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1 #!/usr/bin/perl -w
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2 #
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3 # $RCSfile: SimilarityMatricesFingerprints.pl,v $
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4 # $Date: 2015/02/28 20:46:20 $
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5 # $Revision: 1.21 $
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6 #
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7 # Author: Manish Sud <msud@san.rr.com>
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8 #
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9 # Copyright (C) 2015 Manish Sud. All rights reserved.
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10 #
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11 # This file is part of MayaChemTools.
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12 #
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13 # MayaChemTools is free software; you can redistribute it and/or modify it under
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14 # the terms of the GNU Lesser General Public License as published by the Free
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15 # Software Foundation; either version 3 of the License, or (at your option) any
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16 # later version.
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17 #
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18 # MayaChemTools is distributed in the hope that it will be useful, but without
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19 # any warranty; without even the implied warranty of merchantability of fitness
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20 # for a particular purpose. See the GNU Lesser General Public License for more
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21 # details.
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22 #
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23 # You should have received a copy of the GNU Lesser General Public License
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24 # along with MayaChemTools; if not, see <http://www.gnu.org/licenses/> or
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25 # write to the Free Software Foundation Inc., 59 Temple Place, Suite 330,
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26 # Boston, MA, 02111-1307, USA.
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27 #
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28
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29 use strict;
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30 use FindBin; use lib "$FindBin::Bin/../lib";
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31 use Getopt::Long;
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32 use File::Basename;
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33 use File::Copy;
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34 use Text::ParseWords;
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35 use Benchmark;
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36 use FileUtil;
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37 use TextUtil;
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38 use Fingerprints::FingerprintsFileUtil;
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39 use Fingerprints::FingerprintsBitVector;
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40 use Fingerprints::FingerprintsVector;
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41
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42 my($ScriptName, %Options, $StartTime, $EndTime, $TotalTime);
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43
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44 # Autoflush STDOUT
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45 $| = 1;
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46
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47 # Starting message...
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48 $ScriptName = basename($0);
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49 print "\n$ScriptName: Starting...\n\n";
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50 $StartTime = new Benchmark;
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51
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52 # Get the options and setup script...
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53 SetupScriptUsage();
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54 if ($Options{help} || @ARGV < 1) {
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55 die GetUsageFromPod("$FindBin::Bin/$ScriptName");
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56 }
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57
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58 my(@FingerprintsFilesList);
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59 @FingerprintsFilesList = ExpandFileNames(\@ARGV, "sdf sd fpf fp csv tsv");
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60
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61 # Process options...
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62 print "Processing options...\n";
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63 my(%OptionsInfo);
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64 ProcessOptions();
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65
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66 # Setup information about input files...
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67 print "Checking input fingerprints file(s)...\n";
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68 my(%FingerprintsFilesInfo);
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69 RetrieveFingerprintsFilesInfo();
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70
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71 # Process input files..
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72 my($FileIndex);
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73 if (@FingerprintsFilesList > 1) {
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74 print "\nProcessing fingerprints files...\n";
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75 }
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76 for $FileIndex (0 .. $#FingerprintsFilesList) {
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77 if ($FingerprintsFilesInfo{FileOkay}[$FileIndex]) {
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78 print "\nProcessing file $FingerprintsFilesList[$FileIndex]...\n";
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79 GenerateSimilarityMatrices($FileIndex);
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80 }
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81 }
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82 print "\n$ScriptName:Done...\n\n";
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83
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84 $EndTime = new Benchmark;
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85 $TotalTime = timediff ($EndTime, $StartTime);
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86 print "Total time: ", timestr($TotalTime), "\n";
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87
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88 ###############################################################################
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89
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90 # Generate similarity matrices using fingerprints data in text file...
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91 #
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92 sub GenerateSimilarityMatrices {
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93 my($FileIndex) = @_;
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94
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95 ProcessFingerprintsData($FileIndex);
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96
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97 if ($FingerprintsFilesInfo{FingerprintsBitVectorStringMode}[$FileIndex]) {
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98 GenerateSimilarityMatricesForFingerprintsBitVectors($FileIndex);
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99 }
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100 elsif ($FingerprintsFilesInfo{FingerprintsVectorStringMode}[$FileIndex]) {
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101 GenerateSimilarityMatricesForFingerprintsVectors($FileIndex);
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102 }
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103
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104 CleanupFingerprintsData($FileIndex);
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105 }
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106
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107 # Generate bit vector similarity matrices...
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108 #
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109 sub GenerateSimilarityMatricesForFingerprintsBitVectors {
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110 my($FileIndex) = @_;
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111 my($SpecifiedComparisonMeasure, $ComparisonMeasure, $NewTextFile, $SimilarityMatrixRef, $MethodName, @MethodParameters);
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112
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113 for $SpecifiedComparisonMeasure (@{$OptionsInfo{SpecifiedBitVectorComparisonsRef}}) {
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114 $ComparisonMeasure = $OptionsInfo{SpecifiedBitVectorComparisonsNameRef}->{lc($SpecifiedComparisonMeasure)};
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115 $NewTextFile = $FingerprintsFilesInfo{OutFileRoot}[$FileIndex] . "${ComparisonMeasure}." . $FingerprintsFilesInfo{OutFileExt}[$FileIndex];
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116
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117 $MethodName = $OptionsInfo{SpecifiedBitVectorComparisonsMethodRef}->{lc($ComparisonMeasure)};
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118
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119 @MethodParameters = ();
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120 @MethodParameters = @{$OptionsInfo{SpecifiedBitVectorComparisonsParameterRef}->{lc($ComparisonMeasure)}};
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121
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122 GenerateSimilarityMatrix($FileIndex, $NewTextFile, $MethodName, \@MethodParameters);
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123 }
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124 }
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125
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126 # Generate vector similarity and/or distance matrices...
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127 #
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128 sub GenerateSimilarityMatricesForFingerprintsVectors {
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129 my($FileIndex) = @_;
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130 my($SpecifiedComparisonMeasure, $ComparisonMode, $ComparisonMeasure, $NewTextFile, $MethodName, @MethodParameters);
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131
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132 for $SpecifiedComparisonMeasure (@{$OptionsInfo{SpecifiedVectorComparisonsRef}}) {
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133 $ComparisonMeasure = $OptionsInfo{SpecifiedVectorComparisonsNameRef}->{lc($SpecifiedComparisonMeasure)};
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134
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135 for $ComparisonMode (@{$OptionsInfo{SpecifiedVectorComparisonModesRef}}) {
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136 $NewTextFile = $FingerprintsFilesInfo{OutFileRoot}[$FileIndex] . "${ComparisonMeasure}${ComparisonMode}." . $FingerprintsFilesInfo{OutFileExt}[$FileIndex];
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137
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138 $MethodName = $OptionsInfo{SpecifiedVectorComparisonsMethodRef}->{lc($ComparisonMeasure)};
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139
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140 @MethodParameters = ();
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141 push @MethodParameters, $ComparisonMode;
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142 push @MethodParameters, @{$OptionsInfo{SpecifiedVectorComparisonsParameterRef}->{lc($ComparisonMeasure)}};
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143
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144 GenerateSimilarityMatrix($FileIndex, $NewTextFile, $MethodName, \@MethodParameters);
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145 }
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146 }
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147 }
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148
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149 # Calculate similarity matrix and write it out...
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150 #
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151 sub GenerateSimilarityMatrix {
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152 my($FileIndex, $NewTextFile, $MethodName, $MethodParametersRef) = @_;
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153
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154 print "\nGenerating $NewTextFile...\n";
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155
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156 # Open new file and write out column labels...
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157 open NEWTEXTFILE, ">$NewTextFile" or die "Error: Can't open $NewTextFile: $! \n";
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158 WriteColumnLabels($FileIndex, \*NEWTEXTFILE);
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159
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160 # Calculate and write out similarity matrix values...
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161 if ($OptionsInfo{InputDataMode} =~ /^LoadInMemory$/i) {
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162 GenerateSimilarityMatrixUsingMemoryData($FileIndex, \*NEWTEXTFILE, $MethodName, $MethodParametersRef);
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163 }
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164 elsif ($OptionsInfo{InputDataMode} =~ /^ScanFile$/i) {
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165 GenerateSimilarityMatrixUsingFileData($FileIndex, \*NEWTEXTFILE, $MethodName, $MethodParametersRef);
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166 }
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167 else {
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168 warn "Warning: Input data mode, $OptionsInfo{InputDataMode}, is not supported.\n";
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169 }
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170
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171 # Close new text file...
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172 close NEWTEXTFILE;
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173
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174 }
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175
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176 # Calculate and write out similarity values using fingerprints data already loaded in
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177 # memory...
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178 #
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179 sub GenerateSimilarityMatrixUsingMemoryData {
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180 my($FileIndex, $NewTextFileRef, $MethodName, $MethodParametersRef) = @_;
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181 my($RowIndex, $ColIndex, $CmpdID1, $CmpdID2, $FingerprintsObject1, $FingerprintsObject2, $Value, $Line, @LineWords);
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182
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183 for $RowIndex (0 .. $#{$FingerprintsFilesInfo{FingerprintsObjectsRef}}) {
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184 $FingerprintsObject1 = $FingerprintsFilesInfo{FingerprintsObjectsRef}->[$RowIndex];
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185 $CmpdID1 = $FingerprintsFilesInfo{CompundIDsRef}->[$RowIndex];
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186
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187 if ($OptionsInfo{WriteRowsAndColumns}) {
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188 print $NewTextFileRef "$OptionsInfo{OutQuoteValue}${CmpdID1}$OptionsInfo{OutQuoteValue}";
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189 }
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190
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191 COLINDEX: for $ColIndex (0 .. $#{$FingerprintsFilesInfo{FingerprintsObjectsRef}}) {
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192 if (SkipMatrixData($RowIndex, $ColIndex)) {
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193 next COLINDEX;
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194 }
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195
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196 $FingerprintsObject2 = $FingerprintsFilesInfo{FingerprintsObjectsRef}->[$ColIndex];
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197
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198 $Value = $FingerprintsObject1->$MethodName($FingerprintsObject2, @{$MethodParametersRef});
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199 $Value = (defined($Value) && length($Value)) ? (sprintf("%.$OptionsInfo{Precision}f", $Value) + 0) : '';
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200
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201 if ($OptionsInfo{WriteRowsAndColumns}) {
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202 print $NewTextFileRef "$OptionsInfo{OutDelim}$OptionsInfo{OutQuoteValue}${Value}$OptionsInfo{OutQuoteValue}";
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203 }
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204 elsif ($OptionsInfo{WriteIDPairsAndValue}) {
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205 $CmpdID2 = $FingerprintsFilesInfo{CompundIDsRef}->[$ColIndex];
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206
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207 @LineWords = ();
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208 push @LineWords, ($CmpdID1, $CmpdID2, $Value);
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209 $Line = JoinWords(\@LineWords, $OptionsInfo{OutDelim}, $OptionsInfo{OutQuote});
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210 print $NewTextFileRef "$Line\n";
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211 }
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212 }
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213 if ($OptionsInfo{WriteRowsAndColumns}) {
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214 print $NewTextFileRef "\n";
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215 }
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216 }
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217 }
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218
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219 # Calculate and write out similarity values by retrieving and prcessing data
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220 # from fingerprint file...
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221 #
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222 sub GenerateSimilarityMatrixUsingFileData {
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223 my($FileIndex, $NewTextFileRef, $MethodName, $MethodParametersRef) = @_;
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224 my($RowIndex, $ColIndex, $FingerprintsFileIO, $TmpFingerprintsFileIO, $FingerprintsObject1, $FingerprintsObject2, $CmpdID1, $CmpdID2, $FingerprintsCount, $IgnoredFingerprintsCount, $Value, $Line, @LineWords);
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225
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226 print "\nReading and processing fingerprints data...\n";
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227
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228 $FingerprintsFileIO = Fingerprints::FingerprintsFileUtil::NewFingerprintsFileIO(%{$FingerprintsFilesInfo{FingerprintsFileIOParameters}[$FileIndex]});
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229 $FingerprintsFileIO->Open();
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230
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231 $RowIndex = 0; $ColIndex = 0;
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232 $FingerprintsCount = 0; $IgnoredFingerprintsCount = 0;
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233
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234 FINGERPRINTSFILEIO: while ($FingerprintsFileIO->Read()) {
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235 $FingerprintsCount++;
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236
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237 if (!$FingerprintsFileIO->IsFingerprintsDataValid()) {
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238 $IgnoredFingerprintsCount++;
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239 next FINGERPRINTSFILEIO;
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240 }
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241 $RowIndex++;
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242 $FingerprintsObject1 = $FingerprintsFileIO->GetFingerprints();
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243 $CmpdID1 = $FingerprintsFileIO->GetCompoundID();
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244
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245 if ($OptionsInfo{WriteRowsAndColumns}) {
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246 print $NewTextFileRef "$OptionsInfo{OutQuoteValue}${CmpdID1}$OptionsInfo{OutQuoteValue}";
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247 }
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248
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249 # Force detail level of 1 to avoid duplicate printing of diagnostic messages for invalid
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250 # fingerprints data...
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251 $TmpFingerprintsFileIO = Fingerprints::FingerprintsFileUtil::NewFingerprintsFileIO(%{$FingerprintsFilesInfo{TmpFingerprintsFileIOParameters}[$FileIndex]}, "DetailLevel" => 1);
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252 $TmpFingerprintsFileIO->Open();
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253
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254 $ColIndex = 0;
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255 TMPFINGERPRINTSFILEIO: while ($TmpFingerprintsFileIO->Read()) {
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256 if (!$TmpFingerprintsFileIO->IsFingerprintsDataValid()) {
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257 next TMPFINGERPRINTSFILEIO;
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258 }
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259 $ColIndex++;
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260
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261 if (SkipMatrixData($RowIndex, $ColIndex)) {
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262 next TMPFINGERPRINTSFILEIO;
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263 }
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264
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265 $FingerprintsObject2 = $TmpFingerprintsFileIO->GetFingerprints();
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266
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267 $Value = $FingerprintsObject1->$MethodName($FingerprintsObject2, @{$MethodParametersRef});
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268 $Value = (defined($Value) && length($Value)) ? (sprintf("%.$OptionsInfo{Precision}f", $Value) + 0) : '';
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269
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270 if ($OptionsInfo{WriteRowsAndColumns}) {
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271 print $NewTextFileRef "$OptionsInfo{OutDelim}$OptionsInfo{OutQuoteValue}${Value}$OptionsInfo{OutQuoteValue}";
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272 }
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273 elsif ($OptionsInfo{WriteIDPairsAndValue}) {
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274 $CmpdID2 = $TmpFingerprintsFileIO->GetCompoundID();
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275
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276 @LineWords = ();
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277 push @LineWords, ($CmpdID1, $CmpdID2, $Value);
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278 $Line = JoinWords(\@LineWords, $OptionsInfo{OutDelim}, $OptionsInfo{OutQuote});
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279 print $NewTextFileRef "$Line\n";
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280 }
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281 }
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282 $TmpFingerprintsFileIO->Close();
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283
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284 if ($OptionsInfo{WriteRowsAndColumns}) {
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285 print $NewTextFileRef "\n";
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286 }
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287 }
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288
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289 $FingerprintsFileIO->Close();
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290
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291 print "Number of fingerprints data entries in database fingerprints file: $FingerprintsCount\n";
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292 print "Number of fingerprints date entries processed successfully: ", ($FingerprintsCount - $IgnoredFingerprintsCount) , "\n";
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293 print "Number of fingerprints data entries ignored due to missing/invalid data: $IgnoredFingerprintsCount\n\n";
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294 }
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295
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296 # Check whether matrix data need to be skipped...
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297 #
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298 sub SkipMatrixData {
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299 my($RowIndex, $ColIndex) = @_;
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300
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301 if ($OptionsInfo{WriteFullMatrix}) {
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302 return 0;
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303 }
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304 elsif ($OptionsInfo{WriteUpperTriangularMatrix}) {
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305 return ($RowIndex > $ColIndex) ? 1 : 0;
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306 }
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307 elsif ($OptionsInfo{WriteLowerTriangularMatrix}) {
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308 return ($RowIndex < $ColIndex) ? 1 : 0;
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309 }
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310
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311 return 0;
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312 }
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313
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314 # Write out column labels...
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315 #
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316 sub WriteColumnLabels {
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317 my($FileIndex, $NewTextFileRef) = @_;
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318 my($Line, @LineWords);
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319
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320 if ($OptionsInfo{OutMatrixFormat} =~ /^IDPairsAndValue$/i) {
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321 @LineWords = ();
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322 push @LineWords, ('CmpdID1', 'CmpdID2', 'Coefficient Value');
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323 $Line = JoinWords(\@LineWords, $OptionsInfo{OutDelim}, $OptionsInfo{OutQuote});
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324 print $NewTextFileRef "$Line\n";
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325 }
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326 elsif ($OptionsInfo{OutMatrixFormat} =~ /^RowsAndColumns$/i) {
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327 if ($OptionsInfo{InputDataMode} =~ /^LoadInMemory$/i) {
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328 @LineWords = ();
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329 push @LineWords, '';
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330 push @LineWords, @{$FingerprintsFilesInfo{CompundIDsRef}};
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331 $Line = JoinWords(\@LineWords, $OptionsInfo{OutDelim}, $OptionsInfo{OutQuote});
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332 print $NewTextFileRef "$Line\n";
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333 }
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334 elsif ($OptionsInfo{InputDataMode} =~ /^ScanFile$/i) {
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335 my( $FingerprintsFileIO, $CmpdID);
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336
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337 # Scan file to retrieve compound IDs...
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338 #
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339 print "\nProcessing fingerprints file to generate compound IDs...\n";
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340
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341 # Force detail level of 1 to avoid diagnostics messages for invalid fingeprints data during
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342 # retrieval of compound IDs as these get printed out during calculation of matrix...
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343 #
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344 $FingerprintsFileIO = Fingerprints::FingerprintsFileUtil::NewFingerprintsFileIO(%{$FingerprintsFilesInfo{FingerprintsFileIOParameters}[$FileIndex]}, "DetailLevel" => 1);
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345 $FingerprintsFileIO->Open();
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346
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347 print $NewTextFileRef "$OptionsInfo{OutQuoteValue}$OptionsInfo{OutQuoteValue}";
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348
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349 FINGERPRINTSFILEIO: while ($FingerprintsFileIO->Read()) {
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350 if (!$FingerprintsFileIO->IsFingerprintsDataValid()) {
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351 next FINGERPRINTSFILEIO;
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352 }
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353 $CmpdID = $FingerprintsFileIO->GetCompoundID();
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354 print $NewTextFileRef "$OptionsInfo{OutDelim}$OptionsInfo{OutQuoteValue}${CmpdID}$OptionsInfo{OutQuoteValue}";
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355 }
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356 $FingerprintsFileIO->Close();
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357
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358 print $NewTextFileRef "\n";
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359
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360 print "Processing fingerprints file to generate matrix...\n";
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361 }
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362 }
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363 else {
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364 warn "Warning: Output matrix format, $OptionsInfo{OutMatrixFormat}, is not supported.\n";
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365 }
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366 }
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367
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368 # Process fingerprints data...
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369 #
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370 sub ProcessFingerprintsData {
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371 my($FileIndex) = @_;
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372 my($FingerprintsFileIO);
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373
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374 $FingerprintsFilesInfo{CompundIDsRef} = undef;
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375 $FingerprintsFilesInfo{FingerprintsObjectsRef} = undef;
|
|
|
376
|
|
|
377 if ($OptionsInfo{InputDataMode} =~ /^LoadInMemory$/i) {
|
|
|
378 my($FingerprintsFileIO);
|
|
|
379
|
|
|
380 $FingerprintsFileIO = Fingerprints::FingerprintsFileUtil::NewFingerprintsFileIO(%{$FingerprintsFilesInfo{FingerprintsFileIOParameters}[$FileIndex]});
|
|
|
381 ($FingerprintsFilesInfo{CompundIDsRef}, $FingerprintsFilesInfo{FingerprintsObjectsRef}) = Fingerprints::FingerprintsFileUtil::ReadAndProcessFingerpritsData($FingerprintsFileIO);
|
|
|
382 }
|
|
|
383 elsif ($OptionsInfo{InputDataMode} =~ /^ScanFile$/i) {
|
|
|
384 my($FingerprintsFile, $TmpFingerprintsFile);
|
|
|
385
|
|
|
386 $FingerprintsFile = $FingerprintsFilesList[$FileIndex];
|
|
|
387 $TmpFingerprintsFile = $FingerprintsFilesInfo{TmpFingerprintsFile}[$FileIndex];
|
|
|
388
|
|
|
389 # Copy fingerprints file to a tmp file for calculating similarity matrix...
|
|
|
390 print "\nCopying fingerprints file, $FingerprintsFile, to temporary fingperints file, $TmpFingerprintsFile...\n";
|
|
|
391 copy $FingerprintsFile, $TmpFingerprintsFile or die "Error: Couldn't copy $FingerprintsFile to $TmpFingerprintsFile: $! \n";
|
|
|
392 }
|
|
|
393 }
|
|
|
394
|
|
|
395 # Clean up fingerprints data...
|
|
|
396 #
|
|
|
397 sub CleanupFingerprintsData {
|
|
|
398 my($FileIndex) = @_;
|
|
|
399
|
|
|
400 if ($OptionsInfo{InputDataMode} =~ /^LoadInMemory$/i) {
|
|
|
401 $FingerprintsFilesInfo{CompundIDsRef} = undef;
|
|
|
402 $FingerprintsFilesInfo{FingerprintsObjectsRef} = undef;
|
|
|
403 }
|
|
|
404 elsif ($OptionsInfo{InputDataMode} =~ /^ScanFile$/i) {
|
|
|
405 my($TmpFingerprintsFile);
|
|
|
406
|
|
|
407 # Delete temporary fingerprints file...
|
|
|
408 $TmpFingerprintsFile = $FingerprintsFilesInfo{TmpFingerprintsFile}[$FileIndex];
|
|
|
409
|
|
|
410 print "\nDeleting temporary fingerprints file $TmpFingerprintsFile...\n";
|
|
|
411 unlink $TmpFingerprintsFile or die "Error: Couldn't unlink $TmpFingerprintsFile: $! \n";
|
|
|
412 }
|
|
|
413 }
|
|
|
414
|
|
|
415 # Retrieve information about fingerprints files...
|
|
|
416 #
|
|
|
417 sub RetrieveFingerprintsFilesInfo {
|
|
|
418 my($FingerprintsFile, $TmpFingerprintsFile, $FingerprintsFileIO, $FingerprintsBitVectorStringMode, $FingerprintsVectorStringMode, $FileType, $Index, $FileDir, $FileExt, $FileName, $InDelim, $OutFileRoot, $OutFileExt, %FingerprintsFileIOParameters);
|
|
|
419
|
|
|
420 %FingerprintsFilesInfo = ();
|
|
|
421 @{$FingerprintsFilesInfo{FileOkay}} = ();
|
|
|
422 @{$FingerprintsFilesInfo{FileType}} = ();
|
|
|
423 @{$FingerprintsFilesInfo{InDelim}} = ();
|
|
|
424 @{$FingerprintsFilesInfo{OutFileRoot}} = ();
|
|
|
425 @{$FingerprintsFilesInfo{OutFileExt}} = ();
|
|
|
426
|
|
|
427 @{$FingerprintsFilesInfo{TmpFingerprintsFile}} = ();
|
|
|
428
|
|
|
429 @{$FingerprintsFilesInfo{FingerprintsFileIOParameters}} = ();
|
|
|
430 @{$FingerprintsFilesInfo{TmpFingerprintsFileIOParameters}} = ();
|
|
|
431
|
|
|
432 @{$FingerprintsFilesInfo{FingerprintsBitVectorStringMode}} = ();
|
|
|
433 @{$FingerprintsFilesInfo{FingerprintsVectorStringMode}} = ();
|
|
|
434
|
|
|
435 FILELIST: for $Index (0 .. $#FingerprintsFilesList) {
|
|
|
436 $FingerprintsFilesInfo{FileOkay}[$Index] = 0;
|
|
|
437 $FingerprintsFilesInfo{FileType}[$Index] = '';
|
|
|
438 $FingerprintsFilesInfo{InDelim}[$Index] = "";
|
|
|
439 $FingerprintsFilesInfo{OutFileRoot}[$Index] = '';
|
|
|
440 $FingerprintsFilesInfo{OutFileExt}[$Index] = '';
|
|
|
441
|
|
|
442 %{$FingerprintsFilesInfo{FingerprintsFileIOParameters}[$Index]} = ();
|
|
|
443
|
|
|
444 $FingerprintsFilesInfo{TmpFingerprintsFile}[$Index] = "";
|
|
|
445 %{$FingerprintsFilesInfo{TmpFingerprintsFileIOParameters}[$Index]} = ();
|
|
|
446
|
|
|
447 $FingerprintsFilesInfo{FingerprintsBitVectorStringMode}[$Index] = 0;
|
|
|
448 $FingerprintsFilesInfo{FingerprintsVectorStringMode}[$Index] = 0;
|
|
|
449
|
|
|
450 $FingerprintsFile = $FingerprintsFilesList[$Index];
|
|
|
451 if (!(-e $FingerprintsFile)) {
|
|
|
452 warn "Warning: Ignoring file $FingerprintsFile: It doesn't exist\n";
|
|
|
453 next FILELIST;
|
|
|
454 }
|
|
|
455
|
|
|
456 $FileType = Fingerprints::FingerprintsFileUtil::GetFingerprintsFileType($FingerprintsFile);
|
|
|
457 if (IsEmpty($FileType)) {
|
|
|
458 warn "Warning: Ignoring file $FingerprintsFile: It's not a fingerprints file\n";
|
|
|
459 next FILELIST;
|
|
|
460 }
|
|
|
461
|
|
|
462 $FileDir = ""; $FileName = ""; $FileExt = "";
|
|
|
463 ($FileDir, $FileName, $FileExt) = ParseFileName($FingerprintsFile);
|
|
|
464
|
|
|
465 # Setup temporary fingerprints file name for scan file mode...
|
|
|
466 $TmpFingerprintsFile = "${FileName}Tmp.${FileExt}";
|
|
|
467
|
|
|
468 $InDelim = ($FileExt =~ /^tsv$/i) ? 'Tab' : $OptionsInfo{InDelim};
|
|
|
469
|
|
|
470 # Setup output file names...
|
|
|
471 $OutFileExt = "csv";
|
|
|
472 if ($Options{outdelim} =~ /^tab$/i) {
|
|
|
473 $OutFileExt = "tsv";
|
|
|
474 }
|
|
|
475
|
|
|
476 $OutFileRoot = $FileName;
|
|
|
477 if ($OptionsInfo{OutFileRoot} && (@FingerprintsFilesList == 1)) {
|
|
|
478 my ($RootFileDir, $RootFileName, $RootFileExt) = ParseFileName($OptionsInfo{OutFileRoot});
|
|
|
479 if ($RootFileName && $RootFileExt) {
|
|
|
480 $FileName = $RootFileName;
|
|
|
481 }
|
|
|
482 else {
|
|
|
483 $FileName = $OptionsInfo{OutFileRoot};
|
|
|
484 }
|
|
|
485 $OutFileRoot = $FileName;
|
|
|
486 }
|
|
|
487
|
|
|
488 if (!$Options{overwrite}) {
|
|
|
489 # Similarity matrices output file names for bit-vector strings...
|
|
|
490 my($SpecifiedComparisonMeasure, $ComparisonMeasure);
|
|
|
491 for $SpecifiedComparisonMeasure (@{$OptionsInfo{SpecifiedBitVectorComparisonsRef}}) {
|
|
|
492 $ComparisonMeasure = $OptionsInfo{SpecifiedBitVectorComparisonsNameRef}->{lc($SpecifiedComparisonMeasure)};
|
|
|
493 if (-e "${OutFileRoot}${ComparisonMeasure}.${OutFileExt}") {
|
|
|
494 warn "Warning: Ignoring file $FingerprintsFile: The file ${OutFileRoot}${ComparisonMeasure}.${OutFileExt} already exists.\n";
|
|
|
495 next FILELIST;
|
|
|
496 }
|
|
|
497 }
|
|
|
498 # Similarity matrices output file names for vector strings...
|
|
|
499 my($ComparisonMode);
|
|
|
500 for $SpecifiedComparisonMeasure (@{$OptionsInfo{SpecifiedVectorComparisonsRef}}) {
|
|
|
501 $ComparisonMeasure = $OptionsInfo{SpecifiedVectorComparisonsNameRef}->{lc($SpecifiedComparisonMeasure)};
|
|
|
502 for $ComparisonMode (@{$OptionsInfo{SpecifiedVectorComparisonModesRef}}) {
|
|
|
503 if (-e "${OutFileRoot}${ComparisonMeasure}${ComparisonMode}.${OutFileExt}") {
|
|
|
504 warn "Warning: Ignoring file $FingerprintsFile: The file ${OutFileRoot}${ComparisonMeasure}${ComparisonMode}.${OutFileExt} already exists.\n";
|
|
|
505 next FILELIST;
|
|
|
506 }
|
|
|
507 }
|
|
|
508 }
|
|
|
509 }
|
|
|
510
|
|
|
511 # Setup FingerprintsFileIO parameters...
|
|
|
512 %FingerprintsFileIOParameters = ();
|
|
|
513 FILEIOPARAMETERS: {
|
|
|
514 if ($FileType =~ /^SD$/i) {
|
|
|
515 %FingerprintsFileIOParameters = ('Name' => $FingerprintsFile, 'Mode' => 'Read', 'FingerprintsStringMode' => $OptionsInfo{Mode}, 'ValidateData' => $OptionsInfo{ValidateData}, 'DetailLevel' => $OptionsInfo{Detail}, 'FingerprintsFieldLabel' => $OptionsInfo{FingerprintsField}, 'CompoundIDMode' => $OptionsInfo{CompoundIDMode}, 'CompoundIDFieldLabel' => $OptionsInfo{CompoundIDField}, 'CompoundIDPrefix' => $OptionsInfo{CompoundIDPrefix});
|
|
|
516 last FILEIOPARAMETERS;
|
|
|
517 }
|
|
|
518 if ($FileType =~ /^FP$/i) {
|
|
|
519 %FingerprintsFileIOParameters = ('Name' => $FingerprintsFile, 'Mode' => 'Read', 'FingerprintsStringMode' => $OptionsInfo{Mode}, 'ValidateData' => $OptionsInfo{ValidateData}, 'DetailLevel' => $OptionsInfo{Detail});
|
|
|
520 last FILEIOPARAMETERS;
|
|
|
521 }
|
|
|
522 if ($FileType =~ /^Text$/i) {
|
|
|
523 %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});
|
|
|
524 last FILEIOPARAMETERS;
|
|
|
525 }
|
|
|
526 warn "Warning: File type for fingerprints file, $FingerprintsFile, is not valid. Supported file types: SD, FP or Text\n";
|
|
|
527 next FILELIST;
|
|
|
528 }
|
|
|
529
|
|
|
530 # Retrieve fingerints file string mode information...
|
|
|
531 $FingerprintsFileIO = Fingerprints::FingerprintsFileUtil::NewFingerprintsFileIO(%FingerprintsFileIOParameters);
|
|
|
532
|
|
|
533 if (!$FingerprintsFileIO) {
|
|
|
534 warn "Warning: Ignoring fingerprints file $FingerprintsFile: It contains invalid fingerprints data\n";
|
|
|
535 next FILELIST;
|
|
|
536 }
|
|
|
537 if (!$FingerprintsFileIO->IsFingerprintsFileDataValid()) {
|
|
|
538 warn "Warning: Ignoring fingerprints file $FingerprintsFile: It contains invalid fingerprints data\n";
|
|
|
539 next FILELIST;
|
|
|
540 }
|
|
|
541 $FingerprintsBitVectorStringMode = $FingerprintsFileIO->GetFingerprintsBitVectorStringMode();
|
|
|
542 $FingerprintsVectorStringMode = $FingerprintsFileIO->GetFingerprintsVectorStringMode();
|
|
|
543
|
|
|
544
|
|
|
545 $FingerprintsFilesInfo{FileOkay}[$Index] = 1;
|
|
|
546 $FingerprintsFilesInfo{FileType}[$Index] = $FileType;
|
|
|
547
|
|
|
548 $FingerprintsFilesInfo{InDelim}[$Index] = $InDelim;
|
|
|
549
|
|
|
550 $FingerprintsFilesInfo{OutFileRoot}[$Index] = $OutFileRoot;
|
|
|
551 $FingerprintsFilesInfo{OutFileExt}[$Index] = $OutFileExt;
|
|
|
552
|
|
|
553 %{$FingerprintsFilesInfo{FingerprintsFileIOParameters}[$Index]} = %FingerprintsFileIOParameters;
|
|
|
554
|
|
|
555 $FingerprintsFilesInfo{TmpFingerprintsFile}[$Index] = $TmpFingerprintsFile;
|
|
|
556
|
|
|
557 $FingerprintsFileIOParameters{Name} = $TmpFingerprintsFile;
|
|
|
558 %{$FingerprintsFilesInfo{TmpFingerprintsFileIOParameters}[$Index]} = %FingerprintsFileIOParameters;
|
|
|
559
|
|
|
560 $FingerprintsFilesInfo{FingerprintsBitVectorStringMode}[$Index] = $FingerprintsBitVectorStringMode;
|
|
|
561 $FingerprintsFilesInfo{FingerprintsVectorStringMode}[$Index] = $FingerprintsVectorStringMode;
|
|
|
562 }
|
|
|
563 }
|
|
|
564
|
|
|
565 # Process option values...
|
|
|
566 sub ProcessOptions {
|
|
|
567 %OptionsInfo = ();
|
|
|
568
|
|
|
569 $OptionsInfo{Mode} = $Options{mode};
|
|
|
570
|
|
|
571 $OptionsInfo{InputDataMode} = $Options{inputdatamode};
|
|
|
572
|
|
|
573 ProcessBitVectorComparisonOptions();
|
|
|
574 ProcessVectorComparisonOptions();
|
|
|
575
|
|
|
576 $OptionsInfo{CompoundIDPrefix} = $Options{compoundidprefix} ? $Options{compoundidprefix} : 'Cmpd';
|
|
|
577
|
|
|
578 # Compound ID and fingerprints column options for text files...
|
|
|
579 $OptionsInfo{ColMode} = $Options{colmode};
|
|
|
580
|
|
|
581 if (IsNotEmpty($Options{compoundidcol})) {
|
|
|
582 if ($Options{colmode} =~ /^ColNum$/i) {
|
|
|
583 if (!IsPositiveInteger($Options{compoundidcol})) {
|
|
|
584 die "Error: Column value, $Options{compoundidcol}, specified using \"--CompoundIDCol\" is not valid: Allowed integer values: > 0\n";
|
|
|
585 }
|
|
|
586 }
|
|
|
587 $OptionsInfo{CompoundIDCol} = $Options{compoundidcol};
|
|
|
588 }
|
|
|
589 else {
|
|
|
590 $OptionsInfo{CompoundIDCol} = 'AutoDetect';
|
|
|
591 }
|
|
|
592
|
|
|
593 if (IsNotEmpty($Options{fingerprintscol})) {
|
|
|
594 if ($Options{colmode} =~ /^ColNum$/i) {
|
|
|
595 if (!IsPositiveInteger($Options{fingerprintscol})) {
|
|
|
596 die "Error: Column value, $Options{fingerprintscol}, specified using \"--FingerprintsCol\" is not valid: Allowed integer values: > 0\n";
|
|
|
597 }
|
|
|
598 }
|
|
|
599 $OptionsInfo{FingerprintsCol} = $Options{fingerprintscol};
|
|
|
600 }
|
|
|
601 else {
|
|
|
602 $OptionsInfo{FingerprintsCol} = 'AutoDetect';
|
|
|
603 }
|
|
|
604
|
|
|
605 if (IsNotEmpty($Options{compoundidcol}) && IsNotEmpty($Options{fingerprintscol})) {
|
|
|
606 if (IsPositiveInteger($Options{compoundidcol}) && IsPositiveInteger($Options{fingerprintscol})) {
|
|
|
607 if (($Options{compoundidcol} == $Options{fingerprintscol})) {
|
|
|
608 die "Error: Values specified using \"--CompoundIDCol\" and \"--FingerprintsCol\", $Options{compoundidcol}, must be different.\n";
|
|
|
609 }
|
|
|
610 }
|
|
|
611 else {
|
|
|
612 if (($Options{compoundidcol} eq $Options{fingerprintscol})) {
|
|
|
613 die "Error: Values specified using \"--CompoundIDCol\" and \"--FingerprintsCol\", $Options{compoundidcol}, must be different.\n";
|
|
|
614 }
|
|
|
615 }
|
|
|
616 }
|
|
|
617
|
|
|
618 # Compound ID and fingerprints field options for SD files...
|
|
|
619 $OptionsInfo{CompoundIDMode} = $Options{compoundidmode};
|
|
|
620 $OptionsInfo{CompoundIDField} = '';
|
|
|
621
|
|
|
622 if ($Options{compoundidmode} =~ /^DataField$/i) {
|
|
|
623 if (!$Options{compoundidfield}) {
|
|
|
624 die "Error: You must specify a value for \"--CompoundIDField\" option in \"DataField\" \"--CompoundIDMode\". \n";
|
|
|
625 }
|
|
|
626 $OptionsInfo{CompoundIDField} = $Options{compoundidfield};
|
|
|
627 }
|
|
|
628
|
|
|
629
|
|
|
630 if (IsNotEmpty($Options{fingerprintsfield})) {
|
|
|
631 $OptionsInfo{FingerprintsField} = $Options{fingerprintsfield};
|
|
|
632 }
|
|
|
633 else {
|
|
|
634 $OptionsInfo{FingerprintsField} = 'AutoDetect';
|
|
|
635 }
|
|
|
636
|
|
|
637 if ($Options{compoundidfield} && IsNotEmpty($Options{fingerprintsfield})) {
|
|
|
638 if (($Options{compoundidfield} eq $Options{fingerprintsfield})) {
|
|
|
639 die "Error: Values specified using \"--CompoundIDField\" and \"--Fingerprintsfield\", $Options{compoundidfield}, must be different.\n";
|
|
|
640 }
|
|
|
641 }
|
|
|
642
|
|
|
643 $OptionsInfo{Detail} = $Options{detail};
|
|
|
644
|
|
|
645 $OptionsInfo{InDelim} = $Options{indelim};
|
|
|
646 $OptionsInfo{OutDelim} = ($Options{outdelim} =~ /tab/i ) ? "\t" : (($Options{outdelim} =~ /semicolon/i) ? "\;" : "\,");
|
|
|
647 $OptionsInfo{OutQuote} = ($Options{quote} =~ /^Yes$/i) ? 1 : 0;
|
|
|
648 $OptionsInfo{OutQuoteValue} = ($Options{quote} =~ /^Yes$/i) ? '"' : '';
|
|
|
649
|
|
|
650 $OptionsInfo{OutMatrixFormat} = $Options{outmatrixformat};
|
|
|
651
|
|
|
652 $OptionsInfo{WriteRowsAndColumns} = 0; $OptionsInfo{WriteIDPairsAndValue} = 0;
|
|
|
653 OUTMATRIXFORMAT: {
|
|
|
654 if ($OptionsInfo{OutMatrixFormat} =~ /^RowsAndColumns$/i) {
|
|
|
655 $OptionsInfo{WriteRowsAndColumns} = 1; last OUTMATRIXFORMAT;
|
|
|
656 }
|
|
|
657 if ($OptionsInfo{OutMatrixFormat} =~ /^IDPairsAndValue$/i) {
|
|
|
658 $OptionsInfo{WriteIDPairsAndValue} = 1; last OUTMATRIXFORMAT;
|
|
|
659 }
|
|
|
660 die "Error: The value specified, $Options{outmatrixformat}, for option \"--OutMatrixFormat\" is not valid. Allowed values: RowsAndColumns or IDPairsAndValue\n";
|
|
|
661 }
|
|
|
662
|
|
|
663 $OptionsInfo{OutMatrixType} = $Options{outmatrixtype};
|
|
|
664
|
|
|
665 $OptionsInfo{WriteFullMatrix} = 0;
|
|
|
666 $OptionsInfo{WriteUpperTriangularMatrix} = 0; $OptionsInfo{WriteLowerTriangularMatrix} = 0;
|
|
|
667 OUTMATRIXTYPE: {
|
|
|
668 if ($OptionsInfo{OutMatrixType} =~ /^FullMatrix$/i) {
|
|
|
669 $OptionsInfo{WriteFullMatrix} = 1; last OUTMATRIXTYPE;
|
|
|
670 }
|
|
|
671 if ($OptionsInfo{OutMatrixType} =~ /^UpperTriangularMatrix$/i) {
|
|
|
672 $OptionsInfo{WriteUpperTriangularMatrix} = 1; last OUTMATRIXTYPE;
|
|
|
673 }
|
|
|
674 if ($OptionsInfo{OutMatrixType} =~ /^LowerTriangularMatrix$/i) {
|
|
|
675 $OptionsInfo{WriteLowerTriangularMatrix} = 1; last OUTMATRIXTYPE;
|
|
|
676 }
|
|
|
677 die "Error: The value specified, $Options{outmatrixtype}, for option \"--OutMatrixType\" is not valid. Allowed values: FullMatrix, UpperTriangularMatrix or LowerTriangularMatrix\n";
|
|
|
678 }
|
|
|
679
|
|
|
680 $OptionsInfo{OverwriteFiles} = $Options{overwrite} ? 1 : 0;
|
|
|
681 $OptionsInfo{OutFileRoot} = $Options{root} ? $Options{root} : 0;
|
|
|
682
|
|
|
683 $OptionsInfo{Fast} = $Options{fast} ? 1 : 0;
|
|
|
684 $OptionsInfo{ValidateData} = $Options{fast} ? 0 : 1;
|
|
|
685
|
|
|
686 $OptionsInfo{Precision} = $Options{precision};
|
|
|
687
|
|
|
688 }
|
|
|
689
|
|
|
690 # Process options related to comparion of bit vector strings...
|
|
|
691 #
|
|
|
692 sub ProcessBitVectorComparisonOptions {
|
|
|
693 # Setup supported bit vector similarity coefficients for bit vector strings...
|
|
|
694 my($ComparisonMeasure, $SupportedComparisonMeasure, @SupportedComparisonMeasures, %SupportedComparisonMeasuresNameMap, %SupportedComparisonMeasuresMethodMap);
|
|
|
695
|
|
|
696 @SupportedComparisonMeasures = ();
|
|
|
697 %SupportedComparisonMeasuresNameMap = ();
|
|
|
698 %SupportedComparisonMeasuresMethodMap = ();
|
|
|
699
|
|
|
700 for $SupportedComparisonMeasure (Fingerprints::FingerprintsBitVector::GetSupportedSimilarityCoefficients()) {
|
|
|
701 # Similarity coefficient function/method names contain "Coefficient" in their names.
|
|
|
702 # So take 'em out and setup a map to original function/method name...
|
|
|
703 $ComparisonMeasure = $SupportedComparisonMeasure;
|
|
|
704 $ComparisonMeasure =~ s/Coefficient$//;
|
|
|
705
|
|
|
706 push @SupportedComparisonMeasures, $ComparisonMeasure;
|
|
|
707 $SupportedComparisonMeasuresNameMap{lc($ComparisonMeasure)} = $ComparisonMeasure;
|
|
|
708 $SupportedComparisonMeasuresMethodMap{lc($ComparisonMeasure)} = $SupportedComparisonMeasure;
|
|
|
709 }
|
|
|
710
|
|
|
711 # Setup a list of similarity coefficients to use for calculating similarity matrices for bit vector strings...
|
|
|
712 my($SpecifiedMeasure, @SpecifiedComparisonMeasures, %SpecifiedComparisonMeasuresNameMap, %SpecifiedComparisonMeasuresMethodMap, %SpecifiedComparisonMeasuresParameterMap);
|
|
|
713
|
|
|
714 @SpecifiedComparisonMeasures = ();
|
|
|
715 %SpecifiedComparisonMeasuresNameMap = ();
|
|
|
716 %SpecifiedComparisonMeasuresMethodMap = ();
|
|
|
717 %SpecifiedComparisonMeasuresParameterMap = ();
|
|
|
718
|
|
|
719 if ($Options{bitvectorcomparisonmode} =~ /^All$/i) {
|
|
|
720 push @SpecifiedComparisonMeasures, @SupportedComparisonMeasures;
|
|
|
721 }
|
|
|
722 else {
|
|
|
723 # Comma delimited list of similarity coefficients...
|
|
|
724 my($BitVectorComparisonMode, @SpecifiedMeasures, @UnsupportedSpecifiedMeasures);
|
|
|
725
|
|
|
726 $BitVectorComparisonMode = $Options{bitvectorcomparisonmode};
|
|
|
727 $BitVectorComparisonMode =~ s/ //g;
|
|
|
728 @SpecifiedMeasures = split ",", $BitVectorComparisonMode;
|
|
|
729 @UnsupportedSpecifiedMeasures = ();
|
|
|
730
|
|
|
731 for $SpecifiedMeasure (@SpecifiedMeasures) {
|
|
|
732 if (exists($SupportedComparisonMeasuresMethodMap{lc($SpecifiedMeasure)})) {
|
|
|
733 push @SpecifiedComparisonMeasures, $SpecifiedMeasure;
|
|
|
734 }
|
|
|
735 else {
|
|
|
736 push @UnsupportedSpecifiedMeasures, $SpecifiedMeasure;
|
|
|
737 }
|
|
|
738 }
|
|
|
739 if (@UnsupportedSpecifiedMeasures) {
|
|
|
740 if (@UnsupportedSpecifiedMeasures > 1) {
|
|
|
741 warn "Error: The values specified - ", JoinWords(\@UnsupportedSpecifiedMeasures, ", ", 0)," - for option \"-b --BitVectorComparisonMode\" are not valid.\n";
|
|
|
742 }
|
|
|
743 else {
|
|
|
744 warn "Error: The value specified, @UnsupportedSpecifiedMeasures, for option \"-b --BitVectorComparisonMode\" is not valid.\n";
|
|
|
745 }
|
|
|
746 die "Allowed values:", JoinWords(\@SupportedComparisonMeasures, ", ", 0), "\n";
|
|
|
747 }
|
|
|
748 }
|
|
|
749 for $SpecifiedMeasure (@SpecifiedComparisonMeasures) {
|
|
|
750 $SpecifiedComparisonMeasuresMethodMap{lc($SpecifiedMeasure)} = $SupportedComparisonMeasuresMethodMap{lc($SpecifiedMeasure)};
|
|
|
751 $SpecifiedComparisonMeasuresNameMap{lc($SpecifiedMeasure)} = $SupportedComparisonMeasuresNameMap{lc($SpecifiedMeasure)};
|
|
|
752 }
|
|
|
753
|
|
|
754 $OptionsInfo{BitVectorComparisonMode} = $Options{bitvectorcomparisonmode};
|
|
|
755 $OptionsInfo{SpecifiedBitVectorComparisonsRef} = \@SpecifiedComparisonMeasures;
|
|
|
756 $OptionsInfo{SpecifiedBitVectorComparisonsNameRef} = \%SpecifiedComparisonMeasuresNameMap;
|
|
|
757 $OptionsInfo{SpecifiedBitVectorComparisonsMethodRef} = \%SpecifiedComparisonMeasuresMethodMap;
|
|
|
758
|
|
|
759 # Make sure valid alpha parameter is specified for Tversky calculation...
|
|
|
760 my($SpecifiedMeasure1, $SpecifiedMeasure2);
|
|
|
761 $OptionsInfo{Alpha} = '';
|
|
|
762 $SpecifiedMeasure1 = 'TverskySimilarity';
|
|
|
763 $SpecifiedMeasure2 = 'WeightedTverskySimilarity';
|
|
|
764 if ($SpecifiedComparisonMeasuresNameMap{lc($SpecifiedMeasure1)} || $SpecifiedComparisonMeasuresNameMap{lc($SpecifiedMeasure2)}) {
|
|
|
765 if (IsEmpty($Options{alpha})) {
|
|
|
766 die "Error: You must specify a value for \"-a, --alpha\" option in \"$SpecifiedMeasure1, $SpecifiedMeasure2, or All\" \"-m --mode\". \n";
|
|
|
767 }
|
|
|
768 my($Alpha);
|
|
|
769 $Alpha = $Options{alpha};
|
|
|
770 if (!(IsFloat($Alpha) && $Alpha >=0 && $Alpha <= 1)) {
|
|
|
771 die "Error: The value specified, $Options{alpha}, for option \"-a, --alpha\" is not valid. Allowed values: >= 0 and <= 1\n";
|
|
|
772 }
|
|
|
773 $OptionsInfo{Alpha} = $Alpha;
|
|
|
774 }
|
|
|
775
|
|
|
776 # Make sure valid beta parameter is specified for WeightedTanimoto and WeightedTversky
|
|
|
777 # calculations...
|
|
|
778 $OptionsInfo{Beta} = '';
|
|
|
779 $SpecifiedMeasure1 = 'WeightedTverskySimilarity';
|
|
|
780 $SpecifiedMeasure2 = 'WeightedTanimotoSimilarity';
|
|
|
781 if ($SpecifiedComparisonMeasuresNameMap{lc($SpecifiedMeasure1)} || $SpecifiedComparisonMeasuresNameMap{lc($SpecifiedMeasure2)}) {
|
|
|
782 if (IsEmpty($Options{beta})) {
|
|
|
783 die "Error: You must specify a value for \"-b, --beta\" option in \"$SpecifiedMeasure1, $SpecifiedMeasure2, or All\" \"-m --mode\". \n";
|
|
|
784 }
|
|
|
785 my($Beta);
|
|
|
786 $Beta = $Options{beta};
|
|
|
787 if (!(IsFloat($Beta) && $Beta >=0 && $Beta <= 1)) {
|
|
|
788 die "Error: The value specified, $Options{beta}, for option \"-b, --beta\" is not valid. Allowed values: >= 0 and <= 1\n";
|
|
|
789 }
|
|
|
790 $OptionsInfo{Beta} = $Beta;
|
|
|
791 }
|
|
|
792
|
|
|
793 # Setup any parameters required for specified comparison menthod...
|
|
|
794 for $SpecifiedMeasure (@SpecifiedComparisonMeasures) {
|
|
|
795 @{$SpecifiedComparisonMeasuresParameterMap{lc($SpecifiedMeasure)}} = ();
|
|
|
796 if ($SpecifiedMeasure =~ /^TverskySimilarity$/i) {
|
|
|
797 push @{$SpecifiedComparisonMeasuresParameterMap{lc($SpecifiedMeasure)}}, $OptionsInfo{Alpha};
|
|
|
798 }
|
|
|
799 elsif ($SpecifiedMeasure =~ /^WeightedTverskySimilarity$/i) {
|
|
|
800 push @{$SpecifiedComparisonMeasuresParameterMap{lc($SpecifiedMeasure)}}, $OptionsInfo{Alpha};
|
|
|
801 push @{$SpecifiedComparisonMeasuresParameterMap{lc($SpecifiedMeasure)}}, $OptionsInfo{Beta};
|
|
|
802 }
|
|
|
803 elsif ($SpecifiedMeasure =~ /^WeightedTanimotoSimilarity$/i) {
|
|
|
804 push @{$SpecifiedComparisonMeasuresParameterMap{lc($SpecifiedMeasure)}}, $OptionsInfo{Beta};
|
|
|
805 }
|
|
|
806 }
|
|
|
807 $OptionsInfo{SpecifiedBitVectorComparisonsParameterRef} = \%SpecifiedComparisonMeasuresParameterMap;
|
|
|
808 }
|
|
|
809
|
|
|
810 # Process options related to comparion of vector strings...
|
|
|
811 #
|
|
|
812 sub ProcessVectorComparisonOptions {
|
|
|
813 # Setup specified similarity coefficients for vector strings..
|
|
|
814 my($ComparisonMeasure, $SupportedComparisonMeasure, @SupportedComparisonMeasures, %SupportedComparisonMeasuresNameMap, %SupportedComparisonMeasuresMethodMap);
|
|
|
815
|
|
|
816 @SupportedComparisonMeasures = ();
|
|
|
817 %SupportedComparisonMeasuresNameMap = ();
|
|
|
818 %SupportedComparisonMeasuresMethodMap = ();
|
|
|
819 for $SupportedComparisonMeasure (Fingerprints::FingerprintsVector::GetSupportedDistanceAndSimilarityCoefficients()) {
|
|
|
820 # Similarity and distance coefficient function/method names contain "Coefficient" in their names.
|
|
|
821 # So take 'em out and setup a map to original function/method name...
|
|
|
822 $ComparisonMeasure = $SupportedComparisonMeasure;
|
|
|
823 if ($ComparisonMeasure =~ /Coefficient$/i) {
|
|
|
824 $ComparisonMeasure =~ s/Coefficient$//i;
|
|
|
825 }
|
|
|
826 push @SupportedComparisonMeasures, $ComparisonMeasure;
|
|
|
827 $SupportedComparisonMeasuresNameMap{lc($ComparisonMeasure)} = $ComparisonMeasure;
|
|
|
828 $SupportedComparisonMeasuresMethodMap{lc($ComparisonMeasure)} = $SupportedComparisonMeasure;
|
|
|
829 }
|
|
|
830
|
|
|
831 # Setup a list of similarity coefficients to use for calculating similarity matrices for bit vector strings...
|
|
|
832 my($SpecifiedMeasure, @SpecifiedComparisonMeasures, %SpecifiedComparisonMeasuresNameMap, %SpecifiedComparisonMeasuresMethodMap, %SpecifiedComparisonMeasuresParameterMap);
|
|
|
833
|
|
|
834 @SpecifiedComparisonMeasures = ();
|
|
|
835 %SpecifiedComparisonMeasuresNameMap = ();
|
|
|
836 %SpecifiedComparisonMeasuresMethodMap = ();
|
|
|
837
|
|
|
838 if ($Options{vectorcomparisonmode} =~ /^All$/i) {
|
|
|
839 push @SpecifiedComparisonMeasures, @SupportedComparisonMeasures;
|
|
|
840 }
|
|
|
841 else {
|
|
|
842 # Comma delimited list of similarity coefficients...
|
|
|
843 my($VectorComparisonMode, @SpecifiedMeasures, @UnsupportedSpecifiedMeasures);
|
|
|
844
|
|
|
845 $VectorComparisonMode = $Options{vectorcomparisonmode};
|
|
|
846 $VectorComparisonMode =~ s/ //g;
|
|
|
847 @SpecifiedMeasures = split ",", $VectorComparisonMode;
|
|
|
848 @UnsupportedSpecifiedMeasures = ();
|
|
|
849
|
|
|
850 for $SpecifiedMeasure (@SpecifiedMeasures) {
|
|
|
851 if (exists($SupportedComparisonMeasuresMethodMap{lc($SpecifiedMeasure)})) {
|
|
|
852 push @SpecifiedComparisonMeasures, $SpecifiedMeasure;
|
|
|
853 }
|
|
|
854 else {
|
|
|
855 push @UnsupportedSpecifiedMeasures, $SpecifiedMeasure;
|
|
|
856 }
|
|
|
857 }
|
|
|
858 if (@UnsupportedSpecifiedMeasures) {
|
|
|
859 if (@UnsupportedSpecifiedMeasures > 1) {
|
|
|
860 warn "Error: The values specified - ", JoinWords(\@UnsupportedSpecifiedMeasures, ", ", 0)," - for option \"-v --VectorComparisonMode\" are not valid.\n";
|
|
|
861 }
|
|
|
862 else {
|
|
|
863 warn "Error: The value specified, @UnsupportedSpecifiedMeasures, for option \"-v --VectorComparisonMode\" is not valid.\n";
|
|
|
864 }
|
|
|
865 die "Allowed values:", JoinWords(\@SupportedComparisonMeasures, ", ", 0), "\n";
|
|
|
866 }
|
|
|
867 }
|
|
|
868 for $SpecifiedMeasure (@SpecifiedComparisonMeasures) {
|
|
|
869 $SpecifiedComparisonMeasuresMethodMap{lc($SpecifiedMeasure)} = $SupportedComparisonMeasuresMethodMap{lc($SpecifiedMeasure)};
|
|
|
870 $SpecifiedComparisonMeasuresNameMap{lc($SpecifiedMeasure)} = $SupportedComparisonMeasuresNameMap{lc($SpecifiedMeasure)};
|
|
|
871 }
|
|
|
872
|
|
|
873 $OptionsInfo{VectorComparisonMode} = $Options{vectorcomparisonmode};
|
|
|
874 $OptionsInfo{SpecifiedVectorComparisonsRef} = \@SpecifiedComparisonMeasures;
|
|
|
875 $OptionsInfo{SpecifiedVectorComparisonsNameRef} = \%SpecifiedComparisonMeasuresNameMap;
|
|
|
876 $OptionsInfo{SpecifiedVectorComparisonsMethodRef} = \%SpecifiedComparisonMeasuresMethodMap;
|
|
|
877
|
|
|
878 # Setup specified vector comparison calculation modes...
|
|
|
879 my(@SpecifiedVectorComparisonModes);
|
|
|
880 @SpecifiedVectorComparisonModes = ();
|
|
|
881 if ($Options{vectorcomparisonformulism} =~ /^All$/i) {
|
|
|
882 push @SpecifiedVectorComparisonModes, ("AlgebraicForm", "BinaryForm", "SetTheoreticForm");
|
|
|
883 }
|
|
|
884 else {
|
|
|
885 my($SpecifiedFormulism, @SpecifiedFormulismWords);
|
|
|
886
|
|
|
887 @SpecifiedFormulismWords = split /\,/, $Options{vectorcomparisonformulism};
|
|
|
888 for $SpecifiedFormulism (@SpecifiedFormulismWords) {
|
|
|
889 if ($SpecifiedFormulism !~ /^(AlgebraicForm|BinaryForm|SetTheoreticForm)$/i) {
|
|
|
890 die "Error: The value specified, $SpecifiedFormulism, for option \"--VectorComparisonFormulism\" is not valid. Allowed values: AlgebraicForm, BinaryForm or SetTheoreticForm\n";
|
|
|
891 }
|
|
|
892 push @SpecifiedVectorComparisonModes, $SpecifiedFormulism;
|
|
|
893 }
|
|
|
894 }
|
|
|
895 $OptionsInfo{VectorComparisonFormulism} = $Options{vectorcomparisonformulism};
|
|
|
896 $OptionsInfo{SpecifiedVectorComparisonModesRef} = \@SpecifiedVectorComparisonModes;
|
|
|
897
|
|
|
898 # Setup any parameters required for specified comparison menthod...
|
|
|
899 for $SpecifiedMeasure (@SpecifiedComparisonMeasures) {
|
|
|
900 @{$SpecifiedComparisonMeasuresParameterMap{lc($SpecifiedMeasure)}} = ();
|
|
|
901 push @{$SpecifiedComparisonMeasuresParameterMap{lc($SpecifiedMeasure)}}, ($Options{fast} ? 1 : 0);
|
|
|
902 }
|
|
|
903 $OptionsInfo{SpecifiedVectorComparisonsParameterRef} = \%SpecifiedComparisonMeasuresParameterMap;
|
|
|
904 }
|
|
|
905
|
|
|
906 # Setup script usage and retrieve command line arguments specified using various options...
|
|
|
907 sub SetupScriptUsage {
|
|
|
908
|
|
|
909 # Retrieve all the options...
|
|
|
910 %Options = ();
|
|
|
911
|
|
|
912 $Options{alpha} = 0.5;
|
|
|
913 $Options{beta} = 1;
|
|
|
914
|
|
|
915 $Options{bitvectorcomparisonmode} = "TanimotoSimilarity";
|
|
|
916
|
|
|
917 $Options{colmode} = 'colnum';
|
|
|
918
|
|
|
919 $Options{compoundidprefix} = 'Cmpd';
|
|
|
920 $Options{compoundidmode} = 'LabelPrefix';
|
|
|
921
|
|
|
922 $Options{detail} = 1;
|
|
|
923
|
|
|
924 $Options{indelim} = 'comma';
|
|
|
925 $Options{outdelim} = 'comma';
|
|
|
926
|
|
|
927 $Options{inputdatamode} = 'LoadInMemory';
|
|
|
928
|
|
|
929 $Options{mode} = 'AutoDetect';
|
|
|
930
|
|
|
931 $Options{outmatrixformat} = 'RowsAndColumns';
|
|
|
932
|
|
|
933 $Options{outmatrixtype} = 'FullMatrix';
|
|
|
934
|
|
|
935 $Options{quote} = 'yes';
|
|
|
936 $Options{precision} = 2;
|
|
|
937
|
|
|
938 $Options{vectorcomparisonmode} = "TanimotoSimilarity";
|
|
|
939 $Options{vectorcomparisonformulism} = "AlgebraicForm";
|
|
|
940
|
|
|
941 if (!GetOptions(\%Options, "alpha=f", "beta=f", "bitvectorcomparisonmode|b=s", "colmode|c=s", "compoundidcol=s", "compoundidprefix=s", "compoundidfield=s", "compoundidmode=s", "detail|d=i", "fast|f", "fingerprintscol=s", "fingerprintsfield=s", "help|h", "indelim=s", "inputdatamode=s", "mode|m=s", "outdelim=s", "overwrite|o", "outmatrixformat=s", "outmatrixtype=s", "precision|p=s", "quote|q=s", "root|r=s", "vectorcomparisonmode|v=s", "vectorcomparisonformulism=s", "workingdir|w=s")) {
|
|
|
942 die "\nTo get a list of valid options and their values, use \"$ScriptName -h\" or\n\"perl -S $ScriptName -h\" command and try again...\n";
|
|
|
943 }
|
|
|
944 if ($Options{workingdir}) {
|
|
|
945 if (! -d $Options{workingdir}) {
|
|
|
946 die "Error: The value specified, $Options{workingdir}, for option \"-w --workingdir\" is not a directory name.\n";
|
|
|
947 }
|
|
|
948 chdir $Options{workingdir} or die "Error: Couldn't chdir $Options{workingdir}: $! \n";
|
|
|
949 }
|
|
|
950 if ($Options{colmode} !~ /^(ColNum|ColLabel)$/i) {
|
|
|
951 die "Error: The value specified, $Options{colmode}, for option \"-c, --ColMode\" is not valid. Allowed values: ColNum, or ColLabel\n";
|
|
|
952 }
|
|
|
953 if ($Options{compoundidmode} !~ /^(DataField|MolName|LabelPrefix|MolNameOrLabelPrefix)$/i) {
|
|
|
954 die "Error: The value specified, $Options{compoundidmode}, for option \"--CompoundIDMode\" is not valid. Allowed values: DataField, MolName, LabelPrefix or MolNameOrLabelPrefix\n";
|
|
|
955 }
|
|
|
956 if (!IsPositiveInteger($Options{detail})) {
|
|
|
957 die "Error: The value specified, $Options{detail}, for option \"-d, --detail\" is not valid. Allowed values: > 0 \n";
|
|
|
958 }
|
|
|
959 if ($Options{inputdatamode} !~ /^(LoadInMemory|ScanFile)$/i) {
|
|
|
960 die "Error: The value specified, $Options{inputdatamode}, for option \"--InputDataMode\" is not valid. Allowed values: LoadInMemory or ScanFile\n";
|
|
|
961 }
|
|
|
962 if ($Options{mode} !~ /^(AutoDetect|FingerprintsBitVectorString|FingerprintsVectorString)$/i) {
|
|
|
963 die "Error: The value specified, $Options{mode}, for option \"-m, --mode\" is not valid. Allowed values: AutoDetect, FingerprintsBitVectorString or FingerprintsVectorString \n";
|
|
|
964 }
|
|
|
965 if ($Options{indelim} !~ /^(comma|semicolon)$/i) {
|
|
|
966 die "Error: The value specified, $Options{indelim}, for option \"--InDelim\" is not valid. Allowed values: comma, or semicolon\n";
|
|
|
967 }
|
|
|
968 if ($Options{outdelim} !~ /^(comma|semicolon|tab)$/i) {
|
|
|
969 die "Error: The value specified, $Options{outdelim}, for option \"--OutDelim\" is not valid. Allowed values: comma, tab, or semicolon\n";
|
|
|
970 }
|
|
|
971 if ($Options{outmatrixformat} !~ /^(RowsAndColumns|IDPairsAndValue)$/i) {
|
|
|
972 die "Error: The value specified, $Options{outmatrixformat}, for option \"--OutMatrixFormat\" is not valid. Allowed values: RowsAndColumns or IDPairsAndValue\n";
|
|
|
973 }
|
|
|
974 if ($Options{outmatrixtype} !~ /^(FullMatrix|UpperTriangularMatrix|LowerTriangularMatrix)$/i) {
|
|
|
975 die "Error: The value specified, $Options{outmatrixtype}, for option \"--OutMatrixType\" is not valid. Allowed values: FullMatrix, UpperTriangularMatrix or LowerTriangularMatrix\n";
|
|
|
976 }
|
|
|
977 if ($Options{quote} !~ /^(Yes|No)$/i) {
|
|
|
978 die "Error: The value specified, $Options{quote}, for option \"-q --quote\" is not valid. Allowed values: Yes or No\n";
|
|
|
979 }
|
|
|
980 if (!IsPositiveInteger($Options{precision})) {
|
|
|
981 die "Error: The value specified, $Options{precision}, for option \"--precision\" is not valid. Allowed values: > 0 \n";
|
|
|
982 }
|
|
|
983 }
|
|
|
984
|
|
|
985 __END__
|
|
|
986
|
|
|
987 =head1 NAME
|
|
|
988
|
|
|
989 SimilarityMatricesFingerprints.pl - Calculate similarity matrices using fingerprints strings data in SD, FP and CSV/TSV text file(s)
|
|
|
990
|
|
|
991 =head1 SYNOPSIS
|
|
|
992
|
|
|
993 SimilarityMatricesFingerprints.pl SDFile(s) FPFile(s) TextFile(s)...
|
|
|
994
|
|
|
995 SimilarityMatricesFingerprints.pl [B<--alpha> I<number>] [B<--beta> I<number>]
|
|
|
996 [B<-b, --BitVectorComparisonMode> I<All | "TanimotoSimilarity,[ TverskySimilarity, ... ]">]
|
|
|
997 [B<-c, --ColMode> I<ColNum | ColLabel>] [B<--CompoundIDCol> I<col number | col name>]
|
|
|
998 [B<--CompoundIDPrefix> I<text>] [B<--CompoundIDField> I<DataFieldName>]
|
|
|
999 [B<--CompoundIDMode> I<DataField | MolName | LabelPrefix | MolNameOrLabelPrefix>]
|
|
|
1000 [B<-d, --detail> I<InfoLevel>] [B<-f, --fast>] [B<--FingerprintsCol> I<col number | col name>]
|
|
|
1001 [B<--FingerprintsField> I<FieldLabel>] [B<-h, --help>] [B<--InDelim> I<comma | semicolon>]
|
|
|
1002 [B<--InputDataMode> I<LoadInMemory | ScanFile>]
|
|
|
1003 [B<-m, --mode> I<AutoDetect | FingerprintsBitVectorString | FingerprintsVectorString>]
|
|
|
1004 [B<--OutDelim> I<comma | tab | semicolon>] [B<--OutMatrixFormat> I<RowsAndColumns | IDPairsAndValue>]
|
|
|
1005 [B<--OutMatrixType> I<FullMatrix | UpperTriangularMatrix | LowerTriangularMatrix>]
|
|
|
1006 [B<-o, --overwrite>] [B<-p, --precision> I<number>]
|
|
|
1007 [B<-q, --quote> I<Yes | No>] [B<-r, --root> I<RootName>]
|
|
|
1008 [B<-v, --VectorComparisonMode> I<All | "TanimotoSimilairy, [ ManhattanDistance, ...]">]
|
|
|
1009 [B<--VectorComparisonFormulism> I<All | "AlgebraicForm, [BinaryForm, SetTheoreticForm]">]
|
|
|
1010 [B<-w, --WorkingDir> dirname] SDFile(s) FPFile(s) TextFile(s)...
|
|
|
1011
|
|
|
1012 =head1 DESCRIPTION
|
|
|
1013
|
|
|
1014 Calculate similarity matrices using fingerprint bit-vector or vector strings data in I<SD, FP
|
|
|
1015 and CSV/TSV> text file(s) and generate CSV/TSV text file(s) containing values for specified
|
|
|
1016 similarity and distance coefficients.
|
|
|
1017
|
|
|
1018 The scripts SimilarityMatrixSDFiles.pl and SimilarityMatrixTextFiles.pl have been removed from the
|
|
|
1019 current release of MayaChemTools and their functionality merged with this script.
|
|
|
1020
|
|
|
1021 The valid I<SDFile> extensions are I<.sdf> and I<.sd>. All SD files in a current directory
|
|
|
1022 can be specified either by I<*.sdf> or the current directory name.
|
|
|
1023
|
|
|
1024 The valid I<FPFile> extensions are I<.fpf> and I<.fp>. All FP files in a current directory
|
|
|
1025 can be specified either by I<*.fpf> or the current directory name.
|
|
|
1026
|
|
|
1027 The valid I<TextFile> extensions are I<.csv> and I<.tsv> for comma/semicolon and tab
|
|
|
1028 delimited text files respectively. All other file names are ignored. All text files in a
|
|
|
1029 current directory can be specified by I<*.csv>, I<*.tsv>, or the current directory
|
|
|
1030 name. The B<--indelim> option determines the format of I<TextFile(s)>. Any file
|
|
|
1031 which doesn't correspond to the format indicated by B<--indelim> option is ignored.
|
|
|
1032
|
|
|
1033 Example of I<FP> file containing fingerprints bit-vector string data:
|
|
|
1034
|
|
|
1035 #
|
|
|
1036 # Package = MayaChemTools 7.4
|
|
|
1037 # ReleaseDate = Oct 21, 2010
|
|
|
1038 #
|
|
|
1039 # TimeStamp = Mon Mar 7 15:14:01 2011
|
|
|
1040 #
|
|
|
1041 # FingerprintsStringType = FingerprintsBitVector
|
|
|
1042 #
|
|
|
1043 # Description = PathLengthBits:AtomicInvariantsAtomTypes:MinLength1:...
|
|
|
1044 # Size = 1024
|
|
|
1045 # BitStringFormat = HexadecimalString
|
|
|
1046 # BitsOrder = Ascending
|
|
|
1047 #
|
|
|
1048 Cmpd1 9c8460989ec8a49913991a6603130b0a19e8051c89184414953800cc21510...
|
|
|
1049 Cmpd2 000000249400840040100042011001001980410c000000001010088001120...
|
|
|
1050 ... ...
|
|
|
1051 ... ..
|
|
|
1052
|
|
|
1053 Example of I<FP> file containing fingerprints vector string data:
|
|
|
1054
|
|
|
1055 #
|
|
|
1056 # Package = MayaChemTools 7.4
|
|
|
1057 # ReleaseDate = Oct 21, 2010
|
|
|
1058 #
|
|
|
1059 # TimeStamp = Mon Mar 7 15:14:01 2011
|
|
|
1060 #
|
|
|
1061 # FingerprintsStringType = FingerprintsVector
|
|
|
1062 #
|
|
|
1063 # Description = PathLengthBits:AtomicInvariantsAtomTypes:MinLength1:...
|
|
|
1064 # VectorStringFormat = IDsAndValuesString
|
|
|
1065 # VectorValuesType = NumericalValues
|
|
|
1066 #
|
|
|
1067 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:
|
|
|
1068 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...;
|
|
|
1069 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
|
|
|
1070 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 ...
|
|
|
1071 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
|
|
|
1072 O C CC=O CCCC CCCN CCCO CCNC CNC=N CNC=O CNCN CCCC=O CCCCC CCCCN CC...;
|
|
|
1073 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
|
|
|
1074 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 ...
|
|
|
1075 ... ...
|
|
|
1076 ... ...
|
|
|
1077
|
|
|
1078 Example of I<SD> file containing fingerprints bit-vector string data:
|
|
|
1079
|
|
|
1080 ... ...
|
|
|
1081 ... ...
|
|
|
1082 $$$$
|
|
|
1083 ... ...
|
|
|
1084 ... ...
|
|
|
1085 ... ...
|
|
|
1086 41 44 0 0 0 0 0 0 0 0999 V2000
|
|
|
1087 -3.3652 1.4499 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
|
|
|
1088 ... ...
|
|
|
1089 2 3 1 0 0 0 0
|
|
|
1090 ... ...
|
|
|
1091 M END
|
|
|
1092 > <CmpdID>
|
|
|
1093 Cmpd1
|
|
|
1094
|
|
|
1095 > <PathLengthFingerprints>
|
|
|
1096 FingerprintsBitVector;PathLengthBits:AtomicInvariantsAtomTypes:MinLengt
|
|
|
1097 h1:MaxLength8;1024;HexadecimalString;Ascending;9c8460989ec8a49913991a66
|
|
|
1098 03130b0a19e8051c89184414953800cc2151082844a201042800130860308e8204d4028
|
|
|
1099 00831048940e44281c00060449a5000ac80c894114e006321264401600846c050164462
|
|
|
1100 08190410805000304a10205b0100e04c0038ba0fad0209c0ca8b1200012268b61c0026a
|
|
|
1101 aa0660a11014a011d46
|
|
|
1102
|
|
|
1103 $$$$
|
|
|
1104 ... ...
|
|
|
1105 ... ...
|
|
|
1106
|
|
|
1107 Example of CSV I<Text> file containing fingerprints bit-vector string data:
|
|
|
1108
|
|
|
1109 "CompoundID","PathLengthFingerprints"
|
|
|
1110 "Cmpd1","FingerprintsBitVector;PathLengthBits:AtomicInvariantsAtomTypes
|
|
|
1111 :MinLength1:MaxLength8;1024;HexadecimalString;Ascending;9c8460989ec8a4
|
|
|
1112 9913991a6603130b0a19e8051c89184414953800cc2151082844a20104280013086030
|
|
|
1113 8e8204d402800831048940e44281c00060449a5000ac80c894114e006321264401..."
|
|
|
1114 ... ...
|
|
|
1115 ... ...
|
|
|
1116
|
|
|
1117 The current release of MayaChemTools supports the following types of fingerprint
|
|
|
1118 bit-vector and vector strings:
|
|
|
1119
|
|
|
1120 FingerprintsVector;AtomNeighborhoods:AtomicInvariantsAtomTypes:MinRadi
|
|
|
1121 us0:MaxRadius2;41;AlphaNumericalValues;ValuesString;NR0-C.X1.BO1.H3-AT
|
|
|
1122 C1:NR1-C.X3.BO3.H1-ATC1:NR2-C.X1.BO1.H3-ATC1:NR2-C.X3.BO4-ATC1 NR0-C.X
|
|
|
1123 1.BO1.H3-ATC1:NR1-C.X3.BO3.H1-ATC1:NR2-C.X1.BO1.H3-ATC1:NR2-C.X3.BO4-A
|
|
|
1124 TC1 NR0-C.X2.BO2.H2-ATC1:NR1-C.X2.BO2.H2-ATC1:NR1-C.X3.BO3.H1-ATC1:NR2
|
|
|
1125 -C.X2.BO2.H2-ATC1:NR2-N.X3.BO3-ATC1:NR2-O.X1.BO1.H1-ATC1 NR0-C.X2.B...
|
|
|
1126
|
|
|
1127 FingerprintsVector;AtomTypesCount:AtomicInvariantsAtomTypes:ArbitraryS
|
|
|
1128 ize;10;NumericalValues;IDsAndValuesString;C.X1.BO1.H3 C.X2.BO2.H2 C.X2
|
|
|
1129 .BO3.H1 C.X3.BO3.H1 C.X3.BO4 F.X1.BO1 N.X2.BO2.H1 N.X3.BO3 O.X1.BO1.H1
|
|
|
1130 O.X1.BO2;2 4 14 3 10 1 1 1 3 2
|
|
|
1131
|
|
|
1132 FingerprintsVector;AtomTypesCount:SLogPAtomTypes:ArbitrarySize;16;Nume
|
|
|
1133 ricalValues;IDsAndValuesString;C1 C10 C11 C14 C18 C20 C21 C22 C5 CS F
|
|
|
1134 N11 N4 O10 O2 O9;5 1 1 1 14 4 2 1 2 2 1 1 1 1 3 1
|
|
|
1135
|
|
|
1136 FingerprintsVector;AtomTypesCount:SLogPAtomTypes:FixedSize;67;OrderedN
|
|
|
1137 umericalValues;IDsAndValuesString;C1 C2 C3 C4 C5 C6 C7 C8 C9 C10 C11 C
|
|
|
1138 12 C13 C14 C15 C16 C17 C18 C19 C20 C21 C22 C23 C24 C25 C26 C27 CS N1 N
|
|
|
1139 2 N3 N4 N5 N6 N7 N8 N9 N10 N11 N12 N13 N14 NS O1 O2 O3 O4 O5 O6 O7 O8
|
|
|
1140 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
|
|
|
1141 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...
|
|
|
1142
|
|
|
1143 FingerprintsVector;EStateIndicies:ArbitrarySize;11;NumericalValues;IDs
|
|
|
1144 AndValuesString;SaaCH SaasC SaasN SdO SdssC SsCH3 SsF SsOH SssCH2 SssN
|
|
|
1145 H SsssCH;24.778 4.387 1.993 25.023 -1.435 3.975 14.006 29.759 -0.073 3
|
|
|
1146 .024 -2.270
|
|
|
1147
|
|
|
1148 FingerprintsVector;EStateIndicies:FixedSize;87;OrderedNumericalValues;
|
|
|
1149 ValuesString;0 0 0 0 0 0 0 3.975 0 -0.073 0 0 24.778 -2.270 0 0 -1.435
|
|
|
1150 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
|
|
|
1151 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
|
|
|
1152 0 0 0 0 0 0 0 0 0 0 0 0 0 0
|
|
|
1153
|
|
|
1154 FingerprintsVector;ExtendedConnectivity:AtomicInvariantsAtomTypes:Radi
|
|
|
1155 us2;60;AlphaNumericalValues;ValuesString;73555770 333564680 352413391
|
|
|
1156 666191900 1001270906 1371674323 1481469939 1977749791 2006158649 21414
|
|
|
1157 08799 49532520 64643108 79385615 96062769 273726379 564565671 85514103
|
|
|
1158 5 906706094 988546669 1018231313 1032696425 1197507444 1331250018 1338
|
|
|
1159 532734 1455473691 1607485225 1609687129 1631614296 1670251330 17303...
|
|
|
1160
|
|
|
1161 FingerprintsVector;ExtendedConnectivityCount:AtomicInvariantsAtomTypes
|
|
|
1162 :Radius2;60;NumericalValues;IDsAndValuesString;73555770 333564680 3524
|
|
|
1163 13391 666191900 1001270906 1371674323 1481469939 1977749791 2006158649
|
|
|
1164 2141408799 49532520 64643108 79385615 96062769 273726379 564565671...;
|
|
|
1165 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
|
|
|
1166 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
|
|
|
1167
|
|
|
1168 FingerprintsBitVector;ExtendedConnectivityBits:AtomicInvariantsAtomTyp
|
|
|
1169 es:Radius2;1024;BinaryString;Ascending;0000000000000000000000000000100
|
|
|
1170 0000000001010000000110000011000000000000100000000000000000000000100001
|
|
|
1171 1000000110000000000000000000000000010011000000000000000000000000010000
|
|
|
1172 0000000000000000000000000010000000000000000001000000000000000000000000
|
|
|
1173 0000000000010000100001000000000000101000000000000000100000000000000...
|
|
|
1174
|
|
|
1175 FingerprintsVector;ExtendedConnectivity:FunctionalClassAtomTypes:Radiu
|
|
|
1176 s2;57;AlphaNumericalValues;ValuesString;24769214 508787397 850393286 8
|
|
|
1177 62102353 981185303 1231636850 1649386610 1941540674 263599683 32920567
|
|
|
1178 1 571109041 639579325 683993318 723853089 810600886 885767127 90326012
|
|
|
1179 7 958841485 981022393 1126908698 1152248391 1317567065 1421489994 1455
|
|
|
1180 632544 1557272891 1826413669 1983319256 2015750777 2029559552 20404...
|
|
|
1181
|
|
|
1182 FingerprintsVector;ExtendedConnectivity:EStateAtomTypes:Radius2;62;Alp
|
|
|
1183 haNumericalValues;ValuesString;25189973 528584866 662581668 671034184
|
|
|
1184 926543080 1347067490 1738510057 1759600920 2034425745 2097234755 21450
|
|
|
1185 44754 96779665 180364292 341712110 345278822 386540408 387387308 50430
|
|
|
1186 1706 617094135 771528807 957666640 997798220 1158349170 1291258082 134
|
|
|
1187 1138533 1395329837 1420277211 1479584608 1486476397 1487556246 1566...
|
|
|
1188
|
|
|
1189 FingerprintsBitVector;MACCSKeyBits;166;BinaryString;Ascending;00000000
|
|
|
1190 0000000000000000000000000000000001001000010010000000010010000000011100
|
|
|
1191 0100101010111100011011000100110110000011011110100110111111111111011111
|
|
|
1192 11111111111110111000
|
|
|
1193
|
|
|
1194 FingerprintsBitVector;MACCSKeyBits;322;BinaryString;Ascending;11101011
|
|
|
1195 1110011111100101111111000111101100110000000000000011100010000000000000
|
|
|
1196 0000000000000000000000000000000000000000000000101000000000000000000000
|
|
|
1197 0000000000000000000000000000000000000000000000000000000000000000000000
|
|
|
1198 0000000000000000000000000000000000000011000000000000000000000000000000
|
|
|
1199 0000000000000000000000000000000000000000
|
|
|
1200
|
|
|
1201 FingerprintsVector;MACCSKeyCount;166;OrderedNumericalValues;ValuesStri
|
|
|
1202 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
|
|
|
1203 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
|
|
|
1204 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
|
|
|
1205 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
|
|
|
1206 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
|
|
|
1207
|
|
|
1208 FingerprintsVector;MACCSKeyCount;322;OrderedNumericalValues;ValuesStri
|
|
|
1209 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
|
|
|
1210 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
|
|
|
1211 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
|
|
|
1212 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
|
|
|
1213 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 ...
|
|
|
1214
|
|
|
1215 FingerprintsBitVector;PathLengthBits:AtomicInvariantsAtomTypes:MinLeng
|
|
|
1216 th1:MaxLength8;1024;BinaryString;Ascending;001000010011010101011000110
|
|
|
1217 0100010101011000101001011100110001000010001001101000001001001001001000
|
|
|
1218 0010110100000111001001000001001010100100100000000011000000101001011100
|
|
|
1219 0010000001000101010100000100111100110111011011011000000010110111001101
|
|
|
1220 0101100011000000010001000011000010100011101100001000001000100000000...
|
|
|
1221
|
|
|
1222 FingerprintsVector;PathLengthCount:AtomicInvariantsAtomTypes:MinLength
|
|
|
1223 1:MaxLength8;432;NumericalValues;IDsAndValuesPairsString;C.X1.BO1.H3 2
|
|
|
1224 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
|
|
|
1225 2.BO2.H1 1 N.X3.BO3 1 O.X1.BO1.H1 3 O.X1.BO2 2 C.X1.BO1.H3C.X3.BO3.H1
|
|
|
1226 2 C.X2.BO2.H2C.X2.BO2.H2 1 C.X2.BO2.H2C.X3.BO3.H1 4 C.X2.BO2.H2C.X3.BO
|
|
|
1227 4 1 C.X2.BO2.H2N.X3.BO3 1 C.X2.BO3.H1:C.X2.BO3.H1 10 C.X2.BO3.H1:C....
|
|
|
1228
|
|
|
1229 FingerprintsVector;PathLengthCount:MMFF94AtomTypes:MinLength1:MaxLengt
|
|
|
1230 h8;463;NumericalValues;IDsAndValuesPairsString;C5A 2 C5B 2 C=ON 1 CB 1
|
|
|
1231 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
|
|
|
1232 5 2 C5ACB 1 C5ACR 1 C5B:C5B 1 C5BC=ON 1 C5BCB 1 C=ON=O=CN 1 C=ONNC=O 1
|
|
|
1233 CB:CB 18 CBF 1 CBNC=O 1 COO=O=CO 1 COOCR 1 COOOC=O 1 CRCR 7 CRN5 1 CR
|
|
|
1234 OR 2 C5A:C5B:C5B 2 C5A:C5BC=ON 1 C5A:C5BCB 1 C5A:N5:C5A 1 C5A:N5CR ...
|
|
|
1235
|
|
|
1236 FingerprintsVector;TopologicalAtomPairs:AtomicInvariantsAtomTypes:MinD
|
|
|
1237 istance1:MaxDistance10;223;NumericalValues;IDsAndValuesString;C.X1.BO1
|
|
|
1238 .H3-D1-C.X3.BO3.H1 C.X2.BO2.H2-D1-C.X2.BO2.H2 C.X2.BO2.H2-D1-C.X3.BO3.
|
|
|
1239 H1 C.X2.BO2.H2-D1-C.X3.BO4 C.X2.BO2.H2-D1-N.X3.BO3 C.X2.BO3.H1-D1-...;
|
|
|
1240 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
|
|
|
1241 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...
|
|
|
1242
|
|
|
1243 FingerprintsVector;TopologicalAtomPairs:FunctionalClassAtomTypes:MinDi
|
|
|
1244 stance1:MaxDistance10;144;NumericalValues;IDsAndValuesString;Ar-D1-Ar
|
|
|
1245 Ar-D1-Ar.HBA Ar-D1-HBD Ar-D1-Hal Ar-D1-None Ar.HBA-D1-None HBA-D1-NI H
|
|
|
1246 BA-D1-None HBA.HBD-D1-NI HBA.HBD-D1-None HBD-D1-None NI-D1-None No...;
|
|
|
1247 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
|
|
|
1248 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 ...
|
|
|
1249
|
|
|
1250 FingerprintsVector;TopologicalAtomTorsions:AtomicInvariantsAtomTypes;3
|
|
|
1251 3;NumericalValues;IDsAndValuesString;C.X1.BO1.H3-C.X3.BO3.H1-C.X3.BO4-
|
|
|
1252 C.X3.BO4 C.X1.BO1.H3-C.X3.BO3.H1-C.X3.BO4-N.X3.BO3 C.X2.BO2.H2-C.X2.BO
|
|
|
1253 2.H2-C.X3.BO3.H1-C.X2.BO2.H2 C.X2.BO2.H2-C.X2.BO2.H2-C.X3.BO3.H1-O...;
|
|
|
1254 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
|
|
|
1255
|
|
|
1256 FingerprintsVector;TopologicalAtomTorsions:EStateAtomTypes;36;Numerica
|
|
|
1257 lValues;IDsAndValuesString;aaCH-aaCH-aaCH-aaCH aaCH-aaCH-aaCH-aasC aaC
|
|
|
1258 H-aaCH-aasC-aaCH aaCH-aaCH-aasC-aasC aaCH-aaCH-aasC-sF aaCH-aaCH-aasC-
|
|
|
1259 ssNH aaCH-aasC-aasC-aasC aaCH-aasC-aasC-aasN aaCH-aasC-ssNH-dssC a...;
|
|
|
1260 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
|
|
|
1261
|
|
|
1262 FingerprintsVector;TopologicalAtomTriplets:AtomicInvariantsAtomTypes:M
|
|
|
1263 inDistance1:MaxDistance10;3096;NumericalValues;IDsAndValuesString;C.X1
|
|
|
1264 .BO1.H3-D1-C.X1.BO1.H3-D1-C.X3.BO3.H1-D2 C.X1.BO1.H3-D1-C.X2.BO2.H2-D1
|
|
|
1265 0-C.X3.BO4-D9 C.X1.BO1.H3-D1-C.X2.BO2.H2-D3-N.X3.BO3-D4 C.X1.BO1.H3-D1
|
|
|
1266 -C.X2.BO2.H2-D4-C.X2.BO2.H2-D5 C.X1.BO1.H3-D1-C.X2.BO2.H2-D6-C.X3....;
|
|
|
1267 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
|
|
|
1268 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...
|
|
|
1269
|
|
|
1270 FingerprintsVector;TopologicalAtomTriplets:SYBYLAtomTypes:MinDistance1
|
|
|
1271 :MaxDistance10;2332;NumericalValues;IDsAndValuesString;C.2-D1-C.2-D9-C
|
|
|
1272 .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-
|
|
|
1273 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
|
|
|
1274 -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.
|
|
|
1275 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...
|
|
|
1276
|
|
|
1277 FingerprintsVector;TopologicalPharmacophoreAtomPairs:ArbitrarySize:Min
|
|
|
1278 Distance1:MaxDistance10;54;NumericalValues;IDsAndValuesString;H-D1-H H
|
|
|
1279 -D1-NI HBA-D1-NI HBD-D1-NI H-D2-H H-D2-HBA H-D2-HBD HBA-D2-HBA HBA-D2-
|
|
|
1280 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
|
|
|
1281 BA H-D4-HBD HBA-D4-HBA HBA-D4-HBD HBD-D4-HBD H-D5-H H-D5-HBA H-D5-...;
|
|
|
1282 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
|
|
|
1283 3 4 1 37 10 8 1 35 10 9 3 3 1 28 7 7 4 18 16 12 5 1 2 1
|
|
|
1284
|
|
|
1285 FingerprintsVector;TopologicalPharmacophoreAtomPairs:FixedSize:MinDist
|
|
|
1286 ance1:MaxDistance10;150;OrderedNumericalValues;ValuesString;18 0 0 1 0
|
|
|
1287 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
|
|
|
1288 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
|
|
|
1289 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
|
|
|
1290 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...
|
|
|
1291
|
|
|
1292 FingerprintsVector;TopologicalPharmacophoreAtomTriplets:ArbitrarySize:
|
|
|
1293 MinDistance1:MaxDistance10;696;NumericalValues;IDsAndValuesString;Ar1-
|
|
|
1294 Ar1-Ar1 Ar1-Ar1-H1 Ar1-Ar1-HBA1 Ar1-Ar1-HBD1 Ar1-H1-H1 Ar1-H1-HBA1 Ar1
|
|
|
1295 -H1-HBD1 Ar1-HBA1-HBD1 H1-H1-H1 H1-H1-HBA1 H1-H1-HBD1 H1-HBA1-HBA1 H1-
|
|
|
1296 HBA1-HBD1 H1-HBA1-NI1 H1-HBD1-NI1 HBA1-HBA1-NI1 HBA1-HBD1-NI1 Ar1-...;
|
|
|
1297 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
|
|
|
1298 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
|
|
|
1299 119 123 24 15 185 202 41 25 22 17 3 5 85 95 18 11 23 17 3 1 1 6 4 ...
|
|
|
1300
|
|
|
1301 FingerprintsVector;TopologicalPharmacophoreAtomTriplets:FixedSize:MinD
|
|
|
1302 istance1:MaxDistance10;2692;OrderedNumericalValues;ValuesString;46 106
|
|
|
1303 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
|
|
|
1304 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
|
|
|
1305 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
|
|
|
1306 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 ...
|
|
|
1307
|
|
|
1308 =head1 OPTIONS
|
|
|
1309
|
|
|
1310 =over 4
|
|
|
1311
|
|
|
1312 =item B<--alpha> I<number>
|
|
|
1313
|
|
|
1314 Value of alpha parameter for calculating I<Tversky> similarity coefficient specified for
|
|
|
1315 B<-b, --BitVectorComparisonMode> option. It corresponds to weights assigned for bits set
|
|
|
1316 to "1" in a pair of fingerprint bit-vectors during the calculation of similarity coefficient. Possible
|
|
|
1317 values: I<0 to 1>. Default value: <0.5>.
|
|
|
1318
|
|
|
1319 =item B<--beta> I<number>
|
|
|
1320
|
|
|
1321 Value of beta parameter for calculating I<WeightedTanimoto> and I<WeightedTversky>
|
|
|
1322 similarity coefficients specified for B<-b, --BitVectorComparisonMode> option. It is used to
|
|
|
1323 weight the contributions of bits set to "0" during the calculation of similarity coefficients. Possible
|
|
|
1324 values: I<0 to 1>. Default value of <1> makes I<WeightedTanimoto> and I<WeightedTversky>
|
|
|
1325 equivalent to I<Tanimoto> and I<Tversky>.
|
|
|
1326
|
|
|
1327 =item B<-b, --BitVectorComparisonMode> I<All | "TanimotoSimilarity,[TverskySimilarity,...]">
|
|
|
1328
|
|
|
1329 Specify what similarity coefficients to use for calculating similarity matrices for fingerprints bit-vector
|
|
|
1330 strings data values in I<TextFile(s)>: calculate similarity matrices for all supported similarity
|
|
|
1331 coefficients or specify a comma delimited list of similarity coefficients. Possible values:
|
|
|
1332 I<All | "TanimotoSimilarity,[TverskySimilarity,...]>. Default: I<TanimotoSimilarity>
|
|
|
1333
|
|
|
1334 I<All> uses complete list of supported similarity coefficients: I<BaroniUrbaniSimilarity, BuserSimilarity,
|
|
|
1335 CosineSimilarity, DiceSimilarity, DennisSimilarity, ForbesSimilarity, FossumSimilarity, HamannSimilarity, JacardSimilarity,
|
|
|
1336 Kulczynski1Similarity, Kulczynski2Similarity, MatchingSimilarity, McConnaugheySimilarity, OchiaiSimilarity,
|
|
|
1337 PearsonSimilarity, RogersTanimotoSimilarity, RussellRaoSimilarity, SimpsonSimilarity, SkoalSneath1Similarity,
|
|
|
1338 SkoalSneath2Similarity, SkoalSneath3Similarity, TanimotoSimilarity, TverskySimilarity, YuleSimilarity,
|
|
|
1339 WeightedTanimotoSimilarity, WeightedTverskySimilarity>. These similarity coefficients are described below.
|
|
|
1340
|
|
|
1341 For two fingerprint bit-vectors A and B of same size, let:
|
|
|
1342
|
|
|
1343 Na = Number of bits set to "1" in A
|
|
|
1344 Nb = Number of bits set to "1" in B
|
|
|
1345 Nc = Number of bits set to "1" in both A and B
|
|
|
1346 Nd = Number of bits set to "0" in both A and B
|
|
|
1347
|
|
|
1348 Nt = Number of bits set to "1" or "0" in A or B (Size of A or B)
|
|
|
1349 Nt = Na + Nb - Nc + Nd
|
|
|
1350
|
|
|
1351 Na - Nc = Number of bits set to "1" in A but not in B
|
|
|
1352 Nb - Nc = Number of bits set to "1" in B but not in A
|
|
|
1353
|
|
|
1354 Then, various similarity coefficients [ Ref. 40 - 42 ] for a pair of bit-vectors A and B are
|
|
|
1355 defined as follows:
|
|
|
1356
|
|
|
1357 I<BaroniUrbaniSimilarity>: ( SQRT( Nc * Nd ) + Nc ) / ( SQRT ( Nc * Nd ) + Nc + ( Na - Nc ) + ( Nb - Nc ) ) ( same as Buser )
|
|
|
1358
|
|
|
1359 I<BuserSimilarity>: ( SQRT ( Nc * Nd ) + Nc ) / ( SQRT ( Nc * Nd ) + Nc + ( Na - Nc ) + ( Nb - Nc ) ) ( same as BaroniUrbani )
|
|
|
1360
|
|
|
1361 I<CosineSimilarity>: Nc / SQRT ( Na * Nb ) (same as Ochiai)
|
|
|
1362
|
|
|
1363 I<DiceSimilarity>: (2 * Nc) / ( Na + Nb )
|
|
|
1364
|
|
|
1365 I<DennisSimilarity>: ( Nc * Nd - ( ( Na - Nc ) * ( Nb - Nc ) ) ) / SQRT ( Nt * Na * Nb)
|
|
|
1366
|
|
|
1367 I<ForbesSimilarity>: ( Nt * Nc ) / ( Na * Nb )
|
|
|
1368
|
|
|
1369 I<FossumSimilarity>: ( Nt * ( ( Nc - 1/2 ) ** 2 ) / ( Na * Nb )
|
|
|
1370
|
|
|
1371 I<HamannSimilarity>: ( ( Nc + Nd ) - ( Na - Nc ) - ( Nb - Nc ) ) / Nt
|
|
|
1372
|
|
|
1373 I<JaccardSimilarity>: Nc / ( ( Na - Nc) + ( Nb - Nc ) + Nc ) = Nc / ( Na + Nb - Nc ) (same as Tanimoto)
|
|
|
1374
|
|
|
1375 I<Kulczynski1Similarity>: Nc / ( ( Na - Nc ) + ( Nb - Nc) ) = Nc / ( Na + Nb - 2Nc )
|
|
|
1376
|
|
|
1377 I<Kulczynski2Similarity>: ( ( Nc / 2 ) * ( 2 * Nc + ( Na - Nc ) + ( Nb - Nc) ) ) / ( ( Nc + ( Na - Nc ) ) * ( Nc + ( Nb - Nc ) ) ) = 0.5 * ( Nc / Na + Nc / Nb )
|
|
|
1378
|
|
|
1379 I<MatchingSimilarity>: ( Nc + Nd ) / Nt
|
|
|
1380
|
|
|
1381 I<McConnaugheySimilarity>: ( Nc ** 2 - ( Na - Nc ) * ( Nb - Nc) ) / ( Na * Nb )
|
|
|
1382
|
|
|
1383 I<OchiaiSimilarity>: Nc / SQRT ( Na * Nb ) (same as Cosine)
|
|
|
1384
|
|
|
1385 I<PearsonSimilarity>: ( ( Nc * Nd ) - ( ( Na - Nc ) * ( Nb - Nc ) ) / SQRT ( Na * Nb * ( Na - Nc + Nd ) * ( Nb - Nc + Nd ) )
|
|
|
1386
|
|
|
1387 I<RogersTanimotoSimilarity>: ( Nc + Nd ) / ( ( Na - Nc) + ( Nb - Nc) + Nt) = ( Nc + Nd ) / ( Na + Nb - 2Nc + Nt)
|
|
|
1388
|
|
|
1389 I<RussellRaoSimilarity>: Nc / Nt
|
|
|
1390
|
|
|
1391 I<SimpsonSimilarity>: Nc / MIN ( Na, Nb)
|
|
|
1392
|
|
|
1393 I<SkoalSneath1Similarity>: Nc / ( Nc + 2 * ( Na - Nc) + 2 * ( Nb - Nc) ) = Nc / ( 2 * Na + 2 * Nb - 3 * Nc )
|
|
|
1394
|
|
|
1395 I<SkoalSneath2Similarity>: ( 2 * Nc + 2 * Nd ) / ( Nc + Nd + Nt )
|
|
|
1396
|
|
|
1397 I<SkoalSneath3Similarity>: ( Nc + Nd ) / ( ( Na - Nc ) + ( Nb - Nc ) ) = ( Nc + Nd ) / ( Na + Nb - 2 * Nc )
|
|
|
1398
|
|
|
1399 I<TanimotoSimilarity>: Nc / ( ( Na - Nc) + ( Nb - Nc ) + Nc ) = Nc / ( Na + Nb - Nc ) (same as Jaccard)
|
|
|
1400
|
|
|
1401 I<TverskySimilarity>: Nc / ( alpha * ( Na - Nc ) + ( 1 - alpha) * ( Nb - Nc) + Nc ) = Nc / ( alpha * ( Na - Nb ) + Nb)
|
|
|
1402
|
|
|
1403 I<YuleSimilarity>: ( ( Nc * Nd ) - ( ( Na - Nc ) * ( Nb - Nc ) ) ) / ( ( Nc * Nd ) + ( ( Na - Nc ) * ( Nb - Nc ) ) )
|
|
|
1404
|
|
|
1405 Values of Tanimoto/Jaccard and Tversky coefficients are dependent on only those bit which
|
|
|
1406 are set to "1" in both A and B. In order to take into account all bit positions, modified versions
|
|
|
1407 of Tanimoto [ Ref. 42 ] and Tversky [ Ref. 43 ] have been developed.
|
|
|
1408
|
|
|
1409 Let:
|
|
|
1410
|
|
|
1411 Na' = Number of bits set to "0" in A
|
|
|
1412 Nb' = Number of bits set to "0" in B
|
|
|
1413 Nc' = Number of bits set to "0" in both A and B
|
|
|
1414
|
|
|
1415 Tanimoto': Nc' / ( ( Na' - Nc') + ( Nb' - Nc' ) + Nc' ) = Nc' / ( Na' + Nb' - Nc' )
|
|
|
1416
|
|
|
1417 Tversky': Nc' / ( alpha * ( Na' - Nc' ) + ( 1 - alpha) * ( Nb' - Nc' ) + Nc' ) = Nc' / ( alpha * ( Na' - Nb' ) + Nb')
|
|
|
1418
|
|
|
1419 Then:
|
|
|
1420
|
|
|
1421 I<WeightedTanimotoSimilarity> = beta * Tanimoto + (1 - beta) * Tanimoto'
|
|
|
1422
|
|
|
1423 I<WeightedTverskySimilarity> = beta * Tversky + (1 - beta) * Tversky'
|
|
|
1424
|
|
|
1425 =item B<-c, --ColMode> I<ColNum | ColLabel>
|
|
|
1426
|
|
|
1427 Specify how columns are identified in I<TextFile(s)>: using column number or column
|
|
|
1428 label. Possible values: I<ColNum or ColLabel>. Default value: I<ColNum>.
|
|
|
1429
|
|
|
1430 =item B<--CompoundIDCol> I<col number | col name>
|
|
|
1431
|
|
|
1432 This value is B<-c, --ColMode> mode specific. It specifies input I<TextFile(s)> column to use for
|
|
|
1433 generating compound ID for similarity matrices in output I<TextFile(s)>. Possible values: I<col number
|
|
|
1434 or col label>. Default value: I<first column containing the word compoundID in its column label or sequentially
|
|
|
1435 generated IDs>.
|
|
|
1436
|
|
|
1437 =item B<--CompoundIDPrefix> I<text>
|
|
|
1438
|
|
|
1439 Specify compound ID prefix to use during sequential generation of compound IDs for input I<SDFile(s)>
|
|
|
1440 and I<TextFile(s)>. Default value: I<Cmpd>. The default value generates compound IDs which look
|
|
|
1441 like Cmpd<Number>.
|
|
|
1442
|
|
|
1443 For input I<SDFile(s)>, this value is only used during I<LabelPrefix | MolNameOrLabelPrefix> values
|
|
|
1444 of B<--CompoundIDMode> option; otherwise, it's ignored.
|
|
|
1445
|
|
|
1446 Examples for I<LabelPrefix> or I<MolNameOrLabelPrefix> value of B<--CompoundIDMode>:
|
|
|
1447
|
|
|
1448 Compound
|
|
|
1449
|
|
|
1450 The values specified above generates compound IDs which correspond to Compound<Number>
|
|
|
1451 instead of default value of Cmpd<Number>.
|
|
|
1452
|
|
|
1453 =item B<--CompoundIDField> I<DataFieldName>
|
|
|
1454
|
|
|
1455 Specify input I<SDFile(s)> datafield label for generating compound IDs. This value is only used
|
|
|
1456 during I<DataField> value of B<--CompoundIDMode> option.
|
|
|
1457
|
|
|
1458 Examples for I<DataField> value of B<--CompoundIDMode>:
|
|
|
1459
|
|
|
1460 MolID
|
|
|
1461 ExtReg
|
|
|
1462
|
|
|
1463 =item B<--CompoundIDMode> I<DataField | MolName | LabelPrefix | MolNameOrLabelPrefix>
|
|
|
1464
|
|
|
1465 Specify how to generate compound IDs from input I<SDFile(s)> for similarity matrix CSV/TSV text
|
|
|
1466 file(s): use a I<SDFile(s)> datafield value; use molname line from I<SDFile(s)>; generate a sequential ID
|
|
|
1467 with specific prefix; use combination of both MolName and LabelPrefix with usage of LabelPrefix values
|
|
|
1468 for empty molname lines.
|
|
|
1469
|
|
|
1470 Possible values: I<DataField | MolName | LabelPrefix | MolNameOrLabelPrefix>.
|
|
|
1471 Default: I<LabelPrefix>.
|
|
|
1472
|
|
|
1473 For I<MolNameAndLabelPrefix> value of B<--CompoundIDMode>, molname line in I<SDFile(s)> takes
|
|
|
1474 precedence over sequential compound IDs generated using I<LabelPrefix> and only empty molname
|
|
|
1475 values are replaced with sequential compound IDs.
|
|
|
1476
|
|
|
1477 =item B<-d, --detail> I<InfoLevel>
|
|
|
1478
|
|
|
1479 Level of information to print about lines being ignored. Default: I<1>. Possible values:
|
|
|
1480 I<1, 2 or 3>.
|
|
|
1481
|
|
|
1482 =item B<-f, --fast>
|
|
|
1483
|
|
|
1484 In this mode, fingerprints columns specified using B<--FingerprintsCol> for I<TextFile(s)> and
|
|
|
1485 B<--FingerprintsField> for I<SDFile(s)> are assumed to contain valid fingerprints data and no
|
|
|
1486 checking is performed before calculating similarity matrices. By default, fingerprints data is
|
|
|
1487 validated before computing pairwise similarity and distance coefficients.
|
|
|
1488
|
|
|
1489 =item B<--FingerprintsCol> I<col number | col name>
|
|
|
1490
|
|
|
1491 This value is B<-c, --colmode> specific. It specifies fingerprints column to use during
|
|
|
1492 calculation similarity matrices for I<TextFile(s)>. Possible values: I<col number or col label>.
|
|
|
1493 Default value: I<first column containing the word Fingerprints in its column label>.
|
|
|
1494
|
|
|
1495 =item B<--FingerprintsField> I<FieldLabel>
|
|
|
1496
|
|
|
1497 Fingerprints field label to use during calculation similarity matrices for I<SDFile(s)>.
|
|
|
1498 Default value: I<first data field label containing the word Fingerprints in its label>
|
|
|
1499
|
|
|
1500 =item B<-h, --help>
|
|
|
1501
|
|
|
1502 Print this help message.
|
|
|
1503
|
|
|
1504 =item B<--InDelim> I<comma | semicolon>
|
|
|
1505
|
|
|
1506 Input delimiter for CSV I<TextFile(s)>. Possible values: I<comma or semicolon>.
|
|
|
1507 Default value: I<comma>. For TSV files, this option is ignored and I<tab> is used as a
|
|
|
1508 delimiter.
|
|
|
1509
|
|
|
1510 =item B<--InputDataMode> I<LoadInMemory | ScanFile>
|
|
|
1511
|
|
|
1512 Specify how fingerprints bit-vector or vector strings data from I<SD, FP and CSV/TSV>
|
|
|
1513 fingerprint file(s) is processed: Retrieve, process and load all available fingerprints
|
|
|
1514 data in memory; Retrieve and process data for fingerprints one at a time. Possible values
|
|
|
1515 : I<LoadInMemory | ScanFile>. Default: I<LoadInMemory>.
|
|
|
1516
|
|
|
1517 During I<LoadInMemory> value of B<--InputDataMode>, fingerprints bit-vector or vector
|
|
|
1518 strings data from input file is retrieved, processed, and loaded into memory all at once
|
|
|
1519 as fingerprints objects for generation for similarity matrices.
|
|
|
1520
|
|
|
1521 During I<ScanFile> value of B<--InputDataMode>, multiple passes over the input fingerprints
|
|
|
1522 file are performed to retrieve and process fingerprints bit-vector or vector strings data one at
|
|
|
1523 a time to generate fingerprints objects used during generation of similarity matrices. A temporary
|
|
|
1524 copy of the input fingerprints file is made at the start and deleted after generating the matrices.
|
|
|
1525
|
|
|
1526 I<ScanFile> value of B<--InputDataMode> allows processing of arbitrary large fingerprints files
|
|
|
1527 without any additional memory requirement.
|
|
|
1528
|
|
|
1529 =item B<-m, --mode> I<AutoDetect | FingerprintsBitVectorString | FingerprintsVectorString>
|
|
|
1530
|
|
|
1531 Format of fingerprint strings data in I<TextFile(s)>: automatically detect format of fingerprints
|
|
|
1532 string created by MayaChemTools fingerprints generation scripts or explicitly specify its format.
|
|
|
1533 Possible values: I<AutoDetect | FingerprintsBitVectorString | FingerprintsVectorString>. Default
|
|
|
1534 value: I<AutoDetect>.
|
|
|
1535
|
|
|
1536 =item B<--OutDelim> I<comma | tab | semicolon>
|
|
|
1537
|
|
|
1538 Delimiter for output CSV/TSV text file(s). Possible values: I<comma, tab, or semicolon>
|
|
|
1539 Default value: I<comma>.
|
|
|
1540
|
|
|
1541 =item B<--OutMatrixFormat> I<RowsAndColumns | IDPairsAndValue>
|
|
|
1542
|
|
|
1543 Specify how similarity or distance values calculated for fingerprints vector and bit-vector strings
|
|
|
1544 are written to the output CSV/TSV text file(s): Generate text files containing rows and columns
|
|
|
1545 with their labels corresponding to compound IDs and each matrix element value corresponding to
|
|
|
1546 similarity or distance between corresponding compounds; Generate text files containing rows containing
|
|
|
1547 compoundIDs for two compounds followed by similarity or distance value between these compounds.
|
|
|
1548
|
|
|
1549 Possible values: I<RowsAndColumns, or IDPairsAndValue>. Default value: I<RowsAndColumns>.
|
|
|
1550
|
|
|
1551 The value of B<--OutMatrixFormat> in conjunction with B<--OutMatrixType> determines type
|
|
|
1552 of data written to output files and allows generation of up to 6 different output data formats:
|
|
|
1553
|
|
|
1554 OutMatrixFormat OutMatrixType
|
|
|
1555
|
|
|
1556 RowsAndColumns FullMatrix [ DEFAULT ]
|
|
|
1557 RowsAndColumns UpperTriangularMatrix
|
|
|
1558 RowsAndColumns LowerTriangularMatrix
|
|
|
1559
|
|
|
1560 IDPairsAndValue FullMatrix
|
|
|
1561 IDPairsAndValue UpperTriangularMatrix
|
|
|
1562 IDPairsAndValue LowerTriangularMatrix
|
|
|
1563
|
|
|
1564 Example of data in output file for I<RowsAndColumns> B<--OutMatrixFormat> value for
|
|
|
1565 I<FullMatrix> valueof B<--OutMatrixType>:
|
|
|
1566
|
|
|
1567 "","Cmpd1","Cmpd2","Cmpd3","Cmpd4","Cmpd5","Cmpd6",... ...
|
|
|
1568 "Cmpd1","1","0.04","0.25","0.13","0.11","0.2",... ...
|
|
|
1569 "Cmpd2","0.04","1","0.06","0.05","0.19","0.07",... ...
|
|
|
1570 "Cmpd3","0.25","0.06","1","0.12","0.22","0.25",... ...
|
|
|
1571 "Cmpd4","0.13","0.05","0.12","1","0.11","0.13",... ...
|
|
|
1572 "Cmpd5","0.11","0.19","0.22","0.11","1","0.17",... ...
|
|
|
1573 "Cmpd6","0.2","0.07","0.25","0.13","0.17","1",... ...
|
|
|
1574 ... ... ..
|
|
|
1575 ... ... ..
|
|
|
1576 ... ... ..
|
|
|
1577
|
|
|
1578 Example of data in output file for I<RowsAndColumns> B<--OutMatrixFormat> value for
|
|
|
1579 I<UpperTriangularMatrix> value of B<--OutMatrixType>:
|
|
|
1580
|
|
|
1581 "","Cmpd1","Cmpd2","Cmpd3","Cmpd4","Cmpd5","Cmpd6",... ...
|
|
|
1582 "Cmpd1","1","0.04","0.25","0.13","0.11","0.2",... ...
|
|
|
1583 "Cmpd2","1","0.06","0.05","0.19","0.07",... ...
|
|
|
1584 "Cmpd3","1","0.12","0.22","0.25",... ...
|
|
|
1585 "Cmpd4","1","0.11","0.13",... ...
|
|
|
1586 "Cmpd5","1","0.17",... ...
|
|
|
1587 "Cmpd6","1",... ...
|
|
|
1588 ... ... ..
|
|
|
1589 ... ... ..
|
|
|
1590 ... ... ..
|
|
|
1591
|
|
|
1592 Example of data in output file for I<RowsAndColumns> B<--OutMatrixFormat> value for
|
|
|
1593 I<LowerTriangularMatrix> value of B<--OutMatrixType>:
|
|
|
1594
|
|
|
1595 "","Cmpd1","Cmpd2","Cmpd3","Cmpd4","Cmpd5","Cmpd6",... ...
|
|
|
1596 "Cmpd1","1"
|
|
|
1597 "Cmpd2","0.04","1"
|
|
|
1598 "Cmpd3","0.25","0.06","1"
|
|
|
1599 "Cmpd4","0.13","0.05","0.12","1"
|
|
|
1600 "Cmpd5","0.11","0.19","0.22","0.11","1"
|
|
|
1601 "Cmpd6","0.2","0.07","0.25","0.13","0.17","1"
|
|
|
1602 ... ... ..
|
|
|
1603 ... ... ..
|
|
|
1604 ... ... ..
|
|
|
1605
|
|
|
1606
|
|
|
1607 Example of data in output file for I<IDPairsAndValue> B<--OutMatrixFormat> value for
|
|
|
1608 <FullMatrix> value of B<OutMatrixType>:
|
|
|
1609
|
|
|
1610 "CmpdID1","CmpdID2","Coefficient Value"
|
|
|
1611 "Cmpd1","Cmpd1","1"
|
|
|
1612 "Cmpd1","Cmpd2","0.04"
|
|
|
1613 "Cmpd1","Cmpd3","0.25"
|
|
|
1614 "Cmpd1","Cmpd4","0.13"
|
|
|
1615 ... ... ...
|
|
|
1616 ... ... ...
|
|
|
1617 ... ... ...
|
|
|
1618 "Cmpd2","Cmpd1","0.04"
|
|
|
1619 "Cmpd2","Cmpd2","1"
|
|
|
1620 "Cmpd2","Cmpd3","0.06"
|
|
|
1621 "Cmpd2","Cmpd4","0.05"
|
|
|
1622 ... ... ...
|
|
|
1623 ... ... ...
|
|
|
1624 ... ... ...
|
|
|
1625 "Cmpd3","Cmpd1","0.25"
|
|
|
1626 "Cmpd3","Cmpd2","0.06"
|
|
|
1627 "Cmpd3","Cmpd3","1"
|
|
|
1628 "Cmpd3","Cmpd4","0.12"
|
|
|
1629 ... ... ...
|
|
|
1630 ... ... ...
|
|
|
1631 ... ... ...
|
|
|
1632
|
|
|
1633 Example of data in output file for I<IDPairsAndValue> B<--OutMatrixFormat> value for
|
|
|
1634 <UpperTriangularMatrix> value of B<--OutMatrixType>:
|
|
|
1635
|
|
|
1636 "CmpdID1","CmpdID2","Coefficient Value"
|
|
|
1637 "Cmpd1","Cmpd1","1"
|
|
|
1638 "Cmpd1","Cmpd2","0.04"
|
|
|
1639 "Cmpd1","Cmpd3","0.25"
|
|
|
1640 "Cmpd1","Cmpd4","0.13"
|
|
|
1641 ... ... ...
|
|
|
1642 ... ... ...
|
|
|
1643 ... ... ...
|
|
|
1644 "Cmpd2","Cmpd2","1"
|
|
|
1645 "Cmpd2","Cmpd3","0.06"
|
|
|
1646 "Cmpd2","Cmpd4","0.05"
|
|
|
1647 ... ... ...
|
|
|
1648 ... ... ...
|
|
|
1649 ... ... ...
|
|
|
1650 "Cmpd3","Cmpd3","1"
|
|
|
1651 "Cmpd3","Cmpd4","0.12"
|
|
|
1652 ... ... ...
|
|
|
1653 ... ... ...
|
|
|
1654 ... ... ...
|
|
|
1655
|
|
|
1656 Example of data in output file for I<IDPairsAndValue> B<--OutMatrixFormat> value for
|
|
|
1657 <LowerTriangularMatrix> value of B<--OutMatrixType>:
|
|
|
1658
|
|
|
1659 "CmpdID1","CmpdID2","Coefficient Value"
|
|
|
1660 "Cmpd1","Cmpd1","1"
|
|
|
1661 "Cmpd2","Cmpd1","0.04"
|
|
|
1662 "Cmpd2","Cmpd2","1"
|
|
|
1663 "Cmpd3","Cmpd1","0.25"
|
|
|
1664 "Cmpd3","Cmpd2","0.06"
|
|
|
1665 "Cmpd3","Cmpd3","1"
|
|
|
1666 "Cmpd4","Cmpd1","0.13"
|
|
|
1667 "Cmpd4","Cmpd2","0.05"
|
|
|
1668 "Cmpd4","Cmpd3","0.12"
|
|
|
1669 "Cmpd4","Cmpd4","1"
|
|
|
1670 ... ... ...
|
|
|
1671 ... ... ...
|
|
|
1672 ... ... ...
|
|
|
1673
|
|
|
1674 =item B<--OutMatrixType> I<FullMatrix | UpperTriangularMatrix | LowerTriangularMatrix>
|
|
|
1675
|
|
|
1676 Type of similarity or distance matrix to calculate for fingerprints vector and bit-vector strings:
|
|
|
1677 Calculate full matrix; Calculate lower triangular matrix including diagonal; Calculate upper triangular
|
|
|
1678 matrix including diagonal.
|
|
|
1679
|
|
|
1680 Possible values: I<FullMatrix, UpperTriangularMatrix, or LowerTriangularMatrix>. Default value:
|
|
|
1681 I<FullMatrix>.
|
|
|
1682
|
|
|
1683 The value of B<--OutMatrixType> in conjunction with B<--OutMatrixFormat> determines type
|
|
|
1684 of data written to output files.
|
|
|
1685
|
|
|
1686 =item B<-o, --overwrite>
|
|
|
1687
|
|
|
1688 Overwrite existing files
|
|
|
1689
|
|
|
1690 =item B<-p, --precision> I<number>
|
|
|
1691
|
|
|
1692 Precision of calculated values in the output file. Default: up to I<2> decimal places.
|
|
|
1693 Valid values: positive integers.
|
|
|
1694
|
|
|
1695 =item B<-q, --quote> I<Yes | No>
|
|
|
1696
|
|
|
1697 Put quote around column values in output CSV/TSV text file(s). Possible values:
|
|
|
1698 I<Yes or No>. Default value: I<Yes>.
|
|
|
1699
|
|
|
1700 =item B<-r, --root> I<RootName>
|
|
|
1701
|
|
|
1702 New file name is generated using the root: <Root><BitVectorComparisonMode>.<Ext> or
|
|
|
1703 <Root><VectorComparisonMode><VectorComparisonFormulism>.<Ext>.
|
|
|
1704 The csv, and tsv <Ext> values are used for comma/semicolon, and tab delimited text files
|
|
|
1705 respectively. This option is ignored for multiple input files.
|
|
|
1706
|
|
|
1707 =item B<-v, --VectorComparisonMode> I<All | "TanimotoSimilarity,[ManhattanDistance,...]">
|
|
|
1708
|
|
|
1709 Specify what similarity or distance coefficients to use for calculating similarity matrices for
|
|
|
1710 fingerprint vector strings data values in I<TextFile(s)>: calculate similarity matrices for all
|
|
|
1711 supported similarity and distance coefficients or specify a comma delimited list of similarity
|
|
|
1712 and distance coefficients. Possible values: I<All | "TanimotoSimilairy,[ManhattanDistance,..]">.
|
|
|
1713 Default: I<TanimotoSimilarity>.
|
|
|
1714
|
|
|
1715 The value of B<-v, --VectorComparisonMode>, in conjunction with B<--VectorComparisonFormulism>,
|
|
|
1716 decides which type of similarity and distance coefficient formulism gets used.
|
|
|
1717
|
|
|
1718 I<All> uses complete list of supported similarity and distance coefficients: I<CosineSimilarity,
|
|
|
1719 CzekanowskiSimilarity, DiceSimilarity, OchiaiSimilarity, JaccardSimilarity, SorensonSimilarity, TanimotoSimilarity,
|
|
|
1720 CityBlockDistance, EuclideanDistance, HammingDistance, ManhattanDistance, SoergelDistance>. These
|
|
|
1721 similarity and distance coefficients are described below.
|
|
|
1722
|
|
|
1723 B<FingerprintsVector.pm> module, used to calculate similarity and distance coefficients,
|
|
|
1724 provides support to perform comparison between vectors containing three different types of
|
|
|
1725 values:
|
|
|
1726
|
|
|
1727 Type I: OrderedNumericalValues
|
|
|
1728
|
|
|
1729 . Size of two vectors are same
|
|
|
1730 . Vectors contain real values in a specific order. For example: MACCS keys
|
|
|
1731 count, Topological pharmnacophore atom pairs and so on.
|
|
|
1732
|
|
|
1733 Type II: UnorderedNumericalValues
|
|
|
1734
|
|
|
1735 . Size of two vectors might not be same
|
|
|
1736 . Vectors contain unordered real value identified by value IDs. For example:
|
|
|
1737 Toplogical atom pairs, Topological atom torsions and so on
|
|
|
1738
|
|
|
1739 Type III: AlphaNumericalValues
|
|
|
1740
|
|
|
1741 . Size of two vectors might not be same
|
|
|
1742 . Vectors contain unordered alphanumerical values. For example: Extended
|
|
|
1743 connectivity fingerprints, atom neighborhood fingerprints.
|
|
|
1744
|
|
|
1745 Before performing similarity or distance calculations between vectors containing UnorderedNumericalValues
|
|
|
1746 or AlphaNumericalValues, the vectors are transformed into vectors containing unique OrderedNumericalValues
|
|
|
1747 using value IDs for UnorderedNumericalValues and values itself for AlphaNumericalValues.
|
|
|
1748
|
|
|
1749 Three forms of similarity and distance calculation between two vectors, specified using B<--VectorComparisonFormulism>
|
|
|
1750 option, are supported: I<AlgebraicForm, BinaryForm or SetTheoreticForm>.
|
|
|
1751
|
|
|
1752 For I<BinaryForm>, the ordered list of processed final vector values containing the value or
|
|
|
1753 count of each unique value type is simply converted into a binary vector containing 1s and 0s
|
|
|
1754 corresponding to presence or absence of values before calculating similarity or distance between
|
|
|
1755 two vectors.
|
|
|
1756
|
|
|
1757 For two fingerprint vectors A and B of same size containing OrderedNumericalValues, let:
|
|
|
1758
|
|
|
1759 N = Number values in A or B
|
|
|
1760
|
|
|
1761 Xa = Values of vector A
|
|
|
1762 Xb = Values of vector B
|
|
|
1763
|
|
|
1764 Xai = Value of ith element in A
|
|
|
1765 Xbi = Value of ith element in B
|
|
|
1766
|
|
|
1767 SUM = Sum of i over N values
|
|
|
1768
|
|
|
1769 For SetTheoreticForm of calculation between two vectors, let:
|
|
|
1770
|
|
|
1771 SetIntersectionXaXb = SUM ( MIN ( Xai, Xbi ) )
|
|
|
1772 SetDifferenceXaXb = SUM ( Xai ) + SUM ( Xbi ) - SUM ( MIN ( Xai, Xbi ) )
|
|
|
1773
|
|
|
1774 For BinaryForm of calculation between two vectors, let:
|
|
|
1775
|
|
|
1776 Na = Number of bits set to "1" in A = SUM ( Xai )
|
|
|
1777 Nb = Number of bits set to "1" in B = SUM ( Xbi )
|
|
|
1778 Nc = Number of bits set to "1" in both A and B = SUM ( Xai * Xbi )
|
|
|
1779 Nd = Number of bits set to "0" in both A and B
|
|
|
1780 = SUM ( 1 - Xai - Xbi + Xai * Xbi)
|
|
|
1781
|
|
|
1782 N = Number of bits set to "1" or "0" in A or B = Size of A or B = Na + Nb - Nc + Nd
|
|
|
1783
|
|
|
1784 Additionally, for BinaryForm various values also correspond to:
|
|
|
1785
|
|
|
1786 Na = | Xa |
|
|
|
1787 Nb = | Xb |
|
|
|
1788 Nc = | SetIntersectionXaXb |
|
|
|
1789 Nd = N - | SetDifferenceXaXb |
|
|
|
1790
|
|
|
1791 | SetDifferenceXaXb | = N - Nd = Na + Nb - Nc + Nd - Nd = Na + Nb - Nc
|
|
|
1792 = | Xa | + | Xb | - | SetIntersectionXaXb |
|
|
|
1793
|
|
|
1794 Various similarity and distance coefficients [ Ref 40, Ref 62, Ref 64 ] for a pair of vectors A and B
|
|
|
1795 in I<AlgebraicForm, BinaryForm and SetTheoreticForm> are defined as follows:
|
|
|
1796
|
|
|
1797 B<CityBlockDistance>: ( same as HammingDistance and ManhattanDistance)
|
|
|
1798
|
|
|
1799 I<AlgebraicForm>: SUM ( ABS ( Xai - Xbi ) )
|
|
|
1800
|
|
|
1801 I<BinaryForm>: ( Na - Nc ) + ( Nb - Nc ) = Na + Nb - 2 * Nc
|
|
|
1802
|
|
|
1803 I<SetTheoreticForm>: | SetDifferenceXaXb | - | SetIntersectionXaXb | = SUM ( Xai ) + SUM ( Xbi ) - 2 * ( SUM ( MIN ( Xai, Xbi ) ) )
|
|
|
1804
|
|
|
1805 B<CosineSimilarity>: ( same as OchiaiSimilarityCoefficient)
|
|
|
1806
|
|
|
1807 I<AlgebraicForm>: SUM ( Xai * Xbi ) / SQRT ( SUM ( Xai ** 2) * SUM ( Xbi ** 2) )
|
|
|
1808
|
|
|
1809 I<BinaryForm>: Nc / SQRT ( Na * Nb)
|
|
|
1810
|
|
|
1811 I<SetTheoreticForm>: | SetIntersectionXaXb | / SQRT ( |Xa| * |Xb| ) = SUM ( MIN ( Xai, Xbi ) ) / SQRT ( SUM ( Xai ) * SUM ( Xbi ) )
|
|
|
1812
|
|
|
1813 B<CzekanowskiSimilarity>: ( same as DiceSimilarity and SorensonSimilarity)
|
|
|
1814
|
|
|
1815 I<AlgebraicForm>: ( 2 * ( SUM ( Xai * Xbi ) ) ) / ( SUM ( Xai ** 2) + SUM ( Xbi **2 ) )
|
|
|
1816
|
|
|
1817 I<BinaryForm>: 2 * Nc / ( Na + Nb )
|
|
|
1818
|
|
|
1819 I<SetTheoreticForm>: 2 * | SetIntersectionXaXb | / ( |Xa| + |Xb| ) = 2 * ( SUM ( MIN ( Xai, Xbi ) ) ) / ( SUM ( Xai ) + SUM ( Xbi ) )
|
|
|
1820
|
|
|
1821 B<DiceSimilarity>: ( same as CzekanowskiSimilarity and SorensonSimilarity)
|
|
|
1822
|
|
|
1823 I<AlgebraicForm>: ( 2 * ( SUM ( Xai * Xbi ) ) ) / ( SUM ( Xai ** 2) + SUM ( Xbi **2 ) )
|
|
|
1824
|
|
|
1825 I<BinaryForm>: 2 * Nc / ( Na + Nb )
|
|
|
1826
|
|
|
1827 I<SetTheoreticForm>: 2 * | SetIntersectionXaXb | / ( |Xa| + |Xb| ) = 2 * ( SUM ( MIN ( Xai, Xbi ) ) ) / ( SUM ( Xai ) + SUM ( Xbi ) )
|
|
|
1828
|
|
|
1829 B<EuclideanDistance>:
|
|
|
1830
|
|
|
1831 I<AlgebraicForm>: SQRT ( SUM ( ( ( Xai - Xbi ) ** 2 ) ) )
|
|
|
1832
|
|
|
1833 I<BinaryForm>: SQRT ( ( Na - Nc ) + ( Nb - Nc ) ) = SQRT ( Na + Nb - 2 * Nc )
|
|
|
1834
|
|
|
1835 I<SetTheoreticForm>: SQRT ( | SetDifferenceXaXb | - | SetIntersectionXaXb | ) = SQRT ( SUM ( Xai ) + SUM ( Xbi ) - 2 * ( SUM ( MIN ( Xai, Xbi ) ) ) )
|
|
|
1836
|
|
|
1837 B<HammingDistance>: ( same as CityBlockDistance and ManhattanDistance)
|
|
|
1838
|
|
|
1839 I<AlgebraicForm>: SUM ( ABS ( Xai - Xbi ) )
|
|
|
1840
|
|
|
1841 I<BinaryForm>: ( Na - Nc ) + ( Nb - Nc ) = Na + Nb - 2 * Nc
|
|
|
1842
|
|
|
1843 I<SetTheoreticForm>: | SetDifferenceXaXb | - | SetIntersectionXaXb | = SUM ( Xai ) + SUM ( Xbi ) - 2 * ( SUM ( MIN ( Xai, Xbi ) ) )
|
|
|
1844
|
|
|
1845 B<JaccardSimilarity>: ( same as TanimotoSimilarity)
|
|
|
1846
|
|
|
1847 I<AlgebraicForm>: SUM ( Xai * Xbi ) / ( SUM ( Xai ** 2 ) + SUM ( Xbi ** 2 ) - SUM ( Xai * Xbi ) )
|
|
|
1848
|
|
|
1849 I<BinaryForm>: Nc / ( ( Na - Nc ) + ( Nb - Nc ) + Nc ) = Nc / ( Na + Nb - Nc )
|
|
|
1850
|
|
|
1851 I<SetTheoreticForm>: | SetIntersectionXaXb | / | SetDifferenceXaXb | = SUM ( MIN ( Xai, Xbi ) ) / ( SUM ( Xai ) + SUM ( Xbi ) - SUM ( MIN ( Xai, Xbi ) ) )
|
|
|
1852
|
|
|
1853 B<ManhattanDistance>: ( same as CityBlockDistance and HammingDistance)
|
|
|
1854
|
|
|
1855 I<AlgebraicForm>: SUM ( ABS ( Xai - Xbi ) )
|
|
|
1856
|
|
|
1857 I<BinaryForm>: ( Na - Nc ) + ( Nb - Nc ) = Na + Nb - 2 * Nc
|
|
|
1858
|
|
|
1859 I<SetTheoreticForm>: | SetDifferenceXaXb | - | SetIntersectionXaXb | = SUM ( Xai ) + SUM ( Xbi ) - 2 * ( SUM ( MIN ( Xai, Xbi ) ) )
|
|
|
1860
|
|
|
1861 B<OchiaiSimilarity>: ( same as CosineSimilarity)
|
|
|
1862
|
|
|
1863 I<AlgebraicForm>: SUM ( Xai * Xbi ) / SQRT ( SUM ( Xai ** 2) * SUM ( Xbi ** 2) )
|
|
|
1864
|
|
|
1865 I<BinaryForm>: Nc / SQRT ( Na * Nb)
|
|
|
1866
|
|
|
1867 I<SetTheoreticForm>: | SetIntersectionXaXb | / SQRT ( |Xa| * |Xb| ) = SUM ( MIN ( Xai, Xbi ) ) / SQRT ( SUM ( Xai ) * SUM ( Xbi ) )
|
|
|
1868
|
|
|
1869 B<SorensonSimilarity>: ( same as CzekanowskiSimilarity and DiceSimilarity)
|
|
|
1870
|
|
|
1871 I<AlgebraicForm>: ( 2 * ( SUM ( Xai * Xbi ) ) ) / ( SUM ( Xai ** 2) + SUM ( Xbi **2 ) )
|
|
|
1872
|
|
|
1873 I<BinaryForm>: 2 * Nc / ( Na + Nb )
|
|
|
1874
|
|
|
1875 I<SetTheoreticForm>: 2 * | SetIntersectionXaXb | / ( |Xa| + |Xb| ) = 2 * ( SUM ( MIN ( Xai, Xbi ) ) ) / ( SUM ( Xai ) + SUM ( Xbi ) )
|
|
|
1876
|
|
|
1877 B<SoergelDistance>:
|
|
|
1878
|
|
|
1879 I<AlgebraicForm>: SUM ( ABS ( Xai - Xbi ) ) / SUM ( MAX ( Xai, Xbi ) )
|
|
|
1880
|
|
|
1881 I<BinaryForm>: 1 - Nc / ( Na + Nb - Nc ) = ( Na + Nb - 2 * Nc ) / ( Na + Nb - Nc )
|
|
|
1882
|
|
|
1883 I<SetTheoreticForm>: ( | SetDifferenceXaXb | - | SetIntersectionXaXb | ) / | SetDifferenceXaXb | = ( SUM ( Xai ) + SUM ( Xbi ) - 2 * ( SUM ( MIN ( Xai, Xbi ) ) ) ) / ( SUM ( Xai ) + SUM ( Xbi ) - SUM ( MIN ( Xai, Xbi ) ) )
|
|
|
1884
|
|
|
1885 B<TanimotoSimilarity>: ( same as JaccardSimilarity)
|
|
|
1886
|
|
|
1887 I<AlgebraicForm>: SUM ( Xai * Xbi ) / ( SUM ( Xai ** 2 ) + SUM ( Xbi ** 2 ) - SUM ( Xai * Xbi ) )
|
|
|
1888
|
|
|
1889 I<BinaryForm>: Nc / ( ( Na - Nc ) + ( Nb - Nc ) + Nc ) = Nc / ( Na + Nb - Nc )
|
|
|
1890
|
|
|
1891 I<SetTheoreticForm>: | SetIntersectionXaXb | / | SetDifferenceXaXb | = SUM ( MIN ( Xai, Xbi ) ) / ( SUM ( Xai ) + SUM ( Xbi ) - SUM ( MIN ( Xai, Xbi ) ) )
|
|
|
1892
|
|
|
1893 =item B<--VectorComparisonFormulism> I<All | "AlgebraicForm,[BinaryForm,SetTheoreticForm]">
|
|
|
1894
|
|
|
1895 Specify fingerprints vector comparison formulism to use for calculation similarity and distance
|
|
|
1896 coefficients during B<-v, --VectorComparisonMode>: use all supported comparison formulisms
|
|
|
1897 or specify a comma delimited. Possible values: I<All | "AlgebraicForm,[BinaryForm,SetTheoreticForm]">.
|
|
|
1898 Default value: I<AlgebraicForm>.
|
|
|
1899
|
|
|
1900 I<All> uses all three forms of supported vector comparison formulism for values of B<-v, --VectorComparisonMode>
|
|
|
1901 option.
|
|
|
1902
|
|
|
1903 For fingerprint vector strings containing B<AlphaNumericalValues> data values - B<ExtendedConnectivityFingerprints>,
|
|
|
1904 B<AtomNeighborhoodsFingerprints> and so on - all three formulism result in same value during similarity and distance
|
|
|
1905 calculations.
|
|
|
1906
|
|
|
1907 =item B<-w, --WorkingDir> I<DirName>
|
|
|
1908
|
|
|
1909 Location of working directory. Default: current directory.
|
|
|
1910
|
|
|
1911 =back
|
|
|
1912
|
|
|
1913 =head1 EXAMPLES
|
|
|
1914
|
|
|
1915 To generate a similarity matrix corresponding to Tanimoto similarity coefficient for fingerprints
|
|
|
1916 bit-vector strings data corresponding to supported fingerprints in text file present in a column
|
|
|
1917 name containing Fingerprint substring by loading all fingerprints data into memory and create a
|
|
|
1918 SampleFPHexTanimotoSimilarity.csv file containing compound IDs retrieved from column name
|
|
|
1919 containing CompoundID substring, type:
|
|
|
1920
|
|
|
1921 % SimilarityMatricesFingerprints.pl -o SampleFPHex.csv
|
|
|
1922
|
|
|
1923 To generate a similarity matrix corresponding to Tanimoto similarity coefficient for fingerprints
|
|
|
1924 bit-vector strings data corresponding to supported fingerprints in SD File present in a data field
|
|
|
1925 with Fingerprint substring in its label by loading all fingerprints data into memory and create a
|
|
|
1926 SampleFPHexTanimotoSimilarity.csv file containing sequentially generated compound IDs with
|
|
|
1927 Cmpd prefix, type:
|
|
|
1928
|
|
|
1929 % SimilarityMatricesFingerprints.pl -o SampleFPHex.sdf
|
|
|
1930
|
|
|
1931 To generate a similarity matrix corresponding to Tanimoto similarity coefficient for fingerprints
|
|
|
1932 bit-vector strings data corresponding to supported fingerprints in FP file by loading all fingerprints
|
|
|
1933 data into memory and create a SampleFPHexTanimotoSimilarity.csv file along with compound IDs
|
|
|
1934 retrieved from FP file, type:
|
|
|
1935
|
|
|
1936 % SimilarityMatricesFingerprints.pl -o SampleFPHex.fpf
|
|
|
1937
|
|
|
1938 To generate a lower triangular similarity matrix corresponding to Tanimoto similarity coefficient for
|
|
|
1939 fingerprints bit-vector strings data corresponding to supported fingerprints in text file present in a
|
|
|
1940 column name containing Fingerprint substring by loading all fingerprints data into memory and create
|
|
|
1941 a SampleFPHexTanimotoSimilarity.csv file containing compound IDs retrieved from column name
|
|
|
1942 containing CompoundID substring, type:
|
|
|
1943
|
|
|
1944 % SimilarityMatricesFingerprints.pl -o --InputDataMode LoadInMemory
|
|
|
1945 --OutMatrixFormat RowsAndColumns --OutMatrixType LowerTriangularMatrix
|
|
|
1946 SampleFPHex.csv
|
|
|
1947
|
|
|
1948 To generate a upper triangular similarity matrix corresponding to Tanimoto similarity coefficient for
|
|
|
1949 fingerprints bit-vector strings data corresponding to supported fingerprints in text file present in a
|
|
|
1950 column name containing Fingerprint substring by loading all fingerprints data into memory and create
|
|
|
1951 a SampleFPHexTanimotoSimilarity.csv file in IDPairsAndValue format containing compound IDs retrieved
|
|
|
1952 from column name containing CompoundID substring, type:
|
|
|
1953
|
|
|
1954 % SimilarityMatricesFingerprints.pl -o --InputDataMode LoadInMemory
|
|
|
1955 --OutMatrixFormat IDPairsAndValue --OutMatrixType UpperTriangularMatrix
|
|
|
1956 SampleFPHex.csv
|
|
|
1957
|
|
|
1958 To generate a full similarity matrix corresponding to Tanimoto similarity coefficient for fingerprints
|
|
|
1959 bit-vector strings data corresponding to supported fingerprints in text file present in a column
|
|
|
1960 name containing Fingerprint substring by scanning file without loading all fingerprints data into memory
|
|
|
1961 and create a SampleFPHexTanimotoSimilarity.csv file containing compound IDs retrieved from
|
|
|
1962 column name containing CompoundID substring, type:
|
|
|
1963
|
|
|
1964 % SimilarityMatricesFingerprints.pl -o --InputDataMode ScanFile
|
|
|
1965 --OutMatrixFormat RowsAndColumns --OutMatrixType FullMatrix
|
|
|
1966 SampleFPHex.csv
|
|
|
1967
|
|
|
1968 To generate a lower triangular similarity matrix corresponding to Tanimoto similarity coefficient for
|
|
|
1969 fingerprints bit-vector strings data corresponding to supported fingerprints in text file present in a
|
|
|
1970 column name containing Fingerprint substring by scanning file without loading all fingerprints data into
|
|
|
1971 memory and create a SampleFPHexTanimotoSimilarity.csv file in IDPairsAndValue format containing
|
|
|
1972 compound IDs retrieved from column name containing CompoundID substring, type:
|
|
|
1973
|
|
|
1974 % SimilarityMatricesFingerprints.pl -o --InputDataMode ScanFile
|
|
|
1975 --OutMatrixFormat IDPairsAndValue --OutMatrixType LowerTriangularMatrix
|
|
|
1976 SampleFPHex.csv
|
|
|
1977
|
|
|
1978 To generate a similarity matrix corresponding to Tanimoto similarity coefficient using algebraic formulism
|
|
|
1979 for fingerprints vector strings data corresponding to supported fingerprints in text file present in a column name
|
|
|
1980 containing Fingerprint substring and create a SampleFPCountTanimotoSimilarityAlgebraicForm.csv file
|
|
|
1981 containing compound IDs retrieved from column name containing CompoundID substring, type:
|
|
|
1982
|
|
|
1983 % SimilarityMatricesFingerprints.pl -o SampleFPCount.csv
|
|
|
1984
|
|
|
1985 To generate a similarity matrix corresponding to Tanimoto similarity coefficient using algebraic formulism
|
|
|
1986 for fingerprints vector strings data corresponding to supported fingerprints in SD file present in a data field with
|
|
|
1987 Fingerprint substring in its label and create a SampleFPCountTanimotoSimilarityAlgebraicForm.csv file
|
|
|
1988 containing sequentially generated compound IDs with Cmpd prefix, type:
|
|
|
1989
|
|
|
1990 % SimilarityMatricesFingerprints.pl -o SampleFPCount.sdf
|
|
|
1991
|
|
|
1992 To generate a similarity matrix corresponding to Tanimoto similarity coefficient using algebraic formulism
|
|
|
1993 vector strings data corresponding to supported fingerprints in FP file and create a
|
|
|
1994 SampleFPCountTanimotoSimilarityAlgebraicForm.csv file along with compound IDs retrieved from FP file, type:
|
|
|
1995
|
|
|
1996 % SimilarityMatricesFingerprints.pl -o SampleFPCount.fpf
|
|
|
1997
|
|
|
1998 To generate a similarity matrix corresponding to Tanimoto similarity coefficient for fingerprints
|
|
|
1999 bit-vector strings data corresponding to supported fingerprints in text file present in a column name
|
|
|
2000 containing Fingerprint substring and create a SampleFPHexTanimotoSimilarity.csv file in
|
|
|
2001 IDPairsAndValue format containing compound IDs retrieved from column name containing
|
|
|
2002 CompoundID substring, type:
|
|
|
2003
|
|
|
2004 % SimilarityMatricesFingerprints.pl --OutMatrixFormat IDPairsAndValue -o
|
|
|
2005 SampleFPHex.csv
|
|
|
2006
|
|
|
2007 To generate a similarity matrix corresponding to Tanimoto similarity coefficient for fingerprints
|
|
|
2008 bit-vector strings data corresponding to supported fingerprints in SD file present in a data field with
|
|
|
2009 Fingerprint substring in its label and create a SampleFPHexTanimotoSimilarity.csv file in
|
|
|
2010 IDPairsAndValue format containing sequentially generated compound IDs with Cmpd prefix,
|
|
|
2011 type:
|
|
|
2012
|
|
|
2013 % SimilarityMatricesFingerprints.pl --OutMatrixFormat IDPairsAndValue -o
|
|
|
2014 SampleFPHex.sdf
|
|
|
2015
|
|
|
2016 To generate a similarity matrix corresponding to Tanimoto similarity coefficient for fingerprints
|
|
|
2017 bit-vector strings data corresponding to supported fingerprints in FP file and create a
|
|
|
2018 SampleFPHexTanimotoSimilarity.csv file in IDPairsAndValue format along with compound IDs retrieved
|
|
|
2019 from FP file, type:
|
|
|
2020
|
|
|
2021 % SimilarityMatricesFingerprints.pl --OutMatrixFormat IDPairsAndValue -o
|
|
|
2022 SampleFPHex.fpf
|
|
|
2023
|
|
|
2024 To generate a similarity matrix corresponding to Tanimoto similarity coefficient for fingerprints
|
|
|
2025 bit-vector strings data corresponding to supported fingerprints in SD file present in a data field with
|
|
|
2026 Fingerprint substring in its label and create a SampleFPHexTanimotoSimilarity.csv file
|
|
|
2027 containing compound IDs from mol name line, type:
|
|
|
2028
|
|
|
2029 % SimilarityMatricesFingerprints.pl --CompoundIDMode MolName -o
|
|
|
2030 SampleFPHex.sdf
|
|
|
2031
|
|
|
2032 To generate a similarity matrix corresponding to Tanimoto similarity coefficient for fingerprints
|
|
|
2033 bit-vector strings data corresponding to supported fingerprints present in a data field with
|
|
|
2034 Fingerprint substring in its label and create a SampleFPHexTanimotoSimilarity.csv file
|
|
|
2035 containing compound IDs from data field name Mol_ID, type:
|
|
|
2036
|
|
|
2037 % SimilarityMatricesFingerprints.pl --CompoundIDMode DataField
|
|
|
2038 --CompoundIDField Mol_ID -o SampleFPBin.sdf
|
|
|
2039
|
|
|
2040 To generate similarity matrices corresponding to Buser, Dice and Tanimoto similarity coefficient
|
|
|
2041 for fingerprints bit-vector strings data corresponding to supported fingerprints present in a column
|
|
|
2042 name containing Fingerprint substring and create SampleFPBin[CoefficientName]Similarity.csv files
|
|
|
2043 containing compound IDs retrieved from column name containing CompoundID substring, type:
|
|
|
2044
|
|
|
2045 % SimilarityMatricesFingerprints.pl -b "BuserSimilarity,DiceSimilarity,
|
|
|
2046 TanimotoSimilarity" -o SampleFPBin.csv
|
|
|
2047
|
|
|
2048 To generate similarity matrices corresponding to Buser, Dice and Tanimoto similarity coefficient
|
|
|
2049 for fingerprints bit-vector strings data corresponding to supported fingerprints present in a data field with
|
|
|
2050 Fingerprint substring in its label and create SampleFPBin[CoefficientName]Similarity.csv files
|
|
|
2051 containing sequentially generated compound IDs with Cmpd prefix, type:
|
|
|
2052
|
|
|
2053 % SimilarityMatricesFingerprints.pl -b "BuserSimilarity,DiceSimilarity,
|
|
|
2054 TanimotoSimilarity" -o SampleFPBin.sdf
|
|
|
2055
|
|
|
2056 To generate similarity matrices corresponding to CityBlock distance and Tanimoto similarity coefficients using
|
|
|
2057 algebraic formulism for fingerprints vector strings data corresponding to supported fingerprints present in
|
|
|
2058 a column name containing Fingerprint substring and create SampleFPCount[CoefficientName]AlgebraicForm.csv
|
|
|
2059 files containing compound IDs retrieved from column name containing CompoundID substring, type:
|
|
|
2060
|
|
|
2061 % SimilarityMatricesFingerprints.pl -v "CityBlockDistance,
|
|
|
2062 TanimotoSimilarity" -o SampleFPCount.csv
|
|
|
2063
|
|
|
2064 To generate similarity matrices corresponding to CityBlock distance and Tanimoto similarity coefficients using
|
|
|
2065 algebraic formulism for fingerprints vector strings data corresponding to supported fingerprints present in
|
|
|
2066 a data field with Fingerprint substring in its label and create SampleFPCount[CoefficientName]AlgebraicForm.csv
|
|
|
2067 files containing sequentially generated compound IDs with Cmpd prefix, type:
|
|
|
2068
|
|
|
2069 % SimilarityMatricesFingerprints.pl -v "CityBlockDistance,
|
|
|
2070 TanimotoSimilarity" -o SampleFPCount.sdf
|
|
|
2071
|
|
|
2072 To generate similarity matrices corresponding to CityBlock distance Tanimoto similarity coefficients using
|
|
|
2073 binary formulism for fingerprints vector strings data corresponding to supported fingerprints present in
|
|
|
2074 a column name containing Fingerprint substring and create SampleFPCount[CoefficientName]Binary.csv
|
|
|
2075 files containing compound IDs retrieved from column name containing CompoundID substring, type:
|
|
|
2076
|
|
|
2077 % SimilarityMatricesFingerprints.pl -v "CityBlockDistance,
|
|
|
2078 TanimotoSimilarity" --VectorComparisonFormulism BinaryForm -o
|
|
|
2079 SampleFPCount.csv
|
|
|
2080
|
|
|
2081 To generate similarity matrices corresponding to CityBlock distance Tanimoto similarity coefficients using
|
|
|
2082 binary formulism for fingerprints vector strings data corresponding to supported fingerprints present in
|
|
|
2083 a data field with Fingerprint substring in its label and create SampleFPCount[CoefficientName]Binary.csv
|
|
|
2084 files containing sequentially generated compound IDs with Cmpd prefix, type:
|
|
|
2085
|
|
|
2086 % SimilarityMatricesFingerprints.pl -v "CityBlockDistance,
|
|
|
2087 TanimotoSimilarity" --VectorComparisonFormulism BinaryForm -o
|
|
|
2088 SampleFPCount.sdf
|
|
|
2089
|
|
|
2090 To generate similarity matrices corresponding to CityBlock distance Tanimoto similarity coefficients using
|
|
|
2091 all supported comparison formulisms for fingerprints vector strings data corresponding to supported
|
|
|
2092 fingerprints present in a column name containing Fingerprint substring and create
|
|
|
2093 SampleFPCount[CoefficientName][FormulismName].csv files containing compound IDs retrieved from column
|
|
|
2094 name containing CompoundID substring, type:
|
|
|
2095
|
|
|
2096 % SimilarityMatricesFingerprints.pl -v "CityBlockDistance,
|
|
|
2097 TanimotoSimilarity" --VectorComparisonFormulism All -o SampleFPCount.csv
|
|
|
2098
|
|
|
2099 To generate similarity matrices corresponding to CityBlock distance Tanimoto similarity coefficients using
|
|
|
2100 all supported comparison formulisms for fingerprints vector strings data corresponding to supported
|
|
|
2101 fingerprints present in a data field with Fingerprint substring in its label and create
|
|
|
2102 SampleFPCount[CoefficientName][FormulismName].csv files containing sequentially generated
|
|
|
2103 compound IDs with Cmpd prefix, type:
|
|
|
2104
|
|
|
2105 % SimilarityMatricesFingerprints.pl -v "CityBlockDistance,TanimotoSimilarity"
|
|
|
2106 --VectorComparisonFormulism All -o SampleFPCount.sdf
|
|
|
2107
|
|
|
2108 To generate similarity matrices corresponding to all available similarity coefficient for fingerprints
|
|
|
2109 bit-vector strings data corresponding to supported fingerprints present in a column name
|
|
|
2110 containing Fingerprint substring and create SampleFPHex[CoefficientName].csv files
|
|
|
2111 containing compound IDs retrieved from column name containing CompoundID substring, type:
|
|
|
2112
|
|
|
2113 % SimilarityMatricesFingerprints.pl -m AutoDetect --BitVectorComparisonMode
|
|
|
2114 All --alpha 0.5 -beta 0.5 -o SampleFPHex.csv
|
|
|
2115
|
|
|
2116 To generate similarity matrices corresponding to all available similarity coefficient for fingerprints
|
|
|
2117 bit-vector strings data corresponding to supported fingerprints present in a data field with Fingerprint
|
|
|
2118 substring in its label and create SampleFPHex[CoefficientName].csv files containing sequentially
|
|
|
2119 generated compound IDs with Cmpd prefix, type
|
|
|
2120
|
|
|
2121 % SimilarityMatricesFingerprints.pl -m AutoDetect --BitVectorComparisonMode
|
|
|
2122 All --alpha 0.5 -beta 0.5 -o SampleFPHex.sdf
|
|
|
2123
|
|
|
2124 To generate similarity matrices corresponding to all available similarity and distance coefficients using
|
|
|
2125 all comparison formulism for fingerprints vector strings data corresponding to supported fingerprints
|
|
|
2126 present in a column name containing Fingerprint substring and create
|
|
|
2127 SampleFPCount[CoefficientName][FormulismName].csv files containing compound IDs
|
|
|
2128 retrieved from column name containing CompoundID substring, type:
|
|
|
2129
|
|
|
2130 % SimilarityMatricesFingerprints.pl -m AutoDetect --VectorComparisonMode
|
|
|
2131 All --VectorComparisonFormulism All -o SampleFPCount.csv
|
|
|
2132
|
|
|
2133 To generate similarity matrices corresponding to all available similarity and distance coefficients using
|
|
|
2134 all comparison formulism for fingerprints vector strings data corresponding to supported fingerprints
|
|
|
2135 present in a data field with Fingerprint substring in its label and create
|
|
|
2136 SampleFPCount[CoefficientName][FormulismName].csv files containing sequentially generated
|
|
|
2137 compound IDs with Cmpd prefix, type:
|
|
|
2138
|
|
|
2139 % SimilarityMatricesFingerprints.pl -m AutoDetect --VectorComparisonMode
|
|
|
2140 All --VectorComparisonFormulism All -o SampleFPCount.sdf
|
|
|
2141
|
|
|
2142 To generate a similarity matrix corresponding to Tanimoto similarity coefficient for fingerprints
|
|
|
2143 bit-vector strings data corresponding to supported fingerprints present in a column number 2
|
|
|
2144 and create a SampleFPHexTanimotoSimilarity.csv file containing compound IDs retrieved column
|
|
|
2145 number 1, type:
|
|
|
2146
|
|
|
2147 % SimilarityMatricesFingerprints.pl --ColMode ColNum --CompoundIDCol 1
|
|
|
2148 --FingerprintsCol 2 -o SampleFPHex.csv
|
|
|
2149
|
|
|
2150 To generate a similarity matrix corresponding to Tanimoto similarity coefficient for fingerprints
|
|
|
2151 bit-vector strings data corresponding to supported fingerprints present in a data field name
|
|
|
2152 Fingerprints and create a SampleFPHexTanimotoSimilarity.csv file containing compound IDs
|
|
|
2153 present in data field name Mol_ID, type:
|
|
|
2154
|
|
|
2155 % SimilarityMatricesFingerprints.pl --FingerprintsField Fingerprints
|
|
|
2156 --CompoundIDMode DataField --CompoundIDField Mol_ID -o SampleFPHex.sdf
|
|
|
2157
|
|
|
2158 To generate a similarity matrix corresponding to Tversky similarity coefficient for fingerprints
|
|
|
2159 bit-vector strings data corresponding to supported fingerprints present in a column named Fingerprints
|
|
|
2160 and create a SampleFPHexTverskySimilarity.tsv file containing compound IDs retrieved column named
|
|
|
2161 CompoundID, type:
|
|
|
2162
|
|
|
2163 % SimilarityMatricesFingerprints.pl --BitVectorComparisonMode
|
|
|
2164 TverskySimilarity --alpha 0.5 --ColMode ColLabel --CompoundIDCol
|
|
|
2165 CompoundID --FingerprintsCol Fingerprints --OutDelim Tab --quote No
|
|
|
2166 -o SampleFPHex.csv
|
|
|
2167
|
|
|
2168 To generate a similarity matrix corresponding to Tanimoto similarity coefficient for fingerprints
|
|
|
2169 bit-vector strings data corresponding to supported fingerprints present in a data field
|
|
|
2170 with Fingerprint substring in its label and create a SampleFPHexTanimotoSimilarity.csv file
|
|
|
2171 containing compound IDs from molname line or sequentially generated compound IDs
|
|
|
2172 with Mol prefix, type:
|
|
|
2173
|
|
|
2174 % SimilarityMatricesFingerprints.pl --CompoundIDMode MolnameOrLabelPrefix
|
|
|
2175 --CompoundIDPrefix Mol -o SampleFPHex.sdf
|
|
|
2176
|
|
|
2177 To generate a similarity matrix corresponding to Tanimoto similarity coefficient for fingerprints
|
|
|
2178 bit-vector strings data corresponding to supported fingerprints present in a data field with
|
|
|
2179 Fingerprint substring in its label and create a SampleFPHexTanimotoSimilarity.tsv file
|
|
|
2180 containing sequentially generated compound IDs with Cmpd prefix, type:
|
|
|
2181
|
|
|
2182 % SimilarityMatricesFingerprints.pl -OutDelim Tab --quote No -o SampleFPHex.sdf
|
|
|
2183
|
|
|
2184 =head1 AUTHOR
|
|
|
2185
|
|
|
2186 Manish Sud <msud@san.rr.com>
|
|
|
2187
|
|
|
2188 =head1 SEE ALSO
|
|
|
2189
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2190 InfoFingerprintsFiles.pl, SimilaritySearchingFingerprints.pl, AtomNeighborhoodsFingerprints.pl,
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2191 ExtendedConnectivityFingerprints.pl, MACCSKeysFingerprints.pl, PathLengthFingerprints.pl,
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2192 TopologicalAtomPairsFingerprints.pl, TopologicalAtomTorsionsFingerprints.pl,
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2193 TopologicalPharmacophoreAtomPairsFingerprints.pl, TopologicalPharmacophoreAtomTripletsFingerprints.pl
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2194
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2195 =head1 COPYRIGHT
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2196
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2197 Copyright (C) 2015 Manish Sud. All rights reserved.
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2198
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2199 This file is part of MayaChemTools.
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2200
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2201 MayaChemTools is free software; you can redistribute it and/or modify it under
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2202 the terms of the GNU Lesser General Public License as published by the Free
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2203 Software Foundation; either version 3 of the License, or (at your option)
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2204 any later version.
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2205
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2206 =cut
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