Mercurial > repos > deepakjadmin > r_caret_test
diff mayachemtool/mayachemtools/bin/TopologicalPharmacophoreAtomTripletsFingerprints.pl @ 0:68300206e90d draft default tip
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| author | deepakjadmin |
|---|---|
| date | Thu, 05 Nov 2015 02:41:30 -0500 |
| parents | |
| children |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/mayachemtool/mayachemtools/bin/TopologicalPharmacophoreAtomTripletsFingerprints.pl Thu Nov 05 02:41:30 2015 -0500 @@ -0,0 +1,1343 @@ +#!/usr/bin/perl -w +# +# $RCSfile: TopologicalPharmacophoreAtomTripletsFingerprints.pl,v $ +# $Date: 2015/02/28 20:46:23 $ +# $Revision: 1.34 $ +# +# 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 "$FindBin::Bin/../lib"; +use Getopt::Long; +use File::Basename; +use Text::ParseWords; +use Benchmark; +use FileUtil; +use TextUtil; +use SDFileUtil; +use MoleculeFileIO; +use FileIO::FingerprintsSDFileIO; +use FileIO::FingerprintsTextFileIO; +use FileIO::FingerprintsFPFileIO; +use AtomTypes::FunctionalClassAtomTypes; +use Fingerprints::TopologicalPharmacophoreAtomTripletsFingerprints; + +my($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"; + GenerateTopologicalPharmacophoreAtomTripletsFingerprints($FileIndex); + } +} +print "\n$ScriptName:Done...\n\n"; + +$EndTime = new Benchmark; +$TotalTime = timediff ($EndTime, $StartTime); +print "Total time: ", timestr($TotalTime), "\n"; + +############################################################################### + +# Generate fingerprints for a SD file... +# +sub GenerateTopologicalPharmacophoreAtomTripletsFingerprints { + my($FileIndex) = @_; + my($CmpdCount, $IgnoredCmpdCount, $SDFile, $MoleculeFileIO, $Molecule, $TopologicalPharmacophoreAtomTripletsFingerprints, $NewFPSDFileIO, $NewFPTextFileIO, $NewFPFileIO, $SetupOutputFiles); + + $SDFile = $SDFilesList[$FileIndex]; + + ($NewFPSDFileIO, $NewFPTextFileIO, $NewFPFileIO) = (undef) x 3; + $SetupOutputFiles = 1; + + $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; + } + } + + $TopologicalPharmacophoreAtomTripletsFingerprints = GenerateMoleculeFingerprints($Molecule); + if (!$TopologicalPharmacophoreAtomTripletsFingerprints) { + $IgnoredCmpdCount++; + ProcessIgnoredCompound('FingerprintsGenerationFailed', $CmpdCount, $Molecule); + next COMPOUND; + } + + if ($SetupOutputFiles) { + $SetupOutputFiles = 0; + SetupFingerprintsLabelValueIDs($TopologicalPharmacophoreAtomTripletsFingerprints); + ($NewFPSDFileIO, $NewFPTextFileIO, $NewFPFileIO) = SetupAndOpenOutputFiles($FileIndex); + } + + WriteDataToOutputFiles($FileIndex, $CmpdCount, $Molecule, $TopologicalPharmacophoreAtomTripletsFingerprints, $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: $IgnoredCmpdCount\n"; +} + +# Append atom pair value IDs to fingerprint label... +# +sub SetupFingerprintsLabelValueIDs { + my($TopologicalPharmacophoreAtomTripletsFingerprints) = @_; + + if ($OptionsInfo{AtomTripletsSetSizeToUse} =~ /^ArbitrarySize$/i || + $OptionsInfo{FingerprintsLabelMode} !~ /^FingerprintsLabelWithIDs$/i) { + return; + } + $OptionsInfo{FingerprintsLabel} .= "; Value IDs: " . $TopologicalPharmacophoreAtomTripletsFingerprints->GetFingerprintsVector->GetValueIDsString(); +} + +# Open output files... +# +sub SetupAndOpenOutputFiles { + my($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, $TopologicalPharmacophoreAtomTripletsFingerprints, $NewFPSDFileIO, $NewFPTextFileIO, $NewFPFileIO) = @_; + my($DataFieldLabelAndValuesRef); + + $DataFieldLabelAndValuesRef = undef; + if ($NewFPTextFileIO || $NewFPFileIO) { + $DataFieldLabelAndValuesRef = $Molecule->GetDataFieldLabelAndValues(); + } + + if ($NewFPSDFileIO) { + my($CmpdString); + + $CmpdString = $Molecule->GetInputMoleculeString(); + $NewFPSDFileIO->WriteFingerprints($TopologicalPharmacophoreAtomTripletsFingerprints, $CmpdString); + } + + if ($NewFPTextFileIO) { + my($ColValuesRef); + + $ColValuesRef = SetupFPTextFileCoulmnValues($FileIndex, $CmpdCount, $Molecule, $DataFieldLabelAndValuesRef); + $NewFPTextFileIO->WriteFingerprints($TopologicalPharmacophoreAtomTripletsFingerprints, $ColValuesRef); + } + + if ($NewFPFileIO) { + my($CompoundID); + + $CompoundID = SetupCmpdIDForOutputFiles($CmpdCount, $Molecule, $DataFieldLabelAndValuesRef); + $NewFPFileIO->WriteFingerprints($TopologicalPharmacophoreAtomTripletsFingerprints, $CompoundID); + } +} + +# Generate approriate column labels for FPText output file... +# +sub SetupFPTextFileCoulmnLabels { + my($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($TopologicalPharmacophoreAtomTripletsFingerprints); + + if ($OptionsInfo{KeepLargestComponent}) { + $Molecule->KeepLargestComponent(); + } + if (!$Molecule->DetectRings()) { + return undef; + } + $Molecule->SetAromaticityModel($OptionsInfo{AromaticityModel}); + $Molecule->DetectAromaticity(); + + $TopologicalPharmacophoreAtomTripletsFingerprints = new Fingerprints::TopologicalPharmacophoreAtomTripletsFingerprints('Molecule' => $Molecule, 'AtomTripletsSetSizeToUse' => $OptionsInfo{AtomTripletsSetSizeToUse}, 'MinDistance' => $OptionsInfo{MinDistance}, 'MaxDistance' => $OptionsInfo{MaxDistance}, 'DistanceBinSize' => $OptionsInfo{DistanceBinSize}, 'UseTriangleInequality' => $OptionsInfo{UseTriangleInequality}, 'AtomTypesToUse' => \@{$OptionsInfo{AtomTypesToUse}}); + + # Generate fingerprints... + $TopologicalPharmacophoreAtomTripletsFingerprints->GenerateFingerprints(); + + # Make sure fingerprints generation is successful... + if (!$TopologicalPharmacophoreAtomTripletsFingerprints->IsFingerprintsGenerationSuccessful()) { + return undef; + } + + return $TopologicalPharmacophoreAtomTripletsFingerprints; +} + +# Retrieve information about SD files... +# +sub RetrieveSDFilesInfo { + my($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}TopologicalPharmacophoreAtomTripletsFP"; + } + + $NewSDFileName = "${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 = (); + + ProcessAtomTypesToUseOption(); + + $OptionsInfo{AromaticityModel} = $Options{aromaticitymodel}; + + $OptionsInfo{AtomTripletsSetSizeToUse} = $Options{atomtripletssetsizetouse}; + + $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; + } + + $OptionsInfo{Filter} = ($Options{filter} =~ /^Yes$/i) ? 1 : 0; + + $OptionsInfo{FingerprintsLabelMode} = $Options{fingerprintslabelmode}; + $OptionsInfo{FingerprintsLabel} = $Options{fingerprintslabel} ? $Options{fingerprintslabel} : 'TopologicalPharmacophoreAtomTripletsFingerprints'; + + $OptionsInfo{KeepLargestComponent} = ($Options{keeplargestcomponent} =~ /^Yes$/i) ? 1 : 0; + + $OptionsInfo{DistanceBinSize} = $Options{distancebinsize}; + + $OptionsInfo{MinDistance} = $Options{mindistance}; + $OptionsInfo{MaxDistance} = $Options{maxdistance}; + + $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; + + $OptionsInfo{UseTriangleInequality} = ($Options{usetriangleinequality} =~ /^Yes$/i) ? 1 : 0; + + # Setup default vector string format... + my($VectorStringFormat); + $VectorStringFormat = ''; + + if ($Options{vectorstringformat}) { + $VectorStringFormat = $Options{vectorstringformat}; + + if ($Options{atomtripletssetsizetouse} =~ /^ArbitrarySize$/i && $VectorStringFormat =~ /^ValuesString$/i) { + die "Error: The value specified, $Options{vectorstringformat}, for option \"-v, --VectorStringFormat\" is not valid for $Options{atomtripletssetsizetouse} value of \"--AtomTripletsSetSizeToUse\" option. Allowed values: IDsAndValuesString, IDsAndValuesPairsString, ValuesAndIDsString or ValuesAndIDsPairsString\n"; + } + } + else { + $VectorStringFormat = ($Options{atomtripletssetsizetouse} =~ /^FixedSize$/) ? "ValuesString" : "IDsAndValuesString"; + } + $OptionsInfo{VectorStringFormat} = $VectorStringFormat; +} + +# Process atom type to use option... +# +sub ProcessAtomTypesToUseOption { + my($AtomType, $SpecifiedAtomTypesToUse, @AtomTypesWords); + + @{$OptionsInfo{AtomTypesToUse}} = (); + if (IsEmpty($Options{atomtypestouse})) { + die "Error: Atom types value specified using \"-a, --AtomTypesToUse\" option is empty\n"; + } + + $SpecifiedAtomTypesToUse = $Options{atomtypestouse}; + $SpecifiedAtomTypesToUse =~ s/ //g; + @AtomTypesWords = split /\,/, $SpecifiedAtomTypesToUse; + + for $AtomType (@AtomTypesWords) { + if (!AtomTypes::FunctionalClassAtomTypes::IsFunctionalClassAvailable($AtomType)) { + die "Error: Atom type specified, $AtomType, using \"-a, --AtomTypesToUse\" option is not valid...\n "; + } + push @{$OptionsInfo{AtomTypesToUse}}, $AtomType; + } +} + +# Setup script usage and retrieve command line arguments specified using various options... +sub SetupScriptUsage { + + # Retrieve all the options... + %Options = (); + + $Options{aromaticitymodel} = 'MayaChemToolsAromaticityModel'; + + $Options{atomtripletssetsizetouse} = 'ArbitrarySize'; + + $Options{atomtypestouse} = 'HBD,HBA,PI,NI,H,Ar'; + + $Options{compoundidmode} = 'LabelPrefix'; + $Options{compoundidlabel} = 'CompoundID'; + $Options{datafieldsmode} = 'CompoundID'; + + $Options{filter} = 'Yes'; + + $Options{fingerprintslabelmode} = 'FingerprintsLabelOnly'; + + $Options{keeplargestcomponent} = 'Yes'; + + $Options{mindistance} = 1; + $Options{maxdistance} = 10; + + $Options{distancebinsize} = 2; + + $Options{usetriangleinequality} = 'Yes'; + + $Options{output} = 'text'; + $Options{outdelim} = 'comma'; + $Options{quote} = 'yes'; + + $Options{vectorstringformat} = ''; + + if (!GetOptions(\%Options, "aromaticitymodel=s", "atomtripletssetsizetouse=s", "atomtypestouse|a=s", "compoundid=s", "compoundidlabel=s", "compoundidmode=s", "datafields=s", "datafieldsmode|d=s", "distancebinsize=s", "filter|f=s", "fingerprintslabelmode=s", "fingerprintslabel=s", "help|h", "keeplargestcomponent|k=s", "mindistance=s", "maxdistance=s", "outdelim=s", "output=s", "overwrite|o", "quote|q=s", "root|r=s", "usetriangleinequality|u=s", "vectorstringformat|v=s", "workingdir|w=s")) { + die "\nTo get a list of valid options and their values, use \"$ScriptName -h\" or\n\"perl -S $ScriptName -h\" command and try again...\n"; + } + if ($Options{workingdir}) { + if (! -d $Options{workingdir}) { + die "Error: The value specified, $Options{workingdir}, for option \"-w --workingdir\" is not a directory name.\n"; + } + chdir $Options{workingdir} or die "Error: Couldn't chdir $Options{workingdir}: $! \n"; + } + if (!Molecule::IsSupportedAromaticityModel($Options{aromaticitymodel})) { + my(@SupportedModels) = Molecule::GetSupportedAromaticityModels(); + die "Error: The value specified, $Options{aromaticitymodel}, for option \"--AromaticityModel\" is not valid. Supported aromaticity models in current release of MayaChemTools: @SupportedModels\n"; + } + if ($Options{atomtripletssetsizetouse} !~ /^(ArbitrarySize|FixedSize)$/i) { + die "Error: The value specified, $Options{atomtripletssetsizetouse}, for option \"--AtomTripletsSetSizeToUse\" is not valid. Allowed values: ArbitrarySize or FixedSize\n"; + } + if ($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, $Options{datafieldsmode}, for option \"-d, --DataFieldsMode\" is not valid. Allowed values: All, Common, Specify or CompoundID\n"; + } + if (!IsPositiveInteger($Options{distancebinsize})) { + die "Error: The value specified, $Options{distancebinsize}, for option \"--DistanceBinSize\" is not valid. Allowed values: > 0 \n"; + } + if ($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{fingerprintslabelmode} !~ /^(FingerprintsLabelOnly|FingerprintsLabelWithIDs)$/i) { + die "Error: The value specified, $Options{fingerprintslabelmode}, for option \"--FingerprintsLabelMode\" is not valid. Allowed values: FingerprintsLabelOnly or FingerprintsLabelWithIDs\n"; + } + if ($Options{keeplargestcomponent} !~ /^(Yes|No)$/i) { + die "Error: The value specified, $Options{keeplargestcomponent}, for option \"-k, --KeepLargestComponent\" is not valid. Allowed values: Yes or No\n"; + } + if (!IsPositiveInteger($Options{mindistance})) { + die "Error: The value specified, $Options{mindistance}, for option \"--MinDistance\" is not valid. Allowed values: > 0 \n"; + } + if (!IsPositiveInteger($Options{maxdistance})) { + die "Error: The value specified, $Options{maxdistance}, for option \"--MaxDistance\" is not valid. Allowed values: > 0 \n"; + } + if ($Options{mindistance} > $Options{maxdistance}) { + die "Error: The value specified, specified, $Options{mindistance}, for option \"--MinDistance\" must be less than the value specified, $Options{maxdistance}, for option \"--MaxDistance\" \n"; + } + if ($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, $Options{quote}, for option \"-q --quote\" is not allowed with, semicolon value of \"--outdelim\" option: Fingerprints string use semicolon as delimiter for various data fields and must be quoted.\n"; + } + if ($Options{usetriangleinequality} !~ /^(Yes|No)$/i) { + die "Error: The value specified, $Options{usetriangleinequality}, for option \"-u, --UseTriangleInequality\" is not valid. Allowed values: Yes or No\n"; + } + if ($Options{vectorstringformat} && $Options{vectorstringformat} !~ /^(ValuesString|IDsAndValuesString|IDsAndValuesPairsString|ValuesAndIDsString|ValuesAndIDsPairsString)$/i) { + die "Error: The value specified, $Options{vectorstringformat}, for option \"-v, --VectorStringFormat\" is not valid. Allowed values: ValuesString, IDsAndValuesString, IDsAndValuesPairsString, ValuesAndIDsString or ValuesAndIDsPairsString\n"; + } +} + +__END__ + +=head1 NAME + +TopologicalPharmacophoreAtomTripletsFingerprints.pl - Generate topological pharmacophore atom triplets fingerprints for SD files + +=head1 SYNOPSIS + +TopologicalPharmacophoreAtomTripletsFingerprints.pl SDFile(s)... + +TopologicalPharmacophoreAtomTripletsFingerprints.pl [B<--AromaticityModel> I<AromaticityModelType>] +[B<--AtomTripletsSetSizeToUse> I<ArbitrarySize | FixedSize>] +[B<-a, --AtomTypesToUse> I<"AtomType1, AtomType2...">] +[B<--AtomTypesWeight> I<"AtomType1, Weight1, AtomType2, Weight2...">] +[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<--DistanceBinSize> I<number>] [B<-f, --Filter> I<Yes | No>] +[B<--FingerprintsLabelMode> I<FingerprintsLabelOnly | FingerprintsLabelWithIDs>] [B<--FingerprintsLabel> I<text>] +[B<-h, --help>] [B<-k, --KeepLargestComponent> I<Yes | No>] [B<--MinDistance> I<number>] [B<--MaxDistance> 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<-u, --UseTriangleInequality> I<Yes | No>] +[B<-v, --VectorStringFormat> I<ValuesString, IDsAndValuesString | IDsAndValuesPairsString | ValuesAndIDsString | ValuesAndIDsPairsString>] +[B<-w, --WorkingDir> dirname] SDFile(s)... + +=head1 DESCRIPTION + +Generate topological pharmacophore atom triplets fingerprints [ Ref 66, Ref 68-71 ] 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. + +Based on the values specified for B<--AtomTypesToUse>, pharmacophore atom types are +assigned to all non-hydrogen atoms in a molecule and a distance matrix is generated. +Using B<--MinDistance>, B<--MaxDistance>, and B<--DistanceBinSize> values, a +binned distance matrix is generated with lower bound on the distance bin as the distance +in distance matrix; the lower bound on the distance bin is also used as the distance between +atom pairs for generation of atom triplet identifiers. + +A pharmacophore atom triplets basis set is generated for all unique atom triplets constituting +atom pairs binned distances between B<--MinDistance> and B<--MaxDistance>. The value +of B<--UseTriangleInequality> determines whether the triangle inequality test is applied during +generation of atom triplets basis set. The lower distance bound, along with specified pharmacophore +types, is used during generation of atom triplet IDs. + + Let: + + P = Valid pharmacophore atom type + + Px = Pharmacophore atom x + Py = Pharmacophore atom y + Pz = Pharmacophore atom z + + Dmin = Minimum distance corresponding to number of bonds between two atoms + Dmax = Maximum distance corresponding to number of bonds between two atoms + D = Distance corresponding to number of bonds between two atom + + Bsize = Distance bin size + Nbins = Number of distance bins + + Dxy = Distance or lower bound of binned distance between Px and Py + Dxz = Distance or lower bound of binned distance between Px and Pz + Dyz = Distance or lower bound of binned distance between Py and Pz + + Then: + + PxDyz-PyDxz-PzDxy = Pharmacophore atom triplet IDs for atom types Px, + Py, and Pz + + For example: H1-H1-H1, H2-HBA-H2 and so on + + For default values of Dmin = 1 , Dmax = 10 and Bsize = 2: + + the number of distance bins, Nbins = 5, are: + + [1, 2] [3, 4] [5, 6] [7, 8] [9 10] + + and atom triplet basis set size is 2692. + + Atom triplet basis set size for various values of Dmin, Dmax and Bsize in + conjunction with usage of triangle inequality is: + + Dmin Dmax Bsize UseTriangleInequality TripletBasisSetSize + 1 10 2 No 4960 + 1 10 2 Yes 2692 [ Default ] + 2 12 2 No 8436 + 2 12 2 Yes 4494 + + +Using binned distance matrix and pharmacohore atom types, occurrence of unique pharmacohore +atom triplets is counted. + +The final pharmacophore atom triples count along with atom pair identifiers involving all non-hydrogen +atoms constitute pharmacophore topological atom triplets fingerprints of the molecule. + +For I<ArbitrarySize> value of B<--AtomTripletsSetSizeToUse> option, the fingerprint vector correspond to +only those topological pharmacophore atom triplets which are present and have non-zero count. However, +for I<FixedSize> value of B<--AtomTripletsSetSizeToUse> option, the fingerprint vector contains all possible +valid topological pharmacophore atom triplets with both zero and non-zero count values. + +Example of I<SD> file containing topological pharmacophore atom triplets fingerprints string data: + + ... ... + ... ... + $$$$ + ... ... + ... ... + ... ... + 41 44 0 0 0 0 0 0 0 0999 V2000 + -3.3652 1.4499 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 + ... ... + 2 3 1 0 0 0 0 + ... ... + M END + > <CmpdID> + Cmpd1 + + > <TopologicalPharmacophoreAtomTripletsFingerprints> + FingerprintsVector;TopologicalPharmacophoreAtomTriplets:ArbitrarySize: + MinDistance1:MaxDistance10;696;NumericalValues;IDsAndValuesString;Ar1- + Ar1-Ar1 Ar1-Ar1-H1 Ar1-Ar1-HBA1 Ar1-Ar1-HBD1 Ar1-H1-H1 Ar1-H1-HBA1 Ar1 + -H1-HBD1 Ar1-HBA1-HBD1 H1-H1-H1 H1-H1-HBA1 H1-H1-HBD1 H1-HBA1-HBA1 H1- + HBA1-HBD1 H1-HBA1-NI1 H1-HBD1-NI1 HBA1-HBA1-NI1 HBA1-HBD1-NI1 Ar1-...; + 46 106 8 3 83 11 4 1 21 5 3 1 2 2 1 1 1 100 101 18 11 145 132 26 14 23 + 28 3 3 5 4 61 45 10 4 16 20 7 5 1 3 4 5 3 1 1 1 1 5 4 2 1 2 2 2 1 1 1 + 119 123 24 15 185 202 41 25 22 17 3 5 85 95 18 11 23 17 3 1 1 6 4 ... + + $$$$ + ... ... + ... ... + +Example of I<FP> file containing topological pharmacophore atom triplets fingerprints string data: + + # + # Package = MayaChemTools 7.4 + # Release Date = Oct 21, 2010 + # + # TimeStamp = Fri Mar 11 15:38:58 2011 + # + # FingerprintsStringType = FingerprintsVector + # + # Description = TopologicalPharmacophoreAtomTriplets:ArbitrarySize:M... + # VectorStringFormat = IDsAndValuesString + # VectorValuesType = NumericalValues + # + Cmpd1 696;Ar1-Ar1-Ar1 Ar1-Ar1-H1 Ar1-Ar1-HBA1 Ar1-Ar1-HBD1...;;46 106... + Cmpd2 251;H1-H1-H1 H1-H1-HBA1 H1-H1-HBD1 H1-H1-NI1...;4 1 3 1 1 2 2... + ... ... + ... .. + +Example of CSV I<Text> file containing topological pharmacophore atom triplets fingerprints string data: + + "CompoundID","TopologicalPharmacophoreAtomTripletsFingerprints" + "Cmpd1","FingerprintsVector;TopologicalPharmacophoreAtomTriplets:Arbitr + arySize:MinDistance1:MaxDistance10;696;NumericalValues;IDsAndValuesStri + ng;Ar1-Ar1-Ar1 Ar1-Ar1-H1 Ar1-Ar1-HBA1 Ar1-Ar1-HBD1 Ar1-H1-H1 Ar1-H1-HB + A1 Ar1-H1-HBD1 Ar1-HBA1-HBD1 H1-H1-H1 H1-H1-HBA1 H1-H1-HBD1 H1-HBA1-HBA + 1 H1-HBA1-HBD1 H1-HBA1-NI1 H1-HBD1-NI1 HBA1-HBA1-NI1 HBA1-HBD1-NI1 A...; + 46 106 8 3 83 11 4 1 21 5 3 1 2 2 1 1 1 100 101 18 11 145 132 26 14 23 + 28 3 3 5 4 61 45 10 4 16 20 7 5 1 3 4 5 3 1 1 1 1 5 4 2 1 2 2 2 1 1 1 + 119 123 24 15 185 202 41 25 22 17 3 5 85 95 18 11 23 17 3 1 1 6 4 ... + ... ... + ... ... + +The current release of MayaChemTools generates the following types of topological pharmacophore +atom triplets fingerprints vector strings: + + FingerprintsVector;TopologicalPharmacophoreAtomTriplets:ArbitrarySize: + MinDistance1:MaxDistance10;696;NumericalValues;IDsAndValuesString;Ar1- + Ar1-Ar1 Ar1-Ar1-H1 Ar1-Ar1-HBA1 Ar1-Ar1-HBD1 Ar1-H1-H1 Ar1-H1-HBA1 Ar1 + -H1-HBD1 Ar1-HBA1-HBD1 H1-H1-H1 H1-H1-HBA1 H1-H1-HBD1 H1-HBA1-HBA1 H1- + HBA1-HBD1 H1-HBA1-NI1 H1-HBD1-NI1 HBA1-HBA1-NI1 HBA1-HBD1-NI1 Ar1-...; + 46 106 8 3 83 11 4 1 21 5 3 1 2 2 1 1 1 100 101 18 11 145 132 26 14 23 + 28 3 3 5 4 61 45 10 4 16 20 7 5 1 3 4 5 3 1 1 1 1 5 4 2 1 2 2 2 1 1 1 + 119 123 24 15 185 202 41 25 22 17 3 5 85 95 18 11 23 17 3 1 1 6 4 ... + + FingerprintsVector;TopologicalPharmacophoreAtomTriplets:FixedSize:MinD + istance1:MaxDistance10;2692;OrderedNumericalValues;ValuesString;46 106 + 8 3 0 0 83 11 4 0 0 0 1 0 0 0 0 0 0 0 0 21 5 3 0 0 1 2 2 0 0 1 0 0 0 + 0 0 0 1 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 100 101 18 11 0 0 145 132 26 + 14 0 0 23 28 3 3 0 0 5 4 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 61 45 10 4 0 + 0 16 20 7 5 1 0 3 4 5 3 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 0 5 ... + + FingerprintsVector;TopologicalPharmacophoreAtomTriplets:FixedSize:MinD + istance1:MaxDistance10;2692;OrderedNumericalValues;IDsAndValuesString; + Ar1-Ar1-Ar1 Ar1-Ar1-H1 Ar1-Ar1-HBA1 Ar1-Ar1-HBD1 Ar1-Ar1-NI1 Ar1-Ar1-P + I1 Ar1-H1-H1 Ar1-H1-HBA1 Ar1-H1-HBD1 Ar1-H1-NI1 Ar1-H1-PI1 Ar1-HBA1-HB + A1 Ar1-HBA1-HBD1 Ar1-HBA1-NI1 Ar1-HBA1-PI1 Ar1-HBD1-HBD1 Ar1-HBD1-...; + 46 106 8 3 0 0 83 11 4 0 0 0 1 0 0 0 0 0 0 0 0 21 5 3 0 0 1 2 2 0 0 1 + 0 0 0 0 0 0 1 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 100 101 18 11 0 0 145 + 132 26 14 0 0 23 28 3 3 0 0 5 4 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 61 ... + +=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<--AtomTripletsSetSizeToUse> I<ArbitrarySize | FixedSize> + +Atom triplets set size to use during generation of topological pharmacophore atom triplets +fingerprints. + +Possible values: I<ArbitrarySize | FixedSize>; Default value: I<ArbitrarySize>. + +For I<ArbitrarySize> value of B<--AtomTripletsSetSizeToUse> option, the fingerprint vector +correspond to only those topological pharmacophore atom triplets which are present and +have non-zero count. However, for I<FixedSize> value of B<--AtomTripletsSetSizeToUse> +option, the fingerprint vector contains all possible valid topological pharmacophore atom +triplets with both zero and non-zero count values. + +=item B<-a, --AtomTypesToUse> I<"AtomType1,AtomType2,..."> + +Pharmacophore atom types to use during generation of topological phramacophore +atom triplets. It's a list of comma separated valid pharmacophore atom types. + +Possible values for pharmacophore atom types are: I<Ar, CA, H, HBA, HBD, Hal, NI, PI, RA>. +Default value [ Ref 71 ] : I<HBD,HBA,PI,NI,H,Ar>. + +The pharmacophore atom types abbreviations correspond to: + + HBD: HydrogenBondDonor + HBA: HydrogenBondAcceptor + PI : PositivelyIonizable + NI : NegativelyIonizable + Ar : Aromatic + Hal : Halogen + H : Hydrophobic + RA : RingAtom + CA : ChainAtom + +I<AtomTypes::FunctionalClassAtomTypes> module is used to assign pharmacophore 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 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 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 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 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<--DistanceBinSize> I<number> + +Distance bin size used to bin distances between atom pairs in atom triplets. Default value: I<2>. +Valid values: positive integers. + +For default B<--MinDistance> and B<--MaxDistance> values of 1 and 10 with B<--DistanceBinSize> +of 2 [ Ref 70 ], the following 5 distance bins are generated: + + [1, 2] [3, 4] [5, 6] [7, 8] [9 10] + +The lower distance bound on the distance bin is uses to bin the distance between atom pairs in +atom triplets. So in the previous example, atom pairs with distances 1 and 2 fall in first distance +bin, atom pairs with distances 3 and 4 fall in second distance bin and so on. + +In order to distribute distance bins of equal size, the last bin is allowed to go past B<--MaxDistance> +by up to distance bin size. For example, B<--MinDistance> and B<--MaxDistance> values of 2 and 10 +with B<--DistanceBinSize> of 2 generates the following 6 distance bins: + + [2, 3] [4, 5] [6, 7] [8, 9] [10 11] + +=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<--FingerprintsLabelMode> I<FingerprintsLabelOnly | FingerprintsLabelWithIDs> + +Specify how fingerprints label is generated in conjunction with B<--FingerprintsLabel> option value: +use fingerprints label generated only by B<--FingerprintsLabel> option value or append topological +atom pair count value IDs to B<--FingerprintsLabel> option value. + +Possible values: I<FingerprintsLabelOnly | FingerprintsLabelWithIDs>. Default value: +I<FingerprintsLabelOnly>. + +Topological atom pairs IDs appended to B<--FingerprintsLabel> value during I<FingerprintsLabelWithIDs> +values of B<--FingerprintsLabelMode> correspond to atom pair count values in fingerprint vector string. + +I<FingerprintsLabelWithIDs> value of B<--FingerprintsLabelMode> is ignored during I<ArbitrarySize> value +of B<--AtomTripletsSetSizeToUse> option and topological atom triplets IDs not appended to the label. + +=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<TopologicalPharmacophoreAtomTripletsFingerprints>. + +=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<--MinDistance> I<number> + +Minimum bond distance between atom pairs corresponding to atom triplets for generating +topological pharmacophore atom triplets. Default value: I<1>. Valid values: positive integers and +less than B<--MaxDistance>. + +=item B<--MaxDistance> I<number> + +Maximum bond distance between atom pairs corresponding to atom triplets for generating +topological pharmacophore atom triplets. Default value: I<10>. Valid values: positive integers and +greater than B<--MinDistance>. + +=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><TopologicalPharmacophoreAtomTripletsFP>.<Ext>. The file type determines <Ext> value. +The sdf, fpf, csv, and tsv <Ext> values are used for SD, FP, comma/semicolon, and tab +delimited text files, respectively.This option is ignored for multiple input files. + +=item B<-u, --UseTriangleInequality> I<Yes | No> + +Specify whether to imply triangle distance inequality test to distances between atom pairs in +atom triplets during generation of atom triplets basis set generation. Possible values: +I<Yes or No>. Default value: I<Yes>. + +Triangle distance inequality test implies that distance or binned distance between any two atom +pairs in an atom triplet must be less than the sum of distances or binned distances between other +two atoms pairs and greater than the difference of their distances. + + For atom triplet PxDyz-PyDxz-PzDxy to satisfy triangle inequality: + + Dyz > |Dxz - Dxy| and Dyz < Dxz + Dxy + Dxz > |Dyz - Dxy| and Dyz < Dyz + Dxy + Dxy > |Dyz - Dxz| and Dxy < Dyz + Dxz + +=item B<-v, --VectorStringFormat> I<ValuesString, IDsAndValuesString | IDsAndValuesPairsString | ValuesAndIDsString | ValuesAndIDsPairsString> + +Format of fingerprints vector string data in output SD, FP or CSV/TSV text file(s) specified by +B<--output> option. Possible values: I<ValuesString, IDsAndValuesString | IDsAndValuesPairsString | +ValuesAndIDsString | ValuesAndIDsPairsString>. Defaultvalue: I<ValuesString>. + +Default value during I<FixedSize> value of B<--AtomTripletsSetSizeToUse> option: I<ValuesString>. Default +value during I<ArbitrarySize> value of B<--AtomTripletsSetSizeToUse> option: I<IDsAndValuesString>. + +I<ValuesString> option value is not allowed for I<ArbitrarySize> value of B<--AtomTripletsSetSizeToUse> +option. + +Examples: + + FingerprintsVector;TopologicalPharmacophoreAtomTriplets:ArbitrarySize: + MinDistance1:MaxDistance10;696;NumericalValues;IDsAndValuesString;Ar1- + Ar1-Ar1 Ar1-Ar1-H1 Ar1-Ar1-HBA1 Ar1-Ar1-HBD1 Ar1-H1-H1 Ar1-H1-HBA1 Ar1 + -H1-HBD1 Ar1-HBA1-HBD1 H1-H1-H1 H1-H1-HBA1 H1-H1-HBD1 H1-HBA1-HBA1 H1- + HBA1-HBD1 H1-HBA1-NI1 H1-HBD1-NI1 HBA1-HBA1-NI1 HBA1-HBD1-NI1 Ar1-...; + 46 106 8 3 83 11 4 1 21 5 3 1 2 2 1 1 1 100 101 18 11 145 132 26 14 23 + 28 3 3 5 4 61 45 10 4 16 20 7 5 1 3 4 5 3 1 1 1 1 5 4 2 1 2 2 2 1 1 1 + 119 123 24 15 185 202 41 25 22 17 3 5 85 95 18 11 23 17 3 1 1 6 4 ... + + FingerprintsVector;TopologicalPharmacophoreAtomTriplets:FixedSize:MinD + istance1:MaxDistance10;2692;OrderedNumericalValues;ValuesString;46 106 + 8 3 0 0 83 11 4 0 0 0 1 0 0 0 0 0 0 0 0 21 5 3 0 0 1 2 2 0 0 1 0 0 0 + 0 0 0 1 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 100 101 18 11 0 0 145 132 26 + 14 0 0 23 28 3 3 0 0 5 4 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 61 45 10 4 0 + 0 16 20 7 5 1 0 3 4 5 3 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 0 5 ... + + FingerprintsVector;TopologicalPharmacophoreAtomTriplets:FixedSize:MinD + istance1:MaxDistance10;2692;OrderedNumericalValues;ValuesAndIDsPairsSt + ring;46 Ar1-Ar1-Ar1 106 Ar1-Ar1-H1 8 Ar1-Ar1-HBA1 3 Ar1-Ar1-HBD1 0 Ar1 + -Ar1-NI1 0 Ar1-Ar1-PI1 83 Ar1-H1-H1 11 Ar1-H1-HBA1 4 Ar1-H1-HBD1 0 Ar1 + -H1-NI1 0 Ar1-H1-PI1 0 Ar1-HBA1-HBA1 1 Ar1-HBA1-HBD1 0 Ar1-HBA1-NI1 0 + Ar1-HBA1-PI1 0 Ar1-HBD1-HBD1 0 Ar1-HBD1-NI1 0 Ar1-HBD1-PI1 0 Ar1-NI... + +=item B<-w, --WorkingDir> I<DirName> + +Location of working directory. Default value: current directory. + +=back + +=head1 EXAMPLES + +To generate topological pharmacophore atom triplets fingerprints of arbitrary size corresponding to 5 +distance bins spanning distances from 1 through 10 using default atoms with distances satisfying triangle +inequality and create a SampleTPATFP.csv file containing sequential compound IDs along +with fingerprints vector strings data in ValuesString format, type: + + % TopologicalPharmacophoreAtomTripletsFingerprints.pl -r SampleTPATFP + -o Sample.sdf + +To generate topological pharmacophore atom triplets fingerprints of fixed size corresponding to 5 +distance bins spanning distances from 1 through 10 using default atoms with distances satisfying triangle +inequality and create a SampleTPATFP.csv file containing sequential compound IDs along +with fingerprints vector strings data in ValuesString format, type: + + % TopologicalPharmacophoreAtomTripletsFingerprints.pl + --AtomTripletsSetSizeToUse FixedSize -r SampleTPATFP -o Sample.sdf + +To generate topological pharmacophore atom triplets fingerprints of arbitrary size corresponding to 5 +distance bins spanning distances from 1 through 10 using default atoms with distances satisfying triangle +inequality and create SampleTPATFP.sdf, SampleTPATFP.fpf and SampleTPATFP.csv files with CSV file containing +sequential compound IDs along with fingerprints vector strings data in ValuesString format, type: + + % TopologicalPharmacophoreAtomTripletsFingerprints.pl --output all + -r SampleTPATFP -o Sample.sdf + +To generate topological pharmacophore atom triplets fingerprints of arbitrary size corresponding to 5 +distance bins spanning distances from 1 through 10 using default atoms with distances satisfying triangle +inequality and create a SampleTPATFP.csv file containing sequential compound IDs along +with fingerprints vector strings data in ValuesString format and atom triplets IDs in the +fingerprint data column label starting with Fingerprints, type: + + % TopologicalPharmacophoreAtomTripletsFingerprints.pl + --FingerprintsLabelMode FingerprintsLabelWithIDs --FingerprintsLabel + Fingerprints -r SampleTPATFP -o Sample.sdf + +To generate topological pharmacophore atom triplets fingerprints of arbitrary size corresponding to 5 +distance bins spanning distances from 1 through 10 using default atoms with distances not satisfying triangle +inequality and create a SampleTPATFP.csv file containing sequential compound IDs along +with fingerprints vector strings data in ValuesString format, type: + + % TopologicalPharmacophoreAtomTripletsFingerprints.pl + --UseTriangleInequality No -r SampleTPATFP -o Sample.sdf + +To generate topological pharmacophore atom triplets fingerprints of arbitrary size corresponding to 6 +distance bins spanning distances from 1 through 12 using default atoms with distances satisfying triangle +inequality and create a SampleTPATFP.csv file containing sequential compound IDs along +with fingerprints vector strings data in ValuesString format, type: + + % TopologicalPharmacophoreAtomTripletsFingerprints.pl + --UseTriangleInequality Yes --MinDistance 1 --MaxDistance 12 + --DistanceBinSIze 2 -r SampleTPATFP -o Sample.sdf + +To generate topological pharmacophore atom triplets fingerprints of arbitrary size corresponding to 6 +distance bins spanning distances from 1 through 12 using "HBD,HBA,PI, NI, H, Ar" atoms with distances +satisfying triangle inequality and create a SampleTPATFP.csv file containing sequential compound +IDs along with fingerprints vector strings data in ValuesString format, type: + + % TopologicalPharmacophoreAtomTripletsFingerprints.pl + --AtomTypesToUse "HBD,HBA,PI,NI,H,Ar" --UseTriangleInequality Yes + --MinDistance 1 --MaxDistance 12 --DistanceBinSIze 2 + --VectorStringFormat ValuesString -r SampleTPATFP -o Sample.sdf + +To generate topological pharmacophore atom triplets fingerprints of arbitrary size corresponding to 5 +distance bins spanning distances from 1 through 10 using default atoms with distances satisfying triangle +inequality and create a SampleTPATFP.csv file containing sequential compound IDs from +molecule name line along with fingerprints vector strings data in ValuesString format, type: + + % TopologicalPharmacophoreAtomTripletsFingerprints.pl --DataFieldsMode + CompoundID -CompoundIDMode MolName -r SampleTPATFP -o Sample.sdf + +To generate topological pharmacophore atom triplets fingerprints of arbitrary size corresponding to 5 +distance bins spanning distances from 1 through 10 using default atoms with distances satisfying triangle +inequality and create a SampleTPATFP.csv file containing sequential compound IDs using +specified data field along with fingerprints vector strings data in ValuesString format, type: + + % TopologicalPharmacophoreAtomTripletsFingerprints.pl --DataFieldsMode + CompoundID -CompoundIDMode DataField --CompoundID Mol_ID + -r SampleTPATFP -o Sample.sdf + +To generate topological pharmacophore atom triplets fingerprints of arbitrary size corresponding to 5 +distance bins spanning distances from 1 through 10 using default atoms with distances satisfying triangle +inequality and create a SampleTPATFP.csv file containing sequential compound IDs using +combination of molecule name line and an explicit compound prefix along with fingerprints vector +strings data, type: + + % TopologicalPharmacophoreAtomTripletsFingerprints.pl --DataFieldsMode + CompoundID -CompoundIDMode MolnameOrLabelPrefix + --CompoundID Cmpd --CompoundIDLabel MolID -r SampleSampleTPATFP + -o Sample.sdf + +To generate topological pharmacophore atom triplets fingerprints of arbitrary size corresponding to 5 +distance bins spanning distances from 1 through 10 using default atoms with distances satisfying triangle +inequality and create a SampleTPATFP.csv file containing specific data fields columns along +with fingerprints vector strings data, type: + + % TopologicalPharmacophoreAtomTripletsFingerprints.pl --DataFieldsMode + Specify --DataFields Mol_ID -r SampleTPATFP -o Sample.sdf + +To generate topological pharmacophore atom triplets fingerprints of arbitrary size corresponding to 5 +distance bins spanning distances from 1 through 10 using default atoms with distances satisfying triangle +inequality and create a SampleTPATFP.csv file containing common data fields columns along +with fingerprints vector strings data, type: + + % TopologicalPharmacophoreAtomTripletsFingerprints.pl --DataFieldsMode + Common -r SampleTPATFP -o Sample.sdf + +To generate topological pharmacophore atom triplets fingerprints of arbitrary size corresponding to 5 +distance bins spanning distances from 1 through 10 using default atoms with distances satisfying triangle +inequality and create SampleTPATFP.sdf, SampleTPATFP.fpf and SampleTPATFP.csv files containing all +data fields columns in CSV file along with fingerprints data, type: + + % TopologicalPharmacophoreAtomTripletsFingerprints.pl --DataFieldsMode + All --output all -r SampleTPATFP -o Sample.sdf + +=head1 AUTHOR + +Manish Sud <msud@san.rr.com> + +=head1 SEE ALSO + +InfoFingerprintsFiles.pl, SimilarityMatricesFingerprints.pl, AtomNeighborhoodsFingerprints.pl, +ExtendedConnectivityFingerprints.pl, MACCSKeysFingerprints.pl, PathLengthFingerprints.pl, +TopologicalAtomPairsFingerprints.pl, TopologicalAtomTorsionsFingerprints.pl, +TopologicalPharmacophoreAtomPairsFingerprints.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