Mercurial > repos > deepakjadmin > mayatool3_test3
diff mayachemtools/bin/SimilarityMatricesFingerprints.pl @ 0:73ae111cf86f draft
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| author | deepakjadmin |
|---|---|
| date | Wed, 20 Jan 2016 11:55:01 -0500 |
| parents | |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/mayachemtools/bin/SimilarityMatricesFingerprints.pl Wed Jan 20 11:55:01 2016 -0500 @@ -0,0 +1,2206 @@ +#!/usr/bin/perl -w +# +# $RCSfile: SimilarityMatricesFingerprints.pl,v $ +# $Date: 2015/02/28 20:46:20 $ +# $Revision: 1.21 $ +# +# 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 "$FindBin::Bin/../lib"; +use Getopt::Long; +use File::Basename; +use File::Copy; +use Text::ParseWords; +use Benchmark; +use FileUtil; +use TextUtil; +use Fingerprints::FingerprintsFileUtil; +use Fingerprints::FingerprintsBitVector; +use Fingerprints::FingerprintsVector; + +my($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(@FingerprintsFilesList); +@FingerprintsFilesList = ExpandFileNames(\@ARGV, "sdf sd fpf fp csv tsv"); + +# Process options... +print "Processing options...\n"; +my(%OptionsInfo); +ProcessOptions(); + +# Setup information about input files... +print "Checking input fingerprints file(s)...\n"; +my(%FingerprintsFilesInfo); +RetrieveFingerprintsFilesInfo(); + +# Process input files.. +my($FileIndex); +if (@FingerprintsFilesList > 1) { + print "\nProcessing fingerprints files...\n"; +} +for $FileIndex (0 .. $#FingerprintsFilesList) { + if ($FingerprintsFilesInfo{FileOkay}[$FileIndex]) { + print "\nProcessing file $FingerprintsFilesList[$FileIndex]...\n"; + GenerateSimilarityMatrices($FileIndex); + } +} +print "\n$ScriptName:Done...\n\n"; + +$EndTime = new Benchmark; +$TotalTime = timediff ($EndTime, $StartTime); +print "Total time: ", timestr($TotalTime), "\n"; + +############################################################################### + +# Generate similarity matrices using fingerprints data in text file... +# +sub GenerateSimilarityMatrices { + my($FileIndex) = @_; + + ProcessFingerprintsData($FileIndex); + + if ($FingerprintsFilesInfo{FingerprintsBitVectorStringMode}[$FileIndex]) { + GenerateSimilarityMatricesForFingerprintsBitVectors($FileIndex); + } + elsif ($FingerprintsFilesInfo{FingerprintsVectorStringMode}[$FileIndex]) { + GenerateSimilarityMatricesForFingerprintsVectors($FileIndex); + } + + CleanupFingerprintsData($FileIndex); +} + +# Generate bit vector similarity matrices... +# +sub GenerateSimilarityMatricesForFingerprintsBitVectors { + my($FileIndex) = @_; + my($SpecifiedComparisonMeasure, $ComparisonMeasure, $NewTextFile, $SimilarityMatrixRef, $MethodName, @MethodParameters); + + for $SpecifiedComparisonMeasure (@{$OptionsInfo{SpecifiedBitVectorComparisonsRef}}) { + $ComparisonMeasure = $OptionsInfo{SpecifiedBitVectorComparisonsNameRef}->{lc($SpecifiedComparisonMeasure)}; + $NewTextFile = $FingerprintsFilesInfo{OutFileRoot}[$FileIndex] . "${ComparisonMeasure}." . $FingerprintsFilesInfo{OutFileExt}[$FileIndex]; + + $MethodName = $OptionsInfo{SpecifiedBitVectorComparisonsMethodRef}->{lc($ComparisonMeasure)}; + + @MethodParameters = (); + @MethodParameters = @{$OptionsInfo{SpecifiedBitVectorComparisonsParameterRef}->{lc($ComparisonMeasure)}}; + + GenerateSimilarityMatrix($FileIndex, $NewTextFile, $MethodName, \@MethodParameters); + } +} + +# Generate vector similarity and/or distance matrices... +# +sub GenerateSimilarityMatricesForFingerprintsVectors { + my($FileIndex) = @_; + my($SpecifiedComparisonMeasure, $ComparisonMode, $ComparisonMeasure, $NewTextFile, $MethodName, @MethodParameters); + + for $SpecifiedComparisonMeasure (@{$OptionsInfo{SpecifiedVectorComparisonsRef}}) { + $ComparisonMeasure = $OptionsInfo{SpecifiedVectorComparisonsNameRef}->{lc($SpecifiedComparisonMeasure)}; + + for $ComparisonMode (@{$OptionsInfo{SpecifiedVectorComparisonModesRef}}) { + $NewTextFile = $FingerprintsFilesInfo{OutFileRoot}[$FileIndex] . "${ComparisonMeasure}${ComparisonMode}." . $FingerprintsFilesInfo{OutFileExt}[$FileIndex]; + + $MethodName = $OptionsInfo{SpecifiedVectorComparisonsMethodRef}->{lc($ComparisonMeasure)}; + + @MethodParameters = (); + push @MethodParameters, $ComparisonMode; + push @MethodParameters, @{$OptionsInfo{SpecifiedVectorComparisonsParameterRef}->{lc($ComparisonMeasure)}}; + + GenerateSimilarityMatrix($FileIndex, $NewTextFile, $MethodName, \@MethodParameters); + } + } +} + +# Calculate similarity matrix and write it out... +# +sub GenerateSimilarityMatrix { + my($FileIndex, $NewTextFile, $MethodName, $MethodParametersRef) = @_; + + print "\nGenerating $NewTextFile...\n"; + + # Open new file and write out column labels... + open NEWTEXTFILE, ">$NewTextFile" or die "Error: Can't open $NewTextFile: $! \n"; + WriteColumnLabels($FileIndex, \*NEWTEXTFILE); + + # Calculate and write out similarity matrix values... + if ($OptionsInfo{InputDataMode} =~ /^LoadInMemory$/i) { + GenerateSimilarityMatrixUsingMemoryData($FileIndex, \*NEWTEXTFILE, $MethodName, $MethodParametersRef); + } + elsif ($OptionsInfo{InputDataMode} =~ /^ScanFile$/i) { + GenerateSimilarityMatrixUsingFileData($FileIndex, \*NEWTEXTFILE, $MethodName, $MethodParametersRef); + } + else { + warn "Warning: Input data mode, $OptionsInfo{InputDataMode}, is not supported.\n"; + } + + # Close new text file... + close NEWTEXTFILE; + +} + +# Calculate and write out similarity values using fingerprints data already loaded in +# memory... +# +sub GenerateSimilarityMatrixUsingMemoryData { + my($FileIndex, $NewTextFileRef, $MethodName, $MethodParametersRef) = @_; + my($RowIndex, $ColIndex, $CmpdID1, $CmpdID2, $FingerprintsObject1, $FingerprintsObject2, $Value, $Line, @LineWords); + + for $RowIndex (0 .. $#{$FingerprintsFilesInfo{FingerprintsObjectsRef}}) { + $FingerprintsObject1 = $FingerprintsFilesInfo{FingerprintsObjectsRef}->[$RowIndex]; + $CmpdID1 = $FingerprintsFilesInfo{CompundIDsRef}->[$RowIndex]; + + if ($OptionsInfo{WriteRowsAndColumns}) { + print $NewTextFileRef "$OptionsInfo{OutQuoteValue}${CmpdID1}$OptionsInfo{OutQuoteValue}"; + } + + COLINDEX: for $ColIndex (0 .. $#{$FingerprintsFilesInfo{FingerprintsObjectsRef}}) { + if (SkipMatrixData($RowIndex, $ColIndex)) { + next COLINDEX; + } + + $FingerprintsObject2 = $FingerprintsFilesInfo{FingerprintsObjectsRef}->[$ColIndex]; + + $Value = $FingerprintsObject1->$MethodName($FingerprintsObject2, @{$MethodParametersRef}); + $Value = (defined($Value) && length($Value)) ? (sprintf("%.$OptionsInfo{Precision}f", $Value) + 0) : ''; + + if ($OptionsInfo{WriteRowsAndColumns}) { + print $NewTextFileRef "$OptionsInfo{OutDelim}$OptionsInfo{OutQuoteValue}${Value}$OptionsInfo{OutQuoteValue}"; + } + elsif ($OptionsInfo{WriteIDPairsAndValue}) { + $CmpdID2 = $FingerprintsFilesInfo{CompundIDsRef}->[$ColIndex]; + + @LineWords = (); + push @LineWords, ($CmpdID1, $CmpdID2, $Value); + $Line = JoinWords(\@LineWords, $OptionsInfo{OutDelim}, $OptionsInfo{OutQuote}); + print $NewTextFileRef "$Line\n"; + } + } + if ($OptionsInfo{WriteRowsAndColumns}) { + print $NewTextFileRef "\n"; + } + } +} + +# Calculate and write out similarity values by retrieving and prcessing data +# from fingerprint file... +# +sub GenerateSimilarityMatrixUsingFileData { + my($FileIndex, $NewTextFileRef, $MethodName, $MethodParametersRef) = @_; + my($RowIndex, $ColIndex, $FingerprintsFileIO, $TmpFingerprintsFileIO, $FingerprintsObject1, $FingerprintsObject2, $CmpdID1, $CmpdID2, $FingerprintsCount, $IgnoredFingerprintsCount, $Value, $Line, @LineWords); + + print "\nReading and processing fingerprints data...\n"; + + $FingerprintsFileIO = Fingerprints::FingerprintsFileUtil::NewFingerprintsFileIO(%{$FingerprintsFilesInfo{FingerprintsFileIOParameters}[$FileIndex]}); + $FingerprintsFileIO->Open(); + + $RowIndex = 0; $ColIndex = 0; + $FingerprintsCount = 0; $IgnoredFingerprintsCount = 0; + + FINGERPRINTSFILEIO: while ($FingerprintsFileIO->Read()) { + $FingerprintsCount++; + + if (!$FingerprintsFileIO->IsFingerprintsDataValid()) { + $IgnoredFingerprintsCount++; + next FINGERPRINTSFILEIO; + } + $RowIndex++; + $FingerprintsObject1 = $FingerprintsFileIO->GetFingerprints(); + $CmpdID1 = $FingerprintsFileIO->GetCompoundID(); + + if ($OptionsInfo{WriteRowsAndColumns}) { + print $NewTextFileRef "$OptionsInfo{OutQuoteValue}${CmpdID1}$OptionsInfo{OutQuoteValue}"; + } + + # Force detail level of 1 to avoid duplicate printing of diagnostic messages for invalid + # fingerprints data... + $TmpFingerprintsFileIO = Fingerprints::FingerprintsFileUtil::NewFingerprintsFileIO(%{$FingerprintsFilesInfo{TmpFingerprintsFileIOParameters}[$FileIndex]}, "DetailLevel" => 1); + $TmpFingerprintsFileIO->Open(); + + $ColIndex = 0; + TMPFINGERPRINTSFILEIO: while ($TmpFingerprintsFileIO->Read()) { + if (!$TmpFingerprintsFileIO->IsFingerprintsDataValid()) { + next TMPFINGERPRINTSFILEIO; + } + $ColIndex++; + + if (SkipMatrixData($RowIndex, $ColIndex)) { + next TMPFINGERPRINTSFILEIO; + } + + $FingerprintsObject2 = $TmpFingerprintsFileIO->GetFingerprints(); + + $Value = $FingerprintsObject1->$MethodName($FingerprintsObject2, @{$MethodParametersRef}); + $Value = (defined($Value) && length($Value)) ? (sprintf("%.$OptionsInfo{Precision}f", $Value) + 0) : ''; + + if ($OptionsInfo{WriteRowsAndColumns}) { + print $NewTextFileRef "$OptionsInfo{OutDelim}$OptionsInfo{OutQuoteValue}${Value}$OptionsInfo{OutQuoteValue}"; + } + elsif ($OptionsInfo{WriteIDPairsAndValue}) { + $CmpdID2 = $TmpFingerprintsFileIO->GetCompoundID(); + + @LineWords = (); + push @LineWords, ($CmpdID1, $CmpdID2, $Value); + $Line = JoinWords(\@LineWords, $OptionsInfo{OutDelim}, $OptionsInfo{OutQuote}); + print $NewTextFileRef "$Line\n"; + } + } + $TmpFingerprintsFileIO->Close(); + + if ($OptionsInfo{WriteRowsAndColumns}) { + print $NewTextFileRef "\n"; + } + } + + $FingerprintsFileIO->Close(); + + print "Number of fingerprints data entries in database fingerprints file: $FingerprintsCount\n"; + print "Number of fingerprints date entries processed successfully: ", ($FingerprintsCount - $IgnoredFingerprintsCount) , "\n"; + print "Number of fingerprints data entries ignored due to missing/invalid data: $IgnoredFingerprintsCount\n\n"; +} + +# Check whether matrix data need to be skipped... +# +sub SkipMatrixData { + my($RowIndex, $ColIndex) = @_; + + if ($OptionsInfo{WriteFullMatrix}) { + return 0; + } + elsif ($OptionsInfo{WriteUpperTriangularMatrix}) { + return ($RowIndex > $ColIndex) ? 1 : 0; + } + elsif ($OptionsInfo{WriteLowerTriangularMatrix}) { + return ($RowIndex < $ColIndex) ? 1 : 0; + } + + return 0; +} + +# Write out column labels... +# +sub WriteColumnLabels { + my($FileIndex, $NewTextFileRef) = @_; + my($Line, @LineWords); + + if ($OptionsInfo{OutMatrixFormat} =~ /^IDPairsAndValue$/i) { + @LineWords = (); + push @LineWords, ('CmpdID1', 'CmpdID2', 'Coefficient Value'); + $Line = JoinWords(\@LineWords, $OptionsInfo{OutDelim}, $OptionsInfo{OutQuote}); + print $NewTextFileRef "$Line\n"; + } + elsif ($OptionsInfo{OutMatrixFormat} =~ /^RowsAndColumns$/i) { + if ($OptionsInfo{InputDataMode} =~ /^LoadInMemory$/i) { + @LineWords = (); + push @LineWords, ''; + push @LineWords, @{$FingerprintsFilesInfo{CompundIDsRef}}; + $Line = JoinWords(\@LineWords, $OptionsInfo{OutDelim}, $OptionsInfo{OutQuote}); + print $NewTextFileRef "$Line\n"; + } + elsif ($OptionsInfo{InputDataMode} =~ /^ScanFile$/i) { + my( $FingerprintsFileIO, $CmpdID); + + # Scan file to retrieve compound IDs... + # + print "\nProcessing fingerprints file to generate compound IDs...\n"; + + # Force detail level of 1 to avoid diagnostics messages for invalid fingeprints data during + # retrieval of compound IDs as these get printed out during calculation of matrix... + # + $FingerprintsFileIO = Fingerprints::FingerprintsFileUtil::NewFingerprintsFileIO(%{$FingerprintsFilesInfo{FingerprintsFileIOParameters}[$FileIndex]}, "DetailLevel" => 1); + $FingerprintsFileIO->Open(); + + print $NewTextFileRef "$OptionsInfo{OutQuoteValue}$OptionsInfo{OutQuoteValue}"; + + FINGERPRINTSFILEIO: while ($FingerprintsFileIO->Read()) { + if (!$FingerprintsFileIO->IsFingerprintsDataValid()) { + next FINGERPRINTSFILEIO; + } + $CmpdID = $FingerprintsFileIO->GetCompoundID(); + print $NewTextFileRef "$OptionsInfo{OutDelim}$OptionsInfo{OutQuoteValue}${CmpdID}$OptionsInfo{OutQuoteValue}"; + } + $FingerprintsFileIO->Close(); + + print $NewTextFileRef "\n"; + + print "Processing fingerprints file to generate matrix...\n"; + } + } + else { + warn "Warning: Output matrix format, $OptionsInfo{OutMatrixFormat}, is not supported.\n"; + } +} + +# Process fingerprints data... +# +sub ProcessFingerprintsData { + my($FileIndex) = @_; + my($FingerprintsFileIO); + + $FingerprintsFilesInfo{CompundIDsRef} = undef; + $FingerprintsFilesInfo{FingerprintsObjectsRef} = undef; + + if ($OptionsInfo{InputDataMode} =~ /^LoadInMemory$/i) { + my($FingerprintsFileIO); + + $FingerprintsFileIO = Fingerprints::FingerprintsFileUtil::NewFingerprintsFileIO(%{$FingerprintsFilesInfo{FingerprintsFileIOParameters}[$FileIndex]}); + ($FingerprintsFilesInfo{CompundIDsRef}, $FingerprintsFilesInfo{FingerprintsObjectsRef}) = Fingerprints::FingerprintsFileUtil::ReadAndProcessFingerpritsData($FingerprintsFileIO); + } + elsif ($OptionsInfo{InputDataMode} =~ /^ScanFile$/i) { + my($FingerprintsFile, $TmpFingerprintsFile); + + $FingerprintsFile = $FingerprintsFilesList[$FileIndex]; + $TmpFingerprintsFile = $FingerprintsFilesInfo{TmpFingerprintsFile}[$FileIndex]; + + # Copy fingerprints file to a tmp file for calculating similarity matrix... + print "\nCopying fingerprints file, $FingerprintsFile, to temporary fingperints file, $TmpFingerprintsFile...\n"; + copy $FingerprintsFile, $TmpFingerprintsFile or die "Error: Couldn't copy $FingerprintsFile to $TmpFingerprintsFile: $! \n"; + } +} + +# Clean up fingerprints data... +# +sub CleanupFingerprintsData { + my($FileIndex) = @_; + + if ($OptionsInfo{InputDataMode} =~ /^LoadInMemory$/i) { + $FingerprintsFilesInfo{CompundIDsRef} = undef; + $FingerprintsFilesInfo{FingerprintsObjectsRef} = undef; + } + elsif ($OptionsInfo{InputDataMode} =~ /^ScanFile$/i) { + my($TmpFingerprintsFile); + + # Delete temporary fingerprints file... + $TmpFingerprintsFile = $FingerprintsFilesInfo{TmpFingerprintsFile}[$FileIndex]; + + print "\nDeleting temporary fingerprints file $TmpFingerprintsFile...\n"; + unlink $TmpFingerprintsFile or die "Error: Couldn't unlink $TmpFingerprintsFile: $! \n"; + } +} + +# Retrieve information about fingerprints files... +# +sub RetrieveFingerprintsFilesInfo { + my($FingerprintsFile, $TmpFingerprintsFile, $FingerprintsFileIO, $FingerprintsBitVectorStringMode, $FingerprintsVectorStringMode, $FileType, $Index, $FileDir, $FileExt, $FileName, $InDelim, $OutFileRoot, $OutFileExt, %FingerprintsFileIOParameters); + + %FingerprintsFilesInfo = (); + @{$FingerprintsFilesInfo{FileOkay}} = (); + @{$FingerprintsFilesInfo{FileType}} = (); + @{$FingerprintsFilesInfo{InDelim}} = (); + @{$FingerprintsFilesInfo{OutFileRoot}} = (); + @{$FingerprintsFilesInfo{OutFileExt}} = (); + + @{$FingerprintsFilesInfo{TmpFingerprintsFile}} = (); + + @{$FingerprintsFilesInfo{FingerprintsFileIOParameters}} = (); + @{$FingerprintsFilesInfo{TmpFingerprintsFileIOParameters}} = (); + + @{$FingerprintsFilesInfo{FingerprintsBitVectorStringMode}} = (); + @{$FingerprintsFilesInfo{FingerprintsVectorStringMode}} = (); + + FILELIST: for $Index (0 .. $#FingerprintsFilesList) { + $FingerprintsFilesInfo{FileOkay}[$Index] = 0; + $FingerprintsFilesInfo{FileType}[$Index] = ''; + $FingerprintsFilesInfo{InDelim}[$Index] = ""; + $FingerprintsFilesInfo{OutFileRoot}[$Index] = ''; + $FingerprintsFilesInfo{OutFileExt}[$Index] = ''; + + %{$FingerprintsFilesInfo{FingerprintsFileIOParameters}[$Index]} = (); + + $FingerprintsFilesInfo{TmpFingerprintsFile}[$Index] = ""; + %{$FingerprintsFilesInfo{TmpFingerprintsFileIOParameters}[$Index]} = (); + + $FingerprintsFilesInfo{FingerprintsBitVectorStringMode}[$Index] = 0; + $FingerprintsFilesInfo{FingerprintsVectorStringMode}[$Index] = 0; + + $FingerprintsFile = $FingerprintsFilesList[$Index]; + if (!(-e $FingerprintsFile)) { + warn "Warning: Ignoring file $FingerprintsFile: It doesn't exist\n"; + next FILELIST; + } + + $FileType = Fingerprints::FingerprintsFileUtil::GetFingerprintsFileType($FingerprintsFile); + if (IsEmpty($FileType)) { + warn "Warning: Ignoring file $FingerprintsFile: It's not a fingerprints file\n"; + next FILELIST; + } + + $FileDir = ""; $FileName = ""; $FileExt = ""; + ($FileDir, $FileName, $FileExt) = ParseFileName($FingerprintsFile); + + # Setup temporary fingerprints file name for scan file mode... + $TmpFingerprintsFile = "${FileName}Tmp.${FileExt}"; + + $InDelim = ($FileExt =~ /^tsv$/i) ? 'Tab' : $OptionsInfo{InDelim}; + + # Setup output file names... + $OutFileExt = "csv"; + if ($Options{outdelim} =~ /^tab$/i) { + $OutFileExt = "tsv"; + } + + $OutFileRoot = $FileName; + if ($OptionsInfo{OutFileRoot} && (@FingerprintsFilesList == 1)) { + my ($RootFileDir, $RootFileName, $RootFileExt) = ParseFileName($OptionsInfo{OutFileRoot}); + if ($RootFileName && $RootFileExt) { + $FileName = $RootFileName; + } + else { + $FileName = $OptionsInfo{OutFileRoot}; + } + $OutFileRoot = $FileName; + } + + if (!$Options{overwrite}) { + # Similarity matrices output file names for bit-vector strings... + my($SpecifiedComparisonMeasure, $ComparisonMeasure); + for $SpecifiedComparisonMeasure (@{$OptionsInfo{SpecifiedBitVectorComparisonsRef}}) { + $ComparisonMeasure = $OptionsInfo{SpecifiedBitVectorComparisonsNameRef}->{lc($SpecifiedComparisonMeasure)}; + if (-e "${OutFileRoot}${ComparisonMeasure}.${OutFileExt}") { + warn "Warning: Ignoring file $FingerprintsFile: The file ${OutFileRoot}${ComparisonMeasure}.${OutFileExt} already exists.\n"; + next FILELIST; + } + } + # Similarity matrices output file names for vector strings... + my($ComparisonMode); + for $SpecifiedComparisonMeasure (@{$OptionsInfo{SpecifiedVectorComparisonsRef}}) { + $ComparisonMeasure = $OptionsInfo{SpecifiedVectorComparisonsNameRef}->{lc($SpecifiedComparisonMeasure)}; + for $ComparisonMode (@{$OptionsInfo{SpecifiedVectorComparisonModesRef}}) { + if (-e "${OutFileRoot}${ComparisonMeasure}${ComparisonMode}.${OutFileExt}") { + warn "Warning: Ignoring file $FingerprintsFile: The file ${OutFileRoot}${ComparisonMeasure}${ComparisonMode}.${OutFileExt} already exists.\n"; + next FILELIST; + } + } + } + } + + # Setup FingerprintsFileIO parameters... + %FingerprintsFileIOParameters = (); + FILEIOPARAMETERS: { + if ($FileType =~ /^SD$/i) { + %FingerprintsFileIOParameters = ('Name' => $FingerprintsFile, 'Mode' => 'Read', 'FingerprintsStringMode' => $OptionsInfo{Mode}, 'ValidateData' => $OptionsInfo{ValidateData}, 'DetailLevel' => $OptionsInfo{Detail}, 'FingerprintsFieldLabel' => $OptionsInfo{FingerprintsField}, 'CompoundIDMode' => $OptionsInfo{CompoundIDMode}, 'CompoundIDFieldLabel' => $OptionsInfo{CompoundIDField}, 'CompoundIDPrefix' => $OptionsInfo{CompoundIDPrefix}); + last FILEIOPARAMETERS; + } + if ($FileType =~ /^FP$/i) { + %FingerprintsFileIOParameters = ('Name' => $FingerprintsFile, 'Mode' => 'Read', 'FingerprintsStringMode' => $OptionsInfo{Mode}, 'ValidateData' => $OptionsInfo{ValidateData}, 'DetailLevel' => $OptionsInfo{Detail}); + last FILEIOPARAMETERS; + } + if ($FileType =~ /^Text$/i) { + %FingerprintsFileIOParameters = ('Name' => $FingerprintsFile, 'Mode' => 'Read', 'FingerprintsStringMode' => $OptionsInfo{Mode}, 'ValidateData' => $OptionsInfo{ValidateData}, 'DetailLevel' => $OptionsInfo{Detail}, 'FingerprintsCol' => $OptionsInfo{FingerprintsCol}, 'ColMode' => $OptionsInfo{ColMode}, 'CompoundIDCol' => $OptionsInfo{CompoundIDCol}, 'CompoundIDPrefix' => $OptionsInfo{CompoundIDPrefix}, 'InDelim' => $OptionsInfo{InDelim}); + last FILEIOPARAMETERS; + } + warn "Warning: File type for fingerprints file, $FingerprintsFile, is not valid. Supported file types: SD, FP or Text\n"; + next FILELIST; + } + + # Retrieve fingerints file string mode information... + $FingerprintsFileIO = Fingerprints::FingerprintsFileUtil::NewFingerprintsFileIO(%FingerprintsFileIOParameters); + + if (!$FingerprintsFileIO) { + warn "Warning: Ignoring fingerprints file $FingerprintsFile: It contains invalid fingerprints data\n"; + next FILELIST; + } + if (!$FingerprintsFileIO->IsFingerprintsFileDataValid()) { + warn "Warning: Ignoring fingerprints file $FingerprintsFile: It contains invalid fingerprints data\n"; + next FILELIST; + } + $FingerprintsBitVectorStringMode = $FingerprintsFileIO->GetFingerprintsBitVectorStringMode(); + $FingerprintsVectorStringMode = $FingerprintsFileIO->GetFingerprintsVectorStringMode(); + + + $FingerprintsFilesInfo{FileOkay}[$Index] = 1; + $FingerprintsFilesInfo{FileType}[$Index] = $FileType; + + $FingerprintsFilesInfo{InDelim}[$Index] = $InDelim; + + $FingerprintsFilesInfo{OutFileRoot}[$Index] = $OutFileRoot; + $FingerprintsFilesInfo{OutFileExt}[$Index] = $OutFileExt; + + %{$FingerprintsFilesInfo{FingerprintsFileIOParameters}[$Index]} = %FingerprintsFileIOParameters; + + $FingerprintsFilesInfo{TmpFingerprintsFile}[$Index] = $TmpFingerprintsFile; + + $FingerprintsFileIOParameters{Name} = $TmpFingerprintsFile; + %{$FingerprintsFilesInfo{TmpFingerprintsFileIOParameters}[$Index]} = %FingerprintsFileIOParameters; + + $FingerprintsFilesInfo{FingerprintsBitVectorStringMode}[$Index] = $FingerprintsBitVectorStringMode; + $FingerprintsFilesInfo{FingerprintsVectorStringMode}[$Index] = $FingerprintsVectorStringMode; + } +} + +# Process option values... +sub ProcessOptions { + %OptionsInfo = (); + + $OptionsInfo{Mode} = $Options{mode}; + + $OptionsInfo{InputDataMode} = $Options{inputdatamode}; + + ProcessBitVectorComparisonOptions(); + ProcessVectorComparisonOptions(); + + $OptionsInfo{CompoundIDPrefix} = $Options{compoundidprefix} ? $Options{compoundidprefix} : 'Cmpd'; + + # Compound ID and fingerprints column options for text files... + $OptionsInfo{ColMode} = $Options{colmode}; + + if (IsNotEmpty($Options{compoundidcol})) { + if ($Options{colmode} =~ /^ColNum$/i) { + if (!IsPositiveInteger($Options{compoundidcol})) { + die "Error: Column value, $Options{compoundidcol}, specified using \"--CompoundIDCol\" is not valid: Allowed integer values: > 0\n"; + } + } + $OptionsInfo{CompoundIDCol} = $Options{compoundidcol}; + } + else { + $OptionsInfo{CompoundIDCol} = 'AutoDetect'; + } + + if (IsNotEmpty($Options{fingerprintscol})) { + if ($Options{colmode} =~ /^ColNum$/i) { + if (!IsPositiveInteger($Options{fingerprintscol})) { + die "Error: Column value, $Options{fingerprintscol}, specified using \"--FingerprintsCol\" is not valid: Allowed integer values: > 0\n"; + } + } + $OptionsInfo{FingerprintsCol} = $Options{fingerprintscol}; + } + else { + $OptionsInfo{FingerprintsCol} = 'AutoDetect'; + } + + if (IsNotEmpty($Options{compoundidcol}) && IsNotEmpty($Options{fingerprintscol})) { + if (IsPositiveInteger($Options{compoundidcol}) && IsPositiveInteger($Options{fingerprintscol})) { + if (($Options{compoundidcol} == $Options{fingerprintscol})) { + die "Error: Values specified using \"--CompoundIDCol\" and \"--FingerprintsCol\", $Options{compoundidcol}, must be different.\n"; + } + } + else { + if (($Options{compoundidcol} eq $Options{fingerprintscol})) { + die "Error: Values specified using \"--CompoundIDCol\" and \"--FingerprintsCol\", $Options{compoundidcol}, must be different.\n"; + } + } + } + + # Compound ID and fingerprints field options for SD files... + $OptionsInfo{CompoundIDMode} = $Options{compoundidmode}; + $OptionsInfo{CompoundIDField} = ''; + + if ($Options{compoundidmode} =~ /^DataField$/i) { + if (!$Options{compoundidfield}) { + die "Error: You must specify a value for \"--CompoundIDField\" option in \"DataField\" \"--CompoundIDMode\". \n"; + } + $OptionsInfo{CompoundIDField} = $Options{compoundidfield}; + } + + + if (IsNotEmpty($Options{fingerprintsfield})) { + $OptionsInfo{FingerprintsField} = $Options{fingerprintsfield}; + } + else { + $OptionsInfo{FingerprintsField} = 'AutoDetect'; + } + + if ($Options{compoundidfield} && IsNotEmpty($Options{fingerprintsfield})) { + if (($Options{compoundidfield} eq $Options{fingerprintsfield})) { + die "Error: Values specified using \"--CompoundIDField\" and \"--Fingerprintsfield\", $Options{compoundidfield}, must be different.\n"; + } + } + + $OptionsInfo{Detail} = $Options{detail}; + + $OptionsInfo{InDelim} = $Options{indelim}; + $OptionsInfo{OutDelim} = ($Options{outdelim} =~ /tab/i ) ? "\t" : (($Options{outdelim} =~ /semicolon/i) ? "\;" : "\,"); + $OptionsInfo{OutQuote} = ($Options{quote} =~ /^Yes$/i) ? 1 : 0; + $OptionsInfo{OutQuoteValue} = ($Options{quote} =~ /^Yes$/i) ? '"' : ''; + + $OptionsInfo{OutMatrixFormat} = $Options{outmatrixformat}; + + $OptionsInfo{WriteRowsAndColumns} = 0; $OptionsInfo{WriteIDPairsAndValue} = 0; + OUTMATRIXFORMAT: { + if ($OptionsInfo{OutMatrixFormat} =~ /^RowsAndColumns$/i) { + $OptionsInfo{WriteRowsAndColumns} = 1; last OUTMATRIXFORMAT; + } + if ($OptionsInfo{OutMatrixFormat} =~ /^IDPairsAndValue$/i) { + $OptionsInfo{WriteIDPairsAndValue} = 1; last OUTMATRIXFORMAT; + } + die "Error: The value specified, $Options{outmatrixformat}, for option \"--OutMatrixFormat\" is not valid. Allowed values: RowsAndColumns or IDPairsAndValue\n"; + } + + $OptionsInfo{OutMatrixType} = $Options{outmatrixtype}; + + $OptionsInfo{WriteFullMatrix} = 0; + $OptionsInfo{WriteUpperTriangularMatrix} = 0; $OptionsInfo{WriteLowerTriangularMatrix} = 0; + OUTMATRIXTYPE: { + if ($OptionsInfo{OutMatrixType} =~ /^FullMatrix$/i) { + $OptionsInfo{WriteFullMatrix} = 1; last OUTMATRIXTYPE; + } + if ($OptionsInfo{OutMatrixType} =~ /^UpperTriangularMatrix$/i) { + $OptionsInfo{WriteUpperTriangularMatrix} = 1; last OUTMATRIXTYPE; + } + if ($OptionsInfo{OutMatrixType} =~ /^LowerTriangularMatrix$/i) { + $OptionsInfo{WriteLowerTriangularMatrix} = 1; last OUTMATRIXTYPE; + } + die "Error: The value specified, $Options{outmatrixtype}, for option \"--OutMatrixType\" is not valid. Allowed values: FullMatrix, UpperTriangularMatrix or LowerTriangularMatrix\n"; + } + + $OptionsInfo{OverwriteFiles} = $Options{overwrite} ? 1 : 0; + $OptionsInfo{OutFileRoot} = $Options{root} ? $Options{root} : 0; + + $OptionsInfo{Fast} = $Options{fast} ? 1 : 0; + $OptionsInfo{ValidateData} = $Options{fast} ? 0 : 1; + + $OptionsInfo{Precision} = $Options{precision}; + +} + +# Process options related to comparion of bit vector strings... +# +sub ProcessBitVectorComparisonOptions { + # Setup supported bit vector similarity coefficients for bit vector strings... + my($ComparisonMeasure, $SupportedComparisonMeasure, @SupportedComparisonMeasures, %SupportedComparisonMeasuresNameMap, %SupportedComparisonMeasuresMethodMap); + + @SupportedComparisonMeasures = (); + %SupportedComparisonMeasuresNameMap = (); + %SupportedComparisonMeasuresMethodMap = (); + + for $SupportedComparisonMeasure (Fingerprints::FingerprintsBitVector::GetSupportedSimilarityCoefficients()) { + # Similarity coefficient function/method names contain "Coefficient" in their names. + # So take 'em out and setup a map to original function/method name... + $ComparisonMeasure = $SupportedComparisonMeasure; + $ComparisonMeasure =~ s/Coefficient$//; + + push @SupportedComparisonMeasures, $ComparisonMeasure; + $SupportedComparisonMeasuresNameMap{lc($ComparisonMeasure)} = $ComparisonMeasure; + $SupportedComparisonMeasuresMethodMap{lc($ComparisonMeasure)} = $SupportedComparisonMeasure; + } + + # Setup a list of similarity coefficients to use for calculating similarity matrices for bit vector strings... + my($SpecifiedMeasure, @SpecifiedComparisonMeasures, %SpecifiedComparisonMeasuresNameMap, %SpecifiedComparisonMeasuresMethodMap, %SpecifiedComparisonMeasuresParameterMap); + + @SpecifiedComparisonMeasures = (); + %SpecifiedComparisonMeasuresNameMap = (); + %SpecifiedComparisonMeasuresMethodMap = (); + %SpecifiedComparisonMeasuresParameterMap = (); + + if ($Options{bitvectorcomparisonmode} =~ /^All$/i) { + push @SpecifiedComparisonMeasures, @SupportedComparisonMeasures; + } + else { + # Comma delimited list of similarity coefficients... + my($BitVectorComparisonMode, @SpecifiedMeasures, @UnsupportedSpecifiedMeasures); + + $BitVectorComparisonMode = $Options{bitvectorcomparisonmode}; + $BitVectorComparisonMode =~ s/ //g; + @SpecifiedMeasures = split ",", $BitVectorComparisonMode; + @UnsupportedSpecifiedMeasures = (); + + for $SpecifiedMeasure (@SpecifiedMeasures) { + if (exists($SupportedComparisonMeasuresMethodMap{lc($SpecifiedMeasure)})) { + push @SpecifiedComparisonMeasures, $SpecifiedMeasure; + } + else { + push @UnsupportedSpecifiedMeasures, $SpecifiedMeasure; + } + } + if (@UnsupportedSpecifiedMeasures) { + if (@UnsupportedSpecifiedMeasures > 1) { + warn "Error: The values specified - ", JoinWords(\@UnsupportedSpecifiedMeasures, ", ", 0)," - for option \"-b --BitVectorComparisonMode\" are not valid.\n"; + } + else { + warn "Error: The value specified, @UnsupportedSpecifiedMeasures, for option \"-b --BitVectorComparisonMode\" is not valid.\n"; + } + die "Allowed values:", JoinWords(\@SupportedComparisonMeasures, ", ", 0), "\n"; + } + } + for $SpecifiedMeasure (@SpecifiedComparisonMeasures) { + $SpecifiedComparisonMeasuresMethodMap{lc($SpecifiedMeasure)} = $SupportedComparisonMeasuresMethodMap{lc($SpecifiedMeasure)}; + $SpecifiedComparisonMeasuresNameMap{lc($SpecifiedMeasure)} = $SupportedComparisonMeasuresNameMap{lc($SpecifiedMeasure)}; + } + + $OptionsInfo{BitVectorComparisonMode} = $Options{bitvectorcomparisonmode}; + $OptionsInfo{SpecifiedBitVectorComparisonsRef} = \@SpecifiedComparisonMeasures; + $OptionsInfo{SpecifiedBitVectorComparisonsNameRef} = \%SpecifiedComparisonMeasuresNameMap; + $OptionsInfo{SpecifiedBitVectorComparisonsMethodRef} = \%SpecifiedComparisonMeasuresMethodMap; + + # Make sure valid alpha parameter is specified for Tversky calculation... + my($SpecifiedMeasure1, $SpecifiedMeasure2); + $OptionsInfo{Alpha} = ''; + $SpecifiedMeasure1 = 'TverskySimilarity'; + $SpecifiedMeasure2 = 'WeightedTverskySimilarity'; + if ($SpecifiedComparisonMeasuresNameMap{lc($SpecifiedMeasure1)} || $SpecifiedComparisonMeasuresNameMap{lc($SpecifiedMeasure2)}) { + if (IsEmpty($Options{alpha})) { + die "Error: You must specify a value for \"-a, --alpha\" option in \"$SpecifiedMeasure1, $SpecifiedMeasure2, or All\" \"-m --mode\". \n"; + } + my($Alpha); + $Alpha = $Options{alpha}; + if (!(IsFloat($Alpha) && $Alpha >=0 && $Alpha <= 1)) { + die "Error: The value specified, $Options{alpha}, for option \"-a, --alpha\" is not valid. Allowed values: >= 0 and <= 1\n"; + } + $OptionsInfo{Alpha} = $Alpha; + } + + # Make sure valid beta parameter is specified for WeightedTanimoto and WeightedTversky + # calculations... + $OptionsInfo{Beta} = ''; + $SpecifiedMeasure1 = 'WeightedTverskySimilarity'; + $SpecifiedMeasure2 = 'WeightedTanimotoSimilarity'; + if ($SpecifiedComparisonMeasuresNameMap{lc($SpecifiedMeasure1)} || $SpecifiedComparisonMeasuresNameMap{lc($SpecifiedMeasure2)}) { + if (IsEmpty($Options{beta})) { + die "Error: You must specify a value for \"-b, --beta\" option in \"$SpecifiedMeasure1, $SpecifiedMeasure2, or All\" \"-m --mode\". \n"; + } + my($Beta); + $Beta = $Options{beta}; + if (!(IsFloat($Beta) && $Beta >=0 && $Beta <= 1)) { + die "Error: The value specified, $Options{beta}, for option \"-b, --beta\" is not valid. Allowed values: >= 0 and <= 1\n"; + } + $OptionsInfo{Beta} = $Beta; + } + + # Setup any parameters required for specified comparison menthod... + for $SpecifiedMeasure (@SpecifiedComparisonMeasures) { + @{$SpecifiedComparisonMeasuresParameterMap{lc($SpecifiedMeasure)}} = (); + if ($SpecifiedMeasure =~ /^TverskySimilarity$/i) { + push @{$SpecifiedComparisonMeasuresParameterMap{lc($SpecifiedMeasure)}}, $OptionsInfo{Alpha}; + } + elsif ($SpecifiedMeasure =~ /^WeightedTverskySimilarity$/i) { + push @{$SpecifiedComparisonMeasuresParameterMap{lc($SpecifiedMeasure)}}, $OptionsInfo{Alpha}; + push @{$SpecifiedComparisonMeasuresParameterMap{lc($SpecifiedMeasure)}}, $OptionsInfo{Beta}; + } + elsif ($SpecifiedMeasure =~ /^WeightedTanimotoSimilarity$/i) { + push @{$SpecifiedComparisonMeasuresParameterMap{lc($SpecifiedMeasure)}}, $OptionsInfo{Beta}; + } + } + $OptionsInfo{SpecifiedBitVectorComparisonsParameterRef} = \%SpecifiedComparisonMeasuresParameterMap; +} + +# Process options related to comparion of vector strings... +# +sub ProcessVectorComparisonOptions { + # Setup specified similarity coefficients for vector strings.. + my($ComparisonMeasure, $SupportedComparisonMeasure, @SupportedComparisonMeasures, %SupportedComparisonMeasuresNameMap, %SupportedComparisonMeasuresMethodMap); + + @SupportedComparisonMeasures = (); + %SupportedComparisonMeasuresNameMap = (); + %SupportedComparisonMeasuresMethodMap = (); + for $SupportedComparisonMeasure (Fingerprints::FingerprintsVector::GetSupportedDistanceAndSimilarityCoefficients()) { + # Similarity and distance coefficient function/method names contain "Coefficient" in their names. + # So take 'em out and setup a map to original function/method name... + $ComparisonMeasure = $SupportedComparisonMeasure; + if ($ComparisonMeasure =~ /Coefficient$/i) { + $ComparisonMeasure =~ s/Coefficient$//i; + } + push @SupportedComparisonMeasures, $ComparisonMeasure; + $SupportedComparisonMeasuresNameMap{lc($ComparisonMeasure)} = $ComparisonMeasure; + $SupportedComparisonMeasuresMethodMap{lc($ComparisonMeasure)} = $SupportedComparisonMeasure; + } + + # Setup a list of similarity coefficients to use for calculating similarity matrices for bit vector strings... + my($SpecifiedMeasure, @SpecifiedComparisonMeasures, %SpecifiedComparisonMeasuresNameMap, %SpecifiedComparisonMeasuresMethodMap, %SpecifiedComparisonMeasuresParameterMap); + + @SpecifiedComparisonMeasures = (); + %SpecifiedComparisonMeasuresNameMap = (); + %SpecifiedComparisonMeasuresMethodMap = (); + + if ($Options{vectorcomparisonmode} =~ /^All$/i) { + push @SpecifiedComparisonMeasures, @SupportedComparisonMeasures; + } + else { + # Comma delimited list of similarity coefficients... + my($VectorComparisonMode, @SpecifiedMeasures, @UnsupportedSpecifiedMeasures); + + $VectorComparisonMode = $Options{vectorcomparisonmode}; + $VectorComparisonMode =~ s/ //g; + @SpecifiedMeasures = split ",", $VectorComparisonMode; + @UnsupportedSpecifiedMeasures = (); + + for $SpecifiedMeasure (@SpecifiedMeasures) { + if (exists($SupportedComparisonMeasuresMethodMap{lc($SpecifiedMeasure)})) { + push @SpecifiedComparisonMeasures, $SpecifiedMeasure; + } + else { + push @UnsupportedSpecifiedMeasures, $SpecifiedMeasure; + } + } + if (@UnsupportedSpecifiedMeasures) { + if (@UnsupportedSpecifiedMeasures > 1) { + warn "Error: The values specified - ", JoinWords(\@UnsupportedSpecifiedMeasures, ", ", 0)," - for option \"-v --VectorComparisonMode\" are not valid.\n"; + } + else { + warn "Error: The value specified, @UnsupportedSpecifiedMeasures, for option \"-v --VectorComparisonMode\" is not valid.\n"; + } + die "Allowed values:", JoinWords(\@SupportedComparisonMeasures, ", ", 0), "\n"; + } + } + for $SpecifiedMeasure (@SpecifiedComparisonMeasures) { + $SpecifiedComparisonMeasuresMethodMap{lc($SpecifiedMeasure)} = $SupportedComparisonMeasuresMethodMap{lc($SpecifiedMeasure)}; + $SpecifiedComparisonMeasuresNameMap{lc($SpecifiedMeasure)} = $SupportedComparisonMeasuresNameMap{lc($SpecifiedMeasure)}; + } + + $OptionsInfo{VectorComparisonMode} = $Options{vectorcomparisonmode}; + $OptionsInfo{SpecifiedVectorComparisonsRef} = \@SpecifiedComparisonMeasures; + $OptionsInfo{SpecifiedVectorComparisonsNameRef} = \%SpecifiedComparisonMeasuresNameMap; + $OptionsInfo{SpecifiedVectorComparisonsMethodRef} = \%SpecifiedComparisonMeasuresMethodMap; + + # Setup specified vector comparison calculation modes... + my(@SpecifiedVectorComparisonModes); + @SpecifiedVectorComparisonModes = (); + if ($Options{vectorcomparisonformulism} =~ /^All$/i) { + push @SpecifiedVectorComparisonModes, ("AlgebraicForm", "BinaryForm", "SetTheoreticForm"); + } + else { + my($SpecifiedFormulism, @SpecifiedFormulismWords); + + @SpecifiedFormulismWords = split /\,/, $Options{vectorcomparisonformulism}; + for $SpecifiedFormulism (@SpecifiedFormulismWords) { + if ($SpecifiedFormulism !~ /^(AlgebraicForm|BinaryForm|SetTheoreticForm)$/i) { + die "Error: The value specified, $SpecifiedFormulism, for option \"--VectorComparisonFormulism\" is not valid. Allowed values: AlgebraicForm, BinaryForm or SetTheoreticForm\n"; + } + push @SpecifiedVectorComparisonModes, $SpecifiedFormulism; + } + } + $OptionsInfo{VectorComparisonFormulism} = $Options{vectorcomparisonformulism}; + $OptionsInfo{SpecifiedVectorComparisonModesRef} = \@SpecifiedVectorComparisonModes; + + # Setup any parameters required for specified comparison menthod... + for $SpecifiedMeasure (@SpecifiedComparisonMeasures) { + @{$SpecifiedComparisonMeasuresParameterMap{lc($SpecifiedMeasure)}} = (); + push @{$SpecifiedComparisonMeasuresParameterMap{lc($SpecifiedMeasure)}}, ($Options{fast} ? 1 : 0); + } + $OptionsInfo{SpecifiedVectorComparisonsParameterRef} = \%SpecifiedComparisonMeasuresParameterMap; +} + +# Setup script usage and retrieve command line arguments specified using various options... +sub SetupScriptUsage { + + # Retrieve all the options... + %Options = (); + + $Options{alpha} = 0.5; + $Options{beta} = 1; + + $Options{bitvectorcomparisonmode} = "TanimotoSimilarity"; + + $Options{colmode} = 'colnum'; + + $Options{compoundidprefix} = 'Cmpd'; + $Options{compoundidmode} = 'LabelPrefix'; + + $Options{detail} = 1; + + $Options{indelim} = 'comma'; + $Options{outdelim} = 'comma'; + + $Options{inputdatamode} = 'LoadInMemory'; + + $Options{mode} = 'AutoDetect'; + + $Options{outmatrixformat} = 'RowsAndColumns'; + + $Options{outmatrixtype} = 'FullMatrix'; + + $Options{quote} = 'yes'; + $Options{precision} = 2; + + $Options{vectorcomparisonmode} = "TanimotoSimilarity"; + $Options{vectorcomparisonformulism} = "AlgebraicForm"; + + if (!GetOptions(\%Options, "alpha=f", "beta=f", "bitvectorcomparisonmode|b=s", "colmode|c=s", "compoundidcol=s", "compoundidprefix=s", "compoundidfield=s", "compoundidmode=s", "detail|d=i", "fast|f", "fingerprintscol=s", "fingerprintsfield=s", "help|h", "indelim=s", "inputdatamode=s", "mode|m=s", "outdelim=s", "overwrite|o", "outmatrixformat=s", "outmatrixtype=s", "precision|p=s", "quote|q=s", "root|r=s", "vectorcomparisonmode|v=s", "vectorcomparisonformulism=s", "workingdir|w=s")) { + die "\nTo get a list of valid options and their values, use \"$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}: $! \n"; + } + if ($Options{colmode} !~ /^(ColNum|ColLabel)$/i) { + die "Error: The value specified, $Options{colmode}, for option \"-c, --ColMode\" is not valid. Allowed values: ColNum, or ColLabel\n"; + } + if ($Options{compoundidmode} !~ /^(DataField|MolName|LabelPrefix|MolNameOrLabelPrefix)$/i) { + die "Error: The value specified, $Options{compoundidmode}, for option \"--CompoundIDMode\" is not valid. Allowed values: DataField, MolName, LabelPrefix or MolNameOrLabelPrefix\n"; + } + if (!IsPositiveInteger($Options{detail})) { + die "Error: The value specified, $Options{detail}, for option \"-d, --detail\" is not valid. Allowed values: > 0 \n"; + } + if ($Options{inputdatamode} !~ /^(LoadInMemory|ScanFile)$/i) { + die "Error: The value specified, $Options{inputdatamode}, for option \"--InputDataMode\" is not valid. Allowed values: LoadInMemory or ScanFile\n"; + } + if ($Options{mode} !~ /^(AutoDetect|FingerprintsBitVectorString|FingerprintsVectorString)$/i) { + die "Error: The value specified, $Options{mode}, for option \"-m, --mode\" is not valid. Allowed values: AutoDetect, FingerprintsBitVectorString or FingerprintsVectorString \n"; + } + if ($Options{indelim} !~ /^(comma|semicolon)$/i) { + die "Error: The value specified, $Options{indelim}, for option \"--InDelim\" is not valid. Allowed values: comma, or semicolon\n"; + } + if ($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{outmatrixformat} !~ /^(RowsAndColumns|IDPairsAndValue)$/i) { + die "Error: The value specified, $Options{outmatrixformat}, for option \"--OutMatrixFormat\" is not valid. Allowed values: RowsAndColumns or IDPairsAndValue\n"; + } + if ($Options{outmatrixtype} !~ /^(FullMatrix|UpperTriangularMatrix|LowerTriangularMatrix)$/i) { + die "Error: The value specified, $Options{outmatrixtype}, for option \"--OutMatrixType\" is not valid. Allowed values: FullMatrix, UpperTriangularMatrix or LowerTriangularMatrix\n"; + } + if ($Options{quote} !~ /^(Yes|No)$/i) { + die "Error: The value specified, $Options{quote}, for option \"-q --quote\" is not valid. Allowed values: Yes or No\n"; + } + if (!IsPositiveInteger($Options{precision})) { + die "Error: The value specified, $Options{precision}, for option \"--precision\" is not valid. Allowed values: > 0 \n"; + } +} + +__END__ + +=head1 NAME + +SimilarityMatricesFingerprints.pl - Calculate similarity matrices using fingerprints strings data in SD, FP and CSV/TSV text file(s) + +=head1 SYNOPSIS + +SimilarityMatricesFingerprints.pl SDFile(s) FPFile(s) TextFile(s)... + +SimilarityMatricesFingerprints.pl [B<--alpha> I<number>] [B<--beta> I<number>] +[B<-b, --BitVectorComparisonMode> I<All | "TanimotoSimilarity,[ TverskySimilarity, ... ]">] +[B<-c, --ColMode> I<ColNum | ColLabel>] [B<--CompoundIDCol> I<col number | col name>] +[B<--CompoundIDPrefix> I<text>] [B<--CompoundIDField> I<DataFieldName>] +[B<--CompoundIDMode> I<DataField | MolName | LabelPrefix | MolNameOrLabelPrefix>] +[B<-d, --detail> I<InfoLevel>] [B<-f, --fast>] [B<--FingerprintsCol> I<col number | col name>] +[B<--FingerprintsField> I<FieldLabel>] [B<-h, --help>] [B<--InDelim> I<comma | semicolon>] +[B<--InputDataMode> I<LoadInMemory | ScanFile>] +[B<-m, --mode> I<AutoDetect | FingerprintsBitVectorString | FingerprintsVectorString>] +[B<--OutDelim> I<comma | tab | semicolon>] [B<--OutMatrixFormat> I<RowsAndColumns | IDPairsAndValue>] +[B<--OutMatrixType> I<FullMatrix | UpperTriangularMatrix | LowerTriangularMatrix>] +[B<-o, --overwrite>] [B<-p, --precision> I<number>] +[B<-q, --quote> I<Yes | No>] [B<-r, --root> I<RootName>] +[B<-v, --VectorComparisonMode> I<All | "TanimotoSimilairy, [ ManhattanDistance, ...]">] +[B<--VectorComparisonFormulism> I<All | "AlgebraicForm, [BinaryForm, SetTheoreticForm]">] +[B<-w, --WorkingDir> dirname] SDFile(s) FPFile(s) TextFile(s)... + +=head1 DESCRIPTION + +Calculate similarity matrices using fingerprint bit-vector or vector strings data in I<SD, FP +and CSV/TSV> text file(s) and generate CSV/TSV text file(s) containing values for specified +similarity and distance coefficients. + +The scripts SimilarityMatrixSDFiles.pl and SimilarityMatrixTextFiles.pl have been removed from the +current release of MayaChemTools and their functionality merged with this script. + +The valid I<SDFile> extensions are I<.sdf> and I<.sd>. All SD files in a current directory +can be specified either by I<*.sdf> or the current directory name. + +The valid I<FPFile> extensions are I<.fpf> and I<.fp>. All FP files in a current directory +can be specified either by I<*.fpf> or the current directory name. + +The valid I<TextFile> extensions are I<.csv> and I<.tsv> for comma/semicolon and tab +delimited text files respectively. All other file names are ignored. All text files in a +current directory can be specified by I<*.csv>, I<*.tsv>, or the current directory +name. The B<--indelim> option determines the format of I<TextFile(s)>. Any file +which doesn't correspond to the format indicated by B<--indelim> option is ignored. + +Example of I<FP> file containing fingerprints bit-vector string data: + + # + # Package = MayaChemTools 7.4 + # ReleaseDate = Oct 21, 2010 + # + # TimeStamp = Mon Mar 7 15:14:01 2011 + # + # FingerprintsStringType = FingerprintsBitVector + # + # Description = PathLengthBits:AtomicInvariantsAtomTypes:MinLength1:... + # Size = 1024 + # BitStringFormat = HexadecimalString + # BitsOrder = Ascending + # + Cmpd1 9c8460989ec8a49913991a6603130b0a19e8051c89184414953800cc21510... + Cmpd2 000000249400840040100042011001001980410c000000001010088001120... + ... ... + ... .. + +Example of I<FP> file containing fingerprints vector string data: + + # + # Package = MayaChemTools 7.4 + # ReleaseDate = Oct 21, 2010 + # + # TimeStamp = Mon Mar 7 15:14:01 2011 + # + # FingerprintsStringType = FingerprintsVector + # + # Description = PathLengthBits:AtomicInvariantsAtomTypes:MinLength1:... + # VectorStringFormat = IDsAndValuesString + # VectorValuesType = NumericalValues + # + Cmpd1 338;C F N O C:C C:N C=O CC CF CN CO C:C:C C:C:N C:CC C:CF C:CN C: + N:C C:NC CC:N CC=O CCC CCN CCO CNC NC=O O=CO C:C:C:C C:C:C:N C:C:CC...; + 33 1 2 5 21 2 2 12 1 3 3 20 2 10 2 2 1 2 2 2 8 2 5 1 1 1 19 2 8 2 2 2 2 + 6 2 2 2 2 2 2 2 2 3 2 2 1 4 1 5 1 1 18 6 2 2 1 2 10 2 1 2 1 2 2 2 2 ... + Cmpd2 103;C N O C=N C=O CC CN CO CC=O CCC CCN CCO CNC N=CN NC=O NCN O=C + O C CC=O CCCC CCCN CCCO CCNC CNC=N CNC=O CNCN CCCC=O CCCCC CCCCN CC...; + 15 4 4 1 2 13 5 2 2 15 5 3 2 2 1 1 1 2 17 7 6 5 1 1 1 2 15 8 5 7 2 2 2 2 + 1 2 1 1 3 15 7 6 8 3 4 4 3 2 2 1 2 3 14 2 4 7 4 4 4 4 1 1 1 2 1 1 1 ... + ... ... + ... ... + +Example of I<SD> file containing fingerprints bit-vector string data: + + ... ... + ... ... + $$$$ + ... ... + ... ... + ... ... + 41 44 0 0 0 0 0 0 0 0999 V2000 + -3.3652 1.4499 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 + ... ... + 2 3 1 0 0 0 0 + ... ... + M END + > <CmpdID> + Cmpd1 + + > <PathLengthFingerprints> + FingerprintsBitVector;PathLengthBits:AtomicInvariantsAtomTypes:MinLengt + h1:MaxLength8;1024;HexadecimalString;Ascending;9c8460989ec8a49913991a66 + 03130b0a19e8051c89184414953800cc2151082844a201042800130860308e8204d4028 + 00831048940e44281c00060449a5000ac80c894114e006321264401600846c050164462 + 08190410805000304a10205b0100e04c0038ba0fad0209c0ca8b1200012268b61c0026a + aa0660a11014a011d46 + + $$$$ + ... ... + ... ... + +Example of CSV I<Text> file containing fingerprints bit-vector string data: + + "CompoundID","PathLengthFingerprints" + "Cmpd1","FingerprintsBitVector;PathLengthBits:AtomicInvariantsAtomTypes + :MinLength1:MaxLength8;1024;HexadecimalString;Ascending;9c8460989ec8a4 + 9913991a6603130b0a19e8051c89184414953800cc2151082844a20104280013086030 + 8e8204d402800831048940e44281c00060449a5000ac80c894114e006321264401..." + ... ... + ... ... + +The current release of MayaChemTools supports the following types of fingerprint +bit-vector and vector strings: + + FingerprintsVector;AtomNeighborhoods:AtomicInvariantsAtomTypes:MinRadi + us0:MaxRadius2;41;AlphaNumericalValues;ValuesString;NR0-C.X1.BO1.H3-AT + C1:NR1-C.X3.BO3.H1-ATC1:NR2-C.X1.BO1.H3-ATC1:NR2-C.X3.BO4-ATC1 NR0-C.X + 1.BO1.H3-ATC1:NR1-C.X3.BO3.H1-ATC1:NR2-C.X1.BO1.H3-ATC1:NR2-C.X3.BO4-A + TC1 NR0-C.X2.BO2.H2-ATC1:NR1-C.X2.BO2.H2-ATC1:NR1-C.X3.BO3.H1-ATC1:NR2 + -C.X2.BO2.H2-ATC1:NR2-N.X3.BO3-ATC1:NR2-O.X1.BO1.H1-ATC1 NR0-C.X2.B... + + FingerprintsVector;AtomTypesCount:AtomicInvariantsAtomTypes:ArbitraryS + ize;10;NumericalValues;IDsAndValuesString;C.X1.BO1.H3 C.X2.BO2.H2 C.X2 + .BO3.H1 C.X3.BO3.H1 C.X3.BO4 F.X1.BO1 N.X2.BO2.H1 N.X3.BO3 O.X1.BO1.H1 + O.X1.BO2;2 4 14 3 10 1 1 1 3 2 + + FingerprintsVector;AtomTypesCount:SLogPAtomTypes:ArbitrarySize;16;Nume + ricalValues;IDsAndValuesString;C1 C10 C11 C14 C18 C20 C21 C22 C5 CS F + N11 N4 O10 O2 O9;5 1 1 1 14 4 2 1 2 2 1 1 1 1 3 1 + + FingerprintsVector;AtomTypesCount:SLogPAtomTypes:FixedSize;67;OrderedN + umericalValues;IDsAndValuesString;C1 C2 C3 C4 C5 C6 C7 C8 C9 C10 C11 C + 12 C13 C14 C15 C16 C17 C18 C19 C20 C21 C22 C23 C24 C25 C26 C27 CS N1 N + 2 N3 N4 N5 N6 N7 N8 N9 N10 N11 N12 N13 N14 NS O1 O2 O3 O4 O5 O6 O7 O8 + O9 O10 O11 O12 OS F Cl Br I Hal P S1 S2 S3 Me1 Me2;5 0 0 0 2 0 0 0 0 1 + 1 0 0 1 0 0 0 14 0 4 2 1 0 0 0 0 0 2 0 0 0 1 0 0 0 0 0 0 1 0 0 0 0... + + FingerprintsVector;EStateIndicies:ArbitrarySize;11;NumericalValues;IDs + AndValuesString;SaaCH SaasC SaasN SdO SdssC SsCH3 SsF SsOH SssCH2 SssN + H SsssCH;24.778 4.387 1.993 25.023 -1.435 3.975 14.006 29.759 -0.073 3 + .024 -2.270 + + FingerprintsVector;EStateIndicies:FixedSize;87;OrderedNumericalValues; + ValuesString;0 0 0 0 0 0 0 3.975 0 -0.073 0 0 24.778 -2.270 0 0 -1.435 + 4.387 0 0 0 0 0 0 3.024 0 0 0 0 0 0 0 1.993 0 29.759 25.023 0 0 0 0 1 + 4.006 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 + 0 0 0 0 0 0 0 0 0 0 0 0 0 0 + + FingerprintsVector;ExtendedConnectivity:AtomicInvariantsAtomTypes:Radi + us2;60;AlphaNumericalValues;ValuesString;73555770 333564680 352413391 + 666191900 1001270906 1371674323 1481469939 1977749791 2006158649 21414 + 08799 49532520 64643108 79385615 96062769 273726379 564565671 85514103 + 5 906706094 988546669 1018231313 1032696425 1197507444 1331250018 1338 + 532734 1455473691 1607485225 1609687129 1631614296 1670251330 17303... + + FingerprintsVector;ExtendedConnectivityCount:AtomicInvariantsAtomTypes + :Radius2;60;NumericalValues;IDsAndValuesString;73555770 333564680 3524 + 13391 666191900 1001270906 1371674323 1481469939 1977749791 2006158649 + 2141408799 49532520 64643108 79385615 96062769 273726379 564565671...; + 3 2 1 1 14 1 2 10 4 3 1 1 1 1 2 1 2 1 1 1 2 3 1 1 2 1 3 3 8 2 2 2 6 2 + 1 2 1 1 2 1 1 1 2 1 1 2 1 2 1 1 1 1 1 1 1 1 1 2 1 1 + + FingerprintsBitVector;ExtendedConnectivityBits:AtomicInvariantsAtomTyp + es:Radius2;1024;BinaryString;Ascending;0000000000000000000000000000100 + 0000000001010000000110000011000000000000100000000000000000000000100001 + 1000000110000000000000000000000000010011000000000000000000000000010000 + 0000000000000000000000000010000000000000000001000000000000000000000000 + 0000000000010000100001000000000000101000000000000000100000000000000... + + FingerprintsVector;ExtendedConnectivity:FunctionalClassAtomTypes:Radiu + s2;57;AlphaNumericalValues;ValuesString;24769214 508787397 850393286 8 + 62102353 981185303 1231636850 1649386610 1941540674 263599683 32920567 + 1 571109041 639579325 683993318 723853089 810600886 885767127 90326012 + 7 958841485 981022393 1126908698 1152248391 1317567065 1421489994 1455 + 632544 1557272891 1826413669 1983319256 2015750777 2029559552 20404... + + FingerprintsVector;ExtendedConnectivity:EStateAtomTypes:Radius2;62;Alp + haNumericalValues;ValuesString;25189973 528584866 662581668 671034184 + 926543080 1347067490 1738510057 1759600920 2034425745 2097234755 21450 + 44754 96779665 180364292 341712110 345278822 386540408 387387308 50430 + 1706 617094135 771528807 957666640 997798220 1158349170 1291258082 134 + 1138533 1395329837 1420277211 1479584608 1486476397 1487556246 1566... + + FingerprintsBitVector;MACCSKeyBits;166;BinaryString;Ascending;00000000 + 0000000000000000000000000000000001001000010010000000010010000000011100 + 0100101010111100011011000100110110000011011110100110111111111111011111 + 11111111111110111000 + + FingerprintsBitVector;MACCSKeyBits;322;BinaryString;Ascending;11101011 + 1110011111100101111111000111101100110000000000000011100010000000000000 + 0000000000000000000000000000000000000000000000101000000000000000000000 + 0000000000000000000000000000000000000000000000000000000000000000000000 + 0000000000000000000000000000000000000011000000000000000000000000000000 + 0000000000000000000000000000000000000000 + + FingerprintsVector;MACCSKeyCount;166;OrderedNumericalValues;ValuesStri + ng;0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 + 0 0 0 0 0 0 0 1 0 0 3 0 0 0 0 4 0 0 2 0 0 0 0 0 0 0 0 2 0 0 2 0 0 0 0 + 0 0 0 0 1 1 8 0 0 0 1 0 0 1 0 1 0 1 0 3 1 3 1 0 0 0 1 2 0 11 1 0 0 0 + 5 0 0 1 2 0 1 1 0 0 0 0 0 1 1 0 1 1 1 1 0 4 0 0 1 1 0 4 6 1 1 1 2 1 1 + 3 5 2 2 0 5 3 5 1 1 2 5 1 2 1 2 4 8 3 5 5 2 2 0 3 5 4 1 + + FingerprintsVector;MACCSKeyCount;322;OrderedNumericalValues;ValuesStri + ng;14 8 2 0 2 0 4 4 2 1 4 0 0 2 5 10 5 2 1 0 0 2 0 5 13 3 28 5 5 3 0 0 + 0 4 2 1 1 0 1 1 0 0 2 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 22 5 3 0 0 0 1 0 + 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 + 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 11 0 2 0 0 0 0 0 0 0 0 0 + 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 ... + + FingerprintsBitVector;PathLengthBits:AtomicInvariantsAtomTypes:MinLeng + th1:MaxLength8;1024;BinaryString;Ascending;001000010011010101011000110 + 0100010101011000101001011100110001000010001001101000001001001001001000 + 0010110100000111001001000001001010100100100000000011000000101001011100 + 0010000001000101010100000100111100110111011011011000000010110111001101 + 0101100011000000010001000011000010100011101100001000001000100000000... + + FingerprintsVector;PathLengthCount:AtomicInvariantsAtomTypes:MinLength + 1:MaxLength8;432;NumericalValues;IDsAndValuesPairsString;C.X1.BO1.H3 2 + C.X2.BO2.H2 4 C.X2.BO3.H1 14 C.X3.BO3.H1 3 C.X3.BO4 10 F.X1.BO1 1 N.X + 2.BO2.H1 1 N.X3.BO3 1 O.X1.BO1.H1 3 O.X1.BO2 2 C.X1.BO1.H3C.X3.BO3.H1 + 2 C.X2.BO2.H2C.X2.BO2.H2 1 C.X2.BO2.H2C.X3.BO3.H1 4 C.X2.BO2.H2C.X3.BO + 4 1 C.X2.BO2.H2N.X3.BO3 1 C.X2.BO3.H1:C.X2.BO3.H1 10 C.X2.BO3.H1:C.... + + FingerprintsVector;PathLengthCount:MMFF94AtomTypes:MinLength1:MaxLengt + h8;463;NumericalValues;IDsAndValuesPairsString;C5A 2 C5B 2 C=ON 1 CB 1 + 8 COO 1 CR 9 F 1 N5 1 NC=O 1 O=CN 1 O=CO 1 OC=O 1 OR 2 C5A:C5B 2 C5A:N + 5 2 C5ACB 1 C5ACR 1 C5B:C5B 1 C5BC=ON 1 C5BCB 1 C=ON=O=CN 1 C=ONNC=O 1 + CB:CB 18 CBF 1 CBNC=O 1 COO=O=CO 1 COOCR 1 COOOC=O 1 CRCR 7 CRN5 1 CR + OR 2 C5A:C5B:C5B 2 C5A:C5BC=ON 1 C5A:C5BCB 1 C5A:N5:C5A 1 C5A:N5CR ... + + FingerprintsVector;TopologicalAtomPairs:AtomicInvariantsAtomTypes:MinD + istance1:MaxDistance10;223;NumericalValues;IDsAndValuesString;C.X1.BO1 + .H3-D1-C.X3.BO3.H1 C.X2.BO2.H2-D1-C.X2.BO2.H2 C.X2.BO2.H2-D1-C.X3.BO3. + H1 C.X2.BO2.H2-D1-C.X3.BO4 C.X2.BO2.H2-D1-N.X3.BO3 C.X2.BO3.H1-D1-...; + 2 1 4 1 1 10 8 1 2 6 1 2 2 1 2 1 2 2 1 2 1 5 1 10 12 2 2 1 2 1 9 1 3 1 + 1 1 2 2 1 3 6 1 6 14 2 2 2 3 1 3 1 8 2 2 1 3 2 6 1 2 2 5 1 3 1 23 1... + + FingerprintsVector;TopologicalAtomPairs:FunctionalClassAtomTypes:MinDi + stance1:MaxDistance10;144;NumericalValues;IDsAndValuesString;Ar-D1-Ar + Ar-D1-Ar.HBA Ar-D1-HBD Ar-D1-Hal Ar-D1-None Ar.HBA-D1-None HBA-D1-NI H + BA-D1-None HBA.HBD-D1-NI HBA.HBD-D1-None HBD-D1-None NI-D1-None No...; + 23 2 1 1 2 1 1 1 1 2 1 1 7 28 3 1 3 2 8 2 1 1 1 5 1 5 24 3 3 4 2 13 4 + 1 1 4 1 5 22 4 4 3 1 19 1 1 1 1 1 2 2 3 1 1 8 25 4 5 2 3 1 26 1 4 1 ... + + FingerprintsVector;TopologicalAtomTorsions:AtomicInvariantsAtomTypes;3 + 3;NumericalValues;IDsAndValuesString;C.X1.BO1.H3-C.X3.BO3.H1-C.X3.BO4- + C.X3.BO4 C.X1.BO1.H3-C.X3.BO3.H1-C.X3.BO4-N.X3.BO3 C.X2.BO2.H2-C.X2.BO + 2.H2-C.X3.BO3.H1-C.X2.BO2.H2 C.X2.BO2.H2-C.X2.BO2.H2-C.X3.BO3.H1-O...; + 2 2 1 1 2 2 1 1 3 4 4 8 4 2 2 6 2 2 1 2 1 1 2 1 1 2 6 2 4 2 1 3 1 + + FingerprintsVector;TopologicalAtomTorsions:EStateAtomTypes;36;Numerica + lValues;IDsAndValuesString;aaCH-aaCH-aaCH-aaCH aaCH-aaCH-aaCH-aasC aaC + H-aaCH-aasC-aaCH aaCH-aaCH-aasC-aasC aaCH-aaCH-aasC-sF aaCH-aaCH-aasC- + ssNH aaCH-aasC-aasC-aasC aaCH-aasC-aasC-aasN aaCH-aasC-ssNH-dssC a...; + 4 4 8 4 2 2 6 2 2 2 4 3 2 1 3 3 2 2 2 1 2 1 1 1 2 1 1 1 1 1 1 1 2 1 1 2 + + FingerprintsVector;TopologicalAtomTriplets:AtomicInvariantsAtomTypes:M + inDistance1:MaxDistance10;3096;NumericalValues;IDsAndValuesString;C.X1 + .BO1.H3-D1-C.X1.BO1.H3-D1-C.X3.BO3.H1-D2 C.X1.BO1.H3-D1-C.X2.BO2.H2-D1 + 0-C.X3.BO4-D9 C.X1.BO1.H3-D1-C.X2.BO2.H2-D3-N.X3.BO3-D4 C.X1.BO1.H3-D1 + -C.X2.BO2.H2-D4-C.X2.BO2.H2-D5 C.X1.BO1.H3-D1-C.X2.BO2.H2-D6-C.X3....; + 1 2 2 2 2 2 2 2 8 8 4 8 4 4 2 2 2 2 4 2 2 2 4 2 2 2 2 1 2 2 4 4 4 2 2 + 2 4 4 4 8 4 4 2 4 4 4 2 4 4 2 2 2 2 2 2 2 2 1 2 2 2 2 2 2 2 2 2 2 8... + + FingerprintsVector;TopologicalAtomTriplets:SYBYLAtomTypes:MinDistance1 + :MaxDistance10;2332;NumericalValues;IDsAndValuesString;C.2-D1-C.2-D9-C + .3-D10 C.2-D1-C.2-D9-C.ar-D10 C.2-D1-C.3-D1-C.3-D2 C.2-D1-C.3-D10-C.3- + D9 C.2-D1-C.3-D2-C.3-D3 C.2-D1-C.3-D2-C.ar-D3 C.2-D1-C.3-D3-C.3-D4 C.2 + -D1-C.3-D3-N.ar-D4 C.2-D1-C.3-D3-O.3-D2 C.2-D1-C.3-D4-C.3-D5 C.2-D1-C. + 3-D5-C.3-D6 C.2-D1-C.3-D5-O.3-D4 C.2-D1-C.3-D6-C.3-D7 C.2-D1-C.3-D7... + + 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;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 ... + +=head1 OPTIONS + +=over 4 + +=item B<--alpha> I<number> + +Value of alpha parameter for calculating I<Tversky> similarity coefficient specified for +B<-b, --BitVectorComparisonMode> option. It corresponds to weights assigned for bits set +to "1" in a pair of fingerprint bit-vectors during the calculation of similarity coefficient. Possible +values: I<0 to 1>. Default value: <0.5>. + +=item B<--beta> I<number> + +Value of beta parameter for calculating I<WeightedTanimoto> and I<WeightedTversky> +similarity coefficients specified for B<-b, --BitVectorComparisonMode> option. It is used to +weight the contributions of bits set to "0" during the calculation of similarity coefficients. Possible +values: I<0 to 1>. Default value of <1> makes I<WeightedTanimoto> and I<WeightedTversky> +equivalent to I<Tanimoto> and I<Tversky>. + +=item B<-b, --BitVectorComparisonMode> I<All | "TanimotoSimilarity,[TverskySimilarity,...]"> + +Specify what similarity coefficients to use for calculating similarity matrices for fingerprints bit-vector +strings data values in I<TextFile(s)>: calculate similarity matrices for all supported similarity +coefficients or specify a comma delimited list of similarity coefficients. Possible values: +I<All | "TanimotoSimilarity,[TverskySimilarity,...]>. Default: I<TanimotoSimilarity> + +I<All> uses complete list of supported similarity coefficients: I<BaroniUrbaniSimilarity, BuserSimilarity, +CosineSimilarity, DiceSimilarity, DennisSimilarity, ForbesSimilarity, FossumSimilarity, HamannSimilarity, JacardSimilarity, +Kulczynski1Similarity, Kulczynski2Similarity, MatchingSimilarity, McConnaugheySimilarity, OchiaiSimilarity, +PearsonSimilarity, RogersTanimotoSimilarity, RussellRaoSimilarity, SimpsonSimilarity, SkoalSneath1Similarity, +SkoalSneath2Similarity, SkoalSneath3Similarity, TanimotoSimilarity, TverskySimilarity, YuleSimilarity, +WeightedTanimotoSimilarity, WeightedTverskySimilarity>. These similarity coefficients are described below. + +For two fingerprint bit-vectors A and B of same size, let: + + Na = Number of bits set to "1" in A + Nb = Number of bits set to "1" in B + Nc = Number of bits set to "1" in both A and B + Nd = Number of bits set to "0" in both A and B + + Nt = Number of bits set to "1" or "0" in A or B (Size of A or B) + Nt = Na + Nb - Nc + Nd + + Na - Nc = Number of bits set to "1" in A but not in B + Nb - Nc = Number of bits set to "1" in B but not in A + +Then, various similarity coefficients [ Ref. 40 - 42 ] for a pair of bit-vectors A and B are +defined as follows: + +I<BaroniUrbaniSimilarity>: ( SQRT( Nc * Nd ) + Nc ) / ( SQRT ( Nc * Nd ) + Nc + ( Na - Nc ) + ( Nb - Nc ) ) ( same as Buser ) + +I<BuserSimilarity>: ( SQRT ( Nc * Nd ) + Nc ) / ( SQRT ( Nc * Nd ) + Nc + ( Na - Nc ) + ( Nb - Nc ) ) ( same as BaroniUrbani ) + +I<CosineSimilarity>: Nc / SQRT ( Na * Nb ) (same as Ochiai) + +I<DiceSimilarity>: (2 * Nc) / ( Na + Nb ) + +I<DennisSimilarity>: ( Nc * Nd - ( ( Na - Nc ) * ( Nb - Nc ) ) ) / SQRT ( Nt * Na * Nb) + +I<ForbesSimilarity>: ( Nt * Nc ) / ( Na * Nb ) + +I<FossumSimilarity>: ( Nt * ( ( Nc - 1/2 ) ** 2 ) / ( Na * Nb ) + +I<HamannSimilarity>: ( ( Nc + Nd ) - ( Na - Nc ) - ( Nb - Nc ) ) / Nt + +I<JaccardSimilarity>: Nc / ( ( Na - Nc) + ( Nb - Nc ) + Nc ) = Nc / ( Na + Nb - Nc ) (same as Tanimoto) + +I<Kulczynski1Similarity>: Nc / ( ( Na - Nc ) + ( Nb - Nc) ) = Nc / ( Na + Nb - 2Nc ) + +I<Kulczynski2Similarity>: ( ( Nc / 2 ) * ( 2 * Nc + ( Na - Nc ) + ( Nb - Nc) ) ) / ( ( Nc + ( Na - Nc ) ) * ( Nc + ( Nb - Nc ) ) ) = 0.5 * ( Nc / Na + Nc / Nb ) + +I<MatchingSimilarity>: ( Nc + Nd ) / Nt + +I<McConnaugheySimilarity>: ( Nc ** 2 - ( Na - Nc ) * ( Nb - Nc) ) / ( Na * Nb ) + +I<OchiaiSimilarity>: Nc / SQRT ( Na * Nb ) (same as Cosine) + +I<PearsonSimilarity>: ( ( Nc * Nd ) - ( ( Na - Nc ) * ( Nb - Nc ) ) / SQRT ( Na * Nb * ( Na - Nc + Nd ) * ( Nb - Nc + Nd ) ) + +I<RogersTanimotoSimilarity>: ( Nc + Nd ) / ( ( Na - Nc) + ( Nb - Nc) + Nt) = ( Nc + Nd ) / ( Na + Nb - 2Nc + Nt) + +I<RussellRaoSimilarity>: Nc / Nt + +I<SimpsonSimilarity>: Nc / MIN ( Na, Nb) + +I<SkoalSneath1Similarity>: Nc / ( Nc + 2 * ( Na - Nc) + 2 * ( Nb - Nc) ) = Nc / ( 2 * Na + 2 * Nb - 3 * Nc ) + +I<SkoalSneath2Similarity>: ( 2 * Nc + 2 * Nd ) / ( Nc + Nd + Nt ) + +I<SkoalSneath3Similarity>: ( Nc + Nd ) / ( ( Na - Nc ) + ( Nb - Nc ) ) = ( Nc + Nd ) / ( Na + Nb - 2 * Nc ) + +I<TanimotoSimilarity>: Nc / ( ( Na - Nc) + ( Nb - Nc ) + Nc ) = Nc / ( Na + Nb - Nc ) (same as Jaccard) + +I<TverskySimilarity>: Nc / ( alpha * ( Na - Nc ) + ( 1 - alpha) * ( Nb - Nc) + Nc ) = Nc / ( alpha * ( Na - Nb ) + Nb) + +I<YuleSimilarity>: ( ( Nc * Nd ) - ( ( Na - Nc ) * ( Nb - Nc ) ) ) / ( ( Nc * Nd ) + ( ( Na - Nc ) * ( Nb - Nc ) ) ) + +Values of Tanimoto/Jaccard and Tversky coefficients are dependent on only those bit which +are set to "1" in both A and B. In order to take into account all bit positions, modified versions +of Tanimoto [ Ref. 42 ] and Tversky [ Ref. 43 ] have been developed. + +Let: + + Na' = Number of bits set to "0" in A + Nb' = Number of bits set to "0" in B + Nc' = Number of bits set to "0" in both A and B + +Tanimoto': Nc' / ( ( Na' - Nc') + ( Nb' - Nc' ) + Nc' ) = Nc' / ( Na' + Nb' - Nc' ) + +Tversky': Nc' / ( alpha * ( Na' - Nc' ) + ( 1 - alpha) * ( Nb' - Nc' ) + Nc' ) = Nc' / ( alpha * ( Na' - Nb' ) + Nb') + +Then: + +I<WeightedTanimotoSimilarity> = beta * Tanimoto + (1 - beta) * Tanimoto' + +I<WeightedTverskySimilarity> = beta * Tversky + (1 - beta) * Tversky' + +=item B<-c, --ColMode> I<ColNum | ColLabel> + +Specify how columns are identified in I<TextFile(s)>: using column number or column +label. Possible values: I<ColNum or ColLabel>. Default value: I<ColNum>. + +=item B<--CompoundIDCol> I<col number | col name> + +This value is B<-c, --ColMode> mode specific. It specifies input I<TextFile(s)> column to use for +generating compound ID for similarity matrices in output I<TextFile(s)>. Possible values: I<col number +or col label>. Default value: I<first column containing the word compoundID in its column label or sequentially +generated IDs>. + +=item B<--CompoundIDPrefix> I<text> + +Specify compound ID prefix to use during sequential generation of compound IDs for input I<SDFile(s)> +and I<TextFile(s)>. Default value: I<Cmpd>. The default value generates compound IDs which look +like Cmpd<Number>. + +For input I<SDFile(s)>, this value is only used during I<LabelPrefix | MolNameOrLabelPrefix> values +of B<--CompoundIDMode> option; otherwise, it's ignored. + +Examples for I<LabelPrefix> or I<MolNameOrLabelPrefix> value of B<--CompoundIDMode>: + + Compound + +The values specified above generates compound IDs which correspond to Compound<Number> +instead of default value of Cmpd<Number>. + +=item B<--CompoundIDField> I<DataFieldName> + +Specify input I<SDFile(s)> datafield label for generating compound IDs. This value is only used +during I<DataField> value of B<--CompoundIDMode> option. + +Examples for I<DataField> value of B<--CompoundIDMode>: + + MolID + ExtReg + +=item B<--CompoundIDMode> I<DataField | MolName | LabelPrefix | MolNameOrLabelPrefix> + +Specify how to generate compound IDs from input I<SDFile(s)> for similarity matrix CSV/TSV text +file(s): use a I<SDFile(s)> datafield value; use molname line from I<SDFile(s)>; generate a sequential ID +with specific prefix; use combination of both MolName and LabelPrefix with usage of LabelPrefix values +for empty molname lines. + +Possible values: I<DataField | MolName | LabelPrefix | MolNameOrLabelPrefix>. +Default: I<LabelPrefix>. + +For I<MolNameAndLabelPrefix> value of B<--CompoundIDMode>, molname line in I<SDFile(s)> takes +precedence over sequential compound IDs generated using I<LabelPrefix> and only empty molname +values are replaced with sequential compound IDs. + +=item B<-d, --detail> I<InfoLevel> + +Level of information to print about lines being ignored. Default: I<1>. Possible values: +I<1, 2 or 3>. + +=item B<-f, --fast> + +In this mode, fingerprints columns specified using B<--FingerprintsCol> for I<TextFile(s)> and +B<--FingerprintsField> for I<SDFile(s)> are assumed to contain valid fingerprints data and no +checking is performed before calculating similarity matrices. By default, fingerprints data is +validated before computing pairwise similarity and distance coefficients. + +=item B<--FingerprintsCol> I<col number | col name> + +This value is B<-c, --colmode> specific. It specifies fingerprints column to use during +calculation similarity matrices for I<TextFile(s)>. Possible values: I<col number or col label>. +Default value: I<first column containing the word Fingerprints in its column label>. + +=item B<--FingerprintsField> I<FieldLabel> + +Fingerprints field label to use during calculation similarity matrices for I<SDFile(s)>. +Default value: I<first data field label containing the word Fingerprints in its label> + +=item B<-h, --help> + +Print this help message. + +=item B<--InDelim> I<comma | semicolon> + +Input delimiter for CSV I<TextFile(s)>. Possible values: I<comma or semicolon>. +Default value: I<comma>. For TSV files, this option is ignored and I<tab> is used as a +delimiter. + +=item B<--InputDataMode> I<LoadInMemory | ScanFile> + +Specify how fingerprints bit-vector or vector strings data from I<SD, FP and CSV/TSV> +fingerprint file(s) is processed: Retrieve, process and load all available fingerprints +data in memory; Retrieve and process data for fingerprints one at a time. Possible values +: I<LoadInMemory | ScanFile>. Default: I<LoadInMemory>. + +During I<LoadInMemory> value of B<--InputDataMode>, fingerprints bit-vector or vector +strings data from input file is retrieved, processed, and loaded into memory all at once +as fingerprints objects for generation for similarity matrices. + +During I<ScanFile> value of B<--InputDataMode>, multiple passes over the input fingerprints +file are performed to retrieve and process fingerprints bit-vector or vector strings data one at +a time to generate fingerprints objects used during generation of similarity matrices. A temporary +copy of the input fingerprints file is made at the start and deleted after generating the matrices. + +I<ScanFile> value of B<--InputDataMode> allows processing of arbitrary large fingerprints files +without any additional memory requirement. + +=item B<-m, --mode> I<AutoDetect | FingerprintsBitVectorString | FingerprintsVectorString> + +Format of fingerprint strings data in I<TextFile(s)>: automatically detect format of fingerprints +string created by MayaChemTools fingerprints generation scripts or explicitly specify its format. +Possible values: I<AutoDetect | FingerprintsBitVectorString | FingerprintsVectorString>. Default +value: I<AutoDetect>. + +=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<--OutMatrixFormat> I<RowsAndColumns | IDPairsAndValue> + +Specify how similarity or distance values calculated for fingerprints vector and bit-vector strings +are written to the output CSV/TSV text file(s): Generate text files containing rows and columns +with their labels corresponding to compound IDs and each matrix element value corresponding to +similarity or distance between corresponding compounds; Generate text files containing rows containing +compoundIDs for two compounds followed by similarity or distance value between these compounds. + +Possible values: I<RowsAndColumns, or IDPairsAndValue>. Default value: I<RowsAndColumns>. + +The value of B<--OutMatrixFormat> in conjunction with B<--OutMatrixType> determines type +of data written to output files and allows generation of up to 6 different output data formats: + + OutMatrixFormat OutMatrixType + + RowsAndColumns FullMatrix [ DEFAULT ] + RowsAndColumns UpperTriangularMatrix + RowsAndColumns LowerTriangularMatrix + + IDPairsAndValue FullMatrix + IDPairsAndValue UpperTriangularMatrix + IDPairsAndValue LowerTriangularMatrix + +Example of data in output file for I<RowsAndColumns> B<--OutMatrixFormat> value for +I<FullMatrix> valueof B<--OutMatrixType>: + + "","Cmpd1","Cmpd2","Cmpd3","Cmpd4","Cmpd5","Cmpd6",... ... + "Cmpd1","1","0.04","0.25","0.13","0.11","0.2",... ... + "Cmpd2","0.04","1","0.06","0.05","0.19","0.07",... ... + "Cmpd3","0.25","0.06","1","0.12","0.22","0.25",... ... + "Cmpd4","0.13","0.05","0.12","1","0.11","0.13",... ... + "Cmpd5","0.11","0.19","0.22","0.11","1","0.17",... ... + "Cmpd6","0.2","0.07","0.25","0.13","0.17","1",... ... + ... ... .. + ... ... .. + ... ... .. + +Example of data in output file for I<RowsAndColumns> B<--OutMatrixFormat> value for +I<UpperTriangularMatrix> value of B<--OutMatrixType>: + + "","Cmpd1","Cmpd2","Cmpd3","Cmpd4","Cmpd5","Cmpd6",... ... + "Cmpd1","1","0.04","0.25","0.13","0.11","0.2",... ... + "Cmpd2","1","0.06","0.05","0.19","0.07",... ... + "Cmpd3","1","0.12","0.22","0.25",... ... + "Cmpd4","1","0.11","0.13",... ... + "Cmpd5","1","0.17",... ... + "Cmpd6","1",... ... + ... ... .. + ... ... .. + ... ... .. + +Example of data in output file for I<RowsAndColumns> B<--OutMatrixFormat> value for +I<LowerTriangularMatrix> value of B<--OutMatrixType>: + + "","Cmpd1","Cmpd2","Cmpd3","Cmpd4","Cmpd5","Cmpd6",... ... + "Cmpd1","1" + "Cmpd2","0.04","1" + "Cmpd3","0.25","0.06","1" + "Cmpd4","0.13","0.05","0.12","1" + "Cmpd5","0.11","0.19","0.22","0.11","1" + "Cmpd6","0.2","0.07","0.25","0.13","0.17","1" + ... ... .. + ... ... .. + ... ... .. + + +Example of data in output file for I<IDPairsAndValue> B<--OutMatrixFormat> value for +<FullMatrix> value of B<OutMatrixType>: + + "CmpdID1","CmpdID2","Coefficient Value" + "Cmpd1","Cmpd1","1" + "Cmpd1","Cmpd2","0.04" + "Cmpd1","Cmpd3","0.25" + "Cmpd1","Cmpd4","0.13" + ... ... ... + ... ... ... + ... ... ... + "Cmpd2","Cmpd1","0.04" + "Cmpd2","Cmpd2","1" + "Cmpd2","Cmpd3","0.06" + "Cmpd2","Cmpd4","0.05" + ... ... ... + ... ... ... + ... ... ... + "Cmpd3","Cmpd1","0.25" + "Cmpd3","Cmpd2","0.06" + "Cmpd3","Cmpd3","1" + "Cmpd3","Cmpd4","0.12" + ... ... ... + ... ... ... + ... ... ... + +Example of data in output file for I<IDPairsAndValue> B<--OutMatrixFormat> value for +<UpperTriangularMatrix> value of B<--OutMatrixType>: + + "CmpdID1","CmpdID2","Coefficient Value" + "Cmpd1","Cmpd1","1" + "Cmpd1","Cmpd2","0.04" + "Cmpd1","Cmpd3","0.25" + "Cmpd1","Cmpd4","0.13" + ... ... ... + ... ... ... + ... ... ... + "Cmpd2","Cmpd2","1" + "Cmpd2","Cmpd3","0.06" + "Cmpd2","Cmpd4","0.05" + ... ... ... + ... ... ... + ... ... ... + "Cmpd3","Cmpd3","1" + "Cmpd3","Cmpd4","0.12" + ... ... ... + ... ... ... + ... ... ... + +Example of data in output file for I<IDPairsAndValue> B<--OutMatrixFormat> value for +<LowerTriangularMatrix> value of B<--OutMatrixType>: + + "CmpdID1","CmpdID2","Coefficient Value" + "Cmpd1","Cmpd1","1" + "Cmpd2","Cmpd1","0.04" + "Cmpd2","Cmpd2","1" + "Cmpd3","Cmpd1","0.25" + "Cmpd3","Cmpd2","0.06" + "Cmpd3","Cmpd3","1" + "Cmpd4","Cmpd1","0.13" + "Cmpd4","Cmpd2","0.05" + "Cmpd4","Cmpd3","0.12" + "Cmpd4","Cmpd4","1" + ... ... ... + ... ... ... + ... ... ... + +=item B<--OutMatrixType> I<FullMatrix | UpperTriangularMatrix | LowerTriangularMatrix> + +Type of similarity or distance matrix to calculate for fingerprints vector and bit-vector strings: +Calculate full matrix; Calculate lower triangular matrix including diagonal; Calculate upper triangular +matrix including diagonal. + +Possible values: I<FullMatrix, UpperTriangularMatrix, or LowerTriangularMatrix>. Default value: +I<FullMatrix>. + +The value of B<--OutMatrixType> in conjunction with B<--OutMatrixFormat> determines type +of data written to output files. + +=item B<-o, --overwrite> + +Overwrite existing files + +=item B<-p, --precision> I<number> + +Precision of calculated values in the output file. Default: up to I<2> decimal places. +Valid values: positive integers. + +=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><BitVectorComparisonMode>.<Ext> or +<Root><VectorComparisonMode><VectorComparisonFormulism>.<Ext>. +The csv, and tsv <Ext> values are used for comma/semicolon, and tab delimited text files +respectively. This option is ignored for multiple input files. + +=item B<-v, --VectorComparisonMode> I<All | "TanimotoSimilarity,[ManhattanDistance,...]"> + +Specify what similarity or distance coefficients to use for calculating similarity matrices for +fingerprint vector strings data values in I<TextFile(s)>: calculate similarity matrices for all +supported similarity and distance coefficients or specify a comma delimited list of similarity +and distance coefficients. Possible values: I<All | "TanimotoSimilairy,[ManhattanDistance,..]">. +Default: I<TanimotoSimilarity>. + +The value of B<-v, --VectorComparisonMode>, in conjunction with B<--VectorComparisonFormulism>, +decides which type of similarity and distance coefficient formulism gets used. + +I<All> uses complete list of supported similarity and distance coefficients: I<CosineSimilarity, +CzekanowskiSimilarity, DiceSimilarity, OchiaiSimilarity, JaccardSimilarity, SorensonSimilarity, TanimotoSimilarity, +CityBlockDistance, EuclideanDistance, HammingDistance, ManhattanDistance, SoergelDistance>. These +similarity and distance coefficients are described below. + +B<FingerprintsVector.pm> module, used to calculate similarity and distance coefficients, +provides support to perform comparison between vectors containing three different types of +values: + +Type I: OrderedNumericalValues + + . Size of two vectors are same + . Vectors contain real values in a specific order. For example: MACCS keys + count, Topological pharmnacophore atom pairs and so on. + +Type II: UnorderedNumericalValues + + . Size of two vectors might not be same + . Vectors contain unordered real value identified by value IDs. For example: + Toplogical atom pairs, Topological atom torsions and so on + +Type III: AlphaNumericalValues + + . Size of two vectors might not be same + . Vectors contain unordered alphanumerical values. For example: Extended + connectivity fingerprints, atom neighborhood fingerprints. + +Before performing similarity or distance calculations between vectors containing UnorderedNumericalValues +or AlphaNumericalValues, the vectors are transformed into vectors containing unique OrderedNumericalValues +using value IDs for UnorderedNumericalValues and values itself for AlphaNumericalValues. + +Three forms of similarity and distance calculation between two vectors, specified using B<--VectorComparisonFormulism> +option, are supported: I<AlgebraicForm, BinaryForm or SetTheoreticForm>. + +For I<BinaryForm>, the ordered list of processed final vector values containing the value or +count of each unique value type is simply converted into a binary vector containing 1s and 0s +corresponding to presence or absence of values before calculating similarity or distance between +two vectors. + +For two fingerprint vectors A and B of same size containing OrderedNumericalValues, let: + + N = Number values in A or B + + Xa = Values of vector A + Xb = Values of vector B + + Xai = Value of ith element in A + Xbi = Value of ith element in B + + SUM = Sum of i over N values + +For SetTheoreticForm of calculation between two vectors, let: + + SetIntersectionXaXb = SUM ( MIN ( Xai, Xbi ) ) + SetDifferenceXaXb = SUM ( Xai ) + SUM ( Xbi ) - SUM ( MIN ( Xai, Xbi ) ) + +For BinaryForm of calculation between two vectors, let: + + Na = Number of bits set to "1" in A = SUM ( Xai ) + Nb = Number of bits set to "1" in B = SUM ( Xbi ) + Nc = Number of bits set to "1" in both A and B = SUM ( Xai * Xbi ) + Nd = Number of bits set to "0" in both A and B + = SUM ( 1 - Xai - Xbi + Xai * Xbi) + + N = Number of bits set to "1" or "0" in A or B = Size of A or B = Na + Nb - Nc + Nd + +Additionally, for BinaryForm various values also correspond to: + + Na = | Xa | + Nb = | Xb | + Nc = | SetIntersectionXaXb | + Nd = N - | SetDifferenceXaXb | + + | SetDifferenceXaXb | = N - Nd = Na + Nb - Nc + Nd - Nd = Na + Nb - Nc + = | Xa | + | Xb | - | SetIntersectionXaXb | + +Various similarity and distance coefficients [ Ref 40, Ref 62, Ref 64 ] for a pair of vectors A and B +in I<AlgebraicForm, BinaryForm and SetTheoreticForm> are defined as follows: + +B<CityBlockDistance>: ( same as HammingDistance and ManhattanDistance) + +I<AlgebraicForm>: SUM ( ABS ( Xai - Xbi ) ) + +I<BinaryForm>: ( Na - Nc ) + ( Nb - Nc ) = Na + Nb - 2 * Nc + +I<SetTheoreticForm>: | SetDifferenceXaXb | - | SetIntersectionXaXb | = SUM ( Xai ) + SUM ( Xbi ) - 2 * ( SUM ( MIN ( Xai, Xbi ) ) ) + +B<CosineSimilarity>: ( same as OchiaiSimilarityCoefficient) + +I<AlgebraicForm>: SUM ( Xai * Xbi ) / SQRT ( SUM ( Xai ** 2) * SUM ( Xbi ** 2) ) + +I<BinaryForm>: Nc / SQRT ( Na * Nb) + +I<SetTheoreticForm>: | SetIntersectionXaXb | / SQRT ( |Xa| * |Xb| ) = SUM ( MIN ( Xai, Xbi ) ) / SQRT ( SUM ( Xai ) * SUM ( Xbi ) ) + +B<CzekanowskiSimilarity>: ( same as DiceSimilarity and SorensonSimilarity) + +I<AlgebraicForm>: ( 2 * ( SUM ( Xai * Xbi ) ) ) / ( SUM ( Xai ** 2) + SUM ( Xbi **2 ) ) + +I<BinaryForm>: 2 * Nc / ( Na + Nb ) + +I<SetTheoreticForm>: 2 * | SetIntersectionXaXb | / ( |Xa| + |Xb| ) = 2 * ( SUM ( MIN ( Xai, Xbi ) ) ) / ( SUM ( Xai ) + SUM ( Xbi ) ) + +B<DiceSimilarity>: ( same as CzekanowskiSimilarity and SorensonSimilarity) + +I<AlgebraicForm>: ( 2 * ( SUM ( Xai * Xbi ) ) ) / ( SUM ( Xai ** 2) + SUM ( Xbi **2 ) ) + +I<BinaryForm>: 2 * Nc / ( Na + Nb ) + +I<SetTheoreticForm>: 2 * | SetIntersectionXaXb | / ( |Xa| + |Xb| ) = 2 * ( SUM ( MIN ( Xai, Xbi ) ) ) / ( SUM ( Xai ) + SUM ( Xbi ) ) + +B<EuclideanDistance>: + +I<AlgebraicForm>: SQRT ( SUM ( ( ( Xai - Xbi ) ** 2 ) ) ) + +I<BinaryForm>: SQRT ( ( Na - Nc ) + ( Nb - Nc ) ) = SQRT ( Na + Nb - 2 * Nc ) + +I<SetTheoreticForm>: SQRT ( | SetDifferenceXaXb | - | SetIntersectionXaXb | ) = SQRT ( SUM ( Xai ) + SUM ( Xbi ) - 2 * ( SUM ( MIN ( Xai, Xbi ) ) ) ) + +B<HammingDistance>: ( same as CityBlockDistance and ManhattanDistance) + +I<AlgebraicForm>: SUM ( ABS ( Xai - Xbi ) ) + +I<BinaryForm>: ( Na - Nc ) + ( Nb - Nc ) = Na + Nb - 2 * Nc + +I<SetTheoreticForm>: | SetDifferenceXaXb | - | SetIntersectionXaXb | = SUM ( Xai ) + SUM ( Xbi ) - 2 * ( SUM ( MIN ( Xai, Xbi ) ) ) + +B<JaccardSimilarity>: ( same as TanimotoSimilarity) + +I<AlgebraicForm>: SUM ( Xai * Xbi ) / ( SUM ( Xai ** 2 ) + SUM ( Xbi ** 2 ) - SUM ( Xai * Xbi ) ) + +I<BinaryForm>: Nc / ( ( Na - Nc ) + ( Nb - Nc ) + Nc ) = Nc / ( Na + Nb - Nc ) + +I<SetTheoreticForm>: | SetIntersectionXaXb | / | SetDifferenceXaXb | = SUM ( MIN ( Xai, Xbi ) ) / ( SUM ( Xai ) + SUM ( Xbi ) - SUM ( MIN ( Xai, Xbi ) ) ) + +B<ManhattanDistance>: ( same as CityBlockDistance and HammingDistance) + +I<AlgebraicForm>: SUM ( ABS ( Xai - Xbi ) ) + +I<BinaryForm>: ( Na - Nc ) + ( Nb - Nc ) = Na + Nb - 2 * Nc + +I<SetTheoreticForm>: | SetDifferenceXaXb | - | SetIntersectionXaXb | = SUM ( Xai ) + SUM ( Xbi ) - 2 * ( SUM ( MIN ( Xai, Xbi ) ) ) + +B<OchiaiSimilarity>: ( same as CosineSimilarity) + +I<AlgebraicForm>: SUM ( Xai * Xbi ) / SQRT ( SUM ( Xai ** 2) * SUM ( Xbi ** 2) ) + +I<BinaryForm>: Nc / SQRT ( Na * Nb) + +I<SetTheoreticForm>: | SetIntersectionXaXb | / SQRT ( |Xa| * |Xb| ) = SUM ( MIN ( Xai, Xbi ) ) / SQRT ( SUM ( Xai ) * SUM ( Xbi ) ) + +B<SorensonSimilarity>: ( same as CzekanowskiSimilarity and DiceSimilarity) + +I<AlgebraicForm>: ( 2 * ( SUM ( Xai * Xbi ) ) ) / ( SUM ( Xai ** 2) + SUM ( Xbi **2 ) ) + +I<BinaryForm>: 2 * Nc / ( Na + Nb ) + +I<SetTheoreticForm>: 2 * | SetIntersectionXaXb | / ( |Xa| + |Xb| ) = 2 * ( SUM ( MIN ( Xai, Xbi ) ) ) / ( SUM ( Xai ) + SUM ( Xbi ) ) + +B<SoergelDistance>: + +I<AlgebraicForm>: SUM ( ABS ( Xai - Xbi ) ) / SUM ( MAX ( Xai, Xbi ) ) + +I<BinaryForm>: 1 - Nc / ( Na + Nb - Nc ) = ( Na + Nb - 2 * Nc ) / ( Na + Nb - Nc ) + +I<SetTheoreticForm>: ( | SetDifferenceXaXb | - | SetIntersectionXaXb | ) / | SetDifferenceXaXb | = ( SUM ( Xai ) + SUM ( Xbi ) - 2 * ( SUM ( MIN ( Xai, Xbi ) ) ) ) / ( SUM ( Xai ) + SUM ( Xbi ) - SUM ( MIN ( Xai, Xbi ) ) ) + +B<TanimotoSimilarity>: ( same as JaccardSimilarity) + +I<AlgebraicForm>: SUM ( Xai * Xbi ) / ( SUM ( Xai ** 2 ) + SUM ( Xbi ** 2 ) - SUM ( Xai * Xbi ) ) + +I<BinaryForm>: Nc / ( ( Na - Nc ) + ( Nb - Nc ) + Nc ) = Nc / ( Na + Nb - Nc ) + +I<SetTheoreticForm>: | SetIntersectionXaXb | / | SetDifferenceXaXb | = SUM ( MIN ( Xai, Xbi ) ) / ( SUM ( Xai ) + SUM ( Xbi ) - SUM ( MIN ( Xai, Xbi ) ) ) + +=item B<--VectorComparisonFormulism> I<All | "AlgebraicForm,[BinaryForm,SetTheoreticForm]"> + +Specify fingerprints vector comparison formulism to use for calculation similarity and distance +coefficients during B<-v, --VectorComparisonMode>: use all supported comparison formulisms +or specify a comma delimited. Possible values: I<All | "AlgebraicForm,[BinaryForm,SetTheoreticForm]">. +Default value: I<AlgebraicForm>. + +I<All> uses all three forms of supported vector comparison formulism for values of B<-v, --VectorComparisonMode> +option. + +For fingerprint vector strings containing B<AlphaNumericalValues> data values - B<ExtendedConnectivityFingerprints>, +B<AtomNeighborhoodsFingerprints> and so on - all three formulism result in same value during similarity and distance +calculations. + +=item B<-w, --WorkingDir> I<DirName> + +Location of working directory. Default: current directory. + +=back + +=head1 EXAMPLES + +To generate a similarity matrix corresponding to Tanimoto similarity coefficient for fingerprints +bit-vector strings data corresponding to supported fingerprints in text file present in a column +name containing Fingerprint substring by loading all fingerprints data into memory and create a +SampleFPHexTanimotoSimilarity.csv file containing compound IDs retrieved from column name +containing CompoundID substring, type: + + % SimilarityMatricesFingerprints.pl -o SampleFPHex.csv + +To generate a similarity matrix corresponding to Tanimoto similarity coefficient for fingerprints +bit-vector strings data corresponding to supported fingerprints in SD File present in a data field +with Fingerprint substring in its label by loading all fingerprints data into memory and create a +SampleFPHexTanimotoSimilarity.csv file containing sequentially generated compound IDs with +Cmpd prefix, type: + + % SimilarityMatricesFingerprints.pl -o SampleFPHex.sdf + +To generate a similarity matrix corresponding to Tanimoto similarity coefficient for fingerprints +bit-vector strings data corresponding to supported fingerprints in FP file by loading all fingerprints +data into memory and create a SampleFPHexTanimotoSimilarity.csv file along with compound IDs +retrieved from FP file, type: + + % SimilarityMatricesFingerprints.pl -o SampleFPHex.fpf + +To generate a lower triangular similarity matrix corresponding to Tanimoto similarity coefficient for +fingerprints bit-vector strings data corresponding to supported fingerprints in text file present in a +column name containing Fingerprint substring by loading all fingerprints data into memory and create +a SampleFPHexTanimotoSimilarity.csv file containing compound IDs retrieved from column name +containing CompoundID substring, type: + + % SimilarityMatricesFingerprints.pl -o --InputDataMode LoadInMemory + --OutMatrixFormat RowsAndColumns --OutMatrixType LowerTriangularMatrix + SampleFPHex.csv + +To generate a upper triangular similarity matrix corresponding to Tanimoto similarity coefficient for +fingerprints bit-vector strings data corresponding to supported fingerprints in text file present in a +column name containing Fingerprint substring by loading all fingerprints data into memory and create +a SampleFPHexTanimotoSimilarity.csv file in IDPairsAndValue format containing compound IDs retrieved +from column name containing CompoundID substring, type: + + % SimilarityMatricesFingerprints.pl -o --InputDataMode LoadInMemory + --OutMatrixFormat IDPairsAndValue --OutMatrixType UpperTriangularMatrix + SampleFPHex.csv + +To generate a full similarity matrix corresponding to Tanimoto similarity coefficient for fingerprints +bit-vector strings data corresponding to supported fingerprints in text file present in a column +name containing Fingerprint substring by scanning file without loading all fingerprints data into memory +and create a SampleFPHexTanimotoSimilarity.csv file containing compound IDs retrieved from +column name containing CompoundID substring, type: + + % SimilarityMatricesFingerprints.pl -o --InputDataMode ScanFile + --OutMatrixFormat RowsAndColumns --OutMatrixType FullMatrix + SampleFPHex.csv + +To generate a lower triangular similarity matrix corresponding to Tanimoto similarity coefficient for +fingerprints bit-vector strings data corresponding to supported fingerprints in text file present in a +column name containing Fingerprint substring by scanning file without loading all fingerprints data into +memory and create a SampleFPHexTanimotoSimilarity.csv file in IDPairsAndValue format containing +compound IDs retrieved from column name containing CompoundID substring, type: + + % SimilarityMatricesFingerprints.pl -o --InputDataMode ScanFile + --OutMatrixFormat IDPairsAndValue --OutMatrixType LowerTriangularMatrix + SampleFPHex.csv + +To generate a similarity matrix corresponding to Tanimoto similarity coefficient using algebraic formulism +for fingerprints vector strings data corresponding to supported fingerprints in text file present in a column name +containing Fingerprint substring and create a SampleFPCountTanimotoSimilarityAlgebraicForm.csv file +containing compound IDs retrieved from column name containing CompoundID substring, type: + + % SimilarityMatricesFingerprints.pl -o SampleFPCount.csv + +To generate a similarity matrix corresponding to Tanimoto similarity coefficient using algebraic formulism +for fingerprints vector strings data corresponding to supported fingerprints in SD file present in a data field with +Fingerprint substring in its label and create a SampleFPCountTanimotoSimilarityAlgebraicForm.csv file +containing sequentially generated compound IDs with Cmpd prefix, type: + + % SimilarityMatricesFingerprints.pl -o SampleFPCount.sdf + +To generate a similarity matrix corresponding to Tanimoto similarity coefficient using algebraic formulism +vector strings data corresponding to supported fingerprints in FP file and create a +SampleFPCountTanimotoSimilarityAlgebraicForm.csv file along with compound IDs retrieved from FP file, type: + + % SimilarityMatricesFingerprints.pl -o SampleFPCount.fpf + +To generate a similarity matrix corresponding to Tanimoto similarity coefficient for fingerprints +bit-vector strings data corresponding to supported fingerprints in text file present in a column name +containing Fingerprint substring and create a SampleFPHexTanimotoSimilarity.csv file in +IDPairsAndValue format containing compound IDs retrieved from column name containing +CompoundID substring, type: + + % SimilarityMatricesFingerprints.pl --OutMatrixFormat IDPairsAndValue -o + SampleFPHex.csv + +To generate a similarity matrix corresponding to Tanimoto similarity coefficient for fingerprints +bit-vector strings data corresponding to supported fingerprints in SD file present in a data field with +Fingerprint substring in its label and create a SampleFPHexTanimotoSimilarity.csv file in +IDPairsAndValue format containing sequentially generated compound IDs with Cmpd prefix, +type: + + % SimilarityMatricesFingerprints.pl --OutMatrixFormat IDPairsAndValue -o + SampleFPHex.sdf + +To generate a similarity matrix corresponding to Tanimoto similarity coefficient for fingerprints +bit-vector strings data corresponding to supported fingerprints in FP file and create a +SampleFPHexTanimotoSimilarity.csv file in IDPairsAndValue format along with compound IDs retrieved +from FP file, type: + + % SimilarityMatricesFingerprints.pl --OutMatrixFormat IDPairsAndValue -o + SampleFPHex.fpf + +To generate a similarity matrix corresponding to Tanimoto similarity coefficient for fingerprints +bit-vector strings data corresponding to supported fingerprints in SD file present in a data field with +Fingerprint substring in its label and create a SampleFPHexTanimotoSimilarity.csv file +containing compound IDs from mol name line, type: + + % SimilarityMatricesFingerprints.pl --CompoundIDMode MolName -o + SampleFPHex.sdf + +To generate a similarity matrix corresponding to Tanimoto similarity coefficient for fingerprints +bit-vector strings data corresponding to supported fingerprints present in a data field with +Fingerprint substring in its label and create a SampleFPHexTanimotoSimilarity.csv file +containing compound IDs from data field name Mol_ID, type: + + % SimilarityMatricesFingerprints.pl --CompoundIDMode DataField + --CompoundIDField Mol_ID -o SampleFPBin.sdf + +To generate similarity matrices corresponding to Buser, Dice and Tanimoto similarity coefficient +for fingerprints bit-vector strings data corresponding to supported fingerprints present in a column +name containing Fingerprint substring and create SampleFPBin[CoefficientName]Similarity.csv files +containing compound IDs retrieved from column name containing CompoundID substring, type: + + % SimilarityMatricesFingerprints.pl -b "BuserSimilarity,DiceSimilarity, + TanimotoSimilarity" -o SampleFPBin.csv + +To generate similarity matrices corresponding to Buser, Dice and Tanimoto similarity coefficient +for fingerprints bit-vector strings data corresponding to supported fingerprints present in a data field with +Fingerprint substring in its label and create SampleFPBin[CoefficientName]Similarity.csv files +containing sequentially generated compound IDs with Cmpd prefix, type: + + % SimilarityMatricesFingerprints.pl -b "BuserSimilarity,DiceSimilarity, + TanimotoSimilarity" -o SampleFPBin.sdf + +To generate similarity matrices corresponding to CityBlock distance and Tanimoto similarity coefficients using +algebraic formulism for fingerprints vector strings data corresponding to supported fingerprints present in +a column name containing Fingerprint substring and create SampleFPCount[CoefficientName]AlgebraicForm.csv +files containing compound IDs retrieved from column name containing CompoundID substring, type: + + % SimilarityMatricesFingerprints.pl -v "CityBlockDistance, + TanimotoSimilarity" -o SampleFPCount.csv + +To generate similarity matrices corresponding to CityBlock distance and Tanimoto similarity coefficients using +algebraic formulism for fingerprints vector strings data corresponding to supported fingerprints present in +a data field with Fingerprint substring in its label and create SampleFPCount[CoefficientName]AlgebraicForm.csv +files containing sequentially generated compound IDs with Cmpd prefix, type: + + % SimilarityMatricesFingerprints.pl -v "CityBlockDistance, + TanimotoSimilarity" -o SampleFPCount.sdf + +To generate similarity matrices corresponding to CityBlock distance Tanimoto similarity coefficients using +binary formulism for fingerprints vector strings data corresponding to supported fingerprints present in +a column name containing Fingerprint substring and create SampleFPCount[CoefficientName]Binary.csv +files containing compound IDs retrieved from column name containing CompoundID substring, type: + + % SimilarityMatricesFingerprints.pl -v "CityBlockDistance, + TanimotoSimilarity" --VectorComparisonFormulism BinaryForm -o + SampleFPCount.csv + +To generate similarity matrices corresponding to CityBlock distance Tanimoto similarity coefficients using +binary formulism for fingerprints vector strings data corresponding to supported fingerprints present in +a data field with Fingerprint substring in its label and create SampleFPCount[CoefficientName]Binary.csv +files containing sequentially generated compound IDs with Cmpd prefix, type: + + % SimilarityMatricesFingerprints.pl -v "CityBlockDistance, + TanimotoSimilarity" --VectorComparisonFormulism BinaryForm -o + SampleFPCount.sdf + +To generate similarity matrices corresponding to CityBlock distance Tanimoto similarity coefficients using +all supported comparison formulisms for fingerprints vector strings data corresponding to supported +fingerprints present in a column name containing Fingerprint substring and create +SampleFPCount[CoefficientName][FormulismName].csv files containing compound IDs retrieved from column +name containing CompoundID substring, type: + + % SimilarityMatricesFingerprints.pl -v "CityBlockDistance, + TanimotoSimilarity" --VectorComparisonFormulism All -o SampleFPCount.csv + +To generate similarity matrices corresponding to CityBlock distance Tanimoto similarity coefficients using +all supported comparison formulisms for fingerprints vector strings data corresponding to supported +fingerprints present in a data field with Fingerprint substring in its label and create +SampleFPCount[CoefficientName][FormulismName].csv files containing sequentially generated +compound IDs with Cmpd prefix, type: + + % SimilarityMatricesFingerprints.pl -v "CityBlockDistance,TanimotoSimilarity" + --VectorComparisonFormulism All -o SampleFPCount.sdf + +To generate similarity matrices corresponding to all available similarity coefficient for fingerprints +bit-vector strings data corresponding to supported fingerprints present in a column name +containing Fingerprint substring and create SampleFPHex[CoefficientName].csv files +containing compound IDs retrieved from column name containing CompoundID substring, type: + + % SimilarityMatricesFingerprints.pl -m AutoDetect --BitVectorComparisonMode + All --alpha 0.5 -beta 0.5 -o SampleFPHex.csv + +To generate similarity matrices corresponding to all available similarity coefficient for fingerprints +bit-vector strings data corresponding to supported fingerprints present in a data field with Fingerprint +substring in its label and create SampleFPHex[CoefficientName].csv files containing sequentially +generated compound IDs with Cmpd prefix, type + + % SimilarityMatricesFingerprints.pl -m AutoDetect --BitVectorComparisonMode + All --alpha 0.5 -beta 0.5 -o SampleFPHex.sdf + +To generate similarity matrices corresponding to all available similarity and distance coefficients using +all comparison formulism for fingerprints vector strings data corresponding to supported fingerprints +present in a column name containing Fingerprint substring and create +SampleFPCount[CoefficientName][FormulismName].csv files containing compound IDs +retrieved from column name containing CompoundID substring, type: + + % SimilarityMatricesFingerprints.pl -m AutoDetect --VectorComparisonMode + All --VectorComparisonFormulism All -o SampleFPCount.csv + +To generate similarity matrices corresponding to all available similarity and distance coefficients using +all comparison formulism for fingerprints vector strings data corresponding to supported fingerprints +present in a data field with Fingerprint substring in its label and create +SampleFPCount[CoefficientName][FormulismName].csv files containing sequentially generated +compound IDs with Cmpd prefix, type: + + % SimilarityMatricesFingerprints.pl -m AutoDetect --VectorComparisonMode + All --VectorComparisonFormulism All -o SampleFPCount.sdf + +To generate a similarity matrix corresponding to Tanimoto similarity coefficient for fingerprints +bit-vector strings data corresponding to supported fingerprints present in a column number 2 +and create a SampleFPHexTanimotoSimilarity.csv file containing compound IDs retrieved column +number 1, type: + + % SimilarityMatricesFingerprints.pl --ColMode ColNum --CompoundIDCol 1 + --FingerprintsCol 2 -o SampleFPHex.csv + +To generate a similarity matrix corresponding to Tanimoto similarity coefficient for fingerprints +bit-vector strings data corresponding to supported fingerprints present in a data field name +Fingerprints and create a SampleFPHexTanimotoSimilarity.csv file containing compound IDs +present in data field name Mol_ID, type: + + % SimilarityMatricesFingerprints.pl --FingerprintsField Fingerprints + --CompoundIDMode DataField --CompoundIDField Mol_ID -o SampleFPHex.sdf + +To generate a similarity matrix corresponding to Tversky similarity coefficient for fingerprints +bit-vector strings data corresponding to supported fingerprints present in a column named Fingerprints +and create a SampleFPHexTverskySimilarity.tsv file containing compound IDs retrieved column named +CompoundID, type: + + % SimilarityMatricesFingerprints.pl --BitVectorComparisonMode + TverskySimilarity --alpha 0.5 --ColMode ColLabel --CompoundIDCol + CompoundID --FingerprintsCol Fingerprints --OutDelim Tab --quote No + -o SampleFPHex.csv + +To generate a similarity matrix corresponding to Tanimoto similarity coefficient for fingerprints +bit-vector strings data corresponding to supported fingerprints present in a data field +with Fingerprint substring in its label and create a SampleFPHexTanimotoSimilarity.csv file +containing compound IDs from molname line or sequentially generated compound IDs +with Mol prefix, type: + + % SimilarityMatricesFingerprints.pl --CompoundIDMode MolnameOrLabelPrefix + --CompoundIDPrefix Mol -o SampleFPHex.sdf + +To generate a similarity matrix corresponding to Tanimoto similarity coefficient for fingerprints +bit-vector strings data corresponding to supported fingerprints present in a data field with +Fingerprint substring in its label and create a SampleFPHexTanimotoSimilarity.tsv file +containing sequentially generated compound IDs with Cmpd prefix, type: + + % SimilarityMatricesFingerprints.pl -OutDelim Tab --quote No -o SampleFPHex.sdf + +=head1 AUTHOR + +Manish Sud <msud@san.rr.com> + +=head1 SEE ALSO + +InfoFingerprintsFiles.pl, SimilaritySearchingFingerprints.pl, AtomNeighborhoodsFingerprints.pl, +ExtendedConnectivityFingerprints.pl, MACCSKeysFingerprints.pl, PathLengthFingerprints.pl, +TopologicalAtomPairsFingerprints.pl, TopologicalAtomTorsionsFingerprints.pl, +TopologicalPharmacophoreAtomPairsFingerprints.pl, TopologicalPharmacophoreAtomTripletsFingerprints.pl + +=head1 COPYRIGHT + +Copyright (C) 2015 Manish Sud. All rights reserved. + +This file is part of MayaChemTools. + +MayaChemTools is free software; you can redistribute it and/or modify it under +the terms of the GNU Lesser General Public License as published by the Free +Software Foundation; either version 3 of the License, or (at your option) +any later version. + +=cut