diff mayachemtool/mayachemtools/bin/PathLengthFingerprints.pl @ 0:68300206e90d draft default tip

Uploaded
author deepakjadmin
date Thu, 05 Nov 2015 02:41:30 -0500
parents
children
line wrap: on
line diff
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/mayachemtool/mayachemtools/bin/PathLengthFingerprints.pl	Thu Nov 05 02:41:30 2015 -0500
@@ -0,0 +1,1792 @@
+#!/usr/bin/perl -w
+#
+# $RCSfile: PathLengthFingerprints.pl,v $
+# $Date: 2015/02/28 20:46:20 $
+# $Revision: 1.50 $
+#
+# Author: Manish Sud <msud@san.rr.com>
+#
+# Copyright (C) 2015 Manish Sud. All rights reserved.
+#
+# This file is part of MayaChemTools.
+#
+# MayaChemTools is free software; you can redistribute it and/or modify it under
+# the terms of the GNU Lesser General Public License as published by the Free
+# Software Foundation; either version 3 of the License, or (at your option) any
+# later version.
+#
+# MayaChemTools is distributed in the hope that it will be useful, but without
+# any warranty; without even the implied warranty of merchantability of fitness
+# for a particular purpose.  See the GNU Lesser General Public License for more
+# details.
+#
+# You should have received a copy of the GNU Lesser General Public License
+# along with MayaChemTools; if not, see <http://www.gnu.org/licenses/> or
+# write to the Free Software Foundation Inc., 59 Temple Place, Suite 330,
+# Boston, MA, 02111-1307, USA.
+#
+
+use strict;
+use FindBin; use lib "$FindBin::Bin/../lib";
+use Getopt::Long;
+use File::Basename;
+use Text::ParseWords;
+use Benchmark;
+use FileUtil;
+use TextUtil;
+use SDFileUtil;
+use MoleculeFileIO;
+use FileIO::FingerprintsSDFileIO;
+use FileIO::FingerprintsTextFileIO;
+use FileIO::FingerprintsFPFileIO;
+use AtomTypes::AtomicInvariantsAtomTypes;
+use AtomTypes::FunctionalClassAtomTypes;
+use Fingerprints::PathLengthFingerprints;
+
+my($ScriptName, %Options, $StartTime, $EndTime, $TotalTime);
+
+# Autoflush STDOUT
+$| = 1;
+
+# Starting message...
+$ScriptName = basename($0);
+print "\n$ScriptName: Starting...\n\n";
+$StartTime = new Benchmark;
+
+# Get the options and setup script...
+SetupScriptUsage();
+if ($Options{help} || @ARGV < 1) {
+  die GetUsageFromPod("$FindBin::Bin/$ScriptName");
+}
+
+my(@SDFilesList);
+@SDFilesList = ExpandFileNames(\@ARGV, "sdf sd");
+
+# Process options...
+print "Processing options...\n";
+my(%OptionsInfo);
+ProcessOptions();
+
+# Setup information about input files...
+print "Checking input SD file(s)...\n";
+my(%SDFilesInfo);
+RetrieveSDFilesInfo();
+
+# Process input files..
+my($FileIndex);
+if (@SDFilesList > 1) {
+  print "\nProcessing SD files...\n";
+}
+for $FileIndex (0 .. $#SDFilesList) {
+  if ($SDFilesInfo{FileOkay}[$FileIndex]) {
+    print "\nProcessing file $SDFilesList[$FileIndex]...\n";
+    GeneratePathLengthFingerprints($FileIndex);
+  }
+}
+print "\n$ScriptName:Done...\n\n";
+
+$EndTime = new Benchmark;
+$TotalTime = timediff ($EndTime, $StartTime);
+print "Total time: ", timestr($TotalTime), "\n";
+
+###############################################################################
+
+# Generate fingerprints for a SD file...
+#
+sub GeneratePathLengthFingerprints {
+  my($FileIndex) = @_;
+  my($CmpdCount, $IgnoredCmpdCount, $SDFile, $MoleculeFileIO, $Molecule, $PathLengthFingerprints, $NewFPSDFileIO, $NewFPTextFileIO, $NewFPFileIO);
+
+  $SDFile = $SDFilesList[$FileIndex];
+
+  # Setup output files...
+  #
+  ($NewFPSDFileIO, $NewFPTextFileIO, $NewFPFileIO) = SetupAndOpenOutputFiles($FileIndex);
+
+  $MoleculeFileIO = new MoleculeFileIO('Name' => $SDFile);
+  $MoleculeFileIO->Open();
+
+  $CmpdCount = 0;
+  $IgnoredCmpdCount = 0;
+
+  COMPOUND: while ($Molecule = $MoleculeFileIO->ReadMolecule()) {
+    $CmpdCount++;
+
+    # Filter compound data before calculating fingerprints...
+    if ($OptionsInfo{Filter}) {
+      if (CheckAndFilterCompound($CmpdCount, $Molecule)) {
+	$IgnoredCmpdCount++;
+	next COMPOUND;
+      }
+    }
+
+    $PathLengthFingerprints = GenerateMoleculeFingerprints($Molecule);
+    if (!$PathLengthFingerprints) {
+      $IgnoredCmpdCount++;
+      ProcessIgnoredCompound('FingerprintsGenerationFailed', $CmpdCount, $Molecule);
+      next COMPOUND;
+    }
+
+    WriteDataToOutputFiles($FileIndex, $CmpdCount, $Molecule, $PathLengthFingerprints, $NewFPSDFileIO, $NewFPTextFileIO, $NewFPFileIO);
+  }
+  $MoleculeFileIO->Close();
+
+  if ($NewFPSDFileIO) {
+    $NewFPSDFileIO->Close();
+  }
+  if ($NewFPTextFileIO) {
+    $NewFPTextFileIO->Close();
+  }
+  if ($NewFPFileIO) {
+    $NewFPFileIO->Close();
+  }
+
+  WriteFingerprintsGenerationSummaryStatistics($CmpdCount, $IgnoredCmpdCount);
+}
+
+# Process compound being ignored due to problems in fingerprints geneation...
+#
+sub ProcessIgnoredCompound {
+  my($Mode, $CmpdCount, $Molecule) = @_;
+  my($CmpdID, $DataFieldLabelAndValuesRef);
+
+  $DataFieldLabelAndValuesRef = $Molecule->GetDataFieldLabelAndValues();
+  $CmpdID = SetupCmpdIDForOutputFiles($CmpdCount, $Molecule, $DataFieldLabelAndValuesRef);
+
+  MODE: {
+    if ($Mode =~ /^ContainsNonElementalData$/i) {
+      warn "\nWarning: Ignoring compound record number $CmpdCount with ID $CmpdID: Compound contains atom data corresponding to non-elemental atom symbol(s)...\n\n";
+      next MODE;
+    }
+
+    if ($Mode =~ /^ContainsNoElementalData$/i) {
+      warn "\nWarning: Ignoring compound record number $CmpdCount with ID $CmpdID: Compound contains no atom data...\n\n";
+      next MODE;
+    }
+
+    if ($Mode =~ /^FingerprintsGenerationFailed$/i) {
+      warn "\nWarning: Ignoring compound record number $CmpdCount with ID $CmpdID: Fingerprints generation didn't succeed...\n\n";
+      next MODE;
+    }
+    warn "\nWarning: Ignoring compound record number $CmpdCount with ID $CmpdID: Fingerprints generation didn't succeed...\n\n";
+  }
+}
+
+# Check and filter compounds....
+#
+sub CheckAndFilterCompound {
+  my($CmpdCount, $Molecule) = @_;
+  my($ElementCount, $NonElementCount);
+
+  ($ElementCount, $NonElementCount) = $Molecule->GetNumOfElementsAndNonElements();
+
+  if ($NonElementCount) {
+    ProcessIgnoredCompound('ContainsNonElementalData', $CmpdCount, $Molecule);
+    return 1;
+  }
+
+  if (!$ElementCount) {
+    ProcessIgnoredCompound('ContainsNoElementalData', $CmpdCount, $Molecule);
+    return 1;
+  }
+
+  return 0;
+}
+
+# Write out compounds fingerprints generation summary statistics...
+#
+sub WriteFingerprintsGenerationSummaryStatistics {
+  my($CmpdCount, $IgnoredCmpdCount) = @_;
+  my($ProcessedCmpdCount);
+
+  $ProcessedCmpdCount = $CmpdCount - $IgnoredCmpdCount;
+
+  print "\nNumber of compounds: $CmpdCount\n";
+  print "Number of compounds processed successfully during fingerprints generation: $ProcessedCmpdCount\n";
+  print "Number of compounds ignored during fingerprints generation: $IgnoredCmpdCount\n";
+}
+
+# Open output files...
+#
+sub SetupAndOpenOutputFiles {
+  my($FileIndex) = @_;
+  my($NewFPSDFile, $NewFPFile, $NewFPTextFile, $NewFPSDFileIO, $NewFPTextFileIO, $NewFPFileIO, %FingerprintsFileIOParams);
+
+  ($NewFPSDFileIO, $NewFPTextFileIO, $NewFPFileIO) = (undef) x 3;
+
+  # Setup common parameters for fingerprints file IO objects...
+  #
+  %FingerprintsFileIOParams = ();
+  if ($OptionsInfo{Mode} =~ /^PathLengthBits$/i) {
+    %FingerprintsFileIOParams = ('Mode' => 'Write', 'Overwrite' => $OptionsInfo{OverwriteFiles}, 'FingerprintsStringMode' => 'FingerprintsBitVectorString', 'BitStringFormat' => $OptionsInfo{BitStringFormat}, 'BitsOrder' => $OptionsInfo{BitsOrder});
+  }
+  elsif ($OptionsInfo{Mode} =~ /^PathLengthCount$/i) {
+    %FingerprintsFileIOParams = ('Mode' => 'Write', 'Overwrite' => $OptionsInfo{OverwriteFiles}, 'FingerprintsStringMode' => 'FingerprintsVectorString', 'VectorStringFormat' => $OptionsInfo{VectorStringFormat});
+  }
+
+  if ($OptionsInfo{SDOutput}) {
+    $NewFPSDFile = $SDFilesInfo{SDOutFileNames}[$FileIndex];
+    print "Generating SD file $NewFPSDFile...\n";
+    $NewFPSDFileIO = new FileIO::FingerprintsSDFileIO('Name' => $NewFPSDFile, %FingerprintsFileIOParams, 'FingerprintsFieldLabel' => $OptionsInfo{FingerprintsLabel});
+    $NewFPSDFileIO->Open();
+  }
+
+  if ($OptionsInfo{FPOutput}) {
+    $NewFPFile = $SDFilesInfo{FPOutFileNames}[$FileIndex];
+    print "Generating FP file $NewFPFile...\n";
+    $NewFPFileIO = new FileIO::FingerprintsFPFileIO('Name' => $NewFPFile, %FingerprintsFileIOParams);
+    $NewFPFileIO->Open();
+  }
+
+  if ($OptionsInfo{TextOutput}) {
+    my($ColLabelsRef);
+
+    $NewFPTextFile = $SDFilesInfo{TextOutFileNames}[$FileIndex];
+    $ColLabelsRef = SetupFPTextFileCoulmnLabels($FileIndex);
+
+    print "Generating text file $NewFPTextFile...\n";
+    $NewFPTextFileIO = new FileIO::FingerprintsTextFileIO('Name' => $NewFPTextFile, %FingerprintsFileIOParams, 'DataColLabels' => $ColLabelsRef, 'OutDelim' => $OptionsInfo{OutDelim}, 'OutQuote' => $OptionsInfo{OutQuote});
+    $NewFPTextFileIO->Open();
+  }
+
+  return ($NewFPSDFileIO, $NewFPTextFileIO, $NewFPFileIO);
+}
+
+# Write fingerpritns and other data to appropriate output files...
+#
+sub WriteDataToOutputFiles {
+  my($FileIndex, $CmpdCount, $Molecule, $PathLengthFingerprints, $NewFPSDFileIO, $NewFPTextFileIO, $NewFPFileIO) = @_;
+  my($DataFieldLabelAndValuesRef);
+
+  $DataFieldLabelAndValuesRef = undef;
+  if ($NewFPTextFileIO || $NewFPFileIO) {
+    $DataFieldLabelAndValuesRef = $Molecule->GetDataFieldLabelAndValues();
+  }
+
+  if ($NewFPSDFileIO) {
+    my($CmpdString);
+
+    $CmpdString = $Molecule->GetInputMoleculeString();
+    $NewFPSDFileIO->WriteFingerprints($PathLengthFingerprints, $CmpdString);
+  }
+
+  if ($NewFPTextFileIO) {
+    my($ColValuesRef);
+
+    $ColValuesRef = SetupFPTextFileCoulmnValues($FileIndex, $CmpdCount, $Molecule, $DataFieldLabelAndValuesRef);
+    $NewFPTextFileIO->WriteFingerprints($PathLengthFingerprints, $ColValuesRef);
+  }
+
+  if ($NewFPFileIO) {
+    my($CompoundID);
+
+    $CompoundID = SetupCmpdIDForOutputFiles($CmpdCount, $Molecule, $DataFieldLabelAndValuesRef);
+    $NewFPFileIO->WriteFingerprints($PathLengthFingerprints, $CompoundID);
+  }
+}
+
+# Generate approriate column labels for FPText output file...
+#
+sub SetupFPTextFileCoulmnLabels {
+  my($FileIndex) = @_;
+  my($Line, @ColLabels);
+
+  @ColLabels = ();
+  if ($OptionsInfo{DataFieldsMode} =~ /^All$/i) {
+    push @ColLabels, @{$SDFilesInfo{AllDataFieldsRef}[$FileIndex]};
+  }
+  elsif ($OptionsInfo{DataFieldsMode} =~ /^Common$/i) {
+    push @ColLabels, @{$SDFilesInfo{CommonDataFieldsRef}[$FileIndex]};
+  }
+  elsif ($OptionsInfo{DataFieldsMode} =~ /^Specify$/i) {
+    push @ColLabels, @{$OptionsInfo{SpecifiedDataFields}};
+  }
+  elsif ($OptionsInfo{DataFieldsMode} =~ /^CompoundID$/i) {
+    push @ColLabels, $OptionsInfo{CompoundIDLabel};
+  }
+  # Add fingerprints label...
+  push @ColLabels, $OptionsInfo{FingerprintsLabel};
+
+  return \@ColLabels;
+}
+
+# Generate column values FPText output file..
+#
+sub SetupFPTextFileCoulmnValues {
+  my($FileIndex, $CmpdCount, $Molecule, $DataFieldLabelAndValuesRef) = @_;
+  my(@ColValues);
+
+  @ColValues = ();
+  if ($OptionsInfo{DataFieldsMode} =~ /^CompoundID$/i) {
+    push @ColValues, SetupCmpdIDForOutputFiles($CmpdCount, $Molecule, $DataFieldLabelAndValuesRef);
+  }
+  elsif ($OptionsInfo{DataFieldsMode} =~ /^All$/i) {
+    @ColValues = map { exists $DataFieldLabelAndValuesRef->{$_} ? $DataFieldLabelAndValuesRef->{$_} : ''} @{$SDFilesInfo{AllDataFieldsRef}[$FileIndex]};
+  }
+  elsif ($OptionsInfo{DataFieldsMode} =~ /^Common$/i) {
+    @ColValues = map { exists $DataFieldLabelAndValuesRef->{$_} ? $DataFieldLabelAndValuesRef->{$_} : ''} @{$SDFilesInfo{CommonDataFieldsRef}[$FileIndex]};
+  }
+  elsif ($OptionsInfo{DataFieldsMode} =~ /^Specify$/i) {
+    @ColValues = map { exists $DataFieldLabelAndValuesRef->{$_} ? $DataFieldLabelAndValuesRef->{$_} : ''} @{$OptionsInfo{SpecifiedDataFields}};
+  }
+
+  return \@ColValues;
+}
+
+# Generate compound ID for FP and FPText output files..
+#
+sub SetupCmpdIDForOutputFiles {
+  my($CmpdCount, $Molecule, $DataFieldLabelAndValuesRef) = @_;
+  my($CmpdID);
+
+  $CmpdID = '';
+  if ($OptionsInfo{CompoundIDMode} =~ /^MolNameOrLabelPrefix$/i) {
+    my($MolName);
+    $MolName = $Molecule->GetName();
+    $CmpdID = $MolName ? $MolName : "$OptionsInfo{CompoundID}${CmpdCount}";
+  }
+  elsif ($OptionsInfo{CompoundIDMode} =~ /^LabelPrefix$/i) {
+    $CmpdID = "$OptionsInfo{CompoundID}${CmpdCount}";
+  }
+  elsif ($OptionsInfo{CompoundIDMode} =~ /^DataField$/i) {
+    my($SpecifiedDataField);
+    $SpecifiedDataField = $OptionsInfo{CompoundID};
+    $CmpdID = exists $DataFieldLabelAndValuesRef->{$SpecifiedDataField} ? $DataFieldLabelAndValuesRef->{$SpecifiedDataField} : '';
+  }
+  elsif ($OptionsInfo{CompoundIDMode} =~ /^MolName$/i) {
+    $CmpdID = $Molecule->GetName();
+  }
+  return $CmpdID;
+}
+
+# Generate fingerprints for molecule...
+#
+sub GenerateMoleculeFingerprints {
+  my($Molecule) = @_;
+  my($PathLengthFingerprints);
+
+  if ($OptionsInfo{KeepLargestComponent}) {
+    $Molecule->KeepLargestComponent();
+  }
+  if ($OptionsInfo{IgnoreHydrogens}) {
+    $Molecule->DeleteHydrogens();
+  }
+
+  if ($OptionsInfo{DetectAromaticity}) {
+    if (!$Molecule->DetectRings()) {
+      return undef;
+    }
+    $Molecule->SetAromaticityModel($OptionsInfo{AromaticityModel});
+    $Molecule->DetectAromaticity();
+  }
+
+  $PathLengthFingerprints = undef;
+  if ($OptionsInfo{Mode} =~ /^PathLengthBits$/i) {
+    $PathLengthFingerprints = GeneratePathLengthBitsFingerprints($Molecule);
+  }
+  elsif ($OptionsInfo{Mode} =~ /^PathLengthCount$/i) {
+    $PathLengthFingerprints = GeneratePathLengthCountFingerprints($Molecule);
+  }
+  else {
+    die "Error: The value specified, $Options{mode}, for option \"-m, --mode\" is not valid. Allowed values: PathLengthBits or PathLengthCount\n";
+  }
+
+  return $PathLengthFingerprints;
+}
+
+# Generate pathlength bits finerprints for molecule...
+#
+sub GeneratePathLengthBitsFingerprints {
+  my($Molecule) = @_;
+  my($PathLengthFingerprints);
+
+  $PathLengthFingerprints = new Fingerprints::PathLengthFingerprints('Molecule' => $Molecule, 'Type' => 'PathLengthBits', 'AtomIdentifierType' => $OptionsInfo{AtomIdentifierType}, 'NumOfBitsToSetPerPath' => $OptionsInfo{NumOfBitsToSetPerPath}, 'Size' => $OptionsInfo{Size}, 'MinLength' => $OptionsInfo{MinPathLength}, 'MaxLength' => $OptionsInfo{MaxPathLength}, 'AllowRings' => $OptionsInfo{AllowRings}, 'AllowSharedBonds' => $OptionsInfo{AllowSharedBonds}, 'UseBondSymbols' => $OptionsInfo{UseBondSymbols}, 'UseUniquePaths' => $OptionsInfo{UseUniquePaths}, 'UsePerlCoreRandom' => $OptionsInfo{UsePerlCoreRandom});
+
+  # Set atom identifier type...
+  SetAtomIdentifierTypeValuesToUse($PathLengthFingerprints);
+
+  # Generate fingerprints...
+  $PathLengthFingerprints->GenerateFingerprints();
+
+  # Make sure fingerprints generation is successful...
+  if (!$PathLengthFingerprints->IsFingerprintsGenerationSuccessful()) {
+    return undef;
+  }
+
+  if ($OptionsInfo{Fold}) {
+    my($CheckSizeValue) = 0;
+    $PathLengthFingerprints->FoldFingerprintsBySize($OptionsInfo{FoldedSize}, $CheckSizeValue);
+  }
+
+  return $PathLengthFingerprints;
+}
+
+# Generate pathlength count finerprints for molecule...
+#
+sub GeneratePathLengthCountFingerprints {
+  my($Molecule) = @_;
+  my($PathLengthFingerprints);
+
+  $PathLengthFingerprints = new Fingerprints::PathLengthFingerprints('Molecule' => $Molecule, 'Type' => 'PathLengthCount', 'AtomIdentifierType' => $OptionsInfo{AtomIdentifierType}, 'MinLength' => $OptionsInfo{MinPathLength}, 'MaxLength' => $OptionsInfo{MaxPathLength}, 'AllowRings' => $OptionsInfo{AllowRings}, 'AllowSharedBonds' => $OptionsInfo{AllowSharedBonds}, 'UseBondSymbols' => $OptionsInfo{UseBondSymbols}, 'UseUniquePaths' => $OptionsInfo{UseUniquePaths});
+
+  # Set atom identifier type...
+  SetAtomIdentifierTypeValuesToUse($PathLengthFingerprints);
+
+  # Generate fingerprints...
+  $PathLengthFingerprints->GenerateFingerprints();
+
+  # Make sure fingerprints generation is successful...
+  if (!$PathLengthFingerprints->IsFingerprintsGenerationSuccessful()) {
+    return undef;
+  }
+  return $PathLengthFingerprints;
+}
+
+# Set atom identifier type to use for generating path strings...
+#
+sub SetAtomIdentifierTypeValuesToUse {
+  my($PathLengthFingerprints) = @_;
+
+  if ($OptionsInfo{AtomIdentifierType} =~ /^AtomicInvariantsAtomTypes$/i) {
+    $PathLengthFingerprints->SetAtomicInvariantsToUse(\@{$OptionsInfo{AtomicInvariantsToUse}});
+  }
+  elsif ($OptionsInfo{AtomIdentifierType} =~ /^FunctionalClassAtomTypes$/i) {
+    $PathLengthFingerprints->SetFunctionalClassesToUse(\@{$OptionsInfo{FunctionalClassesToUse}});
+  }
+  elsif ($OptionsInfo{AtomIdentifierType} =~ /^(DREIDINGAtomTypes|EStateAtomTypes|MMFF94AtomTypes|SLogPAtomTypes|SYBYLAtomTypes|TPSAAtomTypes|UFFAtomTypes)$/i) {
+    # Nothing to do for now...
+  }
+  else {
+    die "Error: The value specified, $Options{atomidentifiertype}, for option \"-a, --AtomIdentifierType\" is not valid. Supported atom identifier types in current release of MayaChemTools: AtomicInvariantsAtomTypes, DREIDINGAtomTypes, EStateAtomTypes, FunctionalClassAtomTypes, MMFF94AtomTypes, SLogPAtomTypes, SYBYLAtomTypes, TPSAAtomTypes, UFFAtomTypes\n";
+  }
+}
+
+# Retrieve information about SD files...
+#
+sub RetrieveSDFilesInfo {
+  my($SDFile, $Index, $FileDir, $FileExt, $FileName, $OutFileRoot, $TextOutFileExt, $SDOutFileExt, $FPOutFileExt, $NewSDFileName, $NewFPFileName, $NewTextFileName, $CheckDataField, $CollectDataFields, $AllDataFieldsRef, $CommonDataFieldsRef);
+
+  %SDFilesInfo = ();
+  @{$SDFilesInfo{FileOkay}} = ();
+  @{$SDFilesInfo{OutFileRoot}} = ();
+  @{$SDFilesInfo{SDOutFileNames}} = ();
+  @{$SDFilesInfo{FPOutFileNames}} = ();
+  @{$SDFilesInfo{TextOutFileNames}} = ();
+  @{$SDFilesInfo{AllDataFieldsRef}} = ();
+  @{$SDFilesInfo{CommonDataFieldsRef}} = ();
+
+  $CheckDataField = ($OptionsInfo{TextOutput} && ($OptionsInfo{DataFieldsMode} =~ /^CompoundID$/i) && ($OptionsInfo{CompoundIDMode} =~ /^DataField$/i)) ? 1 : 0;
+  $CollectDataFields = ($OptionsInfo{TextOutput} && ($OptionsInfo{DataFieldsMode} =~ /^(All|Common)$/i)) ? 1 : 0;
+
+  FILELIST: for $Index (0 .. $#SDFilesList) {
+    $SDFile = $SDFilesList[$Index];
+
+    $SDFilesInfo{FileOkay}[$Index] = 0;
+    $SDFilesInfo{OutFileRoot}[$Index] = '';
+    $SDFilesInfo{SDOutFileNames}[$Index] = '';
+    $SDFilesInfo{FPOutFileNames}[$Index] = '';
+    $SDFilesInfo{TextOutFileNames}[$Index] = '';
+
+    $SDFile = $SDFilesList[$Index];
+    if (!(-e $SDFile)) {
+      warn "Warning: Ignoring file $SDFile: It doesn't exist\n";
+      next FILELIST;
+    }
+    if (!CheckFileType($SDFile, "sd sdf")) {
+      warn "Warning: Ignoring file $SDFile: It's not a SD file\n";
+      next FILELIST;
+    }
+
+    if ($CheckDataField) {
+      # Make sure data field exists in SD file..
+      my($CmpdString, $SpecifiedDataField, @CmpdLines, %DataFieldValues);
+
+      @CmpdLines = ();
+      open SDFILE, "$SDFile" or die "Error: Couldn't open $SDFile: $! \n";
+      $CmpdString = ReadCmpdString(\*SDFILE);
+      close SDFILE;
+      @CmpdLines = split "\n", $CmpdString;
+      %DataFieldValues = GetCmpdDataHeaderLabelsAndValues(\@CmpdLines);
+      $SpecifiedDataField = $OptionsInfo{CompoundID};
+      if (!exists $DataFieldValues{$SpecifiedDataField}) {
+	warn "Warning: Ignoring file $SDFile: Data field value, $SpecifiedDataField, using  \"--CompoundID\" option in \"DataField\" \"--CompoundIDMode\" doesn't exist\n";
+	next FILELIST;
+      }
+    }
+
+    $AllDataFieldsRef = '';
+    $CommonDataFieldsRef = '';
+    if ($CollectDataFields) {
+      my($CmpdCount);
+      open SDFILE, "$SDFile" or die "Error: Couldn't open $SDFile: $! \n";
+      ($CmpdCount, $AllDataFieldsRef, $CommonDataFieldsRef) = GetAllAndCommonCmpdDataHeaderLabels(\*SDFILE);
+      close SDFILE;
+    }
+
+    # Setup output file names...
+    $FileDir = ""; $FileName = ""; $FileExt = "";
+    ($FileDir, $FileName, $FileExt) = ParseFileName($SDFile);
+
+    $TextOutFileExt = "csv";
+    if ($Options{outdelim} =~ /^tab$/i) {
+      $TextOutFileExt = "tsv";
+    }
+    $SDOutFileExt = $FileExt;
+    $FPOutFileExt = "fpf";
+
+    if ($OptionsInfo{OutFileRoot} && (@SDFilesList == 1)) {
+      my ($RootFileDir, $RootFileName, $RootFileExt) = ParseFileName($OptionsInfo{OutFileRoot});
+      if ($RootFileName && $RootFileExt) {
+	$FileName = $RootFileName;
+      }
+      else {
+	$FileName = $OptionsInfo{OutFileRoot};
+      }
+      $OutFileRoot = $FileName;
+    }
+    else {
+      $OutFileRoot = "${FileName}PathLengthFP";
+    }
+
+    $NewSDFileName = "${OutFileRoot}.${SDOutFileExt}";
+    $NewFPFileName = "${OutFileRoot}.${FPOutFileExt}";
+    $NewTextFileName = "${OutFileRoot}.${TextOutFileExt}";
+
+    if ($OptionsInfo{SDOutput}) {
+      if ($SDFile =~ /$NewSDFileName/i) {
+	warn "Warning: Ignoring input file $SDFile: Same output, $NewSDFileName, and input file names.\n";
+	print "Specify a different name using \"-r --root\" option or use default name.\n";
+	next FILELIST;
+      }
+    }
+
+    if (!$OptionsInfo{OverwriteFiles}) {
+      # Check SD, FP and text outout files...
+      if ($OptionsInfo{SDOutput}) {
+	if (-e $NewSDFileName) {
+	  warn "Warning: Ignoring file $SDFile: The file $NewSDFileName already exists\n";
+	  next FILELIST;
+	}
+      }
+      if ($OptionsInfo{FPOutput}) {
+	if (-e $NewFPFileName) {
+	  warn "Warning: Ignoring file $SDFile: The file $NewFPFileName already exists\n";
+	  next FILELIST;
+	}
+      }
+      if ($OptionsInfo{TextOutput}) {
+	if (-e $NewTextFileName) {
+	  warn "Warning: Ignoring file $SDFile: The file $NewTextFileName already exists\n";
+	  next FILELIST;
+	}
+      }
+    }
+
+    $SDFilesInfo{FileOkay}[$Index] = 1;
+
+    $SDFilesInfo{OutFileRoot}[$Index] = $OutFileRoot;
+    $SDFilesInfo{SDOutFileNames}[$Index] = $NewSDFileName;
+    $SDFilesInfo{FPOutFileNames}[$Index] = $NewFPFileName;
+    $SDFilesInfo{TextOutFileNames}[$Index] = $NewTextFileName;
+
+    $SDFilesInfo{AllDataFieldsRef}[$Index] = $AllDataFieldsRef;
+    $SDFilesInfo{CommonDataFieldsRef}[$Index] = $CommonDataFieldsRef;
+  }
+}
+
+# Process option values...
+sub ProcessOptions {
+  %OptionsInfo = ();
+
+  $OptionsInfo{Mode} = $Options{mode};
+  $OptionsInfo{AromaticityModel} = $Options{aromaticitymodel};
+  $OptionsInfo{PathMode} = $Options{pathmode};
+
+  ProcessAtomIdentifierTypeOptions();
+
+  $OptionsInfo{BitsOrder} = $Options{bitsorder};
+  $OptionsInfo{BitStringFormat} = $Options{bitstringformat};
+
+  $OptionsInfo{CompoundIDMode} = $Options{compoundidmode};
+  $OptionsInfo{CompoundIDLabel} = $Options{compoundidlabel};
+  $OptionsInfo{DataFieldsMode} = $Options{datafieldsmode};
+
+  my(@SpecifiedDataFields);
+  @SpecifiedDataFields = ();
+
+  @{$OptionsInfo{SpecifiedDataFields}} = ();
+  $OptionsInfo{CompoundID} = '';
+
+  if ($Options{datafieldsmode} =~ /^CompoundID$/i) {
+    if ($Options{compoundidmode} =~ /^DataField$/i) {
+      if (!$Options{compoundid}) {
+	die "Error: You must specify a value for \"--CompoundID\" option in \"DataField\" \"--CompoundIDMode\". \n";
+      }
+      $OptionsInfo{CompoundID} = $Options{compoundid};
+    }
+    elsif ($Options{compoundidmode} =~ /^(LabelPrefix|MolNameOrLabelPrefix)$/i) {
+      $OptionsInfo{CompoundID} = $Options{compoundid} ? $Options{compoundid} : 'Cmpd';
+    }
+  }
+  elsif ($Options{datafieldsmode} =~ /^Specify$/i) {
+    if (!$Options{datafields}) {
+      die "Error: You must specify a value for \"--DataFields\" option in \"Specify\" \"-d, --DataFieldsMode\". \n";
+    }
+    @SpecifiedDataFields = split /\,/, $Options{datafields};
+    push @{$OptionsInfo{SpecifiedDataFields}}, @SpecifiedDataFields;
+  }
+
+  if ($Options{atomidentifiertype} !~ /^AtomicInvariantsAtomTypes$/i) {
+    if ($Options{detectaromaticity} =~ /^No$/i) {
+      die "Error: The value specified, $Options{detectaromaticity}, for option \"--DetectAromaticity\" is not valid. No value is only allowed during AtomicInvariantsAtomTypes value for \"-a, --AtomIdentifierType\" \n";
+    }
+  }
+  $OptionsInfo{DetectAromaticity} = ($Options{detectaromaticity} =~ /^Yes$/i) ? 1 : 0;
+
+  $OptionsInfo{Filter} = ($Options{filter} =~ /^Yes$/i) ? 1 : 0;
+
+  $OptionsInfo{FingerprintsLabel} = $Options{fingerprintslabel} ? $Options{fingerprintslabel} : 'PathLengthFingerprints';
+
+  my($Size, $MinSize, $MaxSize);
+  $MinSize = 32;
+  $MaxSize = 2**32;
+  $Size = $Options{size};
+  if (!(IsPositiveInteger($Size) && $Size >= $MinSize && $Size <= $MaxSize && IsNumberPowerOfNumber($Size, 2))) {
+    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";
+  }
+  $OptionsInfo{Size} = $Size;
+
+  $OptionsInfo{Fold} = ($Options{fold} =~ /^Yes$/i) ? 1 : 0;
+  my($FoldedSize);
+  $FoldedSize = $Options{foldedsize};
+  if ($Options{fold} =~ /^Yes$/i) {
+    if (!(IsPositiveInteger($FoldedSize) && $FoldedSize < $Size && IsNumberPowerOfNumber($FoldedSize, 2))) {
+      die "Error: Invalid folded size value, $FoldedSize, for \"--FoldedSize\" option. Allowed values: power of 2, >= minimum size of $MinSize, and < size value of $Size.\n";
+    }
+  }
+  $OptionsInfo{FoldedSize} = $FoldedSize;
+
+  $OptionsInfo{IgnoreHydrogens} = ($Options{ignorehydrogens} =~ /^Yes$/i) ? 1 : 0;
+  $OptionsInfo{KeepLargestComponent} = ($Options{keeplargestcomponent} =~ /^Yes$/i) ? 1 : 0;
+
+  my($MinPathLength, $MaxPathLength);
+  $MinPathLength = $Options{minpathlength};
+  $MaxPathLength = $Options{maxpathlength};
+  if (!IsPositiveInteger($MinPathLength)) {
+    die "Error: Invalid path length value, $MinPathLength, for \"--MinPathLength\" option. Allowed values: > 0\n";
+  }
+  if (!IsPositiveInteger($MaxPathLength)) {
+    die "Error: Invalid path length value, $MaxPathLength, for \"--MinPathLength\" option. Allowed values: > 0\n";
+  }
+  if ($MinPathLength >= $MaxPathLength) {
+    die "Error: Invalid minimum and maximum path length values, $MinPathLength and $MaxPathLength, for \"--MinPathLength\"  and \"--MaxPathLength\"options. Allowed values: minimum path length value must be smaller than maximum path length value.\n";
+  }
+  $OptionsInfo{MinPathLength} = $MinPathLength;
+  $OptionsInfo{MaxPathLength} = $MaxPathLength;
+
+  my($NumOfBitsToSetPerPath);
+  $NumOfBitsToSetPerPath = $Options{numofbitstosetperpath};
+  if (!IsPositiveInteger($MaxPathLength)) {
+    die "Error: Invalid  value, $NumOfBitsToSetPerPath, for \"-n, --NumOfBitsToSetPerPath\" option. Allowed values: > 0\n";
+  }
+  if ($NumOfBitsToSetPerPath >= $Size) {
+    die "Error: Invalid  value, $NumOfBitsToSetPerPath, for \"-n, --NumOfBitsToSetPerPath\" option. Allowed values: It must be less than the size, $Size, of the fingerprint bit-string.\n";
+  }
+  $OptionsInfo{NumOfBitsToSetPerPath} = $NumOfBitsToSetPerPath;
+
+  $OptionsInfo{Output} = $Options{output};
+  $OptionsInfo{SDOutput} = ($Options{output} =~ /^(SD|All)$/i) ? 1 : 0;
+  $OptionsInfo{FPOutput} = ($Options{output} =~ /^(FP|All)$/i) ? 1 : 0;
+  $OptionsInfo{TextOutput} = ($Options{output} =~ /^(Text|All)$/i) ? 1 : 0;
+
+  $OptionsInfo{OutDelim} = $Options{outdelim};
+  $OptionsInfo{OutQuote} = ($Options{quote} =~ /^Yes$/i) ? 1 : 0;
+
+  $OptionsInfo{OverwriteFiles} = $Options{overwrite} ? 1 : 0;
+  $OptionsInfo{OutFileRoot} = $Options{root} ? $Options{root} : 0;
+
+  $OptionsInfo{UseBondSymbols} = ($Options{usebondsymbols} =~ /^Yes$/i) ? 1 : 0;
+
+  $OptionsInfo{UsePerlCoreRandom} = ($Options{useperlcorerandom} =~ /^Yes$/i) ? 1 : 0;
+
+  $OptionsInfo{UseUniquePaths} = ($Options{useuniquepaths} =~ /^Yes$/i) ? 1 : 0;
+
+  $OptionsInfo{VectorStringFormat} = $Options{vectorstringformat};
+
+  # Setup parameters used during generation of fingerprints by PathLengthFingerprints class...
+  my($AllowRings, $AllowSharedBonds);
+  $AllowRings = 1;
+  $AllowSharedBonds = 1;
+  MODE: {
+    if ($Options{pathmode} =~ /^AtomPathsWithoutRings$/i) { $AllowSharedBonds = 0; $AllowRings = 0; last MODE;}
+    if ($Options{pathmode} =~ /^AtomPathsWithRings$/i) { $AllowSharedBonds = 0; $AllowRings = 1; last MODE;}
+    if ($Options{pathmode} =~ /^AllAtomPathsWithoutRings$/i) { $AllowSharedBonds = 1; $AllowRings = 0; last MODE;}
+    if ($Options{pathmode} =~ /^AllAtomPathsWithRings$/i) { $AllowSharedBonds = 1; $AllowRings = 1; last MODE;}
+    die "Error: ProcessOptions: mode value, $Options{pathmode}, is not supported.\n";
+  }
+  $OptionsInfo{AllowRings} = $AllowRings;
+  $OptionsInfo{AllowSharedBonds} = $AllowSharedBonds;
+}
+
+# Process atom identifier type and related options...
+#
+sub ProcessAtomIdentifierTypeOptions {
+
+  $OptionsInfo{AtomIdentifierType} = $Options{atomidentifiertype};
+
+  if ($Options{atomidentifiertype} =~ /^AtomicInvariantsAtomTypes$/i) {
+    ProcessAtomicInvariantsToUseOption();
+  }
+  elsif ($Options{atomidentifiertype} =~ /^FunctionalClassAtomTypes$/i) {
+    ProcessFunctionalClassesToUse();
+  }
+  elsif ($OptionsInfo{AtomIdentifierType} =~ /^(DREIDINGAtomTypes|EStateAtomTypes|MMFF94AtomTypes|SLogPAtomTypes|SYBYLAtomTypes|TPSAAtomTypes|UFFAtomTypes)$/i) {
+    # Nothing to do for now...
+  }
+  else {
+    die "Error: The value specified, $Options{atomidentifiertype}, for option \"-a, --AtomIdentifierType\" is not valid. Supported atom identifier types in current release of MayaChemTools: AtomicInvariantsAtomTypes, DREIDINGAtomTypes, EStateAtomTypes, FunctionalClassAtomTypes, MMFF94AtomTypes, SLogPAtomTypes, SYBYLAtomTypes, TPSAAtomTypes, UFFAtomTypes\n";
+  }
+}
+
+# Process specified atomic invariants to use...
+#
+sub ProcessAtomicInvariantsToUseOption {
+  my($AtomicInvariant, $AtomSymbolSpecified, @AtomicInvariantsWords);
+
+  @{$OptionsInfo{AtomicInvariantsToUse}} = ();
+  if (IsEmpty($Options{atomicinvariantstouse})) {
+    die "Error: Atomic invariants value specified using \"--AtomicInvariantsToUse\" option is empty\n";
+  }
+  $AtomSymbolSpecified = 0;
+  @AtomicInvariantsWords = split /\,/, $Options{atomicinvariantstouse};
+  for $AtomicInvariant (@AtomicInvariantsWords) {
+    if (!AtomTypes::AtomicInvariantsAtomTypes::IsAtomicInvariantAvailable($AtomicInvariant)) {
+      die "Error: Atomic invariant specified, $AtomicInvariant, using \"--AtomicInvariantsToUse\" option is not valid...\n ";
+    }
+    if ($AtomicInvariant =~ /^(AS|AtomSymbol)$/i) {
+      $AtomSymbolSpecified = 1;
+    }
+    push @{$OptionsInfo{AtomicInvariantsToUse}}, $AtomicInvariant;
+  }
+  if (!$AtomSymbolSpecified) {
+    die "Error: Atomic invariant, AS or AtomSymbol, must be specified as using \"--AtomicInvariantsToUse\" option...\n ";
+  }
+}
+
+# Process specified functional classes invariants to use...
+#
+sub ProcessFunctionalClassesToUse {
+  my($FunctionalClass, @FunctionalClassesToUseWords);
+
+  @{$OptionsInfo{FunctionalClassesToUse}} = ();
+  if (IsEmpty($Options{functionalclassestouse})) {
+    die "Error: Functional classes value specified using \"--FunctionalClassesToUse\" option is empty\n";
+  }
+  @FunctionalClassesToUseWords = split /\,/, $Options{functionalclassestouse};
+  for $FunctionalClass (@FunctionalClassesToUseWords) {
+    if (!AtomTypes::FunctionalClassAtomTypes::IsFunctionalClassAvailable($FunctionalClass)) {
+      die "Error: Functional class specified, $FunctionalClass, using \"--FunctionalClassesToUse\" option is not valid...\n ";
+    }
+    push @{$OptionsInfo{FunctionalClassesToUse}}, $FunctionalClass;
+  }
+}
+
+# Setup script usage  and retrieve command line arguments specified using various options...
+sub SetupScriptUsage {
+
+  # Retrieve all the options...
+  %Options = ();
+
+  $Options{aromaticitymodel} = 'MayaChemToolsAromaticityModel';
+
+  $Options{atomidentifiertype} = 'AtomicInvariantsAtomTypes';
+  $Options{atomicinvariantstouse} = 'AS';
+
+  $Options{functionalclassestouse} = 'HBD,HBA,PI,NI,Ar,Hal';
+
+  $Options{bitsorder} = 'Ascending';
+  $Options{bitstringformat} = 'HexadecimalString';
+
+  $Options{compoundidmode} = 'LabelPrefix';
+  $Options{compoundidlabel} = 'CompoundID';
+  $Options{datafieldsmode} = 'CompoundID';
+  $Options{detectaromaticity} = 'Yes';
+
+  $Options{filter} = 'Yes';
+
+  $Options{fold} = 'No';
+  $Options{foldedsize} = 256;
+
+  $Options{ignorehydrogens} = 'Yes';
+  $Options{keeplargestcomponent} = 'Yes';
+
+  $Options{mode} = 'PathLengthBits';
+  $Options{pathmode} = 'AllAtomPathsWithRings';
+
+  $Options{minpathlength} = 1;
+  $Options{maxpathlength} = 8;
+
+  $Options{numofbitstosetperpath} = 1;
+
+  $Options{output} = 'text';
+  $Options{outdelim} = 'comma';
+  $Options{quote} = 'yes';
+
+  $Options{size} = 1024;
+
+  $Options{usebondsymbols} = 'yes';
+  $Options{useperlcorerandom} = 'yes';
+  $Options{useuniquepaths} = 'yes';
+
+  $Options{vectorstringformat} = 'IDsAndValuesString';
+
+  if (!GetOptions(\%Options, "aromaticitymodel=s", "atomidentifiertype|a=s", "atomicinvariantstouse=s", "functionalclassestouse=s", "bitsorder=s", "bitstringformat|b=s", "compoundid=s", "compoundidlabel=s", "compoundidmode=s", "datafields=s", "datafieldsmode|d=s", "detectaromaticity=s", "filter|f=s", "fingerprintslabel=s", "fold=s", "foldedsize=i", "help|h", "ignorehydrogens|i=s", "keeplargestcomponent|k=s", "mode|m=s", "minpathlength=i", "maxpathlength=i", "numofbitstosetperpath|n=i", "outdelim=s", "output=s", "overwrite|o", "pathmode|p=s", "quote|q=s", "root|r=s", "size|s=i", "usebondsymbols|u=s", "useperlcorerandom=s", "useuniquepaths=s", "vectorstringformat|v=s", "workingdir|w=s")) {
+    die "\nTo get a list of valid options and their values, use \"$ScriptName -h\" or\n\"perl -S $ScriptName -h\" command and try again...\n";
+  }
+  if ($Options{workingdir}) {
+    if (! -d $Options{workingdir}) {
+      die "Error: The value specified, $Options{workingdir}, for option \"-w --workingdir\" is not a directory name.\n";
+    }
+    chdir $Options{workingdir} or die "Error: Couldn't chdir $Options{workingdir}: $! \n";
+  }
+  if (!Molecule::IsSupportedAromaticityModel($Options{aromaticitymodel})) {
+    my(@SupportedModels) = Molecule::GetSupportedAromaticityModels();
+    die "Error: The value specified, $Options{aromaticitymodel}, for option \"--AromaticityModel\" is not valid. Supported aromaticity models in current release of MayaChemTools: @SupportedModels\n";
+  }
+  if ($Options{atomidentifiertype} !~ /^(AtomicInvariantsAtomTypes|DREIDINGAtomTypes|EStateAtomTypes|FunctionalClassAtomTypes|MMFF94AtomTypes|SLogPAtomTypes|SYBYLAtomTypes|TPSAAtomTypes|UFFAtomTypes)$/i) {
+    die "Error: The value specified, $Options{atomidentifiertype}, for option \"-a, --AtomIdentifierType\" is not valid. Supported atom identifier types in current release of MayaChemTools: AtomicInvariantsAtomTypes, DREIDINGAtomTypes, EStateAtomTypes, FunctionalClassAtomTypes, MMFF94AtomTypes, SLogPAtomTypes, SYBYLAtomTypes, TPSAAtomTypes, UFFAtomTypes\n";
+  }
+  if ($Options{bitsorder} !~ /^(Ascending|Descending)$/i) {
+    die "Error: The value specified, $Options{bitsorder}, for option \"--BitsOrder\" is not valid. Allowed values: Ascending or Descending\n";
+  }
+  if ($Options{bitstringformat} !~ /^(BinaryString|HexadecimalString)$/i) {
+    die "Error: The value specified, $Options{bitstringformat}, for option \"-b, --bitstringformat\" is not valid. Allowed values: BinaryString or HexadecimalString\n";
+  }
+  if ($Options{compoundidmode} !~ /^(DataField|MolName|LabelPrefix|MolNameOrLabelPrefix)$/i) {
+    die "Error: The value specified, $Options{compoundidmode}, for option \"--CompoundIDMode\" is not valid. Allowed values: DataField, MolName, LabelPrefix or MolNameOrLabelPrefix\n";
+  }
+  if ($Options{datafieldsmode} !~ /^(All|Common|Specify|CompoundID)$/i) {
+    die "Error: The value specified, $Options{datafieldsmode}, for option \"-d, --DataFieldsMode\" is not valid. Allowed values: All, Common, Specify or CompoundID\n";
+  }
+  if ($Options{detectaromaticity} !~ /^(Yes|No)$/i) {
+    die "Error: The value specified, $Options{detectaromaticity}, for option \"--DetectAromaticity\" is not valid. Allowed values: Yes or No\n";
+  }
+  if ($Options{filter} !~ /^(Yes|No)$/i) {
+    die "Error: The value specified, $Options{filter}, for option \"-f, --Filter\" is not valid. Allowed values: Yes or No\n";
+  }
+  if ($Options{fold} !~ /^(Yes|No)$/i) {
+    die "Error: The value specified, $Options{fold}, for option \"--fold\" is not valid. Allowed values: Yes or No\n";
+  }
+  if (!IsPositiveInteger($Options{foldedsize})) {
+    die "Error: The value specified, $Options{foldedsize}, for option \"--FoldedSize\" is not valid. Allowed values: > 0 \n";
+  }
+  if ($Options{ignorehydrogens} !~ /^(Yes|No)$/i) {
+    die "Error: The value specified, $Options{ignorehydrogens}, for option \"-i, --IgnoreHydrogens\" is not valid. Allowed values: Yes or No\n";
+  }
+  if ($Options{keeplargestcomponent} !~ /^(Yes|No)$/i) {
+    die "Error: The value specified, $Options{keeplargestcomponent}, for option \"-k, --KeepLargestComponent\" is not valid. Allowed values: Yes or No\n";
+  }
+  if ($Options{mode} !~ /^(PathLengthBits|PathLengthCount)$/i) {
+    die "Error: The value specified, $Options{mode}, for option \"-m, --mode\" is not valid. Allowed values: PathLengthBits or PathLengthCount\n";
+  }
+  if (!IsPositiveInteger($Options{minpathlength})) {
+    die "Error: The value specified, $Options{minpathlength}, for option \"--MinPathLength\" is not valid. Allowed values: > 0 \n";
+  }
+  if (!IsPositiveInteger($Options{numofbitstosetperpath})) {
+    die "Error: The value specified, $Options{NumOfBitsToSetPerPath}, for option \"--NumOfBitsToSetPerPath\" is not valid. Allowed values: > 0 \n";
+  }
+  if (!IsPositiveInteger($Options{maxpathlength})) {
+    die "Error: The value specified, $Options{maxpathlength}, for option \"--MaxPathLength\" is not valid. Allowed values: > 0 \n";
+  }
+  if ($Options{output} !~ /^(SD|FP|text|all)$/i) {
+    die "Error: The value specified, $Options{output}, for option \"--output\" is not valid. Allowed values: SD, FP, text, or all\n";
+  }
+  if ($Options{outdelim} !~ /^(comma|semicolon|tab)$/i) {
+    die "Error: The value specified, $Options{outdelim}, for option \"--outdelim\" is not valid. Allowed values: comma, tab, or semicolon\n";
+  }
+  if ($Options{pathmode} !~ /^(AtomPathsWithoutRings|AtomPathsWithRings|AllAtomPathsWithoutRings|AllAtomPathsWithRings)$/i) {
+    die "Error: The value specified, $Options{pathmode}, for option \"-m, --PathMode\" is not valid. Allowed values: AtomPathsWithoutRings, AtomPathsWithRings, AllAtomPathsWithoutRings or AllAtomPathsWithRings\n";
+  }
+  if ($Options{quote} !~ /^(Yes|No)$/i) {
+    die "Error: The value specified, $Options{quote}, for option \"-q --quote\" is not valid. Allowed values: Yes or No\n";
+  }
+  if ($Options{outdelim} =~ /semicolon/i && $Options{quote} =~ /^No$/i) {
+    die "Error: The value specified, $Options{quote}, for option \"-q --quote\" is not allowed with, semicolon value of \"--outdelim\" option: Fingerprints string use semicolon as delimiter for various data fields and must be quoted.\n";
+  }
+
+  if (!IsPositiveInteger($Options{size})) {
+    die "Error: The value specified, $Options{size}, for option \"-s, --size\" is not valid. Allowed values: > 0 \n";
+  }
+  if ($Options{usebondsymbols} !~ /^(Yes|No)$/i) {
+    die "Error: The value specified, $Options{usebondsymbols}, for option \"-u, --UseBondSymbols\" is not valid. Allowed values: Yes or No\n";
+  }
+  if ($Options{useperlcorerandom} !~ /^(Yes|No)$/i) {
+    die "Error: The value specified, $Options{useperlcorerandom}, for option \"--UsePerlCoreRandom\" is not valid. Allowed values: Yes or No\n";
+  }
+  if ($Options{useuniquepaths} !~ /^(Yes|No)$/i) {
+    die "Error: The value specified, $Options{useuniquepaths}, for option \"--UseUniquePaths\" is not valid. Allowed values: Yes or No\n";
+  }
+  if ($Options{vectorstringformat} !~ /^(IDsAndValuesString|IDsAndValuesPairsString|ValuesAndIDsString|ValuesAndIDsPairsString)$/i) {
+    die "Error: The value specified, $Options{vectorstringformat}, for option \"-v, --VectorStringFormat\" is not valid. Allowed values: IDsAndValuesString, IDsAndValuesPairsString, ValuesAndIDsString or ValuesAndIDsPairsString\n";
+  }
+}
+
+__END__
+
+=head1 NAME
+
+PathLengthFingerprints.pl - Generate atom path length based fingerprints for SD files
+
+=head1 SYNOPSIS
+
+PathLengthFingerprints.pl SDFile(s)...
+
+PathLengthFingerprints.pl [B<--AromaticityModel> I<AromaticityModelType>]
+[B<-a, --AtomIdentifierType> I<AtomicInvariantsAtomTypes>]
+[B<--AtomicInvariantsToUse> I<"AtomicInvariant1,AtomicInvariant2...">]
+[B<--FunctionalClassesToUse> I<"FunctionalClass1,FunctionalClass2...">]
+[B<--BitsOrder> I<Ascending | Descending>] [B<-b, --BitStringFormat> I<BinaryString | HexadecimalString>]
+[B<--CompoundID> I<DataFieldName or LabelPrefixString>] [B<--CompoundIDLabel> I<text>]
+[B<--CompoundIDMode> I<DataField | MolName | LabelPrefix | MolNameOrLabelPrefix>]
+[B<--DataFields> I<"FieldLabel1,FieldLabel2,... ">] [B<-d, --DataFieldsMode> I<All | Common | Specify | CompoundID>]
+[B<--DetectAromaticity> I<Yes | No>]  [B<-f, --Filter> I<Yes | No>] [B<--FingerprintsLabel> I<text>]
+[B<--fold> I<Yes | No>] [B<--FoldedSize> I<number>] [B<-h, --help>]
+[B<-i, --IgnoreHydrogens> I<Yes | No>] [B<-k, --KeepLargestComponent> I<Yes | No>]
+[B<-m, --mode> I<PathLengthBits | PathLengthCount>]
+[B<--MinPathLength> I<number>] [B<--MaxPathLength> I<number>] [B<-n, --NumOfBitsToSetPerPath> I<number>]
+[B<--OutDelim> I<comma | tab | semicolon>]
+[B<--output> I<SD | FP | text | all>] [B<-q, --quote> I<Yes | No>] [B<-r, --root> I<RootName>]
+[B<-p, --PathMode> I<AtomPathsWithoutRings | AtomPathsWithRings | AllAtomPathsWithoutRings | AllAtomPathsWithRings>]
+[B<-s, --size> I<number>] [B<-u, --UseBondSymbols> I<Yes | No>] [B<--UsePerlCoreRandom> I<Yes | No>]
+[B<--UseUniquePaths> I<Yes | No>] [B<-q, --quote> I<Yes | No>] [B<-r, --root> I<RootName>]
+[B<-v, --VectorStringFormat> I<IDsAndValuesString | IDsAndValuesPairsString | ValuesAndIDsString | ValuesAndIDsPairsString>]
+[B<-w, --WorkingDir> dirname] SDFile(s)...
+
+=head1 DESCRIPTION
+
+Generate atom path length fingerprints for I<SDFile(s)> and create appropriate SD, FP or
+CSV/TSV text file(s) containing fingerprints bit-vector or vector strings corresponding to
+molecular fingerprints.
+
+Multiple SDFile names are separated by spaces. The valid file extensions are I<.sdf>
+and I<.sd>. All other file names are ignored. All the SD files in a current directory
+can be specified either by I<*.sdf> or the current directory name.
+
+The current release of MayaChemTools supports generation of path length fingerprints
+corresponding to following B<-a, --AtomIdentifierTypes>:
+
+    AtomicInvariantsAtomTypes, DREIDINGAtomTypes, EStateAtomTypes,
+    FunctionalClassAtomTypes, MMFF94AtomTypes, SLogPAtomTypes,
+    SYBYLAtomTypes, TPSAAtomTypes, UFFAtomTypes
+
+Based on the values specified for B<-p, --PathMode>, B<--MinPathLength> and B<--MaxPathLength>,
+all appropriate atom paths are generated for each atom in the molecule and collected in a list and
+the list is filtered to remove any structurally duplicate paths as indicated by the value of
+B<--UseUniquePaths> option.
+
+For each atom path in the filtered atom paths list, an atom path string is created using value of
+B<-a, --AtomIdentifierType> and specified values to use for a particular atom identifier type.
+Value of B<-u, --UseBondSymbols> controls whether bond order symbols are used during generation
+of atom path string. For each atom path, only lexicographically smaller atom path strings are kept.
+
+For I<PathLengthBits> value of B<-m, --mode> option, each atom path is hashed to a 32 bit unsigned
+integer key using B<TextUtil::HashCode> function. Using the hash key as a seed for a random number
+generator, a random integer value between 0 and B<--Size> is used to set corresponding bits
+in the fingerprint bit-vector string. Value of B<--NumOfBitsToSetPerPath> option controls the number
+of time a random number is generated to set corresponding bits.
+
+For I< PathLengthCount> value of B<-m, --mode> option, the number of times an atom path appears
+is tracked and a fingerprints count-string corresponding to count of atom paths is generated.
+
+Example of I<SD> file containing path length fingerprints string data:
+
+    ... ...
+    ... ...
+    $$$$
+    ... ...
+    ... ...
+    ... ...
+    41 44  0  0  0  0  0  0  0  0999 V2000
+     -3.3652    1.4499    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
+    ... ...
+    2  3  1  0  0  0  0
+    ... ...
+    M  END
+    >  <CmpdID>
+    Cmpd1
+
+    >  <PathLengthFingerprints>
+    FingerprintsBitVector;PathLengthBits:AtomicInvariantsAtomTypes:MinLengt
+    h1:MaxLength8;1024;HexadecimalString;Ascending;9c8460989ec8a49913991a66
+    03130b0a19e8051c89184414953800cc2151082844a201042800130860308e8204d4028
+    00831048940e44281c00060449a5000ac80c894114e006321264401600846c050164462
+    08190410805000304a10205b0100e04c0038ba0fad0209c0ca8b1200012268b61c0026a
+    aa0660a11014a011d46
+
+    $$$$
+    ... ...
+    ... ...
+
+Example of I<FP> file containing path length fingerprints string data:
+
+    #
+    # Package = MayaChemTools 7.4
+    # ReleaseDate = Oct 21, 2010
+    #
+    # TimeStamp =  Mon Mar 7 15:14:01 2011
+    #
+    # FingerprintsStringType = FingerprintsBitVector
+    #
+    # Description = PathLengthBits:AtomicInvariantsAtomTypes:MinLength1:...
+    # Size = 1024
+    # BitStringFormat = HexadecimalString
+    # BitsOrder = Ascending
+    #
+    Cmpd1 9c8460989ec8a49913991a6603130b0a19e8051c89184414953800cc21510...
+    Cmpd2 000000249400840040100042011001001980410c000000001010088001120...
+    ... ...
+    ... ..
+
+Example of CSV I<Text> file containing pathlength fingerprints string data:
+
+    "CompoundID","PathLengthFingerprints"
+    "Cmpd1","FingerprintsBitVector;PathLengthBits:AtomicInvariantsAtomTypes
+    :MinLength1:MaxLength8;1024;HexadecimalString;Ascending;9c8460989ec8a4
+    9913991a6603130b0a19e8051c89184414953800cc2151082844a20104280013086030
+    8e8204d402800831048940e44281c00060449a5000ac80c894114e006321264401..."
+    ... ...
+    ... ...
+
+The current release of MayaChemTools generates the following types of path length
+fingerprints bit-vector and vector strings:
+
+    FingerprintsBitVector;PathLengthBits:AtomicInvariantsAtomTypes:MinLeng
+    th1:MaxLength8;1024;BinaryString;Ascending;001000010011010101011000110
+    0100010101011000101001011100110001000010001001101000001001001001001000
+    0010110100000111001001000001001010100100100000000011000000101001011100
+    0010000001000101010100000100111100110111011011011000000010110111001101
+    0101100011000000010001000011000010100011101100001000001000100000000...
+
+    FingerprintsBitVector;PathLengthBits:AtomicInvariantsAtomTypes:MinLeng
+    th1:MaxLength8;1024;HexadecimalString;Ascending;48caa1315d82d91122b029
+    42861c9409a4208182d12015509767bd0867653604481a8b1288000056090583603078
+    9cedae54e26596889ab121309800900490515224208421502120a0dd9200509723ae89
+    00024181b86c0122821d4e4880c38620dab280824b455404009f082003d52c212b4e6d
+    6ea05280140069c780290c43
+
+    FingerprintsVector;PathLengthCount:AtomicInvariantsAtomTypes:MinLength
+    1:MaxLength8;432;NumericalValues;IDsAndValuesPairsString;C.X1.BO1.H3 2
+    C.X2.BO2.H2 4 C.X2.BO3.H1 14 C.X3.BO3.H1 3 C.X3.BO4 10 F.X1.BO1 1 N.X
+    2.BO2.H1 1 N.X3.BO3 1 O.X1.BO1.H1 3 O.X1.BO2 2 C.X1.BO1.H3C.X3.BO3.H1
+    2 C.X2.BO2.H2C.X2.BO2.H2 1 C.X2.BO2.H2C.X3.BO3.H1 4 C.X2.BO2.H2C.X3.BO
+    4 1 C.X2.BO2.H2N.X3.BO3 1 C.X2.BO3.H1:C.X2.BO3.H1 10 C.X2.BO3.H1:C....
+
+    FingerprintsVector;PathLengthCount:DREIDINGAtomTypes:MinLength1:MaxLen
+    gth8;410;NumericalValues;IDsAndValuesPairsString;C_2 2 C_3 9 C_R 22 F_
+    1 N_3 1 N_R 1 O_2 2 O_3 3 C_2=O_2 2 C_2C_3 1 C_2C_R 1 C_2N_3 1 C_2O_3
+    1 C_3C_3 7 C_3C_R 1 C_3N_R 1 C_3O_3 2 C_R:C_R 21 C_R:N_R 2 C_RC_R 2 C
+    _RF_ 1 C_RN_3 1 C_2C_3C_3 1 C_2C_R:C_R 2 C_2N_3C_R 1 C_3C_2=O_2 1 C_3C
+    _2O_3 1 C_3C_3C_3 5 C_3C_3C_R 2 C_3C_3N_R 1 C_3C_3O_3 4 C_3C_R:C_R ...
+
+    FingerprintsVector;PathLengthCount:EStateAtomTypes:MinLength1:MaxLengt
+    h8;454;NumericalValues;IDsAndValuesPairsString;aaCH 14 aasC 8 aasN 1 d
+    O 2 dssC 2 sCH3 2 sF 1 sOH 3 ssCH2 4 ssNH 1 sssCH 3 aaCH:aaCH 10 aaCH:
+    aasC 8 aasC:aasC 3 aasC:aasN 2 aasCaasC 2 aasCdssC 1 aasCsF 1 aasCssNH
+    1 aasCsssCH 1 aasNssCH2 1 dO=dssC 2 dssCsOH 1 dssCssCH2 1 dssCssNH 1
+    sCH3sssCH 2 sOHsssCH 2 ssCH2ssCH2 1 ssCH2sssCH 4 aaCH:aaCH:aaCH 6 a...
+
+    FingerprintsVector;PathLengthCount:FunctionalClassAtomTypes:MinLength1
+    :MaxLength8;404;NumericalValues;IDsAndValuesPairsString;Ar 22 Ar.HBA 1
+    HBA 2 HBA.HBD 3 HBD 1 Hal 1 NI 1 None 10 Ar.HBA:Ar 2 Ar.HBANone 1 Ar:
+    Ar 21 ArAr 2 ArHBD 1 ArHal 1 ArNone 2 HBA.HBDNI 1 HBA.HBDNone 2 HBA=NI
+    1 HBA=None 1 HBDNone 1 NINone 1 NoneNone 7 Ar.HBA:Ar:Ar 2 Ar.HBA:ArAr
+    1 Ar.HBA:ArNone 1 Ar.HBANoneNone 1 Ar:Ar.HBA:Ar 1 Ar:Ar.HBANone 2 ...
+
+    FingerprintsVector;PathLengthCount:MMFF94AtomTypes:MinLength1:MaxLengt
+    h8;463;NumericalValues;IDsAndValuesPairsString;C5A 2 C5B 2 C=ON 1 CB 1
+    8 COO 1 CR 9 F 1 N5 1 NC=O 1 O=CN 1 O=CO 1 OC=O 1 OR 2 C5A:C5B 2 C5A:N
+    5 2 C5ACB 1 C5ACR 1 C5B:C5B 1 C5BC=ON 1 C5BCB 1 C=ON=O=CN 1 C=ONNC=O 1
+    CB:CB 18 CBF 1 CBNC=O 1 COO=O=CO 1 COOCR 1 COOOC=O 1 CRCR 7 CRN5 1 CR
+    OR 2 C5A:C5B:C5B 2 C5A:C5BC=ON 1 C5A:C5BCB 1 C5A:N5:C5A 1 C5A:N5CR ...
+
+    FingerprintsVector;PathLengthCount:SLogPAtomTypes:MinLength1:MaxLength
+    8;518;NumericalValues;IDsAndValuesPairsString;C1 5 C10 1 C11 1 C14 1 C
+    18 14 C20 4 C21 2 C22 1 C5 2 CS 2 F 1 N11 1 N4 1 O10 1 O2 3 O9 1 C10C1
+    1 C10N11 1 C11C1 2 C11C21 1 C14:C18 2 C14F 1 C18:C18 10 C18:C20 4 C18
+    :C22 2 C1C5 1 C1CS 4 C20:C20 1 C20:C21 1 C20:N11 1 C20C20 2 C21:C21 1
+    C21:N11 1 C21C5 1 C22N4 1 C5=O10 1 C5=O9 1 C5N4 1 C5O2 1 CSO2 2 C10...
+
+    FingerprintsVector;PathLengthCount:SYBYLAtomTypes:MinLength1:MaxLength
+    8;412;NumericalValues;IDsAndValuesPairsString;C.2 2 C.3 9 C.ar 22 F 1
+    N.am 1 N.ar 1 O.2 1 O.3 2 O.co2 2 C.2=O.2 1 C.2=O.co2 1 C.2C.3 1 C.2C.
+    ar 1 C.2N.am 1 C.2O.co2 1 C.3C.3 7 C.3C.ar 1 C.3N.ar 1 C.3O.3 2 C.ar:C
+    .ar 21 C.ar:N.ar 2 C.arC.ar 2 C.arF 1 C.arN.am 1 C.2C.3C.3 1 C.2C.ar:C
+    .ar 2 C.2N.amC.ar 1 C.3C.2=O.co2 1 C.3C.2O.co2 1 C.3C.3C.3 5 C.3C.3...
+
+    FingerprintsVector;PathLengthCount:TPSAAtomTypes:MinLength1:MaxLength8
+    ;331;NumericalValues;IDsAndValuesPairsString;N21 1 N7 1 None 34 O3 2 O
+    4 3 N21:None 2 N21None 1 N7None 2 None:None 21 None=O3 2 NoneNone 13 N
+    oneO4 3 N21:None:None 2 N21:NoneNone 2 N21NoneNone 1 N7None:None 2 N7N
+    one=O3 1 N7NoneNone 1 None:N21:None 1 None:N21None 2 None:None:None 20
+    None:NoneNone 12 NoneN7None 1 NoneNone=O3 2 NoneNoneNone 8 NoneNon...
+
+    FingerprintsVector;PathLengthCount:UFFAtomTypes:MinLength1:MaxLength8;
+    410;NumericalValues;IDsAndValuesPairsString;C_2 2 C_3 9 C_R 22 F_ 1 N_
+    3 1 N_R 1 O_2 2 O_3 3 C_2=O_2 2 C_2C_3 1 C_2C_R 1 C_2N_3 1 C_2O_3 1 C_
+    3C_3 7 C_3C_R 1 C_3N_R 1 C_3O_3 2 C_R:C_R 21 C_R:N_R 2 C_RC_R 2 C_RF_
+    1 C_RN_3 1 C_2C_3C_3 1 C_2C_R:C_R 2 C_2N_3C_R 1 C_3C_2=O_2 1 C_3C_2O_3
+    1 C_3C_3C_3 5 C_3C_3C_R 2 C_3C_3N_R 1 C_3C_3O_3 4 C_3C_R:C_R 1 C_3...
+
+=head1 OPTIONS
+
+=over 4
+
+=item B<--AromaticityModel> I<MDLAromaticityModel | TriposAromaticityModel | MMFFAromaticityModel | ChemAxonBasicAromaticityModel | ChemAxonGeneralAromaticityModel | DaylightAromaticityModel | MayaChemToolsAromaticityModel>
+
+Specify aromaticity model to use during detection of aromaticity. Possible values in the current
+release are: I<MDLAromaticityModel, TriposAromaticityModel, MMFFAromaticityModel,
+ChemAxonBasicAromaticityModel, ChemAxonGeneralAromaticityModel, DaylightAromaticityModel
+or MayaChemToolsAromaticityModel>. Default value: I<MayaChemToolsAromaticityModel>.
+
+The supported aromaticity model names along with model specific control parameters
+are defined in B<AromaticityModelsData.csv>, which is distributed with the current release
+and is available under B<lib/data> directory. B<Molecule.pm> module retrieves data from
+this file during class instantiation and makes it available to method B<DetectAromaticity>
+for detecting aromaticity corresponding to a specific model.
+
+This option is ignored during I<No> value of B<--DetectAromaticity> option.
+
+=item B<-a, --AtomIdentifierType> I<AtomicInvariantsAtomTypes | DREIDINGAtomTypes | EStateAtomTypes | FunctionalClassAtomTypes | MMFF94AtomTypes | SLogPAtomTypes | SYBYLAtomTypes | TPSAAtomTypes | UFFAtomTypes>
+
+Specify atom identifier type to use for assignment of atom types to hydrogen and/or
+non-hydrogen atoms during calculation of atom types fingerprints. Possible values in the
+current release are: I<AtomicInvariantsAtomTypes, DREIDINGAtomTypes, EStateAtomTypes,
+FunctionalClassAtomTypes, MMFF94AtomTypes, SLogPAtomTypes, SYBYLAtomTypes,
+TPSAAtomTypes, UFFAtomTypes>. Default value: I<AtomicInvariantsAtomTypes>.
+
+=item B<-a, --AtomIdentifierType> I<AtomicInvariantsAtomTypes | DREIDINGAtomTypes | EStateAtomTypes | FunctionalClassAtomTypes | MMFF94AtomTypes | SLogPAtomTypes | SYBYLAtomTypes | TPSAAtomTypes | UFFAtomTypes>
+
+Specify atom identifier type to use during generation of atom path strings
+corresponding to path length fingerprints. Possible values in the current release are:
+I<AtomicInvariantsAtomTypes, DREIDINGAtomTypes, EStateAtomTypes,
+FunctionalClassAtomTypes, MMFF94AtomTypes, SLogPAtomTypes, SYBYLAtomTypes,
+TPSAAtomTypes, UFFAtomTypes>. Default value: I<AtomicInvariantsAtomTypes>.
+
+=item B<--AtomicInvariantsToUse> I<"AtomicInvariant1,AtomicInvariant2...">
+
+This value is used during I<AtomicInvariantsAtomTypes> value of B<a, --AtomIdentifierType>
+option. It's a list of comma separated valid atomic invariant atom types.
+
+Possible values for atomic invariants are: I<AS, X, BO,  LBO, SB, DB, TB,
+H, Ar, RA, FC, MN, SM>. Default value: I<AS>.
+
+The atomic invariants abbreviations correspond to:
+
+    AS = Atom symbol corresponding to element symbol
+
+    X<n>   = Number of non-hydrogen atom neighbors or heavy atoms
+    BO<n> = Sum of bond orders to non-hydrogen atom neighbors or heavy atoms
+    LBO<n> = Largest bond order of non-hydrogen atom neighbors or heavy atoms
+    SB<n> = Number of single bonds to non-hydrogen atom neighbors or heavy atoms
+    DB<n> = Number of double bonds to non-hydrogen atom neighbors or heavy atoms
+    TB<n> = Number of triple bonds to non-hydrogen atom neighbors or heavy atoms
+    H<n>   = Number of implicit and explicit hydrogens for atom
+    Ar     = Aromatic annotation indicating whether atom is aromatic
+    RA     = Ring atom annotation indicating whether atom is a ring
+    FC<+n/-n> = Formal charge assigned to atom
+    MN<n> = Mass number indicating isotope other than most abundant isotope
+    SM<n> = Spin multiplicity of atom. Possible values: 1 (singlet), 2 (doublet) or
+            3 (triplet)
+
+Atom type generated by AtomTypes::AtomicInvariantsAtomTypes class corresponds to:
+
+    AS.X<n>.BO<n>.LBO<n>.<SB><n>.<DB><n>.<TB><n>.H<n>.Ar.RA.FC<+n/-n>.MN<n>.SM<n>
+
+Except for AS which is a required atomic invariant in atom types, all other atomic invariants are
+optional. Atom type specification doesn't include atomic invariants with zero or undefined values.
+
+In addition to usage of abbreviations for specifying atomic invariants, the following descriptive words
+are also allowed:
+
+    X : NumOfNonHydrogenAtomNeighbors or NumOfHeavyAtomNeighbors
+    BO : SumOfBondOrdersToNonHydrogenAtoms or SumOfBondOrdersToHeavyAtoms
+    LBO : LargestBondOrderToNonHydrogenAtoms or LargestBondOrderToHeavyAtoms
+    SB :  NumOfSingleBondsToNonHydrogenAtoms or NumOfSingleBondsToHeavyAtoms
+    DB : NumOfDoubleBondsToNonHydrogenAtoms or NumOfDoubleBondsToHeavyAtoms
+    TB : NumOfTripleBondsToNonHydrogenAtoms or NumOfTripleBondsToHeavyAtoms
+    H :  NumOfImplicitAndExplicitHydrogens
+    Ar : Aromatic
+    RA : RingAtom
+    FC : FormalCharge
+    MN : MassNumber
+    SM : SpinMultiplicity
+
+Examples:
+
+B<Benzene>: Using value of I<AS> for B<--AtomicInvariantsToUse>, I<Yes> for B<UseBondSymbols>,
+and I< AllAtomPathsWithRings> for B<-p, --PathMode>, atom path strings generated are:
+
+    C C:C C:C:C C:C:C:C C:C:C:C:C C:C:C:C:C:C C:C:C:C:C:C:C
+
+And using I<AS,X,BO> for B<--AtomicInvariantsToUse> generates following atom path
+strings:
+
+    C.X2.BO3 C.X2.BO3:C.X2.BO3 C.X2.BO3:C.X2.BO3:C.X2.BO3
+    C.X2.BO3:C.X2.BO3:C.X2.BO3:C.X2.BO3
+    C.X2.BO3:C.X2.BO3:C.X2.BO3:C.X2.BO3:C.X2.BO3
+    C.X2.BO3:C.X2.BO3:C.X2.BO3:C.X2.BO3:C.X2.BO3:C.X2.BO3
+    C.X2.BO3:C.X2.BO3:C.X2.BO3:C.X2.BO3:C.X2.BO3:C.X2.BO3:C.X2.BO3
+
+B<Urea>: Using value of I<AS> for B<--AtomicInvariantsToUse>, I<Yes> for B<UseBondSymbols>,
+and I< AllAtomPathsWithRings> for B<-p, --PathMode>, atom path strings are:
+
+    C N O C=O CN NC=O NCN
+
+And using I<AS,X,BO> for B<--AtomicInvariantsToUse> generates following atom path
+strings:
+
+    C.X3.BO4 N.X1.BO1 O.X1.BO2 C.X3.BO4=O.X1.BO2
+    C.X3.BO4N.X1.BO1 N.X1.BO1C.X3.BO4=O.X1.BO2
+    N.X1.BO1C.X3.BO4N.X1.BO1
+
+=item B<--FunctionalClassesToUse> I<"FunctionalClass1,FunctionalClass2...">
+
+This value is used during I<FunctionalClassAtomTypes> value of B<a, --AtomIdentifierType>
+option. It's a list of comma separated valid functional classes.
+
+Possible values for atom functional classes are: I<Ar, CA, H, HBA, HBD, Hal, NI, PI, RA>.
+Default value [ Ref 24 ]: I<HBD,HBA,PI,NI,Ar,Hal>.
+
+The functional class abbreviations correspond to:
+
+    HBD: HydrogenBondDonor
+    HBA: HydrogenBondAcceptor
+    PI :  PositivelyIonizable
+    NI : NegativelyIonizable
+    Ar : Aromatic
+    Hal : Halogen
+    H : Hydrophobic
+    RA : RingAtom
+    CA : ChainAtom
+
+ Functional class atom type specification for an atom corresponds to:
+
+    Ar.CA.H.HBA.HBD.Hal.NI.PI.RA
+
+I<AtomTypes::FunctionalClassAtomTypes> module is used to assign functional class atom
+types. It uses following definitions [ Ref 60-61, Ref 65-66 ]:
+
+    HydrogenBondDonor: NH, NH2, OH
+    HydrogenBondAcceptor: N[!H], O
+    PositivelyIonizable: +, NH2
+    NegativelyIonizable: -, C(=O)OH, S(=O)OH, P(=O)OH
+
+=item B<--BitsOrder> I<Ascending | Descending>
+
+Bits order to use during generation of fingerprints bit-vector string for I<PathLengthBits> value of
+B<-m, --mode> option. Possible values: I<Ascending, Descending>. Default: I<Ascending>.
+
+I<Ascending> bit order which corresponds to first bit in each byte as the lowest bit as
+opposed to the highest bit.
+
+Internally, bits are stored in I<Ascending> order using Perl vec function. Regardless
+of machine order, big-endian or little-endian, vec function always considers first
+string byte as the lowest byte and first bit within each byte as the lowest bit.
+
+=item B<-b, --BitStringFormat> I<BinaryString | HexadecimalString>
+
+Format of fingerprints bit-vector string data in output SD, FP or CSV/TSV text file(s) specified by
+B<--output> used during I<PathLengthBits> value of B<-m, --mode> option. Possible
+values: I<BinaryString, HexadecimalString>. Default value: I<HexadecimalString>.
+
+I<BinaryString> corresponds to an ASCII string containing 1s and 0s. I<HexadecimalString>
+contains bit values in ASCII hexadecimal format.
+
+Examples:
+
+    FingerprintsBitVector;PathLengthBits:AtomicInvariantsAtomTypes:MinLeng
+    th1:MaxLength8;1024;BinaryString;Ascending;001000010011010101011000110
+    0100010101011000101001011100110001000010001001101000001001001001001000
+    0010110100000111001001000001001010100100100000000011000000101001011100
+    0010000001000101010100000100111100110111011011011000000010110111001101
+    0101100011000000010001000011000010100011101100001000001000100000000...
+
+    FingerprintsBitVector;PathLengthBits:AtomicInvariantsAtomTypes:MinLeng
+    th1:MaxLength8;1024;HexadecimalString;Ascending;48caa1315d82d91122b029
+    42861c9409a4208182d12015509767bd0867653604481a8b1288000056090583603078
+    9cedae54e26596889ab121309800900490515224208421502120a0dd9200509723ae89
+    00024181b86c0122821d4e4880c38620dab280824b455404009f082003d52c212b4e6d
+    6ea05280140069c780290c43
+
+=item B<--CompoundID> I<DataFieldName or LabelPrefixString>
+
+This value is B<--CompoundIDMode> specific and indicates how compound ID is generated.
+
+For I<DataField> value of B<--CompoundIDMode> option, it corresponds to datafield label name
+whose value is used as compound ID; otherwise, it's a prefix string used for generating compound
+IDs like LabelPrefixString<Number>. Default value, I<Cmpd>, generates compound IDs which
+look like Cmpd<Number>.
+
+Examples for I<DataField> value of B<--CompoundIDMode>:
+
+    MolID
+    ExtReg
+
+Examples for I<LabelPrefix> or I<MolNameOrLabelPrefix> value of B<--CompoundIDMode>:
+
+    Compound
+
+The value specified above generates compound IDs which correspond to Compound<Number>
+instead of default value of Cmpd<Number>.
+
+=item B<--CompoundIDLabel> I<text>
+
+Specify compound ID column label for FP or CSV/TSV text file(s) used during I<CompoundID> value
+of B<--DataFieldsMode> option. Default: I<CompoundID>.
+
+=item B<--CompoundIDMode> I<DataField | MolName | LabelPrefix | MolNameOrLabelPrefix>
+
+Specify how to generate compound IDs and write to FP or CSV/TSV text file(s) along with generated
+fingerprints for I<FP | text | all> values of B<--output> option: use a I<SDFile(s)> datafield value;
+use molname line from I<SDFile(s)>; generate a sequential ID with specific prefix; use combination
+of both MolName and LabelPrefix with usage of LabelPrefix values for empty molname lines.
+
+Possible values: I<DataField | MolName | LabelPrefix | MolNameOrLabelPrefix>.
+Default: I<LabelPrefix>.
+
+For I<MolNameAndLabelPrefix> value of B<--CompoundIDMode>, molname line in I<SDFile(s)> takes
+precedence over sequential compound IDs generated using I<LabelPrefix> and only empty molname
+values are replaced with sequential compound IDs.
+
+This is only used for I<CompoundID> value of B<--DataFieldsMode> option.
+
+=item B<--DataFields> I<"FieldLabel1,FieldLabel2,... ">
+
+Comma delimited list of I<SDFiles(s)> data fields to extract and write to CSV/TSV text file(s) along
+with generated fingerprints for I<text | all> values of B<--output> option.
+
+This is only used for I<Specify> value of B<--DataFieldsMode> option.
+
+Examples:
+
+    Extreg
+    MolID,CompoundName
+
+=item B<-d, --DataFieldsMode> I<All | Common | Specify | CompoundID>
+
+Specify how data fields in I<SDFile(s)> are transferred to output CSV/TSV text file(s) along
+with generated fingerprints for I<text | all> values of B<--output> option: transfer all SD
+data field; transfer SD data files common to all compounds; extract specified data fields;
+generate a compound ID using molname line, a compound prefix, or a combination of both.
+Possible values: I<All | Common | specify | CompoundID>. Default value: I<CompoundID>.
+
+=item B<--DetectAromaticity> I<Yes | No>
+
+Detect aromaticity before generating fingerprints. Possible values: I<Yes or No>.
+Default value: I<Yes>.
+
+I<No> B<--DetectAromaticity> forces usage of atom and bond aromaticity values
+from I<SDFile(s)> and skips the step which detects and assigns aromaticity.
+
+I<No> B<--DetectAromaticity> value is only allowed uring I<AtomicInvariantsAtomTypes>
+value of B<-a, --AtomIdentifierType> options; for all possible values B<-a, --AtomIdentifierType>
+values, it must be I<Yes>.
+
+=item B<-f, --Filter> I<Yes | No>
+
+Specify whether to check and filter compound data in SDFile(s). Possible values: I<Yes or No>.
+Default value: I<Yes>.
+
+By default, compound data is checked before calculating fingerprints and compounds containing
+atom data corresponding to non-element symbols or no atom data are ignored.
+
+=item B<--FingerprintsLabel> I<text>
+
+SD data label or text file column label to use for fingerprints string in output SD or
+CSV/TSV text file(s) specified by B<--output>. Default value: I<PathLenghFingerprints>.
+
+=item B<--fold> I<Yes | No>
+
+Fold fingerprints to increase bit density during I<PathLengthBits> value of
+B<-m, --mode> option. Possible values: I<Yes or No>. Default value: I<No>.
+
+=item B<--FoldedSize> I<number>
+
+Size of folded fingerprint during I<PathLengthBits> value of B<-m, --mode> option. Default
+value: I<256>. Valid values correspond to any positive integer which is less than
+B<-s, --size> and meets the criteria for its value.
+
+Examples:
+
+   128
+   512
+
+=item B<-h, --help>
+
+Print this help message
+
+=item B<-i, --IgnoreHydrogens> I<Yes | No>
+
+Ignore hydrogens during fingerprints generation. Possible values: I<Yes or No>.
+Default value: I<Yes>.
+
+For I<yes> value of B<-i, --IgnoreHydrogens>, any explicit hydrogens are also used for
+generation of atoms path lengths and fingerprints; implicit hydrogens are still ignored.
+
+=item B<-k, --KeepLargestComponent> I<Yes | No>
+
+Generate fingerprints for only the largest component in molecule. Possible values:
+I<Yes or No>. Default value: I<Yes>.
+
+For molecules containing multiple connected components, fingerprints can be generated
+in two different ways: use all connected components or just the largest connected
+component. By default, all atoms except for the largest connected component are
+deleted before generation of fingerprints.
+
+=item B<-m, --mode> I<PathLengthBits | PathLengthCount>
+
+Specify type of path length fingerprints to generate for molecules in I<SDFile(s)>. Possible
+values: I<PathLengthBits, PathLengthCount>. Default value: I<PathLengthBits>.
+
+For I<PathLengthBits> value of B<-m, --mode> option, a fingerprint bit-vector string containing
+zeros and ones is generated and for I<PathLengthCount> value, a fingerprint vector string
+corresponding to number of atom paths is generated.
+
+=item B<--MinPathLength> I<number>
+
+Minimum atom path length to include in fingerprints. Default value: I<1>. Valid values:
+positive integers and less than B<--MaxPathLength>. Path length of 1 correspond to
+a path containing only one atom.
+
+=item B<--MaxPathLength> I<number>
+
+Maximum atom path length to include in fingerprints. Default value: I<8>. Valid values:
+positive integers and greater than B<--MinPathLength>.
+
+=item B<-n, --NumOfBitsToSetPerPath> I<number>
+
+Number of bits to set per path during generation of fingerprints bit-vector string for I<PathLengthBits>
+value of B<-m, --mode> option. Default value: I<1>. Valid values: positive integers.
+
+=item B<--OutDelim> I<comma | tab | semicolon>
+
+Delimiter for output CSV/TSV text file(s). Possible values: I<comma, tab, or semicolon>
+Default value: I<comma>.
+
+=item B<--output> I<SD | FP | text | all>
+
+Type of output files to generate. Possible values: I<SD, FP, text, or all>. Default value: I<text>.
+
+=item B<-o, --overwrite>
+
+Overwrite existing files.
+
+=item B<-p, --PathMode> I<AtomPathsWithoutRings | AtomPathsWithRings | AllAtomPathsWithoutRings | AllAtomPathsWithRings>
+
+Specify type of atom paths to use for generating  pathlength fingerprints for molecules in
+I<SDFile(s)>. Possible values:I<AtomPathsWithoutRings, AtomPathsWithRings,
+AllAtomPathsWithoutRings, AllAtomPathsWithRings>. Default value: I<AllAtomPathsWithRings>.
+
+For molecules with no rings, first two and last two options are equivalent and generate
+same set of atom paths starting from each atom with length between B<--MinPathLength>
+and B<--MaxPathLength>. However, all these four options can result in the same set of
+final atom paths for molecules containing fused, bridged or spiro rings.
+
+For molecules containing rings, atom paths starting from each atom can be traversed in
+four different ways:
+
+I<AtomPathsWithoutRings> - Atom paths containing no rings and without sharing of bonds
+in traversed paths.
+
+I<AtomPathsWithRings> - Atom paths containing rings and without any sharing of bonds in
+traversed paths.
+
+I<AllAtomPathsWithoutRings> - All possible atom paths containing no rings and without any
+sharing of bonds in traversed paths.
+
+I<AllAtomPathsWithRings> - All possible atom paths containing rings and with sharing of
+bonds in traversed paths.
+
+Atom path traversal is terminated at the ring atom.
+
+Based on values specified for for B<-p, --PathMode>, B<--MinPathLength> and
+B<--MaxPathLength>, all appropriate atom paths are generated for each atom in the molecule
+and collected in a list.
+
+For each atom path in the filtered atom paths list, an atom path string is created using value of
+B<-a, --AtomIdentifierType> and specified values to use for a particular atom identifier type.
+Value of B<-u, --UseBondSymbols> controls whether bond order symbols are used during generation
+of atom path string. Atom symbol corresponds to element symbol and characters used to represent
+ bond order are: I<1 - None; 2 - '='; 3 - '#'; 1.5 or aromatic - ':'; others: bond order value>. By default,
+bond symbols are included in atom path strings. Exclusion of bond symbols in atom path strings
+results in fingerprints which correspond purely to atom paths without considering bonds.
+
+B<UseUniquePaths> controls the removal of structurally duplicate atom path strings are removed
+from the list.
+
+For I<PathLengthBits> value of B<-m, --mode> option, each atom path is hashed to a 32 bit unsigned
+integer key using B<TextUtil::HashCode> function. Using the hash key as a seed for a random number
+generator, a random integer value between 0 and B<--Size> is used to set corresponding bits
+in the fingerprint bit-vector string. Value of B<--NumOfBitsToSetPerPaths> option controls the number
+of time a random number is generated to set corresponding bits.
+
+For I< PathLengthCount> value of B<-m, --mode> option, the number of times an atom path appears
+is tracked and a fingerprints count-string corresponding to count of atom paths is generated.
+
+For molecule containing rings, combination of B<-p, --PathMode> and B<--UseBondSymbols> allows
+generation of up to 8 different types of atom path length strings:
+
+    AllowSharedBonds AllowRings UseBondSymbols
+
+    0                0          1   - AtomPathsNoCyclesWithBondSymbols
+    0                1          1   - AtomPathsWithCyclesWithBondSymbols
+
+    1                0          1   - AllAtomPathsNoCyclesWithBondSymbols
+    1                1          1   - AllAtomPathsWithCyclesWithBondSymbols
+                                      [ DEFAULT ]
+
+    0                0          0   - AtomPathsNoCyclesNoBondSymbols
+    0                1          0   - AtomPathsWithCyclesNoBondSymbols
+
+    1                0          0   - AllAtomPathsNoCyclesNoBondSymbols
+    1                1          0   - AllAtomPathsWithCyclesNoWithBondSymbols
+
+Default atom path length fingerprints generation for molecules containing rings with
+I<AllAtomPathsWithRings> value for B<-p, --PathMode>, I<Yes> value for B<--UseBondSymbols>,
+I<2> value for B<--MinPathLength> and I<8> value for B<--MaxPathLength> is the most time
+consuming. Combinations of other options can substantially speed up fingerprint generation
+for molecules containing complex ring systems.
+
+Additionally, value for option B<-a, --AtomIdentifierType> in conjunction with corresponding specified
+values for atom types changes the nature of atom path length strings and the fingerprints.
+
+=item B<-q, --quote> I<Yes | No>
+
+Put quote around column values in output CSV/TSV text file(s). Possible values:
+I<Yes or No>. Default value: I<Yes>.
+
+=item B<-r, --root> I<RootName>
+
+New file name is generated using the root: <Root>.<Ext>. Default for new file
+names: <SDFileName><PathLengthFP>.<Ext>. The file type determines <Ext> value.
+The sdf, fpf, csv, and tsv <Ext> values are used for SD, FP, comma/semicolon, and tab
+delimited text files, respectively.This option is ignored for multiple input files.
+
+=item B<-s, --size> I<number>
+
+Size of fingerprints. Default value: I<1024>. Valid values correspond to any positive
+integer which satisfies the following criteria: power of 2, >= 32 and <= 2 ** 32.
+
+Examples:
+
+   256
+   512
+   2048
+
+=item B<-u, --UseBondSymbols> I<Yes | No>
+
+Specify whether to use bond symbols for atom paths during generation of atom path strings.
+Possible values: I<Yes or No>. Default value: I<Yes>.
+
+I<No> value option for B<-u, --UseBondSymbols> allows the generation of fingerprints corresponding
+purely to atoms disregarding all bonds.
+
+=item B<--UsePerlCoreRandom> I<Yes | No>
+
+Specify whether to use Perl CORE::rand or MayaChemTools MathUtil::random function
+during random number generation for setting bits in fingerprints bit-vector strings. Possible
+values: I<Yes or No>. Default value: I<Yes>.
+
+I<No> value option for B<--UsePerlCoreRandom> allows the generation of fingerprints
+bit-vector strings which are same across different platforms.
+
+The random number generator implemented in MayaChemTools is a variant of
+linear congruential generator (LCG) as described by Miller et al. [ Ref 120 ].
+It is also referred to as Lehmer random number generator or Park-Miller
+random number generator.
+
+Unlike Perl's core random number generator function rand, the random number
+generator implemented in MayaChemTools, MathUtil::random,  generates consistent
+random values across different platforms for a specific random seed and leads
+to generation of portable fingerprints bit-vector strings.
+
+=item B<--UseUniquePaths> I<Yes | No>
+
+Specify whether to use structurally unique atom paths during generation of atom path strings.
+Possible values: I<Yes or No>. Default value: I<Yes>.
+
+I<No> value option for B<--UseUniquePaths> allows usage of all atom paths generated by
+B<-p, --PathMode> option value for generation of atom path strings leading to duplicate
+path count during I<PathLengthCount> value of B<-m, --mode> option. It doesn't change fingerprint
+string generated during I<PathLengthBits> value of B<-m, --mode>.
+
+For example, during I<AllAtomPathsWithRings> value of B<-p, --PathMode> option, benzene has
+12 linear paths of length 2 and 12 cyclic paths length of 7, but only 6 linear paths of length 2 and
+1 cyclic path of length 7 are structurally unique.
+
+=item B<-v, --VectorStringFormat> I<IDsAndValuesString | IDsAndValuesPairsString | ValuesAndIDsString | ValuesAndIDsPairsString>
+
+Format of fingerprints vector string data in output SD, FP or CSV/TSV text file(s) specified by
+B<--output> used during I<PathLengthCount> value of B<-m, --mode> option. Possible
+values: I<IDsAndValuesString | IDsAndValuesPairsString | ValuesAndIDsString |
+ValuesAndIDsPairsString>. Defaultvalue: I<IDsAndValuesString>.
+
+Examples:
+
+    FingerprintsVector;PathLengthCount:AtomicInvariantsAtomTypes:MinLength
+    1:MaxLength8;432;NumericalValues;IDsAndValuesPairsString;C.X1.BO1.H3 2
+     C.X2.BO2.H2 4 C.X2.BO3.H1 14 C.X3.BO3.H1 3 C.X3.BO4 10 F.X1.BO1 1 N.X
+    2.BO2.H1 1 N.X3.BO3 1 O.X1.BO1.H1 3 O.X1.BO2 2 C.X1.BO1.H3C.X3.BO3.H1 
+    2 C.X2.BO2.H2C.X2.BO2.H2 1 C.X2.BO2.H2C.X3.BO3.H1 4 C.X2.BO2.H2C.X3.BO
+    4 1 C.X2.BO2.H2N.X3.BO3 1 C.X2.BO3.H1:C.X2.BO3.H1 10 C.X2.BO3.H1:C....
+
+    FingerprintsVector;PathLengthCount:EStateAtomTypes:MinLength1:MaxLengt
+    h8;454;NumericalValues;IDsAndValuesPairsString;aaCH 14 aasC 8 aasN 1 d
+    O 2 dssC 2 sCH3 2 sF 1 sOH 3 ssCH2 4 ssNH 1 sssCH 3 aaCH:aaCH 10 aaCH:
+    aasC 8 aasC:aasC 3 aasC:aasN 2 aasCaasC 2 aasCdssC 1 aasCsF 1 aasCssNH
+    1 aasCsssCH 1 aasNssCH2 1 dO=dssC 2 dssCsOH 1 dssCssCH2 1 dssCssNH 1
+    sCH3sssCH 2 sOHsssCH 2 ssCH2ssCH2 1 ssCH2sssCH 4 aaCH:aaCH:aaCH 6 a...
+
+=item B<-w, --WorkingDir> I<DirName>
+
+Location of working directory. Default: current directory.
+
+=back
+
+=head1 EXAMPLES
+
+To generate path length fingerprints corresponding to all unique paths from length 1
+through 8 in hexadecimal bit-vector string format of size 1024 and create a
+SamplePLFPHex.csv file containing sequential compound IDs along with fingerprints
+bit-vector strings data, type:
+
+    % PathLengthFingerprints.pl -o -r SamplePLFPHex Sample.sdf
+
+To generate path length fingerprints corresponding to all unique paths from length 1
+through 8 in hexadecimal bit-vector string format of size 1024 and create SamplePLFPHex.sdf,
+SamplePLFPHex.fpf, and SamplePLFPHex.csv files containing sequential compound IDs
+in CSV file along with fingerprints bit-vector strings data, type:
+
+    % PathLengthFingerprints.pl --output all -o -r SamplePLFPHex Sample.sdf
+
+To generate path length fingerprints corresponding to all unique paths from length 1
+through 8 in binary bit-vector string format of size 1024 and create a
+SamplePLFPBin.csv file containing sequential compound IDs along with fingerprints
+bit-vector strings data, type:
+
+    % PathLengthFingerprints.pl --BitStringFormat BinaryString --size 2048
+      -o -r SamplePLFPBin Sample.sdf
+
+To generate path length fingerprints corresponding to count of all unique paths from
+length 1 through 8 in IDsAndValuesString format and create a SamplePLFPCount.csv file
+containing sequential compound IDs along with fingerprints vector strings data, type:
+
+    % PathLengthFingerprints.pl -m PathLengthCount -o -r SamplePLFPCount
+      Sample.sdf
+
+To generate path length fingerprints corresponding to count of all unique paths from
+length 1 through 8 in IDsAndValuesString format using  E-state atom types and
+create a SamplePLFPCount.csv file containing sequential compound IDs along with fingerprints
+vector strings data, type:
+
+    % PathLengthFingerprints.pl -m  PathLengthCount --AtomIdentifierType
+      EStateAtomTypes -o -r SamplePLFPCount Sample.sdf
+
+To generate path length fingerprints corresponding to count of all unique paths from
+length 1 through 8 in IDsAndValuesString format using  SLogP atom types and
+create a SamplePLFPCount.csv file containing sequential compound IDs along with fingerprints
+vector strings data, type:
+
+    % PathLengthFingerprints.pl -m  PathLengthCount --AtomIdentifierType
+      SLogPAtomTypes -o -r SamplePLFPCount Sample.sdf
+
+To generate path length fingerprints corresponding to count of all unique paths from
+length 1 through 8 in IDsAndValuesString format and create a SamplePLFPCount.csv file
+containing sequential compound IDs along with fingerprints vector strings data, type:
+
+    % PathLengthFingerprints.pl -m  PathLengthCount --VectorStringFormat
+      ValuesAndIDsPairsString -o -r SamplePLFPCount Sample.sdf
+
+To generate path length fingerprints corresponding to count of all unique paths from
+length 1 through 8 in IDsAndValuesString format using AS,X,BO as atomic invariants and
+create a SamplePLFPCount.csv file containing sequential compound IDs along with fingerprints
+vector strings data, type:
+
+    % PathLengthFingerprints.pl -m  PathLengthCount --AtomIdentifierType
+      AtomicInvariantsAtomTypes --AtomicInvariantsToUse "AS,X,BO" -o
+      -r SamplePLFPCount Sample.sdf
+
+To generate path length fingerprints corresponding to count of all  paths from
+length 1 through 8 in IDsAndValuesString format and create a SamplePLFPCount.csv file
+containing compound IDs from MolName line along with fingerprints vector strings data, type:
+
+    % PathLengthFingerprints.pl -m  PathLengthCount --UseUniquePaths No
+      -o --CompoundIDMode MolName -r SamplePLFPCount --UseUniquePaths No
+      Sample.sdf
+
+To generate path length fingerprints corresponding to all unique paths from length 1
+through 8 in hexadecimal bit-vector string format of size 512 after folding and create
+SamplePLFPHex.sdf, SamplePLFPHex.fpf, and SamplePLFPHex.sdf  files containing sequential
+compound IDs along with fingerprints bit-vector strings data, type:
+
+    % PathLengthFingerprints.pl --output all --Fold Yes --FoldedSize 512
+       -o -r SamplePLFPHex Sample.sdf
+
+To generate path length fingerprints corresponding to all unique paths from length 1
+through 8 containing no rings and  without sharing of bonds in hexadecimal bit-vector
+string format of size 1024 and create a SamplePLFPHex.csv file containing sequential
+compound IDs along with fingerprints bit-vector strings data and all data fields, type:
+
+    % PathLengthFingerprints.pl -p AtomPathsWithoutRings --DataFieldsMode All
+      -o -r SamplePLFPHex Sample.sdf
+
+To generate path length fingerprints corresponding to all unique paths from length 1
+through 8 containing rings and  without sharing of bonds in hexadecimal bit-vector
+string format of size 1024 and create a SamplePLFPHex.tsv file containing compound IDs
+derived from combination of molecule name line and an explicit compound prefix
+along with fingerprints bit-vector strings data and all data fields, type:
+
+    % PathLengthFingerprints.pl -p AtomPathsWithRings --DataFieldsMode
+      CompoundID --CompoundIDMode MolnameOrLabelPrefix  --CompoundID Cmpd
+      --CompoundIDLabel MolID --FingerprintsLabel PathLengthFP --OutDelim Tab
+      -r SamplePLFPHex -o Sample.sdf
+
+To generate path length fingerprints corresponding to count of all unique paths from
+length 1 through 8 in IDsAndValuesString format and create a SamplePLFPCount.csv file
+containing sequential compound IDs along with fingerprints vector strings data using
+aromaticity specified in SD file, type:
+
+    % PathLengthFingerprints.pl -m PathLengthCount --DetectAromaticity No
+      -o -r SamplePLFPCount Sample.sdf
+
+To generate path length fingerprints corresponding to all unique paths from length 2
+through 6 in hexadecimal bit-vector string format of size 1024 and create a
+SamplePLFPHex.csv file containing sequential compound IDs along with fingerprints
+bit-vector strings data, type:
+
+    % PathLengthFingerprints.pl --MinPathLength 2 --MaxPathLength 6
+      -o -r SamplePLFPHex Sample.sdf
+
+=head1 AUTHOR
+
+Manish Sud <msud@san.rr.com>
+
+=head1 SEE ALSO
+
+InfoFingerprintsFiles.pl, SimilarityMatricesFingerprints.pl, AtomNeighborhoodsFingerprints.pl,
+ExtendedConnectivityFingerprints.pl, MACCSKeysFingerprints.pl,
+TopologicalAtomPairsFingerprints.pl, TopologicalAtomTorsionsFingerprints.pl,
+TopologicalPharmacophoreAtomPairsFingerprints.pl, TopologicalPharmacophoreAtomTripletsFingerprints.pl
+
+=head1 COPYRIGHT
+
+Copyright (C) 2015 Manish Sud. All rights reserved.
+
+This file is part of MayaChemTools.
+
+MayaChemTools is free software; you can redistribute it and/or modify it under
+the terms of the GNU Lesser General Public License as published by the Free
+Software Foundation; either version 3 of the License, or (at your option)
+any later version.
+
+=cut