Mercurial > repos > deepakjadmin > mayatool3_test2
diff bin/TopologicalPharmacophoreAtomPairsFingerprints.pl @ 0:4816e4a8ae95 draft default tip
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| author | deepakjadmin |
|---|---|
| date | Wed, 20 Jan 2016 09:23:18 -0500 |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/bin/TopologicalPharmacophoreAtomPairsFingerprints.pl Wed Jan 20 09:23:18 2016 -0500 @@ -0,0 +1,1483 @@ +#!/usr/bin/perl -w +# +# $RCSfile: TopologicalPharmacophoreAtomPairsFingerprints.pl,v $ +# $Date: 2015/02/28 20:46:23 $ +# $Revision: 1.36 $ +# +# 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 "$FindBin::Bin/../lib"; +use Getopt::Long; +use File::Basename; +use Text::ParseWords; +use Benchmark; +use FileUtil; +use TextUtil; +use SDFileUtil; +use MoleculeFileIO; +use FileIO::FingerprintsSDFileIO; +use FileIO::FingerprintsTextFileIO; +use FileIO::FingerprintsFPFileIO; +use AtomTypes::FunctionalClassAtomTypes; +use Fingerprints::TopologicalPharmacophoreAtomPairsFingerprints; + +my($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"; + GenerateTopologicalPharmacophoreAtomPairsFingerprints($FileIndex); + } +} +print "\n$ScriptName:Done...\n\n"; + +$EndTime = new Benchmark; +$TotalTime = timediff ($EndTime, $StartTime); +print "Total time: ", timestr($TotalTime), "\n"; + +############################################################################### + +# Generate fingerprints for a SD file... +# +sub GenerateTopologicalPharmacophoreAtomPairsFingerprints { + my($FileIndex) = @_; + my($CmpdCount, $IgnoredCmpdCount, $SDFile, $MoleculeFileIO, $Molecule, $TopologicalPharmacophoreAtomPairsFingerprints, $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; + } + } + + $TopologicalPharmacophoreAtomPairsFingerprints = GenerateMoleculeFingerprints($Molecule); + if (!$TopologicalPharmacophoreAtomPairsFingerprints) { + $IgnoredCmpdCount++; + ProcessIgnoredCompound('FingerprintsGenerationFailed', $CmpdCount, $Molecule); + next COMPOUND; + } + + if ($SetupOutputFiles) { + $SetupOutputFiles = 0; + SetupFingerprintsLabelValueIDs($TopologicalPharmacophoreAtomPairsFingerprints); + ($NewFPSDFileIO, $NewFPTextFileIO, $NewFPFileIO) = SetupAndOpenOutputFiles($FileIndex); + } + + WriteDataToOutputFiles($FileIndex, $CmpdCount, $Molecule, $TopologicalPharmacophoreAtomPairsFingerprints, $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: $IgnoredCmpdCount\n"; +} + +# Append atom pair value IDs to fingerprint label... +# +sub SetupFingerprintsLabelValueIDs { + my($TopologicalPharmacophoreAtomPairsFingerprints) = @_; + + if ($OptionsInfo{AtomPairsSetSizeToUse} =~ /^ArbitrarySize$/i || + $OptionsInfo{FingerprintsLabelMode} !~ /^FingerprintsLabelWithIDs$/i) { + return; + } + + $OptionsInfo{FingerprintsLabel} .= "; Value IDs: " . $TopologicalPharmacophoreAtomPairsFingerprints->GetFingerprintsVector->GetValueIDsString(); +} + +# Open output files... +# +sub SetupAndOpenOutputFiles { + my($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, $TopologicalPharmacophoreAtomPairsFingerprints, $NewFPSDFileIO, $NewFPTextFileIO, $NewFPFileIO) = @_; + my($DataFieldLabelAndValuesRef); + + $DataFieldLabelAndValuesRef = undef; + if ($NewFPTextFileIO || $NewFPFileIO) { + $DataFieldLabelAndValuesRef = $Molecule->GetDataFieldLabelAndValues(); + } + + if ($NewFPSDFileIO) { + my($CmpdString); + + $CmpdString = $Molecule->GetInputMoleculeString(); + $NewFPSDFileIO->WriteFingerprints($TopologicalPharmacophoreAtomPairsFingerprints, $CmpdString); + } + + if ($NewFPTextFileIO) { + my($ColValuesRef); + + $ColValuesRef = SetupFPTextFileCoulmnValues($FileIndex, $CmpdCount, $Molecule, $DataFieldLabelAndValuesRef); + $NewFPTextFileIO->WriteFingerprints($TopologicalPharmacophoreAtomPairsFingerprints, $ColValuesRef); + } + + if ($NewFPFileIO) { + my($CompoundID); + + $CompoundID = SetupCmpdIDForOutputFiles($CmpdCount, $Molecule, $DataFieldLabelAndValuesRef); + $NewFPFileIO->WriteFingerprints($TopologicalPharmacophoreAtomPairsFingerprints, $CompoundID); + } +} + +# Generate approriate column labels for FPText output file... +# +sub SetupFPTextFileCoulmnLabels { + my($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($TopologicalPharmacophoreAtomPairsFingerprints); + + if ($OptionsInfo{KeepLargestComponent}) { + $Molecule->KeepLargestComponent(); + } + if (!$Molecule->DetectRings()) { + return undef; + } + $Molecule->SetAromaticityModel($OptionsInfo{AromaticityModel}); + $Molecule->DetectAromaticity(); + + if ($OptionsInfo{FuzzifyAtomPairsCount}) { + $TopologicalPharmacophoreAtomPairsFingerprints = new Fingerprints::TopologicalPharmacophoreAtomPairsFingerprints('Molecule' => $Molecule, 'AtomPairsSetSizeToUse' => $OptionsInfo{AtomPairsSetSizeToUse}, 'MinDistance' => $OptionsInfo{MinDistance}, 'MaxDistance' => $OptionsInfo{MaxDistance}, 'AtomTypesToUse' => \@{$OptionsInfo{AtomTypesToUse}}, , 'NormalizationMethodology' => $OptionsInfo{NormalizationMethodology}, , 'ValuesPrecision' => $OptionsInfo{ValuesPrecision}, 'FuzzifyAtomPairsCount' => $OptionsInfo{FuzzifyAtomPairsCount}, 'FuzzificationMode' => $OptionsInfo{FuzzificationMode}, 'FuzzificationMethodology' => $OptionsInfo{FuzzificationMethodology}, 'FuzzFactor' => $OptionsInfo{FuzzFactor}); + } + else { + $TopologicalPharmacophoreAtomPairsFingerprints = new Fingerprints::TopologicalPharmacophoreAtomPairsFingerprints('Molecule' => $Molecule, 'AtomPairsSetSizeToUse' => $OptionsInfo{AtomPairsSetSizeToUse}, 'MinDistance' => $OptionsInfo{MinDistance}, 'MaxDistance' => $OptionsInfo{MaxDistance}, 'AtomTypesToUse' => \@{$OptionsInfo{AtomTypesToUse}}, 'NormalizationMethodology' => $OptionsInfo{NormalizationMethodology}, 'ValuesPrecision' => $OptionsInfo{ValuesPrecision}); + } + + # Set atom types weights... + if ($OptionsInfo{UseAtomTypesWeight}) { + $TopologicalPharmacophoreAtomPairsFingerprints->SetAtomTypesWeight(%{$OptionsInfo{AtomTypesWeight}}); + } + + # Generate fingerprints... + $TopologicalPharmacophoreAtomPairsFingerprints->GenerateFingerprints(); + + # Make sure fingerprints generation is successful... + if (!$TopologicalPharmacophoreAtomPairsFingerprints->IsFingerprintsGenerationSuccessful()) { + return undef; + } + + return $TopologicalPharmacophoreAtomPairsFingerprints; +} + +# Retrieve information about SD files... +# +sub RetrieveSDFilesInfo { + my($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}TopologicalPharmacophoreAtomPairsFP"; + } + + $NewSDFileName = "${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(); + ProcessAtomTypesWeightOption(); + + $OptionsInfo{AromaticityModel} = $Options{aromaticitymodel}; + + $OptionsInfo{AtomPairsSetSizeToUse} = $Options{atompairssetsizetouse}; + + $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} : 'TopologicalPharmacophoreAtomPairsFingerprints'; + + $OptionsInfo{FuzzifyAtomPairsCount} = ($Options{fuzzifyatompairscount} =~ /^Yes$/i) ? 1 : 0; + $OptionsInfo{FuzzificationMode} = $Options{fuzzificationmode}; + $OptionsInfo{FuzzificationMethodology} = $Options{fuzzificationmethodology}; + $OptionsInfo{FuzzFactor} = $Options{fuzzfactor}; + + $OptionsInfo{KeepLargestComponent} = ($Options{keeplargestcomponent} =~ /^Yes$/i) ? 1 : 0; + + $OptionsInfo{MinDistance} = $Options{mindistance}; + $OptionsInfo{MaxDistance} = $Options{maxdistance}; + + $OptionsInfo{NormalizationMethodology} = $Options{normalizationmethodology}; + + $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{ValuesPrecision} = $Options{valuesprecision}; + + # Setup default vector string format... + my($VectorStringFormat); + $VectorStringFormat = ''; + + if ($Options{vectorstringformat}) { + $VectorStringFormat = $Options{vectorstringformat}; + + if ($Options{atompairssetsizetouse} =~ /^ArbitrarySize$/i && $VectorStringFormat =~ /^ValuesString$/i) { + die "Error: The value specified, $Options{vectorstringformat}, for option \"-v, --VectorStringFormat\" is not valid for $Options{atompairssetsizetouse} value of \"--AtomPairsSetSizeToUse\" option. Allowed values: IDsAndValuesString, IDsAndValuesPairsString, ValuesAndIDsString or ValuesAndIDsPairsString\n"; + } + } + else { + $VectorStringFormat = ($Options{atompairssetsizetouse} =~ /^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: Atomic type specified, $AtomType, using \"-a, --AtomTypesToUse\" option is not valid...\n "; + } + push @{$OptionsInfo{AtomTypesToUse}}, $AtomType; + } +} + +# Process atom types weight option... +# +sub ProcessAtomTypesWeightOption { + my($Index, $AtomType, $AtomTypeWeight, $SpecifiedAtomTypesWeight, @AtomTypesWeightsPairs); + + %{$OptionsInfo{AtomTypesWeight}} = (); + + if (IsEmpty($Options{atomtypesweight})) { + die "Error: Atom types weight value specified using \"--AtomTypesWeight\" option is empty\n"; + } + $OptionsInfo{UseAtomTypesWeight} = ($Options{atomtypesweight} =~ /^None$/i) ? 0 : 1; + if (!$OptionsInfo{UseAtomTypesWeight}) { + return; + } + + # Process specified atom type/weight pairs... + $SpecifiedAtomTypesWeight = $Options{atomtypesweight}; + $SpecifiedAtomTypesWeight =~ s/ //g; + @AtomTypesWeightsPairs = split /\,/, $SpecifiedAtomTypesWeight; + + if (@AtomTypesWeightsPairs % 2) { + die "Error: Invalid number of values specified using \"--AtomTypesWeight\" option: It must contain even number of values.\n"; + } + + for ($Index = 0; $Index < @AtomTypesWeightsPairs; $Index += 2) { + $AtomType = $AtomTypesWeightsPairs[$Index]; $AtomTypeWeight = $AtomTypesWeightsPairs[$Index + 1]; + if (!AtomTypes::FunctionalClassAtomTypes::IsFunctionalClassAvailable($AtomType)) { + die "Error: Atom type specified, $AtomType, using \"--AtomTypesWeight\" option is not valid\n "; + } + if (!(IsFloat($AtomTypeWeight) && $AtomTypeWeight >= 0)) { + die "Error: Atom type weight specified, $AtomTypeWeight, using option \"--AtomTypesWeight\" is not valid. Allowed values: real numbers >= 0 \n"; + } + $OptionsInfo{AtomTypesWeight}{$AtomType} = $AtomTypeWeight; + } +} + +# Setup script usage and retrieve command line arguments specified using various options... +sub SetupScriptUsage { + + # Retrieve all the options... + %Options = (); + + $Options{aromaticitymodel} = 'MayaChemToolsAromaticityModel'; + + $Options{atompairssetsizetouse} = 'ArbitrarySize'; + + $Options{atomtypestouse} = 'HBD,HBA,PI,NI,H'; + $Options{atomtypesweight} = 'None'; + + $Options{compoundidmode} = 'LabelPrefix'; + $Options{compoundidlabel} = 'CompoundID'; + $Options{datafieldsmode} = 'CompoundID'; + + $Options{filter} = 'Yes'; + + $Options{fingerprintslabelmode} = 'FingerprintsLabelOnly'; + + $Options{fuzzifyatompairscount} = 'No'; + $Options{fuzzificationmode} = 'AfterNormalization'; + $Options{fuzzificationmethodology} = 'FuzzyBinning'; + $Options{fuzzfactor} = 0.15; + + $Options{keeplargestcomponent} = 'Yes'; + + $Options{mindistance} = 1; + $Options{maxdistance} = 10; + + $Options{normalizationmethodology} = 'None'; + + $Options{output} = 'text'; + $Options{outdelim} = 'comma'; + $Options{quote} = 'yes'; + + $Options{valuesprecision} = 2; + + $Options{vectorstringformat} = ''; + + if (!GetOptions(\%Options, "aromaticitymodel=s", "atompairssetsizetouse=s", "atomtypestouse|a=s", "atomtypesweight=s", "compoundid=s", "compoundidlabel=s", "compoundidmode=s", "datafields=s", "datafieldsmode|d=s", "filter|f=s", "fingerprintslabelmode=s", "fingerprintslabel=s", "fuzzifyatompairscount=s", "fuzzificationmode=s", "fuzzificationmethodology=s", "fuzzfactor=s", "help|h", "keeplargestcomponent|k=s", "mindistance=s", "maxdistance=s", "normalizationmethodology|n=s", "outdelim=s", "output=s", "overwrite|o", "quote|q=s", "root|r=s", "valuesprecision=s", "vectorstringformat|v=s", "workingdir|w=s")) { + die "\nTo get a list of valid options and their values, use \"$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{atompairssetsizetouse} !~ /^(ArbitrarySize|FixedSize)$/i) { + die "Error: The value specified, $Options{atompairssetsizetouse}, for option \"--AtomPairsSetSizeToUse\" is not valid. Allowed values: ArbitrarySize or FixedSize\n"; + } + if ($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, $Options{datafieldsmode}, for option \"-d, --DataFieldsMode\" is not valid. Allowed values: All, Common, Specify or CompoundID\n"; + } + if ($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{fuzzifyatompairscount} !~ /^(Yes|No)$/i) { + die "Error: The value specified, $Options{fuzzifyatompairscount}, for option \"--FuzzifyAtomPairsCount\" is not valid. Allowed values: Yes or No\n"; + } + if ($Options{fuzzificationmode} !~ /^(BeforeNormalization|AfterNormalization)$/i) { + die "Error: The value specified, $Options{fuzzificationmode}, for option \"--FuzzificationMode\" is not valid. Allowed values: BeforeNormalization or AfterNormalization\n"; + } + if ($Options{fuzzificationmethodology} !~ /^(FuzzyBinning|FuzzyBinSmoothing)$/i) { + die "Error: The value specified, $Options{fuzzificationmethodology}, for option \"--FuzzificationMethodology\" is not valid. Allowed values: FuzzyBinning or FuzzyBinSmoothing\n"; + } + if (!IsFloat($Options{fuzzfactor})) { + die "Error: The value specified, $Options{fuzzfactor}, for option \"--FuzzFactor\" is not valid. Allowed values: real numbers >= 0 \n"; + } + if ($Options{fuzzificationmethodology} !~ /^FuzzyBinning$/i) { + if (!($Options{fuzzfactor} >=0 && $Options{fuzzfactor} <= 1.0)) { + die "Error: The value specified, $Options{fuzzfactor}, for option \"--FuzzFactor\" during FuzzyBinning \"--FuzzificationMethodology\" is not valid. Allowed values: >= 0 and <= 1 \n"; + } + } + elsif ($Options{fuzzificationmethodology} !~ /^FuzzyBinSmoothing$/i) { + if (!($Options{fuzzfactor} >=0 && $Options{fuzzfactor} <= 0.5)) { + die "Error: The value specified, $Options{fuzzfactor}, for option \"--FuzzFactor\" during FuzzyBinSmoothing \"--FuzzificationMethodology\" is not valid. Allowed values: >= 0 and <= 0.5 \n"; + } + } + if ($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{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{normalizationmethodology} !~ /^(None|ByHeavyAtomsCount|ByAtomTypesCount)$/i) { + die "Error: The value specified, $Options{normalizationmethodology}, for option \"--NormalizationMethodology\" is not valid. Allowed values: None, ByHeavyAtomsCount, or ByAtomTypesCount\n"; + } + if ($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, $Options{quote}, for option \"-q --quote\" is not allowed with, semicolon value of \"--outdelim\" option: Fingerprints string use semicolon as delimiter for various data fields and must be quoted.\n"; + } + if (!IsPositiveInteger($Options{valuesprecision})) { + die "Error: The value specified, $Options{valuesprecision}, for option \"--ValuesPrecision\" is not valid. Allowed values: > 0 \n"; + } + if ($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 + +TopologicalPharmacophoreAtomPairsFingerprints.pl - Generate topological pharmacophore atom pairs fingerprints for SD files + +=head1 SYNOPSIS + +TopologicalPharmacophoreAtomPairsFingerprints.pl SDFile(s)... + +TopologicalPharmacophoreAtomPairsFingerprints.pl [B<--AromaticityModel> I<AromaticityModelType>] +[B<--AtomPairsSetSizeToUse> 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<-f, --Filter> I<Yes | No>] +[B<--FingerprintsLabelMode> I<FingerprintsLabelOnly | FingerprintsLabelWithIDs>] [B<--FingerprintsLabel> I<text>] +[B<--FuzzifyAtomPairsCount> I<Yes | No>] [B<--FuzzificationMode> I<FuzzyBinning | FuzzyBinSmoothing>] +[B<--FuzzificationMethodology> I<FuzzyBinning | FuzzyBinSmoothing>] [B<--FuzzFactor> I<number>] +[B<-h, --help>] [B<-k, --KeepLargestComponent> I<Yes | No>] [B<--MinDistance> I<number>] +[B<--MaxDistance> I<number>] [B<-n, --NormalizationMethodology> I<None | ByHeavyAtomsCount | ByAtomTypesCount>] +[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<--ValuesPrecision> I<number>] +[B<-v, --VectorStringFormat> I<ValuesString, IDsAndValuesString | IDsAndValuesPairsString | ValuesAndIDsString | ValuesAndIDsPairsString>] +[B<-w, --WorkingDir> dirname] SDFile(s)... + +=head1 DESCRIPTION + +Generate topological pharmacophore atom pairs fingerprints [ Ref 60-62, Ref 65, Ref 68 ] 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. +A pharmacophore atom pairs basis set is initialized for all unique possible pairs within +B<--MinDistance> and B<--MaxDistance> range. + + Let: + + P = Valid pharmacophore atom type + + Px = Pharmacophore atom type x + Py = Pharmacophore atom type y + + 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 atoms + + Px-Dn-Py = Pharmacophore atom pair ID for atom types Px and Py at + distance Dn + + P = Number of pharmacophore atom types to consider + PPDn = Number of possible unique pharmacophore atom pairs at a distance Dn + + PPT = Total number of possible pharmacophore atom pairs at all distances + between Dmin and Dmax + + Then: + + PPD = (P * (P - 1))/2 + P + + PPT = ((Dmax - Dmin) + 1) * ((P * (P - 1))/2 + P) + = ((Dmax - Dmin) + 1) * PPD + + So for default values of Dmin = 1, Dmax = 10 and P = 5, + + PPD = (5 * (5 - 1))/2 + 5 = 15 + PPT = ((10 - 1) + 1) * 15 = 150 + + The pharmacophore atom pairs bais set includes 150 values. + + The atom pair IDs correspond to: + + Px-Dn-Py = Pharmacophore atom pair ID for atom types Px and Py at + distance Dn + + For example: H-D1-H, H-D2-HBA, PI-D5-PI and so on + +Using distance matrix and pharmacohore atom types, occurrence of unique pharmacohore atom +pairs is counted. The contribution of each atom type to atom pair interaction is optionally +weighted by specified B<--AtomTypesWeight> before assigning its count to appropriate distance +bin. Based on B<--NormalizationMethodology> option, pharmacophore atom pairs count is optionally +normalized. Additionally, pharmacohore atom pairs count is optionally fuzzified before or after +the normalization controlled by values of B<--FuzzifyAtomPairsCount>, B<--FuzzificationMode>, +B<--FuzzificationMethodology> and B<--FuzzFactor> options. + +The final pharmacophore atom pairs count along with atom pair identifiers involving all non-hydrogen +atoms, with optional normalization and fuzzification, constitute pharmacophore topological atom pairs +fingerprints of the molecule. + +For I<ArbitrarySize> value of B<--AtomPairsSetSizeToUse> option, the fingerprint vector correspond to +only those topological pharmacophore atom pairs which are present and have non-zero count. However, +for I<FixedSize> value of B<--AtomPairsSetSizeToUse> option, the fingerprint vector contains all possible +valid topological pharmacophore atom pairs with both zero and non-zero count values. + +Example of I<SD> file containing topological pharmacophore atom pairs fingerprints string data: + + ... ... + ... ... + $$$$ + ... ... + ... ... + ... ... + 41 44 0 0 0 0 0 0 0 0999 V2000 + -3.3652 1.4499 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 + ... ... + 2 3 1 0 0 0 0 + ... ... + M END + > <CmpdID> + Cmpd1 + + > <TopologicalPharmacophoreAtomPairsFingerprints> + FingerprintsVector;TopologicalPharmacophoreAtomPairs:ArbitrarySize:Min + Distance1:MaxDistance10;54;NumericalValues;IDsAndValuesString;H-D1-H H + -D1-NI HBA-D1-NI HBD-D1-NI H-D2-H H-D2-HBA H-D2-HBD HBA-D2-HBA HBA-D2- + HBD H-D3-H H-D3-HBA H-D3-HBD H-D3-NI HBA-D3-NI HBD-D3-NI H-D4-H H-D...; + 18 1 2 1 22 12 8 1 2 18 6 3 1 1 1 22 13 6 5 7 2 28 9 5 1 1 1 36 16 10 3 + 4 1 37 10 8 1 35 10 9 3 3 1 28 7 7 4 18 16 12 5 1 2 1 + + $$$$ + ... ... + ... ... + +Example of I<FP> file containing topological pharmacophore atom pairs fingerprints string data: + + # + # Package = MayaChemTools 7.4 + # Release Date = Oct 21, 2010 + # + # TimeStamp = Fri Mar 11 15:32:48 2011 + # + # FingerprintsStringType = FingerprintsVector + # + # Description = TopologicalPharmacophoreAtomPairs:ArbitrarySize:MinDistance1:MaxDistance10 + # VectorStringFormat = IDsAndValuesString + # VectorValuesType = NumericalValues + # + Cmpd1 54;H-D1-H H-D1-NI HBA-D1-NI HBD-D1-NI H-D2-H H-D2-HBA...;18 1 2... + Cmpd2 61;H-D1-H H-D1-NI HBA-D1-NI HBD-D1-NI H-D2-H H-D2-HBA...;5 1 2 ... + ... ... + ... .. + +Example of CSV I<Text> file containing topological pharmacophore atom pairs fingerprints string data: + + "CompoundID","TopologicalPharmacophoreAtomPairsFingerprints" + "Cmpd1","FingerprintsVector;TopologicalPharmacophoreAtomPairs:Arbitrary + Size:MinDistance1:MaxDistance10;54;NumericalValues;IDsAndValuesString;H + -D1-H H-D1-NI HBA-D1-NI HBD-D1-NI H-D2-H H-D2-HBA H-D2-HBD HBA-D2-HBA H + BA-D2-HBD H-D3-H H-D3-HBA H-D3-HBD H-D3-NI HBA-D3-NI HBD-D3-NI H-D4...; + 18 1 2 1 22 12 8 1 2 18 6 3 1 1 1 22 13 6 5 7 2 28 9 5 1 1 1 36 16 10 3 + 4 1 37 10 8 1 35 10 9 3 3 1 28 7 7 4 18 16 12 5 1 2 1" + ... ... + ... ... + +The current release of MayaChemTools generates the following types of topological pharmacophore +atom pairs fingerprints vector strings: + + FingerprintsVector;TopologicalPharmacophoreAtomPairs:ArbitrarySize:Min + Distance1:MaxDistance10;54;NumericalValues;IDsAndValuesString;H-D1-H H + -D1-NI HBA-D1-NI HBD-D1-NI H-D2-H H-D2-HBA H-D2-HBD HBA-D2-HBA HBA-D2- + HBD H-D3-H H-D3-HBA H-D3-HBD H-D3-NI HBA-D3-NI HBD-D3-NI H-D4-H H-D4-H + BA H-D4-HBD HBA-D4-HBA HBA-D4-HBD HBD-D4-HBD H-D5-H H-D5-HBA H-D5-...; + 18 1 2 1 22 12 8 1 2 18 6 3 1 1 1 22 13 6 5 7 2 28 9 5 1 1 1 36 16 10 + 3 4 1 37 10 8 1 35 10 9 3 3 1 28 7 7 4 18 16 12 5 1 2 1 + + FingerprintsVector;TopologicalPharmacophoreAtomPairs:FixedSize:MinDist + ance1:MaxDistance10;150;OrderedNumericalValues;ValuesString;18 0 0 1 0 + 0 0 2 0 0 1 0 0 0 0 22 12 8 0 0 1 2 0 0 0 0 0 0 0 0 18 6 3 1 0 0 0 1 + 0 0 1 0 0 0 0 22 13 6 0 0 5 7 0 0 2 0 0 0 0 0 28 9 5 1 0 0 0 1 0 0 1 0 + 0 0 0 36 16 10 0 0 3 4 0 0 1 0 0 0 0 0 37 10 8 0 0 0 0 1 0 0 0 0 0 0 + 0 35 10 9 0 0 3 3 0 0 1 0 0 0 0 0 28 7 7 4 0 0 0 0 0 0 0 0 0 0 0 18... + + FingerprintsVector;TopologicalPharmacophoreAtomPairs:FixedSize:MinDist + ance1:MaxDistance10;150;OrderedNumericalValues;IDsAndValuesString;H-D1 + -H H-D1-HBA H-D1-HBD H-D1-NI H-D1-PI HBA-D1-HBA HBA-D1-HBD HBA-D1-NI H + BA-D1-PI HBD-D1-HBD HBD-D1-NI HBD-D1-PI NI-D1-NI NI-D1-PI PI-D1-PI H-D + 2-H H-D2-HBA H-D2-HBD H-D2-NI H-D2-PI HBA-D2-HBA HBA-D2-HBD HBA-D2...; + 18 0 0 1 0 0 0 2 0 0 1 0 0 0 0 22 12 8 0 0 1 2 0 0 0 0 0 0 0 0 18 6 3 + 1 0 0 0 1 0 0 1 0 0 0 0 22 13 6 0 0 5 7 0 0 2 0 0 0 0 0 28 9 5 1 0 0 0 + 1 0 0 1 0 0 0 0 36 16 10 0 0 3 4 0 0 1 0 0 0 0 + + +=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<--AtomPairsSetSizeToUse> I<ArbitrarySize | FixedSize> + +Atom pairs set size to use during generation of topological pharmacophore atom pairs +fingerprints. + +Possible values: I<ArbitrarySize | FixedSize>; Default value: I<ArbitrarySize>. + +For I<ArbitrarySize> value of B<--AtomPairsSetSizeToUse> option, the fingerprint vector +correspond to only those topological pharmacophore atom pairs which are present and +have non-zero count. However, for I<FixedSize> value of B<--AtomPairsSetSizeToUse> +option, the fingerprint vector contains all possible valid topological pharmacophore atom +pairs 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 pairs. 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 60-62 ] : I<HBD,HBA,PI,NI,H>. + +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<--AtomTypesWeight> I<"AtomType1,Weight1,AtomType2,Weight2..."> + +Weights of specified pharmacophore atom types to use during calculation of their contribution +to atom pair count. Default value: I<None>. Valid values: real numbers greater than 0. In general +it's comma delimited list of valid atom type and its weight. + +The weight values allow to increase the importance of specific pharmacophore atom type +in the generated fingerprints. A weight value of 0 for an atom type eliminates its contribution to +atom pair count where as weight value of 2 doubles its contribution. + +=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<-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<--AtomPairsSetSizeToUse> option and topological atom pairs 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<TopologicalPharmacophoreAtomPairsFingerprints>. + +=item B<--FuzzifyAtomPairsCount> I<Yes | No> + +To fuzzify or not to fuzzify atom pairs count. Possible values: I<Yes or No>. Default value: +I<No>. + +=item B<--FuzzificationMode> I<BeforeNormalization | AfterNormalization> + +When to fuzzify atom pairs count. Possible values: I<BeforeNormalization | AfterNormalizationYes>. +Default value: I<AfterNormalization>. + +=item B<--FuzzificationMethodology> I<FuzzyBinning | FuzzyBinSmoothing> + +How to fuzzify atom pairs count. Possible values: I<FuzzyBinning | FuzzyBinSmoothing>. +Default value: I<FuzzyBinning>. + +In conjunction with values for options B<--FuzzifyAtomPairsCount>, B<--FuzzificationMode> and +B<--FuzzFactor>, B<--FuzzificationMethodology> option is used to fuzzify pharmacophore atom +pairs count. + +Let: + + Px = Pharmacophore atom type x + Py = Pharmacophore atom type y + PPxy = Pharmacophore atom pair between atom type Px and Py + + PPxyDn = Pharmacophore atom pairs count between atom type Px and Py + at distance Dn + PPxyDn-1 = Pharmacophore atom pairs count between atom type Px and Py + at distance Dn - 1 + PPxyDn+1 = Pharmacophore atom pairs count between atom type Px and Py + at distance Dn + 1 + + FF = FuzzFactor for FuzzyBinning and FuzzyBinSmoothing + +Then: + +For I<FuzzyBinning>: + + PPxyDn = PPxyDn (Unchanged) + + PPxyDn-1 = PPxyDn-1 + PPxyDn * FF + PPxyDn+1 = PPxyDn+1 + PPxyDn * FF + +For I<FuzzyBinSmoothing>: + + PPxyDn = PPxyDn - PPxyDn * 2FF for Dmin < Dn < Dmax + PPxyDn = PPxyDn - PPxyDn * FF for Dn = Dmin or Dmax + + PPxyDn-1 = PPxyDn-1 + PPxyDn * FF + PPxyDn+1 = PPxyDn+1 + PPxyDn * FF + +In both fuzzification schemes, a value of 0 for FF implies no fuzzification of occurrence counts. +A value of 1 during I<FuzzyBinning> corresponds to maximum fuzzification of occurrence counts; +however, a value of 1 during I<FuzzyBinSmoothing> ends up completely distributing the value over +the previous and next distance bins. + +So for default value of B<--FuzzFactor> (FF) 0.15, the occurrence count of pharmacohore atom pairs +at distance Dn during FuzzyBinning is left unchanged and the counts at distances Dn -1 and Dn + 1 +are incremented by PPxyDn * 0.15. + +And during I<FuzzyBinSmoothing> the occurrence counts at Distance Dn is scaled back using multiplicative +factor of (1 - 2*0.15) and the occurrence counts at distances Dn -1 and Dn + 1 are incremented by +PPxyDn * 0.15. In otherwords, occurrence bin count is smoothed out by distributing it over the +previous and next distance value. + +=item B<--FuzzFactor> I<number> + +Specify by how much to fuzzify atom pairs count. Default value: I<0.15>. Valid values: For +I<FuzzyBinning> value of B<--FuzzificationMethodology> option: I<between 0 and 1.0>; For +I<FuzzyBinSmoothing> value of B<--FuzzificationMethodology> option: I<between 0 and 0.5>. + +=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 for generating topological pharmacophore atom +pairs. Default value: I<1>. Valid values: positive integers including 0 and less than B<--MaxDistance>. + +=item B<--MaxDistance> I<number> + +Maximum bond distance between atom pairs for generating topological pharmacophore atom + pairs. Default value: I<10>. Valid values: positive integers and greater than B<--MinDistance>. + +=item B<-n, --NormalizationMethodology> I<None | ByHeavyAtomsCount | ByAtomTypesCount> + +Normalization methodology to use for scaling the occurrence count of pharmacophore atom +pairs within specified distance range. Possible values: I<None, ByHeavyAtomsCount or +ByAtomTypesCount>. Default value: I<None>. + +=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><TopologicalPharmacophoreAtomPairsFP>.<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<--ValuesPrecision> I<number> + +Precision of atom pairs count real values which might be generated after normalization +or fuzzification. Default value: up to I<2> decimal places. Valid values: positive integers. + +=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>. + +Default value during I<FixedSize> value of B<--AtomPairsSetSizeToUse> option: I<ValuesString>. Default +value during I<ArbitrarySize> value of B<--AtomPairsSetSizeToUse> option: I<IDsAndValuesString>. + +I<ValuesString> option value is not allowed for I<ArbitrarySize> value of B<--AtomPairsSetSizeToUse> +option. + +Examples: + + FingerprintsVector;TopologicalPharmacophoreAtomPairs:ArbitrarySize:Min + Distance1:MaxDistance10;54;NumericalValues;IDsAndValuesString;H-D1-H H + -D1-NI HBA-D1-NI HBD-D1-NI H-D2-H H-D2-HBA H-D2-HBD HBA-D2-HBA HBA-D2- + HBD H-D3-H H-D3-HBA H-D3-HBD H-D3-NI HBA-D3-NI HBD-D3-NI H-D4-H H-D4-H + BA H-D4-HBD HBA-D4-HBA HBA-D4-HBD HBD-D4-HBD H-D5-H H-D5-HBA H-D5-...; + 18 1 2 1 22 12 8 1 2 18 6 3 1 1 1 22 13 6 5 7 2 28 9 5 1 1 1 36 16 10 + 3 4 1 37 10 8 1 35 10 9 3 3 1 28 7 7 4 18 16 12 5 1 2 1 + + FingerprintsVector;TopologicalPharmacophoreAtomPairs:FixedSize:MinDist + ance1:MaxDistance10;150;OrderedNumericalValues;ValuesString;18 0 0 1 0 + 0 0 2 0 0 1 0 0 0 0 22 12 8 0 0 1 2 0 0 0 0 0 0 0 0 18 6 3 1 0 0 0 1 + 0 0 1 0 0 0 0 22 13 6 0 0 5 7 0 0 2 0 0 0 0 0 28 9 5 1 0 0 0 1 0 0 1 0 + 0 0 0 36 16 10 0 0 3 4 0 0 1 0 0 0 0 0 37 10 8 0 0 0 0 1 0 0 0 0 0 0 + 0 35 10 9 0 0 3 3 0 0 1 0 0 0 0 0 28 7 7 4 0 0 0 0 0 0 0 0 0 0 0 18... + + FingerprintsVector;TopologicalPharmacophoreAtomPairs:FixedSize:MinDist + ance1:MaxDistance10;150;OrderedNumericalValues;IDsAndValuesString;H-D1 + -H H-D1-HBA H-D1-HBD H-D1-NI H-D1-PI HBA-D1-HBA HBA-D1-HBD HBA-D1-NI H + BA-D1-PI HBD-D1-HBD HBD-D1-NI HBD-D1-PI NI-D1-NI NI-D1-PI PI-D1-PI H-D + 2-H H-D2-HBA H-D2-HBD H-D2-NI H-D2-PI HBA-D2-HBA HBA-D2-HBD HBA-D2...; + 18 0 0 1 0 0 0 2 0 0 1 0 0 0 0 22 12 8 0 0 1 2 0 0 0 0 0 0 0 0 18 6 3 + 1 0 0 0 1 0 0 1 0 0 0 0 22 13 6 0 0 5 7 0 0 2 0 0 0 0 0 28 9 5 1 0 0 0 + 1 0 0 1 0 0 0 0 36 16 10 0 0 3 4 0 0 1 0 0 0 0 + +=item B<-w, --WorkingDir> I<DirName> + +Location of working directory. Default value: current directory. + +=back + +=head1 EXAMPLES + +To generate topological pharmacophore atom pairs fingerprints of arbitrary size corresponding to distances +from 1 through 10 using default atom types with no weighting, normalization, and fuzzification +of atom pairs count and create a SampleTPAPFP.csv file containing sequential compound IDs along +with fingerprints vector strings data in ValuesString format, type: + + % TopologicalPharmacophoreAtomPairsFingerprints.pl -r SampleTPAPFP + -o Sample.sdf + +To generate topological pharmacophore atom pairs fingerprints of fixed size corresponding to distances +from 1 through 10 using default atom types with no weighting, normalization, and fuzzification +of atom pairs count and create a SampleTPAPFP.csv file containing sequential compound IDs along +with fingerprints vector strings data in ValuesString format, type: + + % TopologicalPharmacophoreAtomPairsFingerprints.pl + --AtomPairsSetSizeToUse FixedSize -r SampleTPAPFP-o Sample.sdf + +To generate topological pharmacophore atom pairs fingerprints of arbitrary size corresponding to distances +from 1 through 10 using default atom types with no weighting, normalization, and fuzzification +of atom pairs count and create SampleTPAPFP.sdf, SampleTPAPFP.fpf and SampleTPAPFP.csv files containing +sequential compound IDs in CSV file along with fingerprints vector strings data in ValuesString +format, type: + + % TopologicalPharmacophoreAtomPairsFingerprints.pl --output all + -r SampleTPAPFP -o Sample.sdf + +To generate topological pharmacophore atom pairs fingerprints of arbitrary size corresponding to distances +from 1 through 10 using default atom types with no weighting, normalization, and fuzzification +of atom pairs count and create a SampleTPAPFP.csv file containing sequential compound IDs along +with fingerprints vector strings data in IDsAndValuesPairsString format, type: + + % TopologicalPharmacophoreAtomPairsFingerprints.pl --VectorStringFormat + IDsAndValuesPairsString -r SampleTPAPFP -o Sample.sdf + +To generate topological pharmacophore atom pairs fingerprints of arbitrary size corresponding to distances +from 1 through 6 using default atom types with no weighting, normalization, and fuzzification +of atom pairs count and create a SampleTPAPFP.csv file containing sequential compound IDs along +with fingerprints vector strings data in ValuesString format, type: + + % TopologicalPharmacophoreAtomPairsFingerprints.pl --MinDistance 1 + -MaxDistance 6 -r SampleTPAPFP -o Sample.sdf + +To generate topological pharmacophore atom pairs fingerprints of arbitrary size corresponding to distances +from 1 through 10 using "HBD,HBA,PI,NI" atom types with double the weighting for "HBD,HBA" and +normalization by HeavyAtomCount but no fuzzification of atom pairs count and create a +SampleTPAPFP.csv file containing sequential compound IDs along with fingerprints vector strings +data in ValuesString format, type: + + % TopologicalPharmacophoreAtomPairsFingerprints.pl --MinDistance 1 + -MaxDistance 10 --AtomTypesToUse "HBD,HBA,PI, NI" --AtomTypesWeight + "HBD,2,HBA,2,PI,1,NI,1" --NormalizationMethodology ByHeavyAtomsCount + --FuzzifyAtomPairsCount No -r SampleTPAPFP -o Sample.sdf + +To generate topological pharmacophore atom pairs fingerprints of arbitrary size corresponding to +distances from 1 through 10 using "HBD,HBA,PI,NI,H" atom types with no weighting of atom types and +normalization but with fuzzification of atom pairs count using FuzzyBinning methodology +with FuzzFactor value 0.15 and create a SampleTPAPFP.csv file containing sequential compound +IDs along with fingerprints vector strings data in ValuesString format, type: + + % TopologicalPharmacophoreAtomPairsFingerprints.pl --MinDistance 1 + --MaxDistance 10 --AtomTypesToUse "HBD,HBA,PI, NI,H" --AtomTypesWeight + "HBD,1,HBA,1,PI,1,NI,1,H,1" --NormalizationMethodology None + --FuzzifyAtomPairsCount Yes --FuzzificationMethodology FuzzyBinning + --FuzzFactor 0.5 -r SampleTPAPFP -o Sample.sdf + +To generate topological pharmacophore atom pairs fingerprints of arbitrary size corresponding to distances +distances from 1 through 10 using default atom types with no weighting, +normalization, and fuzzification of atom pairs count and create a SampleTPAPFP.csv +file containing compound ID from molecule name line along with fingerprints vector strings +data, type: + + % TopologicalPharmacophoreAtomPairsFingerprints.pl --DataFieldsMode + CompoundID -CompoundIDMode MolName -r SampleTPAPFP -o Sample.sdf + +To generate topological pharmacophore atom pairs fingerprints of arbitrary size corresponding +to distances from 1 through 10 using default atom types with no weighting, +normalization, and fuzzification of atom pairs count and create a SampleTPAPFP.csv +file containing compound IDs using specified data field along with fingerprints vector strings +data, type: + + % TopologicalPharmacophoreAtomPairsFingerprints.pl --DataFieldsMode + CompoundID -CompoundIDMode DataField --CompoundID Mol_ID + -r SampleTPAPFP -o Sample.sdf + +To generate topological pharmacophore atom pairs fingerprints of arbitrary size corresponding +to distances from 1 through 10 using default atom types with no weighting, +normalization, and fuzzification of atom pairs count and create a SampleTPAPFP.csv +file containing compound ID using combination of molecule name line and an explicit compound +prefix along with fingerprints vector strings data, type: + + % TopologicalPharmacophoreAtomPairsFingerprints.pl --DataFieldsMode + CompoundID -CompoundIDMode MolnameOrLabelPrefix + --CompoundID Cmpd --CompoundIDLabel MolID -r SampleTPAPFP -o Sample.sdf + +To generate topological pharmacophore atom pairs fingerprints of arbitrary size corresponding +to distances from 1 through 10 using default atom types with no weighting, +normalization, and fuzzification of atom pairs count and create a SampleTPAPFP.csv +file containing specific data fields columns along with fingerprints vector strings +data, type: + + % TopologicalPharmacophoreAtomPairsFingerprints.pl --DataFieldsMode + Specify --DataFields Mol_ID -r SampleTPAPFP -o Sample.sdf + +To generate topological pharmacophore atom pairs fingerprints of arbitrary size corresponding +to distances from 1 through 10 using default atom types with no weighting, +normalization, and fuzzification of atom pairs count and create a SampleTPAPFP.csv +file containing common data fields columns along with fingerprints vector strings +data, type: + + % TopologicalPharmacophoreAtomPairsFingerprints.pl --DataFieldsMode + Common -r SampleTPAPFP -o Sample.sdf + +To generate topological pharmacophore atom pairs fingerprints of arbitrary size corresponding +to distances from 1 through 10 using default atom types with no weighting, +normalization, and fuzzification of atom pairs count and create SampleTPAPFP.sdf, SampleTPAPFP.fpf, +and SampleTPAPFP.csv files containing all data fields columns in CSV file along with fingerprints +data, type: + + % TopologicalPharmacophoreAtomPairsFingerprints.pl --DataFieldsMode + All --output all -r SampleTPAPFP -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, +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