comparison bin/AtomNeighborhoodsFingerprints.pl @ 0:4816e4a8ae95 draft default tip

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#!/usr/bin/perl -w
#
# $RCSfile: AtomNeighborhoodsFingerprints.pl,v $
# $Date: 2015/02/28 20:46:19 $
# $Revision: 1.31 $
#
# Author: Manish Sud <[e-mail]>
#
# 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::AtomNeighborhoodsFingerprints;

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";
    GenerateAtomNeighborhoodsFingerprints($FileIndex);
  }
}
print "\n$ScriptName:Done...\n\n";

$EndTime = new Benchmark;
$TotalTime = timediff ($EndTime, $StartTime);
print "Total time: ", timestr($TotalTime), "\n";

###############################################################################

# Generate fingerprints for a SD file...
#
sub GenerateAtomNeighborhoodsFingerprints {
  my($FileIndex) = @_;
  my($CmpdCount, $IgnoredCmpdCount, $SDFile, $MoleculeFileIO, $Molecule, $AtomNeighborhoodsFingerprints, $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;
      }
    }

    $AtomNeighborhoodsFingerprints = GenerateMoleculeFingerprints($Molecule);
    if (!$AtomNeighborhoodsFingerprints) {
      $IgnoredCmpdCount++;
      ProcessIgnoredCompound('FingerprintsGenerationFailed', $CmpdCount, $Molecule);
      next COMPOUND;
    }

    WriteDataToOutputFiles($FileIndex, $CmpdCount, $Molecule, $AtomNeighborhoodsFingerprints, $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 = ('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, $AtomNeighborhoodsFingerprints, $NewFPSDFileIO, $NewFPTextFileIO, $NewFPFileIO) = @_;
  my($DataFieldLabelAndValuesRef);

  $DataFieldLabelAndValuesRef = undef;
  if ($NewFPTextFileIO || $NewFPFileIO) {
    $DataFieldLabelAndValuesRef = $Molecule->GetDataFieldLabelAndValues();
  }

  if ($NewFPSDFileIO) {
    my($CmpdString);

    $CmpdString = $Molecule->GetInputMoleculeString();
    $NewFPSDFileIO->WriteFingerprints($AtomNeighborhoodsFingerprints, $CmpdString);
  }

  if ($NewFPTextFileIO) {
    my($ColValuesRef);

    $ColValuesRef = SetupFPTextFileCoulmnValues($FileIndex, $CmpdCount, $Molecule, $DataFieldLabelAndValuesRef);
    $NewFPTextFileIO->WriteFingerprints($AtomNeighborhoodsFingerprints, $ColValuesRef);
  }

  if ($NewFPFileIO) {
    my($CompoundID);

    $CompoundID = SetupCmpdIDForOutputFiles($CmpdCount, $Molecule, $DataFieldLabelAndValuesRef);
    $NewFPFileIO->WriteFingerprints($AtomNeighborhoodsFingerprints, $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($Molecule) = @_;
  my($AtomNeighborhoodsFingerprints);

  if ($OptionsInfo{KeepLargestComponent}) {
    $Molecule->KeepLargestComponent();
  }
  if (!$Molecule->DetectRings()) {
    return undef;
  }
  $Molecule->SetAromaticityModel($OptionsInfo{AromaticityModel});
  $Molecule->DetectAromaticity();

  $AtomNeighborhoodsFingerprints = new Fingerprints::AtomNeighborhoodsFingerprints('Molecule' => $Molecule, 'MinNeighborhoodRadius' => $OptionsInfo{MinNeighborhoodRadius},  'MaxNeighborhoodRadius' => $OptionsInfo{MaxNeighborhoodRadius}, 'AtomIdentifierType' => $OptionsInfo{AtomIdentifierType});
  SetAtomIdentifierTypeValuesToUse($AtomNeighborhoodsFingerprints);

  # Generate fingerprints...
  $AtomNeighborhoodsFingerprints->GenerateFingerprints();

  # Make sure fingerprints generation is successful...
  if (!$AtomNeighborhoodsFingerprints->IsFingerprintsGenerationSuccessful()) {
    return undef;
  }

  return $AtomNeighborhoodsFingerprints;
}

# Set atom identifier type to use for generating fingerprints...
#
sub SetAtomIdentifierTypeValuesToUse {
  my($AtomNeighborhoodsFingerprints) = @_;

  if ($OptionsInfo{AtomIdentifierType} =~ /^AtomicInvariantsAtomTypes$/i) {
    $AtomNeighborhoodsFingerprints->SetAtomicInvariantsToUse(\@{$OptionsInfo{AtomicInvariantsToUse}});
  }
  elsif ($OptionsInfo{AtomIdentifierType} =~ /^FunctionalClassAtomTypes$/i) {
    $AtomNeighborhoodsFingerprints->SetFunctionalClassesToUse(\@{$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}AtomNeighborhoodsFP";
    }

    $NewSDFileName = "${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 (!$OptionsInfo{OverwriteFiles}) {
      # Check SD and text outout files...
      if ($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 = ();

  ProcessAtomIdentifierTypeOptions();

  $OptionsInfo{AromaticityModel} = $Options{aromaticitymodel};

  $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;
  }

  $OptionsInfo{FingerprintsLabel} = $Options{fingerprintslabel} ? $Options{fingerprintslabel} : 'AtomNeighborhoodsFingerprints';

  $OptionsInfo{Filter} = ($Options{filter} =~ /^Yes$/i) ? 1 : 0;

  $OptionsInfo{KeepLargestComponent} = ($Options{keeplargestcomponent} =~ /^Yes$/i) ? 1 : 0;

  $OptionsInfo{MinNeighborhoodRadius} = $Options{minneighborhoodradius};
  $OptionsInfo{MaxNeighborhoodRadius} = $Options{maxneighborhoodradius};

  $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{VectorStringFormat} = 'ValuesString';
}

# 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,X,BO,H,FC';
  $Options{functionalclassestouse} = 'HBD,HBA,PI,NI,Ar,Hal';

  $Options{compoundidmode} = 'LabelPrefix';
  $Options{compoundidlabel} = 'CompoundID';
  $Options{datafieldsmode} = 'CompoundID';

  $Options{filter} = 'Yes';

  $Options{keeplargestcomponent} = 'Yes';

  $Options{minneighborhoodradius} = 0;
  $Options{maxneighborhoodradius} = 2;

  $Options{output} = 'text';
  $Options{outdelim} = 'comma';
  $Options{quote} = 'yes';

  if (!GetOptions(\%Options, "aromaticitymodel=s", "atomidentifiertype|a=s", "atomicinvariantstouse=s", "functionalclassestouse=s", "compoundid=s", "compoundidlabel=s", "compoundidmode=s", "datafields=s", "datafieldsmode|d=s", "filter|f=s", "fingerprintslabel=s",  "help|h", "keeplargestcomponent|k=s",  "minneighborhoodradius=s", "maxneighborhoodradius=s", "outdelim=s", "output=s", "overwrite|o", "quote|q=s", "root|r=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{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{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{keeplargestcomponent} !~ /^(Yes|No)$/i) {
    die "Error: The value specified, $Options{keeplargestcomponent}, for option \"-k, --KeepLargestComponent\" is not valid. Allowed values: Yes or No\n";
  }
  if (!(IsInteger($Options{minneighborhoodradius}) && ($Options{minneighborhoodradius} >= 0))) {
    die "Error: The value specified, $Options{minneighborhoodradius}, for option \"--MinNeighborhoodRadius\" is not valid. Allowed values: >= 0 \n";
  }
  if (!(IsInteger($Options{maxneighborhoodradius}) && ($Options{maxneighborhoodradius} >= 0))) {
    die "Error: The value specified, $Options{maxneighborhoodradius}, for option \"--MaxNeighborhoodRadius\" is not valid. Allowed values: >= 0 \n";
  }
  if ($Options{minneighborhoodradius} > $Options{maxneighborhoodradius}) {
    die "Error: The value specified, specified, $Options{minneighborhoodradius}, for option \"--MinNeighborhoodRadius\" must be less than the value specified, $Options{maxneighborhoodradius}, for option \"--MaxNeighborhoodRadius\" \n";
  }
  if ($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{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";
  }
}

__END__

=head1 NAME

AtomNeighborhoodsFingerprints.pl - Generate atom neighborhoods fingerprints for SD files

=head1 SYNOPSIS

AtomNeighborhoodsFingerprints.pl SDFile(s)...

AtomNeighborhoodsFingerprints.pl [B<--AromaticityModel> I<AromaticityModelType>]
[B<-a, --AtomIdentifierType> I<AtomicInvariantsAtomTypes |
DREIDINGAtomTypes | EStateAtomTypes | MMFF94AtomTypes | SLogPAtomTypes | SYBYLAtomTypes | TPSAAtomTypes | UFFAtomTypes>]
[B<--AtomicInvariantsToUse> I<"AtomicInvariant,AtomicInvariant...">]
[B<--FunctionalClassesToUse> I<"FunctionalClass1,FunctionalClass2...">]
[B<--CompoundID> I<DataFieldName or LabelPrefixString>] [B<--CompoundIDLabel> I<text>]
[B<--CompoundIDMode>] [B<--DataFields> I<"FieldLabel1,FieldLabel2,...">]
[B<-d, --DataFieldsMode> I<All | Common | Specify | CompoundID>] [B<-f, --Filter> I<Yes | No>]
[B<--FingerprintsLabel> I<text>] [B<-h, --help>] [B<-k, --KeepLargestComponent> I<Yes | No>]
[B<--MinNeighborhoodRadius> I<number>] [B<--MaxNeighborhoodRadius> I<number>]
[B<--OutDelim> I<comma | tab | semicolon>] [B<--output> I<SD | FP | text | all>] [B<-o, --overwrite>]
[B<-q, --quote> I<Yes | No>] [B<-r, --root> I<RootName>]
[B<-w, --WorkingDir> dirname] SDFile(s)...

=head1 DESCRIPTION

Generate atom neighborhoods fingerprints  [ Ref 53-56, Ref 73 ] for I<SDFile(s)> and create appropriate
SD, FP or CSV/TSV text file(s) containing fingerprints 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 atom neighborhoods fingerprints
corresponding to following B<-a, --AtomIdentifierTypes>:

    AtomicInvariantsAtomTypes, DREIDINGAtomTypes, EStateAtomTypes,
    FunctionalClassAtomTypes, MMFF94AtomTypes, SLogPAtomTypes,
    SYBYLAtomTypes, TPSAAtomTypes, UFFAtomTypes

Based on the values specified for B<-a, --AtomIdentifierType> and B<--AtomicInvariantsToUse>,
initial atom types are assigned to all non-hydrogen atoms in a molecule. Using atom neighborhoods
around each non-hydrogen central atom corresponding to radii between specified values
B<--MinNeighborhoodRadius> and B<--MaxNeighborhoodRadius>, unique atom types at
each radii level are counted and an atom neighborhood identifier is generated.

The format of an atom neighborhood identifier around a central non-hydrogen atom at a
specific radius is:

    NR<n>-<AtomType>-ATC<n>

    NR: Neighborhood radius
    AtomType: Assigned atom type
    ATC: Atom type count

The atom neighborhood identifier for a non-hydrogen central atom corresponding to all specified radii
is generated by concatenating neighborhood identifiers at each radii by colon as a delimiter:

    NR<n>-<AtomType>-ATC<n>:NR<n>-<AtomType>-ATC<n>:...

The atom neighborhood identifiers for all non-hydrogen central atoms at all specified radii are
concatenated using space as a delimiter and constitute atom neighborhood fingerprint of the molecule.

Example of I<SD> file containing atom neighborhood 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

    >  <AtomNeighborhoodsFingerprints>
    FingerprintsVector;AtomNeighborhoods:AtomicInvariantsAtomTypes:MinRadiu
    s0:MaxRadius2;41;AlphaNumericalValues;ValuesString;NR0-C.X1.BO1.H3-ATC1
    :NR1-C.X3.BO3.H1-ATC1:NR2-C.X1.BO1.H3-ATC1:NR2-C.X3.BO4-ATC1 NR0-C.X1.B
    O1.H3-ATC1:NR1-C.X3.BO3.H1-ATC1:NR2-C.X1.BO1.H3-ATC1:NR2-C.X3.BO4-ATC1
    NR0-C.X2.BO2.H2-ATC1:NR1-C.X2.BO2.H2-ATC1:NR1-C.X3.BO3.H1-ATC1:NR2-C...

    $$$$
    ... ...
    ... ...

Example of I<FP> file containing atom neighborhood fingerprints string data:

    #
    # Package = MayaChemTools 7.4
    # Release Date = Oct 21, 2010
    #
    # TimeStamp = Fri Mar 11 14:15:27 2011
    #
    # FingerprintsStringType = FingerprintsVector
    #
    # Description = AtomNeighborhoods:AtomicInvariantsAtomTypes:MinRadiu...
    # VectorStringFormat = ValuesString
    # VectorValuesType = AlphaNumericalValues
    #
    Cmpd1 41;NR0-C.X1.BO1.H3-ATC1:NR1-C.X3.BO3.H1-ATC1:NR2-C.X1.BO1.H3-A...
    Cmpd2 23;NR0-C.X1.BO1.H3-ATC1:NR1-C.X2.BO2.H2-ATC1:NR2-C.X3.BO3.H1-A...
    ... ...
    ... ..

Example of CSV I<Text> file containing atom neighborhood fingerprints string data:

    "CompoundID","AtomNeighborhoodsFingerprints"
    "Cmpd1","FingerprintsVector;AtomNeighborhoods:AtomicInvariantsAtomTypes
    :MinRadius0:MaxRadius2;41;AlphaNumericalValues;ValuesString;NR0-C.X1.B
    O1.H3-ATC1:NR1-C.X3.BO3.H1-ATC1:NR2-C.X1.BO1.H3-ATC1:NR2-C.X3.BO4-ATC1
    NR0-C.X1.BO1.H3-ATC1:NR1-C.X3.BO3.H1-ATC1:NR2-C.X1.BO1.H3-ATC1:NR2-C.X3
    .BO4-ATC1 NR0-C.X2.BO2.H2-ATC1:NR1-C.X2.BO2.H2-ATC1:NR1-C.X3.BO3.H1..."
    ... ...
    ... ...

The current release of MayaChemTools generates the following types of atom neighborhoods
fingerprints vector strings:

    FingerprintsVector;AtomNeighborhoods:AtomicInvariantsAtomTypes:MinRadi
    us0:MaxRadius2;41;AlphaNumericalValues;ValuesString;NR0-C.X1.BO1.H3-AT
    C1:NR1-C.X3.BO3.H1-ATC1:NR2-C.X1.BO1.H3-ATC1:NR2-C.X3.BO4-ATC1 NR0-C.X
    1.BO1.H3-ATC1:NR1-C.X3.BO3.H1-ATC1:NR2-C.X1.BO1.H3-ATC1:NR2-C.X3.BO4-A
    TC1 NR0-C.X2.BO2.H2-ATC1:NR1-C.X2.BO2.H2-ATC1:NR1-C.X3.BO3.H1-ATC1:NR2
    -C.X2.BO2.H2-ATC1:NR2-N.X3.BO3-ATC1:NR2-O.X1.BO1.H1-ATC1 NR0-C.X2.B...

    FingerprintsVector;AtomNeighborhoods:DREIDINGAtomTypes:MinRadius0:MaxR
    adius2;41;AlphaNumericalValues;ValuesString;NR0-C_2-ATC1:NR1-C_3-ATC1:
    NR1-O_2-ATC1:NR1-O_3-ATC1:NR2-C_3-ATC1 NR0-C_2-ATC1:NR1-C_R-ATC1:NR1-N
    _3-ATC1:NR1-O_2-ATC1:NR2-C_R-ATC3 NR0-C_3-ATC1:NR1-C_2-ATC1:NR1-C_3-AT
    C1:NR2-C_3-ATC1:NR2-O_2-ATC1:NR2-O_3-ATC2 NR0-C_3-ATC1:NR1-C_3-ATC1:NR
    1-N_R-ATC1:NR2-C_3-ATC1:NR2-C_R-ATC2 NR0-C_3-ATC1:NR1-C_3-ATC1:NR2-...

    FingerprintsVector;AtomNeighborhoods:EStateAtomTypes:MinRadius0:MaxRad
    ius2;41;AlphaNumericalValues;ValuesString;NR0-aaCH-ATC1:NR1-aaCH-ATC1:
    NR1-aasC-ATC1:NR2-aaCH-ATC1:NR2-aasC-ATC1:NR2-sF-ATC1 NR0-aaCH-ATC1:NR
    1-aaCH-ATC1:NR1-aasC-ATC1:NR2-aaCH-ATC1:NR2-aasC-ATC1:NR2-sF-ATC1 NR0-
    aaCH-ATC1:NR1-aaCH-ATC1:NR1-aasC-ATC1:NR2-aaCH-ATC1:NR2-aasC-ATC2 NR0-
    aaCH-ATC1:NR1-aaCH-ATC1:NR1-aasC-ATC1:NR2-aaCH-ATC1:NR2-aasC-ATC2 N...

    FingerprintsVector;AtomNeighborhoods:FunctionalClassAtomTypes:MinRadiu
    s0:MaxRadius2;41;AlphaNumericalValues;ValuesString;NR0-Ar-ATC1:NR1-Ar-
    ATC1:NR1-Ar.HBA-ATC1:NR1-None-ATC1:NR2-Ar-ATC2:NR2-None-ATC4 NR0-Ar-AT
    C1:NR1-Ar-ATC2:NR1-Ar.HBA-ATC1:NR2-Ar-ATC5:NR2-None-ATC1 NR0-Ar-ATC1:N
    R1-Ar-ATC2:NR1-HBD-ATC1:NR2-Ar-ATC2:NR2-None-ATC1 NR0-Ar-ATC1:NR1-Ar-A
    TC2:NR1-Hal-ATC1:NR2-Ar-ATC2 NR0-Ar-ATC1:NR1-Ar-ATC2:NR1-None-ATC1:...

    FingerprintsVector;AtomNeighborhoods:MMFF94AtomTypes:MinRadius0:MaxRad
    ius2;41;AlphaNumericalValues;ValuesString;NR0-C5A-ATC1:NR1-C5B-ATC1:NR
    1-CB-ATC1:NR1-N5-ATC1:NR2-C5A-ATC1:NR2-C5B-ATC1:NR2-CB-ATC3:NR2-CR-ATC
    1 NR0-C5A-ATC1:NR1-C5B-ATC1:NR1-CR-ATC1:NR1-N5-ATC1:NR2-C5A-ATC1:NR2-C
    5B-ATC1:NR2-C=ON-ATC1:NR2-CR-ATC3 NR0-C5B-ATC1:NR1-C5A-ATC1:NR1-C5B-AT
    C1:NR1-C=ON-ATC1:NR2-C5A-ATC1:NR2-CB-ATC1:NR2-CR-ATC1:NR2-N5-ATC1:N...

    FingerprintsVector;AtomNeighborhoods:SLogPAtomTypes:MinRadius0:MaxRadi
    us2;41;AlphaNumericalValues;ValuesString;NR0-C1-ATC1:NR1-C10-ATC1:NR1-
    CS-ATC1:NR2-C1-ATC1:NR2-N11-ATC1:NR2-O2-ATC1 NR0-C1-ATC1:NR1-C11-ATC1:
    NR2-C1-ATC1:NR2-C21-ATC1 NR0-C1-ATC1:NR1-C11-ATC1:NR2-C1-ATC1:NR2-C21-
    ATC1 NR0-C1-ATC1:NR1-C5-ATC1:NR1-CS-ATC1:NR2-C1-ATC1:NR2-O2-ATC2:NR2-O
    9-ATC1 NR0-C1-ATC1:NR1-CS-ATC2:NR2-C1-ATC2:NR2-O2-ATC2 NR0-C10-ATC1...

    FingerprintsVector;AtomNeighborhoods:SYBYLAtomTypes:MinRadius0:MaxRadi
    us2;41;AlphaNumericalValues;ValuesString;NR0-C.2-ATC1:NR1-C.3-ATC1:NR1
    -O.co2-ATC2:NR2-C.3-ATC1 NR0-C.2-ATC1:NR1-C.ar-ATC1:NR1-N.am-ATC1:NR1-
    O.2-ATC1:NR2-C.ar-ATC3 NR0-C.3-ATC1:NR1-C.2-ATC1:NR1-C.3-ATC1:NR2-C.3-
    ATC1:NR2-O.3-ATC1:NR2-O.co2-ATC2 NR0-C.3-ATC1:NR1-C.3-ATC1:NR1-N.ar-AT
    C1:NR2-C.3-ATC1:NR2-C.ar-ATC2 NR0-C.3-ATC1:NR1-C.3-ATC1:NR2-C.3-ATC...

    FingerprintsVector;AtomNeighborhoods:TPSAAtomTypes:MinRadius0:MaxRadiu
    s2;41;AlphaNumericalValues;ValuesString;NR0-N21-ATC1:NR1-None-ATC3:NR2
    -None-ATC5 NR0-N7-ATC1:NR1-None-ATC2:NR2-None-ATC3:NR2-O3-ATC1 NR0-Non
    e-ATC1:NR1-N21-ATC1:NR1-None-ATC1:NR2-None-ATC3 NR0-None-ATC1:NR1-N21-
    ATC1:NR1-None-ATC2:NR2-None-ATC6 NR0-None-ATC1:NR1-N21-ATC1:NR1-None-A
    TC2:NR2-None-ATC6 NR0-None-ATC1:NR1-N7-ATC1:NR1-None-ATC1:NR1-O3-AT...

    FingerprintsVector;AtomNeighborhoods:UFFAtomTypes:MinRadius0:MaxRadius
    2;41;AlphaNumericalValues;ValuesString;NR0-C_2-ATC1:NR1-C_3-ATC1:NR1-O
    _2-ATC1:NR1-O_3-ATC1:NR2-C_3-ATC1 NR0-C_2-ATC1:NR1-C_R-ATC1:NR1-N_3-AT
    C1:NR1-O_2-ATC1:NR2-C_R-ATC3 NR0-C_3-ATC1:NR1-C_2-ATC1:NR1-C_3-ATC1:NR
    2-C_3-ATC1:NR2-O_2-ATC1:NR2-O_3-ATC2 NR0-C_3-ATC1:NR1-C_3-ATC1:NR1-N_R
    -ATC1:NR2-C_3-ATC1:NR2-C_R-ATC2 NR0-C_3-ATC1:NR1-C_3-ATC1:NR2-C_3-A...

=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.

=item B<-a, --AtomIdentifierType> I<AtomicInvariantsAtomTypes | DREIDINGAtomTypes | EStateAtomTypes | FunctionalClassAtomTypes | MMFF94AtomTypes | SLogPAtomTypes | SYBYLAtomTypes | TPSAAtomTypes | UFFAtomTypes>

Specify atom identifier type to use for assignment of initial atom identifier to non-hydrogen
atoms during calculation of atom neighborhoods 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<"AtomicInvariant,AtomicInvariant...">

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,X,BO,H,FC>.

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

I<AtomTypes::AtomicInvariantsAtomTypes> module is used to assign atomic invariant
atom types.

=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<--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<-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<AtomNeighborhoodsFingerprints>.

=item B<-h, --help>

Print this help message.

=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<--MinNeighborhoodRadius> I<number>

Minimum atom neighborhood radius for generating atom neighborhoods. Default value: I<0>.
Valid values: positive integers and less than B<--MaxNeighborhoodRadius>. Neighborhood
radius of zero corresponds to list of non-hydrogen atoms.

=item B<--MaxNeighborhoodRadius> I<number>

Maximum atom neighborhood radius for generating atom neighborhoods. Default value: I<2>.
Valid values: positive integers and greater than B<--MineighborhoodRadius>.

=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<-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><AtomNeighborhoodsFP>.<Ext>. The file type determines <Ext>
value. The sdf, fpf, csv, and tsv <Ext> values are used for SD, comma/semicolon, and tab
delimited text files, respectively.This option is ignored for multiple input files.

=item B<-w, --WorkingDir> I<DirName>

Location of working directory. Default: current directory.

=back

=head1 EXAMPLES

To generate atom neighborhoods fingerprints corresponding to atom neighborhood radii from 0 to
2 using atomic invariants atom types in vector string format and create a SampleANFP.csv
file containing sequential compound IDs along with fingerprints vector strings data, type:

    % AtomNeighborhoodsFingerprints.pl -r SampleANFP -o Sample.sdf

To generate atom neighborhoods fingerprints corresponding to atom neighborhood radii from 0 to
2 using DREIDING atom types in vector string format and create a SampleANFP.csv
file containing sequential compound IDs along with fingerprints vector strings data, type:

    % AtomNeighborhoodsFingerprints.pl -a DREIDINGAtomTypes -r SampleANFP
      -o Sample.sdf

To generate atom neighborhoods fingerprints corresponding to atom neighborhood radii from 0 to
2 using EStateAtomTypes types in vector string format and create a SampleANFP.csv
file containing sequential compound IDs along with fingerprints vector strings data, type:

    % AtomNeighborhoodsFingerprints.pl -a EStateAtomTypes -r SampleANFP
      -o Sample.sdf

To generate atom neighborhoods fingerprints corresponding to atom neighborhood radii from 0 to
2 using SYBYL atom types in vector string format and create a SampleANFP.csv
file containing sequential compound IDs along with fingerprints vector strings data, type:

    % AtomNeighborhoodsFingerprints.pl -a SYBYLAtomTypes -r SampleANFP
      -o Sample.sdf

To generate atom neighborhoods fingerprints corresponding to atom neighborhood radii from 0 to
2 using FunctionalClass atom types in vector string format and create a SampleANFP.csv
file containing sequential compound IDs along with fingerprints vector strings data, type:

    % AtomNeighborhoodsFingerprints.pl -a FunctionalClassAtomTypes
      -r SampleANFP -o Sample.sdf

To generate atom neighborhoods fingerprints corresponding to atom neighborhood radii from 0 to
2 using MMFF94 atom types in vector string format and create a SampleANFP.csv
file containing sequential compound IDs along with fingerprints vector strings data, type:

    % AtomNeighborhoodsFingerprints.pl -a MMFF94AtomTypes -r SampleANFP
      -o Sample.sdf

To generate atom neighborhoods fingerprints corresponding to atom neighborhood radii from 0 to
2 using SLogP atom types in vector string format and create a SampleANFP.csv
file containing sequential compound IDs along with fingerprints vector strings data, type:

    % AtomNeighborhoodsFingerprints.pl -a SLogPAtomTypes -r SampleANFP
      -o Sample.sdf

To generate atom neighborhoods fingerprints corresponding to atom neighborhood radii from 0 to
2 using SYBYL atom types in vector string format and create a SampleANFP.csv
file containing sequential compound IDs along with fingerprints vector strings data, type:

    % AtomNeighborhoodsFingerprints.pl -a SYBYLAtomTypes -r SampleANFP
      -o Sample.sdf

To generate atom neighborhoods fingerprints corresponding to atom neighborhood radii from 0 to
2 using TPSA atom types in vector string format and create a SampleANFP.csv
file containing sequential compound IDs along with fingerprints vector strings data, type:

    % AtomNeighborhoodsFingerprints.pl -a TPSAAtomTypes -r SampleANFP
      -o Sample.sdf

To generate atom neighborhoods fingerprints corresponding to atom neighborhood radii from 0 to
2 using UFF atom types in vector string format and create a SampleANFP.csv
file containing sequential compound IDs along with fingerprints vector strings data, type:

    % AtomNeighborhoodsFingerprints.pl -a UFFAtomTypes -r SampleANFP
      -o Sample.sdf

To generate atom neighborhoods fingerprints corresponding to atom neighborhood radii from 0 to
2 using atomic invariants atom types in vector string format and create SampleANFP.sdf,
SampleANFP.fpf and SampleANFP.csv files containing sequential compound IDs in CSV file along
with fingerprints vector strings data, type:

    % AtomNeighborhoodsFingerprints.pl --output all -r SampleANFP
      -o Sample.sdf

To generate atom neighborhoods fingerprints corresponding to atom neighborhood radii from 1 to
3 using atomic invariants atom types in vector string format and create a SampleANFP.csv
file containing sequential compound IDs along with fingerprints vector strings data, type:

    % AtomNeighborhoodsFingerprints.pl -a AtomicInvariantsAtomTypes
      --MinNeighborhoodRadius 1 --MaxNeighborhoodRadius 3 -r SampleANFP
      -o Sample.sdf

To generate atom neighborhoods fingerprints corresponding to atom neighborhood radii from 0 to
2 using only AS,X atomic invariants atom types in vector string format and create a SampleANFP.csv
file containing sequential compound IDs along with fingerprints vector strings data, type:

    % AtomNeighborhoodsFingerprints.pl -a AtomicInvariantsAtomTypes
      --AtomicInvariantsToUse "AS,X" --MinNeighborhoodRadius 0
      --MaxNeighborhoodRadius 3 -r SampleANFP -o Sample.sdf

To generate atom neighborhoods fingerprints corresponding to atom neighborhood radii from 0 to
2 using atomic invariants atom types in vector string format and create a SampleANFP.csv
file containing compound ID from molecule name line along with fingerprints vector strings data, type:

    % AtomNeighborhoodsFingerprints.pl -a AtomicInvariantsAtomTypes
      --DataFieldsMode CompoundID --CompoundIDMode MolName
      -r SampleANFP -o Sample.sdf

To generate atom neighborhoods fingerprints corresponding to atom neighborhood radii from 0 to
2 using atomic invariants atom types in vector string format and create a SampleANFP.csv
file containing compound IDs using specified data field along with fingerprints vector strings
data, type:

    % AtomNeighborhoodsFingerprints.pl -a AtomicInvariantsAtomTypes
      --DataFieldsMode CompoundID --CompoundIDMode DataField --CompoundID
      Mol_ID -r SampleANFP -o Sample.sdf

To generate atom neighborhoods fingerprints corresponding to atom neighborhood radii from 0 to
2 using atomic invariants atom types in vector string format and create a SampleANFP.csv
file containing compound ID using combination of molecule name line and an explicit compound
prefix along with fingerprints vector strings data, type:

    % AtomNeighborhoodsFingerprints.pl -a AtomicInvariantsAtomTypes
      --DataFieldsMode CompoundID --CompoundIDMode MolnameOrLabelPrefix
      --CompoundID Cmpd --CompoundIDLabel MolID -r SampleANFP -o Sample.sdf

To generate atom neighborhoods fingerprints corresponding to atom neighborhood radii from 0 to
2 using atomic invariants atom types in vector string format and create a SampleANFP.csv
file containing specific data fields columns along with fingerprints vector strings
data, type:

    % AtomNeighborhoodsFingerprints.pl -a AtomicInvariantsAtomTypes
      --DataFieldsMode Specify --DataFields Mol_ID -r SampleANFP
      -o Sample.sdf

To generate atom neighborhoods fingerprints corresponding to atom neighborhood radii from 0 to
2 using atomic invariants atom types in vector string format and create a SampleANFP.csv
file containing common data fields columns along with fingerprints vector strings
data, type:

    % AtomNeighborhoodsFingerprints.pl -a AtomicInvariantsAtomTypes
      --DataFieldsMode Common -r SampleANFP -o Sample.sdf

To generate atom neighborhoods fingerprints corresponding to atom neighborhood radii from 0 to
2 using atomic invariants atom types in vector string format and create SampleANFP.sdf,
 SampleANFP.fpf and SampleANFP.csv files containing all data fields columns in CSV file along with
fingerprints data, type:

    % AtomNeighborhoodsFingerprints.pl -a AtomicInvariantsAtomTypes
      --DataFieldsMode All  --output all -r SampleANFP
      -o Sample.sdf

=head1 AUTHOR

Manish Sud <[e-mail]>

=head1 SEE ALSO

InfoFingerprintsFiles.pl, SimilarityMatricesFingerprints.pl, SimilaritySearchingFingerprints.pl,
ExtendedConnectivityFingerprints.pl, MACCSKeysFingerprints.pl, PathLengthFingerprints.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