Mercurial > repos > deepakjadmin > mayatool3_test2
diff bin/CalculatePhysicochemicalProperties.pl @ 0:4816e4a8ae95 draft default tip
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| author | deepakjadmin |
|---|---|
| date | Wed, 20 Jan 2016 09:23:18 -0500 |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/bin/CalculatePhysicochemicalProperties.pl Wed Jan 20 09:23:18 2016 -0500 @@ -0,0 +1,1951 @@ +#!/usr/bin/perl -w +# +# $RCSfile: CalculatePhysicochemicalProperties.pl,v $ +# $Date: 2015/02/28 20:46:19 $ +# $Revision: 1.20 $ +# +# 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 "$FindBin::Bin/../lib"; +use Getopt::Long; +use File::Basename; +use Text::ParseWords; +use Benchmark; +use FileUtil; +use TextUtil; +use SDFileUtil; +use MoleculeFileIO; +use Molecule; +use AtomTypes::AtomicInvariantsAtomTypes; +use AtomTypes::FunctionalClassAtomTypes; +use MolecularDescriptors::MolecularDescriptorsGenerator; + +my($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"; + CalculatePhysicochemicalProperties($FileIndex); + } +} +print "\n$ScriptName:Done...\n\n"; + +$EndTime = new Benchmark; +$TotalTime = timediff ($EndTime, $StartTime); +print "Total time: ", timestr($TotalTime), "\n"; + +############################################################################### + +# Calculate physicochemical properties for a SD file... +# +sub CalculatePhysicochemicalProperties { + my($FileIndex) = @_; + my($CmpdCount, $IgnoredCmpdCount, $RuleOf5ViolationsCount, $RuleOf3ViolationsCount, $SDFile, $MoleculeFileIO, $Molecule, $MolecularDescriptorsGenerator, $PhysicochemicalPropertiesDataRef, $NewSDFileRef, $NewTextFileRef); + + $SDFile = $SDFilesList[$FileIndex]; + + # Setup output files... + $NewSDFileRef = ''; $NewTextFileRef = ''; + ($NewSDFileRef, $NewTextFileRef) = SetupAndOpenOutputFiles($FileIndex); + + # Setup molecular descriptor generator to calculate property values for specifed + # property names... + $MolecularDescriptorsGenerator = SetupMolecularDescriptorsGenerator(); + + ($CmpdCount, $IgnoredCmpdCount, $RuleOf5ViolationsCount, $RuleOf3ViolationsCount) = ('0') x 4; + + $MoleculeFileIO = new MoleculeFileIO('Name' => $SDFile); + $MoleculeFileIO->Open(); + + COMPOUND: while ($Molecule = $MoleculeFileIO->ReadMolecule()) { + $CmpdCount++; + + # Filter compound data before calculating physiochemical properties... + if ($OptionsInfo{Filter}) { + if (CheckAndFilterCompound($CmpdCount, $Molecule)) { + $IgnoredCmpdCount++; + next COMPOUND; + } + } + + # Calculate properties... + $PhysicochemicalPropertiesDataRef = CalculateMoleculeProperties($MolecularDescriptorsGenerator, $Molecule); + + if (!defined($PhysicochemicalPropertiesDataRef)) { + $IgnoredCmpdCount++; + ProcessIgnoredCompound('PropertiesCalculationFailed', $CmpdCount, $Molecule); + next COMPOUND; + } + + # Calculate any rule violations... + if ($OptionsInfo{RuleOf5Violations} && $PhysicochemicalPropertiesDataRef->{RuleOf5Violations}) { + $RuleOf5ViolationsCount++; + } + + if ($OptionsInfo{RuleOf3Violations} && $PhysicochemicalPropertiesDataRef->{RuleOf3Violations}) { + $RuleOf3ViolationsCount++; + } + + # Write out calculate properties... + WriteDataToOutputFiles($FileIndex, $CmpdCount, $Molecule, $PhysicochemicalPropertiesDataRef, $NewSDFileRef, $NewTextFileRef); + } + $MoleculeFileIO->Close(); + + if ($OptionsInfo{SDOutput} && $NewSDFileRef) { + close $NewSDFileRef; + } + if ($OptionsInfo{TextOutput} && $NewTextFileRef) { + close $NewTextFileRef; + } + + WriteCalculationSummaryStatistics($CmpdCount, $IgnoredCmpdCount, $RuleOf5ViolationsCount, $RuleOf3ViolationsCount); +} + +# Process compound being ignored due to problems in physicochemical properties calculation... +# +sub ProcessIgnoredCompound { + my($Mode, $CmpdCount, $Molecule) = @_; + my($CmpdID, $DataFieldLabelAndValuesRef); + + $DataFieldLabelAndValuesRef = $Molecule->GetDataFieldLabelAndValues(); + $CmpdID = SetupCmpdIDForTextFiles($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 =~ /^PropertiesCalculationFailed$/i) { + warn "\nWarning: Ignoring compound record number $CmpdCount with ID $CmpdID: Physicochemical properties calculation didn't succeed...\n\n"; + next MODE; + } + warn "\nWarning: Ignoring compound record number $CmpdCount with ID $CmpdID: Physicochemical properties calculation didn't succeed...\n\n"; + } +} + +# Check and filter compounds.... +# +sub CheckAndFilterCompound { + my($CmpdCount, $Molecule) = @_; + my($ElementCount, $NonElementCount); + + ($ElementCount, $NonElementCount) = $Molecule->GetNumOfElementsAndNonElements(); + + if ($NonElementCount) { + ProcessIgnoredCompound('ContainsNonElementalData', $CmpdCount, $Molecule); + return 1; + } + + if (!$ElementCount) { + ProcessIgnoredCompound('ContainsNoElementalData', $CmpdCount, $Molecule); + return 1; + } + + return 0; +} + +# Write out compounds physicochemical properties calculation summary statistics... +# +sub WriteCalculationSummaryStatistics { + my($CmpdCount, $IgnoredCmpdCount, $RuleOf5ViolationsCount, $RuleOf3ViolationsCount) = @_; + my($ProcessedCmpdCount); + + $ProcessedCmpdCount = $CmpdCount - $IgnoredCmpdCount; + + print "\nNumber of compounds: $CmpdCount\n"; + print "Number of compounds processed successfully during physicochemical properties calculation: $ProcessedCmpdCount\n"; + print "Number of compounds ignored during physicochemical properties calculation: $IgnoredCmpdCount\n"; + + if ($OptionsInfo{RuleOf5Violations}) { + print "Number of compounds with one or more RuleOf5 violations: $RuleOf5ViolationsCount\n"; + } + + if ($OptionsInfo{RuleOf3Violations}) { + print "Number of compounds with one or more RuleOf3 violations: $RuleOf3ViolationsCount\n"; + } + +} + +# Open output files... +# +sub SetupAndOpenOutputFiles { + my($FileIndex) = @_; + my($NewSDFile, $NewTextFile, $NewSDFileRef, $NewTextFileRef); + + $NewSDFileRef = ''; + $NewTextFileRef = ''; + + if ($OptionsInfo{SDOutput}) { + $NewSDFile = $SDFilesInfo{SDOutFileNames}[$FileIndex]; + print "Generating SD file $NewSDFile...\n"; + open NEWSDFILE, ">$NewSDFile" or die "Error: Couldn't open $NewSDFile: $! \n"; + $NewSDFileRef = \*NEWSDFILE; + } + if ($OptionsInfo{TextOutput}) { + $NewTextFile = $SDFilesInfo{TextOutFileNames}[$FileIndex]; + print "Generating text file $NewTextFile...\n"; + open NEWTEXTFILE, ">$NewTextFile" or die "Error: Couldn't open $NewTextFile: $! \n"; + WriteTextFileCoulmnLabels($FileIndex, \*NEWTEXTFILE); + $NewTextFileRef = \*NEWTEXTFILE; + } + return ($NewSDFileRef, $NewTextFileRef); +} + +# Write calculated physicochemical properties and other data to appropriate output files... +# +sub WriteDataToOutputFiles { + my($FileIndex, $CmpdCount, $Molecule, $PhysicochemicalPropertiesDataRef, $NewSDFileRef, $NewTextFileRef) = @_; + my($PropertyName, $PropertyValue); + + if ($OptionsInfo{SDOutput}) { + # Retrieve input compound string used to create molecule and write it out + # without last line containing a delimiter... + my($CmpdString); + $CmpdString = $Molecule->GetInputMoleculeString(); + $CmpdString =~ s/\$\$\$\$$//; + print $NewSDFileRef "$CmpdString"; + + # Write out calculated physicochemical properties data... + for $PropertyName (@{$OptionsInfo{SpecifiedPropertyNames}}) { + $PropertyValue = $PhysicochemicalPropertiesDataRef->{$PropertyName}; + print $NewSDFileRef "> <$PropertyName>\n$PropertyValue\n\n"; + } + + # Write out RuleOf5 violations for molecule.... + if ($OptionsInfo{RuleOf5Violations}) { + $PropertyValue = $PhysicochemicalPropertiesDataRef->{RuleOf5Violations}; + print $NewSDFileRef "> <RuleOf5Violations>\n$PropertyValue\n\n"; + } + + # Write out RuleOf3 violations for molecule.... + if ($OptionsInfo{RuleOf3Violations}) { + $PropertyValue = $PhysicochemicalPropertiesDataRef->{RuleOf3Violations}; + print $NewSDFileRef "> <RuleOf3Violations>\n$PropertyValue\n\n"; + } + + # Write out delimiter... + print $NewSDFileRef "\$\$\$\$\n"; + } + + if ($OptionsInfo{TextOutput}) { + my($Line, $DataFieldLabelAndValuesRef, $DataFieldLabel, $DataFieldValue, @LineWords,); + + $DataFieldLabelAndValuesRef = $Molecule->GetDataFieldLabelAndValues(); + @LineWords = (); + if ($OptionsInfo{DataFieldsMode} =~ /^CompoundID$/i) { + push @LineWords, SetupCmpdIDForTextFiles($CmpdCount, $Molecule, $DataFieldLabelAndValuesRef); + } + elsif ($OptionsInfo{DataFieldsMode} =~ /^All$/i) { + @LineWords = map { exists $DataFieldLabelAndValuesRef->{$_} ? $DataFieldLabelAndValuesRef->{$_} : ''} @{$SDFilesInfo{AllDataFieldsRef}[$FileIndex]}; + } + elsif ($OptionsInfo{DataFieldsMode} =~ /^Common$/i) { + @LineWords = map { exists $DataFieldLabelAndValuesRef->{$_} ? $DataFieldLabelAndValuesRef->{$_} : ''} @{$SDFilesInfo{CommonDataFieldsRef}[$FileIndex]}; + } + elsif ($OptionsInfo{DataFieldsMode} =~ /^Specify$/i) { + @LineWords = map { exists $DataFieldLabelAndValuesRef->{$_} ? $DataFieldLabelAndValuesRef->{$_} : ''} @{$OptionsInfo{SpecifiedDataFields}}; + } + + # Append calculated physicochemical properties data... + for $PropertyName (@{$OptionsInfo{SpecifiedPropertyNames}}) { + $PropertyValue = $PhysicochemicalPropertiesDataRef->{$PropertyName}; + push @LineWords, $PropertyValue; + } + + # Write out RuleOf5 violations for molecule.... + if ($OptionsInfo{RuleOf5Violations}) { + $PropertyValue = $PhysicochemicalPropertiesDataRef->{RuleOf5Violations}; + push @LineWords, $PropertyValue; + } + + # Write out RuleOf3 violations for molecule.... + if ($OptionsInfo{RuleOf3Violations}) { + $PropertyValue = $PhysicochemicalPropertiesDataRef->{RuleOf3Violations}; + push @LineWords, $PropertyValue; + } + + $Line = JoinWords(\@LineWords, $OptionsInfo{OutDelim}, $OptionsInfo{OutQuote}); + print $NewTextFileRef "$Line\n"; + } +} + +# Write out approriate column labels to text file... +sub WriteTextFileCoulmnLabels { + my($FileIndex, $NewTextFileRef) = @_; + my($Line, @LineWords); + + @LineWords = (); + if ($OptionsInfo{DataFieldsMode} =~ /^All$/i) { + push @LineWords, @{$SDFilesInfo{AllDataFieldsRef}[$FileIndex]}; + } + elsif ($OptionsInfo{DataFieldsMode} =~ /^Common$/i) { + push @LineWords, @{$SDFilesInfo{CommonDataFieldsRef}[$FileIndex]}; + } + elsif ($OptionsInfo{DataFieldsMode} =~ /^Specify$/i) { + push @LineWords, @{$OptionsInfo{SpecifiedDataFields}}; + } + elsif ($OptionsInfo{DataFieldsMode} =~ /^CompoundID$/i) { + push @LineWords, $OptionsInfo{CompoundIDLabel}; + } + my($SpecifiedPropertyName); + + # Append physicochemical properties column labels... + push @LineWords, @{$OptionsInfo{SpecifiedPropertyNames}}; + + # Write out RuleOf5 violations label... + if ($OptionsInfo{RuleOf5Violations}) { + push @LineWords, 'RuleOf5Violations'; + } + + # Write out RuleOf3 violations label... + if ($OptionsInfo{RuleOf3Violations}) { + push @LineWords, 'RuleOf3Violations'; + } + + $Line = JoinWords(\@LineWords, $OptionsInfo{OutDelim}, $OptionsInfo{OutQuote}); + print $NewTextFileRef "$Line\n"; +} + +# Generate compound ID for text files.. +# +sub SetupCmpdIDForTextFiles { + 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 $CmpdID; +} + +# Calculate physicochemical properties for molecule... +# +sub CalculateMoleculeProperties { + my($MolecularDescriptorsGenerator, $Molecule) = @_; + my($PropertyName, $PropertyValue, $MolecularDescriptorsObject, %CalculatedPhysicochemicalProperties); + + %CalculatedPhysicochemicalProperties = (); + + if ($OptionsInfo{KeepLargestComponent}) { + $Molecule->KeepLargestComponent(); + } + + if (!$Molecule->DetectRings()) { + return undef; + } + $Molecule->SetAromaticityModel($OptionsInfo{AromaticityModel}); + $Molecule->DetectAromaticity(); + + if ($OptionsInfo{AddHydrogens}) { + $Molecule->AddHydrogens(); + } + + # Calculate physicochemical properties... + $MolecularDescriptorsGenerator->SetMolecule($Molecule); + $MolecularDescriptorsGenerator->GenerateDescriptors(); + + if (!$MolecularDescriptorsGenerator->IsDescriptorsGenerationSuccessful()) { + return undef; + } + + %CalculatedPhysicochemicalProperties = $MolecularDescriptorsGenerator->GetDescriptorNamesAndValues(); + + # Count RuleOf3 violations... + if ($OptionsInfo{RuleOf3Violations}) { + CalculateRuleViolationsCount('RuleOf3Violations', \%CalculatedPhysicochemicalProperties); + } + + # Count RuleOf5 violations... + if ($OptionsInfo{RuleOf5Violations}) { + CalculateRuleViolationsCount('RuleOf5Violations', \%CalculatedPhysicochemicalProperties); + } + + return \%CalculatedPhysicochemicalProperties; +} + +# Setup molecular descriptor generator to calculate property values for specifed +# property names... +# +sub SetupMolecularDescriptorsGenerator { + my($PropertyName, $MolecularDescriptorsGenerator); + + $MolecularDescriptorsGenerator = new MolecularDescriptors::MolecularDescriptorsGenerator('Mode' => 'Specify', 'DescriptorNames' => \@{$OptionsInfo{SpecifiedPropertyNames}}); + + # Setup molecular desciptor calculation parameters... + if (exists($OptionsInfo{SpecifiedPropertyNamesMap}{lc('MolecularWeight')}) || exists($OptionsInfo{SpecifiedPropertyNamesMap}{lc('ExactMass')}) ) { + $MolecularDescriptorsGenerator->SetDescriptorClassParameters('DescriptorClassName' => 'WeightAndMassDescriptors', %{$OptionsInfo{PrecisionParametersMap}}); + } + + if (exists($OptionsInfo{SpecifiedPropertyNamesMap}{lc('RotatableBonds')})) { + $MolecularDescriptorsGenerator->SetDescriptorClassParameters('DescriptorClassName' => 'RotatableBondsDescriptors', %{$OptionsInfo{RotatableBondsParametersMap}}); + } + + if (exists($OptionsInfo{SpecifiedPropertyNamesMap}{lc('HydrogenBondDonors')}) || exists($OptionsInfo{SpecifiedPropertyNamesMap}{lc('HydrogenBondAcceptors')}) ) { + $MolecularDescriptorsGenerator->SetDescriptorClassParameters('DescriptorClassName' => 'HydrogenBondsDescriptors', 'HydrogenBondsType' => $OptionsInfo{HydrogenBonds}); + } + + if (exists($OptionsInfo{SpecifiedPropertyNamesMap}{lc('TPSA')})) { + $MolecularDescriptorsGenerator->SetDescriptorClassParameters('DescriptorClassName' => 'TPSADescriptors', %{$OptionsInfo{TPSAParametersMap}}); + } + + if (exists($OptionsInfo{SpecifiedPropertyNamesMap}{lc('MolecularComplexity')})) { + $MolecularDescriptorsGenerator->SetDescriptorClassParameters('DescriptorClassName' => 'MolecularComplexityDescriptors', %{$OptionsInfo{MolecularComplexityParametersMap}}); + } + + return $MolecularDescriptorsGenerator; +} + +# Calculate RuleOf3 or RuleOf5 violations count... +# +sub CalculateRuleViolationsCount { + my($RuleViolationsType, $CalculatedPropertiesMapRef) = @_; + my($RuleViolationsCount, $PropertyName); + + $RuleViolationsCount = 0; + + RULEVIOLATIONSTYPE: { + if ($RuleViolationsType =~ /^RuleOf3Violations$/i) { + for $PropertyName (@{$OptionsInfo{RuleOf3PropertyNames}}) { + if ($CalculatedPropertiesMapRef->{$PropertyName} > $OptionsInfo{RuleOf3MaxPropertyValuesMap}{$PropertyName}) { + $RuleViolationsCount++; + } + } + last RULEVIOLATIONSTYPE; + } + + if ($RuleViolationsType =~ /^RuleOf5Violations$/i) { + for $PropertyName (@{$OptionsInfo{RuleOf5PropertyNames}}) { + if ($CalculatedPropertiesMapRef->{$PropertyName} > $OptionsInfo{RuleOf5MaxPropertyValuesMap}{$PropertyName}) { + $RuleViolationsCount++; + } + } + last RULEVIOLATIONSTYPE; + } + + die "Warning: Unknown rule violation type: $RuleViolationsType..."; + } + + # Set rule violation count... + $CalculatedPropertiesMapRef->{$RuleViolationsType} = $RuleViolationsCount; + +} + +# Retrieve information about SD files... +# +sub RetrieveSDFilesInfo { + my($SDFile, $Index, $FileDir, $FileExt, $FileName, $OutFileRoot, $TextOutFileExt, $SDOutFileExt, $NewSDFileName, $NewTextFileName, $CheckDataField, $CollectDataFields, $AllDataFieldsRef, $CommonDataFieldsRef); + + %SDFilesInfo = (); + @{$SDFilesInfo{FileOkay}} = (); + @{$SDFilesInfo{OutFileRoot}} = (); + @{$SDFilesInfo{SDOutFileNames}} = (); + @{$SDFilesInfo{TextOutFileNames}} = (); + @{$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] = ''; + $SDFilesInfo{TextOutFileNames}[$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 = $FileExt; + + if ($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}PhysicochemicalProperties"; + } + + $NewSDFileName = "${OutFileRoot}.${SDOutFileExt}"; + $NewTextFileName = "${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{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; + $SDFilesInfo{TextOutFileNames}[$Index] = $NewTextFileName; + + $SDFilesInfo{AllDataFieldsRef}[$Index] = $AllDataFieldsRef; + $SDFilesInfo{CommonDataFieldsRef}[$Index] = $CommonDataFieldsRef; + } +} + +# Process option values... +sub ProcessOptions { + %OptionsInfo = (); + + $OptionsInfo{AromaticityModel} = $Options{aromaticitymodel}; + + # Process property name related options... + ProcessPropertyNamesOption(); + + # Setup RuleOf3 and RuleOf5 violation calculations... + $OptionsInfo{RuleOf3Violations} = ($Options{ruleof3violations} =~ /^Yes$/i) ? 1 : 0; + $OptionsInfo{RuleOf5Violations} = ($Options{ruleof5violations} =~ /^Yes$/i) ? 1 : 0; + + $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; + } + + # Types of hydrogen bonds... + $OptionsInfo{HydrogenBonds} = $Options{hydrogenbonds}; + + # Process precision value parameters... + ProcessPrecisionOption(); + + # Process rotatable bonds parameters... + ProcessRotatableBondsOption(); + + # Process TPSA parameters... + ProcessTPSAOption(); + + # Process molecular complexity parameters... + ProcessMolecularComplexityOption(); + + $OptionsInfo{Filter} = ($Options{filter} =~ /^Yes$/i) ? 1 : 0; + + $OptionsInfo{KeepLargestComponent} = ($Options{keeplargestcomponent} =~ /^Yes$/i) ? 1 : 0; + + $OptionsInfo{Output} = $Options{output}; + $OptionsInfo{SDOutput} = ($Options{output} =~ /^(SD|Both)$/i) ? 1 : 0; + $OptionsInfo{TextOutput} = ($Options{output} =~ /^(Text|Both)$/i) ? 1 : 0; + + $OptionsInfo{OutDelim} = ($Options{outdelim} =~ /tab/i ) ? "\t" : (($Options{outdelim} =~ /semicolon/i) ? "\;" : "\,"); + $OptionsInfo{OutQuote} = ($Options{quote} =~ /^Yes$/i) ? 1 : 0; + + $OptionsInfo{OverwriteFiles} = $Options{overwrite} ? 1 : 0; + $OptionsInfo{OutFileRoot} = $Options{root} ? $Options{root} : 0; +} + +# Process property name related options... +# +sub ProcessPropertyNamesOption { + + # Setup supported physicochemical properties... + my($SupportedProperty); + + @{$OptionsInfo{SupportedPropertyNames}} = (); + %{$OptionsInfo{SupportedPropertyNamesMap}} = (); + + @{$OptionsInfo{RuleOf5PropertyNames}} = (); + %{$OptionsInfo{RuleOf5MaxPropertyValuesMap}} = (); + + @{$OptionsInfo{RuleOf3PropertyNames}} = (); + %{$OptionsInfo{RuleOf3MaxPropertyValuesMap}} = (); + + @{$OptionsInfo{DefaultPropertyNames}} = (); + + @{$OptionsInfo{SupportedPropertyNames}} = qw(MolecularWeight ExactMass HeavyAtoms Rings AromaticRings MolecularVolume RotatableBonds HydrogenBondDonors HydrogenBondAcceptors SLogP SMR TPSA Fsp3Carbons Sp3Carbons MolecularComplexity); + + @{$OptionsInfo{RuleOf5PropertyNames}} = qw(MolecularWeight HydrogenBondDonors HydrogenBondAcceptors SLogP); + %{$OptionsInfo{RuleOf5MaxPropertyValuesMap}} = ('MolecularWeight' => 500, 'HydrogenBondDonors' => 5, 'HydrogenBondAcceptors' => 10, 'SLogP' => 5); + + @{$OptionsInfo{RuleOf3PropertyNames}} = qw(MolecularWeight RotatableBonds HydrogenBondDonors HydrogenBondAcceptors SLogP TPSA); + %{$OptionsInfo{RuleOf3MaxPropertyValuesMap}} = ('MolecularWeight' => 300, 'RotatableBonds' => 3, 'HydrogenBondDonors' => 3, 'HydrogenBondAcceptors' => 3, 'SLogP' => 3, 'TPSA' => 60); + + @{$OptionsInfo{DefaultPropertyNames}} = qw(MolecularWeight HeavyAtoms MolecularVolume RotatableBonds HydrogenBondDonors HydrogenBondAcceptors SLogP TPSA); + + for $SupportedProperty (@{$OptionsInfo{SupportedPropertyNames}}) { + $OptionsInfo{SupportedPropertyNamesMap}{lc($SupportedProperty)} = $SupportedProperty; + } + + # Process specified properties.... + my($SpecifiedPropertyName, @SpecifiedPropertyNames, %SpecifiedPropertyNamesMap); + + @SpecifiedPropertyNames = (); + %SpecifiedPropertyNamesMap = (); + + @{$OptionsInfo{SpecifiedPropertyNames}} = (); + %{$OptionsInfo{SpecifiedPropertyNamesMap}} = (); + + if ($Options{mode} =~ /^All$/i) { + @SpecifiedPropertyNames = @{$OptionsInfo{SupportedPropertyNames}}; + } + elsif ($Options{mode} =~ /^RuleOf5$/i) { + @SpecifiedPropertyNames = @{$OptionsInfo{RuleOf5PropertyNames}}; + } + elsif ($Options{mode} =~ /^RuleOf3$/i) { + @SpecifiedPropertyNames = @{$OptionsInfo{RuleOf3PropertyNames}}; + } + elsif (IsEmpty($Options{mode})) { + @SpecifiedPropertyNames = @{$OptionsInfo{DefaultPropertyNames}}; + } + else { + # Comma delimited lisr of specified property names... + my($Mode, $PropertyName, @PropertyNames, @UnsupportedPropertyNames); + + $Mode = $Options{mode}; + $Mode =~ s/ //g; + + @PropertyNames = split ",", $Mode; + @UnsupportedPropertyNames = (); + + for $PropertyName (@PropertyNames) { + if (exists($OptionsInfo{SupportedPropertyNamesMap}{lc($PropertyName)})) { + push @SpecifiedPropertyNames, $PropertyName; + } + else { + push @UnsupportedPropertyNames, $PropertyName; + } + } + if (@UnsupportedPropertyNames) { + if (@UnsupportedPropertyNames > 1) { + warn "Error: The physicochemical property names specified - ", JoinWords(\@UnsupportedPropertyNames, ", ", 0)," - for option \"-m --mode\" are not valid.\n"; + } + else { + warn "Error: The physicochemical property name specified, @UnsupportedPropertyNames , for option \"-m --mode\" is not valid.\n"; + } + die "Allowed values:", JoinWords(\@{$OptionsInfo{SupportedPropertyNames}}, ", ", 0), "\n"; + } + if (!@SpecifiedPropertyNames) { + die "Error: No valid physicochemical property names specified for option \"-m --mode\".\n"; + } + } + + # Set up specified property names map... + PROPERTY: for $SpecifiedPropertyName (@SpecifiedPropertyNames) { + if (exists $SpecifiedPropertyNamesMap{lc($SpecifiedPropertyName)}) { + warn "Warning: The physicochemical property name, $SpecifiedPropertyName, is specified multiple times as value of option \"-m --mode\" .\n"; + next PROPERTY; + } + # Canonical specified property name... + $SpecifiedPropertyNamesMap{lc($SpecifiedPropertyName)} = $OptionsInfo{SupportedPropertyNamesMap}{lc($SpecifiedPropertyName)}; + } + + # Make sure for calculation of RuleOf3Violations, all appropriate property names are specified... + if ($Options{ruleof3violations} =~ /^Yes$/i && $Options{mode} =~ /^RuleOf5$/i) { + die "Error: The value specified, $Options{ruleof3violations}, for \"--RuleOf3Violations\" option in \"RuleOf5\" \"-m --Mode\" is not valid. You must specify RuleOf3 value for \"-m --Mode\" to calculate RuleOf3 violations.\n"; + } + + if ($Options{ruleof3violations} =~ /^Yes$/i) { + my($RuleOf3PropertyName, @MissingRuleOf3Names); + + @MissingRuleOf3Names = (); + PROPERTY: for $RuleOf3PropertyName (@{$OptionsInfo{RuleOf3PropertyNames}}) { + if (exists $SpecifiedPropertyNamesMap{lc($RuleOf3PropertyName)}) { + next PROPERTY; + } + push @MissingRuleOf3Names, $RuleOf3PropertyName; + + # Add property name to specified properties names list and map... + push @SpecifiedPropertyNames, $RuleOf3PropertyName; + $SpecifiedPropertyNamesMap{lc($RuleOf3PropertyName)} = $OptionsInfo{SupportedPropertyNamesMap}{lc($RuleOf3PropertyName)}; + } + if (@MissingRuleOf3Names) { + warn "Warning: The following physicochemical property names not specified in \"-m --Mode\" option are required for calculating RuleOf3Violations and have been added to the list of property names: @MissingRuleOf3Names\n"; + } + } + + # Make sure for calculation of RuleOf5Violations, all appropriate property names are specified... + if ($Options{ruleof5violations} =~ /^Yes$/i && $Options{mode} =~ /^RuleOf3$/i) { + die "Error: The value specified, $Options{ruleof5violations}, for \"--RuleOf5Violations\" option in \"RuleOf3\" \"-m --Mode\" is not valid. You must specify RuleOf5 value for \"-m --Mode\" to calculate RuleOf5 violations.\n"; + } + + if ($Options{ruleof5violations} =~ /^Yes$/i) { + my($RuleOf5PropertyName, @MissingRuleOf5Names); + + @MissingRuleOf5Names = (); + PROPERTY: for $RuleOf5PropertyName (@{$OptionsInfo{RuleOf5PropertyNames}}) { + if (exists $SpecifiedPropertyNamesMap{lc($RuleOf5PropertyName)}) { + next PROPERTY; + } + push @MissingRuleOf5Names, $RuleOf5PropertyName; + + # Add property name to specified properties names list and map... + push @SpecifiedPropertyNames, $RuleOf5PropertyName; + $SpecifiedPropertyNamesMap{lc($RuleOf5PropertyName)} = $OptionsInfo{SupportedPropertyNamesMap}{lc($RuleOf5PropertyName)}; + } + if (@MissingRuleOf5Names) { + warn "Warning: The following physicochemical property names not specified in \"-m --Mode\" option are required for calculating RuleOf5Violations and have been added to the list of property names: @MissingRuleOf5Names\n"; + } + } + $OptionsInfo{Mode} = $Options{mode}; + + # Setup canonical specified property names corresponding to supported names in mixed case... + my(@SpecifiedCanonicalPropertyNames); + + @SpecifiedCanonicalPropertyNames = (); + for $SpecifiedPropertyName (@SpecifiedPropertyNames) { + push @SpecifiedCanonicalPropertyNames, $SpecifiedPropertyNamesMap{lc($SpecifiedPropertyName)}; + } + @{$OptionsInfo{SpecifiedPropertyNames}} = @SpecifiedCanonicalPropertyNames; + %{$OptionsInfo{SpecifiedPropertyNamesMap}} = %SpecifiedPropertyNamesMap; + + # Based on specified property names, figure out whether hydrogens need to be added before + # calculation of properties... + # + $OptionsInfo{AddHydrogens} = 0; + if (exists($SpecifiedPropertyNamesMap{lc('MolecularVolume')}) || exists($SpecifiedPropertyNamesMap{lc('SLogP')}) || exists($SpecifiedPropertyNamesMap{lc('SMR')})) { + $OptionsInfo{AddHydrogens} = 1; + } +} + +# Process precision option... +# +sub ProcessPrecisionOption { + my($ParameterName, $ParameterValue, %PrecisionParametersMap, %PrecisionParameterNamesMap); + + %{$OptionsInfo{PrecisionParametersMap}} = (); + + %PrecisionParametersMap = ('WeightPrecision' => 2, 'MassPrecision' => 4); + %PrecisionParameterNamesMap = ('molecularweight' => 'WeightPrecision', 'exactmass' => 'MassPrecision'); + + if ($Options{precision}) { + # Process specified values... + my($Index, $SpecifiedPrecision, @SpecifiedPrecisionValuePairs); + + $SpecifiedPrecision = $Options{precision}; + $SpecifiedPrecision =~ s/ //g; + @SpecifiedPrecisionValuePairs = split ",", $SpecifiedPrecision; + if (@SpecifiedPrecisionValuePairs % 2) { + die "Error: Invalid number of values specified using \"--Precision\" option: It must contain even number of values.\n"; + } + for ($Index = 0; (($Index + 1) < @SpecifiedPrecisionValuePairs); $Index += 2 ) { + $ParameterName = $SpecifiedPrecisionValuePairs[$Index]; + $ParameterValue = $SpecifiedPrecisionValuePairs[$Index + 1]; + if (!exists $PrecisionParameterNamesMap{lc($ParameterName)}) { + die "Error: The precision parameter name specified, $ParameterName, for option \"--Precision\" is not valid.\n"; + } + if (!IsPositiveInteger($ParameterValue)) { + die "Error: The parameter value specified, $ParameterValue, for parameter name, $ParameterName in option \"--Precision\" is not valid. Allowed values: positive integer. \n"; + } + $ParameterName = $PrecisionParameterNamesMap{lc($ParameterName)}; + $PrecisionParametersMap{$ParameterName} = $ParameterValue; + } + } + $OptionsInfo{Precision} = $Options{precision}; + %{$OptionsInfo{PrecisionParametersMap}} = %PrecisionParametersMap; +} + +# Process rotatable bonds option... +sub ProcessRotatableBondsOption { + my($ParameterName, $ParameterValue, %RotatableBondsParametersMap, %RotatableBondsParameterNamesMap); + + %{$OptionsInfo{RotatableBondsParametersMap}} = (); + %RotatableBondsParametersMap = ('IgnoreTerminalBonds' => 1, 'IgnoreBondsToTripleBonds' => 1, 'IgnoreAmideBonds' => 1, 'IgnoreThioamideBonds' => 1, 'IgnoreSulfonamideBonds' => 1); + + for $ParameterName (keys %RotatableBondsParametersMap) { + $RotatableBondsParameterNamesMap{lc($ParameterName)} = $ParameterName; + } + + if ($Options{rotatablebonds}) { + # Process specified values... + my($Index, $SpecifiedRotatableBonds, @SpecifiedRotatableBondsValuePairs); + + $SpecifiedRotatableBonds = $Options{rotatablebonds}; + $SpecifiedRotatableBonds =~ s/ //g; + @SpecifiedRotatableBondsValuePairs = split ",", $SpecifiedRotatableBonds; + if (@SpecifiedRotatableBondsValuePairs % 2) { + die "Error: Invalid number of values specified using \"--RotatableBonds\" option: It must contain even number of values.\n"; + } + for ($Index = 0; (($Index + 1) < @SpecifiedRotatableBondsValuePairs); $Index += 2 ) { + $ParameterName = $SpecifiedRotatableBondsValuePairs[$Index]; + $ParameterValue = $SpecifiedRotatableBondsValuePairs[$Index + 1]; + if (!exists $RotatableBondsParameterNamesMap{lc($ParameterName)}) { + die "Error: The rotatable bonds parameter name specified, $ParameterName, for option \"--RotatableBonds\" is not valid.\n"; + } + if ($ParameterValue !~ /^(Yes|No)$/i) { + die "Error: The parameter value specified, $ParameterValue, for parameter name, $ParameterName in option \"--RotatableBonds\" is not valid. Allowed values: Yes or No. \n"; + } + $ParameterName = $RotatableBondsParameterNamesMap{lc($ParameterName)}; + $ParameterValue = ($ParameterValue =~ /^Yes$/i) ? 1 : 0; + $RotatableBondsParametersMap{$ParameterName} = $ParameterValue; + } + } + $OptionsInfo{RotatableBonds} = $Options{rotatablebonds}; + %{$OptionsInfo{RotatableBondsParametersMap}} = %RotatableBondsParametersMap; +} + +# Process TPSA option... +# +sub ProcessTPSAOption { + my($ParameterName, $ParameterValue, %TPSAParametersMap, %TPSAParameterNamesMap); + + %{$OptionsInfo{TPSAParametersMap}} = (); + + %TPSAParametersMap = ('IgnorePhosphorus' => 1, 'IgnoreSulfur' => 1); + for $ParameterName (keys %TPSAParametersMap) { + $TPSAParameterNamesMap{lc($ParameterName)} = $ParameterName; + } + + if ($Options{tpsa}) { + # Process specified values... + my($Index, $SpecifiedTPSA, @SpecifiedTPSAValuePairs); + + $SpecifiedTPSA = $Options{tpsa}; + $SpecifiedTPSA =~ s/ //g; + @SpecifiedTPSAValuePairs = split ",", $SpecifiedTPSA; + if (@SpecifiedTPSAValuePairs % 2) { + die "Error: Invalid number of values specified using \"--TPSA\" option: It must contain even number of values.\n"; + } + for ($Index = 0; (($Index + 1) < @SpecifiedTPSAValuePairs); $Index += 2 ) { + $ParameterName = $SpecifiedTPSAValuePairs[$Index]; + $ParameterValue = $SpecifiedTPSAValuePairs[$Index + 1]; + if (!exists $TPSAParameterNamesMap{lc($ParameterName)}) { + die "Error: The TPSA parameter name specified, $ParameterName, for option \"--TPSA\" is not valid.\n"; + } + if ($ParameterValue !~ /^(Yes|No)$/i) { + die "Error: The parameter value specified, $ParameterValue, for parameter name, $ParameterName in option \"--TPSA\" is not valid. Allowed values: Yes or No. \n"; + } + $ParameterName = $TPSAParameterNamesMap{lc($ParameterName)}; + $ParameterValue = ($ParameterValue =~ /^Yes$/i) ? 1 : 0; + $TPSAParametersMap{$ParameterName} = $ParameterValue; + } + } + $OptionsInfo{TPSA} = $Options{tpsa}; + %{$OptionsInfo{TPSAParametersMap}} = %TPSAParametersMap; +} + +# Process molecular complexity parameters... +# +sub ProcessMolecularComplexityOption { + my($MolecularComplexityType, $ParameterName, $ParameterValue, @ParameterNames, @ParameterValues, @AtomIdentifierTypeParameters, %ComplexityParametersMap, %ComplexityParameterNamesMap); + + %{$OptionsInfo{MolecularComplexityParametersMap}} = (); + + %ComplexityParametersMap = ('MolecularComplexityType' => '', 'AtomIdentifierType' => '', + 'AtomicInvariantsToUse' => '', 'FunctionalClassesToUse' => '', + 'MACCSKeysSize' => '166', 'NeighborhoodRadius' => '2', + 'MinPathLength' => '1', 'MaxPathLength' => '8', 'UseBondSymbols' => '1', + 'MinDistance' => '1', 'MaxDistance' => '10', 'UseTriangleInequality' => '', + 'DistanceBinSize' => '2', 'NormalizationMethodology' => 'None'); + + %ComplexityParameterNamesMap = (); + for $ParameterName (keys %ComplexityParametersMap) { + $ComplexityParameterNamesMap{lc($ParameterName)} = $ParameterName; + } + + if ($Options{molecularcomplexity}) { + # Process specified values... + my($Index, $SpecifiedComplexity, @SpecifiedComplexityValuePairs); + + $SpecifiedComplexity = $Options{molecularcomplexity}; + + @SpecifiedComplexityValuePairs = split ",", $SpecifiedComplexity; + if (@SpecifiedComplexityValuePairs % 2) { + die "Error: Invalid number of values specified using \"--MolecularComplexity\" option: It must contain even number of values.\n"; + } + + for ($Index = 0; (($Index + 1) < @SpecifiedComplexityValuePairs); $Index += 2 ) { + $ParameterName = $SpecifiedComplexityValuePairs[$Index]; + $ParameterValue = $SpecifiedComplexityValuePairs[$Index + 1]; + + $ParameterName = RemoveLeadingAndTrailingWhiteSpaces($ParameterName); + $ParameterValue = RemoveLeadingAndTrailingWhiteSpaces($ParameterValue); + + if (!exists $ComplexityParameterNamesMap{lc($ParameterName)}) { + die "Error: The molecular complexity parameter name specified, $ParameterName, for option \"--MolecularComplexity\" is not valid.\n"; + } + $ParameterName = $ComplexityParameterNamesMap{lc($ParameterName)}; + + if ($ParameterName =~ /^AtomicInvariantsToUse$/i) { + my($AtomSymbolFound); + + $AtomSymbolFound = 0; + @ParameterValues = split(' ', $ParameterValue); + for $ParameterValue (@ParameterValues) { + if (!AtomTypes::AtomicInvariantsAtomTypes::IsAtomicInvariantAvailable($ParameterValue)) { + die "Error: The atomic invariant specified, $ParameterValue, for AtomicInvariantsToUse in option \"--MolecularComplexity\" is not valid.\n"; + } + if ($ParameterValue =~ /^(AS|AtomSymbol)$/i) { + $AtomSymbolFound = 1; + } + } + if (!$AtomSymbolFound) { + die "Error: The atomic invariants specified using AtomicInvariantsToUse in option \"--MolecularComplexity\" is not valid: AtomicInvariant atom symbol, AS or AtomSymbol, must be specified.\n"; + } + $ParameterValue = JoinWords(\@ParameterValues, ",", 0); + } + elsif ($ParameterName =~ /^FunctionalClassesToUse$/i) { + @ParameterValues = split(' ', $ParameterValue); + for $ParameterValue (@ParameterValues) { + if (!AtomTypes::FunctionalClassAtomTypes::IsFunctionalClassAvailable($ParameterValue)) { + die "Error: The functional class specified, $ParameterValue, for FunctionalClassesToUse in option \"--MolecularComplexity\" is not valid.\n"; + } + } + $ParameterValue = JoinWords(\@ParameterValues, ",", 0); + } + else { + if ($ParameterValue =~ / /) { + $ParameterValue =~ s/ //g; + } + if ($ParameterValue =~ /^(Yes|No)$/i) { + $ParameterValue = ($ParameterValue =~ /^Yes$/i) ? 1 : 0; + } + } + + if ($ParameterName =~ /^MolecularComplexityType$/i) { + if ($ParameterValue !~ /^(AtomTypesFingerprints|ExtendedConnectivityFingerprints|MACCSKeys|PathLengthFingerprints|TopologicalAtomPairsFingerprints|TopologicalAtomTripletsFingerprints|TopologicalAtomTorsionsFingerprints|TopologicalPharmacophoreAtomPairsFingerprints|TopologicalPharmacophoreAtomTripletsFingerprints)$/i) { + die "Error: The parameter value specified, $ParameterValue, for parameter name, $ParameterName in option \"--MolecularComplexity\" is not valid. Allowed values: AtomTypesFingerprints, ExtendedConnectivityFingerprints, MACCSKeys, PathLengthFingerprints, TopologicalAtomPairsFingerprints, TopologicalAtomTripletsFingerprints, TopologicalAtomTorsionsFingerprints, TopologicalPharmacophoreAtomPairsFingerprints, or TopologicalPharmacophoreAtomTripletsFingerprints..\n"; + } + } + elsif ($ParameterName =~ /^AtomIdentifierType$/i) { + if ($ParameterValue !~ /^(AtomicInvariantsAtomTypes|FunctionalClassAtomTypes|DREIDINGAtomTypes|EStateAtomTypes|MMFF94AtomTypes|SLogPAtomTypes|SYBYLAtomTypes|TPSAAtomTypes|UFFAtomTypes)$/i) { + die "Error: The parameter value specified, $ParameterValue, for parameter name, $ParameterName in option \"--MolecularComplexity\" is not valid. Supported atom identifier types in current release of MayaChemTools: AtomicInvariantsAtomTypes, FunctionalClassAtomTypes, DREIDINGAtomTypes, EStateAtomTypes, MMFF94AtomTypes, SLogPAtomTypes, SYBYLAtomTypes, TPSAAtomTypes and UFFAtomTypes.\n"; + } + } + elsif ($ParameterName =~ /^(MACCSKeysSize|MinPathLength|MaxPathLength|MinDistance|MaxDistance|DistanceBinSize)$/i) { + if (!IsPositiveInteger($ParameterValue)) { + die "Error: The parameter value specified, $ParameterValue, for parameter name, $ParameterName in option \"--MolecularComplexity\" is not valid. Allowed values: positive integer. \n"; + } + } + elsif ($ParameterName =~ /^NeighborhoodRadius$/i) { + if (!(IsInteger($ParameterValue) && $ParameterValue >=0)) { + die "Error: The parameter value specified, $ParameterValue, for parameter name, $ParameterName in option \"--MolecularComplexity\" is not valid. Allowed values: 0 or positive integer. \n"; + } + } + elsif ($ParameterName =~ /^NormalizationMethodology$/i) { + if ($ParameterValue !~ /^(None|ByHeavyAtomsCount|ByPossibleKeysCount)$/i) { + die "Error: The parameter value specified, $ParameterValue, for parameter name, $ParameterName in option \"--MolecularComplexity\" is not valid. Allowed values: None, ByHeavyAtomsCount, or ByPossibleKeysCount\n"; + } + } + $ComplexityParametersMap{$ParameterName} = $ParameterValue; + } + + if ($ComplexityParametersMap{MACCSKeysSize} !~ /^(166|322)$/i) { + die "Error: The parameter value specified, $ComplexityParametersMap{MACCSKeysSize}, for parameter name, MACCSKeysSize in option \"--MolecularComplexity\" is not valid. Allowed values: 166 or 322\n"; + } + if ($ComplexityParametersMap{MinPathLength} > $ComplexityParametersMap{MaxPathLength}) { + die "Error: The parameter value specified for MinPathLength, $ComplexityParametersMap{MinPathLength}, must be <= MaxPathLength, $ComplexityParametersMap{MaxPathLength} ...\n"; + } + if ($ComplexityParametersMap{MinDistance} > $ComplexityParametersMap{MaxDistance}) { + die "Error: The parameter value specified for MinDistance, $ComplexityParametersMap{MinDistance}, must be <= MaxDistance, $ComplexityParametersMap{MaxDistance} ...\n"; + } + } + + # Set default parameter values... + + if (IsEmpty($ComplexityParametersMap{MolecularComplexityType})) { + $ComplexityParametersMap{MolecularComplexityType} = 'MACCSKeys'; + } + $MolecularComplexityType = $ComplexityParametersMap{MolecularComplexityType}; + + + if (IsEmpty($ComplexityParametersMap{AtomIdentifierType})) { + $ComplexityParametersMap{AtomIdentifierType} = ($MolecularComplexityType =~ /^(TopologicalPharmacophoreAtomPairsFingerprints|TopologicalPharmacophoreAtomTripletsFingerprints)$/i) ? "FunctionalClassAtomTypes" : "AtomicInvariantsAtomTypes"; + } + + if (IsEmpty($ComplexityParametersMap{AtomicInvariantsToUse})) { + my($AtomicInvariantsToUse); + + if ($MolecularComplexityType =~ /^(AtomTypesFingerprints|TopologicalAtomPairsFingerprints|TopologicalAtomTripletsFingerprints|TopologicalAtomTorsionsFingerprints)$/i) { + $AtomicInvariantsToUse = "AS,X,BO,H,FC"; + } + elsif ($MolecularComplexityType =~ /^ExtendedConnectivityFingerprints$/i) { + $AtomicInvariantsToUse = "AS,X,BO,H,FC,MN"; + } + else { + $AtomicInvariantsToUse = "AS"; + } + $ComplexityParametersMap{AtomicInvariantsToUse} = $AtomicInvariantsToUse; + } + + if (IsEmpty($ComplexityParametersMap{FunctionalClassesToUse})) { + my($FunctionalClassesToUse); + + if ($MolecularComplexityType =~ /^TopologicalPharmacophoreAtomPairsFingerprints$/i) { + $FunctionalClassesToUse = "HBD,HBA,PI,NI,H"; + } + elsif ($MolecularComplexityType =~ /^TopologicalPharmacophoreAtomTripletsFingerprints$/i) { + $FunctionalClassesToUse = "HBD,HBA,PI,NI,H,Ar"; + } + else { + $FunctionalClassesToUse = "HBD,HBA,PI,NI,H,Ar,Hal"; + } + $ComplexityParametersMap{FunctionalClassesToUse} = $FunctionalClassesToUse; + } + + my(@AtomicInvariantsToUse); + @AtomicInvariantsToUse = split ',', $ComplexityParametersMap{AtomicInvariantsToUse}; + $ComplexityParametersMap{AtomicInvariantsToUse} = \@AtomicInvariantsToUse; + + my(@FunctionalClassesToUse); + @FunctionalClassesToUse = split ',', $ComplexityParametersMap{FunctionalClassesToUse}; + $ComplexityParametersMap{FunctionalClassesToUse} = \@FunctionalClassesToUse; + + if (IsEmpty($ComplexityParametersMap{UseTriangleInequality})) { + $ComplexityParametersMap{UseTriangleInequality} = 0; + if ($MolecularComplexityType =~ /^TopologicalPharmacophoreAtomTripletsFingerprints$/i) { + $ComplexityParametersMap{UseTriangleInequality} = 1; + } + } + + if ($MolecularComplexityType =~ /^(TopologicalPharmacophoreAtomPairsFingerprints|TopologicalPharmacophoreAtomTripletsFingerprints)$/i) { + if ($ComplexityParametersMap{AtomIdentifierType} !~ /^FunctionalClassAtomTypes$/i) { + die "Error: The parameter value specified for AtomIdentifierType, $ComplexityParametersMap{AtomIdentifierType}, in option \"--MolecularComplexity\" is not valid for MolecularComplexityType, $MolecularComplexityType: Allowed value: FunctionalClassAtomTypes...\n"; + } + } + + # Set up approprate paremeter names for specified molecular complexity... + + @ParameterNames = (); + push @ParameterNames, 'MolecularComplexityType'; + + @AtomIdentifierTypeParameters = (); + push @AtomIdentifierTypeParameters, 'AtomIdentifierType'; + if ($ComplexityParametersMap{AtomIdentifierType} =~ /^AtomicInvariantsAtomTypes$/i) { + push @AtomIdentifierTypeParameters, 'AtomicInvariantsToUse'; + } + elsif ($ComplexityParametersMap{AtomIdentifierType} =~ /^FunctionalClassAtomTypes$/i) { + push @AtomIdentifierTypeParameters, 'FunctionalClassesToUse'; + } + + COMPLEXITYTYPE: { + if ($MolecularComplexityType =~ /^AtomTypesFingerprints$/i) { + push @ParameterNames, @AtomIdentifierTypeParameters; + last COMPLEXITYTYPE; + } + if ($MolecularComplexityType =~ /^ExtendedConnectivityFingerprints$/i) { + push @ParameterNames, @AtomIdentifierTypeParameters; + push @ParameterNames, ('NeighborhoodRadius', 'NormalizationMethodology'); + last COMPLEXITYTYPE; + } + if ($MolecularComplexityType =~ /^MACCSKeys$/i) { + push @ParameterNames, 'MACCSKeysSize'; + last COMPLEXITYTYPE; + } + if ($MolecularComplexityType =~ /^PathLengthFingerprints$/i) { + push @ParameterNames, @AtomIdentifierTypeParameters; + push @ParameterNames, ('MinPathLength', 'MaxPathLength', 'UseBondSymbols'); + last COMPLEXITYTYPE; + } + if ($MolecularComplexityType =~ /^TopologicalAtomPairsFingerprints$/i) { + push @ParameterNames, @AtomIdentifierTypeParameters; + push @ParameterNames, ('MinDistance', 'MaxDistance'); + last COMPLEXITYTYPE; + } + if ($MolecularComplexityType =~ /^TopologicalAtomTripletsFingerprints$/i) { + push @ParameterNames, @AtomIdentifierTypeParameters; + push @ParameterNames, ('MinDistance', 'MaxDistance', 'UseTriangleInequality'); + last COMPLEXITYTYPE; + } + if ($MolecularComplexityType =~ /^TopologicalAtomTorsionsFingerprints$/i) { + push @ParameterNames, @AtomIdentifierTypeParameters; + last COMPLEXITYTYPE; + } + if ($MolecularComplexityType =~ /^TopologicalPharmacophoreAtomPairsFingerprints$/i) { + push @ParameterNames, ('AtomIdentifierType', 'FunctionalClassesToUse', 'MinDistance', 'MaxDistance', 'NormalizationMethodology'); + last COMPLEXITYTYPE; + } + if ($MolecularComplexityType =~ /^TopologicalPharmacophoreAtomTripletsFingerprints$/i) { + push @ParameterNames, ('AtomIdentifierType', 'FunctionalClassesToUse', 'MinDistance', 'MaxDistance', 'UseTriangleInequality', 'NormalizationMethodology', 'DistanceBinSize'); + last COMPLEXITYTYPE; + } + die "Error: The parameter value specified, $ParameterValue, for parameter name MolecularComplexityType using \"--MolecularComplexity\" is not valid.\n"; + } + + $OptionsInfo{MolecularComplexity} = $Options{molecularcomplexity}; + + %{$OptionsInfo{MolecularComplexityParametersMap}} = (); + for $ParameterName (@ParameterNames) { + $ParameterValue = $ComplexityParametersMap{$ParameterName}; + $OptionsInfo{MolecularComplexityParametersMap}{$ParameterName} = $ParameterValue; + } +} + +# Setup script usage and retrieve command line arguments specified using various options... +sub SetupScriptUsage { + + # Retrieve all the options... + %Options = (); + + $Options{aromaticitymodel} = 'MayaChemToolsAromaticityModel'; + + $Options{compoundidmode} = 'LabelPrefix'; + $Options{compoundidlabel} = 'CompoundID'; + $Options{datafieldsmode} = 'CompoundID'; + + $Options{filter} = 'Yes'; + + $Options{hydrogenbonds} = 'HBondsType2'; + + $Options{keeplargestcomponent} = 'Yes'; + + # Default mode values are set later... + $Options{mode} = ''; + + # Default moelcular complexity values are set later... + $Options{molecularcomplexity} = ''; + + # Default precision values are set later... + $Options{precision} = ''; + + $Options{output} = 'text'; + $Options{outdelim} = 'comma'; + $Options{quote} = 'yes'; + + # Default rotatable bond parameter values are set later... + $Options{rotatablebonds} = ''; + + $Options{ruleof3violations} = 'No'; + $Options{ruleof5violations} = 'No'; + + # Default TPSA paramater values are set later... + $Options{tpsa} = ''; + + if (!GetOptions(\%Options, "aromaticitymodel=s", "compoundid=s", "compoundidlabel=s", "compoundidmode=s", "datafields=s", "datafieldsmode|d=s", "filter|f=s", "help|h", "hydrogenbonds=s", "keeplargestcomponent|k=s", "mode|m=s", "molecularcomplexity=s", "outdelim=s", "output=s", "overwrite|o", "precision=s", "rotatablebonds=s", "ruleof3violations=s", "ruleof5violations=s", "quote|q=s", "root|r=s", "tpsa=s", "workingdir|w=s")) { + die "\nTo get a list of valid options and their values, use \"$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{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{hydrogenbonds} !~ /^(HBondsType1|HydrogenBondsType1|HBondsType2|HydrogenBondsType2)$/i) { + die "Error: The value specified, $Options{hydrogenbonds}, for option \"--HydrogenBonds\" is not valid. Allowed values: HBondsType1, HydrogenBondsType1, HBondsType2, HydrogenBondsType2\n"; + } + if ($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{output} !~ /^(SD|text|both)$/i) { + die "Error: The value specified, $Options{output}, for option \"--output\" is not valid. Allowed values: SD, text, or both\n"; + } + if ($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{ruleof3violations} !~ /^(Yes|No)$/i) { + die "Error: The value specified, $Options{ruleof3violations}, for option \"--RuleOf3Violations\" is not valid. Allowed values: Yes or No\n"; + } + if ($Options{ruleof5violations} !~ /^(Yes|No)$/i) { + die "Error: The value specified, $Options{ruleof5violations}, for option \"--RuleOf5Violations\" is not valid. Allowed values: Yes or No\n"; + } +} + +__END__ + +=head1 NAME + +CalculatePhysicochemicalProperties.pl - Calculate physicochemical properties for SD files + +=head1 SYNOPSIS + +CalculatePhysicochemicalProperties.pl SDFile(s)... + +PhysicochemicalProperties.pl [B<--AromaticityModel> I<AromaticityModelType>] +[B<--CompoundID> DataFieldName or LabelPrefixString] +[B<--CompoundIDLabel> text] [B<--CompoundIDMode>] [B<--DataFields> "FieldLabel1, FieldLabel2,..."] +[B<-d, --DataFieldsMode> All | Common | Specify | CompoundID] [B<-f, --Filter> Yes | No] [B<-h, --help>] +[B<--HydrogenBonds> HBondsType1 | HBondsType2] [B<-k, --KeepLargestComponent> Yes | No] +[B<-m, --mode> All | RuleOf5 | RuleOf3 | "name1, [name2,...]"] +[B<--MolecularComplexity> I<Name,Value, [Name,Value,...]>] +[B<--OutDelim> comma | tab | semicolon] [B<--output> SD | text | both] [B<-o, --overwrite>] +[B<--Precision> Name,Number,[Name,Number,..]] [B<--RotatableBonds> Name,Value, [Name,Value,...]] +[B<--RuleOf3Violations> Yes | No] [B<--RuleOf5Violations> Yes | No] +[B<-q, --quote> Yes | No] [B<-r, --root> RootName] +[B<-w, --WorkingDir> dirname] SDFile(s)... + +=head1 DESCRIPTION + +Calculate physicochemical properties for I<SDFile(s)> and create appropriate SD or CSV/TSV +text file(s) containing calculated properties. + +The current release of MayaChemTools supports the calculation of these physicochemical +properties: + + MolecularWeight, ExactMass, HeavyAtoms, Rings, AromaticRings, + van der Waals MolecularVolume [ Ref 93 ], RotatableBonds, + HydrogenBondDonors, HydrogenBondAcceptors, LogP and + Molar Refractivity (SLogP and SMR) [ Ref 89 ], Topological Polar + Surface Area (TPSA) [ Ref 90 ], Fraction of SP3 carbons (Fsp3Carbons) + and SP3 carbons (Sp3Carbons) [ Ref 115-116, Ref 119 ], + MolecularComplexity [ Ref 117-119 ] + +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 calculation of molecular complexity using I<MolecularComplexityType> parameter +corresponds to the number of bits-set or unique keys [ Ref 117-119 ] in molecular fingerprints. +Default value for I<MolecularComplexityType>: I<MACCSKeys> of size 166. The calculation +of MACCSKeys is relatively expensive and can take rather substantial amount of time. + +=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<--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 CSV/TSV text file(s) used during I<CompoundID> value +of B<--DataFieldsMode> option. Default value: I<CompoundID>. + +=item B<--CompoundIDMode> I<DataField | MolName | LabelPrefix | MolNameOrLabelPrefix> + +Specify how to generate compound IDs and write to CSV/TSV text file(s) along with calculated +physicochemical properties for I<text | both> 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 value: 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 calculated physicochemical properties for I<text | both> 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 calculated physicochemical properties for I<text | both> 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 physiochemical properties and compounds +containing atom data corresponding to non-element symbols or no atom data are ignored. + +=item B<-h, --help> + +Print this help message. + +=item B<--HydrogenBonds> I<HBondsType1 | HBondsType2> + +Parameters to control calculation of hydrogen bond donors and acceptors. Possible values: +I<HBondsType1, HydrogenBondsType1, HBondsType2, HydrogenBondsType2>. Default value: +I<HBondsType2> which corresponds to B<RuleOf5> definition for number of hydrogen bond +donors and acceptors. + +The current release of MayaChemTools supports identification of two types of hydrogen bond +donor and acceptor atoms with these names: + + HBondsType1 or HydrogenBondsType1 + HBondsType2 or HydrogenBondsType2 + +The names of these hydrogen bond types are rather arbitrary. However, their definitions have +specific meaning and are as follows: + + HydrogenBondsType1 [ Ref 60-61, Ref 65-66 ]: + + Donor: NH, NH2, OH - Any N and O with available H + Acceptor: N[!H], O - Any N without available H and any O + + HydrogenBondsType2 [ Ref 91 ]: + + Donor: NH, NH2, OH - N and O with available H + Acceptor: N, O - And N and O + +=item B<-k, --KeepLargestComponent> I<Yes | No> + +Calculate physicochemical properties for only the largest component in molecule. Possible values: +I<Yes or No>. Default value: I<Yes>. + +For molecules containing multiple connected components, physicochemical properties can be +calculated 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 calculation of physicochemical properties. + +=item B<-m, --mode> I<All | RuleOf5 | RuleOf3 | "name1, [name2,...]"> + +Specify physicochemical properties to calculate for SDFile(s): calculate all available physical +chemical properties; calculate properties corresponding to Rule of 5; or use a comma delimited +list of supported physicochemical properties. Possible values: I<All | RuleOf5 | RuleOf3 | +"name1, [name2,...]">. + +Default value: I<MolecularWeight, HeavyAtoms, MolecularVolume, RotatableBonds, HydrogenBondDonors, +HydrogenBondAcceptors, SLogP, TPSA>. These properties are calculated by default. + +I<RuleOf5> [ Ref 91 ] includes these properties: I<MolecularWeight, HydrogenBondDonors, HydrogenBondAcceptors, +SLogP>. I<RuleOf5> states: MolecularWeight <= 500, HydrogenBondDonors <= 5, HydrogenBondAcceptors <= 10, and +logP <= 5. + +I<RuleOf3> [ Ref 92 ] includes these properties: I<MolecularWeight, RotatableBonds, HydrogenBondDonors, +HydrogenBondAcceptors, SLogP, TPSA>. I<RuleOf3> states: MolecularWeight <= 300, RotatableBonds <= 3, +HydrogenBondDonors <= 3, HydrogenBondAcceptors <= 3, logP <= 3, and TPSA <= 60. + +I<All> calculates all supported physicochemical properties: I<MolecularWeight, ExactMass, +HeavyAtoms, Rings, AromaticRings, MolecularVolume, RotatableBonds, HydrogenBondDonors, +HydrogenBondAcceptors, SLogP, SMR, TPSA, Fsp3Carbons, Sp3Carbons, MolecularComplexity>. + +=item B<--MolecularComplexity> I<Name,Value, [Name,Value,...]> + +Parameters to control calculation of molecular complexity: it's a comma delimited list of parameter +name and value pairs. + +Possible parameter names: I<MolecularComplexityType, AtomIdentifierType, +AtomicInvariantsToUse, FunctionalClassesToUse, MACCSKeysSize, NeighborhoodRadius, +MinPathLength, MaxPathLength, UseBondSymbols, MinDistance, MaxDistance, +UseTriangleInequality, DistanceBinSize, NormalizationMethodology>. + +The valid paramater valuse for each parameter name are described in the following sections. + +The current release of MayaChemTools supports calculation of molecular complexity using +I<MolecularComplexityType> parameter corresponding to the number of bits-set or unique +keys [ Ref 117-119 ] in molecular fingerprints. The valid values for I<MolecularComplexityType> +are: + + AtomTypesFingerprints + ExtendedConnectivityFingerprints + MACCSKeys + PathLengthFingerprints + TopologicalAtomPairsFingerprints + TopologicalAtomTripletsFingerprints + TopologicalAtomTorsionsFingerprints + TopologicalPharmacophoreAtomPairsFingerprints + TopologicalPharmacophoreAtomTripletsFingerprints + +Default value for I<MolecularComplexityType>: I<MACCSKeys>. + +I<AtomIdentifierType> parameter name correspods to atom types used during generation of +fingerprints. The valid values for I<AtomIdentifierType> are: I<AtomicInvariantsAtomTypes, +DREIDINGAtomTypes, EStateAtomTypes, FunctionalClassAtomTypes, MMFF94AtomTypes, +SLogPAtomTypes, SYBYLAtomTypes, TPSAAtomTypes, UFFAtomTypes>. I<AtomicInvariantsAtomTypes> +is not supported for during the following values of I<MolecularComplexityType>: I<MACCSKeys, +TopologicalPharmacophoreAtomPairsFingerprints, TopologicalPharmacophoreAtomTripletsFingerprints>. +I<FunctionalClassAtomTypes> is the only valid value for I<AtomIdentifierType> for topological +pharmacophore fingerprints. + +Default value for I<AtomIdentifierType>: I<AtomicInvariantsAtomTypes> +for all except topological pharmacophore fingerprints where it is I<FunctionalClassAtomTypes>. + +I<AtomicInvariantsToUse> parameter name and values are used during I<AtomicInvariantsAtomTypes> +value of parameter I<AtomIdentifierType>. It's a list of space 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 for I<AtomicInvariantsToUse> parameter are set differently for different fingerprints +using I<MolecularComplexityType> parameter as shown below: + + MolecularComplexityType AtomicInvariantsToUse + + AtomTypesFingerprints AS X BO H FC + TopologicalAtomPairsFingerprints AS X BO H FC + TopologicalAtomTripletsFingerprints AS X BO H FC + TopologicalAtomTorsionsFingerprints AS X BO H FC + + ExtendedConnectivityFingerprints AS X BO H FC MN + PathLengthFingerprints 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 + +I<AtomTypes::AtomicInvariantsAtomTypes> module is used to assign atomic invariant +atom types. + +I<FunctionalClassesToUse> parameter name and values are used during I<FunctionalClassAtomTypes> +value of parameter I<AtomIdentifierType>. It's a list of space separated valid atomic invariant atom types. + +Possible values for atom functional classes are: I<Ar, CA, H, HBA, HBD, Hal, NI, PI, RA>. + +Default value for I<FunctionalClassesToUse> parameter is set to: + + HBD HBA PI NI Ar Hal + +for all fingerprints except for the following two I<MolecularComplexityType> fingerints: + + MolecularComplexityType FunctionalClassesToUse + + TopologicalPharmacophoreAtomPairsFingerprints HBD HBA P, NI H + TopologicalPharmacophoreAtomTripletsFingerprints HBD HBA PI NI H Ar + +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 + +I<MACCSKeysSize> parameter name is only used during I<MACCSKeys> value of +I<MolecularComplexityType> and corresponds to the size of MACCS key set. Possible +values: I<166 or 322>. Default value: I<166>. + +I<NeighborhoodRadius> parameter name is only used during I<ExtendedConnectivityFingerprints> +value of I<MolecularComplexityType> and corresponds to atomic neighborhoods radius for +generating extended connectivity fingerprints. Possible values: positive integer. Default value: +I<2>. + +I<MinPathLength> and I<MaxPathLength> parameters are only used during I<PathLengthFingerprints> +value of I<MolecularComplexityType> and correspond to minimum and maximum path lengths to use +for generating path length fingerprints. Possible values: positive integers. Default value: I<MinPathLength - 1>; +I<MaxPathLength - 8>. + +I<UseBondSymbols> parameter is only used during I<PathLengthFingerprints> value of +I<MolecularComplexityType> and indicates whether bond symbols are included in atom path +strings used to generate path length fingerprints. Possible value: I<Yes or No>. Default value: +I<Yes>. + +I<MinDistance> and I<MaxDistance> parameters are only used during I<TopologicalAtomPairsFingerprints> +and I<TopologicalAtomTripletsFingerprints> values of I<MolecularComplexityType> and correspond to +minimum and maximum bond distance between atom pairs during topological pharmacophore fingerprints. +Possible values: positive integers. Default value: I<MinDistance - 1>; I<MaxDistance - 10>. + +I<UseTriangleInequality> parameter is used during these values for I<MolecularComplexityType>: +I<TopologicalAtomTripletsFingerprints> and I<TopologicalPharmacophoreAtomTripletsFingerprints>. +Possible values: I<Yes or No>. It determines wheter to apply triangle inequality to distance triplets. +Default value: I<TopologicalAtomTripletsFingerprints - No>; +I<TopologicalPharmacophoreAtomTripletsFingerprints - Yes>. + +I<DistanceBinSize> parameter is used during I<TopologicalPharmacophoreAtomTripletsFingerprints> +value of I<MolecularComplexityType> and correspons to distance bin size used for binning +distances during generation of topological pharmacophore atom triplets fingerprints. Possible +value: positive integer. Default value: I<2>. + +I<NormalizationMethodology> is only used for these values for I<MolecularComplexityType>: +I<ExtendedConnectivityFingerprints>, I<TopologicalPharmacophoreAtomPairsFingerprints> +and I<TopologicalPharmacophoreAtomTripletsFingerprints>. It corresponds to normalization +methodology to use for scaling the number of bits-set or unique keys during generation of +fingerprints. Possible values during I<ExtendedConnectivityFingerprints>: I<None or +ByHeavyAtomsCount>; Default value: I<None>. Possible values during topological +pharmacophore atom pairs and tripletes fingerprints: I<None or ByPossibleKeysCount>; +Default value: I<None>. I<ByPossibleKeysCount> corresponds to total number of +possible topological pharmacophore atom pairs or triplets in a molecule. + +Examples of I<MolecularComplexity> name and value parameters: + + MolecularComplexityType,AtomTypesFingerprints,AtomIdentifierType, + AtomicInvariantsAtomTypes,AtomicInvariantsToUse,AS X BO H FC + + MolecularComplexityType,ExtendedConnectivityFingerprints, + AtomIdentifierType,AtomicInvariantsAtomTypes, + AtomicInvariantsToUse,AS X BO H FC MN,NeighborhoodRadius,2, + NormalizationMethodology,None + + MolecularComplexityType,MACCSKeys,MACCSKeysSize,166 + + MolecularComplexityType,PathLengthFingerprints,AtomIdentifierType, + AtomicInvariantsAtomTypes,AtomicInvariantsToUse,AS,MinPathLength, + 1,MaxPathLength,8,UseBondSymbols,Yes + + MolecularComplexityType,TopologicalAtomPairsFingerprints, + AtomIdentifierType,AtomicInvariantsAtomTypes,AtomicInvariantsToUse, + AS X BO H FC,MinDistance,1,MaxDistance,10 + + MolecularComplexityType,TopologicalAtomTripletsFingerprints, + AtomIdentifierType,AtomicInvariantsAtomTypes,AtomicInvariantsToUse, + AS X BO H FC,MinDistance,1,MaxDistance,10,UseTriangleInequality,No + + MolecularComplexityType,TopologicalAtomTorsionsFingerprints, + AtomIdentifierType,AtomicInvariantsAtomTypes,AtomicInvariantsToUse, + AS X BO H FC + + MolecularComplexityType,TopologicalPharmacophoreAtomPairsFingerprints, + AtomIdentifierType,FunctionalClassAtomTypes,FunctionalClassesToUse, + HBD HBA PI NI H,MinDistance,1,MaxDistance,10,NormalizationMethodology, + None + + MolecularComplexityType,TopologicalPharmacophoreAtomTripletsFingerprints, + AtomIdentifierType,FunctionalClassAtomTypes,FunctionalClassesToUse, + HBD HBA PI NI H Ar,MinDistance,1,MaxDistance,10,NormalizationMethodology, + None,UseTriangleInequality,Yes,NormalizationMethodology,None, + DistanceBinSize,2 + +=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 | text | both> + +Type of output files to generate. Possible values: I<SD, text, or both>. Default value: I<text>. + +=item B<-o, --overwrite> + +Overwrite existing files. + +=item B<--Precision> I<Name,Number,[Name,Number,..]> + +Precision of calculated property values in the output file: it's a comma delimited list of +property name and precision value pairs. Possible property names: I<MolecularWeight, +ExactMass>. Possible values: positive intergers. Default value: I<MolecularWeight,2, +ExactMass,4>. + +Examples: + + ExactMass,3 + MolecularWeight,1,ExactMass,2 + +=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><PhysicochemicalProperties>.<Ext>. The file type determines <Ext> value. +The sdf, 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<--RotatableBonds> I<Name,Value, [Name,Value,...]> + +Parameters to control calculation of rotatable bonds [ Ref 92 ]: it's a comma delimited list of parameter +name and value pairs. Possible parameter names: I<IgnoreTerminalBonds, IgnoreBondsToTripleBonds, +IgnoreAmideBonds, IgnoreThioamideBonds, IgnoreSulfonamideBonds>. Possible parameter values: +I<Yes or No>. By default, value of all parameters is set to I<Yes>. + +=item B<--RuleOf3Violations> I<Yes | No> + +Specify whether to calculate B<RuleOf3Violations> for SDFile(s). Possible values: I<Yes or No>. +Default value: I<No>. + +For I<Yes> value of B<RuleOf3Violations>, in addition to calculating total number of B<RuleOf3> violations, +individual violations for compounds are also written to output files. + +B<RuleOf3> [ Ref 92 ] states: MolecularWeight <= 300, RotatableBonds <= 3, HydrogenBondDonors <= 3, +HydrogenBondAcceptors <= 3, logP <= 3, and TPSA <= 60. + +=item B<--RuleOf5Violations> I<Yes | No> + +Specify whether to calculate B<RuleOf5Violations> for SDFile(s). Possible values: I<Yes or No>. +Default value: I<No>. + +For I<Yes> value of B<RuleOf5Violations>, in addition to calculating total number of B<RuleOf5> violations, +individual violations for compounds are also written to output files. + +B<RuleOf5> [ Ref 91 ] states: MolecularWeight <= 500, HydrogenBondDonors <= 5, HydrogenBondAcceptors <= 10, +and logP <= 5. + +=item B<--TPSA> I<Name,Value, [Name,Value,...]> + +Parameters to control calculation of TPSA: it's a comma delimited list of parameter name and value +pairs. Possible parameter names: I<IgnorePhosphorus, IgnoreSulfur>. Possible parameter values: +I<Yes or No>. By default, value of all parameters is set to I<Yes>. + +By default, TPSA atom contributions from Phosphorus and Sulfur atoms are not included during +TPSA calculations. [ Ref 91 ] + +=item B<-w, --WorkingDir> I<DirName> + +Location of working directory. Default value: current directory. + +=back + +=head1 EXAMPLES + +To calculate default set of physicochemical properties - MolecularWeight, HeavyAtoms, +MolecularVolume, RotatableBonds, HydrogenBondDonor, HydrogenBondAcceptors, SLogP, +TPSA - and generate a SamplePhysicochemicalProperties.csv file containing sequential +compound IDs along with properties data, type: + + % CalculatePhysicochemicalProperties.pl -o Sample.sdf + +To calculate all available physicochemical properties and generate both SampleAllProperties.csv +and SampleAllProperties.sdf files containing sequential compound IDs in CSV file along with +properties data, type: + + % CalculatePhysicochemicalProperties.pl -m All --output both + -r SampleAllProperties -o Sample.sdf + +To calculate RuleOf5 physicochemical properties and generate a SampleRuleOf5Properties.csv file +containing sequential compound IDs along with properties data, type: + + % CalculatePhysicochemicalProperties.pl -m RuleOf5 + -r SampleRuleOf5Properties -o Sample.sdf + +To calculate RuleOf5 physicochemical properties along with counting RuleOf5 violations and generate +a SampleRuleOf5Properties.csv file containing sequential compound IDs along with properties data, type: + + % CalculatePhysicochemicalProperties.pl -m RuleOf5 --RuleOf5Violations Yes + -r SampleRuleOf5Properties -o Sample.sdf + +To calculate RuleOf3 physicochemical properties and generate a SampleRuleOf3Properties.csv file +containing sequential compound IDs along with properties data, type: + + % CalculatePhysicochemicalProperties.pl -m RuleOf3 + -r SampleRuleOf3Properties -o Sample.sdf + +To calculate RuleOf3 physicochemical properties along with counting RuleOf3 violations and generate +a SampleRuleOf3Properties.csv file containing sequential compound IDs along with properties data, type: + + % CalculatePhysicochemicalProperties.pl -m RuleOf3 --RuleOf3Violations Yes + -r SampleRuleOf3Properties -o Sample.sdf + +To calculate a specific set of physicochemical properties and generate a SampleProperties.csv file +containing sequential compound IDs along with properties data, type: + + % CalculatePhysicochemicalProperties.pl -m "Rings,AromaticRings" + -r SampleProperties -o Sample.sdf + +To calculate HydrogenBondDonors and HydrogenBondAcceptors using HydrogenBondsType1 definition +and generate a SampleProperties.csv file containing sequential compound IDs along with properties +data, type: + + % CalculatePhysicochemicalProperties.pl -m "HydrogenBondDonors,HydrogenBondAcceptors" + --HydrogenBonds HBondsType1 -r SampleProperties -o Sample.sdf + +To calculate TPSA using sulfur and phosphorus atoms along with nitrogen and oxygen atoms and +generate a SampleProperties.csv file containing sequential compound IDs along with properties +data, type: + + % CalculatePhysicochemicalProperties.pl -m "TPSA" --TPSA "IgnorePhosphorus,No, + IgnoreSulfur,No" -r SampleProperties -o Sample.sdf + +To calculate MolecularComplexity using extendend connectivity fingerprints corresponding +to atom neighborhood radius of 2 with atomic invariant atom types without any scaling and +generate a SampleProperties.csv file containing sequential compound IDs along with properties +data, type: + + % CalculatePhysicochemicalProperties.pl -m MolecularComplexity --MolecularComplexity + "MolecularComplexityType,ExtendedConnectivityFingerprints,NeighborhoodRadius,2, + AtomIdentifierType, AtomicInvariantsAtomTypes, + AtomicInvariantsToUse,AS X BO H FC MN,NormalizationMethodology,None" + -r SampleProperties -o Sample.sdf + +To calculate RuleOf5 physicochemical properties along with counting RuleOf5 violations and generate +a SampleRuleOf5Properties.csv file containing compound IDs from molecule name line along with +properties data, type: + + % CalculatePhysicochemicalProperties.pl -m RuleOf5 --RuleOf5Violations Yes + --DataFieldsMode CompoundID --CompoundIDMode MolName + -r SampleRuleOf5Properties -o Sample.sdf + +To calculate all available physicochemical properties and generate a SampleAllProperties.csv +file containing compound ID using specified data field along with along with properties data, +type: + + % CalculatePhysicochemicalProperties.pl -m All + --DataFieldsMode CompoundID --CompoundIDMode DataField --CompoundID Mol_ID + -r SampleAllProperties -o Sample.sdf + +To calculate all available physicochemical properties and generate a SampleAllProperties.csv +file containing compound ID using combination of molecule name line and an explicit compound +prefix along with properties data, type: + + % CalculatePhysicochemicalProperties.pl -m All + --DataFieldsMode CompoundID --CompoundIDMode MolnameOrLabelPrefix + --CompoundID Cmpd --CompoundIDLabel MolID -r SampleAllProperties + -o Sample.sdf + +To calculate all available physicochemical properties and generate a SampleAllProperties.csv +file containing specific data fields columns along with with properties data, type: + + % CalculatePhysicochemicalProperties.pl -m All + --DataFieldsMode Specify --DataFields Mol_ID -r SampleAllProperties + -o Sample.sdf + +To calculate all available physicochemical properties and generate a SampleAllProperties.csv +file containing common data fields columns along with with properties data, type: + + % CalculatePhysicochemicalProperties.pl -m All + --DataFieldsMode Common -r SampleAllProperties -o Sample.sdf + +To calculate all available physicochemical properties and generate both SampleAllProperties.csv +and CSV files containing all data fields columns in CSV files along with with properties data, type: + + % CalculatePhysicochemicalProperties.pl -m All + --DataFieldsMode All --output both -r SampleAllProperties + -o Sample.sdf + +=head1 AUTHOR + +Manish Sud <msud@san.rr.com> + +=head1 SEE ALSO + +ExtractFromSDtFiles.pl, ExtractFromTextFiles.pl, InfoSDFiles.pl, InfoTextFiles.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