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1 #!/usr/bin/perl -w
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2 #
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3 # $RCSfile: SimilaritySearchingFingerprints.pl,v $
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4 # $Date: 2015/02/28 20:46:21 $
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5 # $Revision: 1.18 $
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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 "$FindBin::Bin/../lib";
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31 use Getopt::Long;
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32 use File::Basename;
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33 use Text::ParseWords;
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34 use Benchmark;
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35 use FileUtil;
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36 use TextUtil;
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37 use SDFileUtil;
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38 use StatisticsUtil;
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39 use PseudoHeap;
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40 use Fingerprints::FingerprintsFileUtil;
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41 use Fingerprints::FingerprintsBitVector;
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42 use Fingerprints::FingerprintsVector;
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43
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44 my($ScriptName, %Options, $StartTime, $EndTime, $TotalTime);
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45
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46 # Autoflush STDOUT
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47 $| = 1;
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48
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49 # Starting message...
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50 $ScriptName = basename($0);
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51 print "\n$ScriptName: Starting...\n\n";
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52 $StartTime = new Benchmark;
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53
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54 # Get the options and setup script...
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55 SetupScriptUsage();
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56 if ($Options{help} || @ARGV != 2) {
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57 die GetUsageFromPod("$FindBin::Bin/$ScriptName");
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58 }
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59
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60 # Process reference and database file names...
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61 my(@FingerprintsFilesList);
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62 ProcessFingerprintsFileNames();
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63
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64 # Process options...
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65 print "Processing options...\n";
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66 my(%OptionsInfo);
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67 ProcessOptions();
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68
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69 # Setup information about fingerprints inut and SD/text output files...
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70 my(%FingerprintsFilesInfo, %OutputFilesInfo, %SimilaritySearchInfo);
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71 print "Checking and retrieving information from reference and database fingerprints files...\n";
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72 RetrieveFingerprintsFilesInfo();
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73
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74 # Perform similarity search...
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75 print "Performing similarity search...\n";
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76 my(%SimilaritySearchResults, %DatabaseFingerprintsFileData);
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77 PerformSimilaritySearch();
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78
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79 print "\n$ScriptName:Done...\n\n";
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80
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81 $EndTime = new Benchmark;
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82 $TotalTime = timediff ($EndTime, $StartTime);
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83 print "Total time: ", timestr($TotalTime), "\n";
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84
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85 ###############################################################################
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86
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87 # Perform similarity search using fingerprints data in reference and database text files...
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88 #
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89 sub PerformSimilaritySearch {
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90
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91 print "\nProcessing fingerprints data for reference molecules...\n";
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92 ReadReferenceFingerprintsData();
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93
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94 InitializeSimilaritySearchResults();
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95 GenerateSimilaritySearchResults();
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96 WriteSimilaritySearchResultFiles();
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97 }
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98
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99 # Find similar molecules from database molecules for individual or multiple reference molecules...
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100 #
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101 sub GenerateSimilaritySearchResults {
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102 my($DatabaseFingerprintsFileIO, $FingerprintsCount, $IgnoredFingerprintsCount, $DatabaseFingerprintsObject, $DatabaseCmpdID, $ReferenceFingerprintsObject, $ReferenceIndex, $ReferenceCmpdID, $ComparisonValue, $FusedComparisonValue, @ComparisonValues);
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103
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104 print "Processing fingerprints data for database molecules...\n";
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105
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106 ($FingerprintsCount, $IgnoredFingerprintsCount) = (0) x 3;
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107
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108 $DatabaseFingerprintsFileIO = Fingerprints::FingerprintsFileUtil::NewFingerprintsFileIO(%{$FingerprintsFilesInfo{Database}{FingerprintsFileIOParameters}});
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109 $DatabaseFingerprintsFileIO->Open();
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110
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111 @ComparisonValues = ();
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112
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113 DATABASEFP: while ($DatabaseFingerprintsFileIO->Read()) {
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114 $FingerprintsCount++;
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115
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116 if (!$DatabaseFingerprintsFileIO->IsFingerprintsDataValid()) {
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117 $IgnoredFingerprintsCount++;
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118 next DATABASEFP;
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119 }
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120 $DatabaseFingerprintsObject = $DatabaseFingerprintsFileIO->GetFingerprints();
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121 $DatabaseCmpdID = $DatabaseFingerprintsFileIO->GetCompoundID();
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122
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123 if ($SimilaritySearchInfo{MultipleReferencesMode}) {
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124 @ComparisonValues = ();
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125 }
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126
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127 REFERENCEFP: for $ReferenceIndex (0 .. $#{$SimilaritySearchInfo{ReferenceCmpdIDsRef}}) {
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128 $ReferenceCmpdID = $SimilaritySearchInfo{ReferenceCmpdIDsRef}->[$ReferenceIndex];
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129 $ReferenceFingerprintsObject = $SimilaritySearchInfo{ReferenceFingerprintsObjectsRef}->[$ReferenceIndex];
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130
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131 $ComparisonValue = CompareReferenceAndDatabaseFingerprintsPair($ReferenceFingerprintsObject, $DatabaseFingerprintsObject);
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132 if (!defined $ComparisonValue) {
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133 next REFERENCEFP;
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134 }
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135
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136 if ($SimilaritySearchInfo{IndividualReferenceMode}) {
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137 CollectSimilaritySearchResults($DatabaseFingerprintsFileIO, $DatabaseCmpdID, $ComparisonValue, $ReferenceCmpdID);
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138 }
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139 elsif ($SimilaritySearchInfo{MultipleReferencesMode}) {
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140 push @ComparisonValues, $ComparisonValue;
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141 }
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142 }
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143
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144 if ($SimilaritySearchInfo{MultipleReferencesMode}) {
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145 $FusedComparisonValue = CalculateGroupFusionComparisonValue(\@ComparisonValues);
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146 if (!defined $FusedComparisonValue) {
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147 next DATABASEFP;
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148 }
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149 CollectSimilaritySearchResults($DatabaseFingerprintsFileIO, $DatabaseCmpdID, $FusedComparisonValue);
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150 }
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151 }
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152 $DatabaseFingerprintsFileIO->Close();
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153
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154 print "Number of fingerprints data entries in database fingerprints file: $FingerprintsCount\n";
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155 print "Number of fingerprints date entries processed successfully: ", ($FingerprintsCount - $IgnoredFingerprintsCount) , "\n";
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156 print "Number of fingerprints data entries ignored due to missing/invalid data: $IgnoredFingerprintsCount\n\n";
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157 }
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158
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159 # Compare a pair of reference and database fingerprints objects corresponding to bit-vector or
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160 # vectors using specified comparison method and comparison cutoff...
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161 #
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162 sub CompareReferenceAndDatabaseFingerprintsPair {
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163 my($ReferenceFingerprintsObject, $DatabaseFingerprintsObject) = @_;
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164 my($ComparisonMethod, $ComparisonValue);
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165
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166 $ComparisonMethod = $SimilaritySearchInfo{ComparisonMethod};
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167 $ComparisonValue = $ReferenceFingerprintsObject->$ComparisonMethod($DatabaseFingerprintsObject, @{$SimilaritySearchInfo{ComparisonMethodParameters}});
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168
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169 if (!defined $ComparisonValue) {
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170 warn "Warning: Ignoring fingerprints data for reference compound ID ", $ReferenceFingerprintsObject->GetID(), ": Its comparison with database compound ID, ", $DatabaseFingerprintsObject->GetID(), ", failed.\n";
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171 return undef;
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172 }
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173
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174 $ComparisonValue = sprintf("%.$OptionsInfo{Precision}f", $ComparisonValue);
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175
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176 # Apply any comparison cutoff...
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177 if ($SimilaritySearchInfo{ApplyComparisonCutoff}) {
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178 return $SimilaritySearchInfo{KeepTop} ? ($ComparisonValue >= $SimilaritySearchInfo{ComparisonCutoff} ? $ComparisonValue : undef) : ($ComparisonValue <= $SimilaritySearchInfo{ComparisonCutoff} ? $ComparisonValue : undef);
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179 }
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180 else {
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181 return $ComparisonValue;
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182 }
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183 }
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184
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185 # Calculate group fusion comparison value...
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186 #
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187 sub CalculateGroupFusionComparisonValue {
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188 my($ComparisonValuesRef) = @_;
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189 my($FusedComparisonValue, @ComparisonValues);
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190
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191 if (!@{$ComparisonValuesRef}) {
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192 return undef;
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193 }
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194
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195 if ($SimilaritySearchInfo{SortComparisonValues}) {
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196 @ComparisonValues = sort { $SimilaritySearchInfo{KeepTop} ? ($b <=> $a) : ($a <=> $b) } @{$ComparisonValuesRef};
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197 if ($SimilaritySearchInfo{UsekNN} && ($OptionsInfo{kNN} < scalar @{$ComparisonValuesRef})) {
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198 # Keep only top kNN values for group fusion...
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199 splice @ComparisonValues, $OptionsInfo{kNN};
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200 }
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201 $ComparisonValuesRef = \@ComparisonValues;
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202 }
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203
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204 $FusedComparisonValue = &{$SimilaritySearchInfo{GroupFusionMethodRef}}($ComparisonValuesRef);
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205 if ($SimilaritySearchInfo{ApplyPrecisionDuringFusion}) {
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206 $FusedComparisonValue = sprintf("%.$OptionsInfo{Precision}f", $FusedComparisonValue);
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207 }
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208
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209 return $FusedComparisonValue;
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210 }
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211
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212 # Collect similarity results for individual reference and multiple references search...
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213 #
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214 sub CollectSimilaritySearchResults {
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215 my($DatabaseFingerprintsFileIO, $DatabaseCmpdID, $ComparisonValue, $ReferenceCmpdID) = @_;
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216
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217 if (defined $ReferenceCmpdID) {
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218 $SimilaritySearchResults{$ReferenceCmpdID}->AddKeyValuePair($ComparisonValue, $DatabaseCmpdID);
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219 }
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220 else {
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221 $SimilaritySearchResults{ResultsPseudoHeap}->AddKeyValuePair($ComparisonValue, $DatabaseCmpdID);
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222 }
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223
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224 if ($FingerprintsFilesInfo{Database}{CollectInputFileData}) {
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225 CollectDatabaseFileData($DatabaseCmpdID, $DatabaseFingerprintsFileIO);
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226 }
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227 }
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228
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229 # Initialize similarity results for individual or multiple reference molecules...
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230 #
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231 sub InitializeSimilaritySearchResults {
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232 my($ReferenceCmpdID);
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233
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234 %SimilaritySearchResults = ();
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235
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236 if ($SimilaritySearchInfo{IndividualReferenceMode}) {
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237 for $ReferenceCmpdID (@{$SimilaritySearchInfo{ReferenceCmpdIDsRef}}) {
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238 $SimilaritySearchResults{$ReferenceCmpdID} = new PseudoHeap('Type' => ($SimilaritySearchInfo{KeepTop} ? 'KeepTopN' : 'KeepBottomN'), 'KeyType' => 'Numeric', 'MaxSize' => $OptionsInfo{MaxSimilarMolecules});
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239 }
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240 }
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241 elsif ($SimilaritySearchInfo{MultipleReferencesMode}) {
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242 $SimilaritySearchResults{ResultsPseudoHeap} = new PseudoHeap('Type' => ($SimilaritySearchInfo{KeepTop} ? 'KeepTopN' : 'KeepBottomN'), 'KeyType' => 'Numeric', 'MaxSize' => $OptionsInfo{MaxSimilarMolecules});
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243 }
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244
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245 %DatabaseFingerprintsFileData = ();
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246 }
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247
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248 # Write out results SD and/or CSV/TSV text files for individual or multiple reference molecules...
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249 #
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250 sub WriteSimilaritySearchResultFiles {
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251 my($NewSDFileRef, $NewTextFileRef, $ReferenceCmpdID, $DatabaseCmpdID, $ComparisonValue);
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252
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253 ($NewSDFileRef, $NewTextFileRef) = SetupAndOpenOutputFiles();
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254
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255 if ($SimilaritySearchInfo{IndividualReferenceMode}) {
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256 for $ReferenceCmpdID (@{$SimilaritySearchInfo{ReferenceCmpdIDsRef}}) {
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257 for $ComparisonValue ($SimilaritySearchResults{$ReferenceCmpdID}->GetSortedKeys()) {
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258 for $DatabaseCmpdID ($SimilaritySearchResults{$ReferenceCmpdID}->GetKeyValues($ComparisonValue)) {
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259 WriteDataToOutputFiles($NewSDFileRef, $NewTextFileRef, $ComparisonValue, $DatabaseCmpdID, $ReferenceCmpdID);
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260 }
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261 }
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262 }
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263 }
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264 elsif ($SimilaritySearchInfo{MultipleReferencesMode}) {
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265 for $ComparisonValue ($SimilaritySearchResults{ResultsPseudoHeap}->GetSortedKeys()) {
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266 for $DatabaseCmpdID ($SimilaritySearchResults{ResultsPseudoHeap}->GetKeyValues($ComparisonValue)) {
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267 WriteDataToOutputFiles($NewSDFileRef, $NewTextFileRef, $ComparisonValue, $DatabaseCmpdID);
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268 }
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269 }
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270 }
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271
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272 if ($NewSDFileRef) {
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273 close $NewSDFileRef;
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274 }
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275 if ($NewTextFileRef) {
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276 close $NewTextFileRef;
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277 }
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278 }
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279
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280 # Write individual reference or multiple references similarity results along with any other data to output files...
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281 #
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282 sub WriteDataToOutputFiles {
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283 my($NewSDFileRef, $NewTextFileRef, $ComparisonValue, $DatabaseCmpdID, $ReferenceCmpdID) = @_;
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284
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285 if ($NewSDFileRef) {
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286 WriteMolStringDataToSDOutputFile($DatabaseCmpdID, $NewSDFileRef);
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287 if (defined $ReferenceCmpdID) {
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288 print $NewSDFileRef "> <ReferenceCmpdID>\n$ReferenceCmpdID\n\n";
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289 }
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290 print $NewSDFileRef "> <DatabaseCmpdID>\n$DatabaseCmpdID\n\n> <ComparisonValue>\n$ComparisonValue\n\n";
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291 WriteDatabaseDataToSDOutputFile($DatabaseCmpdID, $NewSDFileRef);
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292 print $NewSDFileRef "\$\$\$\$\n";
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293 }
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294
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295 if ($NewTextFileRef) {
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296 my(@LineWords);
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297
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298 @LineWords = ();
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299 if (defined $ReferenceCmpdID) {
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300 push @LineWords, $ReferenceCmpdID;
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301 }
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302 push @LineWords, ($DatabaseCmpdID, $ComparisonValue);
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303
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304 if ($FingerprintsFilesInfo{Database}{OutputDataFields} || $FingerprintsFilesInfo{Database}{OutputDataCols}) {
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305 push @LineWords, RetrieveDatabaseDataForTextOutputFile($DatabaseCmpdID);
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306 }
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307 print $NewTextFileRef JoinWords(\@LineWords, $OptionsInfo{OutDelim}, $OptionsInfo{OutQuote}), "\n";
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308 }
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309 }
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310
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311 # Open output files...
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312 #
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313 sub SetupAndOpenOutputFiles {
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314 my($NewSDFileRef, $NewTextFileRef, $NewSDFile, $NewTextFile);
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315
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316 ($NewSDFileRef, $NewTextFileRef) = (undef) x 2;
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317
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318 if ($OptionsInfo{SDOutput}) {
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319 $NewSDFile = $OutputFilesInfo{SDOutFileName};
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320 print "Generating SD file $NewSDFile...\n";
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321 open NEWSDFILE, ">$NewSDFile" or die "Error: Couldn't open $NewSDFile: $! \n";
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322 $NewSDFileRef = \*NEWSDFILE;
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323 }
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324
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325 if ($OptionsInfo{TextOutput}) {
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326 $NewTextFile = $OutputFilesInfo{TextOutFileName};
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327 print "Generating text file $NewTextFile...\n";
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328 open NEWTEXTFILE, ">$NewTextFile" or die "Error: Couldn't open $NewTextFile: $! \n";
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329 $NewTextFileRef = \*NEWTEXTFILE;
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330
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331 WriteTextFileCoulmnLabels(\*NEWTEXTFILE);
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332 }
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333
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334 return ($NewSDFileRef, $NewTextFileRef);
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335 }
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336
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337 # Write out approriate column labels to text file...
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338 #
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339 sub WriteTextFileCoulmnLabels {
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340 my($NewTextFileRef) = @_;
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341 my($Line, @LineWords);
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342
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343 @LineWords = ();
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344
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345 if ($SimilaritySearchInfo{IndividualReferenceMode}) {
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346 push @LineWords, qw(ReferenceCompoundID DatabaseCompoundID ComparisonValue);
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347 }
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348 elsif ($SimilaritySearchInfo{MultipleReferencesMode}) {
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349 push @LineWords, qw(DatabaseCompoundID ComparisonValue);
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350 }
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351
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352 # Add columns for other database fingerprints file data to be written to output file...
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353 if ($FingerprintsFilesInfo{Database}{OutputDataFields}) {
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354 push @LineWords, @{$FingerprintsFilesInfo{Database}{DataFieldsToOutput}};
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355 }
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356 elsif ($FingerprintsFilesInfo{Database}{OutputDataCols}) {
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357 push @LineWords, @{$FingerprintsFilesInfo{Database}{DataColLabelsToOutput}};
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358 }
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359
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360 $Line = JoinWords(\@LineWords, $OptionsInfo{OutDelim}, $OptionsInfo{OutQuote});
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361 print $NewTextFileRef "$Line\n";
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362 }
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363
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364 # Write molecule string data to SD output file...
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365 #
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366 sub WriteMolStringDataToSDOutputFile {
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367 my($DatabaseCmpdID, $NewSDFileRef) = @_;
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368
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369 if ($FingerprintsFilesInfo{Database}{CollectCmpdStringData}) {
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370 my($MolString);
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371
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372 ($MolString) = split /M END/, $DatabaseFingerprintsFileData{$DatabaseCmpdID};
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373 print $NewSDFileRef "$MolString\nM END\n";
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374 }
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375 else {
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376 # Just write out an empty molecule data string...
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377 print $NewSDFileRef SDFileUtil::GenerateEmptyCtabBlockLines(), "\n";
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378 }
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379 }
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380
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381 # Write database data from SD or Text database file to SD output file...
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382 #
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383 sub WriteDatabaseDataToSDOutputFile {
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384 my($DatabaseCmpdID, $NewSDFileRef) = @_;
|
|
|
385
|
|
|
386 if ($FingerprintsFilesInfo{Database}{OutputDataFields}) {
|
|
|
387 my($DataFieldLabel, $DataFieldValue, @CmpdLines, %DataFieldLabelAndValues);
|
|
|
388
|
|
|
389 @CmpdLines = split /\n/, $DatabaseFingerprintsFileData{$DatabaseCmpdID};
|
|
|
390 %DataFieldLabelAndValues = GetCmpdDataHeaderLabelsAndValues(\@CmpdLines);
|
|
|
391
|
|
|
392 for $DataFieldLabel ($FingerprintsFilesInfo{Database}{OutputCurrentDataFields} ? GetCmpdDataHeaderLabels(\@CmpdLines) : @{$FingerprintsFilesInfo{Database}{DataFieldsToOutput}}) {
|
|
|
393 $DataFieldValue = exists $DataFieldLabelAndValues{$DataFieldLabel} ? $DataFieldLabelAndValues{$DataFieldLabel} : '';
|
|
|
394 print $NewSDFileRef "> <$DataFieldLabel>\n$DataFieldValue\n\n";
|
|
|
395 }
|
|
|
396 }
|
|
|
397 elsif ($FingerprintsFilesInfo{Database}{OutputDataCols}) {
|
|
|
398 my($DataColNum, $DataFieldLabel, $DataFieldValue);
|
|
|
399
|
|
|
400 for $DataColNum (@{$FingerprintsFilesInfo{Database}{DataColNumsToOutput}}) {
|
|
|
401 $DataFieldLabel = $FingerprintsFilesInfo{Database}{DataColNumToLabelMap}{$DataColNum};
|
|
|
402 $DataFieldValue = $DatabaseFingerprintsFileData{$DatabaseCmpdID}->[$DataColNum];
|
|
|
403 print $NewSDFileRef "> <$DataFieldLabel>\n$DataFieldValue\n\n";
|
|
|
404 }
|
|
|
405 }
|
|
|
406 }
|
|
|
407
|
|
|
408 # Retriebe database data from SD or Text database file for text output file...
|
|
|
409 #
|
|
|
410 sub RetrieveDatabaseDataForTextOutputFile {
|
|
|
411 my($DatabaseCmpdID) = @_;
|
|
|
412
|
|
|
413 if ($FingerprintsFilesInfo{Database}{OutputDataFields}) {
|
|
|
414 my(@CmpdLines, %DataFieldLabelAndValues);
|
|
|
415
|
|
|
416 @CmpdLines = split /\n/, $DatabaseFingerprintsFileData{$DatabaseCmpdID};
|
|
|
417 %DataFieldLabelAndValues = GetCmpdDataHeaderLabelsAndValues(\@CmpdLines);
|
|
|
418
|
|
|
419 return map { exists $DataFieldLabelAndValues{$_} ? $DataFieldLabelAndValues{$_} : ''} @{$FingerprintsFilesInfo{Database}{DataFieldsToOutput}};
|
|
|
420 }
|
|
|
421 elsif ($FingerprintsFilesInfo{Database}{OutputDataCols}) {
|
|
|
422 if (exists $DatabaseFingerprintsFileData{$DatabaseCmpdID}) {
|
|
|
423 return map { $DatabaseFingerprintsFileData{$DatabaseCmpdID}->[$_] } (0 .. $#{$FingerprintsFilesInfo{Database}{DataColNumsToOutput}});
|
|
|
424 }
|
|
|
425 else {
|
|
|
426 return ('') x $#{$FingerprintsFilesInfo{Database}{DataColNumsToOutput}};
|
|
|
427 }
|
|
|
428 }
|
|
|
429 }
|
|
|
430
|
|
|
431 # Collect database file SD compound string or CSV/TSV data line for generating results
|
|
|
432 # files..
|
|
|
433 #
|
|
|
434 sub CollectDatabaseFileData {
|
|
|
435 my($DatabaseCmpdID, $DatabaseFingerprintsFileIO) = @_;
|
|
|
436
|
|
|
437 if (exists $DatabaseFingerprintsFileData{$DatabaseCmpdID}) {
|
|
|
438 return;
|
|
|
439 }
|
|
|
440
|
|
|
441 if ($FingerprintsFilesInfo{Database}{CollectCmpdStringData}) {
|
|
|
442 $DatabaseFingerprintsFileData{$DatabaseCmpdID} = $DatabaseFingerprintsFileIO->GetCompoundString();
|
|
|
443 }
|
|
|
444
|
|
|
445 if ($FingerprintsFilesInfo{Database}{CollectDataLine}) {
|
|
|
446 my(@DataLineWords);
|
|
|
447 @DataLineWords = $DatabaseFingerprintsFileIO->GetDataLineWords();
|
|
|
448 $DatabaseFingerprintsFileData{$DatabaseCmpdID} = \@DataLineWords;
|
|
|
449 }
|
|
|
450
|
|
|
451 }
|
|
|
452
|
|
|
453 # Read fingerprints data from reference fingerprints file...
|
|
|
454 #
|
|
|
455 sub ReadReferenceFingerprintsData {
|
|
|
456 my($FingerprintsFileIO);
|
|
|
457
|
|
|
458 $FingerprintsFileIO = Fingerprints::FingerprintsFileUtil::NewFingerprintsFileIO(%{$FingerprintsFilesInfo{Reference}{FingerprintsFileIOParameters}});
|
|
|
459 ($SimilaritySearchInfo{ReferenceCmpdIDsRef}, $SimilaritySearchInfo{ReferenceFingerprintsObjectsRef}) = Fingerprints::FingerprintsFileUtil::ReadAndProcessFingerpritsData($FingerprintsFileIO);
|
|
|
460
|
|
|
461 }
|
|
|
462
|
|
|
463 # Retrieve information about fingerprints files...
|
|
|
464 #
|
|
|
465 sub RetrieveFingerprintsFilesInfo {
|
|
|
466
|
|
|
467 %FingerprintsFilesInfo = ();
|
|
|
468 %OutputFilesInfo = ();
|
|
|
469 %SimilaritySearchInfo = ();
|
|
|
470
|
|
|
471 %{$FingerprintsFilesInfo{Reference}} = ();
|
|
|
472 %{$FingerprintsFilesInfo{Database}} = ();
|
|
|
473
|
|
|
474 # Set up reference and database file names...
|
|
|
475 $FingerprintsFilesInfo{Reference}{FileName} = $FingerprintsFilesList[0];
|
|
|
476 $FingerprintsFilesInfo{Database}{FileName} = $FingerprintsFilesList[1];
|
|
|
477
|
|
|
478 # Retrieve information about reference and database fingerprints file...
|
|
|
479 RetrieveReferenceFingerprintsFileInfo();
|
|
|
480 RetrieveDatabaseFingerprintsFileInfo();
|
|
|
481
|
|
|
482 # Setup fingerprints comparison method and associated method parameters...
|
|
|
483 SetupReferenceAndDatabaseFingerprintsComparisonInfo();
|
|
|
484
|
|
|
485 # Retrieve information for output files...
|
|
|
486 RetrieveOutputFilesInfo();
|
|
|
487 }
|
|
|
488
|
|
|
489 # Setup refrerence and database fingerprints comparison method and associated method parameters...
|
|
|
490 #
|
|
|
491 sub SetupReferenceAndDatabaseFingerprintsComparisonInfo {
|
|
|
492
|
|
|
493 # Make sure reference and database fingerprints string match...
|
|
|
494 if (($FingerprintsFilesInfo{Reference}{FirstFingerprintsStringType} !~ /^$FingerprintsFilesInfo{Database}{FirstFingerprintsStringType}$/i) ||
|
|
|
495 ($FingerprintsFilesInfo{Reference}{FingerprintsBitVectorStringMode} != $FingerprintsFilesInfo{Database}{FingerprintsBitVectorStringMode}) ||
|
|
|
496 ($FingerprintsFilesInfo{Reference}{FingerprintsVectorStringMode} != $FingerprintsFilesInfo{Database}{FingerprintsVectorStringMode}) ) {
|
|
|
497 die "Error: First reference fingerprints string type, $FingerprintsFilesInfo{Reference}{FirstFingerprintsStringType}, must match first database fingerprints type, $FingerprintsFilesInfo{Database}{FirstFingerprintsStringType}.\n";
|
|
|
498 }
|
|
|
499
|
|
|
500 if ($FingerprintsFilesInfo{Reference}{FirstFingerprintsStringDescription} !~ /^$FingerprintsFilesInfo{Database}{FirstFingerprintsStringDescription}$/i) {
|
|
|
501 warn "Warning: First reference fingerprints string description, $FingerprintsFilesInfo{Reference}{FirstFingerprintsStringDescription}, doesn't match first database fingerprints string description, $FingerprintsFilesInfo{Database}{FirstFingerprintsStringDescription}.\n";
|
|
|
502 }
|
|
|
503
|
|
|
504 # Setup individual reference and multiple references search mode...
|
|
|
505 $SimilaritySearchInfo{IndividualReferenceMode} = undef;
|
|
|
506 $SimilaritySearchInfo{MultipleReferencesMode} = undef;
|
|
|
507
|
|
|
508 if ($OptionsInfo{Mode} =~ /^IndividualReference$/i) {
|
|
|
509 $SimilaritySearchInfo{IndividualReferenceMode} = 1;
|
|
|
510 }
|
|
|
511 elsif ($OptionsInfo{Mode} =~ /^MultipleReferences$/i) {
|
|
|
512 $SimilaritySearchInfo{MultipleReferencesMode} = 1;
|
|
|
513 }
|
|
|
514 else {
|
|
|
515 die "Error: The value specified, $Options{mode}, for option \"-m, --mode\" is not valid. Allowed values: IndividualReference, MultipleReferences\n";
|
|
|
516 }
|
|
|
517
|
|
|
518 # Set up reference and database fingerprints similarity search method and paramaters...
|
|
|
519 my($ComparisonMeasure, $ComparisonMethod, $ApplyComparisonCutoff, $ComparisonCutoff, $KeepTop, @ComparisonMethodParameters);
|
|
|
520
|
|
|
521 $SimilaritySearchInfo{ComparisonMethod} = '';
|
|
|
522 @{$SimilaritySearchInfo{ComparisonMethodParameters}} = ();
|
|
|
523
|
|
|
524 $SimilaritySearchInfo{ComparisonCutoff} = '';
|
|
|
525 $SimilaritySearchInfo{KeepTop} = '';
|
|
|
526
|
|
|
527 $ComparisonMeasure = ''; $ComparisonMethod = '';
|
|
|
528 @ComparisonMethodParameters = ();
|
|
|
529
|
|
|
530 FINGERPRINTSTYPE: {
|
|
|
531 if ($FingerprintsFilesInfo{Reference}{FingerprintsBitVectorStringMode}) {
|
|
|
532 $ComparisonMeasure = $OptionsInfo{SpecifiedBitVectorComparisonMeasure};
|
|
|
533 $ComparisonMethod = $OptionsInfo{SpecifiedBitVectorComparisonMeasureMethod};
|
|
|
534
|
|
|
535 if ($ComparisonMeasure =~ /^TverskySimilarity$/i) {
|
|
|
536 push @ComparisonMethodParameters, $OptionsInfo{Alpha};
|
|
|
537 }
|
|
|
538 elsif ($ComparisonMeasure =~ /^WeightedTverskySimilarity$/i) {
|
|
|
539 push @ComparisonMethodParameters, $OptionsInfo{Alpha};
|
|
|
540 push @ComparisonMethodParameters, $OptionsInfo{Beta};
|
|
|
541 }
|
|
|
542 elsif ($ComparisonMeasure =~ /^WeightedTanimotoSimilarity$/i) {
|
|
|
543 push @ComparisonMethodParameters, $OptionsInfo{Beta};
|
|
|
544 }
|
|
|
545
|
|
|
546 last FINGERPRINTSTYPE;
|
|
|
547 }
|
|
|
548 if ($FingerprintsFilesInfo{Reference}{FingerprintsVectorStringMode}) {
|
|
|
549 my($SkipValuesCheck);
|
|
|
550
|
|
|
551 $ComparisonMeasure = $OptionsInfo{SpecifiedVectorComparisonMeasure};
|
|
|
552 $ComparisonMethod = $OptionsInfo{SpecifiedVectorComparisonMeasuresMethod};
|
|
|
553
|
|
|
554 push @ComparisonMethodParameters, $OptionsInfo{SpecifiedVectorComparisonMode};
|
|
|
555
|
|
|
556 $SkipValuesCheck = $OptionsInfo{Fast} ? 1 : 0;
|
|
|
557 push @ComparisonMethodParameters, $SkipValuesCheck;
|
|
|
558
|
|
|
559 last FINGERPRINTSTYPE;
|
|
|
560 }
|
|
|
561 die "Error: Uknown fingerprints string type. Supported values: FingerprintsBitVectorString or FingerprintsVectorString.\n";
|
|
|
562 }
|
|
|
563
|
|
|
564 $ApplyComparisonCutoff = $SimilaritySearchInfo{IndividualReferenceMode} ? 1 : (($SimilaritySearchInfo{MultipleReferencesMode} && $OptionsInfo{GroupFusionApplyCutoff}) ? 1 : 0);
|
|
|
565
|
|
|
566 $ComparisonCutoff = ''; $KeepTop = '';
|
|
|
567 if ($ComparisonMethod =~ /Distance/i) {
|
|
|
568 $ComparisonCutoff = $OptionsInfo{DistanceCutoff};
|
|
|
569 $KeepTop = ($OptionsInfo{SearchMode} =~ /^SimilaritySearch$/i) ? 0 : 1;
|
|
|
570 }
|
|
|
571 else {
|
|
|
572 $ComparisonCutoff = $OptionsInfo{SimilarityCutoff};
|
|
|
573 $KeepTop = ($OptionsInfo{SearchMode} =~ /^SimilaritySearch$/i) ? 1 : 0;
|
|
|
574 }
|
|
|
575
|
|
|
576 $SimilaritySearchInfo{ComparisonMethod} = $ComparisonMethod;
|
|
|
577 @{$SimilaritySearchInfo{ComparisonMethodParameters}} = @ComparisonMethodParameters;
|
|
|
578
|
|
|
579 $SimilaritySearchInfo{ComparisonCutoff} = $ComparisonCutoff;
|
|
|
580 $SimilaritySearchInfo{KeepTop} = $KeepTop;
|
|
|
581 $SimilaritySearchInfo{ApplyComparisonCutoff} = $ApplyComparisonCutoff;
|
|
|
582
|
|
|
583 # Setup references to group fusion methods...
|
|
|
584 $SimilaritySearchInfo{GroupFusionMethodRef} = undef;
|
|
|
585 $SimilaritySearchInfo{ApplyPrecisionDuringFusion} = undef;
|
|
|
586
|
|
|
587 FUSIONRULE: {
|
|
|
588 if ($OptionsInfo{GroupFusionRule} =~ /^Max$/i) {
|
|
|
589 # It's always the first value in the appropriated sorted list using value of KeepTop...
|
|
|
590 $SimilaritySearchInfo{GroupFusionMethodRef} = sub { my($ComparisonValuesRef) = @_; return $ComparisonValuesRef->[0]; };
|
|
|
591 last FUSIONRULE;
|
|
|
592 }
|
|
|
593 if ($OptionsInfo{GroupFusionRule} =~ /^Min$/i) {
|
|
|
594 # It's always the last value in the appropriated sorted list using value of KeepTop...
|
|
|
595 $SimilaritySearchInfo{GroupFusionMethodRef} = sub { my($ComparisonValuesRef) = @_; return $ComparisonValuesRef->[$#{$ComparisonValuesRef}]; };
|
|
|
596 last FUSIONRULE;
|
|
|
597 }
|
|
|
598 if ($OptionsInfo{GroupFusionRule} =~ /^Mean$/i) {
|
|
|
599 $SimilaritySearchInfo{GroupFusionMethodRef} = \&StatisticsUtil::Mean;
|
|
|
600 $SimilaritySearchInfo{ApplyPrecisionDuringFusion} = 1;
|
|
|
601 last FUSIONRULE;
|
|
|
602 }
|
|
|
603 if ($OptionsInfo{GroupFusionRule} =~ /^Median$/i) {
|
|
|
604 $SimilaritySearchInfo{GroupFusionMethodRef} = \&StatisticsUtil::Median;
|
|
|
605 $SimilaritySearchInfo{ApplyPrecisionDuringFusion} = 1;
|
|
|
606 last FUSIONRULE;
|
|
|
607 }
|
|
|
608 if ($OptionsInfo{GroupFusionRule} =~ /^Sum$/i) {
|
|
|
609 $SimilaritySearchInfo{GroupFusionMethodRef} = \&StatisticsUtil::Sum;
|
|
|
610 $SimilaritySearchInfo{ApplyPrecisionDuringFusion} = 1;
|
|
|
611 last FUSIONRULE;
|
|
|
612 }
|
|
|
613 if ($OptionsInfo{GroupFusionRule} =~ /^Euclidean$/i) {
|
|
|
614 $SimilaritySearchInfo{GroupFusionMethodRef} = \&StatisticsUtil::Euclidean;
|
|
|
615 $SimilaritySearchInfo{ApplyPrecisionDuringFusion} = 1;
|
|
|
616 last FUSIONRULE;
|
|
|
617 }
|
|
|
618 die "Error: The value specified, $Options{groupfusionrule}, for option \"-g, --GroupFusionRule\" is not valid. Allowed values: Max, Min, Mean, Median, Sum, Euclidean\n";
|
|
|
619 }
|
|
|
620
|
|
|
621 $SimilaritySearchInfo{UsekNN} = ($OptionsInfo{kNN} !~ /^All$/i) ? 1 : 0;
|
|
|
622 $SimilaritySearchInfo{SortComparisonValues} = (($OptionsInfo{GroupFusionRule} =~ /^(Max|Min)$/i) || $SimilaritySearchInfo{UsekNN}) ? 1 : 0;
|
|
|
623 }
|
|
|
624
|
|
|
625 # Retrieve information about reference fingerprints file...
|
|
|
626 #
|
|
|
627 sub RetrieveReferenceFingerprintsFileInfo {
|
|
|
628 my($FingerprintsFile, $FileType, $InDelim, $FingerprintsFileIO, $FingerprintsStringMode, $FingerprintsBitVectorStringMode, $FingerprintsVectorStringMode, $FirstFingerprintsStringType, $FirstFingerprintsStringDescription);
|
|
|
629
|
|
|
630 $FingerprintsFile = $FingerprintsFilesInfo{Reference}{FileName};
|
|
|
631 ($FileType, $InDelim) = RetrieveFingerprintsFileInfo($FingerprintsFile);
|
|
|
632
|
|
|
633 $FingerprintsFilesInfo{Reference}{FileType} = $FileType;
|
|
|
634 $FingerprintsFilesInfo{Reference}{InDelim} = $InDelim;
|
|
|
635
|
|
|
636 # Setup reference FingerprintsFileIO parameters...
|
|
|
637 %{$FingerprintsFilesInfo{Reference}{FingerprintsFileIOParameters}} = RetrieveFingerprintsFileIOParameters('Reference', $FileType, $FingerprintsFile);
|
|
|
638
|
|
|
639 # Make sure reference fingerprints data file contains valid and retrieve fingerprints string mode information...
|
|
|
640 ($FingerprintsStringMode, $FingerprintsBitVectorStringMode, $FingerprintsVectorStringMode, $FirstFingerprintsStringType, $FirstFingerprintsStringDescription) = RetrieveFingerprintsFileFingerprintsStringInfo('Reference', $FingerprintsFile);
|
|
|
641 $FingerprintsFilesInfo{Reference}{FingerprintsStringMode} = $FingerprintsStringMode;
|
|
|
642 $FingerprintsFilesInfo{Reference}{FingerprintsBitVectorStringMode} = $FingerprintsBitVectorStringMode;
|
|
|
643 $FingerprintsFilesInfo{Reference}{FingerprintsVectorStringMode} = $FingerprintsVectorStringMode;
|
|
|
644 $FingerprintsFilesInfo{Reference}{FirstFingerprintsStringType} = $FirstFingerprintsStringType;
|
|
|
645 $FingerprintsFilesInfo{Reference}{FirstFingerprintsStringDescription} = $FirstFingerprintsStringDescription;
|
|
|
646
|
|
|
647 }
|
|
|
648
|
|
|
649 # Retrieve information about database fingerprints file...
|
|
|
650 #
|
|
|
651 sub RetrieveDatabaseFingerprintsFileInfo {
|
|
|
652 my($FingerprintsFile, $FileType, $InDelim, $FingerprintsFileIO, $FingerprintsStringMode, $FingerprintsBitVectorStringMode, $FingerprintsVectorStringMode, $FirstFingerprintsStringType, $FirstFingerprintsStringDescription);
|
|
|
653
|
|
|
654 $FingerprintsFile = $FingerprintsFilesInfo{Database}{FileName};
|
|
|
655 ($FileType, $InDelim) = RetrieveFingerprintsFileInfo($FingerprintsFile);
|
|
|
656
|
|
|
657 $FingerprintsFilesInfo{Database}{FileType} = $FileType;
|
|
|
658 $FingerprintsFilesInfo{Database}{InDelim} = $InDelim;
|
|
|
659
|
|
|
660 # Setup reference FingerprintsFileIO parameters...
|
|
|
661 %{$FingerprintsFilesInfo{Database}{FingerprintsFileIOParameters}} = RetrieveFingerprintsFileIOParameters('Database', $FileType, $FingerprintsFile);
|
|
|
662
|
|
|
663 # Make sure database fingerprints data file contains valid and retrieve fingerprints string mode information...
|
|
|
664 ($FingerprintsStringMode, $FingerprintsBitVectorStringMode, $FingerprintsVectorStringMode, $FirstFingerprintsStringType, $FirstFingerprintsStringDescription) = RetrieveFingerprintsFileFingerprintsStringInfo('Database', $FingerprintsFile);
|
|
|
665 $FingerprintsFilesInfo{Database}{FingerprintsStringMode} = $FingerprintsStringMode;
|
|
|
666 $FingerprintsFilesInfo{Database}{FingerprintsBitVectorStringMode} = $FingerprintsBitVectorStringMode;
|
|
|
667 $FingerprintsFilesInfo{Database}{FingerprintsVectorStringMode} = $FingerprintsVectorStringMode;
|
|
|
668 $FingerprintsFilesInfo{Database}{FirstFingerprintsStringType} = $FirstFingerprintsStringType;
|
|
|
669 $FingerprintsFilesInfo{Database}{FirstFingerprintsStringDescription} = $FirstFingerprintsStringDescription;
|
|
|
670
|
|
|
671 # Retrieve database fingerprints data field information for output file...
|
|
|
672 #
|
|
|
673 RetrieveDatabaseFingerprintsDataFieldsInfo($FingerprintsFile, $FileType, $InDelim);
|
|
|
674
|
|
|
675 # Retrieve database fingerprints text file data columns information for output file...
|
|
|
676 #
|
|
|
677 RetrieveDatabaseFingerprintsDataColsInfo($FingerprintsFile, $FileType, $InDelim);
|
|
|
678
|
|
|
679 # Any need to collect database compound string or data line for generation of results files...
|
|
|
680 $FingerprintsFilesInfo{Database}{CollectCmpdStringData} = ($FileType =~ /^SD$/i) ? 1 : 0;
|
|
|
681 $FingerprintsFilesInfo{Database}{CollectDataLine} = ($FileType =~ /^Text$/i && $OptionsInfo{DatabaseDataColsMode} =~ /^(All|Specify)$/i) ? 1 : 0;
|
|
|
682 $FingerprintsFilesInfo{Database}{CollectInputFileData} = ($FingerprintsFilesInfo{Database}{CollectCmpdStringData} || $FingerprintsFilesInfo{Database}{CollectDataLine}) ? 1 : 0;
|
|
|
683
|
|
|
684 # Set maximum number of similar compounds to find for individual reference of set of multiple
|
|
|
685 # reference compounds...
|
|
|
686 #
|
|
|
687 SetMaximumSimilarMoleculesToRetrieve($FingerprintsFile, $FileType, $InDelim);
|
|
|
688 }
|
|
|
689
|
|
|
690 # Retrieve database fingerprints data field information...
|
|
|
691 #
|
|
|
692 sub RetrieveDatabaseFingerprintsDataFieldsInfo {
|
|
|
693 my($FingerprintsFile, $FileType, $InDelim) = @_;
|
|
|
694 my($CollectDataFields, $CmpdCount, $AllDataFieldsRef, $CommonDataFieldsRef, @DataFieldsToOutput);
|
|
|
695
|
|
|
696 $FingerprintsFilesInfo{Database}{OutputDataFields} = 0;
|
|
|
697 @{$FingerprintsFilesInfo{Database}{DataFieldsToOutput}} = ();
|
|
|
698
|
|
|
699 $FingerprintsFilesInfo{Database}{OutputCurrentDataFields} = 0;
|
|
|
700
|
|
|
701 @{$FingerprintsFilesInfo{Database}{AllDataFields}} = ();
|
|
|
702 @{$FingerprintsFilesInfo{Database}{CommonDataFields}} = ();
|
|
|
703 @{$FingerprintsFilesInfo{Database}{SpecifiedDatabaseDataFields}} = ();
|
|
|
704
|
|
|
705 if ($FileType !~ /^SD$/i) {
|
|
|
706 return;
|
|
|
707 }
|
|
|
708
|
|
|
709 # No need to go over SD file and collect data fields for SD file during All DatabaseDataFieldsMode as
|
|
|
710 # they would be retrieved from database SD file compound string during generation of output files...
|
|
|
711 #
|
|
|
712 $CollectDataFields = (($OptionsInfo{TextOutput} && $OptionsInfo{DatabaseDataFieldsMode} =~ /^(All|Common)$/i) || ($OptionsInfo{SDOutput} && $OptionsInfo{DatabaseDataFieldsMode} =~ /^Common$/i)) ? 1 : 0;
|
|
|
713
|
|
|
714 ($CmpdCount, $AllDataFieldsRef, $CommonDataFieldsRef) = (undef) x 2;
|
|
|
715
|
|
|
716 if ($CollectDataFields) {
|
|
|
717 open SDFILE, "$FingerprintsFile" or die "Error: Couldn't open $FingerprintsFile: $! \n";
|
|
|
718 ($CmpdCount, $AllDataFieldsRef, $CommonDataFieldsRef) = GetAllAndCommonCmpdDataHeaderLabels(\*SDFILE);
|
|
|
719 close SDFILE;
|
|
|
720 }
|
|
|
721
|
|
|
722 @DataFieldsToOutput = ();
|
|
|
723 if ($OptionsInfo{DatabaseDataFieldsMode} =~ /^All$/i) {
|
|
|
724 if (defined $AllDataFieldsRef) {
|
|
|
725 push @DataFieldsToOutput, @{$AllDataFieldsRef};
|
|
|
726 push @{$FingerprintsFilesInfo{Database}{AllDataFields}}, @{$AllDataFieldsRef};
|
|
|
727 }
|
|
|
728 else {
|
|
|
729 # Retrieve and output data fields and values dynamically...
|
|
|
730 $FingerprintsFilesInfo{Database}{OutputCurrentDataFields} = 1;
|
|
|
731 }
|
|
|
732 }
|
|
|
733 elsif ($OptionsInfo{DatabaseDataFieldsMode} =~ /^Common$/i) {
|
|
|
734 if (defined $CommonDataFieldsRef) {
|
|
|
735 push @DataFieldsToOutput, @{$CommonDataFieldsRef};
|
|
|
736 push @{$FingerprintsFilesInfo{Database}{CommonDataFields}}, @{$CommonDataFieldsRef};
|
|
|
737 }
|
|
|
738 }
|
|
|
739 elsif ($OptionsInfo{DatabaseDataFieldsMode} =~ /^Specify$/i) {
|
|
|
740 push @DataFieldsToOutput, @{$OptionsInfo{SpecifiedDatabaseDataFields}};
|
|
|
741 push @{$FingerprintsFilesInfo{Database}{SpecifiedDatabaseDataFields}}, @{$OptionsInfo{SpecifiedDatabaseDataFields}};
|
|
|
742 }
|
|
|
743
|
|
|
744 if ($OptionsInfo{DatabaseDataFieldsMode} !~ /^CompoundID$/i) {
|
|
|
745 $FingerprintsFilesInfo{Database}{OutputDataFields} = 1;
|
|
|
746 }
|
|
|
747
|
|
|
748 push @{$FingerprintsFilesInfo{Database}{DataFieldsToOutput}}, @DataFieldsToOutput;
|
|
|
749
|
|
|
750 }
|
|
|
751
|
|
|
752 # Retrieve database fingerprints data columns information...
|
|
|
753 #
|
|
|
754 sub RetrieveDatabaseFingerprintsDataColsInfo {
|
|
|
755 my($FingerprintsFile, $FileType, $InDelim) = @_;
|
|
|
756 my($Line, $ColNum, $ColLabel, $NumOfCols, @DataColLabels, @DataColLabelsToOutput, @DataColNumsToOutput, %DataColLabelToNumMap, %DataColNumToLabelMap);
|
|
|
757
|
|
|
758 $FingerprintsFilesInfo{Database}{OutputDataCols} = 0;
|
|
|
759
|
|
|
760 @{$FingerprintsFilesInfo{Database}{DataColLabels}} = ();
|
|
|
761 %{$FingerprintsFilesInfo{Database}{DataColLabelToNumMap}} = ();
|
|
|
762 %{$FingerprintsFilesInfo{Database}{DataColNumToLabelMap}} = ();
|
|
|
763
|
|
|
764 @{$FingerprintsFilesInfo{Database}{DataColNumsToOutput}} = ();
|
|
|
765 @{$FingerprintsFilesInfo{Database}{DataColLabelsToOutput}} = ();
|
|
|
766
|
|
|
767 if ($FileType !~ /^Text$/i) {
|
|
|
768 return;
|
|
|
769 }
|
|
|
770
|
|
|
771 @DataColLabels = ();
|
|
|
772 @DataColLabelsToOutput = ();
|
|
|
773 @DataColNumsToOutput = ();
|
|
|
774
|
|
|
775 %DataColLabelToNumMap = ();
|
|
|
776 %DataColNumToLabelMap = ();
|
|
|
777
|
|
|
778 # Get column label line...
|
|
|
779 open TEXTFILE, "$FingerprintsFile" or die "Error: Couldn't open $FingerprintsFile: $! \n";
|
|
|
780 $Line = TextUtil::GetTextLine(\*TEXTFILE);
|
|
|
781 close TEXTFILE;
|
|
|
782
|
|
|
783 $InDelim = ($InDelim =~ /^Tab$/i) ? "\t" : ($InDelim =~ /semicolon/i ? "\;" : "\,");
|
|
|
784
|
|
|
785 @DataColLabels = TextUtil::SplitWords($Line, $InDelim);
|
|
|
786 $NumOfCols = scalar @DataColLabels;
|
|
|
787
|
|
|
788 for $ColNum (0 .. $#DataColLabels) {
|
|
|
789 $ColLabel = $DataColLabels[$ColNum];
|
|
|
790 $DataColLabelToNumMap{$ColLabel} = $ColNum;
|
|
|
791 $DataColNumToLabelMap{$ColNum} = $ColLabel;
|
|
|
792 }
|
|
|
793
|
|
|
794 if ($OptionsInfo{DatabaseDataColsMode} =~ /^Specify$/i) {
|
|
|
795 if ($OptionsInfo{DatabaseColMode} =~ /^ColNum$/i) {
|
|
|
796 for $ColNum (@{$OptionsInfo{SpecifiedDatabaseDataCols}}) {
|
|
|
797 if ($ColNum > $NumOfCols) {
|
|
|
798 die "Error: Column number, $ColNum, specified using \"--DatabaseDataCols\" is not valid: It must be <= $NumOfCols\n";
|
|
|
799 }
|
|
|
800 push @DataColNumsToOutput, ($ColNum - 1);
|
|
|
801 }
|
|
|
802 }
|
|
|
803 elsif ($OptionsInfo{DatabaseColMode} =~ /^ColLabel$/i) {
|
|
|
804 for $ColLabel (@{$OptionsInfo{SpecifiedDatabaseDataCols}}) {
|
|
|
805 if (!exists $DataColLabelToNumMap{$ColLabel}) {
|
|
|
806 die "Error: Column label, $ColLabel, specified using \"--DatabaseDataCols\" is not valid: It doesn't exist\n";
|
|
|
807 }
|
|
|
808 push @DataColNumsToOutput, $DataColLabelToNumMap{$ColLabel};
|
|
|
809 }
|
|
|
810 }
|
|
|
811 }
|
|
|
812 elsif ($OptionsInfo{DatabaseDataColsMode} =~ /^All$/i) {
|
|
|
813 @DataColNumsToOutput = map { $_ } (0 .. $#DataColLabels);
|
|
|
814 }
|
|
|
815
|
|
|
816 # Setup data column labels to output...
|
|
|
817 if (scalar @DataColNumsToOutput) {
|
|
|
818 @DataColLabelsToOutput = map { $DataColNumToLabelMap{$_} } (0 .. $#DataColNumsToOutput);
|
|
|
819 }
|
|
|
820
|
|
|
821 $FingerprintsFilesInfo{Database}{OutputDataCols} = scalar @DataColNumsToOutput ? 1 : 0;
|
|
|
822
|
|
|
823 @{$FingerprintsFilesInfo{Database}{DataColLabels}} = @DataColLabels;
|
|
|
824 %{$FingerprintsFilesInfo{Database}{DataColLabelToNumMap}} = %DataColLabelToNumMap;
|
|
|
825 %{$FingerprintsFilesInfo{Database}{DataColNumToLabelMap}} = %DataColNumToLabelMap;
|
|
|
826
|
|
|
827 @{$FingerprintsFilesInfo{Database}{DataColNumsToOutput}} = @DataColNumsToOutput;
|
|
|
828 @{$FingerprintsFilesInfo{Database}{DataColLabelsToOutput}} = @DataColLabelsToOutput;
|
|
|
829 }
|
|
|
830
|
|
|
831 # Set maximum number of similar compounds to find for individual reference of set of multiple
|
|
|
832 # reference compounds...
|
|
|
833 #
|
|
|
834 sub SetMaximumSimilarMoleculesToRetrieve {
|
|
|
835 my($FingerprintsFile, $FileType, $InDelim) = @_;
|
|
|
836 my($MaxSimilarMolecules, $NumOfDatabaseMolecules, $PercentSimilarMolecules, $Line);
|
|
|
837
|
|
|
838 if ($OptionsInfo{SimilarCountMode} !~ /^PercentSimilar$/i) {
|
|
|
839 return;
|
|
|
840 }
|
|
|
841
|
|
|
842 $PercentSimilarMolecules = $OptionsInfo{PercentSimilarMolecules};
|
|
|
843
|
|
|
844 # Count database entries to figure out MaxSimilarMolecules using PercentSimilarMolecules
|
|
|
845 # value...
|
|
|
846 $NumOfDatabaseMolecules = 0;
|
|
|
847 if ($FileType =~ /^SD$/i && exists($FingerprintsFilesInfo{Database}{NumOfDatabaseMolecules})) {
|
|
|
848 # It might already be counted for SD file...
|
|
|
849 $NumOfDatabaseMolecules = $FingerprintsFilesInfo{Database}{NumOfDatabaseMolecules};
|
|
|
850 }
|
|
|
851 else {
|
|
|
852 print "Calculating maximum number of similar molecules to retrieve for \"PercentSimilar\" value of \"--SimilarCountMode\" option by counting number of molecules in database fingerprints file...\n";
|
|
|
853 open FINGERPRINTSFILE, "$FingerprintsFile" or die "Error: Couldn't open $FingerprintsFile: $! \n";
|
|
|
854 FILETYPE: {
|
|
|
855 if ($FileType =~ /^SD$/i) {
|
|
|
856 while ($Line = TextUtil::GetTextLine(\*FINGERPRINTSFILE)) {
|
|
|
857 if ($Line =~ /^\$\$\$\$/) {
|
|
|
858 $NumOfDatabaseMolecules++;
|
|
|
859 }
|
|
|
860 }
|
|
|
861 last FILETYPE;
|
|
|
862 }
|
|
|
863 if ($FileType =~ /^Text$/i) {
|
|
|
864 # Ignore column label line...
|
|
|
865 $Line = TextUtil::GetTextLine(\*FINGERPRINTSFILE);
|
|
|
866 while ($Line = TextUtil::GetTextLine(\*FINGERPRINTSFILE)) {
|
|
|
867 $NumOfDatabaseMolecules++;
|
|
|
868 }
|
|
|
869 last FILETYPE;
|
|
|
870 }
|
|
|
871 if ($FileType =~ /^FP$/i) {
|
|
|
872 while ($Line = TextUtil::GetTextLine(\*FINGERPRINTSFILE)) {
|
|
|
873 if ($Line !~ /^#/) {
|
|
|
874 $NumOfDatabaseMolecules++;
|
|
|
875 }
|
|
|
876 }
|
|
|
877 last FILETYPE;
|
|
|
878 }
|
|
|
879 $NumOfDatabaseMolecules = 0;
|
|
|
880 }
|
|
|
881 close FINGERPRINTSFILE;
|
|
|
882 $FingerprintsFilesInfo{Database}{NumOfDatabaseMolecules} = $NumOfDatabaseMolecules;
|
|
|
883 }
|
|
|
884
|
|
|
885 $MaxSimilarMolecules = int (($NumOfDatabaseMolecules * $PercentSimilarMolecules)/100);
|
|
|
886 if ($MaxSimilarMolecules < 1) {
|
|
|
887 $MaxSimilarMolecules = 1;
|
|
|
888 }
|
|
|
889
|
|
|
890 $OptionsInfo{MaxSimilarMolecules} = $MaxSimilarMolecules;
|
|
|
891 }
|
|
|
892
|
|
|
893 # Retrieve information about fingerprints file...
|
|
|
894 #
|
|
|
895 sub RetrieveFingerprintsFileInfo {
|
|
|
896 my($FingerprintsFile) = @_;
|
|
|
897 my($FileType, $InDelim, $FileDir, $FileExt, $FileName);
|
|
|
898
|
|
|
899 if (!(-e $FingerprintsFile)) {
|
|
|
900 die "Error: Input fingerprints file, $FingerprintsFile, doesn't exist.\n";
|
|
|
901 }
|
|
|
902
|
|
|
903 $FileType = Fingerprints::FingerprintsFileUtil::GetFingerprintsFileType($FingerprintsFile);
|
|
|
904 if (IsEmpty($FileType)) {
|
|
|
905 die "Error: Input file, $FingerprintsFile, is not a fingerprints file.\n";
|
|
|
906 }
|
|
|
907
|
|
|
908 $InDelim = '';
|
|
|
909 if ($FileType =~ /^Text$/i) {
|
|
|
910 $FileDir = ""; $FileName = ""; $FileExt = "";
|
|
|
911 ($FileDir, $FileName, $FileExt) = ParseFileName($FingerprintsFile);
|
|
|
912 $InDelim = ($FileExt =~ /^tsv$/i) ? 'Tab' : $OptionsInfo{InDelim};
|
|
|
913 }
|
|
|
914
|
|
|
915 return ($FileType, $InDelim);
|
|
|
916 }
|
|
|
917
|
|
|
918 # Retrieve fingerprints file IO parameters...
|
|
|
919 #
|
|
|
920 sub RetrieveFingerprintsFileIOParameters {
|
|
|
921 my($FingerprintsFileMode, $FileType, $FingerprintsFile) = @_;
|
|
|
922 my(%FingerprintsFileIOParams);
|
|
|
923
|
|
|
924 if ($FingerprintsFileMode !~ /^(Reference|Database)$/) {
|
|
|
925 die "Error: Unknown fingerprints file mode: $FingerprintsFileMode. Supported values: Reference or Database\n";
|
|
|
926 }
|
|
|
927
|
|
|
928 %FingerprintsFileIOParams = ();
|
|
|
929
|
|
|
930 FILETYPE: {
|
|
|
931 if ($FileType =~ /^SD$/i) {
|
|
|
932 %FingerprintsFileIOParams = ('Name' => $FingerprintsFile, 'Mode' => 'Read', 'FingerprintsStringMode' => $OptionsInfo{FingerprintsMode}, 'ValidateData' => $OptionsInfo{ValidateData}, 'DetailLevel' => $OptionsInfo{Detail}, 'FingerprintsFieldLabel' => $OptionsInfo{"${FingerprintsFileMode}FingerprintsField"}, 'CompoundIDMode' => $OptionsInfo{"${FingerprintsFileMode}CompoundIDMode"}, 'CompoundIDFieldLabel' => $OptionsInfo{"${FingerprintsFileMode}CompoundIDField"}, 'CompoundIDPrefix' => $OptionsInfo{"${FingerprintsFileMode}CompoundIDPrefix"});
|
|
|
933 last FILETYPE;
|
|
|
934 }
|
|
|
935 if ($FileType =~ /^FP$/i) {
|
|
|
936 %FingerprintsFileIOParams = ('Name' => $FingerprintsFile, 'Mode' => 'Read', 'FingerprintsStringMode' => $OptionsInfo{FingerprintsMode}, 'ValidateData' => $OptionsInfo{ValidateData}, 'DetailLevel' => $OptionsInfo{Detail});
|
|
|
937 last FILETYPE;
|
|
|
938 }
|
|
|
939 if ($FileType =~ /^Text$/i) {
|
|
|
940 %FingerprintsFileIOParams = ('Name' => $FingerprintsFile, 'Mode' => 'Read', 'FingerprintsStringMode' => $OptionsInfo{FingerprintsMode}, 'ValidateData' => $OptionsInfo{ValidateData}, 'DetailLevel' => $OptionsInfo{Detail}, 'FingerprintsCol' => $OptionsInfo{"${FingerprintsFileMode}FingerprintsCol"}, 'ColMode' => $OptionsInfo{"${FingerprintsFileMode}ColMode"}, 'CompoundIDCol' => $OptionsInfo{"${FingerprintsFileMode}CompoundIDCol"}, 'CompoundIDPrefix' => $OptionsInfo{"${FingerprintsFileMode}CompoundIDPrefix"}, 'InDelim' => $FingerprintsFilesInfo{$FingerprintsFileMode}{InDelim});
|
|
|
941 last FILETYPE;
|
|
|
942 }
|
|
|
943 die "Error: Fingerprints file type, $FileType, is not valid. Supported file types: SD, FP or Text\n";
|
|
|
944 }
|
|
|
945
|
|
|
946 return %FingerprintsFileIOParams;
|
|
|
947 }
|
|
|
948
|
|
|
949 # Make sure fingerprints data file contains valid dta and retrieve fingerprints string mode information...
|
|
|
950 #
|
|
|
951 sub RetrieveFingerprintsFileFingerprintsStringInfo {
|
|
|
952 my($FingerprintsFileMode, $FingerprintsFile) = @_;
|
|
|
953 my($FingerprintsFileIO, $FingerprintsStringMode, $FingerprintsBitVectorStringMode, $FingerprintsVectorStringMode, $FirstFingerprintsStringType, $FirstFingerprintsStringDescription);
|
|
|
954
|
|
|
955 $FingerprintsFileIO = Fingerprints::FingerprintsFileUtil::NewFingerprintsFileIO(%{$FingerprintsFilesInfo{$FingerprintsFileMode}{FingerprintsFileIOParameters}});
|
|
|
956 if (!$FingerprintsFileIO) {
|
|
|
957 die "Error: Reference fingerprints file, $FingerprintsFile, contains invalid fingerprints data.\n";
|
|
|
958 }
|
|
|
959 if (!$FingerprintsFileIO->IsFingerprintsFileDataValid()) {
|
|
|
960 die "Error: Reference fingerprints file, $FingerprintsFile, contains invalid fingerprints data.\n";
|
|
|
961 }
|
|
|
962
|
|
|
963 $FingerprintsStringMode = $FingerprintsFileIO->GetFingerprintsStringMode();
|
|
|
964 $FingerprintsBitVectorStringMode = $FingerprintsFileIO->GetFingerprintsBitVectorStringMode();
|
|
|
965 $FingerprintsVectorStringMode = $FingerprintsFileIO->GetFingerprintsVectorStringMode();
|
|
|
966
|
|
|
967 $FirstFingerprintsStringType = $FingerprintsFileIO->GetFirstFingerprintsStringType();
|
|
|
968 $FirstFingerprintsStringDescription = $FingerprintsFileIO->GetFirstFingerprintsStringDescription();
|
|
|
969
|
|
|
970 $FingerprintsFileIO->Close();
|
|
|
971
|
|
|
972 return ($FingerprintsStringMode, $FingerprintsBitVectorStringMode, $FingerprintsVectorStringMode, $FirstFingerprintsStringType, $FirstFingerprintsStringDescription);
|
|
|
973 }
|
|
|
974
|
|
|
975 # Retrieve output files names using reference fingerprints file name...
|
|
|
976 #
|
|
|
977 sub RetrieveOutputFilesInfo {
|
|
|
978 my($FingerprintsFile, $FileDir, $FileExt, $FileName, $OutFileRoot, $SDOutFileName, $TextOutFileName, $SDOutFileExt, $TextOutFileExt, $ReferenceFileName, $DatabaseFileName);
|
|
|
979
|
|
|
980 $OutputFilesInfo{OutFileRoot} = '';
|
|
|
981 $OutputFilesInfo{SDOutFileName} = '';
|
|
|
982 $OutputFilesInfo{TextOutFileName} = '';
|
|
|
983
|
|
|
984 $FingerprintsFile = $FingerprintsFilesInfo{Reference}{FileName};
|
|
|
985
|
|
|
986 $FileDir = ""; $FileName = ""; $FileExt = "";
|
|
|
987 ($FileDir, $FileName, $FileExt) = ParseFileName($FingerprintsFile);
|
|
|
988
|
|
|
989 $SDOutFileExt = "sdf";
|
|
|
990 $TextOutFileExt = ($Options{outdelim} =~ /^tab$/i) ? "tsv" : "csv";
|
|
|
991
|
|
|
992 if ($OptionsInfo{OutFileRoot}) {
|
|
|
993 my ($RootFileDir, $RootFileName, $RootFileExt) = ParseFileName($OptionsInfo{OutFileRoot});
|
|
|
994 if ($RootFileName && $RootFileExt) {
|
|
|
995 $FileName = $RootFileName;
|
|
|
996 }
|
|
|
997 else {
|
|
|
998 $FileName = $OptionsInfo{OutFileRoot};
|
|
|
999 }
|
|
|
1000 $OutFileRoot = $FileName;
|
|
|
1001 }
|
|
|
1002 else {
|
|
|
1003 $OutFileRoot = "${FileName}SimilaritySearching";
|
|
|
1004 }
|
|
|
1005
|
|
|
1006 $SDOutFileName = "${OutFileRoot}.${SDOutFileExt}";
|
|
|
1007 $TextOutFileName = "${OutFileRoot}.${TextOutFileExt}";
|
|
|
1008
|
|
|
1009 $ReferenceFileName = $FingerprintsFilesInfo{Reference}{FileName};
|
|
|
1010 $DatabaseFileName = $FingerprintsFilesInfo{Database}{FileName};
|
|
|
1011
|
|
|
1012 if ($OptionsInfo{SDOutput}) {
|
|
|
1013 if ($SDOutFileName =~ /^$ReferenceFileName$/i) {
|
|
|
1014 die "Error: Same output, $SDOutFileName, and reference input file names.\nSpecify a different name using \"-r --root\" option or use default name.\n";
|
|
|
1015 }
|
|
|
1016 if ($SDOutFileName =~ /^$DatabaseFileName$/i) {
|
|
|
1017 die "Error: Same output, $SDOutFileName, and database input file names.\nSpecify a different name using \"-r --root\" option or use default name.\n";
|
|
|
1018 }
|
|
|
1019 }
|
|
|
1020
|
|
|
1021 if ($OptionsInfo{TextOutput}) {
|
|
|
1022 if ($TextOutFileName =~ /^$ReferenceFileName$/i) {
|
|
|
1023 die "Error: Same output, $TextOutFileName, and reference input file names.\nSpecify a different name using \"-r --root\" option or use default name.\n";
|
|
|
1024 }
|
|
|
1025 if ($TextOutFileName =~ /^$DatabaseFileName$/i) {
|
|
|
1026 die "Error: Same output, $TextOutFileName, and database input file names.\nSpecify a different name using \"-r --root\" option or use default name.\n";
|
|
|
1027 }
|
|
|
1028 }
|
|
|
1029
|
|
|
1030 if (!$OptionsInfo{OverwriteFiles}) {
|
|
|
1031 if ($OptionsInfo{SDOutput}) {
|
|
|
1032 if (-e $SDOutFileName) {
|
|
|
1033 die "Error: The output file $SDOutFileName already exists.\n";
|
|
|
1034 }
|
|
|
1035 }
|
|
|
1036 if ($OptionsInfo{TextOutput}) {
|
|
|
1037 if (-e $TextOutFileName) {
|
|
|
1038 die "Error: The output file $TextOutFileName already exists.\n";
|
|
|
1039 }
|
|
|
1040 }
|
|
|
1041 }
|
|
|
1042
|
|
|
1043 $OutputFilesInfo{OutFileRoot} = $OutFileRoot;
|
|
|
1044 $OutputFilesInfo{SDOutFileName} = $SDOutFileName;
|
|
|
1045 $OutputFilesInfo{TextOutFileName} = $TextOutFileName;
|
|
|
1046
|
|
|
1047 }
|
|
|
1048
|
|
|
1049 # Process input fingerprints file names...
|
|
|
1050 #
|
|
|
1051 sub ProcessFingerprintsFileNames {
|
|
|
1052 @FingerprintsFilesList = ();
|
|
|
1053
|
|
|
1054 if (@ARGV != 2) {
|
|
|
1055 die GetUsageFromPod("$FindBin::Bin/$ScriptName");
|
|
|
1056 }
|
|
|
1057
|
|
|
1058 # Reference fingerprints file name...
|
|
|
1059 push @FingerprintsFilesList, $ARGV[0];
|
|
|
1060
|
|
|
1061 # Database fingerprints file name...
|
|
|
1062 push @FingerprintsFilesList, $ARGV[1];
|
|
|
1063
|
|
|
1064 }
|
|
|
1065
|
|
|
1066 # Process option values...
|
|
|
1067 sub ProcessOptions {
|
|
|
1068 %OptionsInfo = ();
|
|
|
1069
|
|
|
1070 $OptionsInfo{Mode} = $Options{mode};
|
|
|
1071 $OptionsInfo{FingerprintsMode} = $Options{fingerprintsmode};
|
|
|
1072
|
|
|
1073 $OptionsInfo{SearchMode} = $Options{searchmode};
|
|
|
1074
|
|
|
1075 ProcessBitVectorComparisonOptions();
|
|
|
1076 ProcessVectorComparisonOptions();
|
|
|
1077
|
|
|
1078 $OptionsInfo{GroupFusionRule} = $Options{groupfusionrule};
|
|
|
1079 $OptionsInfo{GroupFusionApplyCutoff} = ($Options{groupfusionapplycutoff} =~ /^Yes$/i) ? 1 : 0;;
|
|
|
1080
|
|
|
1081 $OptionsInfo{SimilarCountMode} = $Options{similarcountmode};
|
|
|
1082 $OptionsInfo{NumOfSimilarMolecules} = $Options{numofsimilarmolecules};
|
|
|
1083 $OptionsInfo{PercentSimilarMolecules} = $Options{percentsimilarmolecules};
|
|
|
1084
|
|
|
1085 # Set MaxSimilarMolecules to NumOfSimilarMolecules. For PercentSimilar value of SimilarCountMode,
|
|
|
1086 # it'll be overwritten using number of entries in database fingerprints file and value of PercentSimilarMolecules...
|
|
|
1087 #
|
|
|
1088 $OptionsInfo{MaxSimilarMolecules} = $OptionsInfo{NumOfSimilarMolecules};
|
|
|
1089
|
|
|
1090 $OptionsInfo{SimilarityCutoff} = $Options{similaritycutoff};
|
|
|
1091 $OptionsInfo{DistanceCutoff} = $Options{distancecutoff};
|
|
|
1092
|
|
|
1093 $OptionsInfo{kNN} = $Options{knn};
|
|
|
1094 if ($Options{knn} !~ /^All$/i) {
|
|
|
1095 if (!IsPositiveInteger($Options{knn})) {
|
|
|
1096 die "Error: The value specified, $Options{knn}, for option \"-k, --KNN\" is not valid. Allowed values: > 0 \n";
|
|
|
1097 }
|
|
|
1098 }
|
|
|
1099
|
|
|
1100 ProcessReferenceFingerprintsDataOptions();
|
|
|
1101 ProcessDatabaseFingerprintsDataOptions();
|
|
|
1102
|
|
|
1103 $OptionsInfo{Detail} = $Options{detail};
|
|
|
1104
|
|
|
1105 $OptionsInfo{InDelim} = $Options{indelim};
|
|
|
1106 $OptionsInfo{OutDelim} = ($Options{outdelim} =~ /tab/i ) ? "\t" : (($Options{outdelim} =~ /semicolon/i) ? "\;" : "\,");
|
|
|
1107 $OptionsInfo{OutQuote} = ($Options{quote} =~ /^Yes$/i) ? 1 : 0;
|
|
|
1108
|
|
|
1109 $OptionsInfo{Output} = $Options{output};
|
|
|
1110 $OptionsInfo{SDOutput} = ($Options{output} =~ /^(SD|Both)$/i) ? 1 : 0;
|
|
|
1111 $OptionsInfo{TextOutput} = ($Options{output} =~ /^(Text|Both)$/i) ? 1 : 0;
|
|
|
1112
|
|
|
1113 $OptionsInfo{OverwriteFiles} = $Options{overwrite} ? 1 : 0;
|
|
|
1114 $OptionsInfo{OutFileRoot} = $Options{root} ? $Options{root} : 0;
|
|
|
1115
|
|
|
1116 $OptionsInfo{Fast} = $Options{fast} ? 1 : 0;
|
|
|
1117 $OptionsInfo{ValidateData} = $Options{fast} ? 0 : 1;
|
|
|
1118
|
|
|
1119 $OptionsInfo{Precision} = $Options{precision};
|
|
|
1120 }
|
|
|
1121
|
|
|
1122 # Process options related to comparion of bit vector strings...
|
|
|
1123 #
|
|
|
1124 sub ProcessBitVectorComparisonOptions {
|
|
|
1125 # Setup supported bit vector similarity coefficients for bit vector strings...
|
|
|
1126 my($ComparisonMeasure, $SupportedComparisonMeasure, @SupportedComparisonMeasures, %SupportedComparisonMeasuresNameMap, %SupportedComparisonMeasuresMethodMap);
|
|
|
1127
|
|
|
1128 @SupportedComparisonMeasures = ();
|
|
|
1129 %SupportedComparisonMeasuresNameMap = ();
|
|
|
1130 %SupportedComparisonMeasuresMethodMap = ();
|
|
|
1131
|
|
|
1132 for $SupportedComparisonMeasure (Fingerprints::FingerprintsBitVector::GetSupportedSimilarityCoefficients()) {
|
|
|
1133 # Similarity coefficient function/method names contain "Coefficient" in their names.
|
|
|
1134 # So take 'em out and setup a map to original function/method name...
|
|
|
1135 $ComparisonMeasure = $SupportedComparisonMeasure;
|
|
|
1136 $ComparisonMeasure =~ s/Coefficient$//;
|
|
|
1137
|
|
|
1138 push @SupportedComparisonMeasures, $ComparisonMeasure;
|
|
|
1139 $SupportedComparisonMeasuresNameMap{lc($ComparisonMeasure)} = $ComparisonMeasure;
|
|
|
1140 $SupportedComparisonMeasuresMethodMap{lc($ComparisonMeasure)} = $SupportedComparisonMeasure;
|
|
|
1141 }
|
|
|
1142
|
|
|
1143 # Setup similarity coefficient to use for calculating similarity matrices for bit vector strings...
|
|
|
1144 my($SpecifiedMeasure, $SpecifiedComparisonMeasureName, $SpecifiedComparisonMeasureMethod);
|
|
|
1145
|
|
|
1146 $SpecifiedComparisonMeasureName = '';
|
|
|
1147 $SpecifiedComparisonMeasureMethod = '';
|
|
|
1148
|
|
|
1149 $SpecifiedMeasure = $Options{bitvectorcomparisonmode};
|
|
|
1150
|
|
|
1151 if (! exists $SupportedComparisonMeasuresMethodMap{lc($SpecifiedMeasure)} ) {
|
|
|
1152 die "Error: The value specified, $SpecifiedMeasure, for option \"-b --BitVectorComparisonMode\" is not valid.\nAllowed values:", JoinWords(\@SupportedComparisonMeasures, ", ", 0), "\n";
|
|
|
1153 }
|
|
|
1154
|
|
|
1155 $SpecifiedComparisonMeasureMethod = $SupportedComparisonMeasuresMethodMap{lc($SpecifiedMeasure)};
|
|
|
1156 $SpecifiedComparisonMeasureName = $SupportedComparisonMeasuresNameMap{lc($SpecifiedMeasure)};
|
|
|
1157
|
|
|
1158 $OptionsInfo{BitVectorComparisonMode} = $Options{bitvectorcomparisonmode};
|
|
|
1159
|
|
|
1160 $OptionsInfo{SpecifiedBitVectorComparisonMeasure} = $SpecifiedMeasure;
|
|
|
1161 $OptionsInfo{SpecifiedBitVectorComparisonMeasureName} = $SpecifiedComparisonMeasureName;
|
|
|
1162 $OptionsInfo{SpecifiedBitVectorComparisonMeasureMethod} = $SpecifiedComparisonMeasureMethod;
|
|
|
1163
|
|
|
1164 # Make sure valid alpha parameter is specified for Tversky calculation...
|
|
|
1165 $OptionsInfo{Alpha} = '';
|
|
|
1166 if ($SpecifiedMeasure =~ /^(TverskySimilarity|WeightedTverskySimilarity)$/i) {
|
|
|
1167 if (IsEmpty($Options{alpha})) {
|
|
|
1168 die "Error: You must specify a value for \"-a, --alpha\" option in \"TverskySimilarity or WeightedTverskySimilarity\" \"-m --mode\". \n";
|
|
|
1169 }
|
|
|
1170 my($Alpha);
|
|
|
1171 $Alpha = $Options{alpha};
|
|
|
1172 if (!(IsFloat($Alpha) && $Alpha >=0 && $Alpha <= 1)) {
|
|
|
1173 die "Error: The value specified, $Options{alpha}, for option \"-a, --alpha\" is not valid. Allowed values: >= 0 and <= 1\n";
|
|
|
1174 }
|
|
|
1175 $OptionsInfo{Alpha} = $Alpha;
|
|
|
1176 }
|
|
|
1177
|
|
|
1178 # Make sure valid beta parameter is specified for WeightedTanimoto and WeightedTversky
|
|
|
1179 # calculations...
|
|
|
1180 $OptionsInfo{Beta} = '';
|
|
|
1181 if ($SpecifiedMeasure =~ /^(WeightedTverskySimilarity|WeightedTanimotoSimilarity)$/i) {
|
|
|
1182 if (IsEmpty($Options{beta})) {
|
|
|
1183 die "Error: You must specify a value for \"-b, --beta\" option in \"WeightedTverskySimilarity or WeightedTanimotoSimilarity\" \"-m --mode\". \n";
|
|
|
1184 }
|
|
|
1185 my($Beta);
|
|
|
1186 $Beta = $Options{beta};
|
|
|
1187 if (!(IsFloat($Beta) && $Beta >=0 && $Beta <= 1)) {
|
|
|
1188 die "Error: The value specified, $Options{beta}, for option \"-b, --beta\" is not valid. Allowed values: >= 0 and <= 1\n";
|
|
|
1189 }
|
|
|
1190 $OptionsInfo{Beta} = $Beta;
|
|
|
1191 }
|
|
|
1192 }
|
|
|
1193
|
|
|
1194 # Process options related to comparion of vector strings...
|
|
|
1195 #
|
|
|
1196 sub ProcessVectorComparisonOptions {
|
|
|
1197 # Setup specified similarity coefficients for vector strings..
|
|
|
1198 my($ComparisonMeasure, $SupportedComparisonMeasure, @SupportedComparisonMeasures, %SupportedComparisonMeasuresNameMap, %SupportedComparisonMeasuresMethodMap);
|
|
|
1199
|
|
|
1200 @SupportedComparisonMeasures = ();
|
|
|
1201 %SupportedComparisonMeasuresNameMap = ();
|
|
|
1202 %SupportedComparisonMeasuresMethodMap = ();
|
|
|
1203 for $SupportedComparisonMeasure (Fingerprints::FingerprintsVector::GetSupportedDistanceAndSimilarityCoefficients()) {
|
|
|
1204 # Similarity and distance coefficient function/method names contain "Coefficient" in their names.
|
|
|
1205 # So take 'em out and setup a map to original function/method name...
|
|
|
1206 $ComparisonMeasure = $SupportedComparisonMeasure;
|
|
|
1207 if ($ComparisonMeasure =~ /Coefficient$/i) {
|
|
|
1208 $ComparisonMeasure =~ s/Coefficient$//i;
|
|
|
1209 }
|
|
|
1210 push @SupportedComparisonMeasures, $ComparisonMeasure;
|
|
|
1211 $SupportedComparisonMeasuresNameMap{lc($ComparisonMeasure)} = $ComparisonMeasure;
|
|
|
1212 $SupportedComparisonMeasuresMethodMap{lc($ComparisonMeasure)} = $SupportedComparisonMeasure;
|
|
|
1213 }
|
|
|
1214
|
|
|
1215 # Setup a list of similarity coefficients to use for calculating similarity matrices for bit vector strings...
|
|
|
1216 my($SpecifiedMeasure, $SpecifiedComparisonMeasureName, $SpecifiedComparisonMeasureMethod);
|
|
|
1217
|
|
|
1218 $SpecifiedComparisonMeasureName = '';
|
|
|
1219 $SpecifiedComparisonMeasureMethod = '';
|
|
|
1220
|
|
|
1221 $SpecifiedMeasure = $Options{vectorcomparisonmode};
|
|
|
1222 $SpecifiedMeasure =~ s/ //g;
|
|
|
1223
|
|
|
1224 if (! exists($SupportedComparisonMeasuresMethodMap{lc($SpecifiedMeasure)})) {
|
|
|
1225 die "Error: The value specified, $SpecifiedMeasure, for option \"-v --VectorComparisonMode\" is not valid.\nAllowed values:", JoinWords(\@SupportedComparisonMeasures, ", ", 0), "\n";
|
|
|
1226 }
|
|
|
1227
|
|
|
1228 $SpecifiedComparisonMeasureMethod = $SupportedComparisonMeasuresMethodMap{lc($SpecifiedMeasure)};
|
|
|
1229 $SpecifiedComparisonMeasureName = $SupportedComparisonMeasuresNameMap{lc($SpecifiedMeasure)};
|
|
|
1230
|
|
|
1231 $OptionsInfo{VectorComparisonMode} = $Options{vectorcomparisonmode};
|
|
|
1232
|
|
|
1233 $OptionsInfo{SpecifiedVectorComparisonMeasure} = $SpecifiedMeasure;
|
|
|
1234 $OptionsInfo{SpecifiedVectorComparisonMeasuresName} = $SpecifiedComparisonMeasureName;
|
|
|
1235 $OptionsInfo{SpecifiedVectorComparisonMeasuresMethod} = $SpecifiedComparisonMeasureMethod;
|
|
|
1236
|
|
|
1237 # Setup specified vector comparison calculation modes...
|
|
|
1238 my($SpecifiedFormulism);
|
|
|
1239
|
|
|
1240 $SpecifiedFormulism = $Options{vectorcomparisonformulism};
|
|
|
1241 $SpecifiedFormulism =~ s/ //g;
|
|
|
1242 if ($SpecifiedFormulism !~ /^(AlgebraicForm|BinaryForm|SetTheoreticForm)$/i) {
|
|
|
1243 die "Error: The value specified, $SpecifiedFormulism, for option \"--VectorComparisonFormulism\" is not valid. Allowed values: AlgebraicForm, BinaryForm or SetTheoreticForm\n";
|
|
|
1244 }
|
|
|
1245
|
|
|
1246 $OptionsInfo{VectorComparisonFormulism} = $Options{vectorcomparisonformulism};
|
|
|
1247 $OptionsInfo{SpecifiedVectorComparisonMode} = $SpecifiedFormulism;
|
|
|
1248
|
|
|
1249 }
|
|
|
1250
|
|
|
1251 # Process options related to data retrieval from reference fingerprints SD and CSV/TSV
|
|
|
1252 # text files...
|
|
|
1253 #
|
|
|
1254 sub ProcessReferenceFingerprintsDataOptions {
|
|
|
1255
|
|
|
1256 $OptionsInfo{ReferenceCompoundIDPrefix} = $Options{referencecompoundidprefix} ? $Options{referencecompoundidprefix} : 'Cmpd';
|
|
|
1257
|
|
|
1258 # Compound ID and fingerprints column options for text files...
|
|
|
1259
|
|
|
1260 $OptionsInfo{ReferenceColMode} = $Options{referencecolmode};
|
|
|
1261
|
|
|
1262 if (IsNotEmpty($Options{referencecompoundidcol})) {
|
|
|
1263 if ($Options{referencecolmode} =~ /^ColNum$/i) {
|
|
|
1264 if (!IsPositiveInteger($Options{referencecompoundidcol})) {
|
|
|
1265 die "Error: Column value, $Options{referencecompoundidcol}, specified using \"--ReferenceCompoundIDCol\" is not valid: Allowed integer values: > 0\n";
|
|
|
1266 }
|
|
|
1267 }
|
|
|
1268 $OptionsInfo{ReferenceCompoundIDCol} = $Options{referencecompoundidcol};
|
|
|
1269 }
|
|
|
1270 else {
|
|
|
1271 $OptionsInfo{ReferenceCompoundIDCol} = 'AutoDetect';
|
|
|
1272 }
|
|
|
1273
|
|
|
1274 if (IsNotEmpty($Options{referencefingerprintscol})) {
|
|
|
1275 if ($Options{referencecolmode} =~ /^ColNum$/i) {
|
|
|
1276 if (!IsPositiveInteger($Options{referencefingerprintscol})) {
|
|
|
1277 die "Error: Column value, $Options{referencefingerprintscol}, specified using \"--ReferenceFingerprintsCol\" is not valid: Allowed integer values: > 0\n";
|
|
|
1278 }
|
|
|
1279 }
|
|
|
1280 $OptionsInfo{ReferenceFingerprintsCol} = $Options{referencefingerprintscol};
|
|
|
1281 }
|
|
|
1282 else {
|
|
|
1283 $OptionsInfo{ReferenceFingerprintsCol} = 'AutoDetect';
|
|
|
1284 }
|
|
|
1285
|
|
|
1286 if (IsNotEmpty($Options{referencecompoundidcol}) && IsNotEmpty($Options{referencefingerprintscol})) {
|
|
|
1287 if (IsPositiveInteger($Options{referencecompoundidcol}) && IsPositiveInteger($Options{referencefingerprintscol})) {
|
|
|
1288 if (($Options{referencecompoundidcol} == $Options{referencefingerprintscol})) {
|
|
|
1289 die "Error: Values specified using \"--ReferenceCompoundIDCol\" and \"--ReferenceFingerprintsCol\", $Options{referencecompoundidcol}, must be different.\n";
|
|
|
1290 }
|
|
|
1291 }
|
|
|
1292 else {
|
|
|
1293 if (($Options{referencecompoundidcol} eq $Options{referencefingerprintscol})) {
|
|
|
1294 die "Error: Values specified using \"--ReferenceCompoundIDCol\" and \"--ReferenceFingerprintsCol\", $Options{referencecompoundidcol}, must be different.\n";
|
|
|
1295 }
|
|
|
1296 }
|
|
|
1297 }
|
|
|
1298
|
|
|
1299 # Compound ID and fingerprints field options for SD files...
|
|
|
1300
|
|
|
1301 $OptionsInfo{ReferenceCompoundIDMode} = $Options{referencecompoundidmode};
|
|
|
1302 $OptionsInfo{ReferenceCompoundIDField} = '';
|
|
|
1303
|
|
|
1304 if ($Options{referencecompoundidmode} =~ /^DataField$/i && !$Options{referencecompoundidfield}) {
|
|
|
1305 die "Error: You must specify a value for \"--ReferenceCompoundIDField\" option in \"DataField\" \"--ReferenceCompoundIDMode\". \n";
|
|
|
1306 }
|
|
|
1307 if ($Options{referencecompoundidfield}) {
|
|
|
1308 $OptionsInfo{ReferenceCompoundIDField} = $Options{referencecompoundidfield};
|
|
|
1309 }
|
|
|
1310
|
|
|
1311 if (IsNotEmpty($Options{referencefingerprintsfield})) {
|
|
|
1312 $OptionsInfo{ReferenceFingerprintsField} = $Options{referencefingerprintsfield};
|
|
|
1313 }
|
|
|
1314 else {
|
|
|
1315 $OptionsInfo{ReferenceFingerprintsField} = 'AutoDetect';
|
|
|
1316 }
|
|
|
1317
|
|
|
1318 if ($Options{referencecompoundidfield} && IsNotEmpty($Options{referencefingerprintsfield})) {
|
|
|
1319 if (($Options{referencecompoundidfield} eq $Options{referencefingerprintsfield})) {
|
|
|
1320 die "Error: Values specified using \"--ReferenceCompoundIDField\" and \"--ReferenceFingerprintsfield\", $Options{referencecompoundidfield}, must be different.\n";
|
|
|
1321 }
|
|
|
1322 }
|
|
|
1323
|
|
|
1324 }
|
|
|
1325
|
|
|
1326 # Process options related to data retrieval from database fingerprints SD and CSV/TSV
|
|
|
1327 # text files...
|
|
|
1328 #
|
|
|
1329 sub ProcessDatabaseFingerprintsDataOptions {
|
|
|
1330
|
|
|
1331 $OptionsInfo{DatabaseCompoundIDPrefix} = $Options{databasecompoundidprefix} ? $Options{databasecompoundidprefix} : 'Cmpd';
|
|
|
1332
|
|
|
1333 # Compound ID and fingerprints column options for text files...
|
|
|
1334
|
|
|
1335 $OptionsInfo{DatabaseColMode} = $Options{databasecolmode};
|
|
|
1336
|
|
|
1337 if (IsNotEmpty($Options{databasecompoundidcol})) {
|
|
|
1338 if ($Options{databasecolmode} =~ /^ColNum$/i) {
|
|
|
1339 if (!IsPositiveInteger($Options{databasecompoundidcol})) {
|
|
|
1340 die "Error: Column value, $Options{databasecompoundidcol}, specified using \"--DatabaseCompoundIDCol\" is not valid: Allowed integer values: > 0\n";
|
|
|
1341 }
|
|
|
1342 }
|
|
|
1343 $OptionsInfo{DatabaseCompoundIDCol} = $Options{databasecompoundidcol};
|
|
|
1344 }
|
|
|
1345 else {
|
|
|
1346 $OptionsInfo{DatabaseCompoundIDCol} = 'AutoDetect';
|
|
|
1347 }
|
|
|
1348
|
|
|
1349 if (IsNotEmpty($Options{databasefingerprintscol})) {
|
|
|
1350 if ($Options{databasecolmode} =~ /^ColNum$/i) {
|
|
|
1351 if (!IsPositiveInteger($Options{databasefingerprintscol})) {
|
|
|
1352 die "Error: Column value, $Options{databasefingerprintscol}, specified using \"--DatabaseFingerprintsCol\" is not valid: Allowed integer values: > 0\n";
|
|
|
1353 }
|
|
|
1354 }
|
|
|
1355 $OptionsInfo{DatabaseFingerprintsCol} = $Options{databasefingerprintscol};
|
|
|
1356 }
|
|
|
1357 else {
|
|
|
1358 $OptionsInfo{DatabaseFingerprintsCol} = 'AutoDetect';
|
|
|
1359 }
|
|
|
1360
|
|
|
1361 if (IsNotEmpty($Options{databasecompoundidcol}) && IsNotEmpty($Options{databasefingerprintscol})) {
|
|
|
1362 if (IsPositiveInteger($Options{databasecompoundidcol}) && IsPositiveInteger($Options{databasefingerprintscol})) {
|
|
|
1363 if (($Options{databasecompoundidcol} == $Options{databasefingerprintscol})) {
|
|
|
1364 die "Error: Values specified using \"--DatabaseCompoundIDCol\" and \"--DatabaseFingerprintsCol\", $Options{databasecompoundidcol}, must be different.\n";
|
|
|
1365 }
|
|
|
1366 }
|
|
|
1367 else {
|
|
|
1368 if (($Options{databasecompoundidcol} eq $Options{databasefingerprintscol})) {
|
|
|
1369 die "Error: Values specified using \"--DatabaseCompoundIDCol\" and \"--DatabaseFingerprintsCol\", $Options{databasecompoundidcol}, must be different.\n";
|
|
|
1370 }
|
|
|
1371 }
|
|
|
1372 }
|
|
|
1373
|
|
|
1374 # Database data column options for text files...
|
|
|
1375
|
|
|
1376 $OptionsInfo{DatabaseDataColsMode} = $Options{databasedatacolsmode};
|
|
|
1377 $OptionsInfo{DatabaseDataCols} = '';
|
|
|
1378 @{$OptionsInfo{SpecifiedDatabaseDataCols}} = ();
|
|
|
1379
|
|
|
1380 if ($Options{databasedatacolsmode} =~ /^Specify$/i) {
|
|
|
1381 my($DatabaseDataCols, $DatabaseColNum, @SpecifiedDataCols);
|
|
|
1382
|
|
|
1383 if (!$Options{databasedatacols}) {
|
|
|
1384 die "Error: You must specify a value for \"--DatabaseDataCols\" option in \"Specify\" \"--DatabaseDataColsMode\". \n";
|
|
|
1385 }
|
|
|
1386 $DatabaseDataCols = $Options{databasedatacols};
|
|
|
1387
|
|
|
1388 if ($Options{databasecolmode} =~ /^ColNum$/i) {
|
|
|
1389 $DatabaseDataCols =~ s/ //g;
|
|
|
1390 @SpecifiedDataCols = split /\,/, $DatabaseDataCols;
|
|
|
1391 for $DatabaseColNum (@SpecifiedDataCols) {
|
|
|
1392 if (!IsPositiveInteger($DatabaseColNum)) {
|
|
|
1393 die "Error: Column value, $DatabaseColNum, specified using \"--DatabaseDataCols\" is not valid: Allowed integer values: > 0\n";
|
|
|
1394 }
|
|
|
1395 }
|
|
|
1396 }
|
|
|
1397 else {
|
|
|
1398 @SpecifiedDataCols = split /\,/, $DatabaseDataCols;
|
|
|
1399 }
|
|
|
1400 $OptionsInfo{DatabaseDataCols} = $DatabaseDataCols;
|
|
|
1401 push @{$OptionsInfo{SpecifiedDatabaseDataCols}}, @SpecifiedDataCols;
|
|
|
1402 }
|
|
|
1403 elsif ($Options{databasedatacolsmode} =~ /^All$/i) {
|
|
|
1404 $OptionsInfo{DatabaseDataCols} = 'All';
|
|
|
1405 }
|
|
|
1406
|
|
|
1407 if ($OptionsInfo{DatabaseDataColsMode} =~ /^Specify$/i && !$OptionsInfo{DatabaseDataCols}) {
|
|
|
1408 die "Error: You must specify a value for \"--DatabaseDataCols\" option in \"Specify\" \"--DatabaseDataColsMode\". \n";
|
|
|
1409 }
|
|
|
1410
|
|
|
1411 # Compound ID and fingerprints field options for SD files...
|
|
|
1412
|
|
|
1413 $OptionsInfo{DatabaseCompoundIDMode} = $Options{databasecompoundidmode};
|
|
|
1414 $OptionsInfo{DatabaseCompoundIDField} = $Options{databasecompoundidfield} ? $Options{databasecompoundidfield} : '';
|
|
|
1415
|
|
|
1416 if ($Options{databasecompoundidmode} =~ /^DataField$/i) {
|
|
|
1417 if (!$Options{databasecompoundidfield}) {
|
|
|
1418 die "Error: You must specify a value for \"--DatabaseCompoundIDField\" option in \"DataField\" \"--DatabaseCompoundIDMode\". \n";
|
|
|
1419 }
|
|
|
1420 $OptionsInfo{DatabaseCompoundIDField} = $Options{databasecompoundidfield};
|
|
|
1421 }
|
|
|
1422
|
|
|
1423
|
|
|
1424 if (IsNotEmpty($Options{databasefingerprintsfield})) {
|
|
|
1425 $OptionsInfo{DatabaseFingerprintsField} = $Options{databasefingerprintsfield};
|
|
|
1426 }
|
|
|
1427 else {
|
|
|
1428 $OptionsInfo{DatabaseFingerprintsField} = 'AutoDetect';
|
|
|
1429 }
|
|
|
1430
|
|
|
1431 if ($Options{databasecompoundidfield} && IsNotEmpty($Options{databasefingerprintsfield})) {
|
|
|
1432 if (($Options{databasecompoundidfield} eq $Options{databasefingerprintsfield})) {
|
|
|
1433 die "Error: Values specified using \"--DatabaseCompoundIDField\" and \"--DatabaseFingerprintsfield\", $Options{databasecompoundidfield}, must be different.\n";
|
|
|
1434 }
|
|
|
1435 }
|
|
|
1436
|
|
|
1437 # Database data field options for SD files...
|
|
|
1438
|
|
|
1439 $OptionsInfo{DatabaseDataFieldsMode} = $Options{databasedatafieldsmode};
|
|
|
1440 $OptionsInfo{DatabaseDataFields} = '';
|
|
|
1441 @{$OptionsInfo{SpecifiedDatabaseDataFields}} = ();
|
|
|
1442
|
|
|
1443 if ($Options{databasedatafieldsmode} =~ /^Specify$/i && !$Options{databasedatafields}) {
|
|
|
1444 die "Error: You must specify a value for \"--DatabaseDataFields\" option in \"Specify\" \"--DatabaseDataFieldsMode\". \n";
|
|
|
1445 }
|
|
|
1446 if ($Options{databasedatafields}) {
|
|
|
1447 my(@SpecifiedDataFields);
|
|
|
1448 $OptionsInfo{DatabaseDataFields} = $Options{databasedatafields};
|
|
|
1449
|
|
|
1450 @SpecifiedDataFields = split /\,/, $Options{databasedatafields};
|
|
|
1451 push @{$OptionsInfo{SpecifiedDatabaseDataFields}}, @SpecifiedDataFields;
|
|
|
1452 }
|
|
|
1453 }
|
|
|
1454
|
|
|
1455 # Setup script usage and retrieve command line arguments specified using various options...
|
|
|
1456 sub SetupScriptUsage {
|
|
|
1457
|
|
|
1458 # Retrieve all the options...
|
|
|
1459 %Options = ();
|
|
|
1460
|
|
|
1461 $Options{alpha} = 0.5;
|
|
|
1462 $Options{beta} = 1;
|
|
|
1463
|
|
|
1464 $Options{bitvectorcomparisonmode} = "TanimotoSimilarity";
|
|
|
1465
|
|
|
1466 $Options{databasecolmode} = 'colnum';
|
|
|
1467
|
|
|
1468 $Options{databasecompoundidprefix} = 'Cmpd';
|
|
|
1469 $Options{databasecompoundidmode} = 'LabelPrefix';
|
|
|
1470
|
|
|
1471 $Options{databasedatacolsmode} = 'CompoundID';
|
|
|
1472 $Options{databasedatafieldsmode} = 'CompoundID';
|
|
|
1473
|
|
|
1474 $Options{distancecutoff} = 10;
|
|
|
1475
|
|
|
1476 $Options{referencecolmode} = 'colnum';
|
|
|
1477
|
|
|
1478 $Options{referencecompoundidprefix} = 'Cmpd';
|
|
|
1479 $Options{referencecompoundidmode} = 'LabelPrefix';
|
|
|
1480
|
|
|
1481 $Options{detail} = 1;
|
|
|
1482
|
|
|
1483 $Options{fingerprintsmode} = 'AutoDetect';
|
|
|
1484 $Options{groupfusionrule} = 'Max';
|
|
|
1485 $Options{groupfusionapplycutoff} = 'Yes';
|
|
|
1486
|
|
|
1487 $Options{knn} = 'All';
|
|
|
1488
|
|
|
1489 $Options{mode} = 'MultipleReferences';
|
|
|
1490
|
|
|
1491 $Options{numofsimilarmolecules} = 10;
|
|
|
1492 $Options{percentsimilarmolecules} = 1;
|
|
|
1493
|
|
|
1494 $Options{indelim} = 'comma';
|
|
|
1495 $Options{outdelim} = 'comma';
|
|
|
1496 $Options{quote} = 'yes';
|
|
|
1497
|
|
|
1498 $Options{output} = 'text';
|
|
|
1499
|
|
|
1500 $Options{precision} = 2;
|
|
|
1501
|
|
|
1502 $Options{searchmode} = 'SimilaritySearch';
|
|
|
1503
|
|
|
1504 $Options{similarcountmode} = 'NumOfSimilar';
|
|
|
1505
|
|
|
1506 $Options{similaritycutoff} = 0.75;
|
|
|
1507
|
|
|
1508 $Options{vectorcomparisonmode} = 'TanimotoSimilarity';
|
|
|
1509 $Options{vectorcomparisonformulism} = 'AlgebraicForm';
|
|
|
1510
|
|
|
1511 if (!GetOptions(\%Options, "alpha=f", "beta=f", "bitvectorcomparisonmode|b=s", "databasecolmode=s", "databasecompoundidcol=s", "databasecompoundidprefix=s", "databasecompoundidfield=s", "databasecompoundidmode=s", "databasedatacols=s", "databasedatacolsmode=s", "databasedatafields=s", "databasedatafieldsmode=s", "databasefingerprintscol=s", "databasefingerprintsfield=s", "distancecutoff=f", "detail|d=i", "fast|f", "fingerprintsmode=s", "groupfusionrule|g=s", , "groupfusionapplycutoff=s", "help|h", "indelim=s", "knn|k=s", "mode|m=s", "numofsimilarmolecules|n=i", "outdelim=s", "output=s", "overwrite|o", "percentsimilarmolecules|p=f", "precision=s", "quote|q=s", "referencecolmode=s", "referencecompoundidcol=s", "referencecompoundidprefix=s", "referencecompoundidfield=s", "referencecompoundidmode=s", "referencefingerprintscol=s", "referencefingerprintsfield=s", "root|r=s", "searchmode|s=s", "similarcountmode=s", "similaritycutoff=f", "vectorcomparisonmode|v=s", "vectorcomparisonformulism=s", "workingdir|w=s")) {
|
|
|
1512 die "\nTo get a list of valid options and their values, use \"$ScriptName -h\" or\n\"perl -S $ScriptName -h\" command and try again...\n";
|
|
|
1513 }
|
|
|
1514 if ($Options{workingdir}) {
|
|
|
1515 if (! -d $Options{workingdir}) {
|
|
|
1516 die "Error: The value specified, $Options{workingdir}, for option \"-w --workingdir\" is not a directory name.\n";
|
|
|
1517 }
|
|
|
1518 chdir $Options{workingdir} or die "Error: Couldn't chdir $Options{workingdir}: $! \n";
|
|
|
1519 }
|
|
|
1520 if ($Options{databasecolmode} !~ /^(ColNum|ColLabel)$/i) {
|
|
|
1521 die "Error: The value specified, $Options{databasecolmode}, for option \"--DatabaseColMode\" is not valid. Allowed values: ColNum, or ColLabel\n";
|
|
|
1522 }
|
|
|
1523 if ($Options{databasecompoundidmode} !~ /^(DataField|MolName|LabelPrefix|MolNameOrLabelPrefix)$/i) {
|
|
|
1524 die "Error: The value specified, $Options{databasecompoundidmode}, for option \"--DatabaseCompoundIDMode\" is not valid. Allowed values: DataField, MolName, LabelPrefix or MolNameOrLabelPrefix\n";
|
|
|
1525 }
|
|
|
1526 if ($Options{databasedatacolsmode} !~ /^(All|Specify|CompoundID)$/i) {
|
|
|
1527 die "Error: The value specified, $Options{databasedatacolsmode}, for option \"--DatabaseDataColsMode\" is not valid. Allowed values: All, Specify, or CompoundID\n";
|
|
|
1528 }
|
|
|
1529 if ($Options{databasedatafieldsmode} !~ /^(All|Common|Specify|CompoundID)$/i) {
|
|
|
1530 die "Error: The value specified, $Options{databasedatafieldsmode}, for option \"--DatabaseDataFieldsMode\" is not valid. Allowed values: All, Common, Specify, or CompoundID\n";
|
|
|
1531 }
|
|
|
1532 if (!IsPositiveInteger($Options{detail})) {
|
|
|
1533 die "Error: The value specified, $Options{detail}, for option \"-d, --detail\" is not valid. Allowed values: > 0 \n";
|
|
|
1534 }
|
|
|
1535 if ($Options{fingerprintsmode} !~ /^(AutoDetect|FingerprintsBitVectorString|FingerprintsVectorString)$/i) {
|
|
|
1536 die "Error: The value specified, $Options{fingerprintsmode}, for option \"--FingerprintsMode\" is not valid. Allowed values: AutoDetect, FingerprintsBitVectorString or FingerprintsVectorString \n";
|
|
|
1537 }
|
|
|
1538 if ($Options{groupfusionrule} !~ /^(Max|Min|Mean|Median|Sum|Euclidean)$/i) {
|
|
|
1539 die "Error: The value specified, $Options{groupfusionrule}, for option \"-g, --GroupFusionRule\" is not valid. Allowed values: Max, Min, Mean, Median, Sum, Euclidean\n";
|
|
|
1540 }
|
|
|
1541 if ($Options{groupfusionapplycutoff} !~ /^(Yes|No)$/i) {
|
|
|
1542 die "Error: The value specified, $Options{quote}, for option \"--GroupFusionApplyCutoff\" is not valid. Allowed values: Yes or No\n";
|
|
|
1543 }
|
|
|
1544 if ($Options{indelim} !~ /^(comma|semicolon)$/i) {
|
|
|
1545 die "Error: The value specified, $Options{indelim}, for option \"--InDelim\" is not valid. Allowed values: comma, or semicolon\n";
|
|
|
1546 }
|
|
|
1547 if ($Options{mode} !~ /^(IndividualReference|MultipleReferences)$/i) {
|
|
|
1548 die "Error: The value specified, $Options{mode}, for option \"-m, --mode\" is not valid. Allowed values: IndividualReference, MultipleReferences\n";
|
|
|
1549 }
|
|
|
1550 if (!IsPositiveInteger($Options{numofsimilarmolecules})) {
|
|
|
1551 die "Error: The value specified, $Options{numofsimilarmolecules}, for option \"-n, --NumOfSimilarMolecules\" is not valid. Allowed values: > 0 \n";
|
|
|
1552 }
|
|
|
1553 if ($Options{outdelim} !~ /^(comma|semicolon|tab)$/i) {
|
|
|
1554 die "Error: The value specified, $Options{outdelim}, for option \"--OutDelim\" is not valid. Allowed values: comma, tab, or semicolon\n";
|
|
|
1555 }
|
|
|
1556 if ($Options{output} !~ /^(SD|text|both)$/i) {
|
|
|
1557 die "Error: The value specified, $Options{output}, for option \"--output\" is not valid. Allowed values: SD, text, or both\n";
|
|
|
1558 }
|
|
|
1559 if (!(IsFloat($Options{percentsimilarmolecules}) && $Options{percentsimilarmolecules} > 0 && $Options{percentsimilarmolecules} <= 100)) {
|
|
|
1560 die "Error: The value specified, $Options{percentsimilarmolecules}, for option \"-p, --PercentSimilarMolecules\" is not valid. Allowed values: > 0 and <= 100 \n";
|
|
|
1561 }
|
|
|
1562 if ($Options{quote} !~ /^(Yes|No)$/i) {
|
|
|
1563 die "Error: The value specified, $Options{quote}, for option \"-q --quote\" is not valid. Allowed values: Yes or No\n";
|
|
|
1564 }
|
|
|
1565 if (!IsPositiveInteger($Options{precision})) {
|
|
|
1566 die "Error: The value specified, $Options{precision}, for option \"--precision\" is not valid. Allowed values: > 0 \n";
|
|
|
1567 }
|
|
|
1568 if ($Options{referencecolmode} !~ /^(ColNum|ColLabel)$/i) {
|
|
|
1569 die "Error: The value specified, $Options{referencecolmode}, for option \"--ReferenceColMode\" is not valid. Allowed values: ColNum, or ColLabel\n";
|
|
|
1570 }
|
|
|
1571 if ($Options{referencecompoundidmode} !~ /^(DataField|MolName|LabelPrefix|MolNameOrLabelPrefix)$/i) {
|
|
|
1572 die "Error: The value specified, $Options{referencecompoundidmode}, for option \"--ReferenceCompoundIDMode\" is not valid. Allowed values: DataField, MolName, LabelPrefix or MolNameOrLabelPrefix\n";
|
|
|
1573 }
|
|
|
1574 if ($Options{searchmode} !~ /^(SimilaritySearch|DissimilaritySearch)$/i) {
|
|
|
1575 die "Error: The value specified, $Options{searchmode}, for option \"-s, --SearchMode\" is not valid. Allowed values: SimilaritySearch, DissimilaritySearch \n";
|
|
|
1576 }
|
|
|
1577 if ($Options{similarcountmode} !~ /^(NumOfSimilar|PercentSimilar)$/i) {
|
|
|
1578 die "Error: The value specified, $Options{similarcountmode}, for option \"--SimilarCountMode\" is not valid. Allowed values: NumOfSimilar, PercentSimilar \n";
|
|
|
1579 }
|
|
|
1580 }
|
|
|
1581
|
|
|
1582 __END__
|
|
|
1583
|
|
|
1584 =head1 NAME
|
|
|
1585
|
|
|
1586 SimilaritySearchingFingerprints.pl - Perform similarity search using fingerprints strings data in SD, FP and CSV/TSV text file(s)
|
|
|
1587
|
|
|
1588 =head1 SYNOPSIS
|
|
|
1589
|
|
|
1590 SimilaritySearchingFingerprints.pl ReferenceFPFile DatabaseFPFile
|
|
|
1591
|
|
|
1592 SimilaritySearchingFingerprints.pl [B<--alpha> I<number>] [B<--beta> I<number>]
|
|
|
1593 [B<-b, --BitVectorComparisonMode> I<TanimotoSimilarity | TverskySimilarity | ...>]
|
|
|
1594 [B<--DatabaseColMode> I<ColNum | ColLabel>] [B<--DatabaseCompoundIDCol> I<col number | col name>]
|
|
|
1595 [B<--DatabaseCompoundIDPrefix> I<text>] [B<--DatabaseCompoundIDField> I<DataFieldName>]
|
|
|
1596 [B<--DatabaseCompoundIDMode> I<DataField | MolName | LabelPrefix | MolNameOrLabelPrefix>]
|
|
|
1597 [B<--DatabaseDataCols> I<"DataColNum1, DataColNum2,... " | DataColLabel1, DataCoLabel2,... ">]
|
|
|
1598 [B<--DatabaseDataColsMode> I<All | Specify | CompoundID>] [B<--DatabaseDataFields> I<"FieldLabel1, FieldLabel2,... ">]
|
|
|
1599 [B<--DatabaseDataFieldsMode> I<All | Common | Specify | CompoundID>]
|
|
|
1600 [B<--DatabaseFingerprintsCol> I<col number | col name>] [B<--DatabaseFingerprintsField> I<FieldLabel>]
|
|
|
1601 []B<--DistanceCutoff> I<number>] [B<-d, --detail> I<InfoLevel>] [B<-f, --fast>]
|
|
|
1602 [B<--FingerprintsMode> I<AutoDetect | FingerprintsBitVectorString | FingerprintsVectorString>]
|
|
|
1603 [B<-g, --GroupFusionRule> I<Max, Mean, Median, Min, Sum, Euclidean>] [B<--GroupFusionApplyCutoff> I<Yes | No>]
|
|
|
1604 [B<-h, --help>] [B<--InDelim> I<comma | semicolon>] [B<-k, --KNN> I<all | number>]
|
|
|
1605 [B<-m, --mode> I<IndividualReference | MultipleReferences>]
|
|
|
1606 [B<-n, --NumOfSimilarMolecules> I<number>] [B<--OutDelim> I<comma | tab | semicolon>]
|
|
|
1607 [B<--output> I<SD | text | both>] [B<-o, --overwrite>]
|
|
|
1608 [B<-p, --PercentSimilarMolecules> I<number>] [B<--precision> I<number>] [B<-q, --quote> I<Yes | No>]
|
|
|
1609 [B<--ReferenceColMode> I<ColNum | ColLabel>] [B<--ReferenceCompoundIDCol> I<col number | col name>]
|
|
|
1610 [B<--ReferenceCompoundIDPrefix> I<text>] [B<--ReferenceCompoundIDField> I<DataFieldName>]
|
|
|
1611 [B<--ReferenceCompoundIDMode> I<DataField | MolName | LabelPrefix | MolNameOrLabelPrefix>]
|
|
|
1612 [B<--ReferenceFingerprintsCol> I<col number | col name>] [B<--ReferenceFingerprintsField> I<FieldLabel>]
|
|
|
1613 [B<-r, --root> I<RootName>] [B<-s, --SearchMode> I<SimilaritySearch | DissimilaritySearch>]
|
|
|
1614 [B<--SimilarCountMode> I<NumOfSimilar | PercentSimilar>] [B<--SimilarityCutoff> I<number>]
|
|
|
1615 [B<-v, --VectorComparisonMode> I<TanimotoSimilairy | ... | ManhattanDistance | ...>]
|
|
|
1616 [B<--VectorComparisonFormulism> I<AlgebraicForm | BinaryForm | SetTheoreticForm>]
|
|
|
1617 [B<-w, --WorkingDir> dirname] ReferenceFingerprintsFile DatabaseFingerprintsFile
|
|
|
1618
|
|
|
1619 =head1 DESCRIPTION
|
|
|
1620
|
|
|
1621 Perform molecular similarity search [ Ref 94-113 ] using fingerprint bit-vector or vector strings
|
|
|
1622 data in I<SD, FP, or CSV/TSV text> files corresponding to I<ReferenceFingerprintsFile> and
|
|
|
1623 I<DatabaseFingerprintsFile>, and generate SD and CSV/TSV text file(s) containing database
|
|
|
1624 molecules which are similar to reference molecule(s). The reference molecules are also referred
|
|
|
1625 to as query or seed molecules and database molecules as target molecules in the literature.
|
|
|
1626
|
|
|
1627 The current release of MayaChemTools supports two types of similarity search modes:
|
|
|
1628 I<IndividualReference or MultipleReferences>. For default value of I<MultipleReferences> for B<-m, --mode>
|
|
|
1629 option, reference molecules are considered as a set and B<-g, --GroupFusionRule> is used to calculate
|
|
|
1630 similarity of a database molecule against reference molecules set. The group fusion rule is also
|
|
|
1631 referred to as data fusion of consensus scoring in the literature. However, for I<IndividualReference>
|
|
|
1632 value of B<-m, --mode> option, reference molecules are treated as individual molecules and each reference
|
|
|
1633 molecule is compared against a database molecule by itself to identify similar molecules.
|
|
|
1634
|
|
|
1635 The molecular dissimilarity search can also be performed using I<DissimilaritySearch> value for
|
|
|
1636 B<-s, --SearchMode> option. During dissimilarity search or usage of distance comparison coefficient
|
|
|
1637 in similarity similarity search, the meaning of fingerprints comparison value is automatically reversed
|
|
|
1638 as shown below:
|
|
|
1639
|
|
|
1640 SeachMode ComparisonCoefficient ResultsSort ComparisonValues
|
|
|
1641
|
|
|
1642 Similarity SimilarityCoefficient Descending Higher value imples
|
|
|
1643 high similarity
|
|
|
1644 Similarity DistanceCoefficient Ascending Lower value implies
|
|
|
1645 high similarity
|
|
|
1646
|
|
|
1647 Dissimilarity SimilarityCoefficient Ascending Lower value implies
|
|
|
1648 high dissimilarity
|
|
|
1649 Dissimilarity DistanceCoefficient Descending Higher value implies
|
|
|
1650 high dissimilarity
|
|
|
1651
|
|
|
1652 During I<IndividualReference> value of B<-m, --Mode> option for similarity search, fingerprints bit-vector
|
|
|
1653 or vector string of each reference molecule is compared with database molecules using specified
|
|
|
1654 similarity or distance coefficients to identify most similar molecules for each reference molecule.
|
|
|
1655 Based on value of B<--SimilarCountMode>, up to B<--n, --NumOfSimilarMolecules> or B<-p,
|
|
|
1656 --PercentSimilarMolecules> at specified B<--SimilarityCutoff> or B<--DistanceCutoff> are
|
|
|
1657 identified for each reference molecule.
|
|
|
1658
|
|
|
1659 During I<MultipleReferences> value B<-m, --mode> option for similarity search, all reference molecules
|
|
|
1660 are considered as a set and B<-g, --GroupFusionRule> is used to calculate similarity of a database
|
|
|
1661 molecule against reference molecules set either using all reference molecules or number of k-nearest
|
|
|
1662 neighbors (k-NN) to a database molecule specified using B<-k, --kNN>. The fingerprints bit-vector
|
|
|
1663 or vector string of each reference molecule in a set is compared with a database molecule using
|
|
|
1664 a similarity or distance coefficient specified via B<-b, --BitVectorComparisonMode> or B<-v,
|
|
|
1665 --VectorComparisonMode>. The reference molecules whose comparison values with a database
|
|
|
1666 molecule fall outside specified B<--SimilarityCutoff> or B<--DistanceCutoff> are ignored during I<Yes>
|
|
|
1667 value of B<--GroupFusionApplyCutoff>. The specified B<-g, --GroupFusionRule> is applied to
|
|
|
1668 B<-k, --kNN> reference molecules to calculate final similarity value between a database molecule
|
|
|
1669 and reference molecules set.
|
|
|
1670
|
|
|
1671 The input fingerprints I<SD, FP, or Text (CSV/TSV)> files for I<ReferenceFingerprintsFile> and
|
|
|
1672 I<DatabaseTextFile> must contain valid fingerprint bit-vector or vector strings data corresponding to
|
|
|
1673 same type of fingerprints.
|
|
|
1674
|
|
|
1675 The valid fingerprints I<SDFile> extensions are I<.sdf> and I<.sd>. The valid fingerprints I<FPFile>
|
|
|
1676 extensions are I<.fpf> and I<.fp>. The valid fingerprints I<TextFile (CSV/TSV)> extensions are
|
|
|
1677 I<.csv> and I<.tsv> for comma/semicolon and tab delimited text files respectively. The B<--indelim>
|
|
|
1678 option determines the format of I<TextFile>. Any file which doesn't correspond to the format indicated
|
|
|
1679 by B<--indelim> option is ignored.
|
|
|
1680
|
|
|
1681 Example of I<FP> file containing fingerprints bit-vector string data:
|
|
|
1682
|
|
|
1683 #
|
|
|
1684 # Package = MayaChemTools 7.4
|
|
|
1685 # ReleaseDate = Oct 21, 2010
|
|
|
1686 #
|
|
|
1687 # TimeStamp = Mon Mar 7 15:14:01 2011
|
|
|
1688 #
|
|
|
1689 # FingerprintsStringType = FingerprintsBitVector
|
|
|
1690 #
|
|
|
1691 # Description = PathLengthBits:AtomicInvariantsAtomTypes:MinLength1:...
|
|
|
1692 # Size = 1024
|
|
|
1693 # BitStringFormat = HexadecimalString
|
|
|
1694 # BitsOrder = Ascending
|
|
|
1695 #
|
|
|
1696 Cmpd1 9c8460989ec8a49913991a6603130b0a19e8051c89184414953800cc21510...
|
|
|
1697 Cmpd2 000000249400840040100042011001001980410c000000001010088001120...
|
|
|
1698 ... ...
|
|
|
1699 ... ..
|
|
|
1700
|
|
|
1701 Example of I<FP> file containing fingerprints vector string data:
|
|
|
1702
|
|
|
1703 #
|
|
|
1704 # Package = MayaChemTools 7.4
|
|
|
1705 # ReleaseDate = Oct 21, 2010
|
|
|
1706 #
|
|
|
1707 # TimeStamp = Mon Mar 7 15:14:01 2011
|
|
|
1708 #
|
|
|
1709 # FingerprintsStringType = FingerprintsVector
|
|
|
1710 #
|
|
|
1711 # Description = PathLengthBits:AtomicInvariantsAtomTypes:MinLength1:...
|
|
|
1712 # VectorStringFormat = IDsAndValuesString
|
|
|
1713 # VectorValuesType = NumericalValues
|
|
|
1714 #
|
|
|
1715 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:
|
|
|
1716 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...;
|
|
|
1717 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
|
|
|
1718 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 ...
|
|
|
1719 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
|
|
|
1720 O C CC=O CCCC CCCN CCCO CCNC CNC=N CNC=O CNCN CCCC=O CCCCC CCCCN CC...;
|
|
|
1721 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
|
|
|
1722 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 ...
|
|
|
1723 ... ...
|
|
|
1724 ... ...
|
|
|
1725
|
|
|
1726 Example of I<SD> file containing fingerprints bit-vector string data:
|
|
|
1727
|
|
|
1728 ... ...
|
|
|
1729 ... ...
|
|
|
1730 $$$$
|
|
|
1731 ... ...
|
|
|
1732 ... ...
|
|
|
1733 ... ...
|
|
|
1734 41 44 0 0 0 0 0 0 0 0999 V2000
|
|
|
1735 -3.3652 1.4499 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
|
|
|
1736 ... ...
|
|
|
1737 2 3 1 0 0 0 0
|
|
|
1738 ... ...
|
|
|
1739 M END
|
|
|
1740 > <CmpdID>
|
|
|
1741 Cmpd1
|
|
|
1742
|
|
|
1743 > <PathLengthFingerprints>
|
|
|
1744 FingerprintsBitVector;PathLengthBits:AtomicInvariantsAtomTypes:MinLengt
|
|
|
1745 h1:MaxLength8;1024;HexadecimalString;Ascending;9c8460989ec8a49913991a66
|
|
|
1746 03130b0a19e8051c89184414953800cc2151082844a201042800130860308e8204d4028
|
|
|
1747 00831048940e44281c00060449a5000ac80c894114e006321264401600846c050164462
|
|
|
1748 08190410805000304a10205b0100e04c0038ba0fad0209c0ca8b1200012268b61c0026a
|
|
|
1749 aa0660a11014a011d46
|
|
|
1750
|
|
|
1751 $$$$
|
|
|
1752 ... ...
|
|
|
1753 ... ...
|
|
|
1754
|
|
|
1755 Example of CSV I<TextFile> containing fingerprints bit-vector string data:
|
|
|
1756
|
|
|
1757 "CompoundID","PathLengthFingerprints"
|
|
|
1758 "Cmpd1","FingerprintsBitVector;PathLengthBits:AtomicInvariantsAtomTypes
|
|
|
1759 :MinLength1:MaxLength8;1024;HexadecimalString;Ascending;9c8460989ec8a4
|
|
|
1760 9913991a6603130b0a19e8051c89184414953800cc2151082844a20104280013086030
|
|
|
1761 8e8204d402800831048940e44281c00060449a5000ac80c894114e006321264401..."
|
|
|
1762 ... ...
|
|
|
1763 ... ...
|
|
|
1764
|
|
|
1765 The current release of MayaChemTools supports the following types of fingerprint
|
|
|
1766 bit-vector and vector strings:
|
|
|
1767
|
|
|
1768 FingerprintsVector;AtomNeighborhoods:AtomicInvariantsAtomTypes:MinRadi
|
|
|
1769 us0:MaxRadius2;41;AlphaNumericalValues;ValuesString;NR0-C.X1.BO1.H3-AT
|
|
|
1770 C1:NR1-C.X3.BO3.H1-ATC1:NR2-C.X1.BO1.H3-ATC1:NR2-C.X3.BO4-ATC1 NR0-C.X
|
|
|
1771 1.BO1.H3-ATC1:NR1-C.X3.BO3.H1-ATC1:NR2-C.X1.BO1.H3-ATC1:NR2-C.X3.BO4-A
|
|
|
1772 TC1 NR0-C.X2.BO2.H2-ATC1:NR1-C.X2.BO2.H2-ATC1:NR1-C.X3.BO3.H1-ATC1:NR2
|
|
|
1773 -C.X2.BO2.H2-ATC1:NR2-N.X3.BO3-ATC1:NR2-O.X1.BO1.H1-ATC1 NR0-C.X2.B...
|
|
|
1774
|
|
|
1775 FingerprintsVector;AtomTypesCount:AtomicInvariantsAtomTypes:ArbitraryS
|
|
|
1776 ize;10;NumericalValues;IDsAndValuesString;C.X1.BO1.H3 C.X2.BO2.H2 C.X2
|
|
|
1777 .BO3.H1 C.X3.BO3.H1 C.X3.BO4 F.X1.BO1 N.X2.BO2.H1 N.X3.BO3 O.X1.BO1.H1
|
|
|
1778 O.X1.BO2;2 4 14 3 10 1 1 1 3 2
|
|
|
1779
|
|
|
1780 FingerprintsVector;AtomTypesCount:SLogPAtomTypes:ArbitrarySize;16;Nume
|
|
|
1781 ricalValues;IDsAndValuesString;C1 C10 C11 C14 C18 C20 C21 C22 C5 CS F
|
|
|
1782 N11 N4 O10 O2 O9;5 1 1 1 14 4 2 1 2 2 1 1 1 1 3 1
|
|
|
1783
|
|
|
1784 FingerprintsVector;AtomTypesCount:SLogPAtomTypes:FixedSize;67;OrderedN
|
|
|
1785 umericalValues;IDsAndValuesString;C1 C2 C3 C4 C5 C6 C7 C8 C9 C10 C11 C
|
|
|
1786 12 C13 C14 C15 C16 C17 C18 C19 C20 C21 C22 C23 C24 C25 C26 C27 CS N1 N
|
|
|
1787 2 N3 N4 N5 N6 N7 N8 N9 N10 N11 N12 N13 N14 NS O1 O2 O3 O4 O5 O6 O7 O8
|
|
|
1788 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
|
|
|
1789 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...
|
|
|
1790
|
|
|
1791 FingerprintsVector;EStateIndicies:ArbitrarySize;11;NumericalValues;IDs
|
|
|
1792 AndValuesString;SaaCH SaasC SaasN SdO SdssC SsCH3 SsF SsOH SssCH2 SssN
|
|
|
1793 H SsssCH;24.778 4.387 1.993 25.023 -1.435 3.975 14.006 29.759 -0.073 3
|
|
|
1794 .024 -2.270
|
|
|
1795
|
|
|
1796 FingerprintsVector;EStateIndicies:FixedSize;87;OrderedNumericalValues;
|
|
|
1797 ValuesString;0 0 0 0 0 0 0 3.975 0 -0.073 0 0 24.778 -2.270 0 0 -1.435
|
|
|
1798 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
|
|
|
1799 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
|
|
|
1800 0 0 0 0 0 0 0 0 0 0 0 0 0 0
|
|
|
1801
|
|
|
1802 FingerprintsVector;ExtendedConnectivity:AtomicInvariantsAtomTypes:Radi
|
|
|
1803 us2;60;AlphaNumericalValues;ValuesString;73555770 333564680 352413391
|
|
|
1804 666191900 1001270906 1371674323 1481469939 1977749791 2006158649 21414
|
|
|
1805 08799 49532520 64643108 79385615 96062769 273726379 564565671 85514103
|
|
|
1806 5 906706094 988546669 1018231313 1032696425 1197507444 1331250018 1338
|
|
|
1807 532734 1455473691 1607485225 1609687129 1631614296 1670251330 17303...
|
|
|
1808
|
|
|
1809 FingerprintsVector;ExtendedConnectivityCount:AtomicInvariantsAtomTypes
|
|
|
1810 :Radius2;60;NumericalValues;IDsAndValuesString;73555770 333564680 3524
|
|
|
1811 13391 666191900 1001270906 1371674323 1481469939 1977749791 2006158649
|
|
|
1812 2141408799 49532520 64643108 79385615 96062769 273726379 564565671...;
|
|
|
1813 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
|
|
|
1814 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
|
|
|
1815
|
|
|
1816 FingerprintsBitVector;ExtendedConnectivityBits:AtomicInvariantsAtomTyp
|
|
|
1817 es:Radius2;1024;BinaryString;Ascending;0000000000000000000000000000100
|
|
|
1818 0000000001010000000110000011000000000000100000000000000000000000100001
|
|
|
1819 1000000110000000000000000000000000010011000000000000000000000000010000
|
|
|
1820 0000000000000000000000000010000000000000000001000000000000000000000000
|
|
|
1821 0000000000010000100001000000000000101000000000000000100000000000000...
|
|
|
1822
|
|
|
1823 FingerprintsVector;ExtendedConnectivity:FunctionalClassAtomTypes:Radiu
|
|
|
1824 s2;57;AlphaNumericalValues;ValuesString;24769214 508787397 850393286 8
|
|
|
1825 62102353 981185303 1231636850 1649386610 1941540674 263599683 32920567
|
|
|
1826 1 571109041 639579325 683993318 723853089 810600886 885767127 90326012
|
|
|
1827 7 958841485 981022393 1126908698 1152248391 1317567065 1421489994 1455
|
|
|
1828 632544 1557272891 1826413669 1983319256 2015750777 2029559552 20404...
|
|
|
1829
|
|
|
1830 FingerprintsVector;ExtendedConnectivity:EStateAtomTypes:Radius2;62;Alp
|
|
|
1831 haNumericalValues;ValuesString;25189973 528584866 662581668 671034184
|
|
|
1832 926543080 1347067490 1738510057 1759600920 2034425745 2097234755 21450
|
|
|
1833 44754 96779665 180364292 341712110 345278822 386540408 387387308 50430
|
|
|
1834 1706 617094135 771528807 957666640 997798220 1158349170 1291258082 134
|
|
|
1835 1138533 1395329837 1420277211 1479584608 1486476397 1487556246 1566...
|
|
|
1836
|
|
|
1837 FingerprintsBitVector;MACCSKeyBits;166;BinaryString;Ascending;00000000
|
|
|
1838 0000000000000000000000000000000001001000010010000000010010000000011100
|
|
|
1839 0100101010111100011011000100110110000011011110100110111111111111011111
|
|
|
1840 11111111111110111000
|
|
|
1841
|
|
|
1842 FingerprintsBitVector;MACCSKeyBits;322;BinaryString;Ascending;11101011
|
|
|
1843 1110011111100101111111000111101100110000000000000011100010000000000000
|
|
|
1844 0000000000000000000000000000000000000000000000101000000000000000000000
|
|
|
1845 0000000000000000000000000000000000000000000000000000000000000000000000
|
|
|
1846 0000000000000000000000000000000000000011000000000000000000000000000000
|
|
|
1847 0000000000000000000000000000000000000000
|
|
|
1848
|
|
|
1849 FingerprintsVector;MACCSKeyCount;166;OrderedNumericalValues;ValuesStri
|
|
|
1850 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
|
|
|
1851 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
|
|
|
1852 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
|
|
|
1853 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
|
|
|
1854 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
|
|
|
1855
|
|
|
1856 FingerprintsVector;MACCSKeyCount;322;OrderedNumericalValues;ValuesStri
|
|
|
1857 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
|
|
|
1858 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
|
|
|
1859 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
|
|
|
1860 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
|
|
|
1861 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 ...
|
|
|
1862
|
|
|
1863 FingerprintsBitVector;PathLengthBits:AtomicInvariantsAtomTypes:MinLeng
|
|
|
1864 th1:MaxLength8;1024;BinaryString;Ascending;001000010011010101011000110
|
|
|
1865 0100010101011000101001011100110001000010001001101000001001001001001000
|
|
|
1866 0010110100000111001001000001001010100100100000000011000000101001011100
|
|
|
1867 0010000001000101010100000100111100110111011011011000000010110111001101
|
|
|
1868 0101100011000000010001000011000010100011101100001000001000100000000...
|
|
|
1869
|
|
|
1870 FingerprintsVector;PathLengthCount:AtomicInvariantsAtomTypes:MinLength
|
|
|
1871 1:MaxLength8;432;NumericalValues;IDsAndValuesPairsString;C.X1.BO1.H3 2
|
|
|
1872 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
|
|
|
1873 2.BO2.H1 1 N.X3.BO3 1 O.X1.BO1.H1 3 O.X1.BO2 2 C.X1.BO1.H3C.X3.BO3.H1
|
|
|
1874 2 C.X2.BO2.H2C.X2.BO2.H2 1 C.X2.BO2.H2C.X3.BO3.H1 4 C.X2.BO2.H2C.X3.BO
|
|
|
1875 4 1 C.X2.BO2.H2N.X3.BO3 1 C.X2.BO3.H1:C.X2.BO3.H1 10 C.X2.BO3.H1:C....
|
|
|
1876
|
|
|
1877 FingerprintsVector;PathLengthCount:MMFF94AtomTypes:MinLength1:MaxLengt
|
|
|
1878 h8;463;NumericalValues;IDsAndValuesPairsString;C5A 2 C5B 2 C=ON 1 CB 1
|
|
|
1879 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
|
|
|
1880 5 2 C5ACB 1 C5ACR 1 C5B:C5B 1 C5BC=ON 1 C5BCB 1 C=ON=O=CN 1 C=ONNC=O 1
|
|
|
1881 CB:CB 18 CBF 1 CBNC=O 1 COO=O=CO 1 COOCR 1 COOOC=O 1 CRCR 7 CRN5 1 CR
|
|
|
1882 OR 2 C5A:C5B:C5B 2 C5A:C5BC=ON 1 C5A:C5BCB 1 C5A:N5:C5A 1 C5A:N5CR ...
|
|
|
1883
|
|
|
1884 FingerprintsVector;TopologicalAtomPairs:AtomicInvariantsAtomTypes:MinD
|
|
|
1885 istance1:MaxDistance10;223;NumericalValues;IDsAndValuesString;C.X1.BO1
|
|
|
1886 .H3-D1-C.X3.BO3.H1 C.X2.BO2.H2-D1-C.X2.BO2.H2 C.X2.BO2.H2-D1-C.X3.BO3.
|
|
|
1887 H1 C.X2.BO2.H2-D1-C.X3.BO4 C.X2.BO2.H2-D1-N.X3.BO3 C.X2.BO3.H1-D1-...;
|
|
|
1888 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
|
|
|
1889 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...
|
|
|
1890
|
|
|
1891 FingerprintsVector;TopologicalAtomPairs:FunctionalClassAtomTypes:MinDi
|
|
|
1892 stance1:MaxDistance10;144;NumericalValues;IDsAndValuesString;Ar-D1-Ar
|
|
|
1893 Ar-D1-Ar.HBA Ar-D1-HBD Ar-D1-Hal Ar-D1-None Ar.HBA-D1-None HBA-D1-NI H
|
|
|
1894 BA-D1-None HBA.HBD-D1-NI HBA.HBD-D1-None HBD-D1-None NI-D1-None No...;
|
|
|
1895 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
|
|
|
1896 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 ...
|
|
|
1897
|
|
|
1898 FingerprintsVector;TopologicalAtomTorsions:AtomicInvariantsAtomTypes;3
|
|
|
1899 3;NumericalValues;IDsAndValuesString;C.X1.BO1.H3-C.X3.BO3.H1-C.X3.BO4-
|
|
|
1900 C.X3.BO4 C.X1.BO1.H3-C.X3.BO3.H1-C.X3.BO4-N.X3.BO3 C.X2.BO2.H2-C.X2.BO
|
|
|
1901 2.H2-C.X3.BO3.H1-C.X2.BO2.H2 C.X2.BO2.H2-C.X2.BO2.H2-C.X3.BO3.H1-O...;
|
|
|
1902 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
|
|
|
1903
|
|
|
1904 FingerprintsVector;TopologicalAtomTorsions:EStateAtomTypes;36;Numerica
|
|
|
1905 lValues;IDsAndValuesString;aaCH-aaCH-aaCH-aaCH aaCH-aaCH-aaCH-aasC aaC
|
|
|
1906 H-aaCH-aasC-aaCH aaCH-aaCH-aasC-aasC aaCH-aaCH-aasC-sF aaCH-aaCH-aasC-
|
|
|
1907 ssNH aaCH-aasC-aasC-aasC aaCH-aasC-aasC-aasN aaCH-aasC-ssNH-dssC a...;
|
|
|
1908 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
|
|
|
1909
|
|
|
1910 FingerprintsVector;TopologicalAtomTriplets:AtomicInvariantsAtomTypes:M
|
|
|
1911 inDistance1:MaxDistance10;3096;NumericalValues;IDsAndValuesString;C.X1
|
|
|
1912 .BO1.H3-D1-C.X1.BO1.H3-D1-C.X3.BO3.H1-D2 C.X1.BO1.H3-D1-C.X2.BO2.H2-D1
|
|
|
1913 0-C.X3.BO4-D9 C.X1.BO1.H3-D1-C.X2.BO2.H2-D3-N.X3.BO3-D4 C.X1.BO1.H3-D1
|
|
|
1914 -C.X2.BO2.H2-D4-C.X2.BO2.H2-D5 C.X1.BO1.H3-D1-C.X2.BO2.H2-D6-C.X3....;
|
|
|
1915 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
|
|
|
1916 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...
|
|
|
1917
|
|
|
1918 FingerprintsVector;TopologicalAtomTriplets:SYBYLAtomTypes:MinDistance1
|
|
|
1919 :MaxDistance10;2332;NumericalValues;IDsAndValuesString;C.2-D1-C.2-D9-C
|
|
|
1920 .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-
|
|
|
1921 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
|
|
|
1922 -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.
|
|
|
1923 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...
|
|
|
1924
|
|
|
1925 FingerprintsVector;TopologicalPharmacophoreAtomPairs:ArbitrarySize:Min
|
|
|
1926 Distance1:MaxDistance10;54;NumericalValues;IDsAndValuesString;H-D1-H H
|
|
|
1927 -D1-NI HBA-D1-NI HBD-D1-NI H-D2-H H-D2-HBA H-D2-HBD HBA-D2-HBA HBA-D2-
|
|
|
1928 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
|
|
|
1929 BA H-D4-HBD HBA-D4-HBA HBA-D4-HBD HBD-D4-HBD H-D5-H H-D5-HBA H-D5-...;
|
|
|
1930 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
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|
|
1931 3 4 1 37 10 8 1 35 10 9 3 3 1 28 7 7 4 18 16 12 5 1 2 1
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|
|
1932
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|
1933 FingerprintsVector;TopologicalPharmacophoreAtomPairs:FixedSize:MinDist
|
|
|
1934 ance1:MaxDistance10;150;OrderedNumericalValues;ValuesString;18 0 0 1 0
|
|
|
1935 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
|
|
|
1936 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
|
|
|
1937 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
|
|
|
1938 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...
|
|
|
1939
|
|
|
1940 FingerprintsVector;TopologicalPharmacophoreAtomTriplets:ArbitrarySize:
|
|
|
1941 MinDistance1:MaxDistance10;696;NumericalValues;IDsAndValuesString;Ar1-
|
|
|
1942 Ar1-Ar1 Ar1-Ar1-H1 Ar1-Ar1-HBA1 Ar1-Ar1-HBD1 Ar1-H1-H1 Ar1-H1-HBA1 Ar1
|
|
|
1943 -H1-HBD1 Ar1-HBA1-HBD1 H1-H1-H1 H1-H1-HBA1 H1-H1-HBD1 H1-HBA1-HBA1 H1-
|
|
|
1944 HBA1-HBD1 H1-HBA1-NI1 H1-HBD1-NI1 HBA1-HBA1-NI1 HBA1-HBD1-NI1 Ar1-...;
|
|
|
1945 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
|
|
|
1946 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
|
|
|
1947 119 123 24 15 185 202 41 25 22 17 3 5 85 95 18 11 23 17 3 1 1 6 4 ...
|
|
|
1948
|
|
|
1949 FingerprintsVector;TopologicalPharmacophoreAtomTriplets:FixedSize:MinD
|
|
|
1950 istance1:MaxDistance10;2692;OrderedNumericalValues;ValuesString;46 106
|
|
|
1951 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
|
|
|
1952 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
|
|
|
1953 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
|
|
|
1954 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 ...
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|
|
1955
|
|
|
1956 =head1 OPTIONS
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|
1957
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|
1958 =over 4
|
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|
1959
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1960 =item B<--alpha> I<number>
|
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|
1961
|
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1962 Value of alpha parameter for calculating I<Tversky> similarity coefficient specified for
|
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|
1963 B<-b, --BitVectorComparisonMode> option. It corresponds to weights assigned for bits set
|
|
|
1964 to "1" in a pair of fingerprint bit-vectors during the calculation of similarity coefficient. Possible
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|
|
1965 values: I<0 to 1>. Default value: <0.5>.
|
|
|
1966
|
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|
1967 =item B<--beta> I<number>
|
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|
1968
|
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|
1969 Value of beta parameter for calculating I<WeightedTanimoto> and I<WeightedTversky>
|
|
|
1970 similarity coefficients specified for B<-b, --BitVectorComparisonMode> option. It is used to
|
|
|
1971 weight the contributions of bits set to "0" during the calculation of similarity coefficients. Possible
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|
|
1972 values: I<0 to 1>. Default value of <1> makes I<WeightedTanimoto> and I<WeightedTversky>
|
|
|
1973 equivalent to I<Tanimoto> and I<Tversky>.
|
|
|
1974
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|
1975 =item B<-b, --BitVectorComparisonMode> I<TanimotoSimilarity | TverskySimilarity | ...>
|
|
|
1976
|
|
|
1977 Specify what similarity coefficient to use for calculating similarity between fingerprints bit-vector
|
|
|
1978 string data values in I<ReferenceFingerprintsFile> and I<DatabaseFingerprintsFile> during similarity
|
|
|
1979 search. Possible values: I<TanimotoSimilarity | TverskySimilarity | ...>. Default: I<TanimotoSimilarity>
|
|
|
1980
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1981 The current release supports the following similarity coefficients: I<BaroniUrbaniSimilarity, BuserSimilarity,
|
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|
1982 CosineSimilarity, DiceSimilarity, DennisSimilarity, ForbesSimilarity, FossumSimilarity, HamannSimilarity, JacardSimilarity,
|
|
|
1983 Kulczynski1Similarity, Kulczynski2Similarity, MatchingSimilarity, McConnaugheySimilarity, OchiaiSimilarity,
|
|
|
1984 PearsonSimilarity, RogersTanimotoSimilarity, RussellRaoSimilarity, SimpsonSimilarity, SkoalSneath1Similarity,
|
|
|
1985 SkoalSneath2Similarity, SkoalSneath3Similarity, TanimotoSimilarity, TverskySimilarity, YuleSimilarity,
|
|
|
1986 WeightedTanimotoSimilarity, WeightedTverskySimilarity>. These similarity coefficients are described below.
|
|
|
1987
|
|
|
1988 For two fingerprint bit-vectors A and B of same size, let:
|
|
|
1989
|
|
|
1990 Na = Number of bits set to "1" in A
|
|
|
1991 Nb = Number of bits set to "1" in B
|
|
|
1992 Nc = Number of bits set to "1" in both A and B
|
|
|
1993 Nd = Number of bits set to "0" in both A and B
|
|
|
1994
|
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|
1995 Nt = Number of bits set to "1" or "0" in A or B (Size of A or B)
|
|
|
1996 Nt = Na + Nb - Nc + Nd
|
|
|
1997
|
|
|
1998 Na - Nc = Number of bits set to "1" in A but not in B
|
|
|
1999 Nb - Nc = Number of bits set to "1" in B but not in A
|
|
|
2000
|
|
|
2001 Then, various similarity coefficients [ Ref. 40 - 42 ] for a pair of bit-vectors A and B are
|
|
|
2002 defined as follows:
|
|
|
2003
|
|
|
2004 I<BaroniUrbaniSimilarity>: ( SQRT( Nc * Nd ) + Nc ) / ( SQRT ( Nc * Nd ) + Nc + ( Na - Nc ) + ( Nb - Nc ) ) ( same as Buser )
|
|
|
2005
|
|
|
2006 I<BuserSimilarity>: ( SQRT ( Nc * Nd ) + Nc ) / ( SQRT ( Nc * Nd ) + Nc + ( Na - Nc ) + ( Nb - Nc ) ) ( same as BaroniUrbani )
|
|
|
2007
|
|
|
2008 I<CosineSimilarity>: Nc / SQRT ( Na * Nb ) (same as Ochiai)
|
|
|
2009
|
|
|
2010 I<DiceSimilarity>: (2 * Nc) / ( Na + Nb )
|
|
|
2011
|
|
|
2012 I<DennisSimilarity>: ( Nc * Nd - ( ( Na - Nc ) * ( Nb - Nc ) ) ) / SQRT ( Nt * Na * Nb)
|
|
|
2013
|
|
|
2014 I<ForbesSimilarity>: ( Nt * Nc ) / ( Na * Nb )
|
|
|
2015
|
|
|
2016 I<FossumSimilarity>: ( Nt * ( ( Nc - 1/2 ) ** 2 ) / ( Na * Nb )
|
|
|
2017
|
|
|
2018 I<HamannSimilarity>: ( ( Nc + Nd ) - ( Na - Nc ) - ( Nb - Nc ) ) / Nt
|
|
|
2019
|
|
|
2020 I<JaccardSimilarity>: Nc / ( ( Na - Nc) + ( Nb - Nc ) + Nc ) = Nc / ( Na + Nb - Nc ) (same as Tanimoto)
|
|
|
2021
|
|
|
2022 I<Kulczynski1Similarity>: Nc / ( ( Na - Nc ) + ( Nb - Nc) ) = Nc / ( Na + Nb - 2Nc )
|
|
|
2023
|
|
|
2024 I<Kulczynski2Similarity>: ( ( Nc / 2 ) * ( 2 * Nc + ( Na - Nc ) + ( Nb - Nc) ) ) / ( ( Nc + ( Na - Nc ) ) * ( Nc + ( Nb - Nc ) ) ) = 0.5 * ( Nc / Na + Nc / Nb )
|
|
|
2025
|
|
|
2026 I<MatchingSimilarity>: ( Nc + Nd ) / Nt
|
|
|
2027
|
|
|
2028 I<McConnaugheySimilarity>: ( Nc ** 2 - ( Na - Nc ) * ( Nb - Nc) ) / ( Na * Nb )
|
|
|
2029
|
|
|
2030 I<OchiaiSimilarity>: Nc / SQRT ( Na * Nb ) (same as Cosine)
|
|
|
2031
|
|
|
2032 I<PearsonSimilarity>: ( ( Nc * Nd ) - ( ( Na - Nc ) * ( Nb - Nc ) ) / SQRT ( Na * Nb * ( Na - Nc + Nd ) * ( Nb - Nc + Nd ) )
|
|
|
2033
|
|
|
2034 I<RogersTanimotoSimilarity>: ( Nc + Nd ) / ( ( Na - Nc) + ( Nb - Nc) + Nt) = ( Nc + Nd ) / ( Na + Nb - 2Nc + Nt)
|
|
|
2035
|
|
|
2036 I<RussellRaoSimilarity>: Nc / Nt
|
|
|
2037
|
|
|
2038 I<SimpsonSimilarity>: Nc / MIN ( Na, Nb)
|
|
|
2039
|
|
|
2040 I<SkoalSneath1Similarity>: Nc / ( Nc + 2 * ( Na - Nc) + 2 * ( Nb - Nc) ) = Nc / ( 2 * Na + 2 * Nb - 3 * Nc )
|
|
|
2041
|
|
|
2042 I<SkoalSneath2Similarity>: ( 2 * Nc + 2 * Nd ) / ( Nc + Nd + Nt )
|
|
|
2043
|
|
|
2044 I<SkoalSneath3Similarity>: ( Nc + Nd ) / ( ( Na - Nc ) + ( Nb - Nc ) ) = ( Nc + Nd ) / ( Na + Nb - 2 * Nc )
|
|
|
2045
|
|
|
2046 I<TanimotoSimilarity>: Nc / ( ( Na - Nc) + ( Nb - Nc ) + Nc ) = Nc / ( Na + Nb - Nc ) (same as Jaccard)
|
|
|
2047
|
|
|
2048 I<TverskySimilarity>: Nc / ( alpha * ( Na - Nc ) + ( 1 - alpha) * ( Nb - Nc) + Nc ) = Nc / ( alpha * ( Na - Nb ) + Nb)
|
|
|
2049
|
|
|
2050 I<YuleSimilarity>: ( ( Nc * Nd ) - ( ( Na - Nc ) * ( Nb - Nc ) ) ) / ( ( Nc * Nd ) + ( ( Na - Nc ) * ( Nb - Nc ) ) )
|
|
|
2051
|
|
|
2052 Values of Tanimoto/Jaccard and Tversky coefficients are dependent on only those bit which
|
|
|
2053 are set to "1" in both A and B. In order to take into account all bit positions, modified versions
|
|
|
2054 of Tanimoto [ Ref. 42 ] and Tversky [ Ref. 43 ] have been developed.
|
|
|
2055
|
|
|
2056 Let:
|
|
|
2057
|
|
|
2058 Na' = Number of bits set to "0" in A
|
|
|
2059 Nb' = Number of bits set to "0" in B
|
|
|
2060 Nc' = Number of bits set to "0" in both A and B
|
|
|
2061
|
|
|
2062 Tanimoto': Nc' / ( ( Na' - Nc') + ( Nb' - Nc' ) + Nc' ) = Nc' / ( Na' + Nb' - Nc' )
|
|
|
2063
|
|
|
2064 Tversky': Nc' / ( alpha * ( Na' - Nc' ) + ( 1 - alpha) * ( Nb' - Nc' ) + Nc' ) = Nc' / ( alpha * ( Na' - Nb' ) + Nb')
|
|
|
2065
|
|
|
2066 Then:
|
|
|
2067
|
|
|
2068 I<WeightedTanimotoSimilarity> = beta * Tanimoto + (1 - beta) * Tanimoto'
|
|
|
2069
|
|
|
2070 I<WeightedTverskySimilarity> = beta * Tversky + (1 - beta) * Tversky'
|
|
|
2071
|
|
|
2072 =item B<--DatabaseColMode> I<ColNum | ColLabel>
|
|
|
2073
|
|
|
2074 Specify how columns are identified in database fingerprints I<TextFile>: using column
|
|
|
2075 number or column label. Possible values: I<ColNum or ColLabel>. Default value: I<ColNum>.
|
|
|
2076
|
|
|
2077 =item B<--DatabaseCompoundIDCol> I<col number | col name>
|
|
|
2078
|
|
|
2079 This value is B<--DatabaseColMode> mode specific. It specifies column to use for retrieving compound
|
|
|
2080 ID from database fingerprints I<TextFile> during similarity and dissimilarity search for output SD and
|
|
|
2081 CSV/TSV text files. Possible values: I<col number or col label>. Default value: I<first column containing
|
|
|
2082 the word compoundID in its column label or sequentially generated IDs>.
|
|
|
2083
|
|
|
2084 This is only used for I<CompoundID> value of B<--DatabaseDataColsMode> option.
|
|
|
2085
|
|
|
2086 =item B<--DatabaseCompoundIDPrefix> I<text>
|
|
|
2087
|
|
|
2088 Specify compound ID prefix to use during sequential generation of compound IDs for database fingerprints
|
|
|
2089 I<SDFile> and I<TextFile>. Default value: I<Cmpd>. The default value generates compound IDs which look
|
|
|
2090 like Cmpd<Number>.
|
|
|
2091
|
|
|
2092 For database fingerprints I<SDFile>, this value is only used during I<LabelPrefix | MolNameOrLabelPrefix>
|
|
|
2093 values of B<--DatabaseCompoundIDMode> option; otherwise, it's ignored.
|
|
|
2094
|
|
|
2095 Examples for I<LabelPrefix> or I<MolNameOrLabelPrefix> value of B<--DatabaseCompoundIDMode>:
|
|
|
2096
|
|
|
2097 Compound
|
|
|
2098
|
|
|
2099 The values specified above generates compound IDs which correspond to Compound<Number>
|
|
|
2100 instead of default value of Cmpd<Number>.
|
|
|
2101
|
|
|
2102 =item B<--DatabaseCompoundIDField> I<DataFieldName>
|
|
|
2103
|
|
|
2104 Specify database fingerprints I<SDFile> datafield label for generating compound IDs. This value is
|
|
|
2105 only used during I<DataField> value of B<--DatabaseCompoundIDMode> option.
|
|
|
2106
|
|
|
2107 Examples for I<DataField> value of B<--DatabaseCompoundIDMode>:
|
|
|
2108
|
|
|
2109 MolID
|
|
|
2110 ExtReg
|
|
|
2111
|
|
|
2112 =item B<--DatabaseCompoundIDMode> I<DataField | MolName | LabelPrefix | MolNameOrLabelPrefix>
|
|
|
2113
|
|
|
2114 Specify how to generate compound IDs from database fingerprints I<SDFile> during similarity and
|
|
|
2115 dissimilarity search for output SD and CSV/TSV text files: use a I<SDFile> datafield value; use
|
|
|
2116 molname line from I<SDFile>; generate a sequential ID with specific prefix; use combination of both
|
|
|
2117 MolName and LabelPrefix with usage of LabelPrefix values for empty molname lines.
|
|
|
2118
|
|
|
2119 Possible values: I<DataField | MolName | LabelPrefix | MolNameOrLabelPrefix>.
|
|
|
2120 Default: I<LabelPrefix>.
|
|
|
2121
|
|
|
2122 For I<MolNameAndLabelPrefix> value of B<--DatabaseCompoundIDMode>, molname line in I<SDFile> takes
|
|
|
2123 precedence over sequential compound IDs generated using I<LabelPrefix> and only empty molname
|
|
|
2124 values are replaced with sequential compound IDs.
|
|
|
2125
|
|
|
2126 This is only used for I<CompoundID> value of B<--DatabaseDataFieldsMode> option.
|
|
|
2127
|
|
|
2128 =item B<--DatabaseDataCols> I<"DataColNum1,DataColNum2,... " | DataColLabel1,DataCoLabel2,... ">
|
|
|
2129
|
|
|
2130 This value is B<--DatabaseColMode> mode specific. It is a comma delimited list of database fingerprints
|
|
|
2131 I<TextFile> data column numbers or labels to extract and write to SD and CSV/TSV text files along with
|
|
|
2132 other information for I<SD | text | both> values of B<--output> option.
|
|
|
2133
|
|
|
2134 This is only used for I<Specify> value of B<--DatabaseDataColsMode> option.
|
|
|
2135
|
|
|
2136 Examples:
|
|
|
2137
|
|
|
2138 1,2,3
|
|
|
2139 CompoundName,MolWt
|
|
|
2140
|
|
|
2141 =item B<--DatabaseDataColsMode> I<All | Specify | CompoundID>
|
|
|
2142
|
|
|
2143 Specify how data columns from database fingerprints I<TextFile> are transferred to output SD and
|
|
|
2144 CSV/TSV text files along with other information for I<SD | text | both> values of B<--output> option:
|
|
|
2145 transfer all data columns; extract specified data columns; generate a compound ID database compound
|
|
|
2146 prefix. Possible values: I<All | Specify | CompoundID>. Default value: I<CompoundID>.
|
|
|
2147
|
|
|
2148 =item B<--DatabaseDataFields> I<"FieldLabel1,FieldLabel2,... ">
|
|
|
2149
|
|
|
2150 Comma delimited list of database fingerprints I<SDFile> data fields to extract and write to SD
|
|
|
2151 and CSV/TSV text files along with other information for I<SD | text | both> values of
|
|
|
2152 B<--output> option.
|
|
|
2153
|
|
|
2154 This is only used for I<Specify> value of B<--DatabaseDataFieldsMode> option.
|
|
|
2155
|
|
|
2156 Examples:
|
|
|
2157
|
|
|
2158 Extreg
|
|
|
2159 MolID,CompoundName
|
|
|
2160
|
|
|
2161 =item B<--DatabaseDataFieldsMode> I<All | Common | Specify | CompoundID>
|
|
|
2162
|
|
|
2163 Specify how data fields from database fingerprints I<SDFile> are transferred to output SD and
|
|
|
2164 CSV/TSV text files along with other information for I<SD | text | both> values of B<--output>
|
|
|
2165 option: transfer all SD data field; transfer SD data files common to all compounds; extract
|
|
|
2166 specified data fields; generate a compound ID using molname line, a compound prefix, or a
|
|
|
2167 combination of both. Possible values: I<All | Common | specify | CompoundID>. Default value:
|
|
|
2168 I<CompoundID>.
|
|
|
2169
|
|
|
2170 =item B<--DatabaseFingerprintsCol> I<col number | col name>
|
|
|
2171
|
|
|
2172 This value is B<--DatabaseColMode> specific. It specifies fingerprints column to use during similarity
|
|
|
2173 and dissimilarity search for database fingerprints I<TextFile>. Possible values: I<col number or col label>.
|
|
|
2174 Default value: I<first column containing the word Fingerprints in its column label>.
|
|
|
2175
|
|
|
2176 =item B<--DatabaseFingerprintsField> I<FieldLabel>
|
|
|
2177
|
|
|
2178 Fingerprints field label to use during similarity and dissimilarity search for database fingerprints I<SDFile>.
|
|
|
2179 Default value: I<first data field label containing the word Fingerprints in its label>
|
|
|
2180
|
|
|
2181 =item B<--DistanceCutoff> I<number>
|
|
|
2182
|
|
|
2183 Distance cutoff value to use during comparison of distance value between a pair of database
|
|
|
2184 and reference molecule calculated by distance comparison methods for fingerprints vector
|
|
|
2185 string data values. Possible values: I<Any valid number>. Default value: I<10>.
|
|
|
2186
|
|
|
2187 The comparison value between a pair of database and reference molecule must meet the cutoff
|
|
|
2188 criterion as shown below:
|
|
|
2189
|
|
|
2190 SeachMode CutoffCriterion ComparisonValues
|
|
|
2191
|
|
|
2192 Similarity <= Lower value implies high similarity
|
|
|
2193 Dissimilarity >= Higher value implies high dissimilarity
|
|
|
2194
|
|
|
2195 This option is only used during distance coefficients values of B<-v, --VectorComparisonMode>
|
|
|
2196 option.
|
|
|
2197
|
|
|
2198 This option is ignored during I<No> value of B<--GroupFusionApplyCutoff> for I<MultipleReferences>
|
|
|
2199 B<-m, --mode>.
|
|
|
2200
|
|
|
2201 =item B<-d, --detail> I<InfoLevel>
|
|
|
2202
|
|
|
2203 Level of information to print about lines being ignored. Default: I<1>. Possible values:
|
|
|
2204 I<1, 2 or 3>.
|
|
|
2205
|
|
|
2206 =item B<-f, --fast>
|
|
|
2207
|
|
|
2208 In this mode, fingerprints columns specified using B<--FingerprintsCol> for reference and database
|
|
|
2209 fingerprints I<TextFile(s)>, and B<--FingerprintsField> for reference and database fingerprints I<SDFile(s)>
|
|
|
2210 are assumed to contain valid fingerprints data and no checking is performed before performing similarity
|
|
|
2211 and dissimilarity search. By default, fingerprints data is validated before computing pairwise similarity and
|
|
|
2212 distance coefficients.
|
|
|
2213
|
|
|
2214 =item B<--FingerprintsMode> I<AutoDetect | FingerprintsBitVectorString | FingerprintsVectorString>
|
|
|
2215
|
|
|
2216 Format of fingerprint strings data in reference and database fingerprints I<SD, FP, or Text (CSV/TSV)>
|
|
|
2217 files: automatically detect format of fingerprints string created by MayaChemTools fingerprints
|
|
|
2218 generation scripts or explicitly specify its format. Possible values: I<AutoDetect | FingerprintsBitVectorString |
|
|
|
2219 FingerprintsVectorString>. Default value: I<AutoDetect>.
|
|
|
2220
|
|
|
2221 =item B<-g, --GroupFusionRule> I<Max, Min, Mean, Median, Sum, Euclidean>
|
|
|
2222
|
|
|
2223 Specify what group fusion [ Ref 94-97, Ref 100, Ref 105 ] rule to use for calculating similarity of
|
|
|
2224 a database molecule against a set of reference molecules during I<MultipleReferences> value of
|
|
|
2225 similarity search B<-m, --mode>. Possible values: I<Max, Min, Mean, Median, Sum, Euclidean>. Default
|
|
|
2226 value: I<Max>. I<Mean> value corresponds to average or arithmetic mean. The group fusion rule is
|
|
|
2227 also referred to as data fusion of consensus scoring in the literature.
|
|
|
2228
|
|
|
2229 For a reference molecules set and a database molecule, let:
|
|
|
2230
|
|
|
2231 N = Number of reference molecules in a set
|
|
|
2232
|
|
|
2233 i = ith reference reference molecule in a set
|
|
|
2234 n = Nth reference reference molecule in a set
|
|
|
2235
|
|
|
2236 d = dth database molecule
|
|
|
2237
|
|
|
2238 Crd = Fingerprints comparison value between rth reference and dth database
|
|
|
2239 molecule - similarity/dissimilarity comparison using similarity or
|
|
|
2240 distance coefficient
|
|
|
2241
|
|
|
2242 Then, various group fusion rules to calculate fused similarity between a database molecule and
|
|
|
2243 reference molecules set are defined as follows:
|
|
|
2244
|
|
|
2245 B<Max>: MAX ( C1d, C2d, ..., Cid, ..., Cnd )
|
|
|
2246
|
|
|
2247 B<Min>: MIN ( C1d, C2d, ..., Cid, ..., Cnd )
|
|
|
2248
|
|
|
2249 B<Mean>: SUM ( C1d, C2d, ..., Cid, ..., Cnd ) / N
|
|
|
2250
|
|
|
2251 B<Median>: MEDIAN ( C1d, C2d, ..., Cid, ..., Cnd )
|
|
|
2252
|
|
|
2253 B<Sum>: SUM ( C1d, C2d, ..., Cid, ..., Cnd )
|
|
|
2254
|
|
|
2255 B<Euclidean>: SQRT( SUM( C1d ** 2, C2d ** 2, ..., Cid ** 2, ..., Cnd *** 2) )
|
|
|
2256
|
|
|
2257 The fingerprints bit-vector or vector string of each reference molecule in a set is compared
|
|
|
2258 with a database molecule using a similarity or distance coefficient specified via B<-b,
|
|
|
2259 --BitVectorComparisonMode> or B<-v, --VectorComparisonMode>. The reference molecules
|
|
|
2260 whose comparison values with a database molecule fall outside specified B<--SimilarityCutoff>
|
|
|
2261 or B<--DistanceCutoff> are ignored during I<Yes> value of B<--GroupFusionApplyCutoff>. The
|
|
|
2262 specified B<-g, --GroupFusionRule> is applied to B<-k, --kNN> reference molecules to calculate
|
|
|
2263 final fused similarity value between a database molecule and reference molecules set.
|
|
|
2264
|
|
|
2265 During dissimilarity search or usage of distance comparison coefficient in similarity search,
|
|
|
2266 the meaning of fingerprints comaprison value is automatically reversed as shown below:
|
|
|
2267
|
|
|
2268 SeachMode ComparisonCoefficient ComparisonValues
|
|
|
2269
|
|
|
2270 Similarity SimilarityCoefficient Higher value imples high similarity
|
|
|
2271 Similarity DistanceCoefficient Lower value implies high similarity
|
|
|
2272
|
|
|
2273 Dissimilarity SimilarityCoefficient Lower value implies high
|
|
|
2274 dissimilarity
|
|
|
2275 Dissimilarity DistanceCoefficient Higher value implies high
|
|
|
2276 dissimilarity
|
|
|
2277
|
|
|
2278 Consequently, I<Max> implies highest and lowest comparison value for usage of similarity and
|
|
|
2279 distance coefficient respectively during similarity search. And it corresponds to lowest and highest
|
|
|
2280 comparison value for usage of similarity and distance coefficient respectively during dissimilarity
|
|
|
2281 search. During I<Min> fusion rule, the highest and lowest comparison values are appropriately
|
|
|
2282 reversed.
|
|
|
2283
|
|
|
2284 =item B<--GroupFusionApplyCutoff> I<Yes | No>
|
|
|
2285
|
|
|
2286 Specify whether to apply B<--SimilarityCutoff> or B<--DistanceCutoff> values during application
|
|
|
2287 of B<-g, --GroupFusionRule> to reference molecules set. Possible values: I<Yes or No>. Default
|
|
|
2288 value: I<Yes>.
|
|
|
2289
|
|
|
2290 During I<Yes> value of B<--GroupFusionApplyCutoff>, the reference molecules whose comparison
|
|
|
2291 values with a database molecule fall outside specified B<--SimilarityCutoff> or B<--DistanceCutoff>
|
|
|
2292 are not used to calculate final fused similarity value between a database molecule and reference
|
|
|
2293 molecules set.
|
|
|
2294
|
|
|
2295 =item B<-h, --help>
|
|
|
2296
|
|
|
2297 Print this help message.
|
|
|
2298
|
|
|
2299 =item B<--InDelim> I<comma | semicolon>
|
|
|
2300
|
|
|
2301 Input delimiter for reference and database fingerprints CSV I<TextFile(s)>. Possible values:
|
|
|
2302 I<comma or semicolon>. Default value: I<comma>. For TSV files, this option is ignored
|
|
|
2303 and I<tab> is used as a delimiter.
|
|
|
2304
|
|
|
2305 =item B<-k, --kNN> I<all | number>
|
|
|
2306
|
|
|
2307 Number of k-nearest neighbors (k-NN) reference molecules to use during B<-g, --GroupFusionRule>
|
|
|
2308 for calculating similarity of a database molecule against a set of reference molecules. Possible values:
|
|
|
2309 I<all | positive integers>. Default: I<all>.
|
|
|
2310
|
|
|
2311 After ranking similarity values between a database molecule and reference molecules during
|
|
|
2312 I<MultipleReferences> value of similarity search B<-m, --mode> option, a top B<-k, --KNN> reference
|
|
|
2313 molecule are selected and used during B<-g, --GroupFusionRule>.
|
|
|
2314
|
|
|
2315 This option is B<-s, --SearchMode> dependent: It corresponds to dissimilar molecules during
|
|
|
2316 I<DissimilaritySearch> value of B<-s, --SearchMode> option.
|
|
|
2317
|
|
|
2318 =item B<-m, --mode> I<IndividualReference | MultipleReferences>
|
|
|
2319
|
|
|
2320 Specify how to treat reference molecules in I<ReferenceFingerprintsFile> during similarity search:
|
|
|
2321 Treat each reference molecule individually during similarity search or perform similarity
|
|
|
2322 search by treating multiple reference molecules as a set. Possible values: I<IndividualReference
|
|
|
2323 | MultipleReferences>. Default value: I<MultipleReferences>.
|
|
|
2324
|
|
|
2325 During I<IndividualReference> value of B<-m, --Mode> for similarity search, fingerprints bit-vector
|
|
|
2326 or vector string of each reference molecule is compared with database molecules using specified
|
|
|
2327 similarity or distance coefficients to identify most similar molecules for each reference molecule.
|
|
|
2328 Based on value of B<--SimilarCountMode>, upto B<--n, NumOfSimilarMolecules> or B<-p,
|
|
|
2329 --PercentSimilarMolecules> at specified <--SimilarityCutoff> or B<--DistanceCutoff> are
|
|
|
2330 identified for each reference molecule.
|
|
|
2331
|
|
|
2332 During I<MultipleReferences> value B<-m, --mode> for similarity search, all reference molecules
|
|
|
2333 are considered as a set and B<-g, --GroupFusionRule> is used to calculate similarity of a database
|
|
|
2334 molecule against reference molecules set either using all reference molecules or number of k-nearest
|
|
|
2335 neighbors (k-NN) to a database molecule specified using B<-k, --kNN>. The fingerprints bit-vector
|
|
|
2336 or vector string of each reference molecule in a set is compared with a database molecule using
|
|
|
2337 a similarity or distance coefficient specified via B<-b, --BitVectorComparisonMode> or B<-v,
|
|
|
2338 --VectorComparisonMode>. The reference molecules whose comparison values with a database
|
|
|
2339 molecule fall outside specified B<--SimilarityCutoff> or B<--DistanceCutoff> are ignored. The
|
|
|
2340 specified B<-g, --GroupFusionRule> is applied to rest of B<-k, --kNN> reference molecules to calculate
|
|
|
2341 final similarity value between a database molecule and reference molecules set.
|
|
|
2342
|
|
|
2343 The meaning of similarity and distance is automatically reversed during I<DissimilaritySearch> value
|
|
|
2344 of B<-s, --SearchMode> along with appropriate handling of B<--SimilarityCutoff> or
|
|
|
2345 B<--DistanceCutoff> values.
|
|
|
2346
|
|
|
2347 =item B<-n, --NumOfSimilarMolecules> I<number>
|
|
|
2348
|
|
|
2349 Maximum number of most similar database molecules to find for each reference molecule or set of
|
|
|
2350 reference molecules based on I<IndividualReference> or I<MultipleReferences> value of similarity
|
|
|
2351 search B<-m, --mode> option. Default: I<10>. Valid values: positive integers.
|
|
|
2352
|
|
|
2353 This option is ignored during I<PercentSimilar> value of B<--SimilarCountMode> option.
|
|
|
2354
|
|
|
2355 This option is B<-s, --SearchMode> dependent: It corresponds to dissimilar molecules during
|
|
|
2356 I<DissimilaritySearch> value of B<-s, --SearchMode> option.
|
|
|
2357
|
|
|
2358 =item B<--OutDelim> I<comma | tab | semicolon>
|
|
|
2359
|
|
|
2360 Delimiter for output CSV/TSV text file. Possible values: I<comma, tab, or semicolon>
|
|
|
2361 Default value: I<comma>.
|
|
|
2362
|
|
|
2363 =item B<--output> I<SD | text | both>
|
|
|
2364
|
|
|
2365 Type of output files to generate. Possible values: I<SD, text, or both>. Default value: I<text>.
|
|
|
2366
|
|
|
2367 =item B<-o, --overwrite>
|
|
|
2368
|
|
|
2369 Overwrite existing files
|
|
|
2370
|
|
|
2371 =item B<-p, --PercentSimilarMolecules> I<number>
|
|
|
2372
|
|
|
2373 Maximum percent of mosy similar database molecules to find for each reference molecule or set of
|
|
|
2374 reference molecules based on I<IndividualReference> or I<MultipleReferences> value of similarity
|
|
|
2375 search B<-m, --mode> option. Default: I<1> percent of database molecules. Valid values: non-zero values
|
|
|
2376 in between I<0 to 100>.
|
|
|
2377
|
|
|
2378 This option is ignored during I<NumOfSimilar> value of B<--SimilarCountMode> option.
|
|
|
2379
|
|
|
2380 During I<PercentSimilar> value of B<--SimilarCountMode> option, the number of molecules
|
|
|
2381 in I<DatabaseFingerprintsFile> is counted and number of similar molecules correspond to
|
|
|
2382 B<--PercentSimilarMolecules> of the total number of database molecules.
|
|
|
2383
|
|
|
2384 This option is B<-s, --SearchMode> dependent: It corresponds to dissimilar molecules during
|
|
|
2385 I<DissimilaritySearch> value of B<-s, --SearchMode> option.
|
|
|
2386
|
|
|
2387 =item B<--precision> I<number>
|
|
|
2388
|
|
|
2389 Precision of calculated similarity values for comparison and generating output files. Default: up to I<2>
|
|
|
2390 decimal places. Valid values: positive integers.
|
|
|
2391
|
|
|
2392 =item B<-q, --quote> I<Yes | No>
|
|
|
2393
|
|
|
2394 Put quote around column values in output CSV/TSV text file. Possible values:
|
|
|
2395 I<Yes or No>. Default value: I<Yes>.
|
|
|
2396
|
|
|
2397 =item B<--ReferenceColMode> I<ColNum | ColLabel>
|
|
|
2398
|
|
|
2399 Specify how columns are identified in reference fingerprints I<TextFile>: using column
|
|
|
2400 number or column label. Possible values: I<ColNum or ColLabel>. Default value: I<ColNum>.
|
|
|
2401
|
|
|
2402 =item B<--ReferenceCompoundIDCol> I<col number | col name>
|
|
|
2403
|
|
|
2404 This value is B<--ReferenceColMode> mode specific. It specifies column to use for retrieving compound
|
|
|
2405 ID from reference fingerprints I<TextFile> during similarity and dissimilarity search for output SD and CSV/TSV
|
|
|
2406 text files. Possible values: I<col number or col label>. Default value: I<first column containing the word compoundID
|
|
|
2407 in its column label or sequentially generated IDs>.
|
|
|
2408
|
|
|
2409 =item B<--ReferenceCompoundIDPrefix> I<text>
|
|
|
2410
|
|
|
2411 Specify compound ID prefix to use during sequential generation of compound IDs for reference fingerprints
|
|
|
2412 I<SDFile> and I<TextFile>. Default value: I<Cmpd>. The default value generates compound IDs which looks
|
|
|
2413 like Cmpd<Number>.
|
|
|
2414
|
|
|
2415 For reference fingerprints I<SDFile>, this value is only used during I<LabelPrefix | MolNameOrLabelPrefix>
|
|
|
2416 values of B<--ReferenceCompoundIDMode> option; otherwise, it's ignored.
|
|
|
2417
|
|
|
2418 Examples for I<LabelPrefix> or I<MolNameOrLabelPrefix> value of B<--DatabaseCompoundIDMode>:
|
|
|
2419
|
|
|
2420 Compound
|
|
|
2421
|
|
|
2422 The values specified above generates compound IDs which correspond to Compound<Number>
|
|
|
2423 instead of default value of Cmpd<Number>.
|
|
|
2424
|
|
|
2425 =item B<--ReferenceCompoundIDField> I<DataFieldName>
|
|
|
2426
|
|
|
2427 Specify reference fingerprints I<SDFile> datafield label for generating compound IDs.
|
|
|
2428 This value is only used during I<DataField> value of B<--ReferenceCompoundIDMode> option.
|
|
|
2429
|
|
|
2430 Examples for I<DataField> value of B<--ReferenceCompoundIDMode>:
|
|
|
2431
|
|
|
2432 MolID
|
|
|
2433 ExtReg
|
|
|
2434
|
|
|
2435 =item B<--ReferenceCompoundIDMode> I<DataField | MolName | LabelPrefix | MolNameOrLabelPrefix>
|
|
|
2436
|
|
|
2437 Specify how to generate compound IDs from reference fingerprints I<SDFile> during similarity and
|
|
|
2438 dissimilarity search for output SD and CSV/TSV text files: use a I<SDFile> datafield value; use
|
|
|
2439 molname line from I<SDFile>; generate a sequential ID with specific prefix; use combination of both
|
|
|
2440 MolName and LabelPrefix with usage of LabelPrefix values for empty molname lines.
|
|
|
2441
|
|
|
2442 Possible values: I<DataField | MolName | LabelPrefix | MolNameOrLabelPrefix>.
|
|
|
2443 Default: I<LabelPrefix>.
|
|
|
2444
|
|
|
2445 For I<MolNameAndLabelPrefix> value of B<--ReferenceCompoundIDMode>, molname line in I<SDFiles>
|
|
|
2446 takes precedence over sequential compound IDs generated using I<LabelPrefix> and only empty molname
|
|
|
2447 values are replaced with sequential compound IDs.
|
|
|
2448
|
|
|
2449 =item B<--ReferenceFingerprintsCol> I<col number | col name>
|
|
|
2450
|
|
|
2451 This value is B<--ReferenceColMode> specific. It specifies fingerprints column to use during similarity
|
|
|
2452 and dissimilarity search for reference fingerprints I<TextFile>. Possible values: I<col number or col label>.
|
|
|
2453 Default value: I<first column containing the word Fingerprints in its column label>.
|
|
|
2454
|
|
|
2455 =item B<--ReferenceFingerprintsField> I<FieldLabel>
|
|
|
2456
|
|
|
2457 Fingerprints field label to use during similarity and dissimilarity search for reference fingerprints I<SDFile>.
|
|
|
2458 Default value: I<first data field label containing the word Fingerprints in its label>
|
|
|
2459
|
|
|
2460 =item B<-r, --root> I<RootName>
|
|
|
2461
|
|
|
2462 New file name is generated using the root: <Root>.<Ext>. Default for new file name:
|
|
|
2463 <ReferenceFileName>SimilaritySearching.<Ext>. The output file type determines <Ext>
|
|
|
2464 value. The sdf, csv, and tsv <Ext> values are used for SD, comma/semicolon, and tab delimited
|
|
|
2465 text files respectively.
|
|
|
2466
|
|
|
2467 =item B<-s, --SearchMode> I<SimilaritySearch | DissimilaritySearch>
|
|
|
2468
|
|
|
2469 Specify how to find molecules from database molecules for individual reference molecules or
|
|
|
2470 set of reference molecules: Find similar molecules or dissimilar molecules from database molecules.
|
|
|
2471 Possible values: I<SimilaritySearch | DissimilaritySearch>. Default value: I<SimilaritySearch>.
|
|
|
2472
|
|
|
2473 During I<DissimilaritySearch> value of B<-s, --SearchMode> option, the meaning of the following
|
|
|
2474 options is switched and they correspond to dissimilar molecules instead of similar molecules:
|
|
|
2475 B<--SimilarCountMode>, B<-n, --NumOfSimilarMolecules>, B<--PercentSimilarMolecules>,
|
|
|
2476 B<-k, --kNN>.
|
|
|
2477
|
|
|
2478 =item B<--SimilarCountMode> I<NumOfSimilar | PercentSimilar>
|
|
|
2479
|
|
|
2480 Specify method used to count similar molecules found from database molecules for individual
|
|
|
2481 reference molecules or set of reference molecules: Find number of similar molecules or percent
|
|
|
2482 of similar molecules from database molecules. Possible values: I<NumOfSimilar | PercentSimilar>.
|
|
|
2483 Default value: I<NumOfSimilar>.
|
|
|
2484
|
|
|
2485 The values for number of similar molecules and percent similar molecules are specified
|
|
|
2486 using options B<-n, NumOfSimilarMolecule> and B<--PercentSimilarMolecules>.
|
|
|
2487
|
|
|
2488 This option is B<-s, --SearchMode> dependent: It corresponds to dissimilar molecules during
|
|
|
2489 I<DissimilaritySearch> value of B<-s, --SearchMode> option.
|
|
|
2490
|
|
|
2491 =item B<--SimilarityCutoff> I<number>
|
|
|
2492
|
|
|
2493 Similarity cutoff value to use during comparison of similarity value between a pair of database
|
|
|
2494 and reference molecules calculated by similarity comparison methods for fingerprints bit-vector
|
|
|
2495 vector strings data values. Possible values: I<Any valid number>. Default value: I<0.75>.
|
|
|
2496
|
|
|
2497 The comparison value between a pair of database and reference molecule must meet the cutoff
|
|
|
2498 criterion as shown below:
|
|
|
2499
|
|
|
2500 SeachMode CutoffCriterion ComparisonValues
|
|
|
2501
|
|
|
2502 Similarity >= Higher value implies high similarity
|
|
|
2503 Dissimilarity <= Lower value implies high dissimilarity
|
|
|
2504
|
|
|
2505 This option is ignored during I<No> value of B<--GroupFusionApplyCutoff> for I<MultipleReferences>
|
|
|
2506 B<-m, --mode>.
|
|
|
2507
|
|
|
2508 This option is B<-s, --SearchMode> dependent: It corresponds to dissimilar molecules during
|
|
|
2509 I<DissimilaritySearch> value of B<-s, --SearchMode> option.
|
|
|
2510
|
|
|
2511 =item B<-v, --VectorComparisonMode> I<SupportedSimilarityName | SupportedDistanceName>
|
|
|
2512
|
|
|
2513 Specify what similarity or distance coefficient to use for calculating similarity between fingerprint
|
|
|
2514 vector strings data values in I<ReferenceFingerprintsFile> and I<DatabaseFingerprintsFile> during
|
|
|
2515 similarity search. Possible values: I<TanimotoSimilairy | ... | ManhattanDistance | ...>. Default
|
|
|
2516 value: I<TanimotoSimilarity>.
|
|
|
2517
|
|
|
2518 The value of B<-v, --VectorComparisonMode>, in conjunction with B<--VectorComparisonFormulism>,
|
|
|
2519 decides which type of similarity and distance coefficient formulism gets used.
|
|
|
2520
|
|
|
2521 The current releases supports the following similarity and distance coefficients: I<CosineSimilarity,
|
|
|
2522 CzekanowskiSimilarity, DiceSimilarity, OchiaiSimilarity, JaccardSimilarity, SorensonSimilarity, TanimotoSimilarity,
|
|
|
2523 CityBlockDistance, EuclideanDistance, HammingDistance, ManhattanDistance, SoergelDistance>. These
|
|
|
2524 similarity and distance coefficients are described below.
|
|
|
2525
|
|
|
2526 B<FingerprintsVector.pm> module, used to calculate similarity and distance coefficients,
|
|
|
2527 provides support to perform comparison between vectors containing three different types of
|
|
|
2528 values:
|
|
|
2529
|
|
|
2530 Type I: OrderedNumericalValues
|
|
|
2531
|
|
|
2532 . Size of two vectors are same
|
|
|
2533 . Vectors contain real values in a specific order. For example: MACCS keys
|
|
|
2534 count, Topological pharmnacophore atom pairs and so on.
|
|
|
2535
|
|
|
2536 Type II: UnorderedNumericalValues
|
|
|
2537
|
|
|
2538 . Size of two vectors might not be same
|
|
|
2539 . Vectors contain unordered real value identified by value IDs. For example:
|
|
|
2540 Toplogical atom pairs, Topological atom torsions and so on
|
|
|
2541
|
|
|
2542 Type III: AlphaNumericalValues
|
|
|
2543
|
|
|
2544 . Size of two vectors might not be same
|
|
|
2545 . Vectors contain unordered alphanumerical values. For example: Extended
|
|
|
2546 connectivity fingerprints, atom neighborhood fingerprints.
|
|
|
2547
|
|
|
2548 Before performing similarity or distance calculations between vectors containing UnorderedNumericalValues
|
|
|
2549 or AlphaNumericalValues, the vectors are transformed into vectors containing unique OrderedNumericalValues
|
|
|
2550 using value IDs for UnorderedNumericalValues and values itself for AlphaNumericalValues.
|
|
|
2551
|
|
|
2552 Three forms of similarity and distance calculation between two vectors, specified using B<--VectorComparisonFormulism>
|
|
|
2553 option, are supported: I<AlgebraicForm, BinaryForm or SetTheoreticForm>.
|
|
|
2554
|
|
|
2555 For I<BinaryForm>, the ordered list of processed final vector values containing the value or
|
|
|
2556 count of each unique value type is simply converted into a binary vector containing 1s and 0s
|
|
|
2557 corresponding to presence or absence of values before calculating similarity or distance between
|
|
|
2558 two vectors.
|
|
|
2559
|
|
|
2560 For two fingerprint vectors A and B of same size containing OrderedNumericalValues, let:
|
|
|
2561
|
|
|
2562 N = Number values in A or B
|
|
|
2563
|
|
|
2564 Xa = Values of vector A
|
|
|
2565 Xb = Values of vector B
|
|
|
2566
|
|
|
2567 Xai = Value of ith element in A
|
|
|
2568 Xbi = Value of ith element in B
|
|
|
2569
|
|
|
2570 SUM = Sum of i over N values
|
|
|
2571
|
|
|
2572 For SetTheoreticForm of calculation between two vectors, let:
|
|
|
2573
|
|
|
2574 SetIntersectionXaXb = SUM ( MIN ( Xai, Xbi ) )
|
|
|
2575 SetDifferenceXaXb = SUM ( Xai ) + SUM ( Xbi ) - SUM ( MIN ( Xai, Xbi ) )
|
|
|
2576
|
|
|
2577 For BinaryForm of calculation between two vectors, let:
|
|
|
2578
|
|
|
2579 Na = Number of bits set to "1" in A = SUM ( Xai )
|
|
|
2580 Nb = Number of bits set to "1" in B = SUM ( Xbi )
|
|
|
2581 Nc = Number of bits set to "1" in both A and B = SUM ( Xai * Xbi )
|
|
|
2582 Nd = Number of bits set to "0" in both A and B
|
|
|
2583 = SUM ( 1 - Xai - Xbi + Xai * Xbi)
|
|
|
2584
|
|
|
2585 N = Number of bits set to "1" or "0" in A or B = Size of A or B = Na + Nb - Nc + Nd
|
|
|
2586
|
|
|
2587 Additionally, for BinaryForm various values also correspond to:
|
|
|
2588
|
|
|
2589 Na = | Xa |
|
|
|
2590 Nb = | Xb |
|
|
|
2591 Nc = | SetIntersectionXaXb |
|
|
|
2592 Nd = N - | SetDifferenceXaXb |
|
|
|
2593
|
|
|
2594 | SetDifferenceXaXb | = N - Nd = Na + Nb - Nc + Nd - Nd = Na + Nb - Nc
|
|
|
2595 = | Xa | + | Xb | - | SetIntersectionXaXb |
|
|
|
2596
|
|
|
2597 Various similarity and distance coefficients [ Ref 40, Ref 62, Ref 64 ] for a pair of vectors A and B
|
|
|
2598 in I<AlgebraicForm, BinaryForm and SetTheoreticForm> are defined as follows:
|
|
|
2599
|
|
|
2600 B<CityBlockDistance>: ( same as HammingDistance and ManhattanDistance)
|
|
|
2601
|
|
|
2602 I<AlgebraicForm>: SUM ( ABS ( Xai - Xbi ) )
|
|
|
2603
|
|
|
2604 I<BinaryForm>: ( Na - Nc ) + ( Nb - Nc ) = Na + Nb - 2 * Nc
|
|
|
2605
|
|
|
2606 I<SetTheoreticForm>: | SetDifferenceXaXb | - | SetIntersectionXaXb | = SUM ( Xai ) + SUM ( Xbi ) - 2 * ( SUM ( MIN ( Xai, Xbi ) ) )
|
|
|
2607
|
|
|
2608 B<CosineSimilarity>: ( same as OchiaiSimilarityCoefficient)
|
|
|
2609
|
|
|
2610 I<AlgebraicForm>: SUM ( Xai * Xbi ) / SQRT ( SUM ( Xai ** 2) * SUM ( Xbi ** 2) )
|
|
|
2611
|
|
|
2612 I<BinaryForm>: Nc / SQRT ( Na * Nb)
|
|
|
2613
|
|
|
2614 I<SetTheoreticForm>: | SetIntersectionXaXb | / SQRT ( |Xa| * |Xb| ) = SUM ( MIN ( Xai, Xbi ) ) / SQRT ( SUM ( Xai ) * SUM ( Xbi ) )
|
|
|
2615
|
|
|
2616 B<CzekanowskiSimilarity>: ( same as DiceSimilarity and SorensonSimilarity)
|
|
|
2617
|
|
|
2618 I<AlgebraicForm>: ( 2 * ( SUM ( Xai * Xbi ) ) ) / ( SUM ( Xai ** 2) + SUM ( Xbi **2 ) )
|
|
|
2619
|
|
|
2620 I<BinaryForm>: 2 * Nc / ( Na + Nb )
|
|
|
2621
|
|
|
2622 I<SetTheoreticForm>: 2 * | SetIntersectionXaXb | / ( |Xa| + |Xb| ) = 2 * ( SUM ( MIN ( Xai, Xbi ) ) ) / ( SUM ( Xai ) + SUM ( Xbi ) )
|
|
|
2623
|
|
|
2624 B<DiceSimilarity>: ( same as CzekanowskiSimilarity and SorensonSimilarity)
|
|
|
2625
|
|
|
2626 I<AlgebraicForm>: ( 2 * ( SUM ( Xai * Xbi ) ) ) / ( SUM ( Xai ** 2) + SUM ( Xbi **2 ) )
|
|
|
2627
|
|
|
2628 I<BinaryForm>: 2 * Nc / ( Na + Nb )
|
|
|
2629
|
|
|
2630 I<SetTheoreticForm>: 2 * | SetIntersectionXaXb | / ( |Xa| + |Xb| ) = 2 * ( SUM ( MIN ( Xai, Xbi ) ) ) / ( SUM ( Xai ) + SUM ( Xbi ) )
|
|
|
2631
|
|
|
2632 B<EuclideanDistance>:
|
|
|
2633
|
|
|
2634 I<AlgebraicForm>: SQRT ( SUM ( ( ( Xai - Xbi ) ** 2 ) ) )
|
|
|
2635
|
|
|
2636 I<BinaryForm>: SQRT ( ( Na - Nc ) + ( Nb - Nc ) ) = SQRT ( Na + Nb - 2 * Nc )
|
|
|
2637
|
|
|
2638 I<SetTheoreticForm>: SQRT ( | SetDifferenceXaXb | - | SetIntersectionXaXb | ) = SQRT ( SUM ( Xai ) + SUM ( Xbi ) - 2 * ( SUM ( MIN ( Xai, Xbi ) ) ) )
|
|
|
2639
|
|
|
2640 B<HammingDistance>: ( same as CityBlockDistance and ManhattanDistance)
|
|
|
2641
|
|
|
2642 I<AlgebraicForm>: SUM ( ABS ( Xai - Xbi ) )
|
|
|
2643
|
|
|
2644 I<BinaryForm>: ( Na - Nc ) + ( Nb - Nc ) = Na + Nb - 2 * Nc
|
|
|
2645
|
|
|
2646 I<SetTheoreticForm>: | SetDifferenceXaXb | - | SetIntersectionXaXb | = SUM ( Xai ) + SUM ( Xbi ) - 2 * ( SUM ( MIN ( Xai, Xbi ) ) )
|
|
|
2647
|
|
|
2648 B<JaccardSimilarity>: ( same as TanimotoSimilarity)
|
|
|
2649
|
|
|
2650 I<AlgebraicForm>: SUM ( Xai * Xbi ) / ( SUM ( Xai ** 2 ) + SUM ( Xbi ** 2 ) - SUM ( Xai * Xbi ) )
|
|
|
2651
|
|
|
2652 I<BinaryForm>: Nc / ( ( Na - Nc ) + ( Nb - Nc ) + Nc ) = Nc / ( Na + Nb - Nc )
|
|
|
2653
|
|
|
2654 I<SetTheoreticForm>: | SetIntersectionXaXb | / | SetDifferenceXaXb | = SUM ( MIN ( Xai, Xbi ) ) / ( SUM ( Xai ) + SUM ( Xbi ) - SUM ( MIN ( Xai, Xbi ) ) )
|
|
|
2655
|
|
|
2656 B<ManhattanDistance>: ( same as CityBlockDistance and HammingDistance)
|
|
|
2657
|
|
|
2658 I<AlgebraicForm>: SUM ( ABS ( Xai - Xbi ) )
|
|
|
2659
|
|
|
2660 I<BinaryForm>: ( Na - Nc ) + ( Nb - Nc ) = Na + Nb - 2 * Nc
|
|
|
2661
|
|
|
2662 I<SetTheoreticForm>: | SetDifferenceXaXb | - | SetIntersectionXaXb | = SUM ( Xai ) + SUM ( Xbi ) - 2 * ( SUM ( MIN ( Xai, Xbi ) ) )
|
|
|
2663
|
|
|
2664 B<OchiaiSimilarity>: ( same as CosineSimilarity)
|
|
|
2665
|
|
|
2666 I<AlgebraicForm>: SUM ( Xai * Xbi ) / SQRT ( SUM ( Xai ** 2) * SUM ( Xbi ** 2) )
|
|
|
2667
|
|
|
2668 I<BinaryForm>: Nc / SQRT ( Na * Nb)
|
|
|
2669
|
|
|
2670 I<SetTheoreticForm>: | SetIntersectionXaXb | / SQRT ( |Xa| * |Xb| ) = SUM ( MIN ( Xai, Xbi ) ) / SQRT ( SUM ( Xai ) * SUM ( Xbi ) )
|
|
|
2671
|
|
|
2672 B<SorensonSimilarity>: ( same as CzekanowskiSimilarity and DiceSimilarity)
|
|
|
2673
|
|
|
2674 I<AlgebraicForm>: ( 2 * ( SUM ( Xai * Xbi ) ) ) / ( SUM ( Xai ** 2) + SUM ( Xbi **2 ) )
|
|
|
2675
|
|
|
2676 I<BinaryForm>: 2 * Nc / ( Na + Nb )
|
|
|
2677
|
|
|
2678 I<SetTheoreticForm>: 2 * | SetIntersectionXaXb | / ( |Xa| + |Xb| ) = 2 * ( SUM ( MIN ( Xai, Xbi ) ) ) / ( SUM ( Xai ) + SUM ( Xbi ) )
|
|
|
2679
|
|
|
2680 B<SoergelDistance>:
|
|
|
2681
|
|
|
2682 I<AlgebraicForm>: SUM ( ABS ( Xai - Xbi ) ) / SUM ( MAX ( Xai, Xbi ) )
|
|
|
2683
|
|
|
2684 I<BinaryForm>: 1 - Nc / ( Na + Nb - Nc ) = ( Na + Nb - 2 * Nc ) / ( Na + Nb - Nc )
|
|
|
2685
|
|
|
2686 I<SetTheoreticForm>: ( | SetDifferenceXaXb | - | SetIntersectionXaXb | ) / | SetDifferenceXaXb | = ( SUM ( Xai ) + SUM ( Xbi ) - 2 * ( SUM ( MIN ( Xai, Xbi ) ) ) ) / ( SUM ( Xai ) + SUM ( Xbi ) - SUM ( MIN ( Xai, Xbi ) ) )
|
|
|
2687
|
|
|
2688 B<TanimotoSimilarity>: ( same as JaccardSimilarity)
|
|
|
2689
|
|
|
2690 I<AlgebraicForm>: SUM ( Xai * Xbi ) / ( SUM ( Xai ** 2 ) + SUM ( Xbi ** 2 ) - SUM ( Xai * Xbi ) )
|
|
|
2691
|
|
|
2692 I<BinaryForm>: Nc / ( ( Na - Nc ) + ( Nb - Nc ) + Nc ) = Nc / ( Na + Nb - Nc )
|
|
|
2693
|
|
|
2694 I<SetTheoreticForm>: | SetIntersectionXaXb | / | SetDifferenceXaXb | = SUM ( MIN ( Xai, Xbi ) ) / ( SUM ( Xai ) + SUM ( Xbi ) - SUM ( MIN ( Xai, Xbi ) ) )
|
|
|
2695
|
|
|
2696 =item B<--VectorComparisonFormulism> I<AlgebraicForm | BinaryForm | SetTheoreticForm>
|
|
|
2697
|
|
|
2698 Specify fingerprints vector comparison formulism to use for calculation similarity and distance
|
|
|
2699 coefficients during B<-v, --VectorComparisonMode>. Possible values: I<AlgebraicForm | BinaryForm |
|
|
|
2700 SetTheoreticForm>. Default value: I<AlgebraicForm>.
|
|
|
2701
|
|
|
2702 For fingerprint vector strings containing B<AlphaNumericalValues> data values - B<ExtendedConnectivityFingerprints>,
|
|
|
2703 B<AtomNeighborhoodsFingerprints> and so on - all three formulism result in same value during similarity and distance
|
|
|
2704 calculations.
|
|
|
2705
|
|
|
2706 =item B<-w, --WorkingDir> I<DirName>
|
|
|
2707
|
|
|
2708 Location of working directory. Default: current directory.
|
|
|
2709
|
|
|
2710 =back
|
|
|
2711
|
|
|
2712 =head1 EXAMPLES
|
|
|
2713
|
|
|
2714 To perform similarity search using Tanimoto coefficient by treating all reference molecules as a set
|
|
|
2715 to find 10 most similar database molecules with application of Max group fusion rule and similarity
|
|
|
2716 cutoff to supported fingerprints strings data in SD fingerprints files present in a data fields with
|
|
|
2717 Fingerprint substring in their labels, and create a ReferenceFPHexSimilaritySearching.csv file containing
|
|
|
2718 sequentially generated database compound IDs with Cmpd prefix, type:
|
|
|
2719
|
|
|
2720 % SimilaritySearchingFingerprints.pl -o ReferenceSampleFPHex.sdf
|
|
|
2721 DatabaseSampleFPHex.sdf
|
|
|
2722
|
|
|
2723 To perform similarity search using Tanimoto coefficient by treating all reference molecules as a set
|
|
|
2724 to find 10 most similar database molecules with application of Max group fusion rule and similarity
|
|
|
2725 cutoff to supported fingerprints strings data in FP fingerprints files, and create a
|
|
|
2726 SimilaritySearchResults.csv file containing database compound IDs retireved from FP file, type:
|
|
|
2727
|
|
|
2728 % SimilaritySearchingFingerprints.pl -r SimilaritySearchResults -o
|
|
|
2729 ReferenceSampleFPBin.fpf DatabaseSampleFPBin.fpf
|
|
|
2730
|
|
|
2731 To perform similarity search using Tanimoto coefficient by treating all reference molecules as a set
|
|
|
2732 to find 10 most similar database database molecules with application of Max group fusion rule and
|
|
|
2733 similarity cutoff to supported fingerprints strings data in text fingerprints files present in a column
|
|
|
2734 names containing Fingerprint substring in their names, and create a ReferenceFPHexSimilaritySearching.csv
|
|
|
2735 file containing database compound IDs retireved column name containing CompoundID substring or
|
|
|
2736 sequentially generated compound IDs, type:
|
|
|
2737
|
|
|
2738 % SimilaritySearchingFingerprints.pl -o ReferenceSampleFPCount.csv
|
|
|
2739 DatabaseSampleFPCount.csv
|
|
|
2740
|
|
|
2741 To perform similarity search using Tanimoto coefficient by treating reference molecules as individual molecules
|
|
|
2742 to find 10 most similar database molecules for each reference molecule with application of similarity cutoff to
|
|
|
2743 supported fingerprints strings data in SD fingerprints files present in a data fields with Fingerprint substring
|
|
|
2744 in their labels, and create a ReferenceFPHexSimilaritySearching.csv file containing sequentially generated
|
|
|
2745 reference and database compound IDs with Cmpd prefix, type:
|
|
|
2746
|
|
|
2747 % SimilaritySearchingFingerprints.pl -mode IndividualReference -o
|
|
|
2748 ReferenceSampleFPHex.sdf DatabaseSampleFPHex.sdf
|
|
|
2749
|
|
|
2750 To perform similarity search using Tanimoto coefficient by treating reference molecules as individual molecules
|
|
|
2751 to find 10 most similar database molecules for each reference molecule with application of similarity cutoff to
|
|
|
2752 supported fingerprints strings data in FP fingerprints files, and create a ReferenceFPHexSimilaritySearching.csv
|
|
|
2753 file containing references and database compound IDs retireved from FP file, type:
|
|
|
2754
|
|
|
2755 % SimilaritySearchingFingerprints.pl -mode IndividualReference -o
|
|
|
2756 ReferenceSampleFPHex.fpf DatabaseSampleFPHex.fpf
|
|
|
2757
|
|
|
2758 To perform similarity search using Tanimoto coefficient by treating reference molecules as individual molecules
|
|
|
2759 to find 10 most similar database molecules for each reference molecule with application of similarity cutoff to
|
|
|
2760 supported fingerprints strings data in text fingerprints files present in a column names containing Fingerprint
|
|
|
2761 substring in their names, and create a ReferenceFPHexSimilaritySearching.csv file containing reference and
|
|
|
2762 database compound IDs retrieved column name containing CompoundID substring or sequentially generated
|
|
|
2763 compound IDs, type:
|
|
|
2764
|
|
|
2765 % SimilaritySearchingFingerprints.pl -mode IndividualReference -o
|
|
|
2766 ReferenceSampleFPHex.csv DatabaseSampleFPHex.csv
|
|
|
2767
|
|
|
2768 To perform dissimilarity search using Tanimoto coefficient by treating all reference molecules as a set
|
|
|
2769 to find 10 most dissimilar database molecules with application of Max group fusion rule and similarity
|
|
|
2770 cutoff to supported fingerprints strings data in SD fingerprints files present in a data fields with
|
|
|
2771 Fingerprint substring in their labels, and create a ReferenceFPHexSimilaritySearching.csv file containing
|
|
|
2772 sequentially generated database compound IDs with Cmpd prefix, type:
|
|
|
2773
|
|
|
2774 % SimilaritySearchingFingerprints.pl --mode MultipleReferences --SearchMode
|
|
|
2775 DissimilaritySearch -o ReferenceSampleFPHex.sdf DatabaseSampleFPHex.sdf
|
|
|
2776
|
|
|
2777 To perform similarity search using CityBlock distance by treating reference molecules as individual molecules
|
|
|
2778 to find 10 most similar database molecules for each reference molecule with application of distance cutoff
|
|
|
2779 to supported vector fingerprints strings data in SD fingerprints files present in a data fields with Fingerprint
|
|
|
2780 substring in their labels, and create a ReferenceFPHexSimilaritySearching.csv file containing sequentially generated
|
|
|
2781 reference and database compound IDs with Cmpd prefix, type:
|
|
|
2782
|
|
|
2783 % SimilaritySearchingFingerprints.pl -mode IndividualReference
|
|
|
2784 --VectorComparisonMode CityBlockDistance --VectorComparisonFormulism
|
|
|
2785 AlgebraicForm --DistanceCutoff 10 -o
|
|
|
2786 ReferenceSampleFPCount.sdf DatabaseSampleFPCount.sdf
|
|
|
2787
|
|
|
2788 To perform similarity search using Tanimoto coefficient by treating all reference molecules as a set
|
|
|
2789 to find 100 most similar database molecules with application of Mean group fusion rule to to top 10
|
|
|
2790 reference molecules with in similarity cutoff of 0.75 to supported fingerprints strings data in FP fingerprints
|
|
|
2791 files, and create a ReferenceFPHexSimilaritySearching.csv file containing database compound IDs retrieved
|
|
|
2792 from FP file, type:
|
|
|
2793
|
|
|
2794 % SimilaritySearchingFingerprints.pl --mode MultipleReferences --SearchMode
|
|
|
2795 SimilaritySearch --BitVectorComparisonMode TanimotoSimilarity
|
|
|
2796 --GroupFusionRule Mean --GroupFusionApplyCutoff Yes --kNN 10
|
|
|
2797 --SimilarityCutoff 0.75 --SimilarCountMode NumOfSimilar
|
|
|
2798 --NumOfSimilarMolecules 100 -o
|
|
|
2799 ReferenceSampleFPHex.fpf DatabaseSampleFPHex.fpf
|
|
|
2800
|
|
|
2801 To perform similarity search using Tanimoto coefficient by treating reference molecules as individual molecules
|
|
|
2802 to find 2 percent of most similar database molecules for each reference molecule with application of similarity
|
|
|
2803 cutoff of 0.85 to supported fingerprints strings data in text fingerprints files present in specific columns and
|
|
|
2804 create a ReferenceFPHexSimilaritySearching.csv file containing reference and database compoundIDs retrieved
|
|
|
2805 from specific columns, type:
|
|
|
2806
|
|
|
2807 % SimilaritySearchingFingerprints.pl --mode IndividualReference --SearchMode
|
|
|
2808 SimilaritySearch --BitVectorComparisonMode TanimotoSimilarity
|
|
|
2809 --ReferenceColMode ColLabel --ReferenceFingerprintsCol Fingerprints
|
|
|
2810 --ReferenceCompoundIDCol CompoundID --DatabaseColMode Collabel
|
|
|
2811 --DatabaseCompoundIDCol CompoundID --DatabaseFingerprintsCol
|
|
|
2812 Fingerprints --SimilarityCutoff 0.85 --SimilarCountMode PercentSimilar
|
|
|
2813 --PercentSimilarMolecules 2 -o
|
|
|
2814 ReferenceSampleFPHex.csv DatabaseSampleFPHex.csv
|
|
|
2815
|
|
|
2816 To perform similarity search using Tanimoto coefficient by treating reference molecules as individual molecules
|
|
|
2817 to find top 50 most similar database molecules for each reference molecule with application of similarity
|
|
|
2818 cutoff of 0.85 to supported fingerprints strings data in SD fingerprints files present in specific data fields and
|
|
|
2819 create both ReferenceFPHexSimilaritySearching.csv and ReferenceFPHexSimilaritySearching.sdf files containing
|
|
|
2820 reference and database compoundIDs retrieved from specific data fields, type:
|
|
|
2821
|
|
|
2822 % SimilaritySearchingFingerprints.pl --mode IndividualReference --SearchMode
|
|
|
2823 SimilaritySearch --BitVectorComparisonMode TanimotoSimilarity
|
|
|
2824 --ReferenceFingerprintsField Fingerprints
|
|
|
2825 --DatabaseFingerprintsField Fingerprints
|
|
|
2826 --ReferenceCompoundIDMode DataField --ReferenceCompoundIDField CmpdID
|
|
|
2827 --DatabaseCompoundIDMode DataField --DatabaseCompoundIDField CmpdID
|
|
|
2828 --SimilarityCutoff 0.85 --SimilarCountMode NumOfSimilar
|
|
|
2829 --NumOfSimilarMolecules 50 --output both -o
|
|
|
2830 ReferenceSampleFPHex.sdf DatabaseSampleFPHex.sdf
|
|
|
2831
|
|
|
2832 To perform similarity search using Tanimoto coefficient by treating reference molecules as individual molecules
|
|
|
2833 to find 1 percent of most similar database molecules for each reference molecule with application of similarity
|
|
|
2834 cutoff to supported fingerprints strings data in SD fingerprints files present in specific data field labels, and create
|
|
|
2835 both ReferenceFPHexSimilaritySearching.csv ReferenceFPHexSimilaritySearching.sdf files containing reference and
|
|
|
2836 database compound IDs retrieved from specific data field labels along with other specific data for database
|
|
|
2837 molecules, type:
|
|
|
2838
|
|
|
2839 % SimilaritySearchingFingerprints.pl --mode IndividualReference --SearchMode
|
|
|
2840 SimilaritySearch --BitVectorComparisonMode TanimotoSimilarity
|
|
|
2841 --ReferenceFingerprintsField Fingerprints
|
|
|
2842 --DatabaseFingerprintsField Fingerprints
|
|
|
2843 --ReferenceCompoundIDMode DataField --ReferenceCompoundIDField CmpdID
|
|
|
2844 --DatabaseCompoundIDMode DataField --DatabaseCompoundIDField CmpdID
|
|
|
2845 --DatabaseDataFieldsMode Specify --DatabaseDataFields "TPSA,SLogP"
|
|
|
2846 --SimilarityCutoff 0.75 --SimilarCountMode PercentSimilar
|
|
|
2847 --PercentSimilarMolecules 1 --output both --OutDelim comma --quote Yes
|
|
|
2848 --precision 3 -o ReferenceSampleFPHex.sdf DatabaseSampleFPHex.sdf
|
|
|
2849
|
|
|
2850 =head1 AUTHOR
|
|
|
2851
|
|
|
2852 Manish Sud <msud@san.rr.com>
|
|
|
2853
|
|
|
2854 =head1 SEE ALSO
|
|
|
2855
|
|
|
2856 InfoFingerprintsFiles.pl, SimilarityMatricesFingerprints.pl, AtomNeighborhoodsFingerprints.pl,
|
|
|
2857 ExtendedConnectivityFingerprints.pl, MACCSKeysFingerprints.pl, PathLengthFingerprints.pl,
|
|
|
2858 TopologicalAtomPairsFingerprints.pl, TopologicalAtomTorsionsFingerprints.pl,
|
|
|
2859 TopologicalPharmacophoreAtomPairsFingerprints.pl, TopologicalPharmacophoreAtomTripletsFingerprints.pl
|
|
|
2860
|
|
|
2861 =head1 COPYRIGHT
|
|
|
2862
|
|
|
2863 Copyright (C) 2015 Manish Sud. All rights reserved.
|
|
|
2864
|
|
|
2865 This file is part of MayaChemTools.
|
|
|
2866
|
|
|
2867 MayaChemTools is free software; you can redistribute it and/or modify it under
|
|
|
2868 the terms of the GNU Lesser General Public License as published by the Free
|
|
|
2869 Software Foundation; either version 3 of the License, or (at your option)
|
|
|
2870 any later version.
|
|
|
2871
|
|
|
2872 =cut
|
