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