Mercurial > repos > deepakjadmin > r_caret_test
diff mayachemtool/mayachemtools/bin/PathLengthFingerprints.pl @ 0:68300206e90d draft default tip
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| author | deepakjadmin |
|---|---|
| date | Thu, 05 Nov 2015 02:41:30 -0500 |
| parents | |
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--- /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