $! \n";
     477       ($CmpdCount, $AllDataFieldsRef, $CommonDataFieldsRef) = GetAllAndCommonCmpdDataHeaderLabels(\*SDFILE);
     478       close SDFILE;
     479     }
     480
     481     # Setup output file names...
     482     $FileDir = ""; $FileName = ""; $FileExt = "";
     483     ($FileDir, $FileName, $FileExt) = ParseFileName($SDFile);
     484
     485     $TextOutFileExt = "csv";
     486     if ($Options{outdelim} =~ /^tab$/i) {
     487       $TextOutFileExt = "tsv";
     488     }
     489     $SDOutFileExt = $FileExt;
     490     $FPOutFileExt = "fpf";
     491
     492     if ($OptionsInfo{OutFileRoot} && (@SDFilesList == 1)) {
     493       my ($RootFileDir, $RootFileName, $RootFileExt) = ParseFileName($OptionsInfo{OutFileRoot});
     494       if ($RootFileName && $RootFileExt) {
     495         $FileName = $RootFileName;
     496       }
     497       else {
     498         $FileName = $OptionsInfo{OutFileRoot};
     499       }
     500       $OutFileRoot = $FileName;
     501     }
     502     else {
     503       $OutFileRoot = "${FileName}ExtendedConnectivityFP";
     504     }
     505
     506     $NewSDFileName = "${OutFileRoot}.${SDOutFileExt}";
     507     $NewFPFileName = "${OutFileRoot}.${FPOutFileExt}";
     508     $NewTextFileName = "${OutFileRoot}.${TextOutFileExt}";
     509
     510     if ($OptionsInfo{SDOutput}) {
     511       if ($SDFile =~ /$NewSDFileName/i) {
     512         warn "Warning: Ignoring input file $SDFile: Same output, $NewSDFileName, and input file names.\n";
     513         print "Specify a different name using \"-r --root\" option or use default name.\n";
     514         next FILELIST;
     515       }
     516     }
     517
     518     if (!$OptionsInfo{OverwriteFiles}) {
     519       # Check SD and text outout files...
     520       if ($OptionsInfo{SDOutput}) {
     521         if (-e $NewSDFileName) {
     522           warn "Warning: Ignoring file $SDFile: The file $NewSDFileName already exists\n";
     523           next FILELIST;
     524         }
     525       }
     526       if ($OptionsInfo{FPOutput}) {
     527         if (-e $NewFPFileName) {
     528           warn "Warning: Ignoring file $SDFile: The file $NewFPFileName already exists\n";
     529           next FILELIST;
     530         }
     531       }
     532       if ($OptionsInfo{TextOutput}) {
     533         if (-e $NewTextFileName) {
     534           warn "Warning: Ignoring file $SDFile: The file $NewTextFileName already exists\n";
     535           next FILELIST;
     536         }
     537       }
     538     }
     539
     540     $SDFilesInfo{FileOkay}[$Index] = 1;
     541
     542     $SDFilesInfo{OutFileRoot}[$Index] = $OutFileRoot;
     543     $SDFilesInfo{SDOutFileNames}[$Index] = $NewSDFileName;
     544     $SDFilesInfo{FPOutFileNames}[$Index] = $NewFPFileName;
     545     $SDFilesInfo{TextOutFileNames}[$Index] = $NewTextFileName;
     546
     547     $SDFilesInfo{AllDataFieldsRef}[$Index] = $AllDataFieldsRef;
     548     $SDFilesInfo{CommonDataFieldsRef}[$Index] = $CommonDataFieldsRef;
     549   }
     550 }
     551
     552 # Process option values...
     553 sub ProcessOptions {
     554   %OptionsInfo = ();
     555
     556   ProcessAtomIdentifierTypeOptions();
     557
     558   $OptionsInfo{AromaticityModel} = $Options{aromaticitymodel};
     559
     560   $OptionsInfo{BitsOrder} = $Options{bitsorder};
     561   $OptionsInfo{BitStringFormat} = $Options{bitstringformat};
     562
     563   $OptionsInfo{CompoundIDMode} = $Options{compoundidmode};
     564   $OptionsInfo{CompoundIDLabel} = $Options{compoundidlabel};
     565   $OptionsInfo{DataFieldsMode} = $Options{datafieldsmode};
     566
     567   my(@SpecifiedDataFields);
     568   @SpecifiedDataFields = ();
     569
     570   @{$OptionsInfo{SpecifiedDataFields}} = ();
     571   $OptionsInfo{CompoundID} = '';
     572
     573   if ($Options{datafieldsmode} =~ /^CompoundID$/i) {
     574     if ($Options{compoundidmode} =~ /^DataField$/i) {
     575       if (!$Options{compoundid}) {
     576         die "Error: You must specify a value for \"--CompoundID\" option in \"DataField\" \"--CompoundIDMode\". \n";
     577       }
     578       $OptionsInfo{CompoundID} = $Options{compoundid};
     579     }
     580     elsif ($Options{compoundidmode} =~ /^(LabelPrefix|MolNameOrLabelPrefix)$/i) {
     581       $OptionsInfo{CompoundID} = $Options{compoundid} ? $Options{compoundid} : 'Cmpd';
     582     }
     583   }
     584   elsif ($Options{datafieldsmode} =~ /^Specify$/i) {
     585     if (!$Options{datafields}) {
     586       die "Error: You must specify a value for \"--DataFields\" option in \"Specify\" \"-d, --DataFieldsMode\". \n";
     587     }
     588     @SpecifiedDataFields = split /\,/, $Options{datafields};
     589     push @{$OptionsInfo{SpecifiedDataFields}}, @SpecifiedDataFields;
     590   }
     591
     592   $OptionsInfo{FingerprintsLabel} = $Options{fingerprintslabel} ? $Options{fingerprintslabel} : 'ExtendedConnectivityFingerprints';
     593
     594   $OptionsInfo{Filter} = ($Options{filter} =~ /^Yes$/i) ? 1 : 0;
     595
     596   $OptionsInfo{KeepLargestComponent} = ($Options{keeplargestcomponent} =~ /^Yes$/i) ? 1 : 0;
     597
     598   $OptionsInfo{Mode} = $Options{mode};
     599
     600   $OptionsInfo{NeighborhoodRadius} = $Options{neighborhoodradius};
     601
     602   $OptionsInfo{UsePerlCoreRandom} = ($Options{useperlcorerandom} =~ /^Yes$/i) ? 1 : 0;
     603
     604   $OptionsInfo{Output} = $Options{output};
     605   $OptionsInfo{SDOutput} = ($Options{output} =~ /^(SD|All)$/i) ? 1 : 0;
     606   $OptionsInfo{FPOutput} = ($Options{output} =~ /^(FP|All)$/i) ? 1 : 0;
     607   $OptionsInfo{TextOutput} = ($Options{output} =~ /^(Text|All)$/i) ? 1 : 0;
     608
     609   $OptionsInfo{OutDelim} = $Options{outdelim};
     610   $OptionsInfo{OutQuote} = ($Options{quote} =~ /^Yes$/i) ? 1 : 0;
     611
     612   $OptionsInfo{OverwriteFiles} = $Options{overwrite} ? 1 : 0;
     613   $OptionsInfo{OutFileRoot} = $Options{root} ? $Options{root} : 0;
     614
     615   my($Size, $MinSize, $MaxSize);
     616   $MinSize = 32;
     617   $MaxSize = 2**32;
     618   $Size = $Options{size};
     619   if (!(IsPositiveInteger($Size) && $Size >= $MinSize && $Size <= $MaxSize && IsNumberPowerOfNumber($Size, 2))) {
     620     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";
     621   }
     622   $OptionsInfo{Size} = $Size;
     623
     624   # Setup default vector string format...
     625   #
     626   my($VectorStringFormat);
     627   $VectorStringFormat = '';
     628   if ($Options{vectorstringformat}) {
     629     $VectorStringFormat = $Options{vectorstringformat};
     630   }
     631   else {
     632     $VectorStringFormat = ($Options{mode} =~ /^ExtendedConnectivity$/) ? "ValuesString" : "IDsAndValuesString";
     633   }
     634   $OptionsInfo{VectorStringFormat} = $VectorStringFormat;
     635 }
     636
     637 # Process atom identifier type and related options...
     638 #
     639 sub ProcessAtomIdentifierTypeOptions {
     640
     641   $OptionsInfo{AtomIdentifierType} = $Options{atomidentifiertype};
     642
     643   if ($Options{atomidentifiertype} =~ /^AtomicInvariantsAtomTypes$/i) {
     644     ProcessAtomicInvariantsToUseOption();
     645   }
     646   elsif ($Options{atomidentifiertype} =~ /^FunctionalClassAtomTypes$/i) {
     647     ProcessFunctionalClassesToUse();
     648   }
     649   elsif ($Options{atomidentifiertype} =~ /^(DREIDINGAtomTypes|EStateAtomTypes|MMFF94AtomTypes|SLogPAtomTypes|SYBYLAtomTypes|TPSAAtomTypes|UFFAtomTypes)$/i) {
     650     # Nothing to do for now...
     651   }
     652   else {
     653     die "Error: The value specified, $Options{atomidentifiertype}, for option \"-a, --AtomIdentifierType\" is not valid. Supported atom identifier types in current release of MayaChemTools: AtomicInvariantsAtomTypes, DREIDINGAtomTypes, EStateAtomTypes, FunctionalClassAtomTypes, MMFF94AtomTypes, SLogPAtomTypes, SYBYLAtomTypes, TPSAAtomTypes, UFFAtomTypes\n";
     654   }
     655 }
     656
     657 # Process specified atomic invariants to use...
     658 #
     659 sub ProcessAtomicInvariantsToUseOption {
     660   my($AtomicInvariant, $AtomSymbolSpecified, @AtomicInvariantsWords);
     661
     662   @{$OptionsInfo{AtomicInvariantsToUse}} = ();
     663   if (IsEmpty($Options{atomicinvariantstouse})) {
     664     die "Error: Atomic invariants value specified using \"--AtomicInvariantsToUse\" option is empty\n";
     665   }
     666   $AtomSymbolSpecified = 0;
     667   @AtomicInvariantsWords = split /\,/, $Options{atomicinvariantstouse};
     668   for $AtomicInvariant (@AtomicInvariantsWords) {
     669     if (!AtomTypes::AtomicInvariantsAtomTypes::IsAtomicInvariantAvailable($AtomicInvariant)) {
     670       die "Error: Atomic invariant specified, $AtomicInvariant, using \"--AtomicInvariantsToUse\" option is not valid...\n ";
     671     }
     672     if ($AtomicInvariant =~ /^(AS|AtomSymbol)$/i) {
     673       $AtomSymbolSpecified = 1;
     674     }
     675     push @{$OptionsInfo{AtomicInvariantsToUse}}, $AtomicInvariant;
     676   }
     677   if (!$AtomSymbolSpecified) {
     678     die "Error: Atomic invariant, AS or AtomSymbol, must be specified as using \"--AtomicInvariantsToUse\" option...\n ";
     679   }
     680 }
     681
     682 # Process specified functional classes invariants to use...
     683 #
     684 sub ProcessFunctionalClassesToUse {
     685   my($FunctionalClass, @FunctionalClassesToUseWords);
     686
     687   @{$OptionsInfo{FunctionalClassesToUse}} = ();
     688   if (IsEmpty($Options{functionalclassestouse})) {
     689     die "Error: Functional classes value specified using \"--FunctionalClassesToUse\" option is empty\n";
     690   }
     691   @FunctionalClassesToUseWords = split /\,/, $Options{functionalclassestouse};
     692   for $FunctionalClass (@FunctionalClassesToUseWords) {
     693     if (!AtomTypes::FunctionalClassAtomTypes::IsFunctionalClassAvailable($FunctionalClass)) {
     694       die "Error: Functional class specified, $FunctionalClass, using \"--FunctionalClassesToUse\" option is not valid...\n ";
     695     }
     696     push @{$OptionsInfo{FunctionalClassesToUse}}, $FunctionalClass;
     697   }
     698 }
     699
     700 # Setup script usage  and retrieve command line arguments specified using various options...
     701 sub SetupScriptUsage {
     702
     703   # Retrieve all the options...
     704   %Options = ();
     705
     706   $Options{aromaticitymodel} = 'MayaChemToolsAromaticityModel';
     707
     708   $Options{atomidentifiertype} = 'AtomicInvariantsAtomTypes';
     709   $Options{atomicinvariantstouse} = 'AS,X,BO,H,FC,MN';
     710   $Options{functionalclassestouse} = 'HBD,HBA,PI,NI,Ar,Hal';
     711
     712   $Options{bitsorder} = 'Ascending';
     713   $Options{bitstringformat} = 'HexadecimalString';
     714
     715   $Options{compoundidmode} = 'LabelPrefix';
     716   $Options{compoundidlabel} = 'CompoundID';
     717   $Options{datafieldsmode} = 'CompoundID';
     718
     719   $Options{filter} = 'Yes';
     720
     721   $Options{keeplargestcomponent} = 'Yes';
     722
     723   $Options{mode} = 'ExtendedConnectivity';
     724
     725   $Options{neighborhoodradius} = 2;
     726
     727   $Options{useperlcorerandom} = 'yes';
     728
     729   $Options{output} = 'text';
     730   $Options{outdelim} = 'comma';
     731   $Options{quote} = 'yes';
     732
     733   $Options{size} = 1024;
     734
     735   $Options{vectorstringformat} = '';
     736
     737   if (!GetOptions(\%Options, "aromaticitymodel=s", "atomidentifiertype|a=s", "atomicinvariantstouse=s", "functionalclassestouse=s", "bitsorder=s", "bitstringformat|b=s", "compoundid=s", "compoundidlabel=s", "compoundidmode=s", "datafields=s", "datafieldsmode|d=s", "filter|f=s", "fingerprintslabel=s",  "help|h", "keeplargestcomponent|k=s",  "mode|m=s", "neighborhoodradius|n=s", "outdelim=s", "output=s", "overwrite|o", "quote|q=s", "root|r=s", "size|s=i", "useperlcorerandom=s", "vectorstringformat|v=s", "workingdir|w=s")) {
     738     die "\nTo get a list of valid options and their values, use \"$ScriptName -h\" or\n\"perl -S $ScriptName -h\" command and try again...\n";
     739   }
     740   if ($Options{workingdir}) {
     741     if (! -d $Options{workingdir}) {
     742       die "Error: The value specified, $Options{workingdir}, for option \"-w --workingdir\" is not a directory name.\n";
     743     }
     744     chdir $Options{workingdir} or die "Error: Couldn't chdir $Options{workingdir}: $! \n";
     745   }
     746   if (!Molecule::IsSupportedAromaticityModel($Options{aromaticitymodel})) {
     747     my(@SupportedModels) = Molecule::GetSupportedAromaticityModels();
     748     die "Error: The value specified, $Options{aromaticitymodel}, for option \"--AromaticityModel\" is not valid. Supported aromaticity models in current release of MayaChemTools: @SupportedModels\n";
     749   }
     750   if ($Options{atomidentifiertype} !~ /^(AtomicInvariantsAtomTypes|FunctionalClassAtomTypes|DREIDINGAtomTypes|EStateAtomTypes|MMFF94AtomTypes|SLogPAtomTypes|SYBYLAtomTypes|TPSAAtomTypes|UFFAtomTypes)$/i) {
     751     die "Error: The value specified, $Options{atomidentifiertype}, for option \"-a, --AtomIdentifierType\" is not valid. Supported atom identifier types in current release of MayaChemTools: AtomicInvariantsAtomTypes, FunctionalClassAtomTypes, DREIDINGAtomTypes, EStateAtomTypes, MMFF94AtomTypes, SLogPAtomTypes, SYBYLAtomTypes, TPSAAtomTypes, UFFAtomTypes\n";
     752   }
     753   if ($Options{bitsorder} !~ /^(Ascending|Descending)$/i) {
     754     die "Error: The value specified, $Options{bitsorder}, for option \"--BitsOrder\" is not valid. Allowed values: Ascending or Descending\n";
     755   }
     756   if ($Options{bitstringformat} !~ /^(BinaryString|HexadecimalString)$/i) {
     757     die "Error: The value specified, $Options{bitstringformat}, for option \"-b, --bitstringformat\" is not valid. Allowed values: BinaryString or HexadecimalString\n";
     758   }
     759   if ($Options{compoundidmode} !~ /^(DataField|MolName|LabelPrefix|MolNameOrLabelPrefix)$/i) {
     760     die "Error: The value specified, $Options{compoundidmode}, for option \"--CompoundIDMode\" is not valid. Allowed values: DataField, MolName, LabelPrefix or MolNameOrLabelPrefix\n";
     761   }
     762   if ($Options{datafieldsmode} !~ /^(All|Common|Specify|CompoundID)$/i) {
     763     die "Error: The value specified, $Options{datafieldsmode}, for option \"-d, --DataFieldsMode\" is not valid. Allowed values: All, Common, Specify or CompoundID\n";
     764   }
     765   if ($Options{filter} !~ /^(Yes|No)$/i) {
     766     die "Error: The value specified, $Options{filter}, for option \"-f, --Filter\" is not valid. Allowed values: Yes or No\n";
     767   }
     768   if ($Options{keeplargestcomponent} !~ /^(Yes|No)$/i) {
     769     die "Error: The value specified, $Options{keeplargestcomponent}, for option \"-k, --KeepLargestComponent\" is not valid. Allowed values: Yes or No\n";
     770   }
     771   if ($Options{mode} !~ /^(ExtendedConnectivity|ExtendedConnectivityCount|ExtendedConnectivityBits)$/i) {
     772     die "Error: The value specified, $Options{mode}, for option \"-m, --mode\" is not valid. Allowed values: ExtendedConnectivity, ExtendedConnecticityCount, or ExtendedConnectivityBits\n";
     773   }
     774   if (!(IsInteger($Options{neighborhoodradius}) && ($Options{neighborhoodradius} >= 0))) {
     775     die "Error: The value specified, $Options{neighborhoodradius}, for option \"-n, --NeighborhoodRadius\" is not valid. Allowed values: >= 0 \n";
     776   }
     777   if ($Options{output} !~ /^(SD|FP|text|all)$/i) {
     778     die "Error: The value specified, $Options{output}, for option \"--output\" is not valid. Allowed values: SD, FP, text, or all\n";
     779   }
     780   if ($Options{outdelim} !~ /^(comma|semicolon|tab)$/i) {
     781     die "Error: The value specified, $Options{outdelim}, for option \"--outdelim\" is not valid. Allowed values: comma, tab, or semicolon\n";
     782   }
     783   if ($Options{quote} !~ /^(Yes|No)$/i) {
     784     die "Error: The value specified, $Options{quote}, for option \"-q --quote\" is not valid. Allowed values: Yes or No\n";
     785   }
     786   if (!IsPositiveInteger($Options{size})) {
     787     die "Error: The value specified, $Options{size}, for option \"-s, --size\" is not valid. Allowed values: > 0 \n";
     788   }
     789   if ($Options{outdelim} =~ /semicolon/i && $Options{quote} =~ /^No$/i) {
     790     die "Error: The value specified, $Options{quote}, for option \"-q --quote\" is not allowed with, semicolon value of \"--outdelim\" option: Fingerprints string use semicolon as delimiter for various data fields and must be quoted.\n";
     791   }
     792   if ($Options{useperlcorerandom} !~ /^(Yes|No)$/i) {
     793     die "Error: The value specified, $Options{useperlcorerandom}, for option \"--UsePerlCoreRandom\" is not valid. Allowed values: Yes or No\n";
     794   }
     795   if ($Options{vectorstringformat} && $Options{vectorstringformat} !~ /^(ValuesString|IDsAndValuesString|IDsAndValuesPairsString|ValuesAndIDsString|ValuesAndIDsPairsString)$/i) {
     796     die "Error: The value specified, $Options{vectorstringformat}, for option \"-v, --VectorStringFormat\" is not valid. Allowed values: ValuesString, IDsAndValuesString, IDsAndValuesPairsString, ValuesAndIDsString or ValuesAndIDsPairsString\n";
     797   }
     798 }
     799