Mercurial > repos > deepakjadmin > mayatool3_test2
diff bin/AtomNeighborhoodsFingerprints.pl @ 0:4816e4a8ae95 draft default tip
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| author | deepakjadmin |
|---|---|
| date | Wed, 20 Jan 2016 09:23:18 -0500 |
| parents | |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/bin/AtomNeighborhoodsFingerprints.pl Wed Jan 20 09:23:18 2016 -0500 @@ -0,0 +1,1335 @@ +#!/usr/bin/perl -w +# +# $RCSfile: AtomNeighborhoodsFingerprints.pl,v $ +# $Date: 2015/02/28 20:46:19 $ +# $Revision: 1.31 $ +# +# 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 "$FindBin::Bin/../lib"; +use Getopt::Long; +use File::Basename; +use Text::ParseWords; +use Benchmark; +use FileUtil; +use TextUtil; +use SDFileUtil; +use MoleculeFileIO; +use FileIO::FingerprintsSDFileIO; +use FileIO::FingerprintsTextFileIO; +use FileIO::FingerprintsFPFileIO; +use AtomTypes::AtomicInvariantsAtomTypes; +use AtomTypes::FunctionalClassAtomTypes; +use Fingerprints::AtomNeighborhoodsFingerprints; + +my($ScriptName, %Options, $StartTime, $EndTime, $TotalTime); + +# Autoflush STDOUT +$| = 1; + +# Starting message... +$ScriptName = basename($0); +print "\n$ScriptName: Starting...\n\n"; +$StartTime = new Benchmark; + +# Get the options and setup script... +SetupScriptUsage(); +if ($Options{help} || @ARGV < 1) { + die GetUsageFromPod("$FindBin::Bin/$ScriptName"); +} + +my(@SDFilesList); +@SDFilesList = ExpandFileNames(\@ARGV, "sdf sd"); + +# Process options... +print "Processing options...\n"; +my(%OptionsInfo); +ProcessOptions(); + +# Setup information about input files... +print "Checking input SD file(s)...\n"; +my(%SDFilesInfo); +RetrieveSDFilesInfo(); + +# Process input files.. +my($FileIndex); +if (@SDFilesList > 1) { + print "\nProcessing SD files...\n"; +} +for $FileIndex (0 .. $#SDFilesList) { + if ($SDFilesInfo{FileOkay}[$FileIndex]) { + print "\nProcessing file $SDFilesList[$FileIndex]...\n"; + GenerateAtomNeighborhoodsFingerprints($FileIndex); + } +} +print "\n$ScriptName:Done...\n\n"; + +$EndTime = new Benchmark; +$TotalTime = timediff ($EndTime, $StartTime); +print "Total time: ", timestr($TotalTime), "\n"; + +############################################################################### + +# Generate fingerprints for a SD file... +# +sub GenerateAtomNeighborhoodsFingerprints { + my($FileIndex) = @_; + my($CmpdCount, $IgnoredCmpdCount, $SDFile, $MoleculeFileIO, $Molecule, $AtomNeighborhoodsFingerprints, $NewFPSDFileIO, $NewFPTextFileIO, $NewFPFileIO); + + $SDFile = $SDFilesList[$FileIndex]; + + # Setup output files... + # + ($NewFPSDFileIO, $NewFPTextFileIO, $NewFPFileIO) = SetupAndOpenOutputFiles($FileIndex); + + $MoleculeFileIO = new MoleculeFileIO('Name' => $SDFile); + $MoleculeFileIO->Open(); + + $CmpdCount = 0; + $IgnoredCmpdCount = 0; + + COMPOUND: while ($Molecule = $MoleculeFileIO->ReadMolecule()) { + $CmpdCount++; + + # Filter compound data before calculating fingerprints... + if ($OptionsInfo{Filter}) { + if (CheckAndFilterCompound($CmpdCount, $Molecule)) { + $IgnoredCmpdCount++; + next COMPOUND; + } + } + + $AtomNeighborhoodsFingerprints = GenerateMoleculeFingerprints($Molecule); + if (!$AtomNeighborhoodsFingerprints) { + $IgnoredCmpdCount++; + ProcessIgnoredCompound('FingerprintsGenerationFailed', $CmpdCount, $Molecule); + next COMPOUND; + } + + WriteDataToOutputFiles($FileIndex, $CmpdCount, $Molecule, $AtomNeighborhoodsFingerprints, $NewFPSDFileIO, $NewFPTextFileIO, $NewFPFileIO); + } + $MoleculeFileIO->Close(); + + if ($NewFPSDFileIO) { + $NewFPSDFileIO->Close(); + } + if ($NewFPTextFileIO) { + $NewFPTextFileIO->Close(); + } + if ($NewFPFileIO) { + $NewFPFileIO->Close(); + } + + WriteFingerprintsGenerationSummaryStatistics($CmpdCount, $IgnoredCmpdCount); +} + +# Process compound being ignored due to problems in fingerprints geneation... +# +sub ProcessIgnoredCompound { + my($Mode, $CmpdCount, $Molecule) = @_; + my($CmpdID, $DataFieldLabelAndValuesRef); + + $DataFieldLabelAndValuesRef = $Molecule->GetDataFieldLabelAndValues(); + $CmpdID = SetupCmpdIDForOutputFiles($CmpdCount, $Molecule, $DataFieldLabelAndValuesRef); + + MODE: { + if ($Mode =~ /^ContainsNonElementalData$/i) { + warn "\nWarning: Ignoring compound record number $CmpdCount with ID $CmpdID: Compound contains atom data corresponding to non-elemental atom symbol(s)...\n\n"; + next MODE; + } + + if ($Mode =~ /^ContainsNoElementalData$/i) { + warn "\nWarning: Ignoring compound record number $CmpdCount with ID $CmpdID: Compound contains no atom data...\n\n"; + next MODE; + } + + if ($Mode =~ /^FingerprintsGenerationFailed$/i) { + warn "\nWarning: Ignoring compound record number $CmpdCount with ID $CmpdID: Fingerprints generation didn't succeed...\n\n"; + next MODE; + } + warn "\nWarning: Ignoring compound record number $CmpdCount with ID $CmpdID: Fingerprints generation didn't succeed...\n\n"; + } +} + +# Check and filter compounds.... +# +sub CheckAndFilterCompound { + my($CmpdCount, $Molecule) = @_; + my($ElementCount, $NonElementCount); + + ($ElementCount, $NonElementCount) = $Molecule->GetNumOfElementsAndNonElements(); + + if ($NonElementCount) { + ProcessIgnoredCompound('ContainsNonElementalData', $CmpdCount, $Molecule); + return 1; + } + + if (!$ElementCount) { + ProcessIgnoredCompound('ContainsNoElementalData', $CmpdCount, $Molecule); + return 1; + } + + return 0; +} + +# Write out compounds fingerprints generation summary statistics... +# +sub WriteFingerprintsGenerationSummaryStatistics { + my($CmpdCount, $IgnoredCmpdCount) = @_; + my($ProcessedCmpdCount); + + $ProcessedCmpdCount = $CmpdCount - $IgnoredCmpdCount; + + print "\nNumber of compounds: $CmpdCount\n"; + print "Number of compounds processed successfully during fingerprints generation: $ProcessedCmpdCount\n"; + print "Number of compounds ignored during fingerprints generation: $IgnoredCmpdCount\n"; +} + +# Open output files... +# +sub SetupAndOpenOutputFiles { + my($FileIndex) = @_; + my($NewFPSDFile, $NewFPFile, $NewFPTextFile, $NewFPSDFileIO, $NewFPTextFileIO, $NewFPFileIO, %FingerprintsFileIOParams); + + ($NewFPSDFileIO, $NewFPTextFileIO, $NewFPFileIO) = (undef) x 3; + + # Setup common parameters for fingerprints file IO objects... + # + %FingerprintsFileIOParams = ('Mode' => 'Write', 'Overwrite' => $OptionsInfo{OverwriteFiles}, 'FingerprintsStringMode' => 'FingerprintsVectorString', 'VectorStringFormat' => $OptionsInfo{VectorStringFormat}); + + if ($OptionsInfo{SDOutput}) { + $NewFPSDFile = $SDFilesInfo{SDOutFileNames}[$FileIndex]; + print "Generating SD file $NewFPSDFile...\n"; + $NewFPSDFileIO = new FileIO::FingerprintsSDFileIO('Name' => $NewFPSDFile, %FingerprintsFileIOParams, 'FingerprintsFieldLabel' => $OptionsInfo{FingerprintsLabel}); + $NewFPSDFileIO->Open(); + } + + if ($OptionsInfo{FPOutput}) { + $NewFPFile = $SDFilesInfo{FPOutFileNames}[$FileIndex]; + print "Generating FP file $NewFPFile...\n"; + $NewFPFileIO = new FileIO::FingerprintsFPFileIO('Name' => $NewFPFile, %FingerprintsFileIOParams); + $NewFPFileIO->Open(); + } + + if ($OptionsInfo{TextOutput}) { + my($ColLabelsRef); + + $NewFPTextFile = $SDFilesInfo{TextOutFileNames}[$FileIndex]; + $ColLabelsRef = SetupFPTextFileCoulmnLabels($FileIndex); + + print "Generating text file $NewFPTextFile...\n"; + $NewFPTextFileIO = new FileIO::FingerprintsTextFileIO('Name' => $NewFPTextFile, %FingerprintsFileIOParams, 'DataColLabels' => $ColLabelsRef, 'OutDelim' => $OptionsInfo{OutDelim}, 'OutQuote' => $OptionsInfo{OutQuote}); + $NewFPTextFileIO->Open(); + } + + return ($NewFPSDFileIO, $NewFPTextFileIO, $NewFPFileIO); +} + +# Write fingerpritns and other data to appropriate output files... +# +sub WriteDataToOutputFiles { + my($FileIndex, $CmpdCount, $Molecule, $AtomNeighborhoodsFingerprints, $NewFPSDFileIO, $NewFPTextFileIO, $NewFPFileIO) = @_; + my($DataFieldLabelAndValuesRef); + + $DataFieldLabelAndValuesRef = undef; + if ($NewFPTextFileIO || $NewFPFileIO) { + $DataFieldLabelAndValuesRef = $Molecule->GetDataFieldLabelAndValues(); + } + + if ($NewFPSDFileIO) { + my($CmpdString); + + $CmpdString = $Molecule->GetInputMoleculeString(); + $NewFPSDFileIO->WriteFingerprints($AtomNeighborhoodsFingerprints, $CmpdString); + } + + if ($NewFPTextFileIO) { + my($ColValuesRef); + + $ColValuesRef = SetupFPTextFileCoulmnValues($FileIndex, $CmpdCount, $Molecule, $DataFieldLabelAndValuesRef); + $NewFPTextFileIO->WriteFingerprints($AtomNeighborhoodsFingerprints, $ColValuesRef); + } + + if ($NewFPFileIO) { + my($CompoundID); + + $CompoundID = SetupCmpdIDForOutputFiles($CmpdCount, $Molecule, $DataFieldLabelAndValuesRef); + $NewFPFileIO->WriteFingerprints($AtomNeighborhoodsFingerprints, $CompoundID); + } +} + +# Generate approriate column labels for FPText output file... +# +sub SetupFPTextFileCoulmnLabels { + my($FileIndex) = @_; + my($Line, @ColLabels); + + @ColLabels = (); + if ($OptionsInfo{DataFieldsMode} =~ /^All$/i) { + push @ColLabels, @{$SDFilesInfo{AllDataFieldsRef}[$FileIndex]}; + } + elsif ($OptionsInfo{DataFieldsMode} =~ /^Common$/i) { + push @ColLabels, @{$SDFilesInfo{CommonDataFieldsRef}[$FileIndex]}; + } + elsif ($OptionsInfo{DataFieldsMode} =~ /^Specify$/i) { + push @ColLabels, @{$OptionsInfo{SpecifiedDataFields}}; + } + elsif ($OptionsInfo{DataFieldsMode} =~ /^CompoundID$/i) { + push @ColLabels, $OptionsInfo{CompoundIDLabel}; + } + # Add fingerprints label... + push @ColLabels, $OptionsInfo{FingerprintsLabel}; + + return \@ColLabels; +} + +# Generate column values FPText output file.. +# +sub SetupFPTextFileCoulmnValues { + my($FileIndex, $CmpdCount, $Molecule, $DataFieldLabelAndValuesRef) = @_; + my(@ColValues); + + @ColValues = (); + if ($OptionsInfo{DataFieldsMode} =~ /^CompoundID$/i) { + push @ColValues, SetupCmpdIDForOutputFiles($CmpdCount, $Molecule, $DataFieldLabelAndValuesRef); + } + elsif ($OptionsInfo{DataFieldsMode} =~ /^All$/i) { + @ColValues = map { exists $DataFieldLabelAndValuesRef->{$_} ? $DataFieldLabelAndValuesRef->{$_} : ''} @{$SDFilesInfo{AllDataFieldsRef}[$FileIndex]}; + } + elsif ($OptionsInfo{DataFieldsMode} =~ /^Common$/i) { + @ColValues = map { exists $DataFieldLabelAndValuesRef->{$_} ? $DataFieldLabelAndValuesRef->{$_} : ''} @{$SDFilesInfo{CommonDataFieldsRef}[$FileIndex]}; + } + elsif ($OptionsInfo{DataFieldsMode} =~ /^Specify$/i) { + @ColValues = map { exists $DataFieldLabelAndValuesRef->{$_} ? $DataFieldLabelAndValuesRef->{$_} : ''} @{$OptionsInfo{SpecifiedDataFields}}; + } + + return \@ColValues; +} + +# Generate compound ID for FP and FPText output files.. +# +sub SetupCmpdIDForOutputFiles { + my($CmpdCount, $Molecule, $DataFieldLabelAndValuesRef) = @_; + my($CmpdID); + + $CmpdID = ''; + if ($OptionsInfo{CompoundIDMode} =~ /^MolNameOrLabelPrefix$/i) { + my($MolName); + $MolName = $Molecule->GetName(); + $CmpdID = $MolName ? $MolName : "$OptionsInfo{CompoundID}${CmpdCount}"; + } + elsif ($OptionsInfo{CompoundIDMode} =~ /^LabelPrefix$/i) { + $CmpdID = "$OptionsInfo{CompoundID}${CmpdCount}"; + } + elsif ($OptionsInfo{CompoundIDMode} =~ /^DataField$/i) { + my($SpecifiedDataField); + $SpecifiedDataField = $OptionsInfo{CompoundID}; + $CmpdID = exists $DataFieldLabelAndValuesRef->{$SpecifiedDataField} ? $DataFieldLabelAndValuesRef->{$SpecifiedDataField} : ''; + } + elsif ($OptionsInfo{CompoundIDMode} =~ /^MolName$/i) { + $CmpdID = $Molecule->GetName(); + } + return $CmpdID; +} + +# Generate fingerprints for molecule... +# +sub GenerateMoleculeFingerprints { + my($Molecule) = @_; + my($AtomNeighborhoodsFingerprints); + + if ($OptionsInfo{KeepLargestComponent}) { + $Molecule->KeepLargestComponent(); + } + if (!$Molecule->DetectRings()) { + return undef; + } + $Molecule->SetAromaticityModel($OptionsInfo{AromaticityModel}); + $Molecule->DetectAromaticity(); + + $AtomNeighborhoodsFingerprints = new Fingerprints::AtomNeighborhoodsFingerprints('Molecule' => $Molecule, 'MinNeighborhoodRadius' => $OptionsInfo{MinNeighborhoodRadius}, 'MaxNeighborhoodRadius' => $OptionsInfo{MaxNeighborhoodRadius}, 'AtomIdentifierType' => $OptionsInfo{AtomIdentifierType}); + SetAtomIdentifierTypeValuesToUse($AtomNeighborhoodsFingerprints); + + # Generate fingerprints... + $AtomNeighborhoodsFingerprints->GenerateFingerprints(); + + # Make sure fingerprints generation is successful... + if (!$AtomNeighborhoodsFingerprints->IsFingerprintsGenerationSuccessful()) { + return undef; + } + + return $AtomNeighborhoodsFingerprints; +} + +# Set atom identifier type to use for generating fingerprints... +# +sub SetAtomIdentifierTypeValuesToUse { + my($AtomNeighborhoodsFingerprints) = @_; + + if ($OptionsInfo{AtomIdentifierType} =~ /^AtomicInvariantsAtomTypes$/i) { + $AtomNeighborhoodsFingerprints->SetAtomicInvariantsToUse(\@{$OptionsInfo{AtomicInvariantsToUse}}); + } + elsif ($OptionsInfo{AtomIdentifierType} =~ /^FunctionalClassAtomTypes$/i) { + $AtomNeighborhoodsFingerprints->SetFunctionalClassesToUse(\@{$OptionsInfo{FunctionalClassesToUse}}); + } + elsif ($OptionsInfo{AtomIdentifierType} =~ /^(DREIDINGAtomTypes|EStateAtomTypes|MMFF94AtomTypes|SLogPAtomTypes|SYBYLAtomTypes|TPSAAtomTypes|UFFAtomTypes)$/i) { + # Nothing to do for now... + } + else { + die "Error: The value specified, $Options{atomidentifiertype}, for option \"-a, --AtomIdentifierType\" is not valid. Supported atom identifier types in current release of MayaChemTools: AtomicInvariantsAtomTypes, DREIDINGAtomTypes, EStateAtomTypes, FunctionalClassAtomTypes, MMFF94AtomTypes, SLogPAtomTypes, SYBYLAtomTypes, TPSAAtomTypes, UFFAtomTypes\n"; + } +} + +# Retrieve information about SD files... +# +sub RetrieveSDFilesInfo { + my($SDFile, $Index, $FileDir, $FileExt, $FileName, $OutFileRoot, $TextOutFileExt, $SDOutFileExt, $FPOutFileExt, $NewSDFileName, $NewFPFileName, $NewTextFileName, $CheckDataField, $CollectDataFields, $AllDataFieldsRef, $CommonDataFieldsRef); + + %SDFilesInfo = (); + @{$SDFilesInfo{FileOkay}} = (); + @{$SDFilesInfo{OutFileRoot}} = (); + @{$SDFilesInfo{SDOutFileNames}} = (); + @{$SDFilesInfo{FPOutFileNames}} = (); + @{$SDFilesInfo{TextOutFileNames}} = (); + @{$SDFilesInfo{AllDataFieldsRef}} = (); + @{$SDFilesInfo{CommonDataFieldsRef}} = (); + + $CheckDataField = ($OptionsInfo{TextOutput} && ($OptionsInfo{DataFieldsMode} =~ /^CompoundID$/i) && ($OptionsInfo{CompoundIDMode} =~ /^DataField$/i)) ? 1 : 0; + $CollectDataFields = ($OptionsInfo{TextOutput} && ($OptionsInfo{DataFieldsMode} =~ /^(All|Common)$/i)) ? 1 : 0; + + FILELIST: for $Index (0 .. $#SDFilesList) { + $SDFile = $SDFilesList[$Index]; + + $SDFilesInfo{FileOkay}[$Index] = 0; + $SDFilesInfo{OutFileRoot}[$Index] = ''; + $SDFilesInfo{SDOutFileNames}[$Index] = ''; + $SDFilesInfo{FPOutFileNames}[$Index] = ''; + $SDFilesInfo{TextOutFileNames}[$Index] = ''; + + $SDFile = $SDFilesList[$Index]; + if (!(-e $SDFile)) { + warn "Warning: Ignoring file $SDFile: It doesn't exist\n"; + next FILELIST; + } + if (!CheckFileType($SDFile, "sd sdf")) { + warn "Warning: Ignoring file $SDFile: It's not a SD file\n"; + next FILELIST; + } + + if ($CheckDataField) { + # Make sure data field exists in SD file.. + my($CmpdString, $SpecifiedDataField, @CmpdLines, %DataFieldValues); + + @CmpdLines = (); + open SDFILE, "$SDFile" or die "Error: Couldn't open $SDFile: $! \n"; + $CmpdString = ReadCmpdString(\*SDFILE); + close SDFILE; + @CmpdLines = split "\n", $CmpdString; + %DataFieldValues = GetCmpdDataHeaderLabelsAndValues(\@CmpdLines); + $SpecifiedDataField = $OptionsInfo{CompoundID}; + if (!exists $DataFieldValues{$SpecifiedDataField}) { + warn "Warning: Ignoring file $SDFile: Data field value, $SpecifiedDataField, using \"--CompoundID\" option in \"DataField\" \"--CompoundIDMode\" doesn't exist\n"; + next FILELIST; + } + } + + $AllDataFieldsRef = ''; + $CommonDataFieldsRef = ''; + if ($CollectDataFields) { + my($CmpdCount); + open SDFILE, "$SDFile" or die "Error: Couldn't open $SDFile: $! \n"; + ($CmpdCount, $AllDataFieldsRef, $CommonDataFieldsRef) = GetAllAndCommonCmpdDataHeaderLabels(\*SDFILE); + close SDFILE; + } + + # Setup output file names... + $FileDir = ""; $FileName = ""; $FileExt = ""; + ($FileDir, $FileName, $FileExt) = ParseFileName($SDFile); + + $TextOutFileExt = "csv"; + if ($Options{outdelim} =~ /^tab$/i) { + $TextOutFileExt = "tsv"; + } + $SDOutFileExt = $FileExt; + $FPOutFileExt = "fpf"; + + if ($OptionsInfo{OutFileRoot} && (@SDFilesList == 1)) { + my ($RootFileDir, $RootFileName, $RootFileExt) = ParseFileName($OptionsInfo{OutFileRoot}); + if ($RootFileName && $RootFileExt) { + $FileName = $RootFileName; + } + else { + $FileName = $OptionsInfo{OutFileRoot}; + } + $OutFileRoot = $FileName; + } + else { + $OutFileRoot = "${FileName}AtomNeighborhoodsFP"; + } + + $NewSDFileName = "${OutFileRoot}.${SDOutFileExt}"; + $NewFPFileName = "${OutFileRoot}.${FPOutFileExt}"; + $NewTextFileName = "${OutFileRoot}.${TextOutFileExt}"; + + if ($OptionsInfo{SDOutput}) { + if ($SDFile =~ /$NewSDFileName/i) { + warn "Warning: Ignoring input file $SDFile: Same output, $NewSDFileName, and input file names.\n"; + print "Specify a different name using \"-r --root\" option or use default name.\n"; + next FILELIST; + } + } + + if (!$OptionsInfo{OverwriteFiles}) { + # Check SD and text outout files... + if ($OptionsInfo{SDOutput}) { + if (-e $NewSDFileName) { + warn "Warning: Ignoring file $SDFile: The file $NewSDFileName already exists\n"; + next FILELIST; + } + } + if ($OptionsInfo{FPOutput}) { + if (-e $NewFPFileName) { + warn "Warning: Ignoring file $SDFile: The file $NewFPFileName already exists\n"; + next FILELIST; + } + } + if ($OptionsInfo{TextOutput}) { + if (-e $NewTextFileName) { + warn "Warning: Ignoring file $SDFile: The file $NewTextFileName already exists\n"; + next FILELIST; + } + } + } + + $SDFilesInfo{FileOkay}[$Index] = 1; + + $SDFilesInfo{OutFileRoot}[$Index] = $OutFileRoot; + $SDFilesInfo{SDOutFileNames}[$Index] = $NewSDFileName; + $SDFilesInfo{FPOutFileNames}[$Index] = $NewFPFileName; + $SDFilesInfo{TextOutFileNames}[$Index] = $NewTextFileName; + + $SDFilesInfo{AllDataFieldsRef}[$Index] = $AllDataFieldsRef; + $SDFilesInfo{CommonDataFieldsRef}[$Index] = $CommonDataFieldsRef; + } +} + +# Process option values... +sub ProcessOptions { + %OptionsInfo = (); + + ProcessAtomIdentifierTypeOptions(); + + $OptionsInfo{AromaticityModel} = $Options{aromaticitymodel}; + + $OptionsInfo{CompoundIDMode} = $Options{compoundidmode}; + $OptionsInfo{CompoundIDLabel} = $Options{compoundidlabel}; + $OptionsInfo{DataFieldsMode} = $Options{datafieldsmode}; + + my(@SpecifiedDataFields); + @SpecifiedDataFields = (); + + @{$OptionsInfo{SpecifiedDataFields}} = (); + $OptionsInfo{CompoundID} = ''; + + if ($Options{datafieldsmode} =~ /^CompoundID$/i) { + if ($Options{compoundidmode} =~ /^DataField$/i) { + if (!$Options{compoundid}) { + die "Error: You must specify a value for \"--CompoundID\" option in \"DataField\" \"--CompoundIDMode\". \n"; + } + $OptionsInfo{CompoundID} = $Options{compoundid}; + } + elsif ($Options{compoundidmode} =~ /^(LabelPrefix|MolNameOrLabelPrefix)$/i) { + $OptionsInfo{CompoundID} = $Options{compoundid} ? $Options{compoundid} : 'Cmpd'; + } + } + elsif ($Options{datafieldsmode} =~ /^Specify$/i) { + if (!$Options{datafields}) { + die "Error: You must specify a value for \"--DataFields\" option in \"Specify\" \"-d, --DataFieldsMode\". \n"; + } + @SpecifiedDataFields = split /\,/, $Options{datafields}; + push @{$OptionsInfo{SpecifiedDataFields}}, @SpecifiedDataFields; + } + + $OptionsInfo{FingerprintsLabel} = $Options{fingerprintslabel} ? $Options{fingerprintslabel} : 'AtomNeighborhoodsFingerprints'; + + $OptionsInfo{Filter} = ($Options{filter} =~ /^Yes$/i) ? 1 : 0; + + $OptionsInfo{KeepLargestComponent} = ($Options{keeplargestcomponent} =~ /^Yes$/i) ? 1 : 0; + + $OptionsInfo{MinNeighborhoodRadius} = $Options{minneighborhoodradius}; + $OptionsInfo{MaxNeighborhoodRadius} = $Options{maxneighborhoodradius}; + + $OptionsInfo{Output} = $Options{output}; + $OptionsInfo{SDOutput} = ($Options{output} =~ /^(SD|All)$/i) ? 1 : 0; + $OptionsInfo{FPOutput} = ($Options{output} =~ /^(FP|All)$/i) ? 1 : 0; + $OptionsInfo{TextOutput} = ($Options{output} =~ /^(Text|All)$/i) ? 1 : 0; + + $OptionsInfo{OutDelim} = $Options{outdelim}; + $OptionsInfo{OutQuote} = ($Options{quote} =~ /^Yes$/i) ? 1 : 0; + + $OptionsInfo{OverwriteFiles} = $Options{overwrite} ? 1 : 0; + $OptionsInfo{OutFileRoot} = $Options{root} ? $Options{root} : 0; + + $OptionsInfo{VectorStringFormat} = 'ValuesString'; +} + +# Process atom identifier type and related options... +# +sub ProcessAtomIdentifierTypeOptions { + + $OptionsInfo{AtomIdentifierType} = $Options{atomidentifiertype}; + + if ($Options{atomidentifiertype} =~ /^AtomicInvariantsAtomTypes$/i) { + ProcessAtomicInvariantsToUseOption(); + } + elsif ($Options{atomidentifiertype} =~ /^FunctionalClassAtomTypes$/i) { + ProcessFunctionalClassesToUse(); + } + elsif ($OptionsInfo{AtomIdentifierType} =~ /^(DREIDINGAtomTypes|EStateAtomTypes|MMFF94AtomTypes|SLogPAtomTypes|SYBYLAtomTypes|TPSAAtomTypes|UFFAtomTypes)$/i) { + # Nothing to do for now... + } + else { + die "Error: The value specified, $Options{atomidentifiertype}, for option \"-a, --AtomIdentifierType\" is not valid. Supported atom identifier types in current release of MayaChemTools: AtomicInvariantsAtomTypes, DREIDINGAtomTypes, EStateAtomTypes, FunctionalClassAtomTypes, MMFF94AtomTypes, SLogPAtomTypes, SYBYLAtomTypes, TPSAAtomTypes, UFFAtomTypes\n"; + } +} + +# Process specified atomic invariants to use... +# +sub ProcessAtomicInvariantsToUseOption { + my($AtomicInvariant, $AtomSymbolSpecified, @AtomicInvariantsWords); + + @{$OptionsInfo{AtomicInvariantsToUse}} = (); + if (IsEmpty($Options{atomicinvariantstouse})) { + die "Error: Atomic invariants value specified using \"--AtomicInvariantsToUse\" option is empty\n"; + } + $AtomSymbolSpecified = 0; + @AtomicInvariantsWords = split /\,/, $Options{atomicinvariantstouse}; + for $AtomicInvariant (@AtomicInvariantsWords) { + if (!AtomTypes::AtomicInvariantsAtomTypes::IsAtomicInvariantAvailable($AtomicInvariant)) { + die "Error: Atomic invariant specified, $AtomicInvariant, using \"--AtomicInvariantsToUse\" option is not valid...\n "; + } + if ($AtomicInvariant =~ /^(AS|AtomSymbol)$/i) { + $AtomSymbolSpecified = 1; + } + push @{$OptionsInfo{AtomicInvariantsToUse}}, $AtomicInvariant; + } + if (!$AtomSymbolSpecified) { + die "Error: Atomic invariant, AS or AtomSymbol, must be specified as using \"--AtomicInvariantsToUse\" option...\n "; + } +} + +# Process specified functional classes invariants to use... +# +sub ProcessFunctionalClassesToUse { + my($FunctionalClass, @FunctionalClassesToUseWords); + + @{$OptionsInfo{FunctionalClassesToUse}} = (); + if (IsEmpty($Options{functionalclassestouse})) { + die "Error: Functional classes value specified using \"--FunctionalClassesToUse\" option is empty\n"; + } + @FunctionalClassesToUseWords = split /\,/, $Options{functionalclassestouse}; + for $FunctionalClass (@FunctionalClassesToUseWords) { + if (!AtomTypes::FunctionalClassAtomTypes::IsFunctionalClassAvailable($FunctionalClass)) { + die "Error: Functional class specified, $FunctionalClass, using \"--FunctionalClassesToUse\" option is not valid...\n "; + } + push @{$OptionsInfo{FunctionalClassesToUse}}, $FunctionalClass; + } +} + +# Setup script usage and retrieve command line arguments specified using various options... +sub SetupScriptUsage { + + # Retrieve all the options... + %Options = (); + + $Options{aromaticitymodel} = 'MayaChemToolsAromaticityModel'; + + $Options{atomidentifiertype} = 'AtomicInvariantsAtomTypes'; + $Options{atomicinvariantstouse} = 'AS,X,BO,H,FC'; + $Options{functionalclassestouse} = 'HBD,HBA,PI,NI,Ar,Hal'; + + $Options{compoundidmode} = 'LabelPrefix'; + $Options{compoundidlabel} = 'CompoundID'; + $Options{datafieldsmode} = 'CompoundID'; + + $Options{filter} = 'Yes'; + + $Options{keeplargestcomponent} = 'Yes'; + + $Options{minneighborhoodradius} = 0; + $Options{maxneighborhoodradius} = 2; + + $Options{output} = 'text'; + $Options{outdelim} = 'comma'; + $Options{quote} = 'yes'; + + if (!GetOptions(\%Options, "aromaticitymodel=s", "atomidentifiertype|a=s", "atomicinvariantstouse=s", "functionalclassestouse=s", "compoundid=s", "compoundidlabel=s", "compoundidmode=s", "datafields=s", "datafieldsmode|d=s", "filter|f=s", "fingerprintslabel=s", "help|h", "keeplargestcomponent|k=s", "minneighborhoodradius=s", "maxneighborhoodradius=s", "outdelim=s", "output=s", "overwrite|o", "quote|q=s", "root|r=s", "workingdir|w=s")) { + die "\nTo get a list of valid options and their values, use \"$ScriptName -h\" or\n\"perl -S $ScriptName -h\" command and try again...\n"; + } + if ($Options{workingdir}) { + if (! -d $Options{workingdir}) { + die "Error: The value specified, $Options{workingdir}, for option \"-w --workingdir\" is not a directory name.\n"; + } + chdir $Options{workingdir} or die "Error: Couldn't chdir $Options{workingdir}: $! \n"; + } + if (!Molecule::IsSupportedAromaticityModel($Options{aromaticitymodel})) { + my(@SupportedModels) = Molecule::GetSupportedAromaticityModels(); + die "Error: The value specified, $Options{aromaticitymodel}, for option \"--AromaticityModel\" is not valid. Supported aromaticity models in current release of MayaChemTools: @SupportedModels\n"; + } + if ($Options{atomidentifiertype} !~ /^(AtomicInvariantsAtomTypes|DREIDINGAtomTypes|EStateAtomTypes|FunctionalClassAtomTypes|MMFF94AtomTypes|SLogPAtomTypes|SYBYLAtomTypes|TPSAAtomTypes|UFFAtomTypes)$/i) { + die "Error: The value specified, $Options{atomidentifiertype}, for option \"-a, --AtomIdentifierType\" is not valid. Supported atom identifier types in current release of MayaChemTools: AtomicInvariantsAtomTypes, DREIDINGAtomTypes, EStateAtomTypes, FunctionalClassAtomTypes, MMFF94AtomTypes, SLogPAtomTypes, SYBYLAtomTypes, TPSAAtomTypes, UFFAtomTypes\n"; + } + if ($Options{compoundidmode} !~ /^(DataField|MolName|LabelPrefix|MolNameOrLabelPrefix)$/i) { + die "Error: The value specified, $Options{compoundidmode}, for option \"--CompoundIDMode\" is not valid. Allowed values: DataField, MolName, LabelPrefix or MolNameOrLabelPrefix\n"; + } + if ($Options{datafieldsmode} !~ /^(All|Common|Specify|CompoundID)$/i) { + die "Error: The value specified, $Options{datafieldsmode}, for option \"-d, --DataFieldsMode\" is not valid. Allowed values: All, Common, Specify or CompoundID\n"; + } + if ($Options{filter} !~ /^(Yes|No)$/i) { + die "Error: The value specified, $Options{filter}, for option \"-f, --Filter\" is not valid. Allowed values: Yes or No\n"; + } + if ($Options{keeplargestcomponent} !~ /^(Yes|No)$/i) { + die "Error: The value specified, $Options{keeplargestcomponent}, for option \"-k, --KeepLargestComponent\" is not valid. Allowed values: Yes or No\n"; + } + if (!(IsInteger($Options{minneighborhoodradius}) && ($Options{minneighborhoodradius} >= 0))) { + die "Error: The value specified, $Options{minneighborhoodradius}, for option \"--MinNeighborhoodRadius\" is not valid. Allowed values: >= 0 \n"; + } + if (!(IsInteger($Options{maxneighborhoodradius}) && ($Options{maxneighborhoodradius} >= 0))) { + die "Error: The value specified, $Options{maxneighborhoodradius}, for option \"--MaxNeighborhoodRadius\" is not valid. Allowed values: >= 0 \n"; + } + if ($Options{minneighborhoodradius} > $Options{maxneighborhoodradius}) { + die "Error: The value specified, specified, $Options{minneighborhoodradius}, for option \"--MinNeighborhoodRadius\" must be less than the value specified, $Options{maxneighborhoodradius}, for option \"--MaxNeighborhoodRadius\" \n"; + } + if ($Options{output} !~ /^(SD|FP|text|all)$/i) { + die "Error: The value specified, $Options{output}, for option \"--output\" is not valid. Allowed values: SD, FP, text, or all\n"; + } + if ($Options{outdelim} !~ /^(comma|semicolon|tab)$/i) { + die "Error: The value specified, $Options{outdelim}, for option \"--outdelim\" is not valid. Allowed values: comma, tab, or semicolon\n"; + } + if ($Options{quote} !~ /^(Yes|No)$/i) { + die "Error: The value specified, $Options{quote}, for option \"-q --quote\" is not valid. Allowed values: Yes or No\n"; + } + if ($Options{outdelim} =~ /semicolon/i && $Options{quote} =~ /^No$/i) { + die "Error: The value specified, $Options{quote}, for option \"-q --quote\" is not allowed with, semicolon value of \"--outdelim\" option: Fingerprints string use semicolon as delimiter for various data fields and must be quoted.\n"; + } +} + +__END__ + +=head1 NAME + +AtomNeighborhoodsFingerprints.pl - Generate atom neighborhoods fingerprints for SD files + +=head1 SYNOPSIS + +AtomNeighborhoodsFingerprints.pl SDFile(s)... + +AtomNeighborhoodsFingerprints.pl [B<--AromaticityModel> I<AromaticityModelType>] +[B<-a, --AtomIdentifierType> I<AtomicInvariantsAtomTypes | +DREIDINGAtomTypes | EStateAtomTypes | MMFF94AtomTypes | SLogPAtomTypes | SYBYLAtomTypes | TPSAAtomTypes | UFFAtomTypes>] +[B<--AtomicInvariantsToUse> I<"AtomicInvariant,AtomicInvariant...">] +[B<--FunctionalClassesToUse> I<"FunctionalClass1,FunctionalClass2...">] +[B<--CompoundID> I<DataFieldName or LabelPrefixString>] [B<--CompoundIDLabel> I<text>] +[B<--CompoundIDMode>] [B<--DataFields> I<"FieldLabel1,FieldLabel2,...">] +[B<-d, --DataFieldsMode> I<All | Common | Specify | CompoundID>] [B<-f, --Filter> I<Yes | No>] +[B<--FingerprintsLabel> I<text>] [B<-h, --help>] [B<-k, --KeepLargestComponent> I<Yes | No>] +[B<--MinNeighborhoodRadius> I<number>] [B<--MaxNeighborhoodRadius> I<number>] +[B<--OutDelim> I<comma | tab | semicolon>] [B<--output> I<SD | FP | text | all>] [B<-o, --overwrite>] +[B<-q, --quote> I<Yes | No>] [B<-r, --root> I<RootName>] +[B<-w, --WorkingDir> dirname] SDFile(s)... + +=head1 DESCRIPTION + +Generate atom neighborhoods fingerprints [ Ref 53-56, Ref 73 ] for I<SDFile(s)> and create appropriate +SD, FP or CSV/TSV text file(s) containing fingerprints vector strings corresponding to molecular fingerprints. + +Multiple SDFile names are separated by spaces. The valid file extensions are I<.sdf> +and I<.sd>. All other file names are ignored. All the SD files in a current directory +can be specified either by I<*.sdf> or the current directory name. + +The current release of MayaChemTools supports generation of atom neighborhoods fingerprints +corresponding to following B<-a, --AtomIdentifierTypes>: + + AtomicInvariantsAtomTypes, DREIDINGAtomTypes, EStateAtomTypes, + FunctionalClassAtomTypes, MMFF94AtomTypes, SLogPAtomTypes, + SYBYLAtomTypes, TPSAAtomTypes, UFFAtomTypes + +Based on the values specified for B<-a, --AtomIdentifierType> and B<--AtomicInvariantsToUse>, +initial atom types are assigned to all non-hydrogen atoms in a molecule. Using atom neighborhoods +around each non-hydrogen central atom corresponding to radii between specified values +B<--MinNeighborhoodRadius> and B<--MaxNeighborhoodRadius>, unique atom types at +each radii level are counted and an atom neighborhood identifier is generated. + +The format of an atom neighborhood identifier around a central non-hydrogen atom at a +specific radius is: + + NR<n>-<AtomType>-ATC<n> + + NR: Neighborhood radius + AtomType: Assigned atom type + ATC: Atom type count + +The atom neighborhood identifier for a non-hydrogen central atom corresponding to all specified radii +is generated by concatenating neighborhood identifiers at each radii by colon as a delimiter: + + NR<n>-<AtomType>-ATC<n>:NR<n>-<AtomType>-ATC<n>:... + +The atom neighborhood identifiers for all non-hydrogen central atoms at all specified radii are +concatenated using space as a delimiter and constitute atom neighborhood fingerprint of the molecule. + +Example of I<SD> file containing atom neighborhood fingerprints string data: + + ... ... + ... ... + $$$$ + ... ... + ... ... + ... ... + 41 44 0 0 0 0 0 0 0 0999 V2000 + -3.3652 1.4499 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 + ... ... + 2 3 1 0 0 0 0 + ... ... + M END + > <CmpdID> + Cmpd1 + + > <AtomNeighborhoodsFingerprints> + FingerprintsVector;AtomNeighborhoods:AtomicInvariantsAtomTypes:MinRadiu + s0:MaxRadius2;41;AlphaNumericalValues;ValuesString;NR0-C.X1.BO1.H3-ATC1 + :NR1-C.X3.BO3.H1-ATC1:NR2-C.X1.BO1.H3-ATC1:NR2-C.X3.BO4-ATC1 NR0-C.X1.B + O1.H3-ATC1:NR1-C.X3.BO3.H1-ATC1:NR2-C.X1.BO1.H3-ATC1:NR2-C.X3.BO4-ATC1 + NR0-C.X2.BO2.H2-ATC1:NR1-C.X2.BO2.H2-ATC1:NR1-C.X3.BO3.H1-ATC1:NR2-C... + + $$$$ + ... ... + ... ... + +Example of I<FP> file containing atom neighborhood fingerprints string data: + + # + # Package = MayaChemTools 7.4 + # Release Date = Oct 21, 2010 + # + # TimeStamp = Fri Mar 11 14:15:27 2011 + # + # FingerprintsStringType = FingerprintsVector + # + # Description = AtomNeighborhoods:AtomicInvariantsAtomTypes:MinRadiu... + # VectorStringFormat = ValuesString + # VectorValuesType = AlphaNumericalValues + # + Cmpd1 41;NR0-C.X1.BO1.H3-ATC1:NR1-C.X3.BO3.H1-ATC1:NR2-C.X1.BO1.H3-A... + Cmpd2 23;NR0-C.X1.BO1.H3-ATC1:NR1-C.X2.BO2.H2-ATC1:NR2-C.X3.BO3.H1-A... + ... ... + ... .. + +Example of CSV I<Text> file containing atom neighborhood fingerprints string data: + + "CompoundID","AtomNeighborhoodsFingerprints" + "Cmpd1","FingerprintsVector;AtomNeighborhoods:AtomicInvariantsAtomTypes + :MinRadius0:MaxRadius2;41;AlphaNumericalValues;ValuesString;NR0-C.X1.B + O1.H3-ATC1:NR1-C.X3.BO3.H1-ATC1:NR2-C.X1.BO1.H3-ATC1:NR2-C.X3.BO4-ATC1 + NR0-C.X1.BO1.H3-ATC1:NR1-C.X3.BO3.H1-ATC1:NR2-C.X1.BO1.H3-ATC1:NR2-C.X3 + .BO4-ATC1 NR0-C.X2.BO2.H2-ATC1:NR1-C.X2.BO2.H2-ATC1:NR1-C.X3.BO3.H1..." + ... ... + ... ... + +The current release of MayaChemTools generates the following types of atom neighborhoods +fingerprints vector strings: + + FingerprintsVector;AtomNeighborhoods:AtomicInvariantsAtomTypes:MinRadi + us0:MaxRadius2;41;AlphaNumericalValues;ValuesString;NR0-C.X1.BO1.H3-AT + C1:NR1-C.X3.BO3.H1-ATC1:NR2-C.X1.BO1.H3-ATC1:NR2-C.X3.BO4-ATC1 NR0-C.X + 1.BO1.H3-ATC1:NR1-C.X3.BO3.H1-ATC1:NR2-C.X1.BO1.H3-ATC1:NR2-C.X3.BO4-A + TC1 NR0-C.X2.BO2.H2-ATC1:NR1-C.X2.BO2.H2-ATC1:NR1-C.X3.BO3.H1-ATC1:NR2 + -C.X2.BO2.H2-ATC1:NR2-N.X3.BO3-ATC1:NR2-O.X1.BO1.H1-ATC1 NR0-C.X2.B... + + FingerprintsVector;AtomNeighborhoods:DREIDINGAtomTypes:MinRadius0:MaxR + adius2;41;AlphaNumericalValues;ValuesString;NR0-C_2-ATC1:NR1-C_3-ATC1: + NR1-O_2-ATC1:NR1-O_3-ATC1:NR2-C_3-ATC1 NR0-C_2-ATC1:NR1-C_R-ATC1:NR1-N + _3-ATC1:NR1-O_2-ATC1:NR2-C_R-ATC3 NR0-C_3-ATC1:NR1-C_2-ATC1:NR1-C_3-AT + C1:NR2-C_3-ATC1:NR2-O_2-ATC1:NR2-O_3-ATC2 NR0-C_3-ATC1:NR1-C_3-ATC1:NR + 1-N_R-ATC1:NR2-C_3-ATC1:NR2-C_R-ATC2 NR0-C_3-ATC1:NR1-C_3-ATC1:NR2-... + + FingerprintsVector;AtomNeighborhoods:EStateAtomTypes:MinRadius0:MaxRad + ius2;41;AlphaNumericalValues;ValuesString;NR0-aaCH-ATC1:NR1-aaCH-ATC1: + NR1-aasC-ATC1:NR2-aaCH-ATC1:NR2-aasC-ATC1:NR2-sF-ATC1 NR0-aaCH-ATC1:NR + 1-aaCH-ATC1:NR1-aasC-ATC1:NR2-aaCH-ATC1:NR2-aasC-ATC1:NR2-sF-ATC1 NR0- + aaCH-ATC1:NR1-aaCH-ATC1:NR1-aasC-ATC1:NR2-aaCH-ATC1:NR2-aasC-ATC2 NR0- + aaCH-ATC1:NR1-aaCH-ATC1:NR1-aasC-ATC1:NR2-aaCH-ATC1:NR2-aasC-ATC2 N... + + FingerprintsVector;AtomNeighborhoods:FunctionalClassAtomTypes:MinRadiu + s0:MaxRadius2;41;AlphaNumericalValues;ValuesString;NR0-Ar-ATC1:NR1-Ar- + ATC1:NR1-Ar.HBA-ATC1:NR1-None-ATC1:NR2-Ar-ATC2:NR2-None-ATC4 NR0-Ar-AT + C1:NR1-Ar-ATC2:NR1-Ar.HBA-ATC1:NR2-Ar-ATC5:NR2-None-ATC1 NR0-Ar-ATC1:N + R1-Ar-ATC2:NR1-HBD-ATC1:NR2-Ar-ATC2:NR2-None-ATC1 NR0-Ar-ATC1:NR1-Ar-A + TC2:NR1-Hal-ATC1:NR2-Ar-ATC2 NR0-Ar-ATC1:NR1-Ar-ATC2:NR1-None-ATC1:... + + FingerprintsVector;AtomNeighborhoods:MMFF94AtomTypes:MinRadius0:MaxRad + ius2;41;AlphaNumericalValues;ValuesString;NR0-C5A-ATC1:NR1-C5B-ATC1:NR + 1-CB-ATC1:NR1-N5-ATC1:NR2-C5A-ATC1:NR2-C5B-ATC1:NR2-CB-ATC3:NR2-CR-ATC + 1 NR0-C5A-ATC1:NR1-C5B-ATC1:NR1-CR-ATC1:NR1-N5-ATC1:NR2-C5A-ATC1:NR2-C + 5B-ATC1:NR2-C=ON-ATC1:NR2-CR-ATC3 NR0-C5B-ATC1:NR1-C5A-ATC1:NR1-C5B-AT + C1:NR1-C=ON-ATC1:NR2-C5A-ATC1:NR2-CB-ATC1:NR2-CR-ATC1:NR2-N5-ATC1:N... + + FingerprintsVector;AtomNeighborhoods:SLogPAtomTypes:MinRadius0:MaxRadi + us2;41;AlphaNumericalValues;ValuesString;NR0-C1-ATC1:NR1-C10-ATC1:NR1- + CS-ATC1:NR2-C1-ATC1:NR2-N11-ATC1:NR2-O2-ATC1 NR0-C1-ATC1:NR1-C11-ATC1: + NR2-C1-ATC1:NR2-C21-ATC1 NR0-C1-ATC1:NR1-C11-ATC1:NR2-C1-ATC1:NR2-C21- + ATC1 NR0-C1-ATC1:NR1-C5-ATC1:NR1-CS-ATC1:NR2-C1-ATC1:NR2-O2-ATC2:NR2-O + 9-ATC1 NR0-C1-ATC1:NR1-CS-ATC2:NR2-C1-ATC2:NR2-O2-ATC2 NR0-C10-ATC1... + + FingerprintsVector;AtomNeighborhoods:SYBYLAtomTypes:MinRadius0:MaxRadi + us2;41;AlphaNumericalValues;ValuesString;NR0-C.2-ATC1:NR1-C.3-ATC1:NR1 + -O.co2-ATC2:NR2-C.3-ATC1 NR0-C.2-ATC1:NR1-C.ar-ATC1:NR1-N.am-ATC1:NR1- + O.2-ATC1:NR2-C.ar-ATC3 NR0-C.3-ATC1:NR1-C.2-ATC1:NR1-C.3-ATC1:NR2-C.3- + ATC1:NR2-O.3-ATC1:NR2-O.co2-ATC2 NR0-C.3-ATC1:NR1-C.3-ATC1:NR1-N.ar-AT + C1:NR2-C.3-ATC1:NR2-C.ar-ATC2 NR0-C.3-ATC1:NR1-C.3-ATC1:NR2-C.3-ATC... + + FingerprintsVector;AtomNeighborhoods:TPSAAtomTypes:MinRadius0:MaxRadiu + s2;41;AlphaNumericalValues;ValuesString;NR0-N21-ATC1:NR1-None-ATC3:NR2 + -None-ATC5 NR0-N7-ATC1:NR1-None-ATC2:NR2-None-ATC3:NR2-O3-ATC1 NR0-Non + e-ATC1:NR1-N21-ATC1:NR1-None-ATC1:NR2-None-ATC3 NR0-None-ATC1:NR1-N21- + ATC1:NR1-None-ATC2:NR2-None-ATC6 NR0-None-ATC1:NR1-N21-ATC1:NR1-None-A + TC2:NR2-None-ATC6 NR0-None-ATC1:NR1-N7-ATC1:NR1-None-ATC1:NR1-O3-AT... + + FingerprintsVector;AtomNeighborhoods:UFFAtomTypes:MinRadius0:MaxRadius + 2;41;AlphaNumericalValues;ValuesString;NR0-C_2-ATC1:NR1-C_3-ATC1:NR1-O + _2-ATC1:NR1-O_3-ATC1:NR2-C_3-ATC1 NR0-C_2-ATC1:NR1-C_R-ATC1:NR1-N_3-AT + C1:NR1-O_2-ATC1:NR2-C_R-ATC3 NR0-C_3-ATC1:NR1-C_2-ATC1:NR1-C_3-ATC1:NR + 2-C_3-ATC1:NR2-O_2-ATC1:NR2-O_3-ATC2 NR0-C_3-ATC1:NR1-C_3-ATC1:NR1-N_R + -ATC1:NR2-C_3-ATC1:NR2-C_R-ATC2 NR0-C_3-ATC1:NR1-C_3-ATC1:NR2-C_3-A... + +=head1 OPTIONS + +=over 4 + +=item B<--AromaticityModel> I<MDLAromaticityModel | TriposAromaticityModel | MMFFAromaticityModel | ChemAxonBasicAromaticityModel | ChemAxonGeneralAromaticityModel | DaylightAromaticityModel | MayaChemToolsAromaticityModel> + +Specify aromaticity model to use during detection of aromaticity. Possible values in the current +release are: I<MDLAromaticityModel, TriposAromaticityModel, MMFFAromaticityModel, +ChemAxonBasicAromaticityModel, ChemAxonGeneralAromaticityModel, DaylightAromaticityModel +or MayaChemToolsAromaticityModel>. Default value: I<MayaChemToolsAromaticityModel>. + +The supported aromaticity model names along with model specific control parameters +are defined in B<AromaticityModelsData.csv>, which is distributed with the current release +and is available under B<lib/data> directory. B<Molecule.pm> module retrieves data from +this file during class instantiation and makes it available to method B<DetectAromaticity> +for detecting aromaticity corresponding to a specific model. + +=item B<-a, --AtomIdentifierType> I<AtomicInvariantsAtomTypes | DREIDINGAtomTypes | EStateAtomTypes | FunctionalClassAtomTypes | MMFF94AtomTypes | SLogPAtomTypes | SYBYLAtomTypes | TPSAAtomTypes | UFFAtomTypes> + +Specify atom identifier type to use for assignment of initial atom identifier to non-hydrogen +atoms during calculation of atom neighborhoods fingerprints. Possible values in the current +release are: I<AtomicInvariantsAtomTypes, DREIDINGAtomTypes, EStateAtomTypes, +FunctionalClassAtomTypes, MMFF94AtomTypes, SLogPAtomTypes, SYBYLAtomTypes, +TPSAAtomTypes, UFFAtomTypes>. Default value: I<AtomicInvariantsAtomTypes>. + +=item B<--AtomicInvariantsToUse> I<"AtomicInvariant,AtomicInvariant..."> + +This value is used during I<AtomicInvariantsAtomTypes> value of B<a, --AtomIdentifierType> +option. It's a list of comma separated valid atomic invariant atom types. + +Possible values for atomic invariants are: I<AS, X, BO, LBO, SB, DB, TB, +H, Ar, RA, FC, MN, SM>. Default value: I<AS,X,BO,H,FC>. + +The atomic invariants abbreviations correspond to: + + AS = Atom symbol corresponding to element symbol + + X<n> = Number of non-hydrogen atom neighbors or heavy atoms + BO<n> = Sum of bond orders to non-hydrogen atom neighbors or heavy atoms + LBO<n> = Largest bond order of non-hydrogen atom neighbors or heavy atoms + SB<n> = Number of single bonds to non-hydrogen atom neighbors or heavy atoms + DB<n> = Number of double bonds to non-hydrogen atom neighbors or heavy atoms + TB<n> = Number of triple bonds to non-hydrogen atom neighbors or heavy atoms + H<n> = Number of implicit and explicit hydrogens for atom + Ar = Aromatic annotation indicating whether atom is aromatic + RA = Ring atom annotation indicating whether atom is a ring + FC<+n/-n> = Formal charge assigned to atom + MN<n> = Mass number indicating isotope other than most abundant isotope + SM<n> = Spin multiplicity of atom. Possible values: 1 (singlet), 2 (doublet) or + 3 (triplet) + +Atom type generated by AtomTypes::AtomicInvariantsAtomTypes class corresponds to: + + AS.X<n>.BO<n>.LBO<n>.<SB><n>.<DB><n>.<TB><n>.H<n>.Ar.RA.FC<+n/-n>.MN<n>.SM<n> + +Except for AS which is a required atomic invariant in atom types, all other atomic invariants are +optional. Atom type specification doesn't include atomic invariants with zero or undefined values. + +In addition to usage of abbreviations for specifying atomic invariants, the following descriptive words +are also allowed: + + X : NumOfNonHydrogenAtomNeighbors or NumOfHeavyAtomNeighbors + BO : SumOfBondOrdersToNonHydrogenAtoms or SumOfBondOrdersToHeavyAtoms + LBO : LargestBondOrderToNonHydrogenAtoms or LargestBondOrderToHeavyAtoms + SB : NumOfSingleBondsToNonHydrogenAtoms or NumOfSingleBondsToHeavyAtoms + DB : NumOfDoubleBondsToNonHydrogenAtoms or NumOfDoubleBondsToHeavyAtoms + TB : NumOfTripleBondsToNonHydrogenAtoms or NumOfTripleBondsToHeavyAtoms + H : NumOfImplicitAndExplicitHydrogens + Ar : Aromatic + RA : RingAtom + FC : FormalCharge + MN : MassNumber + SM : SpinMultiplicity + +I<AtomTypes::AtomicInvariantsAtomTypes> module is used to assign atomic invariant +atom types. + +=item B<--FunctionalClassesToUse> I<"FunctionalClass1,FunctionalClass2..."> + +This value is used during I<FunctionalClassAtomTypes> value of B<a, --AtomIdentifierType> +option. It's a list of comma separated valid functional classes. + +Possible values for atom functional classes are: I<Ar, CA, H, HBA, HBD, Hal, NI, PI, RA>. +Default value [ Ref 24 ]: I<HBD,HBA,PI,NI,Ar,Hal>. + +The functional class abbreviations correspond to: + + HBD: HydrogenBondDonor + HBA: HydrogenBondAcceptor + PI : PositivelyIonizable + NI : NegativelyIonizable + Ar : Aromatic + Hal : Halogen + H : Hydrophobic + RA : RingAtom + CA : ChainAtom + + Functional class atom type specification for an atom corresponds to: + + Ar.CA.H.HBA.HBD.Hal.NI.PI.RA + +I<AtomTypes::FunctionalClassAtomTypes> module is used to assign functional class atom +types. It uses following definitions [ Ref 60-61, Ref 65-66 ]: + + HydrogenBondDonor: NH, NH2, OH + HydrogenBondAcceptor: N[!H], O + PositivelyIonizable: +, NH2 + NegativelyIonizable: -, C(=O)OH, S(=O)OH, P(=O)OH + +=item B<--CompoundID> I<DataFieldName or LabelPrefixString> + +This value is B<--CompoundIDMode> specific and indicates how compound ID is generated. + +For I<DataField> value of B<--CompoundIDMode> option, it corresponds to datafield label name +whose value is used as compound ID; otherwise, it's a prefix string used for generating compound +IDs like LabelPrefixString<Number>. Default value, I<Cmpd>, generates compound IDs which +look like Cmpd<Number>. + +Examples for I<DataField> value of B<--CompoundIDMode>: + + MolID + ExtReg + +Examples for I<LabelPrefix> or I<MolNameOrLabelPrefix> value of B<--CompoundIDMode>: + + Compound + +The value specified above generates compound IDs which correspond to Compound<Number> +instead of default value of Cmpd<Number>. + + +=item B<--CompoundIDLabel> I<text> + +Specify compound ID column label for FP or CSV/TSV text file(s) used during I<CompoundID> value +of B<--DataFieldsMode> option. Default: I<CompoundID>. + +=item B<--CompoundIDMode> I<DataField | MolName | LabelPrefix | MolNameOrLabelPrefix> + +Specify how to generate compound IDs and write to FP or CSV/TSV text file(s) along with generated +fingerprints for I<FP | text | all> values of B<--output> option: use a I<SDFile(s)> datafield value; +use molname line from I<SDFile(s)>; generate a sequential ID with specific prefix; use combination +of both MolName and LabelPrefix with usage of LabelPrefix values for empty molname lines. + +Possible values: I<DataField | MolName | LabelPrefix | MolNameOrLabelPrefix>. +Default: I<LabelPrefix>. + +For I<MolNameAndLabelPrefix> value of B<--CompoundIDMode>, molname line in I<SDFile(s)> takes +precedence over sequential compound IDs generated using I<LabelPrefix> and only empty molname +values are replaced with sequential compound IDs. + +This is only used for I<CompoundID> value of B<--DataFieldsMode> option. + +=item B<--DataFields> I<"FieldLabel1,FieldLabel2,..."> + +Comma delimited list of I<SDFiles(s)> data fields to extract and write to CSV/TSV text file(s) along +with generated fingerprints for I<text | all> values of B<--output> option. + +This is only used for I<Specify> value of B<--DataFieldsMode> option. + +Examples: + + Extreg + MolID,CompoundName + +=item B<-d, --DataFieldsMode> I<All | Common | Specify | CompoundID> + +Specify how data fields in I<SDFile(s)> are transferred to output CSV/TSV text file(s) along +with generated fingerprints for I<text | all> values of B<--output> option: transfer all SD +data field; transfer SD data files common to all compounds; extract specified data fields; +generate a compound ID using molname line, a compound prefix, or a combination of both. +Possible values: I<All | Common | specify | CompoundID>. Default value: I<CompoundID>. + +=item B<-f, --Filter> I<Yes | No> + +Specify whether to check and filter compound data in SDFile(s). Possible values: I<Yes or No>. +Default value: I<Yes>. + +By default, compound data is checked before calculating fingerprints and compounds containing +atom data corresponding to non-element symbols or no atom data are ignored. + +=item B<--FingerprintsLabel> I<text> + +SD data label or text file column label to use for fingerprints string in output SD or +CSV/TSV text file(s) specified by B<--output>. Default value: I<AtomNeighborhoodsFingerprints>. + +=item B<-h, --help> + +Print this help message. + +=item B<-k, --KeepLargestComponent> I<Yes | No> + +Generate fingerprints for only the largest component in molecule. Possible values: +I<Yes or No>. Default value: I<Yes>. + +For molecules containing multiple connected components, fingerprints can be generated +in two different ways: use all connected components or just the largest connected +component. By default, all atoms except for the largest connected component are +deleted before generation of fingerprints. + +=item B<--MinNeighborhoodRadius> I<number> + +Minimum atom neighborhood radius for generating atom neighborhoods. Default value: I<0>. +Valid values: positive integers and less than B<--MaxNeighborhoodRadius>. Neighborhood +radius of zero corresponds to list of non-hydrogen atoms. + +=item B<--MaxNeighborhoodRadius> I<number> + +Maximum atom neighborhood radius for generating atom neighborhoods. Default value: I<2>. +Valid values: positive integers and greater than B<--MineighborhoodRadius>. + +=item B<--OutDelim> I<comma | tab | semicolon> + +Delimiter for output CSV/TSV text file(s). Possible values: I<comma, tab, or semicolon> +Default value: I<comma>. + +=item B<--output> I<SD | FP | text | all> + +Type of output files to generate. Possible values: I<SD, FP, text, or all>. Default value: I<text>. + +=item B<-o, --overwrite> + +Overwrite existing files. + +=item B<-q, --quote> I<Yes | No> + +Put quote around column values in output CSV/TSV text file(s). Possible values: +I<Yes or No>. Default value: I<Yes>. + +=item B<-r, --root> I<RootName> + +New file name is generated using the root: <Root>.<Ext>. Default for new file names: +<SDFileName><AtomNeighborhoodsFP>.<Ext>. The file type determines <Ext> +value. The sdf, fpf, csv, and tsv <Ext> values are used for SD, comma/semicolon, and tab +delimited text files, respectively.This option is ignored for multiple input files. + +=item B<-w, --WorkingDir> I<DirName> + +Location of working directory. Default: current directory. + +=back + +=head1 EXAMPLES + +To generate atom neighborhoods fingerprints corresponding to atom neighborhood radii from 0 to +2 using atomic invariants atom types in vector string format and create a SampleANFP.csv +file containing sequential compound IDs along with fingerprints vector strings data, type: + + % AtomNeighborhoodsFingerprints.pl -r SampleANFP -o Sample.sdf + +To generate atom neighborhoods fingerprints corresponding to atom neighborhood radii from 0 to +2 using DREIDING atom types in vector string format and create a SampleANFP.csv +file containing sequential compound IDs along with fingerprints vector strings data, type: + + % AtomNeighborhoodsFingerprints.pl -a DREIDINGAtomTypes -r SampleANFP + -o Sample.sdf + +To generate atom neighborhoods fingerprints corresponding to atom neighborhood radii from 0 to +2 using EStateAtomTypes types in vector string format and create a SampleANFP.csv +file containing sequential compound IDs along with fingerprints vector strings data, type: + + % AtomNeighborhoodsFingerprints.pl -a EStateAtomTypes -r SampleANFP + -o Sample.sdf + +To generate atom neighborhoods fingerprints corresponding to atom neighborhood radii from 0 to +2 using SYBYL atom types in vector string format and create a SampleANFP.csv +file containing sequential compound IDs along with fingerprints vector strings data, type: + + % AtomNeighborhoodsFingerprints.pl -a SYBYLAtomTypes -r SampleANFP + -o Sample.sdf + +To generate atom neighborhoods fingerprints corresponding to atom neighborhood radii from 0 to +2 using FunctionalClass atom types in vector string format and create a SampleANFP.csv +file containing sequential compound IDs along with fingerprints vector strings data, type: + + % AtomNeighborhoodsFingerprints.pl -a FunctionalClassAtomTypes + -r SampleANFP -o Sample.sdf + +To generate atom neighborhoods fingerprints corresponding to atom neighborhood radii from 0 to +2 using MMFF94 atom types in vector string format and create a SampleANFP.csv +file containing sequential compound IDs along with fingerprints vector strings data, type: + + % AtomNeighborhoodsFingerprints.pl -a MMFF94AtomTypes -r SampleANFP + -o Sample.sdf + +To generate atom neighborhoods fingerprints corresponding to atom neighborhood radii from 0 to +2 using SLogP atom types in vector string format and create a SampleANFP.csv +file containing sequential compound IDs along with fingerprints vector strings data, type: + + % AtomNeighborhoodsFingerprints.pl -a SLogPAtomTypes -r SampleANFP + -o Sample.sdf + +To generate atom neighborhoods fingerprints corresponding to atom neighborhood radii from 0 to +2 using SYBYL atom types in vector string format and create a SampleANFP.csv +file containing sequential compound IDs along with fingerprints vector strings data, type: + + % AtomNeighborhoodsFingerprints.pl -a SYBYLAtomTypes -r SampleANFP + -o Sample.sdf + +To generate atom neighborhoods fingerprints corresponding to atom neighborhood radii from 0 to +2 using TPSA atom types in vector string format and create a SampleANFP.csv +file containing sequential compound IDs along with fingerprints vector strings data, type: + + % AtomNeighborhoodsFingerprints.pl -a TPSAAtomTypes -r SampleANFP + -o Sample.sdf + +To generate atom neighborhoods fingerprints corresponding to atom neighborhood radii from 0 to +2 using UFF atom types in vector string format and create a SampleANFP.csv +file containing sequential compound IDs along with fingerprints vector strings data, type: + + % AtomNeighborhoodsFingerprints.pl -a UFFAtomTypes -r SampleANFP + -o Sample.sdf + +To generate atom neighborhoods fingerprints corresponding to atom neighborhood radii from 0 to +2 using atomic invariants atom types in vector string format and create SampleANFP.sdf, +SampleANFP.fpf and SampleANFP.csv files containing sequential compound IDs in CSV file along +with fingerprints vector strings data, type: + + % AtomNeighborhoodsFingerprints.pl --output all -r SampleANFP + -o Sample.sdf + +To generate atom neighborhoods fingerprints corresponding to atom neighborhood radii from 1 to +3 using atomic invariants atom types in vector string format and create a SampleANFP.csv +file containing sequential compound IDs along with fingerprints vector strings data, type: + + % AtomNeighborhoodsFingerprints.pl -a AtomicInvariantsAtomTypes + --MinNeighborhoodRadius 1 --MaxNeighborhoodRadius 3 -r SampleANFP + -o Sample.sdf + +To generate atom neighborhoods fingerprints corresponding to atom neighborhood radii from 0 to +2 using only AS,X atomic invariants atom types in vector string format and create a SampleANFP.csv +file containing sequential compound IDs along with fingerprints vector strings data, type: + + % AtomNeighborhoodsFingerprints.pl -a AtomicInvariantsAtomTypes + --AtomicInvariantsToUse "AS,X" --MinNeighborhoodRadius 0 + --MaxNeighborhoodRadius 3 -r SampleANFP -o Sample.sdf + +To generate atom neighborhoods fingerprints corresponding to atom neighborhood radii from 0 to +2 using atomic invariants atom types in vector string format and create a SampleANFP.csv +file containing compound ID from molecule name line along with fingerprints vector strings data, type: + + % AtomNeighborhoodsFingerprints.pl -a AtomicInvariantsAtomTypes + --DataFieldsMode CompoundID --CompoundIDMode MolName + -r SampleANFP -o Sample.sdf + +To generate atom neighborhoods fingerprints corresponding to atom neighborhood radii from 0 to +2 using atomic invariants atom types in vector string format and create a SampleANFP.csv +file containing compound IDs using specified data field along with fingerprints vector strings +data, type: + + % AtomNeighborhoodsFingerprints.pl -a AtomicInvariantsAtomTypes + --DataFieldsMode CompoundID --CompoundIDMode DataField --CompoundID + Mol_ID -r SampleANFP -o Sample.sdf + +To generate atom neighborhoods fingerprints corresponding to atom neighborhood radii from 0 to +2 using atomic invariants atom types in vector string format and create a SampleANFP.csv +file containing compound ID using combination of molecule name line and an explicit compound +prefix along with fingerprints vector strings data, type: + + % AtomNeighborhoodsFingerprints.pl -a AtomicInvariantsAtomTypes + --DataFieldsMode CompoundID --CompoundIDMode MolnameOrLabelPrefix + --CompoundID Cmpd --CompoundIDLabel MolID -r SampleANFP -o Sample.sdf + +To generate atom neighborhoods fingerprints corresponding to atom neighborhood radii from 0 to +2 using atomic invariants atom types in vector string format and create a SampleANFP.csv +file containing specific data fields columns along with fingerprints vector strings +data, type: + + % AtomNeighborhoodsFingerprints.pl -a AtomicInvariantsAtomTypes + --DataFieldsMode Specify --DataFields Mol_ID -r SampleANFP + -o Sample.sdf + +To generate atom neighborhoods fingerprints corresponding to atom neighborhood radii from 0 to +2 using atomic invariants atom types in vector string format and create a SampleANFP.csv +file containing common data fields columns along with fingerprints vector strings +data, type: + + % AtomNeighborhoodsFingerprints.pl -a AtomicInvariantsAtomTypes + --DataFieldsMode Common -r SampleANFP -o Sample.sdf + +To generate atom neighborhoods fingerprints corresponding to atom neighborhood radii from 0 to +2 using atomic invariants atom types in vector string format and create SampleANFP.sdf, + SampleANFP.fpf and SampleANFP.csv files containing all data fields columns in CSV file along with +fingerprints data, type: + + % AtomNeighborhoodsFingerprints.pl -a AtomicInvariantsAtomTypes + --DataFieldsMode All --output all -r SampleANFP + -o Sample.sdf + +=head1 AUTHOR + +Manish Sud <msud@san.rr.com> + +=head1 SEE ALSO + +InfoFingerprintsFiles.pl, SimilarityMatricesFingerprints.pl, SimilaritySearchingFingerprints.pl, +ExtendedConnectivityFingerprints.pl, MACCSKeysFingerprints.pl, PathLengthFingerprints.pl, +TopologicalAtomPairsFingerprints.pl, TopologicalAtomTorsionsFingerprints.pl, +TopologicalPharmacophoreAtomPairsFingerprints.pl, TopologicalPharmacophoreAtomTripletsFingerprints.pl + +=head1 COPYRIGHT + +Copyright (C) 2015 Manish Sud. All rights reserved. + +This file is part of MayaChemTools. + +MayaChemTools is free software; you can redistribute it and/or modify it under +the terms of the GNU Lesser General Public License as published by the Free +Software Foundation; either version 3 of the License, or (at your option) +any later version. + +=cut